diff --git "a/metadata/all_metadata.json" "b/metadata/all_metadata.json" new file mode 100644--- /dev/null +++ "b/metadata/all_metadata.json" @@ -0,0 +1,43645 @@ +[ + { + "pmid": "37420170", + "title": "The 16S rDNA high-throughput sequencing correlation analysis of milk and gut microbial communities in mastitis Holstein cows.", + "year": 2023, + "journal": "BMC microbiology", + "authors": [ + "Jiang C", + "Hou X", + "Gao X", + "Liu P", + "Guo X", + "Hu G", + "Li Q", + "Huang C", + "Li G", + "Fang W", + "Mai W", + "Wu C", + "Xu Z", + "Liu P" + ], + "bacteria": "Pygmaiobacter", + "condition": "healthy", + "relevance_score": 0.22521245646707666, + "mesh_terms": [ + "Female", + "Cattle", + "Animals", + "Humans", + "Milk", + "DNA, Ribosomal", + "Microbiota", + "Lactobacillales", + "High-Throughput Nucleotide Sequencing", + "Mastitis" + ], + "raw_abstract": "This study aimed to understand the changes in the milk and gut microbiota of dairy cows with mastitis, and to further explore the relationship between mastitis and the microbiota. In this study, we extracted microbial DNA from healthy and mastitis cows and performed high-throughput sequencing using the Illumina NovaSeq sequencing platform. OTU clustering was performed to analyze complexity, multi-sample comparisons, differences in community structure between groups, and differential analysis of species composition and abundance. The results showed that there were differences in microbial diversity and community composition in the milk and feces of normal and mastitis cows, where the diversity of microbiota decreased and species abundance increased in the mastitis group. There was a significant difference in the flora composition of the two groups of samples (P\u2009<\u20090.05), especially at the genus level, the difference in the milk samples was Sphingomonas (P\u2009<\u20090.05) and Stenotrophomonas (P\u2009<\u20090.05), the differences in stool samples were Alistipes (P\u2009<\u20090.05), Flavonifractor (P\u2009<\u20090.05), Agathobacter (P\u2009<\u20090.05) and Pygmaiobacter (P\u2009<\u20090.05). In conclusion, the microbiota of the udder and intestinal tissues of dairy cows suffering from mastitis will change significantly. This suggests that the development of mastitis is related to the endogenous pathway of microbial intestinal mammary glands, but the mechanisms involved need further study.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29653723", + "title": "Characterization of the duodenal bacterial microbiota in patients with pancreatic head cancer vs. healthy controls.", + "year": 2018, + "journal": "Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]", + "authors": [ + "Mei QX", + "Huang CL", + "Luo SZ", + "Zhang XM", + "Zeng Y", + "Lu YY" + ], + "bacteria": "Enhydrobacter", + "condition": "healthy", + "relevance_score": 0.2854002956392609, + "mesh_terms": [ + "Aged", + "C-Reactive Protein", + "Duodenum", + "Endotoxins", + "Enteritis", + "Female", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Incidence", + "Interleukin-6", + "Male", + "Middle Aged", + "Pancreas", + "Pancreatic Neoplasms", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "An increasing number of reports have demonstrated that there is an association between the presence of pathogenic microorganisms and pancreatic cancer. However, the role of the duodenal microbiota in pancreatic carcinogenesis remains unknown. In this study, duodenal mucosal microbiota was analyzed in 14 patients with pancreatic head cancer and 14 healthy controls using 16S rRNA gene pyrosequencing methods. Plasma endotoxin activity and the concentrations of the proinflammatory cytokine IL-6 and C-reactive protein (CRP) were measured in blood samples. The urea breath test was used to detect Helicobacter pylori infections. Endoscopic duodenal mucosal biopsies were evaluated by histological examinations. Statistical comparisons of inflammatory factors revealed significantly higher levels of CRP and IL-6 in the pancreatic cancer group as compared to healthy controls. Patients with pancreatic cancer also had a higher incidence of H.\u00a0pylori infections and showed mucosal changes, including villous abnormalities and diffuse inflammatory cell infiltration in the lamina propria. The sequences analysis showed that based on linear discriminant analysis effect size (LEfSe) analysis at the genus level, Acinetobacter, Aquabacterium, Oceanobacillus, Rahnella, Massilia, Delftia, Deinococcus, and Sphingobium were more abundant in the duodenal mucosa of pancreatic cancer patients, whereas the duodenal microbiotas of healthy controls were enriched with Porphyromonas, Paenibacillus, Enhydrobacter, Escherichia, Shigella, and Pseudomonas. These results reveal a picture of duodenal microbiota in pancreatic head cancer patients that could be useful in future trials investigating the role of gut microbiota in pancreatic cancer.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35312122", + "title": "Gut microbiome: New biomarkers in early screening of colorectal cancer.", + "year": 2022, + "journal": "Journal of clinical laboratory analysis", + "authors": [ + "Zhou P", + "Yang D", + "Sun D", + "Zhou Y" + ], + "bacteria": "Enhydrobacter", + "condition": "healthy", + "relevance_score": 0.2292474113773472, + "mesh_terms": [ + "Adenoma", + "Biomarkers", + "Colorectal Neoplasms", + "Early Detection of Cancer", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Reproducibility of Results" + ], + "raw_abstract": "BACKGROUND: Certain \"star intestinal bacteria\" have been found to act as a contributor to the development of colorectal cancer (CRC). Besides, given that the gut microbiome can be detected in a diverse range of samples (stool, tissue, blood, etc), it is categorized into fecal microbiome, blood microbiome, and tissue microbiome. METHODS: To provide an overview of the recent research progress, this review summarizes the characteristics of the gut microbiome in different samples at each stage of CRC and their screening efficiency. RESULTS: The screening models constructed from different sample microbiomes (healthy/colorectal adenoma, healthy/CRC, and colorectal adenoma/CRC) have both strengths and constraints in terms of biomarker reproducibility and area under the receiver-operating characteristic curve (AUC) of the screening models. Many bacteria, such as Bifidobacteria, Fusobacterium nucleatum (F. n), Geotrichum candidum, Porphyromonas asaccharolytica, Escherichia coli, Rhodococcus, Anaerostipes caccae, Enhydrobacter, Lachnoclostridiumsp. m3, Bacteroides clarus, Clostridium hathewayi, Ruminococcaceae, Bacteroides thetaiotaomicron, Culinariside, and enterotoxigenic Bacteroides fragilis (ETBF), show favorable diagnostic efficacy in early screening of colorectal cancer. CONCLUSIONS: This review highlights stool, blood, tissue, and bowel fluid are the main sample sources for biomarkers, each with its own advantages and limitations. Moreover, other samples such as extracellular vesicles and biofilms also should been deserved further attention.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39307134", + "title": "Comparison of Tissue and Urine Microbiota in Male, Intervention Naive Patients with and without Non-Invasive Bladder Cancer.", + "year": 2025, + "journal": "Urologia internationalis", + "authors": [ + "Ozer MS", + "Incir C", + "Yildiz HA", + "Deger MD", + "Sarikaya AE", + "Tuncok Y", + "Ergor G", + "Esen N", + "Sen V", + "Bozkurt O", + "Esen A" + ], + "bacteria": "Enhydrobacter", + "condition": "healthy", + "relevance_score": 0.21158208292129949, + "mesh_terms": [ + "Humans", + "Male", + "Urinary Bladder Neoplasms", + "Microbiota", + "Middle Aged", + "Aged", + "Dysbiosis", + "Urine", + "Case-Control Studies" + ], + "raw_abstract": "INTRODUCTION: To investigate the presence of dysbiosis in patients with naive bladder cancer. METHODS: Twelve male patients with non-invasive bladder cancer and twelve age-matched healthy males had midstream urine and tissue samples taken. A history of endourological interventions was determined as an exclusion criterion, ensuring that the study was designed solely with na\u00efve participants. The bacterial 16s ribosomal RNA V3-V4 regions were used to examine urine and tissue samples. We compared the microbiota composition of the bladder cancer and control groups. RESULTS: Escherichia Shigella (p < 0.001), Staphylococcus (p < 0.001), Delftia (p < 0.001), Acinetobacter (p < 0.001), Corynebacterium (p < 0.001), and Enhydrobacter (p < 0.001) were abundant in bladder cancer tissue samples. Escherichia Shigella (p < 0.001), Ureaplasma (p < 0.001), Lactobacillus (p = 0.005), Stenotrophomonas (p < 0.001), Streptococcus (p < 0.001), Corynebacterium (p < 0.001), and Prevotella (p = 0.039) were abundant in bladder cancer urine samples. Midstream urine has a sensitivity of 83% for detecting dysbiotic bacteria in cancer tissue. CONCLUSIONS: Our research is the first microbiota study of bladder cancer done with naive patients who have never had an endourological intervention. Escherichia Shigella, Staphylococcus, Acinetobacter, Enhydrobacter, Delftia, Corynebacterium, and Pseudomonas were detected as dysbiotic bacteria in bladder cancer. The sensitivity of the midstream urine sample in detecting dysbiosis in tissue is 83%.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28429209", + "title": "Analysis of Gut Microbiota in Patients with Parkinson's Disease.", + "year": 2017, + "journal": "Bulletin of experimental biology and medicine", + "authors": [ + "Petrov VA", + "Saltykova IV", + "Zhukova IA", + "Alifirova VM", + "Zhukova NG", + "Dorofeeva YB", + "Tyakht AV", + "Kovarsky BA", + "Alekseev DG", + "Kostryukova ES", + "Mironova YS", + "Izhboldina OP", + "Nikitina MA", + "Perevozchikova TV", + "Fait EA", + "Babenko VV", + "Vakhitova MT", + "Govorun VM", + "Sazonov AE" + ], + "bacteria": "Papillibacter", + "condition": "healthy", + "relevance_score": 0.5043502526460152, + "mesh_terms": [ + "Aged", + "Biodiversity", + "Case-Control Studies", + "DNA Barcoding, Taxonomic", + "DNA, Bacterial", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gram-Negative Bacteria", + "Gram-Positive Bacteria", + "Humans", + "Male", + "Middle Aged", + "Parkinson Disease", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "Gut microbiota of patients with Parkinson's disease and healthy volunteers was analyzed by the method of high throughput 16S rRNA sequencing of bacterial genomes. In patients with Parkinson's diseases, changes in the content of 9 genera and 15 species of microorganisms were revealed: reduced content of Dorea, Bacteroides, Prevotella, Faecalibacterium, Bacteroides massiliensis, Stoquefichus massiliensis, Bacteroides coprocola, Blautia glucerasea, Dorea longicatena, Bacteroides dorei, Bacteroides plebeus, Prevotella copri, Coprococcus eutactus, and Ruminococcus callidus, and increased content of Christensenella, Catabacter, Lactobacillus, Oscillospira, Bifidobacterium, Christensenella minuta, Catabacter hongkongensis, Lactobacillus mucosae, Ruminococcus bromii, and Papillibacter cinnamivorans. This microbiological pattern of gut microflora can trigger local inflammation followed by aggregation of \u03b1-synuclein and generation of Lewy bodies.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39488083", + "title": "Assessment of the fecal microbiome of healthy rabbits (Oryctolagus cuniculus domesticus) compared with rabbits with gastrointestinal disease using next-generation DNA sequencing.", + "year": 2025, + "journal": "American journal of veterinary research", + "authors": [ + "Vecere G", + "Malka S", + "Sands N", + "Lee M", + "Krumbeck JA" + ], + "bacteria": "Papillibacter", + "condition": "healthy", + "relevance_score": 0.3460662960440057, + "mesh_terms": [ + "Animals", + "Rabbits", + "Feces", + "Gastrointestinal Diseases", + "High-Throughput Nucleotide Sequencing", + "Bacteria", + "RNA, Ribosomal, 16S", + "Microbiota", + "Fungi", + "Sequence Analysis, DNA", + "Male", + "Female" + ], + "raw_abstract": "OBJECTIVE: To determine the normal fecal microbiome of healthy rabbits in comparison to rabbits with gastrointestinal (GI) disease. Next-generation DNA sequencing was used to identify the primary bacteria and fungi in the microbiome. METHODS: Fecal pellets from 25 clinically healthy rabbits and 25 rabbits experiencing GI disease were collected. Next-generation DNA sequencing was performed targeting the ITS-2 region for mycobiome, and the V1-V3 region of the 16S rRNA for bacteriome analysis. ITS-2 stands for internal transcribed spacer 2, a region of DNA in fungi that is used to identify and classify species. RESULTS: In healthy rabbit feces, Bacteroidales sp, Odoribacter sp, Paraprevotella xylaniphila, Lachnospiraceae sp, Papillibacter sp, Akkermansia sp, and Ruminococcus sp were noted to be more prevalent. Comparatively, Lachnoclostridium sp, Anaerotruncus sp, Subdoligranulum sp, and B uniformis were found in greater abundance in rabbits with GI disease. Only 1 fungal species, Malassezia restricta, was significantly enriched in the GI disease group. CONCLUSIONS: Next-generation DNA sequencing technology can be used to evaluate the microbiome of the rabbit GI tract through fecal material and can provide a clinically accessible testing method for veterinarians. CLINICAL RELEVANCE: Numerous bacteria and fungi in the fecal samples of healthy rabbits were identified that could be considered markers of gastrointestinal health; similarly, specific bacteria and fungi were noted in greater abundance in rabbits with GI disease, which should be further investigated for their importance in causing, contributing to, or as the result of clinical disease. These findings support the use of next-generation DNA sequencing in order to diversify our understanding of the microbiome of rabbit feces, aid in clinical diagnosis, and provide support for the need for more specific probiotic supplements for rabbits.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30088332", + "title": "Altered gut microbiota and microbial biomarkers associated with chronic kidney disease.", + "year": 2019, + "journal": "MicrobiologyOpen", + "authors": [ + "Lun H", + "Yang W", + "Zhao S", + "Jiang M", + "Xu M", + "Liu F", + "Wang Y" + ], + "bacteria": "Dielma", + "condition": "healthy", + "relevance_score": 0.39496699901383897, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteria", + "Biodiversity", + "Biomarkers", + "Case-Control Studies", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "Renal Insufficiency, Chronic" + ], + "raw_abstract": "The present study aimed to determine the differences in gut microbiota between patients with chronic kidney disease (CKD) and healthy controls (HC) and search for better microbial biomarkers associated with CKD. The 16S rRNA gene sequencing approach was used to investigate the differences in gut microbiota between the CKD and HC groups. The study found that 12 phylotypes were overrepresented in the CKD group and 19 in the HC group at the genus level. Furthermore, genera Lachnospira and Ruminococcus_gnavus performed the best in differentiating between HC and CKD populations. In addition, this novel study found that the genera Holdemanella, Megamonas, Prevotella 2, Dielma, and Scardovia were associated with the progression of CKD and hemodialysis. In conclusion, the composition of gut microbiota was different in CKD populations compared with healthy populations, and Lachnospira and R._gnavus were better microbial biomarkers. In addition, five phylotypes, including Holdemanella, Megamonas, Prevotella2, Dielma, and Scardovia, served as an indicator of the progression of CKD and hemodialysis. However, large-scale prospective studies should be performed to identify the reliability of the set of these phylotypes as biomarkers.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33124578", + "title": "Intestinal microbiota composition of patients with Beh\u00e7et's disease: differences between eye, mucocutaneous and vascular involvement. The Rheuma-BIOTA study.", + "year": 2020, + "journal": "Clinical and experimental rheumatology", + "authors": [ + "Yasar Bilge NS", + "P\u00e9rez Brocal V", + "Kasifoglu T", + "Bilge U", + "Kasifoglu N", + "Moya A", + "Dinleyici EC" + ], + "bacteria": "Dielma", + "condition": "healthy", + "relevance_score": 0.27484843161521166, + "mesh_terms": [ + "Adult", + "Behcet Syndrome", + "Gastrointestinal Microbiome", + "Humans", + "Prospective Studies" + ], + "raw_abstract": "OBJECTIVES: Changes in microbiota composition affect the aetiology and patho-genesis of chronic diseases, including Beh\u00e7et's disease (BD). However, no studies have analysed the potential gut microbiota changes among different clinical forms of BD. This study evaluated the intestinal microbiota composition of patients with BD and healthy controls and also compared differences between patients with BD with respect to eye, mucocutaneous, and vascular involvement. METHODS: In this prospective cohort study, 27 patients diagnosed with BD according to the International Study Group criteria and 10 age- and sex-matched healthy controls were included. Detailed intestinal microbiota analysis was performed. RESULTS: There were no differences between the BD group and the control group in terms of alpha and beta microbial diversity and abundance indices (p>0.05). Actinomyces, Libanicoccus, Collinsella, Eggerthella, Enetrohabdus, Catenibacterium, and Enterobacter were significantly higher in the BD group than in the control group. In addition, Bacteroides, Cricetibacter, Alistipes, Lachnospira, Dielma, Akkermansia, Sutterella, Anaerofilum, Ruminococcease-UCG007, Acetanaerobacterium, and Copropaacter were lower in the BD group than in the control group. When we compared three different system involvement (eye, mucocutaneous, and vascular), the linear discriminant analysis effective size revealed a difference for the following genera: Lachnospiraceae NK4A136 in the uveitis group; Dialister, Intestinomonas, and Marvinbryantia in the mucocutaneous group; and Gemella in the vascular group. CONCLUSIONS: The composition of intestinal microbiota was significantly different in patients with BD compared with healthy adults. Ours is the first study to show differences in microbiota composition in isolated mucocutaneous, eye, and vascular involvement. These findings should be evaluated in a larger series.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35108565", + "title": "Alteration of gut microbiota composition and function of Indian major carp, rohu (Labeo rohita) infected with Argulus siamensis.", + "year": 2022, + "journal": "Microbial pathogenesis", + "authors": [ + "Mondal HK", + "Maji UJ", + "Mohanty S", + "Sahoo PK", + "Maiti NK" + ], + "bacteria": "Dielma", + "condition": "healthy", + "relevance_score": 0.20492888440752827, + "mesh_terms": [ + "Animals", + "Arguloida", + "Carps", + "Fish Diseases", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Gut microbiome homeostasis is critical in preventing diseases. However, the effect of disease on gut microbiota assembly remains unclear. At present, there are no reports on the composition and functional analysis of intestinal microbiota of Indian major carp, rohu (L. rohita) infected with ectoparasite, Argulus. In this study, we analysed and compared the intestinal microbiota of healthy and Argulus-infected rohu by 16S rRNA amplicon sequencing. Argulus infection could significantly influence the diversity and richness of the gut microbiota. However, abundance of Actinobacteria and Patescibacteria were enriched significantly in Argulus-infected fish. Venn diagram revealed that there were many more unique genera in the infected group as compared to control fish. The genera, Stenotrophomonas and Pirellula were significantly increased in infected fish while the abundance of Reyranella was decreased. LEfSe analysis showed a significant enrichment in abundances of 11 taxa in healthy group and 17 taxa in infected group. Furthermore, genera Rubellimicrobium, Dielma, Hyphomicrobium, Reyranella, Streptomyces and Cloacibacterium performed the best in differentiating between both the groups. Predicted microbiota function by PICRUSt revealed that the gut microbiota of infected fish was mainly associated with enriched synthesis of chitinases, chitin binding proteins, osmoprotectant proteins and sulfatases enzymes. There was a positive association between the structural and functional composition of the gut microbiota. The results indicated that the Argulus infection could affect the intestinal microbiota composition and function of rohu.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36241691", + "title": "Profile of gut microbiota and serum metabolites associated with metabolic syndrome in a remote island most afflicted by obesity in Japan.", + "year": 2022, + "journal": "Scientific reports", + "authors": [ + "Uema T", + "Millman JF", + "Okamoto S", + "Nakamura T", + "Yamashiro K", + "Uehara M", + "Honma KI", + "Miyazato M", + "Ashikari A", + "Saito S", + "Maeda S", + "Imamura M", + "Ishida H", + "Matsushita M", + "Nakamura K", + "Masuzaki H" + ], + "bacteria": "Brachyspira", + "condition": "healthy", + "relevance_score": 0.33047962826972493, + "mesh_terms": [ + "Body Mass Index", + "Creatine", + "Gastrointestinal Microbiome", + "Glycated Hemoglobin", + "Humans", + "Insulins", + "Japan", + "Metabolic Syndrome", + "Obesity", + "Pyruvic Acid", + "Triglycerides" + ], + "raw_abstract": "Numerous studies have revealed distinct differences in the profiles of gut microbiota between non-obese and obese individuals. To date, however, little is known if any disparities in the community of gut microbiota exist between metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO) subjects. We therefore aimed to comprehensively characterize the gut microbiota and circulating metabolites in serum from both MHO and MUO residing in the remote island, Kumejima, where the prevalence of obesity is one of the highest in Japan, and explored possible correlations between the gut microbiota profile and markers of metabolic syndrome. Results revealed that MUO showed significantly higher levels of genera such as g_Succinivibrio, g_Granulicatella, g_Brachyspira, g_Oribacterium and g_Atopobium in comparison to MHO. Moreover, abundance of g_Succinivibrio, g_Brachyspira and g_Atopobium were positively correlated with value of fasting insulin, HOMA-R, circulating triglycerides, diastolic blood pressure, BMI, body weight, waist circumference and HbA1c. In addition, MUO compared to MHO showed an imbalance of serum metabolites, with a significant elevation in 2-oxoisovaleric acid, pyruvic acid, 2-hydroxybutyric acid, and creatine. Our data highlight unmet needs in precision approaches for the treatment of obesity, targeting the gut microbiota profile and serum metabolites in a distinct population affected by obesity.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37451531", + "title": "Multi-omics analyses of serum metabolome, urine metabolome and gut microbiome reveal dysregulated glycerophospholipid metabolism in subacute cadmium-exposed wistar rats.", + "year": 2023, + "journal": "Toxicology", + "authors": [ + "Wu C", + "Fang F", + "Yu Y", + "Wang B", + "Gao H", + "Cui W" + ], + "bacteria": "Brachyspira", + "condition": "healthy", + "relevance_score": 0.3070880492648327, + "mesh_terms": [ + "Rats", + "Animals", + "Gastrointestinal Microbiome", + "Rats, Wistar", + "Cadmium", + "Multiomics", + "Metabolome", + "Metabolomics" + ], + "raw_abstract": "Data is limited on intestinal microbiota and metabolites in healthy residents exposed to cadmium (Cd), a population uniquely susceptible to Cd toxicity through contaminated foods. In this study, the 16\u00a0S rRNA gene sequencing, serum metabolomics and urine metabolomics were performed to examine the alterations of gut microbiota and metabolomics profile of wistar rats exposed to Cd. These findings indicated that Cd exposure markedly altered the structure of gut microbial community, reduced significantly microbiome diversity, and identified 5 phyla and 6 genera with significant changes. Specifically, the levels of Pseudoxanthomonas and Anaerovibrio upregulated and that of Akkermansia, Brachyspira, Aggregatibacter and SMB53 reduced in rats treated with Cd. Metabolomics profiles of the urine and serum of Cd-treated rats revealed that the abundance of glycerophospholipid metabolites and their derivatives were markedly altered. Glycerophospholipid metabolic pathways that were markedly enriched in metabolomics in both samples was also significantly predicted in gut microbiota analysis. Further, interaction analysis predicted that there might be a relationship between the differential glycerophospholipid metabolites and affected bacteria genera induced by Cd. These results suggested that subacute Cd could disrupt the intestinal microecologica equilibrium and glycerophospholipid metabolic homeostasis, and also provided potential differential microbiota and glycerophospholipid biomarkers between subacute Cd-exposed rats and healthy rats.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27907102", + "title": "An Investigation into the Etiological Agents of Swine Dysentery in Australian Pig Herds.", + "year": 2016, + "journal": "PloS one", + "authors": [ + "La T", + "Phillips ND", + "Hampson DJ" + ], + "bacteria": "Brachyspira", + "condition": "healthy", + "relevance_score": 0.22766632296753372, + "mesh_terms": [ + "Animals", + "Australia", + "Brachyspira", + "Dysentery", + "Feces", + "Swine", + "Swine Diseases", + "Virulence" + ], + "raw_abstract": "Swine dysentery (SD) is a mucohemorrhagic colitis, classically seen in grower/finisher pigs and caused by infection with the anaerobic intestinal spirochete Brachyspira hyodysenteriae. More recently, however, the newly described species Brachyspira hampsonii and Brachyspira suanatina have been identified as causing SD in North America and/or Europe. Furthermore, there have been occasions where strains of B. hyodysenteriae have been recovered from healthy pigs, including in multiplier herds with high health status. This study investigated whether cases of SD in Australia may be caused by the newly described species; how isolates of B. hyodysenteriae recovered from healthy herds compared to isolates from herds with disease; and how contemporary isolates compare to those recovered in previous decades, including in their plasmid gene content and antimicrobial resistance profiles. In total 1103 fecal and colon samples from pigs in 97 Australian herds were collected and tested. Of the agents of SD only B. hyodysenteriae was found, being present in 34 (35.1%) of the herds, including in 14 of 24 (58%) herds that had been considered to be free of SD. Multilocus sequence typing applied to 96 isolates from 30 herds and to 53 Australian isolates dating from the 1980s through the early 2000s showed that they were diverse, distinct from those reported in other countries, and that the 2014/16 isolates generally were different from those from earlier decades. These findings provided evidence for ongoing evolution of B. hyodysenteriae strains in Australia. In seven of the 20 herds where multiple isolates were available, two to four different sequence types (STs) were identified. Isolates with the same STs also were found in some herds with epidemiological links. Analysis of a block of six plasmid virulence-associated genes showed a lack of consistency between their presence or absence and their origin from herds currently with or without disease; however, significantly fewer isolates from the 2000s and from 2014/16 had this block of genes compared to isolates from the 1980s and 1990s. It is speculated that loss of these genes may have been responsible for the occurrence of milder disease occurring in recent years. In addition, fewer isolates from 2014/16 were susceptible to the antimicrobials lincomycin, and to a lesser extent tiamulin, than those from earlier Australian studies. Four distinct multi-drug resistant strains were identified in five herds, posing a threat to disease control.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28126042", + "title": "Fournierella massiliensis gen. nov., sp. nov., a new human-associated member of the family Ruminococcaceae.", + "year": 2017, + "journal": "International journal of systematic and evolutionary microbiology", + "authors": [ + "Togo AH", + "Durand G", + "Khelaifia S", + "Armstrong N", + "Robert C", + "Cadoret F", + "Di Pinto F", + "Delerce J", + "Levasseur A", + "Raoult D", + "Million M" + ], + "bacteria": "Fournierella", + "condition": "healthy", + "relevance_score": 0.2252680648636692, + "mesh_terms": [ + "Bacterial Typing Techniques", + "Base Composition", + "DNA, Bacterial", + "Fatty Acids", + "Feces", + "France", + "Gram-Positive Bacteria", + "Humans", + "Male", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "An anaerobic bacterium, strain AT2T, was isolated from the fresh stool sample of a healthy French man using the culturomics approach. The 16S rRNA gene sequence analysis showed that strain AT2T had 95.2\u200a% nucleotide sequence similarity with Gemmiger formicilisATCC 27749T, the phylogenetically closest species with standing in nomenclature. Cells are Gram-stain-negative, catalase- and oxidase-negative, obligately anaerobic, non-motile, non-spore-forming, rod-shaped, and the bacilli were mesothermophilic. The major fatty acids were C16\u200a:\u200a0 (43.8\u200a%) and C18\u200a:\u200a1n9 (20\u200a%). The DNA G+C content of the strain based on its genome sequence was 56.8\u2009mol%. Based on the phenotypic, biochemical and phylogenetic analysis, we propose the creation of the genus Fournierella gen. nov., which contains strain AT2T (=CSUR P2014T=DSM 100451T) as the type strain of the type species Fournierella massiliensis gen. nov., sp. nov.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38331300", + "title": "Alterations in the diversity, composition and function of the gut microbiota in Uyghur individuals with sarcopenia.", + "year": 2024, + "journal": "Experimental gerontology", + "authors": [ + "Zhang Q", + "Li X", + "Huang T", + "Zhang S", + "Teng K", + "Rousitemu N", + "Lan T", + "Wen Y" + ], + "bacteria": "GCA-900066575", + "condition": "healthy", + "relevance_score": 0.2756242663260786, + "mesh_terms": [ + "Humans", + "Sarcopenia", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Aging", + "Bacteroidetes" + ], + "raw_abstract": "BACKGROUND: Research on the gut microbiota has emerged as a new direction for understanding pathophysiologic changes in diseases associated with aging, such as sarcopenia. Several studies have shown that there are differences in the gut microbiota between individuals with sarcopenia and without sarcopenia. However, these differences are not consistent across regions and ethnic groups, and additional research is needed. METHODS: In this study, we collected fresh fecal samples from 31 Uyghur individuals with sarcopenia and 31 healthy controls. We used 16S rRNA sequencing to obtain fecal base sequences and analyzed the diversity, composition and function of the gut microbiota. RESULTS: There was no significant difference in alpha diversity between the sarcopenia group and the healthy control group (P\u00a0>\u00a00.05). There was a significant difference in beta diversity between the groups (P\u00a0<\u00a00.05). In the sarcopenia group, the abundances of Alloprevotella, un_f_Prevotellaceae, Anaerovibrio, Prevotellaceae_NK3B31_group, Mitsuokella, Prevotella and Allisonella were lower than those in the heathy control group, and the abundances of Flavobacteriales, Flavobacteriaceae, Catenibacterium, Romboutsia, Erysipelotrichaceae_UCG-003, GCA-900066575, Lachnospiraceae_FCS020_group, and un_f_Flavobacteriaceae were higher than those in the heathy control group. Linear discriminant analysis effect size (LEfSe) revealed that the microbial species in the control group that were significantly different from those in the sarcopenia group were concentrated in the genus Alloprevotella, while the species in the sarcopenia group were concentrated in the genus Catenibacterium. Functional prediction analysis revealed that D-alanine, glycine, serine, and threonine metabolism and transcription machinery, among others, were enriched in the sarcopenia group, which indicated that metabolic pathways related to amino acid metabolism and nutrient transport may be regulated to varying degrees in the pathophysiological context of sarcopenia. CONCLUSIONS: There were significant differences in the composition and function of the gut microbiota between Xinjiang Uyghur sarcopenia individuals and healthy individuals. These findings might aid in the development of probiotics or microbial-based therapies for sarcopenia in Uyhur individuals.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38085410", + "title": "Characterization of gut microbiota in patients with stage 3-4 chronic kidney disease: a retrospective cohort study.", + "year": 2024, + "journal": "International urology and nephrology", + "authors": [ + "Yang X", + "Cai S", + "Gong J", + "Zhang J", + "Lian M", + "Chen R", + "Zhou L", + "Bai P", + "Liu B", + "Zhuang M", + "Tan H", + "Xu J", + "Li M" + ], + "bacteria": "Coprobacillus", + "condition": "healthy", + "relevance_score": 0.3764260351704308, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Retrospective Studies", + "Dysbiosis", + "Renal Insufficiency, Chronic", + "Feces", + "Bacteria" + ], + "raw_abstract": "PURPOSE: Multiple factors, such as dietary patterns, pharmaceutical interventions, and exposure to harmful substances, possess the capacity to influence gut microbiota composition. Gut microbiota dysbiosis has emerged as a significant contributor to the progression of chronic kidney disease (CKD) and its associated complications. By comprehending the intricacies of the intestinal microbiota, this research endeavor holds the potential to offer novel perspectives on potential strategies for mitigating CKD progression. METHODS: In this retrospective analysis, we assessed gut microbiota composition in CKD patients. Fecal samples were collected from a cohort of 44 patients with stage 3-4 CKD, alongside a control group consisting of 132 healthy volunteers. Subsequently, 16\u00a0s rDNA sequencing was conducted to examine the composition of the gut microbiota. RESULTS: Our findings revealed significant alterations in the diversity of intestinal microbiota in fecal samples between patients with stage 3-4 CKD and healthy subjects. Among the 475 bacterial genera, 164 were shared, while 242 dominant genera were exclusive to healthy subjects and 69 to CKD stages 3-4 samples. Notably, healthy volunteers exhibited a prevalence of intestinal Firmicutes and Bacteroidetes, whereas stage 3-4 CKD patients displayed higher abundance of Proteobacteria and Actinobacteria. The presence of uncultured Coprobacillus sp. notably contributed to distinguishing between the two groups. ROC curve analysis identified distinct microbiota with superior diagnostic efficacy for discriminating stage 3-4 CKD patients from healthy individuals. Metabolic pathway analysis revealed differing dominant pathways between the two groups-the NADH dehydrogenase pathway in healthy individuals and the phosphate acetyltransferase pathway in stage 3-4 CKD patients. Moreover, the CKD cohort displayed a higher proportion of Gram-negative bacteria and facultative anaerobes. CONCLUSIONS: In conclusion, our study underscores the profound influence of gut microbiota dysbiosis on CKD progression. The distinct microbial profiles observed in CKD patients highlight the potential efficacy of microbiota-based interventions in mitigating CKD advancement.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30101990", + "title": "Gut microbiota alterations in moderate to severe acne vulgaris patients.", + "year": 2018, + "journal": "The Journal of dermatology", + "authors": [ + "Yan HM", + "Zhao HJ", + "Guo DY", + "Zhu PQ", + "Zhang CL", + "Jiang W" + ], + "bacteria": "Coprobacillus", + "condition": "healthy", + "relevance_score": 0.2506740633577749, + "mesh_terms": [ + "Acne Vulgaris", + "Adolescent", + "Adult", + "Bacteria", + "Case-Control Studies", + "DNA, Bacterial", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Male", + "RNA, Bacterial", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA", + "Severity of Illness Index", + "Young Adult" + ], + "raw_abstract": "Acne vulgaris is a chronic inflammatory dermatosis affecting approximately 85% of adolescents. There are many factors contributing to the development of this ailment. A recent study indicated that gut microbiota takes part in the pathogenesis of acne. We aimed to investigate the link between acne vulgaris and gut microbiota. A total of 31 moderate to severe acne vulgaris patients and 31 healthy controls were enrolled. We collected their feces, and gut microbiota was evaluated by the hypervariable regions of 16S rRNA genes through high-throughput sequencing. We identified links between acne vulgaris and changes of gut microbiota. At the phylum level, Actinobacteria (0.89% in acne patients and 2.84% in normal controls, P = 0.004) was decreased and Proteobacteria (8.35% in acne patients and 7.01% in normal controls, P = 0.031) was increased. At the genus level, Bifidobacterium, Butyricicoccus, Coprobacillus, Lactobacillus and Allobaculum were all decreased. The observed difference in genera between acne patients and healthy controls provides a new insight into the link between gut microbiota changes and acne vulgaris risk.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35662119", + "title": "Intestinal Microflora Changes in Patients with Mild Alzheimer's Disease in a Chinese Cohort.", + "year": 2022, + "journal": "Journal of Alzheimer's disease : JAD", + "authors": [ + "Wang Y", + "Li L", + "Zhao X", + "Sui S", + "Wang Q", + "Shi G", + "Xu H", + "Zhang X", + "He Y", + "Gu J" + ], + "bacteria": "Coprobacillus", + "condition": "healthy", + "relevance_score": 0.2065108384953541, + "mesh_terms": [ + "Alzheimer Disease", + "China", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Understanding the relationship between Alzheimer's disease (AD) and intestinal flora is still a major scientific topic that continues to advance. OBJECTIVE: To determine characterized changes in the intestinal microbe community of patients with mild AD. METHODS: Comparison of the 16S ribosomal RNA (rRNA) high-throughput sequencing data was obtained from the Illumina MiSeq platform of fecal microorganisms of the patients and healthy controls (HC) which were selected from cohabiting caregivers of AD patients to exclude environmental and dietary factors. RESULTS: We found that the abundance of several bacteria taxa in AD patients was different from that in HC at the genus level, such as Anaerostipes, Mitsuokella, Prevotella, Bosea, Fusobacterium, Anaerotruncus, Clostridium, and Coprobacillus. Interestingly, the abundance of Akkermansia, an emerging probiotic, increased significantly in the AD group compared with that in the HC group. Meanwhile, the quantity of traditional probiotic Bifidobacteria of the AD group also rose. CONCLUSION: These alterations in fecal microbiome of the AD group indicate that patients with mild AD have unique gut microbial characteristics. These specific AD-associated intestinal microbes could serve as novel potential targets for early intervention of AD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36615708", + "title": "Probiotic ", + "year": 2022, + "journal": "Nutrients", + "authors": [ + "Shi S", + "Zhang Q", + "Sang Y", + "Ge S", + "Wang Q", + "Wang R", + "He J" + ], + "bacteria": "Granulicatella", + "condition": "healthy", + "relevance_score": 0.6892467102177692, + "mesh_terms": [ + "Humans", + "Aged", + "Bifidobacterium longum", + "Probiotics", + "Cognition", + "Bifidobacterium", + "Cognitive Dysfunction", + "Double-Blind Method" + ], + "raw_abstract": "Probiotics could improve cognitive functions in patients with neurological disorders such as Alzheimer\u2019s disease, but the effects on cognitive function in healthy older adults without cognitive impairment need further study. The purpose of this study was to investigate the effect of Bifidobacterium longum BB68S (BB68S) on cognitive functions among healthy older adults without cognitive impairment. A randomized, double-blind, placebo-controlled trial was conducted with 60 healthy older adults without cognitive impairment who were divided into probiotic or placebo groups and required to consume either a sachet of probiotic (BB68S, 5 \u00d7 1010 CFU/sachet) or placebo once daily for 8 weeks. The Montreal Cognitive Assessment (MoCA) was used as an inclusion screening tool to screen elderly participants with healthy cognitive function in our study, and the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) was used to assess cognitive function in subjects before and after intervention as an assessment tool. BB68S significantly improved subjects\u2019 cognitive functions (total RBANS score increased by 18.89 points after intervention, p < 0.0001), especially immediate memory, visuospatial/constructional, attention, and delayed memory domains. BB68S intervention increased the relative abundances of beneficial bacteria Lachnospira, Bifidobacterium, Dorea, and Cellulosilyticum, while decreasing those of bacteria related to cognition impairment, such as Collinsella, Parabacteroides, Tyzzerella, Bilophila, unclassified_c_Negativicutes, Epulopiscium, Porphyromonas, and Granulicatella. In conclusion, BB68S could improve cognitive functions in healthy elderly adults without cognitive impairment, along with having beneficial regulatory effects on their gut microbiota. This study supports probiotics as a strategy to promote healthy aging and advances cognitive aging research.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39895585", + "title": "Alterations in the Tongue Coating Microbiome in Patients With Diarrhea-Predominant Irritable Bowel Syndrome: A Cross-Sectional Study.", + "year": 2025, + "journal": "APMIS : acta pathologica, microbiologica, et immunologica Scandinavica", + "authors": [ + "Li Y", + "Mai Y", + "Jiao Y", + "Yuan Y", + "Qu Y", + "Zhang Y", + "Wang M", + "Zhang W", + "Lu X", + "Lin Z", + "Liang C", + "Li J", + "Mao T", + "Xie C" + ], + "bacteria": "Granulicatella", + "condition": "healthy", + "relevance_score": 0.6328835236971281, + "mesh_terms": [ + "Humans", + "Irritable Bowel Syndrome", + "Adult", + "Male", + "Female", + "Tongue", + "Cross-Sectional Studies", + "RNA, Ribosomal, 16S", + "Middle Aged", + "Diarrhea", + "Microbiota", + "Dysbiosis", + "Bacteria", + "Young Adult", + "High-Throughput Nucleotide Sequencing", + "DNA, Bacterial", + "Gastrointestinal Microbiome", + "Sequence Analysis, DNA" + ], + "raw_abstract": "The gut microbiota plays a critical role in the occurrence and development of IBS-D, however, IBS-D-associated tongue coating microbiome dysbiosis has not yet been clearly defined. To address this, we analyzed the structure and composition of the tongue coating microbiome in 23 IBS-D patients and 12 healthy controls using 16S rRNA high-throughput sequencing analysis. The 16S rRNA sequencing results revealed that the overall observed OTUs of tongue coating microbiome in IBS-D patients exhibited a significant decrease compared with the healthy controls. Alpha diversity analysis showed that the diversity and community richness were significantly reduced in IBS-D patients, and PCoA revealed a distinct clustering of tongue coating microbiome between the IBS-D patients and healthy controls. Microbial comparisons at the genus level showed that the abundance of Veillonella, Prevotella in IBS-D patients was higher than those in healthy controls, while Streptococcus, Haemophilus, Granulicatella, and Rothia were significantly reduced compared with the healthy volunteers. Functional analysis results showed significant differences in 88 functional metabolic pathways between the IBS-D patients and the healthy controls, including fatty acid biosynthesis. These findings identified the structure, composition, functionality of tongue coating microbiome in IBS-D patients, and hold promise the potential for therapeutic targets during IBS-D management.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33452946", + "title": "Characteristics of the vaginal microbiomes in prepubertal girls with and without vulvovaginitis.", + "year": 2021, + "journal": "European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology", + "authors": [ + "Xiaoming W", + "Jing L", + "Yuchen P", + "Huili L", + "Miao Z", + "Jing S" + ], + "bacteria": "Granulicatella", + "condition": "healthy", + "relevance_score": 0.5756048985114303, + "mesh_terms": [ + "Bacteria", + "Child", + "Child, Preschool", + "Female", + "Humans", + "Microbiota", + "Phylogeny", + "Vagina", + "Vulvovaginitis" + ], + "raw_abstract": "The present study focused on the characteristics of the vaginal microbiomes in prepubertal girls with and without vulvovaginitis. We collected 24 vaginal samples and 16 fecal samples from 10 girls aged 3-9 years with vulvovaginitis and 16 healthy girls of the same age. The samples were divided into three groups: fecal swabs from healthy controls (HF), vaginal swabs from healthy controls (HVS), and vaginal swabs from girls with vulvovaginitis (VVS). Sequencing of the V3-V4 region of the 16S rDNA gene was performed with the NovaSeq PE250 platform to reveal the vaginal microbial community structure in healthy prepubertal girls and vulvovaginitis-associated microbiota. The intestinal microbiomes of healthy children were also analyzed for comparison. This study revealed that the healthy vaginal tract in prepubertal girls was dominated by Prevotella, Porphyromonas, Ezakiella, and Peptoniphilus species, with a high diversity of microbiota. The vulvovaginitis-associated microbiota were dominated by Streptococcus, Prevotella, Haemophilus, and Granulicatella, with lower diversity than that in healthy girls. Furthermore, the compositions of the vaginal and intestinal microbiomes were completely different. ANOSIM, MRPP, Adonis, and AMOVA were used to analyze the beta diversity, and the results showed that there were significant differences in the microbial communities among the three groups. Lactobacillus deficiency and high bacterial diversity were characteristics of the vaginal microbiome in healthy prepubertal girls; this is inconsistent with that in reproductive-age women. The vulvovaginitis-associated vaginal microbiota differed dramatically from normal microbiota, and the main causative agents were not fecal in origin.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34294722", + "title": "Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization.", + "year": 2021, + "journal": "NPJ biofilms and microbiomes", + "authors": [ + "Wu Y", + "Cheng X", + "Jiang G", + "Tang H", + "Ming S", + "Tang L", + "Lu J", + "Guo C", + "Shan H", + "Huang X" + ], + "bacteria": "Granulicatella", + "condition": "healthy", + "relevance_score": 0.34461681101212344, + "mesh_terms": [ + "Bacteria", + "COVID-19", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Hospitalization", + "Humans", + "Male", + "Mouth", + "RNA, Ribosomal, 16S", + "SARS-CoV-2", + "Viral Load" + ], + "raw_abstract": "The human oral and gut commensal microbes play vital roles in the development and maintenance of immune homeostasis, while its association with susceptibility and severity of SARS-CoV-2 infection is barely understood. In this study, we investigated the dynamics of the oral and intestinal flora before and after the clearance of SARS-CoV-2 in 53 COVID-19 patients, and then examined their microbiome alterations in comparison to 76 healthy individuals. A total of 140 throat swab samples and 81 fecal samples from these COVID-19 patients during hospitalization, and 44 throat swab samples and 32 fecal samples from sex and age-matched healthy individuals were collected and then subjected to 16S rRNA sequencing and viral load inspection. We found that SARS-CoV-2 infection was associated with alterations of the microbiome community in patients as indicated by both alpha and beta diversity indexes. Several bacterial taxa were identified related to SARS-CoV-2 infection, wherein elevated Granulicatella and Rothia mucilaginosa were found in both oral and gut microbiome. The SARS-CoV-2 viral load in those samples was also calculated to identify potential dynamics between COVID-19 and the microbiome. These findings provide a meaningful baseline for microbes in the digestive tract of COVID-19 patients and will shed light on new dimensions for disease pathophysiology, potential microbial biomarkers, and treatment strategies for COVID-19.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39089446", + "title": "Temporal effects of lascufloxacin on human gut and salivary microbiota: Analysis using next-generation sequencing method.", + "year": 2025, + "journal": "Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy", + "authors": [ + "Mukuda K", + "Inoue R", + "Takata M", + "Takazawa K", + "Noma H", + "Morishima S", + "Oda M", + "Ma'arif AS", + "Endo Y", + "Sunada H", + "Doi A", + "Matsuda R", + "Nishikawa Y", + "Okada K", + "Kitaura T", + "Nakamoto M", + "Yamasaki A", + "Chikumi H" + ], + "bacteria": "Granulicatella", + "condition": "healthy", + "relevance_score": 0.33200532403576616, + "mesh_terms": [ + "Humans", + "Saliva", + "Gastrointestinal Microbiome", + "Male", + "High-Throughput Nucleotide Sequencing", + "Female", + "Middle Aged", + "Adult", + "Fluoroquinolones", + "Anti-Bacterial Agents", + "Feces", + "Microbiota", + "Aged", + "Bacteria", + "Pneumonia", + "Young Adult" + ], + "raw_abstract": "INTRODUCTION: Antimicrobial treatment disrupts human microbiota. The effects of lascufloxacin (LSFX), a new fluoroquinolone, on human microbiota remains unknown. Therefore, in this study, we aimed to evaluate the effects of LSFX administration on the gut and salivary microbiota of healthy participants and those with pneumonia. METHODS: LSFX (75\u00a0mg, once a day, orally) was administered to healthy adults (healthy group) and adult patients with pneumonia (pneumonia group), and fecal and saliva samples were collected at five time points (Days 0, 3, 7, 14, and 28). Using the collected samples, \u03b1- and \u03b2-diversity indices, as well as bacterial composition of the gut microbiota and salivary microbiota were analyzed using next-generation sequencing. RESULTS: In the healthy group, \u03b1-diversity indices of the gut and salivary microbiota were reduced and the lowest values on Day 3. For the gut microbiota, the Chao1 index (richness) recovered on Day 28, whereas the Shannon index (evenness) did not. In the salivary microbiota, the Chao1 and Shannon indices did not recover within the 28 day period. The \u03b2-diversity indices changed after LSFX administration and subsequently recovered on Day 28. After LSFX administration, the abundance of the Lachnospiraceae family decreased in the gut microbiota, and the abundance of Granulicatella, Streptococcus, Prevotella, Absconditabacteriales(SR1), and Saccharimonadales decreased in the salivary microbiota. In the pneumonia group, the \u03b1-diversity indices were lowest on Day 14 after LSFX administration. CONCLUSIONS: We elucidated that LSFX administration differentially affected the gut and salivary microbiota; however, the richness and beta diversity recovered within 28 days.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36241691", + "title": "Profile of gut microbiota and serum metabolites associated with metabolic syndrome in a remote island most afflicted by obesity in Japan.", + "year": 2022, + "journal": "Scientific reports", + "authors": [ + "Uema T", + "Millman JF", + "Okamoto S", + "Nakamura T", + "Yamashiro K", + "Uehara M", + "Honma KI", + "Miyazato M", + "Ashikari A", + "Saito S", + "Maeda S", + "Imamura M", + "Ishida H", + "Matsushita M", + "Nakamura K", + "Masuzaki H" + ], + "bacteria": "Granulicatella", + "condition": "healthy", + "relevance_score": 0.22762248541258207, + "mesh_terms": [ + "Body Mass Index", + "Creatine", + "Gastrointestinal Microbiome", + "Glycated Hemoglobin", + "Humans", + "Insulins", + "Japan", + "Metabolic Syndrome", + "Obesity", + "Pyruvic Acid", + "Triglycerides" + ], + "raw_abstract": "Numerous studies have revealed distinct differences in the profiles of gut microbiota between non-obese and obese individuals. To date, however, little is known if any disparities in the community of gut microbiota exist between metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO) subjects. We therefore aimed to comprehensively characterize the gut microbiota and circulating metabolites in serum from both MHO and MUO residing in the remote island, Kumejima, where the prevalence of obesity is one of the highest in Japan, and explored possible correlations between the gut microbiota profile and markers of metabolic syndrome. Results revealed that MUO showed significantly higher levels of genera such as g_Succinivibrio, g_Granulicatella, g_Brachyspira, g_Oribacterium and g_Atopobium in comparison to MHO. Moreover, abundance of g_Succinivibrio, g_Brachyspira and g_Atopobium were positively correlated with value of fasting insulin, HOMA-R, circulating triglycerides, diastolic blood pressure, BMI, body weight, waist circumference and HbA1c. In addition, MUO compared to MHO showed an imbalance of serum metabolites, with a significant elevation in 2-oxoisovaleric acid, pyruvic acid, 2-hydroxybutyric acid, and creatine. Our data highlight unmet needs in precision approaches for the treatment of obesity, targeting the gut microbiota profile and serum metabolites in a distinct population affected by obesity.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31211854", + "title": "The imbalance of gut microbiota and its correlation with plasma inflammatory cytokines in pemphigus vulgaris patients.", + "year": 2019, + "journal": "Scandinavian journal of immunology", + "authors": [ + "Huang S", + "Mao J", + "Zhou L", + "Xiong X", + "Deng Y" + ], + "bacteria": "Granulicatella", + "condition": "healthy", + "relevance_score": 0.22206138871951084, + "mesh_terms": [ + "Adult", + "Autoantibodies", + "Autoimmune Diseases", + "Cytokines", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Male", + "Middle Aged", + "Pemphigus", + "Plasma", + "T-Lymphocytes, Regulatory", + "Th1 Cells", + "Th17 Cells", + "Th2 Cells" + ], + "raw_abstract": "Pemphigus vulgaris (PV) is an autoimmune disease characterized by the production of IgG autoantibodies owing to an imbalance in the Th1/Th2 and Th17/Tregs cell pathways. The role of gut microbiota in the development of immune system and autoimmune diseases has been unraveled in the last two decades. However, data pertaining to gut microbiota of PV patients is largely lacking. We aimed to compare the gut microbiota of PV patients and healthy\u2009controls and assessed potential correlation with circulating cytokines of Th1/Th2/Th17 cell. Faecal bacterial diversity was analysed in 18 PV patients and 14 age- and gender-matched healthy individuals using hypervariable\u2009tag\u2009sequencing\u2009of the\u2009V3-V4 region\u2009of the\u200916S\u2009rRNA\u2009gene. Plasma levels of 20 inflammatory cytokines were assessed using the Luminex screening system. As a result, we identified 10 differentially abundant taxa between patients and controls. At the genera level, Lachnospiracea_incertae_sedis and Coprococcus decreased, while Granulicatella, Flavonifractor enriched in PV. Plasma levels of C5a, interleukin (IL)-2R, IL-6, IL-8, IL-7, IL-1\u03b2, IL17A, IL-5 and IL-21 were significantly increased in PV Flavonifractor exhibited a positive correlation with C5a, IL-6, IL-8, IL-7, IL-1\u03b2, IL17A and IL-21. Lachnospiracea_incertae_sedis and Coprococcus showed a negative correlation with IL-17A. Our results are consistent with the hypothesis that PV patients have gut microbial dysbiosis which might contribute to the immune disorder and the development of PV.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32352710", + "title": "Increased Ileal Immunoglobulin A Production and Immunoglobulin A-Coated Bacteria in Diarrhea-Predominant Irritable Bowel Syndrome.", + "year": 2020, + "journal": "Clinical and translational gastroenterology", + "authors": [ + "Liu Y", + "Yuan X", + "Li L", + "Lin L", + "Zuo X", + "Cong Y", + "Li Y" + ], + "bacteria": "Granulicatella", + "condition": "healthy", + "relevance_score": 0.20583476897832279, + "mesh_terms": [ + "Adult", + "Case-Control Studies", + "DNA, Bacterial", + "Diarrhea", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Ileum", + "Immunoglobulin A", + "Intestinal Mucosa", + "Irritable Bowel Syndrome", + "Male", + "Middle Aged", + "Prospective Studies", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVES: Immune activation and intestinal microbial dysbiosis could induce diarrhea-predominant irritable bowel syndrome (IBS-D). We examined the roles of ileal immunoglobulin A (IgA) and IgA-coated bacteria in IBS-D pathogenesis. METHODS: Peripheral blood, fecal samples, and ileal and cecal biopsies were collected from 32 healthy volunteers and 44 patients with IBS-D. Quantitative reverse transcriptase polymerase chain reaction was used to assess differential gene expression. IgA levels in the blood and fecal samples were quantified by an enzyme-linked immunosorbent assay. IgA cells were assessed by immunofluorescence imaging. Flow-cytometry-based IgA bacterial cell sorting and 16S rRNA gene sequencing (IgA-SEQ) was used to isolate and identify fecal IgA bacteria. RESULTS: Fecal IgA, particularly IgA1, was upregulated in patients with IBS-D. IgA class switch and B cell-activating factor-receptor were increased in the terminal ileum of patients. The intestinal microbiota composition was altered in patients compared with that in controls. IgA-SEQ showed that the proportion of fecal IgA-coated bacteria was increased significantly in patients with IBS-D. IgA bacteria in patients with IBS-D showed higher abundances of Escherichia-Shigella, Granulicatella, and Haemophilus compared with healthy controls and IgA bacteria in patients with IBS-D. The Escherichia-Shigella IgA coating index was positively correlated with anxiety and depression. The Escherichia-Shigella relative abundance, luminal IgA activity, and some altered IgA-coated bacteria were positively associated with the clinical manifestations of IBS-D. DISCUSSION: Microbial dysbiosis may promote the terminal ileal mucosa to produce higher levels of IgA, increasing the proportion of IgA-coated bacteria by activating IgA class switching, which might regulate local inflammation and clinical manifestations in IBS-D. IgA may mediate the effects of microbial dysbiosis on the pathogenesis of IBS-D.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39895585", + "title": "Alterations in the Tongue Coating Microbiome in Patients With Diarrhea-Predominant Irritable Bowel Syndrome: A Cross-Sectional Study.", + "year": 2025, + "journal": "APMIS : acta pathologica, microbiologica, et immunologica Scandinavica", + "authors": [ + "Li Y", + "Mai Y", + "Jiao Y", + "Yuan Y", + "Qu Y", + "Zhang Y", + "Wang M", + "Zhang W", + "Lu X", + "Lin Z", + "Liang C", + "Li J", + "Mao T", + "Xie C" + ], + "bacteria": "Rothia", + "condition": "healthy", + "relevance_score": 0.6328835236971281, + "mesh_terms": [ + "Humans", + "Irritable Bowel Syndrome", + "Adult", + "Male", + "Female", + "Tongue", + "Cross-Sectional Studies", + "RNA, Ribosomal, 16S", + "Middle Aged", + "Diarrhea", + "Microbiota", + "Dysbiosis", + "Bacteria", + "Young Adult", + "High-Throughput Nucleotide Sequencing", + "DNA, Bacterial", + "Gastrointestinal Microbiome", + "Sequence Analysis, DNA" + ], + "raw_abstract": "The gut microbiota plays a critical role in the occurrence and development of IBS-D, however, IBS-D-associated tongue coating microbiome dysbiosis has not yet been clearly defined. To address this, we analyzed the structure and composition of the tongue coating microbiome in 23 IBS-D patients and 12 healthy controls using 16S rRNA high-throughput sequencing analysis. The 16S rRNA sequencing results revealed that the overall observed OTUs of tongue coating microbiome in IBS-D patients exhibited a significant decrease compared with the healthy controls. Alpha diversity analysis showed that the diversity and community richness were significantly reduced in IBS-D patients, and PCoA revealed a distinct clustering of tongue coating microbiome between the IBS-D patients and healthy controls. Microbial comparisons at the genus level showed that the abundance of Veillonella, Prevotella in IBS-D patients was higher than those in healthy controls, while Streptococcus, Haemophilus, Granulicatella, and Rothia were significantly reduced compared with the healthy volunteers. Functional analysis results showed significant differences in 88 functional metabolic pathways between the IBS-D patients and the healthy controls, including fatty acid biosynthesis. These findings identified the structure, composition, functionality of tongue coating microbiome in IBS-D patients, and hold promise the potential for therapeutic targets during IBS-D management.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30918225", + "title": "Next-generation sequencing analysis of bacterial flora in bovine protothecal mastitic milk and feces.", + "year": 2019, + "journal": "The Journal of veterinary medical science", + "authors": [ + "Miura A", + "Kurumisawa T", + "Kano R", + "Ito T", + "Suzuki K", + "Kamata H" + ], + "bacteria": "Rothia", + "condition": "healthy", + "relevance_score": 0.5814247314512323, + "mesh_terms": [ + "Animals", + "Cattle", + "Feces", + "Female", + "High-Throughput Nucleotide Sequencing", + "Mastitis, Bovine", + "RNA, Bacterial", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "The aim of the present study was to evaluate the bacterial flora in the udder and intestinal environments in cows with and without protothecal mastitis. We used next-generation sequencing (NGS) analysis to identify 16S rRNA genes from bacterial flora present in 13 milk and 13 fecal samples from protothecal mastitic and healthy dairy cows in the Aichi region of Japan. Sequences associated with 5 species (Calothrix desertica, Corynebacterium simulans, Corynebacterium striatum, Empedobacter falsenii, and Rothia endophytica) showed the highest prevalence in samples of milk and feces from animals with protothecal mastitis. This range of species differed from those detected in the milk and feces from healthy cows.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37700874", + "title": "Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing.", + "year": 2023, + "journal": "Journal of asthma and allergy", + "authors": [ + "Wan J", + "Song J", + "Lv Q", + "Zhang H", + "Xiang Q", + "Dai H", + "Zheng H", + "Lin X", + "Zhang W" + ], + "bacteria": "Rothia", + "condition": "healthy", + "relevance_score": 0.4092405953598793, + "mesh_terms": [], + "raw_abstract": "PURPOSE: Recent studies had shown that gut microbiota played a significant role in the development of the immune system and may affect the course of airway allergic disease. We conducted this study to determine unique gut microbial associated with allergic disease in children by shotgun gene sequencing. METHODS: We collected fecal samples from children with allergic asthma (n = 23) and allergic rhinitis (n = 18), and healthy control (n = 19). The gut microbiota of specimens was analyzed by high-throughput metagenomic shotgun gene sequencing. RESULTS: The intestinal microbiota of children with allergic asthma and allergic rhinitis was characterized by increased microbial richness and diversity. Simpson and Shannon were significantly elevated in children with allergic asthma. Principal coordinates analysis (PCoA) showed that the gut microbial communities cluster patterns of children with asthma or rhinitis were significantly different from those of healthy controls. However, no significant difference was found between asthma group and rhinitis group At the phylum level, higher relative abundance of Firmicutes was found in the allergic rhinitis group and allergic asthma group, while the level of Bacteroidetes was significantly lower. At the genus level, Corynebacterium, Streptococcus, Dorea, Actinomyces, Bifidobacterium, Blautia, and Rothia were significantly enriched in the allergic asthma group. Finally, a random forest classifier model selected 16 general signatures to discriminate the allergic asthma group from the healthy control group. CONCLUSION: In conclusion, children in the allergic rhinitis group and allergic asthma group had altered gut microbiomes in comparison with the healthy control group. Compared to healthy children, the gut microbiome in children with allergic diseases has higher pro-inflammatory potential and increased production of pro-inflammatory molecules.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33773586", + "title": "The gut microbial composition in polycystic ovary syndrome with insulin resistance: findings from a normal-weight population.", + "year": 2021, + "journal": "Journal of ovarian research", + "authors": [ + "He F", + "Li Y" + ], + "bacteria": "Rothia", + "condition": "healthy", + "relevance_score": 0.3643156816969864, + "mesh_terms": [ + "Adult", + "Female", + "Gastrointestinal Microbiome", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Insulin Resistance", + "Polycystic Ovary Syndrome" + ], + "raw_abstract": "BACKGROUND: Limited studies have reported the relationship between intestinal flora dysbiosis and clinical characteristics in polycystic ovary syndrome (PCOS). However, the structure and characteristics of gut microbiota in PCOS have not been fully elucidated. OBJECTIVE: To analyze the composition of the Intestinal flora population in normal-weight women with PCOS and insulin resistance(IR) compared to PCOS alone and healthy women. METHODS: A total of 14 PCOS patients with insulin resistant(PCOS-IR) and 12 PCOS alone (PCOS-NIR), and 10 age- and body mass index-matched healthy control women (HC). BMI: 18.5-23.9\u00a0kg/m RESULTS: No significant difference in diversity was observed between PCOA and sample cluster analysis among the three groups (Beta-diversity) and Alpha-diversity. The relative abundance of Rothia, Ruminococcus, and Enterococcus was significantly higher in the PCOS-IR group than in the other two groups (P\u2009<\u20090.05), while that of Prevotella was dramatically decreased (P\u2009<\u20090.05). The abundance of Enterococcus was positively correlated with waist circumference, hip circumference, diastolic blood pressure, and insulin resistance index. Meanwhile, Rothia abundance is positively associated with waist circumference and free fatty acids. CONCLUSIONS: The gut microbial composition of PCOS patients with insulin resistance is different from that of PCOS alone and healthy women. The difference is correlated with the clinical characteristics of PCOS, with regards to insulin resistance, abdominal obesity, free fatty acids, and other indicators. PCOS-IR patients have an increased abundance of Enterococcus which potentially the intestinal environment of the host by enriching the metabolic pathways related to insulin resistance, causing the occurrence and development of PCOS.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34294722", + "title": "Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization.", + "year": 2021, + "journal": "NPJ biofilms and microbiomes", + "authors": [ + "Wu Y", + "Cheng X", + "Jiang G", + "Tang H", + "Ming S", + "Tang L", + "Lu J", + "Guo C", + "Shan H", + "Huang X" + ], + "bacteria": "Rothia", + "condition": "healthy", + "relevance_score": 0.34461681101212344, + "mesh_terms": [ + "Bacteria", + "COVID-19", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Hospitalization", + "Humans", + "Male", + "Mouth", + "RNA, Ribosomal, 16S", + "SARS-CoV-2", + "Viral Load" + ], + "raw_abstract": "The human oral and gut commensal microbes play vital roles in the development and maintenance of immune homeostasis, while its association with susceptibility and severity of SARS-CoV-2 infection is barely understood. In this study, we investigated the dynamics of the oral and intestinal flora before and after the clearance of SARS-CoV-2 in 53 COVID-19 patients, and then examined their microbiome alterations in comparison to 76 healthy individuals. A total of 140 throat swab samples and 81 fecal samples from these COVID-19 patients during hospitalization, and 44 throat swab samples and 32 fecal samples from sex and age-matched healthy individuals were collected and then subjected to 16S rRNA sequencing and viral load inspection. We found that SARS-CoV-2 infection was associated with alterations of the microbiome community in patients as indicated by both alpha and beta diversity indexes. Several bacterial taxa were identified related to SARS-CoV-2 infection, wherein elevated Granulicatella and Rothia mucilaginosa were found in both oral and gut microbiome. The SARS-CoV-2 viral load in those samples was also calculated to identify potential dynamics between COVID-19 and the microbiome. These findings provide a meaningful baseline for microbes in the digestive tract of COVID-19 patients and will shed light on new dimensions for disease pathophysiology, potential microbial biomarkers, and treatment strategies for COVID-19.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39415150", + "title": "Oral microbiome dysbiosis may be associated with intra cranial aneurysms.", + "year": 2024, + "journal": "BMC oral health", + "authors": [ + "Ma J", + "Wang F", + "Zhu Y", + "Tian Y", + "Du C", + "Yan L", + "Ding C", + "Wang D" + ], + "bacteria": "Rothia", + "condition": "healthy", + "relevance_score": 0.2952069971335803, + "mesh_terms": [ + "Humans", + "Intracranial Aneurysm", + "Female", + "Male", + "Middle Aged", + "Dysbiosis", + "Microbiota", + "Case-Control Studies", + "Saliva", + "Mouth", + "RNA, Ribosomal, 16S", + "Adult", + "Aged", + "High-Throughput Nucleotide Sequencing" + ], + "raw_abstract": "BACKGROUND: Although the etiology of aneurysms remains elusive, recent advances in high-throughput sequencing technology and ongoing human microbiome investigations suggest a potential link between microbiome composition and the onset of various human diseases. OBJECTIVE: This study aimed to utilize high-throughput 16\u00a0S rRNA gene sequencing to analyze the oral flora bacterial profiles of individuals, comparing patients with intracranial aneurysms to a healthy control group. Importantly, we sought to identify differences in the oral microbiota and offer novel insights and methods for early diagnosis and identification of intracranial aneurysms. METHOD: Saliva samples were collected from 60 patients with cerebral aneurysms (case group) and 130 healthy individuals (control group). The V3-V4 region of the bacterial 16\u00a0S rRNA gene was amplified and sequenced using the HiSeq high-throughput sequencing platform to establish the bacterial profile. Sequencing data were analyzed using QIIME2 and Metastats software to compare composition differences and relative abundance at the phylum and genus levels in the oral microbiota of the two groups. RESULTS: Significant differences in oral microbiota composition were observed between patients in the case and control groups (P\u2009<\u20090.05). Genus-level identification highlighted key positions occupied by Eubacterium, Saccharimonadaceae, Rothia, Gemella, Streptococcus, Lactobacillales, Phocaeicola, Bacteroides, Saccharimonadales, and Abiotrophia. CONCLUSION: This study revealed noteworthy distinctions in the composition, abundance, and diversity of oral microbiota between intracranial aneurysm patients and healthy controls. These disparities suggest a potential correlation between oral microbiota and the development of intracranial aneurysms, offering new avenues for early diagnosis and intervention. However, limitations such as a small sample size, lack of prospective design, and absence of causal inference warrant further validation and exploration.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29615776", + "title": "Dysbiosis of the salivary microbiota in pediatric-onset primary sclerosing cholangitis and its potential as a biomarker.", + "year": 2018, + "journal": "Scientific reports", + "authors": [ + "Iwasawa K", + "Suda W", + "Tsunoda T", + "Oikawa-Kawamoto M", + "Umetsu S", + "Takayasu L", + "Inui A", + "Fujisawa T", + "Morita H", + "Sogo T", + "Hattori M" + ], + "bacteria": "Rothia", + "condition": "healthy", + "relevance_score": 0.255189596239146, + "mesh_terms": [ + "Adolescent", + "Biomarkers", + "Case-Control Studies", + "Child", + "Cholangitis, Sclerosing", + "Dysbiosis", + "Female", + "Humans", + "Male", + "Phenotype", + "RNA, Ribosomal, 16S", + "Saliva" + ], + "raw_abstract": "Primary sclerosing cholangitis (PSC) is a liver disease known for its frequent concurrence with inflammatory bowel disease. Dysbiosis of the gut microbiota in PSC was reported in several studies, but the microbiological features of the salivary microbiota in PSC have not been established. Here we compared the salivary microbial communities of 24 pediatric-onset PSC patients, 16 age-matched ulcerative colitis (UC) patients, and 24 healthy controls (HCs) by analyzing the bacterial 16S rRNA gene sequence data. The species-richness (\u03b1-diversity) showed no significant between-group differences, whereas the overall salivary microbiota structure (\u03b2-diversity) showed significant differences among the three groups. Taxonomic assignment revealed that the PSC salivary microbiota were characterized by significant decreases in the abundance of Rothia and Haemophilus compared to the HC group, and significantly decreased Haemophilus and increased Oribacterium compared to the UC group. By combining the genera selected by the random forest algorithm in machine learning, followed by confirmation with 10-fold cross-validation, we were able to distinguish the PSC group from the HC group with the area under the curve (AUC) of 0.7423, and from the UC group with the AUC of 0.8756. Our results indicate the potential of salivary microbiota as biomarkers for a noninvasive diagnosis of PSC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33782445", + "title": "Potential role of microbiome in Chronic Fatigue Syndrome/Myalgic Encephalomyelits (CFS/ME).", + "year": 2021, + "journal": "Scientific reports", + "authors": [ + "Lupo GFD", + "Rocchetti G", + "Lucini L", + "Lorusso L", + "Manara E", + "Bertelli M", + "Puglisi E", + "Capelli E" + ], + "bacteria": "Rothia", + "condition": "healthy", + "relevance_score": 0.24194261844933657, + "mesh_terms": [ + "Adult", + "Case-Control Studies", + "Chromatography, High Pressure Liquid", + "Dysbiosis", + "Fatigue Syndrome, Chronic", + "Feces", + "Female", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Male", + "Mass Spectrometry", + "Metabolomics", + "Microbiota", + "Middle Aged", + "Pilot Projects", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME) is a severe multisystemic disease characterized by immunological abnormalities and dysfunction of energy metabolism. Recent evidences suggest strong correlations between dysbiosis and pathological condition. The present research explored the composition of the intestinal and oral microbiota in CFS/ME patients as compared to healthy controls. The fecal metabolomic profile of a subgroup of CFS/ME patients was also compared with the one of healthy controls. The fecal and salivary bacterial composition in CFS/ME patients was investigated by Illumina sequencing of 16S rRNA gene amplicons. The metabolomic analysis was performed by an UHPLC-MS. The fecal microbiota of CFS/ME patients showed a reduction of Lachnospiraceae, particularly Anaerostipes, and an increased abundance of genera Bacteroides and Phascolarctobacterium compared to the non-CFS/ME groups. The oral microbiota of CFS/ME patients showed an increase of Rothia dentocariosa. The fecal metabolomic profile of CFS/ME patients revealed high levels of glutamic acid and argininosuccinic acid, together with a decrease of alpha-tocopherol. Our results reveal microbial signatures of dysbiosis in the intestinal microbiota of CFS/ME patients. Further studies are needed to better understand if the microbial composition changes are cause or consequence of the onset of CFS/ME and if they are related to any of the several secondary symptoms.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33839797", + "title": "Gut microbiota profiles and characterization of cultivable fungal isolates in IBS patients.", + "year": 2021, + "journal": "Applied microbiology and biotechnology", + "authors": [ + "Sciavilla P", + "Strati F", + "Di Paola M", + "Modesto M", + "Vitali F", + "Cavalieri D", + "Prati GM", + "Di Vito M", + "Aragona G", + "De Filippo C", + "Mattarelli P" + ], + "bacteria": "Rothia", + "condition": "healthy", + "relevance_score": 0.2345233303677031, + "mesh_terms": [ + "Dysbiosis", + "Ecosystem", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Irritable Bowel Syndrome", + "Quality of Life" + ], + "raw_abstract": "Studies so far conducted on irritable bowel syndrome (IBS) have been focused mainly on the role of gut bacterial dysbiosis in modulating the intestinal permeability, inflammation, and motility, with consequences on the quality of life. Limited evidences showed a potential involvement of gut fungal communities. Here, the gut bacterial and fungal microbiota of a cohort of IBS patients have been characterized and compared with that of healthy subjects (HS). The IBS microbial community structure differed significantly compared to HS. In particular, we observed an enrichment of bacterial taxa involved in gut inflammation, such as Enterobacteriaceae, Streptococcus, Fusobacteria, Gemella, and Rothia, as well as depletion of health-promoting bacterial genera, such as Roseburia and Faecalibacterium. Gut microbial profiles in IBS patients differed also in accordance with constipation. Sequence analysis of the gut mycobiota showed enrichment of Saccharomycetes in IBS. Culturomics analysis of fungal isolates from feces showed enrichment of Candida spp. displaying from IBS a clonal expansion and a distinct genotypic profiles and different phenotypical features when compared to HS of Candida albicans isolates. Alongside the well-characterized gut bacterial dysbiosis in IBS, this study shed light on a yet poorly explored fungal component of the intestinal ecosystem, the gut mycobiota. Our results showed a differential fungal community in IBS compared to HS, suggesting potential for new insights on the involvement of the gut mycobiota in IBS. KEY POINTS: \u2022 Comparison of gut microbiota and mycobiota between IBS and healthy subjects \u2022 Investigation of cultivable fungi in IBS and healthy subjects \u2022 Candida albicans isolates result more virulent in IBS subjects compared to healthy subjects.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39333290", + "title": "Altered gut microbial profile accompanied by abnormal short chain fatty acid metabolism exacerbates nonalcoholic fatty liver disease progression.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Yang C", + "Wu J", + "Yang L", + "Hu Q", + "Li L", + "Yang Y", + "Hu J", + "Pan D", + "Zhao Q" + ], + "bacteria": "Rothia", + "condition": "healthy", + "relevance_score": 0.2200727677545431, + "mesh_terms": [ + "Non-alcoholic Fatty Liver Disease", + "Humans", + "Gastrointestinal Microbiome", + "Fatty Acids, Volatile", + "Male", + "Female", + "Middle Aged", + "Feces", + "Adult", + "Disease Progression", + "RNA, Ribosomal, 16S", + "Bacteria" + ], + "raw_abstract": "Dysregulation of the gut microbiome has associated with the occurrence and progression of non-alcoholic fatty liver disease (NAFLD). To determine the diagnostic capacity of this association, we compared fecal microbiomes across 104 participants including non-NAFLD controls and NAFLD subtypes patients that were distinguished by magnetic resonance imaging. We measured their blood biochemical parameters, 16\u00a0S rRNA-based gut microbiota and fecal short-chain fatty acids (SCFAs). Multi-omic analyses revealed that NAFLD patients exhibited specific changes in gut microbiota and fecal SCFAs as compared to non-NAFLD subjects. Four bacterial genera (Faecalibacterium, Subdoligranulum, Haemophilus, and Roseburia) and two fecal SCFAs profiles (acetic acid, and butyric acid) were closely related to NAFLD phenotypes and could accurately distinguish NAFLD patients from healthy non-NAFLD subjects. Twelve genera belonging to Faecalibacterium, Subdoligranulum, Haemophilus, Intestinibacter, Agathobacter, Lachnospiraceae_UCG-004, Roseburia, Butyricicoccus, Actinomycetales_unclassified, [Eubacterium]_ventriosum_group, Rothia, and Rhodococcus were effective to distinguish NAFLD subtypes. Of them, combination of five genera can distinguish effectively mild NAFLD from non-NAFLD with an area under curve (AUC) of 0.84. Seven genera distinguish moderate NAFLD with an AUC of 0.83. Eight genera distinguish severe NAFLD with an AUC of 0.90. In our study, butyric acid distinguished mild-NAFLD from non-NAFLD with AUC value of 0.83. And acetic acid distinguished moderate-NAFLD and severe-NAFLD from non-NAFLD with AUC value of 0.84 and 0.70. In summary, our study and further analysis showed that gut microbiota and fecal SCFAs maybe a method with convenient detection advantages and invasive manner that are not only a good prediction model for early warning of NAFLD occurrence, but also have a strong ability to distinguish NAFLD subtypes.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26424567", + "title": "Early infancy microbial and metabolic alterations affect risk of childhood asthma.", + "year": 2015, + "journal": "Science translational medicine", + "authors": [ + "Arrieta MC", + "Stiemsma LT", + "Dimitriu PA", + "Thorson L", + "Russell S", + "Yurist-Doutsch S", + "Kuzeljevic B", + "Gold MJ", + "Britton HM", + "Lefebvre DL", + "Subbarao P", + "Mandhane P", + "Becker A", + "McNagny KM", + "Sears MR", + "Kollmann T", + "Mohn WW", + "Turvey SE", + "Finlay BB" + ], + "bacteria": "Rothia", + "condition": "healthy", + "relevance_score": 0.20163300771382248, + "mesh_terms": [ + "Animals", + "Asthma", + "Child", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Infant", + "Metabolome", + "Mice", + "Microbiota", + "Phenotype", + "Pneumonia", + "Risk Factors", + "Software" + ], + "raw_abstract": "Asthma is the most prevalent pediatric chronic disease and affects more than 300 million people worldwide. Recent evidence in mice has identified a \"critical window\" early in life where gut microbial changes (dysbiosis) are most influential in experimental asthma. However, current research has yet to establish whether these changes precede or are involved in human asthma. We compared the gut microbiota of 319 subjects enrolled in the Canadian Healthy Infant Longitudinal Development (CHILD) Study, and show that infants at risk of asthma exhibited transient gut microbial dysbiosis during the first 100 days of life. The relative abundance of the bacterial genera Lachnospira, Veillonella, Faecalibacterium, and Rothia was significantly decreased in children at risk of asthma. This reduction in bacterial taxa was accompanied by reduced levels of fecal acetate and dysregulation of enterohepatic metabolites. Inoculation of germ-free mice with these four bacterial taxa ameliorated airway inflammation in their adult progeny, demonstrating a causal role of these bacterial taxa in averting asthma development. These results enhance the potential for future microbe-based diagnostics and therapies, potentially in the form of probiotics, to prevent the development of asthma and other related allergic diseases in children.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38177971", + "title": "Gut microbiota alteration and its association with immune function in post-COVID-19 patients.", + "year": 2024, + "journal": "Folia microbiologica", + "authors": [ + "Cai J", + "Xu J", + "Tan Y", + "Xiang Y", + "Li Z", + "Zheng J", + "Li Y" + ], + "bacteria": "Hungatella", + "condition": "healthy", + "relevance_score": 0.6030254942603244, + "mesh_terms": [ + "Humans", + "COVID-19", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "SARS-CoV-2", + "Male", + "Middle Aged", + "Female", + "Adult", + "Bacteria", + "Aged", + "Interleukin-8", + "Killer Cells, Natural", + "Feces", + "Interleukin-1beta" + ], + "raw_abstract": "To reveal the variation of gut microbiota and its association with immune function in cured patients with coronavirus 2019 (COVID-19) disease, gut microbiota of patients discharged from hospital for 20\u2009~\u200923\u00a0months and healthy volunteers was analyzed by high throughput 16S rRNA sequencing. The diversity and abundance were compared, and the correlation with immunity factors was investigated, and changes in the content of 6 genera microorganisms with proportion higher than 0.1% were revealed in patients with COVID-19 disease: reduced content of Subdoligranulum, Haemophilus, Coprococcus, Eubacterium vertriosum group, and Lachnospiraceae ND3007 group and increased content of Hungatella. NK cells were negatively correlated to Subdoligranulum, while CD8 cells were positively correlated to Subdoligranulum but negative to Hungatella. IL-8 concentration was negatively correlated to Subdoligranulum, Haemophilus, Coprococcus, Eubacterium vertriosum group, and Lachnospiraceae ND3007 group but positively to Hungatella, while IL-1\u03b2 concentration was negatively correlated to Haemophilus and Eubacterium ventriosum group but positively to Hungatella. The variation of probiotics and potential pathogenic bacteria implies a higher risk in diseases and inflammation, and the modulation of the gut microbiota may help the healing of COVID-19 patients.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38782999", + "title": "Uncovering the characteristics of the gut microbiota in patients with ischemic stroke and hemorrhagic stroke.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Chen YZ", + "Huang ZY", + "Zhou WW", + "Li ZY", + "Li XP", + "Chen SS", + "Ma JK" + ], + "bacteria": "Hungatella", + "condition": "healthy", + "relevance_score": 0.3528206515139304, + "mesh_terms": [ + "Gastrointestinal Microbiome", + "Humans", + "Ischemic Stroke", + "Male", + "Hemorrhagic Stroke", + "Female", + "Case-Control Studies", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Aged", + "Bacteria", + "High-Throughput Nucleotide Sequencing" + ], + "raw_abstract": "This study aimed to explore the gut microbiota characteristics of ischemic and hemorrhagic stroke patients. A case-control study was conducted, and high-throughput sequencing of the V4-V5 region of 16S rRNA was used to analyze the differences in gut microbiota. The results showed that Proteobacteria was significantly increased in the ischemic stroke group compared with the healthy control group, while Fusobacteria was significantly increased in the hemorrhagic stroke group. In the ischemic stroke group, Butyricimonas, Alloprevotella, and Escherichia were significantly more abundant than in the healthy control group. In the hemorrhagic stroke group, Atopobium, Hungatella, Eisenbergiella, Butyricimonas, Odonbacter, Lachnociostridium, Alistipes, Parabacteroides, and Fusobacterium were significantly more abundant than in the healthy control group. Additionally, Alloprevotella, Ruminococcus, and Prevotella were significantly more abundant in the ischemic stroke group than in the hemorrhagic stroke group. The gut microbiota of ischemic and hemorrhagic stroke patients has significant diversity characteristics. These results provide new theoretical basis for exploring the prevention and treatment of different types of stroke through gut microbiota research.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36113426", + "title": "Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course.", + "year": 2022, + "journal": "Cell", + "authors": [], + "bacteria": "Hungatella", + "condition": "healthy", + "relevance_score": 0.3208181431713567, + "mesh_terms": [ + "Fatty Acids, Volatile", + "Gastrointestinal Microbiome", + "Humans", + "Interferon-beta", + "Multiple Sclerosis", + "Phytic Acid", + "Pyruvates" + ], + "raw_abstract": "Changes in gut microbiota have been associated with several diseases. Here, the International Multiple Sclerosis Microbiome Study (iMSMS) studied the gut microbiome of 576 MS patients (36% untreated) and genetically unrelated household healthy controls (1,152 total subjects). We observed a significantly increased proportion of Akkermansia muciniphila, Ruthenibacterium lactatiformans, Hungatella hathewayi, and Eisenbergiella tayi and decreased Faecalibacterium prausnitzii and Blautia species. The phytate degradation pathway was over-represented in untreated MS, while pyruvate-producing carbohydrate metabolism pathways were significantly reduced. Microbiome composition, function, and derived metabolites also differed in response to disease-modifying treatments. The therapeutic activity of interferon-\u03b2 may in part be associated with upregulation of short-chain fatty acid transporters. Distinct microbial networks were observed in untreated MS and healthy controls. These results strongly support specific gut microbiome associations with MS risk, course and progression, and functional changes in response to treatment.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38822184", + "title": "Alteration in gut microbial characteristics of patients with acromegaly.", + "year": 2024, + "journal": "Endocrine", + "authors": [ + "Babayeva A", + "Ozkul C", + "Coskun M", + "Uzun A", + "Yalcin MM", + "Yalinay M", + "Akturk M", + "Toruner FB", + "Karakoc MA", + "Yetkin I", + "Altinova AE" + ], + "bacteria": "Hungatella", + "condition": "healthy", + "relevance_score": 0.32037779856361365, + "mesh_terms": [ + "Humans", + "Acromegaly", + "Gastrointestinal Microbiome", + "Male", + "Female", + "Middle Aged", + "Adult", + "Feces", + "RNA, Ribosomal, 16S", + "Aged", + "Case-Control Studies" + ], + "raw_abstract": "PURPOSE: Studies on intestinal microbiota in acromegaly are scant. This study aimed to characterize the gut microbiome in patients with acromegaly. METHOD: Stool samples were collected from 11 patients newly diagnosed with acromegaly and 12 healthy controls matched for body mass index (BMI) and age after three days on a standard diet. Clinical and gut microbial composition assessments were performed for the two participant groups using 16S rRNA gene amplicon sequencing. RESULTS: There was no difference in the alpha diversity of the microbiota between the samples from patients with acromegaly and those from the healthy controls. Based on beta diversity measurements, differences in microbial community structures were found to be significant only when compared using the Jaccard similarity index. The corresponding Firmicutes/Bacteroidota ratio tended to be higher in individuals with acromegaly than in healthy controls. The mean relative abundance of Actinobacteriota was 2.3 times higher in the acromegaly patient group than in the control group. Eggerthellaceae, Christensenellaceae, and Bacteroidaceae were among the significantly abundant bacterial families in the samples from the acromegaly patient group, while Butyricicoccaceae and Tannerellaceae were decreased. At the level of the genus, the most discriminative features were the abundance of Prevotella 7, Bacteroides, Senegalimassilia, Enterohabdus, the Family XIII AD3011 group, Howardella, and Hungatella in the samples from the acromegaly patient group. In contrast, the Butyrivibrio and the Eubacterium eligens group were the most discriminative genera for the healthy controls and were significantly less abundant in patients with acromegaly. While there were no significantly differentiated taxa between the diabetic and non-diabetic subgroups, Prevotella_7 was significantly enriched in the osteoarthritis (OA) subgroup. No significant association was found between individual genera and growth hormone (GH) levels and insulin-like growth factor-1 (IGF-1) levels as well as the upper limit of normal (ULN). CONCLUSION: Although alpha and beta diversity were mainly similar between the two groups, significant differences were observed between the acromegaly group and the control group at the family and genus levels. These results suggest that the differences between the microbial communities in patients with acromegaly and those in healthy individuals consist primarily of compositional differences independent of abundance. Prospective studies are needed to further explore the clinical implications of gut microbiome dysbiosis in patients with acromegaly.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32169051", + "title": "Fecal microbiota characteristics of Chinese patients with primary IgA nephropathy: a cross-sectional study.", + "year": 2020, + "journal": "BMC nephrology", + "authors": [ + "Hu X", + "Du J", + "Xie Y", + "Huang Q", + "Xiao Y", + "Chen J", + "Yan S", + "Gong Z", + "Ouyang S" + ], + "bacteria": "Hungatella", + "condition": "healthy", + "relevance_score": 0.30247742379654774, + "mesh_terms": [ + "Adult", + "Albuminuria", + "Asian People", + "Bacteria", + "Creatinine", + "Cross-Sectional Studies", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Glomerular Filtration Rate", + "Glomerulonephritis, IGA", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Sequence Analysis, RNA" + ], + "raw_abstract": "BACKGROUND: Growing evidence has shown that the gut-renal connection and gut microbiota dysbiosis play a critical role in immunoglobulin A nephropathy (IgAN). However, the fecal microbiome profile in Chinese patients with IgAN remains unknown. A cross-sectional study was designed for the first time to investigate the fecal microbiota compositions in patients with primary IgAN in China and to evaluate the relationship between the fecal microbiome and IgAN clinical presentation. METHODS: Fecal samples were collected from 17 IgAN patients and 18 age-, sex-, and body mass index-matched healthy controls, and bacterial DNA was extracted for 16S ribosomal RNA gene sequencing targeting the V3-V4 region. RESULTS: Fecal samples from the IgAN patients and healthy controls showed differences in gut microbiota community richness and compositions. Compared to the healthy controls, IgAN patients at the phylum level had an increased abundance of Fusobacteria, but a decreased abundance of Synergistetes. The significantly increased genera in the IgAN group were Escherichia-Shigella, Hungatella, and Eggerthella, all of which possess pathogenic potential. Furthermore, the genus Escherichia-Shigella was negatively associated with the estimated glomerular filtration rate (eGFR) but was positively associated with the urinary albumin-to-creatinine ratio (uACR). However, the genus rectale_group was present in the IgAN group with a low abundance and was negatively associated with the uACR. Functional analysis disclosed that infection-related pathways were enriched in the IgAN group. CONCLUSIONS: We demonstrate that gut microbiota dysbiosis occurs in patients with IgAN, and that changes in gut bacterial populations are closely related to IgAN clinical features, suggesting that certain specific gut microbiota may be a potential therapeutic target for IgAN.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35417758", + "title": "Effects of a Low-Carbohydrate, High-Protein Diet on Gut Microbiome Composition in Insulin-Resistant Individuals With Chronic Spinal Cord Injury: Preliminary Results From a Randomized Controlled Trial.", + "year": 2022, + "journal": "Archives of physical medicine and rehabilitation", + "authors": [ + "Li J", + "Morrow C", + "McLain A", + "Womack ED", + "Yarar-Fisher C" + ], + "bacteria": "Hungatella", + "condition": "healthy", + "relevance_score": 0.21260509974062974, + "mesh_terms": [ + "Adult", + "Carbohydrates", + "Diet", + "Diet, High-Protein", + "Gastrointestinal Microbiome", + "Humans", + "Insulin", + "Phylogeny", + "Spinal Cord Injuries" + ], + "raw_abstract": "OBJECTIVE: To evaluate the effect of a low-carbohydrate, high-protein (LC/HP) diet that includes healthy dietary components (eg, lean meat, whole grains, fruits and vegetables, fiber, etc) on the gut microbiome composition in individuals with chronic spinal cord injury (SCI). DESIGN: A single-center randomized parallel controlled trial. SETTING: Research University. PARTICIPANTS: Adult participants with chronic SCI (N=19, 3 years or more after the injury, C2-L2, American Spinal Injury Association Impairment Scale A-D). Participants were insulin resistant and had not received antibiotics within 4 weeks before enrolling in the study. INTERVENTIONS: Participants were randomized to the LC/HP diet group (40% energy from carbohydrates, 30% energy from protein, and 30% energy from fat and met dietary guideline recommendations) or the control group for 8 weeks. Participants assigned to the LC/HP group were provided with all meals delivered weekly to their homes. Participants assigned to the control group were asked to continue their usual diet. MAIN OUTCOME MEASURES: Stool samples were collected at baseline and the end of week 8. The gut microbiome 16S ribosomal RNA V4 region was sequenced, and gut microbiome diversity and taxonomical abundance were computed using the QIIME2 suite. RESULTS: Participants in the LC/HP group had significant changes in alpha-diversity (reduced operational taxonomic unit and Faith's phylogenetic diversity) and beta-diversity (unweighted UniFrac), while no significant differences were observed among participants in the control group after the intervention. Moreover, several taxa changed differently over time between groups, including increased Bacteroides thetaiotaomicron, Coprococcus 3, Fusicatenibacter, Tannerellaceae, and decreased Tyzzerella, Phascolarctobacterium, Romboutsia, Clostridium sensu stricto 1, Hungatella, Ruminococcus gauvreauii, family XI, and Bacillales among participants in the diet group, while these taxa did not change in the control group. CONCLUSIONS: An LC/HP diet with healthy dietary components improved gut microbiome composition in individuals with SCI, including increased bacteria implicated in fiber metabolism and reduced bacteria communities linked to cardiometabolic disorders.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39143364", + "title": "Identification and comparison of intestinal microbial diversity in patients at different stages of hepatic cystic echinococcosis.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Akhlaghi E", + "Salari E", + "Mansouri M", + "Shafiei M", + "Kalantar-Neyestanaki D", + "Aghassi H", + "Fasihi Harandi M" + ], + "bacteria": "Gemella", + "condition": "healthy", + "relevance_score": 0.3218633471242415, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Echinococcosis, Hepatic", + "Male", + "Female", + "RNA, Ribosomal, 16S", + "Adult", + "Middle Aged", + "Feces", + "Bacteria", + "Biodiversity", + "High-Throughput Nucleotide Sequencing" + ], + "raw_abstract": "There is a significant focus on the role of the host microbiome in different outcomes of human parasitic diseases, including cystic echinococcosis (CE). This study was conducted to identify the intestinal microbiome of patients with CE at different stages of hydatid cyst compared to healthy individuals. Stool samples from CE patients as well as healthy individuals were collected. The samples were divided into three groups representing various stages of hepatic hydatid cyst: active (CE1 and CE2), transitional\u00a0(CE3), and inactive (CE4 and CE5). One family member from each group was selected to serve as a control. The gut microbiome of patients with different stages of hydatid cysts was investigated using metagenomic next-generation amplicon sequencing of the V3-V4 region of the 16S rRNA gene. In this study, we identified 4862 Operational Taxonomic Units from three stages of hydatid cysts in CE patients and healthy individuals with a combined frequency of 2,955,291. The most abundant genera observed in all the subjects were Blautia, Agathobacter, Faecalibacterium, Bacteroides, Bifidobacterium, and Prevotella. The highest microbial frequency was related to inactive forms of CE, and the lowest frequency was observed in the group with active forms. However, the lowest OTU diversity was found in patients with inactive cysts compared with those with active and\u00a0transitional cyst stages. The genus Agatobacter had the highest OTU frequency. Pseudomonas, Gemella, and Ligilactobacillus showed significant differences among the patients with different stages of hydatid cysts. Additionally, Anaerostipes and Candidatus showed significantly different reads in CE patients compared to healthy individuals. Our findings indicate that several bacterial genera can play a role in the fate of hydatid cysts in patients at different stages of the disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33789570", + "title": "Bacterial community structure alterations within the colorectal cancer gut microbiome.", + "year": 2021, + "journal": "BMC microbiology", + "authors": [ + "Loftus M", + "Hassouneh SA", + "Yooseph S" + ], + "bacteria": "Gemella", + "condition": "healthy", + "relevance_score": 0.30450074230992036, + "mesh_terms": [ + "Bacteria", + "Biodiversity", + "Colorectal Neoplasms", + "Feces", + "Gastrointestinal Microbiome", + "Genome, Bacterial", + "High-Throughput Nucleotide Sequencing", + "Humans" + ], + "raw_abstract": "BACKGROUND: Colorectal cancer is a leading cause of cancer-related deaths worldwide. The human gut microbiome has become an active area of research for understanding the initiation, progression, and treatment of colorectal cancer. Despite multiple studies having found significant alterations in the carriage of specific bacteria within the gut microbiome of colorectal cancer patients, no single bacterium has been unequivocally connected to all cases. Whether alterations in species carriages are the cause or outcome of cancer formation is still unclear, but what is clear is that focus should be placed on understanding changes to the bacterial community structure within the cancer-associated gut microbiome. RESULTS: By applying a novel set of analyses on 252 previously published whole-genome shotgun sequenced fecal samples from healthy and late-stage colorectal cancer subjects, we identify taxonomic, functional, and structural changes within the cancer-associated human gut microbiome. Bacterial association networks constructed from these data exhibited widespread differences in the underlying bacterial community structure between healthy and colorectal cancer associated gut microbiomes. Within the cancer-associated ecosystem, bacterial species were found to form associations with other species that are taxonomically and functionally dissimilar to themselves, as well as form modules functionally geared towards potential changes in the tumor-associated ecosystem. Bacterial community profiling of these samples revealed a significant increase in species diversity within the cancer-associated gut microbiome, and an elevated relative abundance of species classified as originating from the oral microbiome including, but not limited to, Fusobacterium nucleatum, Peptostreptococcus stomatis, Gemella morbillorum, and Parvimonas micra. Differential abundance analyses of community functional capabilities revealed an elevation in functions linked to virulence factors and peptide degradation, and a reduction in functions involved in amino-acid biosynthesis within the colorectal cancer gut microbiome. CONCLUSIONS: We utilize whole-genome shotgun sequenced fecal samples provided from a large cohort of late-stage colorectal cancer and healthy subjects to identify a number of potentially important taxonomic, functional, and structural alterations occurring within the colorectal cancer associated gut microbiome. Our analyses indicate that the cancer-associated ecosystem influences bacterial partner selection in the native microbiota, and we highlight specific oral bacteria and their associations as potentially relevant towards aiding tumor progression.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39415150", + "title": "Oral microbiome dysbiosis may be associated with intra cranial aneurysms.", + "year": 2024, + "journal": "BMC oral health", + "authors": [ + "Ma J", + "Wang F", + "Zhu Y", + "Tian Y", + "Du C", + "Yan L", + "Ding C", + "Wang D" + ], + "bacteria": "Gemella", + "condition": "healthy", + "relevance_score": 0.2952069971335803, + "mesh_terms": [ + "Humans", + "Intracranial Aneurysm", + "Female", + "Male", + "Middle Aged", + "Dysbiosis", + "Microbiota", + "Case-Control Studies", + "Saliva", + "Mouth", + "RNA, Ribosomal, 16S", + "Adult", + "Aged", + "High-Throughput Nucleotide Sequencing" + ], + "raw_abstract": "BACKGROUND: Although the etiology of aneurysms remains elusive, recent advances in high-throughput sequencing technology and ongoing human microbiome investigations suggest a potential link between microbiome composition and the onset of various human diseases. OBJECTIVE: This study aimed to utilize high-throughput 16\u00a0S rRNA gene sequencing to analyze the oral flora bacterial profiles of individuals, comparing patients with intracranial aneurysms to a healthy control group. Importantly, we sought to identify differences in the oral microbiota and offer novel insights and methods for early diagnosis and identification of intracranial aneurysms. METHOD: Saliva samples were collected from 60 patients with cerebral aneurysms (case group) and 130 healthy individuals (control group). The V3-V4 region of the bacterial 16\u00a0S rRNA gene was amplified and sequenced using the HiSeq high-throughput sequencing platform to establish the bacterial profile. Sequencing data were analyzed using QIIME2 and Metastats software to compare composition differences and relative abundance at the phylum and genus levels in the oral microbiota of the two groups. RESULTS: Significant differences in oral microbiota composition were observed between patients in the case and control groups (P\u2009<\u20090.05). Genus-level identification highlighted key positions occupied by Eubacterium, Saccharimonadaceae, Rothia, Gemella, Streptococcus, Lactobacillales, Phocaeicola, Bacteroides, Saccharimonadales, and Abiotrophia. CONCLUSION: This study revealed noteworthy distinctions in the composition, abundance, and diversity of oral microbiota between intracranial aneurysm patients and healthy controls. These disparities suggest a potential correlation between oral microbiota and the development of intracranial aneurysms, offering new avenues for early diagnosis and intervention. However, limitations such as a small sample size, lack of prospective design, and absence of causal inference warrant further validation and exploration.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33124578", + "title": "Intestinal microbiota composition of patients with Beh\u00e7et's disease: differences between eye, mucocutaneous and vascular involvement. The Rheuma-BIOTA study.", + "year": 2020, + "journal": "Clinical and experimental rheumatology", + "authors": [ + "Yasar Bilge NS", + "P\u00e9rez Brocal V", + "Kasifoglu T", + "Bilge U", + "Kasifoglu N", + "Moya A", + "Dinleyici EC" + ], + "bacteria": "Gemella", + "condition": "healthy", + "relevance_score": 0.27484843161521166, + "mesh_terms": [ + "Adult", + "Behcet Syndrome", + "Gastrointestinal Microbiome", + "Humans", + "Prospective Studies" + ], + "raw_abstract": "OBJECTIVES: Changes in microbiota composition affect the aetiology and patho-genesis of chronic diseases, including Beh\u00e7et's disease (BD). However, no studies have analysed the potential gut microbiota changes among different clinical forms of BD. This study evaluated the intestinal microbiota composition of patients with BD and healthy controls and also compared differences between patients with BD with respect to eye, mucocutaneous, and vascular involvement. METHODS: In this prospective cohort study, 27 patients diagnosed with BD according to the International Study Group criteria and 10 age- and sex-matched healthy controls were included. Detailed intestinal microbiota analysis was performed. RESULTS: There were no differences between the BD group and the control group in terms of alpha and beta microbial diversity and abundance indices (p>0.05). Actinomyces, Libanicoccus, Collinsella, Eggerthella, Enetrohabdus, Catenibacterium, and Enterobacter were significantly higher in the BD group than in the control group. In addition, Bacteroides, Cricetibacter, Alistipes, Lachnospira, Dielma, Akkermansia, Sutterella, Anaerofilum, Ruminococcease-UCG007, Acetanaerobacterium, and Copropaacter were lower in the BD group than in the control group. When we compared three different system involvement (eye, mucocutaneous, and vascular), the linear discriminant analysis effective size revealed a difference for the following genera: Lachnospiraceae NK4A136 in the uveitis group; Dialister, Intestinomonas, and Marvinbryantia in the mucocutaneous group; and Gemella in the vascular group. CONCLUSIONS: The composition of intestinal microbiota was significantly different in patients with BD compared with healthy adults. Ours is the first study to show differences in microbiota composition in isolated mucocutaneous, eye, and vascular involvement. These findings should be evaluated in a larger series.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26891226", + "title": "Association between intestinal permeability and faecal microbiota composition in Italian children with beta cell autoimmunity at risk for type 1 diabetes.", + "year": 2016, + "journal": "Diabetes/metabolism research and reviews", + "authors": [ + "Maffeis C", + "Martina A", + "Corradi M", + "Quarella S", + "Nori N", + "Torriani S", + "Plebani M", + "Contreas G", + "Felis GE" + ], + "bacteria": "Gemella", + "condition": "healthy", + "relevance_score": 0.25239552884932515, + "mesh_terms": [ + "Adolescent", + "Autoimmunity", + "Bacteria", + "Biomarkers", + "Case-Control Studies", + "Cell Membrane Permeability", + "Child", + "Diabetes Mellitus, Type 1", + "Feces", + "Female", + "Follow-Up Studies", + "Humans", + "Intestines", + "Male", + "Metagenome", + "Microbiota", + "Prognosis", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Pancreatic organ-specific autoimmunity in subjects at risk for type 1 diabetes (T1D) is associated with increased intestinal permeability and an aberrant gut microbiota, but these factors have not yet been simultaneously investigated in the same subjects. Thus, the aim of this study was to assess both intestinal permeability and gut microbiota composition in an Italian sample of children at risk for T1D. METHODS: Ten Italian children with beta cell autoimmunity at risk for T1D and 10 healthy children were involved in a case-control study. The lactulose/mannitol test was used to assess intestinal permeability. Analysis of microbiota composition was performed using polymerase chain reaction followed by denaturing gradient gel electrophoresis, based on the 16S rRNA gene. RESULTS: Intestinal permeability was significantly higher in children at risk for T1D than in healthy controls. Moreover, the gut microbiota of the former differed from that of the latter group: Three microorganisms were detected - Dialister invisus, Gemella sanguinis and Bifidobacterium longum - in association with the pre-pathologic state. CONCLUSIONS: The results of this study validated the hypothesis that increased intestinal permeability together with differences in microbiota composition are contemporaneously associated with the pre-pathological condition of T1D in a sample of Italian children. Further studies are necessary to confirm the microbial markers identified in this sample of children as well as to clarify the involvement of microbiota modifications in the mechanisms leading to increased permeability and the autoimmune mechanisms that promote diabetes onset. Copyright \u00a9 2016 John Wiley & Sons, Ltd.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "24939571", + "title": "The HLA-DQ2 genotype selects for early intestinal microbiota composition in infants at high risk of developing coeliac disease.", + "year": 2015, + "journal": "Gut", + "authors": [ + "Olivares M", + "Neef A", + "Castillejo G", + "Palma GD", + "Varea V", + "Capilla A", + "Palau F", + "Nova E", + "Marcos A", + "Polanco I", + "Ribes-Koninckx C", + "Ortigosa L", + "Izquierdo L", + "Sanz Y" + ], + "bacteria": "Gemella", + "condition": "healthy", + "relevance_score": 0.23991188542475606, + "mesh_terms": [ + "Celiac Disease", + "Clostridium", + "Feces", + "Female", + "Genetic Markers", + "Genotype", + "HLA-DQ Antigens", + "Haplotypes", + "Humans", + "Infant", + "Intestines", + "Male", + "Microbiota", + "Prospective Studies", + "Real-Time Polymerase Chain Reaction", + "Risk Factors" + ], + "raw_abstract": "OBJECTIVE: Intestinal dysbiosis has been associated with coeliac disease (CD), but whether the alterations are cause or consequence of the disease is unknown. This study investigated whether the human leukocyte antigen (HLA)-DQ2 genotype is an independent factor influencing the early gut microbiota composition of healthy infants at family risk of CD. DESIGN: As part of a larger prospective study, a subset (n=22) of exclusively breastfed and vaginally delivered infants with either high genetic risk (HLA-DQ2 carriers) or low genetic risk (non-HLA-DQ2/8 carriers) of developing CD were selected from a cohort of healthy infants with at least one first-degree relative with CD. Infant faecal microbiota was analysed by 16S rRNA gene pyrosequencing and real time quantitative PCR. RESULTS: Infants with a high genetic risk had significantly higher proportions of Firmicutes and Proteobacteria and lower proportions of Actinobacteria compared with low-risk infants. At genus level, high-risk infants had significantly less Bifidobacterium and unclassified Bifidobacteriaceae proportions and more Corynebacterium, Gemella, Clostridium sensu stricto, unclassified Clostridiaceae, unclassified Enterobacteriaceae and Raoultella proportions. Quantitative real time PCR also revealed lower numbers of Bifidobacterium species in infants with high genetic risk than in those with low genetic risk. In high-risk infants negative correlations were identified between Bifidobacterium species and several genera of Proteobacteria (Escherichia/Shigella) and Firmicutes (Clostridium). CONCLUSIONS: The genotype of infants at family risk of developing CD, carrying the HLA-DQ2 haplotypes, influences the early gut microbiota composition. This finding suggests that a specific disease-biased host genotype may also select for the first gut colonisers and could contribute to determining disease risk.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33839797", + "title": "Gut microbiota profiles and characterization of cultivable fungal isolates in IBS patients.", + "year": 2021, + "journal": "Applied microbiology and biotechnology", + "authors": [ + "Sciavilla P", + "Strati F", + "Di Paola M", + "Modesto M", + "Vitali F", + "Cavalieri D", + "Prati GM", + "Di Vito M", + "Aragona G", + "De Filippo C", + "Mattarelli P" + ], + "bacteria": "Gemella", + "condition": "healthy", + "relevance_score": 0.2345233303677031, + "mesh_terms": [ + "Dysbiosis", + "Ecosystem", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Irritable Bowel Syndrome", + "Quality of Life" + ], + "raw_abstract": "Studies so far conducted on irritable bowel syndrome (IBS) have been focused mainly on the role of gut bacterial dysbiosis in modulating the intestinal permeability, inflammation, and motility, with consequences on the quality of life. Limited evidences showed a potential involvement of gut fungal communities. Here, the gut bacterial and fungal microbiota of a cohort of IBS patients have been characterized and compared with that of healthy subjects (HS). The IBS microbial community structure differed significantly compared to HS. In particular, we observed an enrichment of bacterial taxa involved in gut inflammation, such as Enterobacteriaceae, Streptococcus, Fusobacteria, Gemella, and Rothia, as well as depletion of health-promoting bacterial genera, such as Roseburia and Faecalibacterium. Gut microbial profiles in IBS patients differed also in accordance with constipation. Sequence analysis of the gut mycobiota showed enrichment of Saccharomycetes in IBS. Culturomics analysis of fungal isolates from feces showed enrichment of Candida spp. displaying from IBS a clonal expansion and a distinct genotypic profiles and different phenotypical features when compared to HS of Candida albicans isolates. Alongside the well-characterized gut bacterial dysbiosis in IBS, this study shed light on a yet poorly explored fungal component of the intestinal ecosystem, the gut mycobiota. Our results showed a differential fungal community in IBS compared to HS, suggesting potential for new insights on the involvement of the gut mycobiota in IBS. KEY POINTS: \u2022 Comparison of gut microbiota and mycobiota between IBS and healthy subjects \u2022 Investigation of cultivable fungi in IBS and healthy subjects \u2022 Candida albicans isolates result more virulent in IBS subjects compared to healthy subjects.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33410957", + "title": "Metagenomic Analyses Expand Bacterial and Functional Profiling Biomarkers for Colorectal Cancer in a Hainan Cohort, China.", + "year": 2021, + "journal": "Current microbiology", + "authors": [ + "Chang H", + "Mishra R", + "Cen C", + "Tang Y", + "Ma C", + "Wasti S", + "Wang Y", + "Ou Q", + "Chen K", + "Zhang J" + ], + "bacteria": "Gemella", + "condition": "healthy", + "relevance_score": 0.20124375480992626, + "mesh_terms": [ + "Biomarkers", + "China", + "Citrobacter", + "Colorectal Neoplasms", + "Firmicutes", + "Gemella", + "Humans" + ], + "raw_abstract": "This study was conducted for the metagenomic analysis of stool samples from CRC affected individuals to identify biomarkers for CRC in Hainan, the only tropical island province of China. The gut microbiota of CRC patients differed significantly from that of healthy and reference database cohorts based on Aitchison distance and Bray-Cutis distance but there was no significant difference in alpha diversity. Furthermore, at the species level, 68 species were significantly altered including 37 CRC-enriched, such as, Fusobacterium nucleatum, Parvimonas micra, Gemella morbillorum, Citrobacter portucalensis, Alloprevotella sp., Shigella sonnei, Coriobacteriaceae bacterium, etc. Sixty-seven different metabolic pathways were acquired, and pathways involved in the synthesis of many amino acids were significantly declined. Besides, 2 identified antibiotic resistance genes performed well (area under the receive-operation curve AUC\u2009=\u20090.833, 95% CI 58.51-100%) compared with virulence factor genes. The results of the present study provide region-specific bacterial and functional biomarkers of gut microbiota for CRC patients in Hainan. Microbiota is considered as a non-invasive biomarker for the detection of CRC. Gut microbiota of different geographic regions should be further studied to expand the understanding of markers, especially for the China cohort due to diverse nationalities and lifestyles.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38970464", + "title": "Detection of colorectal-cancer-associated bacterial taxa in fecal samples using next-generation sequencing and 19 newly established qPCR assays.", + "year": 2025, + "journal": "Molecular oncology", + "authors": [ + "Senthakumaran T", + "Tann\u00e6s TM", + "Moen AEF", + "Brackmann SA", + "Jahanlu D", + "Rounge TB", + "Bemanian V", + "Tunsj\u00f8 HS" + ], + "bacteria": "Gemella", + "condition": "healthy", + "relevance_score": 0.20040861092972392, + "mesh_terms": [ + "Humans", + "Feces", + "Colorectal Neoplasms", + "High-Throughput Nucleotide Sequencing", + "Bacteria", + "Real-Time Polymerase Chain Reaction", + "Female", + "Middle Aged", + "Male", + "Aged", + "RNA, Ribosomal, 16S", + "Adult" + ], + "raw_abstract": "We have previously identified increased levels of distinct bacterial taxa within mucosal biopsies from colorectal cancer (CRC) patients. Following prior research, the aim of this study was to investigate the detection of the same CRC-associated bacteria in fecal samples and to evaluate the suitability of fecal samples as a non-invasive material for the detection of CRC-associated bacteria. Next-generation sequencing (NGS) of the 16S ribosomal RNA (rRNA) V4 region was performed to evaluate the detection of the CRC-associated bacteria in the fecal microbiota of cancer patients, patients with adenomatous polyp and healthy controls. Furthermore, 19 novel species-specific quantitative PCR (qPCR) assays were established to detect the CRC-associated bacteria. Approximately, 75% of the bacterial taxa identified in biopsies were reflected in fecal samples. NGS failed to detect low-abundance CRC-associated taxa in fecal samples, whereas qPCR exhibited high sensitivity and specificity in identifying all targeted taxa. Comparison of fecal microbial composition between the different patient groups showed enrichment of Fusobacterium\u2009nucleatum, Parvimonas\u2009micra, and Gemella\u2009morbillorum in cancer patients. Our findings suggest that low-abundance mucosa-associated bacteria can be detected in fecal samples using sensitive qPCR assays.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27679525", + "title": "Systematic Review of the Human Milk Microbiota.", + "year": 2017, + "journal": "Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition", + "authors": [ + "Fitzstevens JL", + "Smith KC", + "Hagadorn JI", + "Caimano MJ", + "Matson AP", + "Brownell EA" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.4077535348707427, + "mesh_terms": [ + "Food Microbiology", + "Humans", + "Infant", + "Microbiota", + "Milk, Human", + "Staphylococcus", + "Streptococcus" + ], + "raw_abstract": "Human milk-associated microbes are among the first to colonize the infant gut and may help to shape both short- and long-term infant health outcomes. We performed a systematic review to characterize the microbiota of human milk. Relevant primary studies were identified through a comprehensive search of PubMed (January 1, 1964, to June 31, 2015). Included studies were conducted among healthy mothers, were written in English, identified bacteria in human milk, used culture-independent methods, and reported primary results at the genus level. Twelve studies satisfied inclusion criteria. All varied in geographic location and human milk collection/storage/analytic methods. Streptococcus was identified in human milk samples in 11 studies (91.6%) and Staphylococcus in 10 (83.3%); both were predominant genera in 6 (50%). Eight of the 12 studies used conventional ribosomal RNA (rRNA) polymerase chain reaction (PCR), of which 7 (87.5%) identified Streptococcus and 6 (80%) identified Staphylococcus as present. Of these 8 studies, 2 (25%) identified Streptococcus and Staphylococcus as predominant genera. Four of the 12 studies used next-generation sequencing (NGS), all of which identified Streptococcus and Staphylococcus as present and predominant genera. Relative to conventional rRNA PCR, NGS is a more sensitive method to identify/quantify bacterial genera in human milk, suggesting the predominance of Streptococcus and Staphylococcus may be underestimated in studies using older methods. These genera, Streptococcus and Staphylococcus, may be universally predominant in human milk, regardless of differences in geographic location or analytic methods. Primary studies designed to evaluate the effect of these 2 genera on short- and long-term infant outcomes are warranted.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32709038", + "title": "Evolution of Gut Microbiome and Metabolome in Suspected Necrotizing Enterocolitis: A Case-Control Study.", + "year": 2020, + "journal": "Journal of clinical medicine", + "authors": [ + "Brehin C", + "Dubois D", + "Dicky O", + "Breinig S", + "Oswald E", + "Serino M" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.3670779713210499, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Necrotizing enterocolitis (NEC) is a devastating condition in preterm infants due to multiple factors, including gut microbiota dysbiosis. NEC development is poorly understood, due to the focus on severe NEC (NEC-2/3). METHODS: We studied the gut microbiota, microbiome and metabolome of children with suspected NEC (NEC-1). RESULTS: NEC-1 gut microbiota had a higher abundance of the Streptococcus (second 10-days of life) and Staphylococcus (third 10-days of life) species. NEC-1 children showed a microbiome evolution in the third 10-days of life being the most divergent, and were associated with a different metabolomic signature than in healthy children. The NEC-1 microbiome had increased glycosaminoglycan degradation and lysosome activity by the first 10-days of life, and was more sensitive to childbirth, low birth weight and gestational age, than healthy microbiome. NEC-1 fecal metabolome was more divergent by the second month of life. CONCLUSIONS: NEC-1 gut microbiota and microbiome modifications appear more distinguishable by the third 10-days of life, compared to healthy children. These data identify a precise window of time (i.e., the third 10-days of life) and provide microbial targets to fight/blunt NEC-1 progression.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32301919", + "title": "Risk Factors for Carriage of Antibiotic-resistant Bacteria in Healthy Children in the Community: A Systematic Review.", + "year": 2020, + "journal": "The Pediatric infectious disease journal", + "authors": [ + "Messina NL", + "Williamson DA", + "Robins-Browne R", + "Bryant PA", + "Curtis N" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.35444405646034055, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Bacteria", + "Bacterial Infections", + "Carrier State", + "Child", + "Drug Resistance, Bacterial", + "Healthy Volunteers", + "Humans", + "Nasopharynx", + "Risk Factors" + ], + "raw_abstract": "BACKGROUND: In addition to health care settings, antibiotic resistance has also been increasing in the community. Healthy children represent an important potential reservoir of antibiotic-resistant (AR) bacteria. However, strategies to reduce the spread of AR bacteria often fail to specifically address the factors that promote the carriage of AR bacteria in this population.The objective of this review was to Identify risk factors for carriage of AR bacteria by healthy children. METHODS: We did a systematic search of MEDLINE, Embase and PubMed for studies in developed (OECD) countries that assessed risk factors for carriage of AR bacteria in healthy children in the community. We excluded studies done before 1998 and studies of AR Streptococcus pneumoniae carriage in the absence of pneumococcal conjugate vaccination. RESULTS: Of 1234 studies identified, 30 were eligible for inclusion. These studies assessed the impact of 49 risk factors on AR strains of S. pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Streptococcus pyogenes and Escherichia coli. The majority of these risk factors were assessed in 2 or fewer studies per bacteria. Recent antibiotic consumption was associated with carriage of resistant respiratory bacteria (S. pneumoniae, H. influenzae); however, it was not consistently associated with carriage of AR bacteria in skin or stool (S. aureus and E. coli). For AR S. aureus, transmission within households appeared to have a greater impact than individual antibiotic use. CONCLUSIONS: The factors that promote carriage of AR bacteria by healthy children differed between bacterial species. To reduce reservoirs of AR bacteria in the community, it is essential for intervention strategies to target the specific risk factors for different bacteria.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30681124", + "title": "Geographical location specific composition of cultured microbiota and Lactobacillus occurrence in human breast milk in China.", + "year": 2019, + "journal": "Food & function", + "authors": [ + "Ding M", + "Qi C", + "Yang Z", + "Jiang S", + "Bi Y", + "Lai J", + "Sun J" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.35410308909556737, + "mesh_terms": [ + "Adult", + "Bacteria", + "China", + "Demography", + "Female", + "Humans", + "Microbiota", + "Milk, Human", + "Polymerase Chain Reaction", + "RNA, Bacterial", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Breast milk bacteria play an important role in the early development of the gut microbiota and the immune system. Dominant living bacteria of 89 healthy Chinese women from 11 cities in five regions were analysed by broad-range yeast extract, casitone, and fatty acid and de Man, Rogosa, and Sharpe-based culturing coupled with 16S rRNA sequence and quantitative polymerase chain reaction. Principal coordinate analysis showed that human breast milk samples were classified into three groups, driven by Enterococcus (abundance in group 1, 63.13%), Streptococcus (abundance in group 2, 68.16%) and Staphylococcus (abundance in group 3, 55.17%). The microbiota profile was highly region-specific. Samples from the Northwest and North of China showed higher alpha diversity compared to other regions (p < 0.05). Staphylococcus, Streptococcus, and Enterococcus were the dominant genera in all samples. Lactobacillus had a high occurrence in samples from the Northwest and North, dominated by Lactobacillus reuteri and Lactobacillus gasseri. Samples of mothers with a high postpartum body mass index showed more Staphylococcus and less Lactobacillus and Streptococcus. Staphylococcus was negatively correlated with Lactobacillus and Streptococcus. The mode of delivery also affected the composition of microbiota, even after culture. These findings indicate differences between the North and South, provide effective information for collection of samples in which Lactobacillus is the predominant genus, and lower the detection limit for small amounts of bacteria.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26905350", + "title": "Prevalence and risk factors of early fecal carriage of Enterococcus faecalis and Staphylococcus spp and their antimicrobial resistant patterns among healthy neonates born in a hospital setting in central Saudi Arabia.", + "year": 2016, + "journal": "Saudi medical journal", + "authors": [ + "El-Kersh TA", + "Marie MA", + "Al-Sheikh YA", + "Al-Agamy MH", + "Al Bloushy AA" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.346763512289104, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Birth Weight", + "Carrier State", + "Cesarean Section", + "Delivery, Obstetric", + "Drug Resistance, Bacterial", + "Drug Resistance, Multiple, Bacterial", + "Enterococcus faecalis", + "Female", + "Gentamicins", + "Gram-Positive Bacterial Infections", + "Humans", + "Infant, Newborn", + "Male", + "Methicillin-Resistant Staphylococcus aureus", + "Microbial Sensitivity Tests", + "Oxacillin", + "Prevalence", + "Prospective Studies", + "Risk Factors", + "Saudi Arabia", + "Staphylococcal Infections", + "Staphylococcus aureus", + "Staphylococcus epidermidis", + "Streptomycin" + ], + "raw_abstract": "OBJECTIVES: To investigate the prevalence, antibiotic resistant profiles, and risk factors of early fecal carriage of Enterococcus faecalis (E. faecalis) and staphylococci among 150 healthy Saudi neonates born in a hospital setting in central Saudi Arabia. METHODS: This prospective study was conducted in Al-Bukayriyah General Hospital, Qassim, Saudi Arabia, between June 2012 and January 2013. The E. faecalis and Staphylococcus spp. isolates were identified manually, and Vitek2 system was used for identity confirmation at the species level and minimum inhibitory concentration-susceptibility testing. RESULTS: Enterococcus faecalis (n=73) and Staphylococcus spp. (n=18) were recovered. Unlike staphylococci, E. faecalis colonization did not significantly vary from day one up to 7 days of life, regardless of the type of feeding, but it was relatively higher among vaginally versus cesarean delivery. Both Staphylococcus epidermidis (S. epidermidis) and Staphylococcus aureus (S. aureus) carriage increase as the body weight increases, and this difference was significant (p=0.025) for S. epidermidis. High-level resistance in Gentamycin among E. faecalis isolates was 25% and 11% to Streptomycin. Thirty percent of S. epidermidis were resistant to oxacillin and exhibited multidrug-resistant (MDR) patterns of 5 resistant markers, which were also observed among 2/5 (40%) of Methicillin-resistant Staphylococcus aureus isolates. CONCLUSION: Enterococcus faecalis did not significantly vary in relation to type of delivery, age up to 7 days, and type of feeding. The neonatal fecal carriage of MDR isolates should be considered as a crucial reservoir to the further spread of antimicrobial resistance genes among hospitals, cross infections, and the community.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36315327", + "title": "Characterization of the mucosal microbiota in patients with nodular lymphoid hyperplasia with concurrent irritable bowel syndrome compared to healthy controls.", + "year": 2023, + "journal": "Molecular biology reports", + "authors": [ + "Salarieh N", + "Emami Meibodi A", + "Alipour S", + "Azimirad M", + "Looha MA", + "Asadzadeh Aghdaei H", + "Yadegar A", + "Shahrokh S", + "Zali MR" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.3305962563601991, + "mesh_terms": [ + "Humans", + "Irritable Bowel Syndrome", + "Hyperplasia", + "Intestines", + "Microbiota", + "Ileum", + "Bacteria", + "Feces" + ], + "raw_abstract": "BACKGROUND: Nodular lymphoid hyperplasia (NLH) is known as a lymphoproliferative lesion in which multiple small nodules appear on the intestinal wall. It has been documented that patients who struggle with irritable bowel syndrome (IBS) are at greater risk of developing NLH. Here, we aimed to investigate the previously reported pathogens and the abundance of a selection of mucosal microbiota in IBS\u2009+\u2009NLH patients compared to IBS, and healthy controls. METHODS AND RESULTS: Terminal ileum biopsies were collected from 37 IBS\u2009+\u2009NLH, 37 IBS, and 29 healthy controls. Bacterial culture and PCR was performed to detect the presence of pathogens in biopsies. A qPCR assay was applied to assess the abundance of a selection of bacterial taxa. Totally, five bacterial isolates including two enteropathogenic and one enteroaggregative Escherichia coli (EPEC, EAEC), one enterotoxigenic Staphylococcus aureus (SEA), and one Yersinia enterocolitica strains were detected among the IBS\u2009+\u2009NLH cases. The relative abundance of Bacteroidetes and Streptococcus spp. in IBS\u2009+\u2009NLH patients was significantly less than IBS and healthy controls. Firmicutes, Pseudomonas spp., Haemophilus spp., and Campylobacter spp. were notably more abundant in IBS\u2009+\u2009NLH than in IBS patients. The abundance of Verrucomicrobia was higher in NLH\u2009+\u2009IBS than in healthy controls. Actinobacteria was also significantly more abundant among NLH\u2009+\u2009IBS patients than the controls. CONCLUSION: Our results demonstrated that mucosal microbiota composition in NLH\u2009+\u2009IBS patients slightly differs from that of IBS patients and healthy controls. Further research using large-scale cohorts are needed to enhance current understanding of the contribution of the mucosal microbiota to NLH pathogenesis with concurrent IBS.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30076401", + "title": "Higher intake of coagulase-negative staphylococci from maternal milk promotes gut colonization with mecA-negative Staphylococcus epidermidis in preterm neonates.", + "year": 2018, + "journal": "Journal of perinatology : official journal of the California Perinatal Association", + "authors": [ + "Soeorg H", + "Treumuth S", + "Metsvaht HK", + "Eelm\u00e4e I", + "Merila M", + "Ilmoja ML", + "Lutsar I", + "Metsvaht T" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.3091318428218451, + "mesh_terms": [ + "Adult", + "Breast Feeding", + "Coagulase", + "Feces", + "Female", + "Gastrointestinal Tract", + "Humans", + "Infant, Newborn", + "Infant, Premature", + "Intensive Care Units, Neonatal", + "Longitudinal Studies", + "Milk, Human", + "Multilocus Sequence Typing", + "Neonatal Sepsis", + "Proportional Hazards Models", + "Prospective Studies", + "Skin", + "Staphylococcus epidermidis", + "Staphylococcus haemolyticus", + "Term Birth" + ], + "raw_abstract": "OBJECTIVE: We aimed to determine factors associated with gut colonization of preterm neonates with coagulase-negative staphylococci (CoNS) from maternal milk (MM). STUDY DESIGN: CoNS isolated from weekly collected stool and MM of hospitalized preterm (n\u2009=\u200949) and healthy term neonates (n\u2009=\u200920) were genotyped. Colonization-related factors were determined by Cox proportional hazards regression. RESULT: Gut colonization with mecA-negative Staphylococcus epidermidis from MM was less prevalent (40.8% vs. 95%) and delayed (median age 15.5 vs. 2 days) in preterm compared with term neonates. Enhanced colonization was associated with higher intake of CoNS from MM (hazard ratio (95% confidence interval) 1.006 (1.00-1.01) for 10 CONCLUSION: Enteral feeding with larger proportion of unpasteurized MM and limiting spread of predominant strains may promote colonization with CoNS from MM.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28665928", + "title": "The role of breast milk in the colonization of neonatal gut and skin with coagulase-negative staphylococci.", + "year": 2017, + "journal": "Pediatric research", + "authors": [ + "Soeorg H", + "Metsvaht T", + "Eelm\u00e4e I", + "Merila M", + "Treumuth S", + "Huik K", + "J\u00fcrna-Ellam M", + "Ilmoja ML", + "Lutsar I" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.3085262407673057, + "mesh_terms": [ + "Age Factors", + "Bacterial Proteins", + "Child Development", + "DNA, Bacterial", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Genotype", + "Gestational Age", + "Hospitalization", + "Humans", + "Infant", + "Infant, Newborn", + "Infant, Premature", + "Male", + "Milk, Human", + "Minisatellite Repeats", + "Phenotype", + "Pregnancy", + "Skin", + "Staphylococcus epidermidis", + "Term Birth", + "Virulence" + ], + "raw_abstract": "BackgroundWe aimed to determine the genetic relatedness between Staphylococcus epidermidis colonizing breast milk (BM) and BM-fed neonates during the first month of life.MethodsS. epidermidis was isolated from the stool and skin swabs of 20 healthy term and 49 preterm neonates hospitalized in the neonatal intensive care unit and from the BM of mothers once a week and typed by multilocus variable-number tandem-repeat analysis. Virulence-related genes were determined by PCR.ResultsThe gut (95%) and skin (100%) of term neonates were colonized with strains genetically similar to those in BM and carrying mecA and IS256 at low rate (both <6.7%). In preterm neonates, colonization with strains genetically similar to those in BM was low on the skin (34.7%) and in the gut in the first week of life (14.3%), but the prevalence of mecA (>90.6%) and IS256 (>61.7%) was high. By the fourth week, in the gut of preterm neonates the prevalence of mecA (73.8%) and IS256 (18.4%) decreased, but colonization with strains genetically similar to those in BM increased (83.7%).ConclusionDuring early life, the skin and gut of preterm neonates is colonized with S. epidermidis that is distinct from strains found in BM, but gradually the gut is enriched with strains genetically similar to those in BM, as in term neonates.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26466455", + "title": "[THE MICRO-ECOLOGY OF DIGESTIVE TRACT AS AN INDICATOR OF HUMAN HEALTH CONDITIONS].", + "year": 2015, + "journal": "Klinicheskaia laboratornaia diagnostika", + "authors": [ + "Samoukina AM", + "Mikhailova ES", + "Chervinets VM", + "Mironov A Yu", + "Alekseeva YA" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.30615626585712213, + "mesh_terms": [ + "Adolescent", + "Age Factors", + "Bacillus", + "Bacterial Typing Techniques", + "Bifidobacterium", + "Candida", + "Child", + "Escherichia coli", + "Feces", + "Female", + "Gastrointestinal Tract", + "Health Status", + "Humans", + "Lactobacillus", + "Male", + "Microbiota", + "Mouth", + "Staphylococcus" + ], + "raw_abstract": "The study was carried out to analyze qualitative and quantitative parameters of oral fluid and feces in 74 healthy individuals of different age groups. In most of the cases, alterations of micro-ecology are established characterizing by decreasing of amount of indigenous micro-flora and increasing of number of opportunistic pathogenic microorganisms of genera of Staphylococcus, Bacillus, Candida. The degree of evidence of these alterations reliably increases with age. It is established that microbiota, initial and terminal biotopes of digestive tract are closely interrelated and have number of common characteristics depending on age, hormonal and immune status and reflect conditions of micro-biocenosis of digestive tract in general. The character and degree of evidence of alterations of micro-biocenosis can be an effective diagnostic criterion for complex evaluation of human health conditions with following formation of risk groups in need of particular volume of correction activities.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28418301", + "title": "Severe MRSA Enterocolitis Caused by a Strain Harboring Enterotoxins D, G, and I.", + "year": 2017, + "journal": "Emerging infectious diseases", + "authors": [ + "Bergevin M", + "Marion A", + "Farber D", + "Golding GR", + "L\u00e9vesque S" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.3025085157023462, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Biopsy", + "Endoscopy, Gastrointestinal", + "Enterocolitis", + "Enterotoxins", + "Gene Expression", + "Humans", + "Intestinal Mucosa", + "Methicillin-Resistant Staphylococcus aureus", + "Staphylococcal Infections", + "Treatment Outcome" + ], + "raw_abstract": "We describe a case of methicillin-resistant Staphylococcus aureus (MRSA) enterocolitis in a healthy adult with previous antibiotic exposure. Colonoscopy revealed diffuse colitis and mild ileitis without ulceration. Stool cultures demonstrated abundant growth of MRSA and absent normal flora. Oral vancomycin treatment was effective and seems to be the consensus choice for therapy.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "25909606", + "title": "[Microbiological monitoring of oral fluid of clinically healthy children].", + "year": 2015, + "journal": "Stomatologiia", + "authors": [ + "Samoukina AM", + "Mikha\u012dlova ES", + "Chervinets VM", + "Alekseeva IA", + "Zhmakin IA", + "Andreeva OV" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.29409004780900627, + "mesh_terms": [ + "Bacillus", + "Bifidobacterium", + "Candida", + "Child", + "Child, Preschool", + "Feces", + "Female", + "Gastrointestinal Tract", + "Humans", + "Lactobacillus", + "Male", + "Monitoring, Physiologic", + "Saliva", + "Staphylococcus" + ], + "raw_abstract": "The article presents qualitative and quantitative parameters of microbiocenosis of oral fluid and feces of clinically healthy children in different age groups. In most of the cases compensated disbiotic changes were found, which were characterized by reduction in the number of indigenous microflora (lactobacilli and bifidobacteria) and increase of representatives of opportunistic pathogens (Staphylococcus, Bacillus and Candida). Microecological changes in different gastrointestinal biotopes are closely interrelated. Saliva may be considered as a specimen of integral fluid of human environment and can be used for complex assessment of the state of gastrointestinal tract microflora. \u041f\u0440\u0435\u0434\u0441\u0442\u0430\u0432\u043b\u0435\u043d\u044b \u043a\u0430\u0447\u0435\u0441\u0442\u0432\u0435\u043d\u043d\u044b\u0435 \u0438 \u043a\u043e\u043b\u0438\u0447\u0435\u0441\u0442\u0432\u0435\u043d\u043d\u044b\u0435 \u043f\u0430\u0440\u0430\u043c\u0435\u0442\u0440\u044b \u043c\u0438\u043a\u0440\u043e\u0431\u0438\u043e\u0446\u0435\u043d\u043e\u0437\u043e\u0432 \u0440\u043e\u0442\u043e\u0432\u043e\u0439 \u0436\u0438\u0434\u043a\u043e\u0441\u0442\u0438 (\u0420\u0416) \u0438 \u043a\u0430\u043b\u0430 \u0443 \u043a\u043b\u0438\u043d\u0438\u0447\u0435\u0441\u043a\u0438 \u0437\u0434\u043e\u0440\u043e\u0432\u044b\u0445 \u0434\u0435\u0442\u0435\u0439 \u0440\u0430\u0437\u043d\u044b\u0445 \u0432\u043e\u0437\u0440\u0430\u0441\u0442\u043d\u044b\u0445 \u0433\u0440\u0443\u043f\u043f. \u0412 \u0431\u043e\u043b\u044c\u0448\u0438\u043d\u0441\u0442\u0432\u0435 \u0441\u043b\u0443\u0447\u0430\u0435\u0432 \u0432\u044b\u044f\u0432\u043b\u0435\u043d\u044b \u043a\u043e\u043c\u043f\u0435\u043d\u0441\u0438\u0440\u043e\u0432\u0430\u043d\u043d\u044b\u0435 \u0434\u0438\u0441\u0431\u0438\u043e\u0442\u0438\u0447\u0435\u0441\u043a\u0438\u0435 \u0438\u0437\u043c\u0435\u043d\u0435\u043d\u0438\u044f, \u0445\u0430\u0440\u0430\u043a\u0442\u0435\u0440\u0438\u0437\u0443\u044e\u0449\u0438\u0435\u0441\u044f \u0441\u043d\u0438\u0436\u0435\u043d\u0438\u0435\u043c \u043a\u043e\u043b\u0438\u0447\u0435\u0441\u0442\u0432\u0430 \u0438\u043d\u0434\u0438\u0433\u0435\u043d\u043d\u043e\u0439 \u043c\u0438\u043a\u0440\u043e\u0444\u043b\u043e\u0440\u044b (\u043b\u0430\u043a\u0442\u043e- \u0438 \u0431\u0438\u0444\u0438\u0434\u043e\u0431\u0430\u043a\u0442\u0435\u0440\u0438\u0439) \u0438 \u0443\u0432\u0435\u043b\u0438\u0447\u0435\u043d\u0438\u0435\u043c \u043a\u043e\u043b\u0438\u0447\u0435\u0441\u0442\u0432\u0430 \u043f\u0440\u0435\u0434\u0441\u0442\u0430\u0432\u0438\u0442\u0435\u043b\u0435\u0439 \u0443\u0441\u043b\u043e\u0432\u043d\u043e-\u043f\u0430\u0442\u043e\u0433\u0435\u043d\u043d\u044b\u0445 \u043c\u0438\u043a\u0440\u043e\u043e\u0440\u0433\u0430\u043d\u0438\u0437\u043c\u043e\u0432 (Staphylococcus, Bacillus \u0438 Candida). \u041c\u0438\u043a\u0440\u043e\u044d\u043a\u043e\u043b\u043e\u0433\u0438\u0447\u0435\u0441\u043a\u0438\u0435 \u0438\u0437\u043c\u0435\u043d\u0435\u043d\u0438\u044f \u0432 \u0440\u0430\u0437\u043b\u0438\u0447\u043d\u044b\u0445 \u0431\u0438\u043e\u0442\u043e\u043f\u0430\u0445 \u0436\u0435\u043b\u0443\u0434\u043e\u0447\u043d\u043e-\u043a\u0438\u0448\u0435\u0447\u043d\u043e\u0433\u043e \u0442\u0440\u0430\u043a\u0442\u0430 (\u0416\u041a\u0422) \u0442\u0435\u0441\u043d\u043e \u0432\u0437\u0430\u0438\u043c\u043e\u0441\u0432\u044f\u0437\u0430\u043d\u044b \u043c\u0435\u0436\u0434\u0443 \u0441\u043e\u0431\u043e\u0439. \u0420\u0416, \u044f\u0432\u043b\u044f\u044f\u0441\u044c \u0438\u043d\u0442\u0435\u0433\u0440\u0430\u043b\u044c\u043d\u043e\u0439 \u0441\u0440\u0435\u0434\u043e\u0439 \u043e\u0440\u0433\u0430\u043d\u0438\u0437\u043c\u0430 \u0447\u0435\u043b\u043e\u0432\u0435\u043a\u0430, \u043c\u043e\u0436\u0435\u0442 \u0431\u044b\u0442\u044c \u0438\u0441\u043f\u043e\u043b\u044c\u0437\u043e\u0432\u0430\u043d\u0430 \u0432 \u043a\u0430\u0447\u0435\u0441\u0442\u0432\u0435 \u0431\u0438\u043e\u043c\u0430\u0442\u0435\u0440\u0438\u0430\u043b\u0430, \u043a\u043e\u043c\u043f\u043b\u0435\u043a\u0441\u043d\u043e \u0445\u0430\u0440\u0430\u043a\u0442\u0435\u0440\u0438\u0437\u0443\u044e\u0449\u0435\u0433\u043e \u0441\u043e\u0441\u0442\u043e\u044f\u043d\u0438\u0435 \u043c\u0438\u043a\u0440\u043e\u0444\u043b\u043e\u0440\u044b \u0416\u041a\u0422.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26068542", + "title": "Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes.", + "year": 2015, + "journal": "Diabetes", + "authors": [ + "Alkanani AK", + "Hara N", + "Gottlieb PA", + "Ir D", + "Robertson CE", + "Wagner BD", + "Frank DN", + "Zipris D" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.29336796382779523, + "mesh_terms": [ + "Adolescent", + "Adult", + "Autoantibodies", + "Autoimmunity", + "Bacteria", + "Case-Control Studies", + "Child", + "Child, Preschool", + "Cohort Studies", + "Diabetes Mellitus, Type 1", + "Disease Susceptibility", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Islets of Langerhans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "United States", + "Young Adult" + ], + "raw_abstract": "We tested the hypothesis that alterations in the intestinal microbiota are linked with the progression of type 1 diabetes (T1D). Herein, we present results from a study performed in subjects with islet autoimmunity living in the U.S. High-throughput sequencing of bacterial 16S rRNA genes and adjustment for sex, age, autoantibody presence, and HLA indicated that the gut microbiomes of seropositive subjects differed from those of autoantibody-free first-degree relatives (FDRs) in the abundance of four taxa. Furthermore, subjects with autoantibodies, seronegative FDRs, and new-onset patients had different levels of the Firmicutes genera Lactobacillus and Staphylococcus compared with healthy control subjects with no family history of autoimmunity. Further analysis revealed trends toward increased and reduced abundances of the Bacteroidetes genera Bacteroides and Prevotella, respectively, in seropositive subjects with multiple versus one autoantibody. Canonical discriminant analysis suggested that the gut microbiomes of autoantibody-positive individuals and seronegative FDRs clustered together but separate from those of new-onset patients and unrelated healthy control subjects. Finally, no differences in biodiversity were evident in seropositive versus seronegative FDRs. These observations suggest that altered intestinal microbiota may be associated with disease susceptibility.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32884012", + "title": "Altered gut microbiota correlated with systemic inflammation in children with Kawasaki disease.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Chen J", + "Yue Y", + "Wang L", + "Deng Z", + "Yuan Y", + "Zhao M", + "Yuan Z", + "Tan C", + "Cao Y" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.2894806313455323, + "mesh_terms": [ + "Acinetobacter", + "Child, Preschool", + "Computational Biology", + "Enterococcus", + "Female", + "Gastrointestinal Microbiome", + "Helicobacter", + "Humans", + "Infant", + "Inflammation", + "Lactococcus", + "Male", + "Mucocutaneous Lymph Node Syndrome", + "Polymerase Chain Reaction", + "Staphylococcus" + ], + "raw_abstract": "Kawasaki disease (KD) is a multi-systemic vasculitis of unknown etiology that occurs mainly in children, and the disturbance of gut microbiota is generally believed to cause a hyperimmune reaction triggering KD. The aim of the study was to investigate the alterations in the fecal microbiota and assess its relationship with systemic inflammation. Totally 30 KD children were enrolled and followed up for 6\u00a0months, with another group of 30 age- and sex-matched healthy children as controls. Phylotype profiles of fecal microbial communities were analyzed using 16S rRNA gene sequencing. Serum inflammatory markers were detected by flow cytometer. We showed that KD children exhibited a significant reduction in fecal microbial diversity in the acute phase compared with the healthy controls. Enterococcus, Acinetobacter, Helicobacter, Lactococcus, Staphylococcus and Butyricimonas in acute KD children were significantly higher than the healthy children. Levels of systemic inflammation biomarkers, including IL-2, IL-4, IL-6, IL-10, TNF-\u03b1, and INF-\u03b3, were significantly elevated in the acute KD children. Altered microbiota genera Enterococcus and Helicobacter abundances were shown to be correlated positively with IL-6, which were never previously reported in KD. This study suggested that gut microbiota alteration is closely associated with systemic inflammation, which provides a new perspective on the etiology and pathogenesis of KD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36853067", + "title": "Fecal microbiome in dogs with lymphoid and nonlymphoid tumors.", + "year": 2023, + "journal": "Journal of veterinary internal medicine", + "authors": [ + "Bae H", + "Lim SK", + "Jo HE", + "Oh Y", + "Park J", + "Choi HJ", + "Yu D" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.2805173393386912, + "mesh_terms": [ + "Humans", + "Dogs", + "Animals", + "RNA, Ribosomal, 16S", + "Retrospective Studies", + "Microbiota", + "Lymphoma", + "Feces", + "Dog Diseases" + ], + "raw_abstract": "BACKGROUND: The association of gut microbiota with cancer etiology and prognosis has been demonstrated in humans and rodents but has not been studied in dogs with different types of tumors. HYPOTHESIS/OBJECTIVES: To analyze microbiome composition according to tumor progression based on metastasis, recurrence, and therapeutic response in canine tumors. ANIMALS: Thirty-two client-owned dogs were divided into 3 groups: healthy (n\u00a0=\u00a09), with lymphoma (n\u00a0=\u00a012), with nonlymphoid tumors (n\u00a0=\u00a011). METHODS: Retrospective case series included animals were divided into subgroups according to the nature and severity of their tumors. Feces were screened for the 16S rRNA gene. RESULTS: Overall, alpha diversity was significantly reduced in dogs with tumors (n\u00a0=\u00a023; 12 lymphoid and 11 nonlymphoid) compared to healthy dogs (n\u00a0=\u00a09). Bacteroides had lower abundance in canine tumors at genus level. Staphylococcus showed significantly reduced abundance in dogs with aggressive tumor progression. Higher white blood cell (WBC) and neutrophil counts and lower hematocrit were significant in dogs with aggressive tumor. Spearman's rank correlation coefficient analysis revealed several measurements that showed moderate to strong correlations, including Coprococcus with total WBC count, neutrophil count, and hematocrit in the aggressive tumor group, and Saccharimonas with serum albumin and sodium concentration in all tumor dogs. CONCLUSION AND CLINICAL IMPORTANCE: The diversity of the gut microbiome was significantly reduced in dogs with tumors compared to healthy dogs. Correlations were found between changes in blood measurements and changes in microbiome composition in relation to paraneoplastic syndrome.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39614169", + "title": "Nasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Tang H", + "Du S", + "Niu Z", + "Zhang D", + "Tang Z", + "Chen H", + "Chen Z", + "Zhang M", + "Xu Y", + "Sun Y", + "Fu X", + "Norback D", + "Shao J", + "Zhao Z" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.2791173108283521, + "mesh_terms": [ + "Humans", + "Dust", + "Male", + "Child", + "Female", + "Rhinitis, Allergic", + "Case-Control Studies", + "RNA, Ribosomal, 16S", + "Bacteria", + "Skin", + "Mouth", + "Microbiota", + "Nasal Cavity", + "Air Pollution, Indoor", + "Child, Preschool", + "Metagenomics", + "Nose" + ], + "raw_abstract": "BACKGROUND: Allergic rhinitis (AR) subjects might have their microenvironment changed due to pathogenesis and living environment. Whether the nasal microbe in AR children differs from healthy subjects and how it interplays with dermal, oral and indoor dust microbe needs to be elucidated. METHODS: In this case-control study, we analyzed and compared the bacterial characterization and associations in nasal, dermal, oral swab samples and dust samples in 62 children with physician-diagnosed AR(cases) and 51 age- and gender-matched healthy ones with no history of allergic diseases(controls). Full-length 16S rRNA sequencing(swabs) and shotgun metagenomics(dust) were applied. Bacterial diversity, composition, abundance difference characteristics and fast expectation-maximization for microbial source tracking(FEAST) analysis were performed and compared between cases and controls. RESULTS: The \u03b1-diversity of dust microorganisms in AR was lower than that in control group (P\u2009=\u20090.034), and the \u03b2-diversity indices of microorganisms in nasal cavity (P\u2009=\u20090.020), skin (P\u2009=\u20090.001) and dust (P\u2009=\u20090.004) were significantly different from those in control group. At species levels, a total of 10, 15, 12, and 15 bacterial species were differentially enriched in either cases or controls in nasal, dermal, oral, and dust samples, respectively(Linear Discriminant Analysis(LDA) score\u2009>\u20092, P\u2009<\u20090.05). Staphylococcus epidermidis was the single species simultaneously more abundant in nasal, dermal and dust samples in AR children. By FEAST analysis, 8.85% and 10.11% of S. epidermidis in AR dermal and dust samples came from nasal cavity. These proportions were significantly higher than those in controls (2.70% and 3.86%) (P\u2009<\u20090.05). The same significantly higher transfer proportions(P\u2009<\u20090.05) were observed for Staphylococcus aureus enriched in the nasal cavity in AR children. Classification models by random forest regression at species levels showed, bacterial species enriched in indoor dust, nasal and dermal samples had substantial power in distinguishing AR children from healthy ones, with the highest power in the dust samples (AUC\u2009=\u20090.88) followed by nasal(AUC\u2009=\u20090.81) and dermal ones(AUC\u2009=\u20090.80). CONCLUSIONS: Our study presented the microbial enrichment characteristics in AR children both in the living environment(dust) and body sites exposed to environment through inhalation(nasal cavity), contact(skin) and ingestion(oral cavity) pathways, respectively. Nasal S.epidermidis and S.aureus had dominant influences on dust and other body sites in AR children.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36557565", + "title": "Microbiome in Male Genital Mucosa (Prepuce, Glans, and Coronal Sulcus): A Systematic Review.", + "year": 2022, + "journal": "Microorganisms", + "authors": [ + "Gon\u00e7alves MFM", + "Fernandes \u00c2R", + "Rodrigues AG", + "Lisboa C" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.27758917252397663, + "mesh_terms": [], + "raw_abstract": "The human body represents a complex and diverse reservoir of microorganisms. Although the human microbiome remains poorly characterized and understood, it should not be underestimated, since recent studies have highlighted its importance in health. This is especially evident when considering microbiota in the male reproductive system, responsible for men\u2019s fertility and sexual behavior. Therefore, the aim of this systematic review is to provide an overview of the microbial communities of the healthy male genital mucosa and its role in disease. This study was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The search was limited to the English language and studies published until August 2022 that included culture-independent techniques for microbiome characterization in male genital mucosa. Ten articles were included. The bacterial composition of the male genital mucosa consists of several genera including Prevotella, Finegoldia, Peptoniphilus, Staphylococcus, Corynebacterium, and Anaerococcus, suggesting that the male genital microbiome composition shows similarities with the adjacent anatomical sites and is related with sexual intercourse. Moreover, male circumcision appears to influence the penile microbiome. Despite the lack of knowledge on the male genital mucosa microbiome in disease, it was reported that Staphylococcus warneri and Prevotella bivia were associated with balanoposthitis, whereas Enterobacteriaceae, Prevotella, and Fusobacterium were more abundant in male genital lichen sclerosus. The limited data and paucity of prospective controlled studies highlight the need for additional studies and established criteria for sampling methods and the microbiome assay procedure. Such a consensus would foster the knowledge about the composition of the genital microbiome of healthy males and its role in disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29724187", + "title": "Effects of intestinal colonization by Clostridium difficile and Staphylococcus aureus on microbiota diversity in healthy individuals in China.", + "year": 2018, + "journal": "BMC infectious diseases", + "authors": [ + "Dong D", + "Ni Q", + "Wang C", + "Zhang L", + "Li Z", + "Jiang C", + "EnqiangMao", + "Peng Y" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.2724443737376959, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Bacteroides", + "Biodiversity", + "China", + "Clostridioides difficile", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestines", + "Male", + "Methicillin-Resistant Staphylococcus aureus", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Staphylococcus aureus" + ], + "raw_abstract": "BACKGROUND: Intestinal colonization by pathogenic bacteria is a risk factor for infection, and contributes to environmental contamination and disease dissemination. Alteration of gut microbiota also plays a pivotal role in the development of disease. Although Clostridium difficile and Staphylococcus aureus are well-recognized pathogens causing nosocomial and community infections, the intestinal colonization was not fully investigated. Herein, we explored their overall carriage rates in healthy adults from the community, and characterized the gut microbiomes of C. difficile and S. aureus carriers. METHODS: Fecal samples were collected from 1709 healthy volunteers from communities in Shanghai, China, and tested for the presence of C. difficile, methicillin-sensitive S. aureus (MSSA), and methicillin-resistant S. aureus (MRSA) using culture-based techniques. To explore differences in the gut microbiome, 16S rRNA gene sequencing was conducted using samples from non-carriers (CH), C. difficile carriers (CCD), MRSA carriers (CM), and MSSA carriers (CS). RESULTS: Overall, we detected 12 C. difficile and 60\u00a0S. aureus isolates, accounting for 0.70% and 3.51% of total isolates, respectively. Eight isolates were determined to be MRSA, accounting for 13.3% of the S. aureus population. Sequencing data revealed that the microbial diversity and richness were similar among the four groups. However, at the phylum level, carriage of C. difficile or MRSA was associated with a paucity of Bacteroidetes and an overabundance of Proteobacteria compared with non-carriers. At the genus level, the prevalence of the genera Bacteroides, Prevotella, Faecalibacterium, and Roseburia was decreased in C. difficile-positive samples compared with the controls, while the proportion of Clostridium cluster XIVa species was increased. MRSA carriers exhibited a higher proportion of the genera Parasutterella and Klebsiella, but a decreased prevalence of Bacteroides. Compared with MSSA carriers, Klebsiella was the only genus found to be significantly enriched in MRSA carriers. CONCLUSIONS: In healthy adults, colonization by C. difficile or S. aureus did not significantly affect gut microbiota diversity. However, the alteration of the gut microbiota composition in C. difficile carriers could indicate a predisposition to further infection. Our study provides essential data on the prevalence and effects of C. difficile and S. aureus colonization on gut microbiota composition in healthy adults.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32747701", + "title": "Analysis of the human breast milk microbiome and bacterial extracellular vesicles in healthy mothers.", + "year": 2020, + "journal": "Experimental & molecular medicine", + "authors": [ + "Kim SY", + "Yi DY" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.2529106453484697, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biodiversity", + "Extracellular Vesicles", + "Female", + "Humans", + "Microbiota", + "Milk, Human", + "Mothers", + "Principal Component Analysis" + ], + "raw_abstract": "The microbiota of human breast milk (HBM) contribute to infant gut colonization; however, whether bacterial extracellular vesicles (EVs) are present in HBM or might contribute to this process remains unknown. In this study, we characterized the HBM microbiota of healthy Korean mothers and measured the key bacteria likely affecting infant gut colonization by analyzing both the microbiota and bacterial EVs. A total of 22 HBM samples were collected from lactating mothers. The DNA of bacteria and bacteria-derived EVs was extracted from each sample. In alpha-diversity analyses, bacterial samples showed higher richness and evenness than bacterial EV samples, and beta-diversity analyses showed significant differences between bacteria and bacterial EVs within identical individual samples. Firmicutes accounted for the largest proportion among the phyla, followed by Proteobacteria, Bacteroidetes, and Actinobacteria, in both bacteria and bacterial EV samples. At the genus level, Streptococcus (25.1%) and Staphylococcus (10.7%) were predominant in bacterial samples, whereas Bacteroides (9.1%), Acinetobacter (6.9%), and Lactobacillaceae(f) (5.5%) were prevalent in bacterial EV samples. Several genera, including Bifidobacterium, were significantly positively correlated between the two samples. This study revealed the diverse bacterial communities in the HBM of healthy lactating mothers, and found that gut-associated genera accounted for a high proportion in bacterial EV samples. Our findings suggest the existence of key bacteria with metabolic activity that are independent of the major bacterial populations that inhabit HBM, and the possibility that EVs derived from these bacteria are involved in the vertical transfer of gut microbiota.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38938502", + "title": "A pilot study on the characterization and correlation of oropharyngeal and intestinal microbiota in children with type 1 diabetes mellitus.", + "year": 2024, + "journal": "Frontiers in pediatrics", + "authors": [ + "Wang L", + "Gong C", + "Wang R", + "Wang J", + "Yang Z", + "Wang X" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.24579511967526815, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Type 1 Diabetes Mellitus (T1DM) is one of the most common endocrine disorders of childhood and adolescence, showing a rapidly increasing prevalence worldwide. A study indicated that the composition of the oropharyngeal and gut microbiota changed in T1DM. However, no studies have yet associated the changes between the microbiomes of the oropharyngeal and intestinal sites, nor between the flora and clinical indicators. In this study, we examined the composition and characteristics of oropharyngeal and intestinal flora in patients with T1DM in compared to healthy children. We identified correlations between oropharyngeal and intestinal flora and evaluated their association with clinical laboratory tests in patients with T1DM. METHODS: The oropharyngeal and fecal samples from 13 T1DM and 20 healthy children were analyzed by high-throughput sequencing of the V3-V4 region of 16S rRNA. The associations between microbes and microorganisms in oropharyngeal and fecal ecological niches, as well as the correlation between these and clinical indicators were further analyzed. RESULTS: It was revealed that T1DM children had distinct microbiological characteristics, and the dominant oropharyngeal microbiota genus included Streptococcus, Prevotella, Leptotrichia, and Neisseria; that of intestinal microbiota included Blautia, Fusicatenibacter, Bacteroides, and Eubacterium_hallii_group. Furthermore, oropharyngeal Staphylococcus was significantly positively correlated with intestinal norank_f__Ruminococcaceae and Ruminococcus_torques_group in TIDM children. Moreover, in these children, differential genes in oropharyngeal and intestinal samples were enriched in metabolic pathways such as amino acid generation, fatty acid metabolism, and nucleotide sugar biosynthesis. Additionally, correlation analysis between the oropharyngeal/intestinal microbiome with laboratory tests showed significant correlations between several bacterial taxa in the oropharynx and intestines and glycated hemoglobin and C-peptide. CONCLUSION: Unique microbial characteristics were found in the oropharynx and intestine in children with T1DM compared to healthy children. Positive correlations were found between changes in the relative abundance of oropharyngeal and gut microbiota in children with T1DM. Associations between the oropharyngeal/intestinal microbiota and laboratory investigations in children with T1DM suggest that the composition of the oropharyngeal and intestinal flora in children with T1DM may have some impact on glycemic control.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28049493", + "title": "Presence of foodborne pathogens, extended-spectrum \u03b2-lactamase -producing Enterobacteriaceae, and methicillin-resistant Staphylococcus aureus in slaughtered reindeer in northern Finland and Norway.", + "year": 2017, + "journal": "Acta veterinaria Scandinavica", + "authors": [ + "Laaksonen S", + "Oksanen A", + "Julmi J", + "Zweifel C", + "Fredriksson-Ahomaa M", + "Stephan R" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.241070177765028, + "mesh_terms": [ + "Animals", + "Enterobacteriaceae", + "Finland", + "Food Handling", + "Food Microbiology", + "Meat", + "Methicillin-Resistant Staphylococcus aureus", + "Norway", + "Reindeer", + "beta-Lactamases" + ], + "raw_abstract": "BACKGROUND: Various food-producing animals were recognized in recent years as healthy carriers of bacterial pathogens causing human illness. In northern Fennoscandia, the husbandry of semi-domesticated reindeer (Rangifer tarandus tarandus) is a traditional livelihood and meat is the main product. This study determined the presence of selected foodborne pathogens, methicillin-resistant Staphylococcus aureus (MRSA), and extended-spectrum \u03b2-lactamase (ESBL)-producing Enterobacteriaceae in healthy semi-domesticated reindeer at slaughter in northern Finland and Norway. RESULTS: All 470 reindeer fecal samples tested negative for Salmonella spp., whereas L. monocytogenes was detected in 3%, Yersinia spp. in 10%, and Shiga toxins genes (stx1 and/or stx2) in 33% of the samples. Listeria monocytogenes isolates belonged to the serotype 1/2a (14/15) and 4b, Yersinia spp. were identified mainly as Y. kristensenii (30/46) and Y. enterocolitica (8/46), and stx2 predominated among the Shiga toxin genes (stx2 alone or in combination with stx1 was found in 25% of the samples). With regard to the frequency and distribution of stx1/stx2, striking differences were evident among the 10 different areas of origin. Hence, reindeer could constitute a reservoir for Shiga toxin-producing E. coli (STEC), but strain isolation and characterization is required for verification purposes and to assess the potential human pathogenicity of strains. On the other hand, the favorable antibiotic resistance profiles (only 5% of 95 E. coli isolates were resistant to one or more of the tested antibiotics) and the absence of MRSA and ESBL-producing Enterobacteriaceae (when applying selective methods) suggest only a limited risk of transmission to humans. CONCLUSIONS: Healthy semi-domesticated reindeer in northern Finland and Norway can be carriers of certain bacterial foodborne pathogens. Strict compliance with good hygiene practices during any step of slaughter (in particular during dehiding and evisceration) is therefore of central importance to avoid carcass contamination and to prevent foodborne pathogens from entering the food chain.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38964239", + "title": "The hidden link: How oral and respiratory microbiomes affect multiple sclerosis.", + "year": 2024, + "journal": "Multiple sclerosis and related disorders", + "authors": [ + "Jameie M", + "Ahli B", + "Ghadir S", + "Azami M", + "Amanollahi M", + "Ebadi R", + "Rafati A", + "Naser Moghadasi A" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.24058568016472215, + "mesh_terms": [ + "Humans", + "Multiple Sclerosis", + "Microbiota", + "Mouth", + "Lung", + "Animals", + "Respiratory System" + ], + "raw_abstract": "BACKGROUND: Extensive research has explored the role of gut microbiota in multiple sclerosis (MS). However, the impact of microbial communities in the oral cavity and respiratory tract on MS is an emerging area of investigation. PURPOSE: We aimed to review the current literature related to the nasal, oral, and lung microbiota in people with MS (PwMS). METHODS: We conducted a narrative review of clinical and preclinical original studies on PubMed that explored the relationship between the bacterial or viral composition of the nasal, lung, and oral microbiota and MS. Additionally, to find relevant studies not retrieved initially, we also searched for references in related review papers, as well as the references cited within the included studies. RESULTS AND CONCLUSIONS: Thirteen studies were meticulously reviewed in three sections; oral microbiota (n = 8), nasal microbiota (n = 3), and lung microbiota (n = 2), highlighting considerable alterations in the oral and respiratory microbiome of PwMS compared to healthy controls (HCs). Genera like Aggregatibacter and Streptococcus were less abundant in the oral microbiota of PwMS compared to HCs, while Staphylococcus, Leptotrichia, Fusobacterium, and Bacteroides showed increased abundance in PwMS. Additionally, the presence of specific bacteria, including Streptococcus sanguinis, within the oral microbiota was suggested to influence Epstein-Barr virus reactivation, a well-established risk factor for MS. Studies related to the nasal microbiome indicated elevated levels of specific Staphylococcus aureus toxins, as well as nasal glial cell infection with human herpes virus (HHV)-6 in PwMS. Emerging research on lung microbiome in animal models demonstrated that manipulating the lung microbiome towards lipopolysaccharide-producing bacteria might suppress MS symptoms. These findings open avenues for potential therapeutic strategies. However, further research is crucial to fully understand the complex interactions between the microbiome and MS. This will help identify the most effective timing, bacterial strains, and modulation techniques.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39174731", + "title": "Gut Microbiome in Children with Congenital Heart Disease After Cardiopulmonary Bypass Surgery (GuMiBear Study).", + "year": 2024, + "journal": "Pediatric cardiology", + "authors": [ + "Koc F", + "Magner C", + "Murphy K", + "Kelleher ST", + "Tan MH", + "O'Toole M", + "Jenkins D", + "Boyle J", + "Lavelle M", + "Maguire N", + "Ross PR", + "Stanton C", + "McMahon CJ" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.23771593308263975, + "mesh_terms": [], + "raw_abstract": "The gut microbiome of infants with congenital heart disease (CHD) undergoing cardiopulmonary bypass surgery (CPB) is at risk of profound alteration. The aim of this study was to examine the gut microbiome pre- and post-bypass surgery to explore potential implications of altered gut biodiversity.\u00a0A prospective cohort study involving infants with CHD who underwent CPB\u00a0was performed. Faecal samples were collected from infants alongside the collection of demographic and clinical data in order to examine gut microbiome changes before and after surgery. 16S rRNA sequencing analysis was performed on DNA isolated from stool samples to determine changes in gut microbiome composition. Thirty-three patients were recruited, with samples from thirteen of these available for final analysis. Compared with healthy, matched controls, at a genus level, pre-operative samples for infants with CHD demonstrated a higher relative abundance of Escherichia-Shigella (31% vs 2-6%) and a lower relative abundance of Bifidobacterium (13% vs 40-60%). In post-operative samples, the relative abundance of Escherichia-Shigella (35%), Enterococcus (11%), Akkermansia (6%), and Staphylococcus (5%) were higher than pre-op samples. One infant developed post-operative necrotising-enterocolitis (NEC). They displayed a marked abundance of the Enterococcus (93%) genus pre-operatively. This study demonstrates that infants with CHD have an altered gut\u00a0microbiome when compared with healthy controls and there might be a possible link between an abundance of virulent species and NEC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37973865", + "title": "Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra.", + "year": 2023, + "journal": "Nature microbiology", + "authors": [ + "King AM", + "Zhang Z", + "Glassey E", + "Siuti P", + "Clardy J", + "Voigt CA" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.2364413601690739, + "mesh_terms": [ + "Humans", + "Antimicrobial Peptides", + "Methicillin-Resistant Staphylococcus aureus", + "Escherichia coli", + "Peptides", + "Bacteria", + "Microbiota", + "Anti-Bacterial Agents" + ], + "raw_abstract": "Human-associated bacteria secrete modified peptides to control host physiology and remodel the microbiota species composition. Here we scanned 2,229 Human Microbiome Project genomes of species colonizing skin, gastrointestinal tract, urogenital tract, mouth and trachea for gene clusters encoding RiPPs (ribosomally synthesized and post-translationally modified peptides). We found 218 lanthipeptides and 25 lasso peptides, 70 of which were synthesized and expressed in E. coli and 23 could be purified and functionally characterized. They were tested for activity against bacteria associated with healthy human flora and pathogens. New antibiotics were identified against strains implicated in skin, nasal and vaginal dysbiosis as well as from oral strains selectively targeting those in the gut. Extended- and narrow-spectrum antibiotics were found against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci. Mining natural products produced by human-associated microbes will enable the elucidation of ecological relationships and may be a rich resource for antimicrobial discovery.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27344596", + "title": "Identification of Infantile Diarrhea Caused by Breast Milk-Transmitted Staphylococcus aureus Infection.", + "year": 2016, + "journal": "Current microbiology", + "authors": [ + "Chen Z", + "Pan WG", + "Xian WY", + "Cheng H", + "Zheng JX", + "Hu QH", + "Yu ZJ", + "Deng QW" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.23368729511169195, + "mesh_terms": [ + "Adult", + "Breast Feeding", + "China", + "Diarrhea, Infantile", + "Feces", + "Female", + "Humans", + "Infant", + "Infant, Newborn", + "Infectious Disease Transmission, Vertical", + "Male", + "Milk, Human", + "Multilocus Sequence Typing", + "Staphylococcal Infections", + "Staphylococcus aureus", + "Young Adult" + ], + "raw_abstract": "Staphylococcus aureus is a well-known organism which is responsible for a variety of human infectious diseases including skin infections, pneumonia, bacteremia, and endocarditis. Few of the microorganisms can be transmitted from mother to the newborn or infant by milk breastfeeding. This study aims to identify transmission of S. aureus from healthy, lactating mothers to their infants by breastfeeding. Stool specimens of diarrheal infants and breast milk of their mother (totally three pairs) were collected and six Staphylococcus aureus isolates were cultured positively. Homology and molecular characters of isolated strains were tested using pulsed-field gel electrophoresis (PFGE), spa typing, and multilocus sequence typing. Furthermore, toxin genes detection was also performed. Each pair of isolates has the same PFGE type and spa type. Four Sequence types (STs) were found among all the isolates; they are ST15, ST188, and ST59, respectively. Among the strains, seb, sec, and tst genes were found, and all were negative for pvl gene. The homology of the S. aureus strains isolated from the infants' stool and the mothers' milk was genetically demonstrated, which indicated that breastfeeding may be important in the transmission of S. aureus infection, and the character of S. aureus needed to be further evaluated.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35149000", + "title": "Predominance of Staphylococcus Correlates with Wound Burden and Disease Activity in Dystrophic Epidermolysis Bullosa: A Prospective Case-Control Study.", + "year": 2022, + "journal": "The Journal of investigative dermatology", + "authors": [ + "Reimer-Taschenbrecker A", + "K\u00fcnstner A", + "Hirose M", + "H\u00fcbner S", + "Gewert S", + "Ibrahim S", + "Busch H", + "Has C" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.2330350396014756, + "mesh_terms": [ + "Case-Control Studies", + "Child", + "Epidermolysis Bullosa", + "Epidermolysis Bullosa Dystrophica", + "Humans", + "Skin", + "Staphylococcus", + "Staphylococcus aureus" + ], + "raw_abstract": "Recessive dystrophic epidermolysis bullosa is characterized by skin blistering and wounds. To uncover the changes in the skin and mucosal microbiome related to age and disease progression and microbiome impact on clinical and inflammatory laboratory parameters, swabs from wounded and unwounded skin, oral mucosa, and stool samples of 28 children with recessive dystrophic epidermolysis bullosa and 28 healthy controls were subjected to 16S-ribosomal RNA gene sequencing. Skin microbiome of patients with recessive dystrophic epidermolysis bullosa showed significantly reduced alpha diversity compared with that of healthy controls and showed significantly early, age-dependent predominance of Staphylococcus aureus, first in wounded skin and then in unwounded skin. These findings were more pronounced in the severe disease with higher abundances of S.\u00a0aureus than in intermediate disease. S.\u00a0aureus abundance correlated significantly with both acute and chronic wound burden. Changes in oral mucosal and gut microbiome were discrete, with no significant differences in alpha diversity. Our findings show that children with recessive dystrophic epidermolysis bullosa experience skin microbiome changes early in life. Longitudinal studies should confirm that dysbiosis starts in wounds and later extends to unwounded skin. The predominance of S.\u00a0aureus significantly correlates with wound burden and disease activity and, to some extent, with systemic inflammation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32472074", + "title": "Station and train surface microbiomes of Mexico City's metro (subway/underground).", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Hern\u00e1ndez AM", + "Vargas-Robles D", + "Alcaraz LD", + "Peimbert M" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.23033472489751913, + "mesh_terms": [ + "Bacteria", + "DNA, Bacterial", + "DNA, Ribosomal", + "Environmental Microbiology", + "Equipment Contamination", + "Humans", + "Mexico", + "Microbiota", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Railroads", + "Sequence Analysis, DNA", + "Transportation", + "Urban Renewal" + ], + "raw_abstract": "The metro is one of the more representative urban transportation systems of Mexico City, and it transports approximately 4.5 million commuters every day. Large crowds promote the exchange of microbes between humans. In this study, we determined the bacterial diversity profile of the Mexico City metro by massive sequencing of the 16S rRNA gene. We identified a total of 50,174 operational taxonomic units (OTUs) and 1058 genera. The metro microbiome was dominated by the phylum Actinobacteria and by the genera Cutibacterium (15%) (C. acnes 13%), Corynebacterium (13%), Streptococcus (9%), and Staphylococcus (5%) (S. epidermidis; 4%), reflecting the microbe composition of healthy human skin. The metro likely microbial sources were skin, dust, saliva, and vaginal, with no fecal contribution detected. A total of 420 bacterial genera were universal to the twelve metro lines tested, and those genera contributed to 99.10% of the abundance. The annual 1.6 billion ridership makes this public transport a main hub for microbe-host-environment interactions. Finally, this study shows that the microbial composition of the Mexico City metro comes from a mixture of environmental and human sources and that commuters are exposed to healthy composition of the human microbiota.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27148183", + "title": "Relationship between Milk Microbiota, Bacterial Load, Macronutrients, and Human Cells during Lactation.", + "year": 2016, + "journal": "Frontiers in microbiology", + "authors": [ + "Boix-Amor\u00f3s A", + "Collado MC", + "Mira A" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.22677899818042024, + "mesh_terms": [], + "raw_abstract": "Human breast milk is considered the optimal nutrition for infants, providing essential nutrients and a broad range of bioactive compounds, as well as its own microbiota. However, the interaction among those components and the biological role of milk microorganisms is still uncovered. Thus, our aim was to identify the relationships between milk microbiota composition, bacterial load, macronutrients, and human cells during lactation. Bacterial load was estimated in milk samples from a total of 21 healthy mothers through lactation time by bacteria-specific qPCR targeted to the single-copy gene fusA. Milk microbiome composition and diversity was estimated by 16S-pyrosequencing and the structure of these bacteria in the fluid was studied by flow cytometry, qPCR, and microscopy. Fat, protein, lactose, and dry extract of milk as well as the number of somatic cells were also analyzed. We observed that milk bacterial communities were generally complex, and showed individual-specific profiles. Milk microbiota was dominated by Staphylococcus, Pseudomonas, Streptococcus, and Acinetobacter. Staphylococcus aureus was not detected in any of these samples from healthy mothers. There was high variability in composition and number of bacteria per milliliter among mothers and in some cases even within mothers at different time points. The median bacterial load was 10(6) bacterial cells/ml through time, higher than those numbers reported by 16S gene PCR and culture methods. Furthermore, milk bacteria were present in a free-living, \"planktonic\" state, but also in equal proportion associated to human immune cells. There was no correlation between bacterial load and the amount of immune cells in milk, strengthening the idea that milk bacteria are not sensed as an infection by the immune system.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35889029", + "title": "Profile of the Gut Microbiome Containing Carbapenem-Resistant Enterobacteriaceae in ICU Patients.", + "year": 2022, + "journal": "Microorganisms", + "authors": [ + "Sindi AA", + "Alsayed SM", + "Abushoshah I", + "Bokhary DH", + "Tashkandy NR" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.22591425641222077, + "mesh_terms": [], + "raw_abstract": "Carbapenem-resistant Enterobacteriaceae (CRE) is a risk to public health worldwide and causes epidemic outbreaks in hospitals. The identification of alterations in the gut microbial profile can potentially serve as an early diagnostic tool to prevent harmful bacterial colonization. The purpose of this study was to characterize the gut microbiota profile of CRE-positive stool samples using 16S rRNA gene sequencing and to compare it with that of healthy control groups at King AbdulAziz University Hospital. Our results demonstrate that compared to the control group samples, the CRE-positive and CRE-negative group samples were less diverse and were dominated by a few operational taxonomic clusters of Enterococcus, Sphingomonas, and Staphylococcus. An analysis of samples from CRE-positive patients revealed Pseudomonas as the most abundant taxon. The existence of Pseudomonas in clinical samples undoubtedly indicates the development of resistance to a variety of antimicrobial drugs, with a less diverse microbiota. In our study, we found that the co-occurrence patterns of Klebsiella, Parabacteroides, Proteus and Pseudomonas differed between the CRE-negative and control stool groups.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32921446", + "title": "Distribution of non-aureus staphylococci from quarter milk, teat apices, and rectal feces of dairy cows, and their virulence potential.", + "year": 2020, + "journal": "Journal of dairy science", + "authors": [ + "Wuytack A", + "De Visscher A", + "Piepers S", + "Boyen F", + "Haesebrouck F", + "De Vliegher S" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.22525837420299927, + "mesh_terms": [ + "Animals", + "Cattle", + "Cell Count", + "Cross-Sectional Studies", + "Feces", + "Female", + "Lactation", + "Mammary Glands, Animal", + "Mastitis, Bovine", + "Milk", + "Staphylococcal Infections", + "Staphylococcus", + "Staphylococcus haemolyticus", + "Staphylococcus hominis", + "Virulence" + ], + "raw_abstract": "Non-aureus staphylococci (NAS) are predominantly isolated from bovine milk samples of quarters suffering from subclinical mastitis. They are also abundantly present on dairy cows' teat apices and can be recovered from bovine fecal samples, as recently described. Differences in ecology, epidemiology, effect on udder health, and virulence or protective traits have been reported among the species within this group. The objectives of this study were (1) to describe the species-specific distribution of NAS in 3 bovine-associated habitats, namely quarter milk, teat apices, and rectal feces, and (2) to evaluate the virulence potential of NAS by comparing their distribution in contrasting milk sample strata and the presence of selected virulence genes. A cross-sectional, systematic sampling procedure was followed in 8 dairy herds that participated in the local Dairy Herd Improvement program in Flanders, Belgium. Quarter milk samples (n = 573) were collected from 144 lactating cows in 8 herds. In 5 of the 8 herds, teat apex swabs (n = 192) were taken from 15 lactating cows, before and after milking, and from 18 dry cows. In the same 5 herds, rectal feces were sampled from 80 lactating cows (n = 80), taking into account that a cow could only serve as the source of one type of sample. In addition, milk samples of all clinical mastitis cases were continuously collected during the 1-yr study period from March 2017 to March 2018 in the 8 herds. In total, 1,676 Staphylococcus isolates were phenotypically identified and subjected to MALDI-TOF mass spectrometry. Thirty-three, 98, and 28% of all quarter milk, teat apex, and rectal fecal samples were NAS-positive, respectively, reaffirming the presence of NAS in rectal feces. The overall predominant species in the 3 habitats combined were Staphylococcus haemolyticus, Staphylococcus chromogenes, and Staphylococcus hominis. Four, 16, and 12% of the healthy quarters (quarter milk somatic cell count \u226450,000 cells/mL of milk), quarters with subclinical mastitis (quarter milk somatic cell count >50,000 cells/mL of milk), and quarters with clinical mastitis, respectively, were NAS-positive, suggesting that the potential to cause (mild) clinical mastitis is present among NAS. This was substantiated by comparing the presence of virulence genes of NAS isolates originating from contrasting milk sample strata (healthy quarters and quarters with clinical mastitis).", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33972766", + "title": "Fetal meconium does not have a detectable microbiota before birth.", + "year": 2021, + "journal": "Nature microbiology", + "authors": [ + "Kennedy KM", + "Gerlach MJ", + "Adam T", + "Heimesaat MM", + "Rossi L", + "Surette MG", + "Sloboda DM", + "Braun T" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.22241787743719962, + "mesh_terms": [ + "Bacteria", + "Cesarean Section", + "Feces", + "Female", + "Fetus", + "Gestational Age", + "Humans", + "Infant", + "Infant, Newborn", + "Male", + "Meconium", + "Microbiota", + "Pregnancy", + "Rectum" + ], + "raw_abstract": "Microbial colonization of the human intestine impacts host metabolism and immunity; however, exactly when colonization occurs is unclear. Although many studies have reported bacterial DNA in first-pass meconium samples, these samples are typically collected hours to days after birth. Here, we investigated whether bacteria could be detected in meconium before birth. Fetal meconium (n\u2009=\u200920) was collected by rectal swab during elective breech caesarean deliveries without labour and before antibiotics and compared to technical and procedural controls (n\u2009=\u20095), first-pass meconium (neonatal meconium; n\u2009=\u200914) and infant stool (n\u2009=\u200925). Unlike first-pass meconium, no microbial signal distinct from negative controls was detected in fetal meconium by 16S ribosomal RNA gene sequencing. Additionally, positive aerobic (n\u2009=\u200910 of 20) and anaerobic (n\u2009=\u200912 of 20) clinical cultures of fetal meconium (13 of 20 samples positive in at least one culture) were identified as likely skin contaminants, most frequently Staphylococcus epidermidis, and not detected by sequencing in most samples (same genera detected by culture and sequencing in 2 of 13 samples with positive culture). We conclude that fetal gut colonization of healthy term infants does not occur before birth and that microbial profiles of neonatal meconium reflect populations acquired during and after birth.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32441784", + "title": "Impact of Clinical Factors on the Intestinal Microbiome in Infants With Gastroschisis.", + "year": 2021, + "journal": "JPEN. Journal of parenteral and enteral nutrition", + "authors": [ + "Wu AJ", + "Lee DJ", + "Li F", + "Tobin NH", + "Aldrovandi GM", + "Shew SB", + "Calkins KL" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.21463924172206258, + "mesh_terms": [ + "Cesarean Section", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Gastroschisis", + "Humans", + "Infant", + "Pregnancy", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Infants with gastroschisis require operations and lengthy hospitalizations due to intestinal dysmotility. Dysbiosis may contribute to these problems. Little is known on the microbiome of gastroschisis infants. METHODS: The purpose of this study was to investigate the fecal microbiome in gastroschisis infants. Microbiome profiling was performed by sequencing the V4 region of the 16S rRNA gene. The microbiome of gastroschisis infants was compared with the microbiome of healthy controls, and the effects of mode of birth delivery, gestational age, antibiotic duration, and nutrition type on microbial composition and diversity were investigated. RESULTS: The microbiome of gastroschisis infants (n = 13) was less diverse (Chao1, P < .001), lacked Bifidobacterium (P = .001), and had increased Staphylococcus (P = .007) compared with controls (n = 83). Mode of delivery (R CONCLUSION: The microbiome of gastroschisis infants is dysbiotic, and mode of birth delivery, antibiotic duration, and gestational age appear to contribute to microbial variation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35093554", + "title": "Gut microbiome alterations in hereditary angioedema.", + "year": 2022, + "journal": "Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology", + "authors": [ + "Cao Y", + "Kan H", + "Wang X", + "Zhi Y" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.21320678457304004, + "mesh_terms": [ + "Angioedemas, Hereditary", + "Complement C1 Inhibitor Protein", + "Danazol", + "Dysbiosis", + "Family", + "Gastrointestinal Microbiome", + "Humans", + "Tranexamic Acid" + ], + "raw_abstract": "BACKGROUND: Hereditary angioedema (HAE) is a rare disease with wide intra- and interindividual clinical variation. There are no reliable indicators available in clinical practice to predict the onset and severity of HAE. Uncovering the changes in the gut microbiota in HAE patients may offer insight into a missing piece of the pathogenesis and help explain the clinical heterogeneity. OBJECTIVE: Explore whether dysbiosis exists in patients with HAE and whether there are biomarkers to indicate the episodes. METHODS: Fecal samples and clinical data were collected from patients with C1-inhibitor-related HAE and their healthy family members. Patients were grouped on the basis of the most recent conditions of HAE episodes and major clinical manifestations. The gut microbiota was evaluated by sequencing the 16S ribosomal RNA gene and analyzed for diversity. RESULTS: Microbial richness and diversity were significantly reduced among patients who had recent HAE attacks, especially for those presenting with abdominal symptoms (P\u00a0=\u00a0.003 and P\u00a0=\u00a0.048 compared with healthy controls and patients with no recent episodes, respectively). Decreased Firmicutes and increased Proteobacteria were found among the individuals with a recent episode, along with a marked increase of pathogenic bacteria on the basis of the predictive functional profiling. Dysbiosis was restored after regular use of danazol or tranexamic acid. A combined biomarker composed of Bifidobacterium, Lachnospira, Paraprevotella, Desulfovibrio, and Staphylococcus was proposed to detect the recent edema episodes. CONCLUSION: We reported alterations of the gut microbiome in patients with HAE and explored the possible role of bacteria in the etiology of edema episodes, which may provide new clues for the prediction of disease course, clinical treatment, and therapeutic evaluation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31421888", + "title": "Non-aureus staphylococci in fecal samples of dairy cows: First report and phenotypic and genotypic characterization.", + "year": 2019, + "journal": "Journal of dairy science", + "authors": [ + "Wuytack A", + "De Visscher A", + "Piepers S", + "Boyen F", + "Haesebrouck F", + "De Vliegher S" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.20848400886488636, + "mesh_terms": [ + "Animals", + "Cattle", + "Feces", + "Female", + "Genotype", + "Mammary Glands, Animal", + "Milk", + "Molecular Typing", + "Prevalence", + "RNA, Ribosomal, 16S", + "Random Amplified Polymorphic DNA Technique", + "Staphylococcus", + "Staphylococcus haemolyticus", + "Streptococcus", + "beta-Lactamases" + ], + "raw_abstract": "The aims of this study were to determine whether non-aureus staphylococci (NAS) are present in rectal feces of healthy dairy cows, and if so, to delineate species to which they belong and to study several phenotypic and genotypic traits as a first step toward determining the potential impact of fecal shedding of NAS on bovine udder health. Fecal samples were aseptically collected from the rectum of 25 randomly selected clinically healthy dairy cows in a commercial dairy herd using an automated milking system. Fecal NAS were isolated and then identified at the species level using transfer RNA-intergenic spacer PCR and sequencing of the 16S rRNA housekeeping gene. Strain typing was performed using random amplification of polymorphic DNA (RAPD)-PCR. The antimicrobial resistance profiles, biofilm formation, and growth and inhibitory characteristics of all NAS isolates were evaluated. Half of the cows were shedding NAS, resulting in 31 NAS isolates belonging to 11 different species. The most prevalent species were Staphylococcus rostri (23%, n = 7), Staphylococcus cohnii (16%, n = 5), and Staphylococcus haemolyticus (13%, n = 4) with all Staphylococcus agnetis, Staphylococcus chromogenes, and Staph. rostri isolates belonging to the same strain according to RAPD banding patterns. Acquired antimicrobial resistance was observed in 28 of the 31 NAS isolates, mainly due to \u03b2-lactamase production. Most of the isolates (84%, n = 27) had a weak biofilm-forming potential, but only 2 contained the bap gene. The ica and aap genes were not detected in any of the isolates. In vitro growth of Staphylococcus aureus and Streptococcus dysgalactiae was inhibited by Staph. agnetis isolates, and Staph. chromogenes isolates were able to inhibit the growth of Strep. dysgalactiae and Streptococcus uberis. All fecal isolates were able to grow when oxygen and iron were limitedly available, mimicking the growth conditions in the mammary gland.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29205422", + "title": "Systematic review: ileoanal pouch microbiota in health and disease.", + "year": 2018, + "journal": "Alimentary pharmacology & therapeutics", + "authors": [ + "Segal JP", + "Oke S", + "Hold GL", + "Clark SK", + "Faiz OD", + "Hart AL" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.20754353811371182, + "mesh_terms": [ + "Adult", + "Colonic Pouches", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Health", + "Humans", + "Longitudinal Studies", + "Male", + "Pouchitis" + ], + "raw_abstract": "BACKGROUND: The resident gut microbiota is essential for physiological processes; the disturbance of its balance is linked to intestinal inflammation. The ileoanal pouch is a model for the study of intestinal inflammation, as inflammation of the pouch is common and mostly develops within 12\u00a0months following ileostomy closure. This allows the longitudinal study of the microbiota, giving insight into the microbiota changes during transition from a normal to an inflamed pouch. AIM: To explore the literature on the microbiota of the ileoanal pouch in health and disease. METHODS: A systematic computer search of the on-line bibliographic databases MEDLINE and EMBASE was performed between 1966 and February 2017. Randomised controlled trials, cohort studies and observational studies were included. Studies were included if they reported microbiota analysis on faecal samples or tissue from the ileoanal pouch. RESULTS: Twenty-six papers were eligible. Following ileostomy closure, anaerobic bacteria are the abundant species in the ileoanal pouch with presence of a diverse microbiota key to maintaining a healthy ileoanal pouch. Acute pouchitis is associated with an increase in Clostridia species, while chronic pouchitis is associated with an increase in Staphylococcus aureus. In the treatment of pouchitis, a decrease in Clostridia species appears to be associated with treatment response. CONCLUSION: The microbiota plays an important role in both the inflamed and the healthy ileoanal pouch. A direct causal relationship between individual microbiota changes and inflammation has not yet been established, but manipulation of the ileoanal pouch microbiota may be a novel therapeutic avenue to explore.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35622224", + "title": "Dynamic colonization of gut microbiota and its influencing factors among the breast-feeding infants during the first two years of life.", + "year": 2022, + "journal": "Journal of microbiology (Seoul, Korea)", + "authors": [ + "Li P", + "Chang X", + "Chen X", + "Tang T", + "Liu Y", + "Shang Y", + "Qi K" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.2041901168485065, + "mesh_terms": [ + "Adult", + "Bacteria", + "Bifidobacterium", + "Breast Feeding", + "Feces", + "Female", + "Firmicutes", + "Gastrointestinal Microbiome", + "Humans", + "Infant", + "Infant, Newborn", + "Pregnancy", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "The maturation of infant gut microbiota has lifelong implications on health, which has been proposed as the major events during the first year of life. However, little is known about their dynamic colonization and influencing elements among the first two-year infancy as well as into the adulthood. So based on the 16S rRNA sequencing data among 30 healthy breast-feeding mother-infant pairs with normal ranges of growth and development indicators from birth to two years old, the dynamic colonization of gut microbiota and its influencing factors were discussed using this birth cohort. Among these, we identified that the diversity of gut microbiota was significantly increased from six-month to two-year subgroups. The significantly dynamic trends of gut microbiota at the phylum (genus) level were that the percents of Firmicutes (Faecalibacterium, Blautia, Enterococcus, Subdoligranulum, Agathobacter, unidentified_Erysipelotrichaceae, Staphylococcus, unidentified_Ruminococcaceae, and Fusicatenibacter), Bacteroidetes and Verrucomicrobia were increased, while Actinobacteria (Bifidobacterium) and Proteobacteria (unidentified-Enterobacteriaceae and Klebsiella) were decreased with the increased ages from six months to two years old, which might simultaneously modulate the host pathways, such as the higher percents of chemoheterotrophy and fermentation, and lower percentages of nitrate_reduction, aerobic_chemoheterotrophy and so on. Furthermore, there were significant associations between maternal (milk microbiota, pre-pregnancy BMI, BMI increment during the pregnancy)/infant characteristics (BMI at birth and BMI gain), and the compositions of gut microbiota. However, no differences of gut microbiota were shown between the different sex and productive mode subgroups. Overall, the colonization of gut microbiota is significantly matured into the adulthood with the increased ages to two-years old and regulated by the above maternal/infant characteristics, which will provide a new direction for the host-gut microbiota interplay during the first two years of life.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35689701", + "title": "Features of the gut prokaryotic virome of Japanese patients with Crohn's disease.", + "year": 2022, + "journal": "Journal of gastroenterology", + "authors": [ + "Imai T", + "Inoue R", + "Nishida A", + "Yokota Y", + "Morishima S", + "Kawahara M", + "Kusada H", + "Tamaki H", + "Andoh A" + ], + "bacteria": "Staphylococcus", + "condition": "healthy", + "relevance_score": 0.20021960081514537, + "mesh_terms": [ + "Bacteria", + "Crohn Disease", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Japan", + "RNA, Ribosomal, 16S", + "Virome" + ], + "raw_abstract": "BACKGROUND/AIMS: The gut virome is mainly composed of bacteriophages and influences gut homeostasis and pathogenic conditions. In this study, we analyzed the gut prokaryotic virome in Japanese patients with Crohn's disease (CD). MATERIALS/METHODS: We collected 19 fecal samples from CD patients and 16 samples from healthy controls. The gut bacteriome was analyzed by 16S rRNA gene sequencing and the virome was profiled by shotgun metagenomic sequencing. RESULTS: Despite no differences in richness and evenness, there was a significant difference in the overall structure of the gut virome between CD patients and controls (P\u2009=\u20090.013). CrAssphage and Staphylococcus virus, belonging to the order Caudovirales, were dominant in the gut virome of controls and CD patients. The abundance of crAssphage was significantly greater in CD patients than controls (P\u2009=\u20090.021). Lactococcus, Enterococcus and Lactobacillus phages were present only in CD patients, while Xanthomonas and Escherichia phages were unique to the controls. In the gut bacteriome of CD patients, richness and evenness were significantly lower, and a significant difference in the overall structure was observed between groups (P\u2009=\u20090.014). The gut bacteriome of CD patients was characterized by a decrease of the genera Faecalibacterium, Roseburia, and Ruminococcus and an increase of the family Enterobacteriaceae. There were more significant correlations between viruses and bacteria in CD patients than controls. CONCLUSIONS: The gut virome of CD patients was distinct from that of healthy controls in a Japanese population. An altered gut virome may be one of the factors associated with the bacterial dysbiosis of CD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37728722", + "title": "Gut microbiota, a potential cause of higher insulin sensitivity in children with Prader-Willi syndrome.", + "year": 2024, + "journal": "Journal of endocrinological investigation", + "authors": [ + "Zhong ML", + "Cai YQ", + "Tang YF", + "Dai YL", + "Jiang YH", + "Ni Y", + "Zou CC" + ], + "bacteria": "Frisingicoccus", + "condition": "healthy", + "relevance_score": 0.2412084751933096, + "mesh_terms": [ + "Child", + "Humans", + "Prader-Willi Syndrome", + "Insulin Resistance", + "Gastrointestinal Microbiome", + "Cross-Sectional Studies", + "Obesity" + ], + "raw_abstract": "PURPOSE: Obesity is the main driving factor for comorbidities in Prader-Willi syndrome (PWS) patients due to overeating behaviors. The gut microbiota has been implicated in the etiology of obesity and associated comorbidities. The purpose of the present study was to characterize the fecal microbiota in Chinese patients with PWS and compare it to that of patients with obesity as well as healthy controls. METHODS: We conducted a cross-sectional study with 35 PWS patients (PWS), 35 patients with obesity (OB), and 35 healthy controls (HC). Metagenomic sequencing was performed in stool samples. RESULTS: The composition of the fecal microbiota in PWS patients differed from that of participants in the OB and HC groups. It was characterized by increased Akkermansia Eubacterium, Eubacterium rectale, and Roseburia intestinalis and decreased Parabacteroides and Phascolarctobacterium. Additionally, the homeostatic model assessment of insulin resistance (HOMA-IR) was lower in PWS patients than in patients with obesity. Spearman rank correlation analysis showed that Achromobacter, Acidiphilium, Xylophilus, and Frisingicoccus were significantly negatively correlated with HOMA-IR. CONCLUSION: The composition of the gut microbiota in Chinese PWS patients differed from that in patients with obesity, which might contribute to higher insulin sensitivity in PWS patients.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34062226", + "title": "Microbiome analysis reveals the significant changes in gut microbiota of diarrheic Baer's Pochards (Aythya baeri).", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Xi L", + "Song Y", + "Han J", + "Qin X" + ], + "bacteria": "Elusimicrobium", + "condition": "healthy", + "relevance_score": 0.4555303886737918, + "mesh_terms": [ + "Bacteroidetes", + "Feces", + "Firmicutes", + "Gastrointestinal Microbiome", + "Microbiota" + ], + "raw_abstract": "Gut microbiota has been demonstrated to play multiple crucial roles in immunity, physiology, metabolism, and health maintenance. Diarrhea was closely related to the gut microbiota, but information regarding the alterations in gut microbial composition and structure in Baer's Pochard (Aythya baeri) with diarrhea remains scarce. Here, 16S rDNA amplicon sequencing was performed to investigate the gut microbial variability between diarrheic and healthy Baer's Pochard. Results indicated that the gut bacterial community of diarrheic Baer's Pochard showed a distinct decrease in alpha diversity, accompanied by evident changes in taxonomic compositions. Microbial taxonomic analysis revealed that Firmicutes, Proteobacteria and Bacteroidetes were the most dominant phyla in all the fecal samples regardless of health status. At the genus level, the differences in gut bacterial abundance between healthy and diarrheic populations were gradually observed. Specifically, the proportion of Elusimicrobia in the diarrheic Baer's Pochard was increased in comparison with healthy populations, while Acidobacteria, Rokubacteria, Cyanobacteria and Patescibacteria were dramatically decreased. Additionally, the relative proportion of 23 bacterial genera significantly decreased in diarrheic Baer's Pochard, whereas the relative percentage of 4 bacterial genera (Alkanindiges, Elusimicrobium, Spirosoma and Exiguobacterium) observably increased as compared to healthy populations. Taken together, the present study revealed that there were distinct differences in the gut microbial composition and diversity between the healthy and diarrheic Baer's Pochard. Remarkably, this is the first report on the differences in the gut microbiota of Baer's Pochard under different health states and may contribute to provide better insight into gut microbial composition and diversity of Baer's Pochard.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38689063", + "title": "Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development.", + "year": 2024, + "journal": "Nature medicine", + "authors": [ + "Tito RY", + "Verbandt S", + "Aguirre Vazquez M", + "Lahti L", + "Verspecht C", + "Llor\u00e9ns-Rico V", + "Vieira-Silva S", + "Arts J", + "Falony G", + "Dekker E", + "Reumers J", + "Tejpar S", + "Raes J" + ], + "bacteria": "Peptostreptococcus", + "condition": "healthy", + "relevance_score": 0.34974533439543126, + "mesh_terms": [ + "Humans", + "Colorectal Neoplasms", + "Middle Aged", + "Feces", + "Female", + "Aged", + "Male", + "RNA, Ribosomal, 16S", + "Adult", + "Gastrointestinal Microbiome", + "Aged, 80 and over", + "Young Adult", + "Microbiota", + "Leukocyte L1 Antigen Complex" + ], + "raw_abstract": "Despite substantial progress in cancer microbiome research, recognized confounders and advances in absolute microbiome quantification remain underused; this raises concerns regarding potential spurious associations. Here we study the fecal microbiota of 589 patients at different colorectal cancer (CRC) stages and compare observations with up to 15 published studies (4,439 patients and controls total). Using quantitative microbiome profiling based on 16S ribosomal RNA amplicon sequencing, combined with rigorous confounder control, we identified transit time, fecal calprotectin (intestinal inflammation) and body mass index as primary microbial covariates, superseding variance explained by CRC diagnostic groups. Well-established microbiome CRC targets, such as Fusobacterium nucleatum, did not significantly associate with CRC diagnostic groups (healthy, adenoma and carcinoma) when controlling for these covariates. In contrast, the associations of Anaerococcus vaginalis, Dialister pneumosintes, Parvimonas micra, Peptostreptococcus anaerobius, Porphyromonas asaccharolytica and Prevotella intermedia remained robust, highlighting their future target potential. Finally, control individuals (age 22-80\u2009years, mean 57.7\u2009years, standard deviation 11.3) meeting criteria for colonoscopy (for example, through a positive fecal immunochemical test) but without colonic lesions are enriched for the dysbiotic Bacteroides2 enterotype, emphasizing uncertainties in defining healthy controls in cancer microbiome research. Together, these results indicate the importance of quantitative microbiome profiling and covariate control for biomarker identification in CRC microbiome studies.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33789570", + "title": "Bacterial community structure alterations within the colorectal cancer gut microbiome.", + "year": 2021, + "journal": "BMC microbiology", + "authors": [ + "Loftus M", + "Hassouneh SA", + "Yooseph S" + ], + "bacteria": "Peptostreptococcus", + "condition": "healthy", + "relevance_score": 0.30450074230992036, + "mesh_terms": [ + "Bacteria", + "Biodiversity", + "Colorectal Neoplasms", + "Feces", + "Gastrointestinal Microbiome", + "Genome, Bacterial", + "High-Throughput Nucleotide Sequencing", + "Humans" + ], + "raw_abstract": "BACKGROUND: Colorectal cancer is a leading cause of cancer-related deaths worldwide. The human gut microbiome has become an active area of research for understanding the initiation, progression, and treatment of colorectal cancer. Despite multiple studies having found significant alterations in the carriage of specific bacteria within the gut microbiome of colorectal cancer patients, no single bacterium has been unequivocally connected to all cases. Whether alterations in species carriages are the cause or outcome of cancer formation is still unclear, but what is clear is that focus should be placed on understanding changes to the bacterial community structure within the cancer-associated gut microbiome. RESULTS: By applying a novel set of analyses on 252 previously published whole-genome shotgun sequenced fecal samples from healthy and late-stage colorectal cancer subjects, we identify taxonomic, functional, and structural changes within the cancer-associated human gut microbiome. Bacterial association networks constructed from these data exhibited widespread differences in the underlying bacterial community structure between healthy and colorectal cancer associated gut microbiomes. Within the cancer-associated ecosystem, bacterial species were found to form associations with other species that are taxonomically and functionally dissimilar to themselves, as well as form modules functionally geared towards potential changes in the tumor-associated ecosystem. Bacterial community profiling of these samples revealed a significant increase in species diversity within the cancer-associated gut microbiome, and an elevated relative abundance of species classified as originating from the oral microbiome including, but not limited to, Fusobacterium nucleatum, Peptostreptococcus stomatis, Gemella morbillorum, and Parvimonas micra. Differential abundance analyses of community functional capabilities revealed an elevation in functions linked to virulence factors and peptide degradation, and a reduction in functions involved in amino-acid biosynthesis within the colorectal cancer gut microbiome. CONCLUSIONS: We utilize whole-genome shotgun sequenced fecal samples provided from a large cohort of late-stage colorectal cancer and healthy subjects to identify a number of potentially important taxonomic, functional, and structural alterations occurring within the colorectal cancer associated gut microbiome. Our analyses indicate that the cancer-associated ecosystem influences bacterial partner selection in the native microbiota, and we highlight specific oral bacteria and their associations as potentially relevant towards aiding tumor progression.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33990174", + "title": "Association of gestational diabetes mellitus with changes in gut microbiota composition at the species level.", + "year": 2021, + "journal": "BMC microbiology", + "authors": [ + "Chen F", + "Gan Y", + "Li Y", + "He W", + "Wu W", + "Wang K", + "Li Q" + ], + "bacteria": "Peptostreptococcus", + "condition": "healthy", + "relevance_score": 0.2023230034156815, + "mesh_terms": [ + "Adult", + "Bacteria", + "Blood Glucose", + "Cohort Studies", + "DNA, Bacterial", + "Diabetes, Gestational", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Middle Aged", + "Pilot Projects", + "Pregnancy", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Gestational diabetes mellitus (GDM), a common endocrine disorder with rising prevalence in pregnancy, has been reported to be associated with alteration of gut microbiota in recent years. However, the role of gut microbiome in GDM physiopathology remains unclear. This pilot study aims to characterize the alteration of gut microbiota in GDM on species-level resolution and evaluate the relationship with occurrence of GDM. METHODS: An analysis based on 16S rRNA microarray was performed on fecal samples obtained from 30 women with GDM and 28 healthy pregnant women. RESULTS: We found 54 and 141 differentially abundant taxa between GDM and control group at the genus and the species level respectively. Among GDM patients, Peptostreptococcus anaerobius was inversely correlated with fasting glucose while certain species (e.g., Aureimonas altamirensis, Kosakonia cowanii) were positively correlated with fasting glucose. CONCLUSIONS: This study suggests that there are large amounts of differentially abundant taxa between GDM and control group at the genus and the species level. Some of these taxa were correlated with blood glucose level and might be used as biomarkers for diagnoses and therapeutic targets for probiotics or synbiotics.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26994772", + "title": "Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India.", + "year": 2016, + "journal": "Journal of gastroenterology", + "authors": [ + "Kedia S", + "Rampal R", + "Paul J", + "Ahuja V" + ], + "bacteria": "Peptostreptococcus", + "condition": "healthy", + "relevance_score": 0.2011520873386664, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Dysentery, Amebic", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "India", + "Intestinal Mucosa" + ], + "raw_abstract": "The disease profile in the Indian population provides a unique opportunity for studying the host microbiome interaction in both infectious (amebiasis) and autoimmune diseases\u00a0like inflammatory bowel disease (IBD) from a similar environment and genetic background. Analysis of fecal samples from untreated amebic liver abscess (ALA) patients, Entamoeba histolytica (Eh)-negative and -positive asymptomatic individuals, and pus samples from naive ALA patients revealed a significant reduction in Lactobacillus in asymptomatic individuals (Eh +ve) and ALA patients. Two anaerobic genera, namely Bacteroides and Peptostreptococcus, were detected in naive ALA pus samples. Analysis of fecal samples from amoebic colitis patients showed a significant decline in population of Bacteroides, Clostridium coccoides and leptum subgroup, Lactobacillus, Campylobacter, and Eubacterium, whereas a significant increase in Bifidobacterium was observed. Mucosa-associated bacterial flora analysis from IBD patients and healthy controls revealed a significant difference in concentration of bacteria among predominating and subdominating genera between ulcerative colitis (UC), Crohn's disease (CD) patients, and controls. In contrast to the mucosal studies, we found a significant increase in lactobacilli population in fecal samples of active UC patients. Another study revealed a significant decrease of Clostridium coccoides and leptum clusters in fecal samples of active UC patients along with decreased concentrations of fecal SCFAs, especially of n-butyrate, iso-butyrate, and acetate. We therefore found similar perturbations in gut microbiome in both infectious and autoimmune diseases, indicating inflammation to be the major driver for changes in gut microbiome.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36034695", + "title": "Saliva microbiome changes in thyroid cancer and thyroid nodules patients.", + "year": 2022, + "journal": "Frontiers in cellular and infection microbiology", + "authors": [ + "Jiao J", + "Zheng Y", + "Zhang Q", + "Xia D", + "Zhang L", + "Ma N" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.48048451706860523, + "mesh_terms": [ + "Animals", + "Cats", + "Humans", + "Microbiota", + "RNA, Ribosomal, 16S", + "Saliva", + "Thyroid Neoplasms", + "Thyroid Nodule" + ], + "raw_abstract": "OBJECTIVE: Thyroid disease has been reported to associate with gut microbiota, but the effects of thyroid cancer and thyroid nodules on the oral microbiota are still largely unknown. This study aimed to identify the variation in salivary microbiota and their potential association with thyroid cancer and thyroid nodules. METHODS: We used 16S rRNA high-throughput sequencing to examine the salivary microbiota of thyroid cancer patients (n = 14), thyroid nodules patients (n = 9), and healthy controls (n = 15). RESULTS: The alpha-diversity indices Chao1 and ACE were found to be relatively higher in patients with thyroid cancer and thyroid nodules compared to healthy controls. The beta diversity in both the thyroid cancer and thyroid nodules groups was divergent from the healthy control group. The genera Alloprevotella, Anaeroglobus, Acinetobacter, unclassified Bacteroidales, and unclassified Cyanobacteriales were significantly enriched in the thyroid cancer group compared with the healthy control group. In contrast, the microbiome of the healthy controls was mainly composed of the genera Haemophilus, Lautropia, Allorhizobium Neorhizobium Pararhizobium Rhizobium, Escherichia Shigella, and unclassified Rhodobacteraceae. The thyroid nodules group was dominated by genre uncultured Candidatus Saccharibacteria bacterium, unclassified Clostridiales bacterium feline oral taxon 148, Treponema, unclassified Prevotellaceae, Mobiluncus, and Acholeplasma. In contrast, the genera unclassified Rhodobacteraceae and Aggregatibacter dominated the healthy control group. The study also found that clinical indicators were correlated with the saliva microbiome. CONCLUSION: The salivary microbiota variation may be connected with thyroid cancer and thyroid nodules.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31357852", + "title": "Dental hypofunction alters subgingival microorganisms: a pilot study.", + "year": 2019, + "journal": "Minerva stomatologica", + "authors": [ + "Karatas O", + "Balci Yuce H", + "Aydemir Turkal H" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.46368296150563215, + "mesh_terms": [ + "Aggregatibacter actinomycetemcomitans", + "Humans", + "Pilot Projects", + "Porphyromonas gingivalis", + "Prevotella intermedia", + "Vascular Endothelial Growth Factor A" + ], + "raw_abstract": "BACKGROUND: The aim of this study was to evaluate dental plaque compositions, vascular endothelial growth factor (VEGF) and hypoxia-inducible factor (HIF) 1-alpha levels in gingival crevicular fluid (GCF) at hypofunctional and normofunctional teeth in healthy individuals and chronic periodontitis patients. METHODS: Sixty systemically healthy individuals were enrolled. Study groups were: group 1 hypofunctional healthy group (group 1, N.=15); group 2 hypofunctional periodontitis group (group 2, N.=15); group 3 normofunctional healthy group (group 3, N.=15); and group 4 normofunctional periodontitis group (group 4, N.=15). Clinical periodontal measurements (plaque index, gingival index and clinical attachment level) were recorded. Dental plaque and GCF samples were taken. VEGF and HIF 1-alpha levels in GCF were determined. Subgingival plaque samples were evaluated for 11 different bacterial species as, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Prevotella intermedia, Peptostreptococcus micros, Fusobacterium nucleatum, Campylobacter rectus, Eubacterium nodatum, Eikenella corrodens and Capnocytophaga species. RESULTS: Tannerella forsythia, Peptostreptococcus micros, Eubacterium nodatum levels decreased in hypofunctional healthy and periodontitis groups (P<0.05). Porphyromonas gingivalis levels increased in hypofunctional healthy group and decreased in hypofunctional periodontitis group (P<0.05). There was also a decrease in Eikenella corrodens levels in hypofunctional periodontitis group (P<0.05). There were no difference regarding the Aggregatibacter actinomycetemcomitans, Capnocytophaga spp., Prevotella intermedia and Fusobacterium nucleatum levels among the groups (P>0.05). VEGF and HIF-1\u03b1 levels in both GCF and serum samples were also similar (P>0.05). CONCLUSIONS: Within the limits of this study, the authors found that the levels of four significant bacterial strains were decreased in both hypofunctional healthy and hypofunctional periodontitis groups compared to normofunctional equivalents. Though not evaluated in this study, this situation could be due to periodontal ligament atrophy and related physiological alterations.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29340343", + "title": "What is the Impact of Epstein-Barr Virus in Peri-implant Infection?", + "year": 2018, + "journal": "The International journal of oral & maxillofacial implants", + "authors": [ + "Canullo L", + "Pesce P", + "Botticelli D", + "Covani U", + "Jankovic S", + "Jovanovic T", + "Rakic M" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.44228570274353185, + "mesh_terms": [ + "Adult", + "Aged", + "Aggregatibacter actinomycetemcomitans", + "Campylobacter rectus", + "Cross-Sectional Studies", + "Dental Implants", + "Epstein-Barr Virus Infections", + "Female", + "Fusobacterium nucleatum", + "Gram-Negative Bacteria", + "Gram-Negative Bacterial Infections", + "Herpesvirus 4, Human", + "Humans", + "Male", + "Middle Aged", + "Peri-Implantitis", + "Prevalence", + "Prevotella intermedia" + ], + "raw_abstract": "PURPOSE: To compare the qualitative and quantitative profile of Epstein-Barr virus (EBV) at external and internal implant surfaces between participants with peri-implantitis and healthy peri-implant tissues and to quantitatively assess the relation between EBV and periopathogens inside the microbiologic profile associated with peri-implantitis. MATERIALS AND METHODS: Microbiologic specimens were retrieved from 84 patients wearing 190 implants to estimate the levels of EBV and 10 periopathogens in the peri-implant pocket and internal-implant connection using quantitative polymerase chain reaction. RESULTS: The study sample consisted of 113 healthy and 77 peri-implantitis-affected implants. Statistical significance was not reached in EBV prevalence between peri-implantitis and healthy controls. EBV-positive participants demonstrated higher levels of Prevotella intermedia (Pi) and Campylobacter rectus (Cr) compared with EBV-negative participants. A positive correlation was demonstrated among EBV and Tannerella forsythia (Tf), Parvimonas micra (Pm), Fusobacterium nucleatum (Fn), and Cr levels in peri-implantitis-affected implants, while healthy controls demonstrated a positive correlation between EBV and Aggregatibacter actinomycetemcomitans (Aa), Pi, and Pm. CONCLUSION: EBV cannot be considered as a microbiologic marker of peri-implantitis. However, EBV could be considered as a risk factor and a peri-implantitis enhancer based on its positive correlations with pathogens associated with peri-implantitis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33084948", + "title": "Taxonomic profiling and functional characterization of the healthy human oral bacterial microbiome from the north Indian urban sub-population.", + "year": 2021, + "journal": "Archives of microbiology", + "authors": [ + "Verma D", + "Srivastava A", + "Garg PK", + "Akhter Y", + "Dubey AK", + "Mishra S", + "Deo SVS" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.38165800523304444, + "mesh_terms": [ + "Adolescent", + "Adult", + "Bacteria", + "Female", + "High-Throughput Nucleotide Sequencing", + "Humans", + "India", + "Male", + "Metagenome", + "Microbiota", + "Middle Aged", + "Mouth", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Poor oral health has broad consequences that can be seen at personal as well as societal levels, especially in developing countries like India. We have limited information on the healthy oral cavity's inhabitant microorganisms that play a crucial role in overall oral health. In a comprehensive culture-independent approach, the bacterial composition of healthy human oral cavities was determined from a sub-population of northern India. During this study, 20 mouthwash-derived metagenomes were explored for identifying bacterial diversity using the 16S rRNA hypervariable V3 region with the MiSeq Illumina platform. On the taxonomy assignment of operational taxonomic units (OTUs), 20 assigned phyla and 162 genera were recovered among the participants. The mean relative abundance revealed that Streptococcus was the dominant genera among the participants. However, at inter-individual analysis, Neisseria and Haemophilus exhibited first-order dominance among five and three healthy individuals, respectively. Correlation studies indicate that Streptococcus shares a strong relationship with Rothia, Corynebacterium, Prevotella, and Veillonella, whereas it was negatively correlated with Neisseria, Aggregatibacter, Porphyromonas, and Fusobacteria like Gram-negative bacteria. Bacterial diversity showed insignificant differences at the level of age and gender within and between the participants. The results support several of the major findings of previous reports on the healthy oral microbiome of the Indian population, however, the present investigation further illustrates that demographic region leaves an impact on overall bacterial composition. The study will assist in a better understanding of the oral microbiome from region-specific Indian population that was otherwise highly under-represented.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29857043", + "title": "Qualitative, quantitative and genotypic evaluation of Aggregatibacter actinomycetemcomitans and Fusobacterium nucleatum isolated from individuals with different periodontal clinical conditions.", + "year": 2018, + "journal": "Anaerobe", + "authors": [ + "Arenas Rodrigues VA", + "de Avila ED", + "Nakano V", + "Avila-Campos MJ" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.34673170062370945, + "mesh_terms": [ + "Adult", + "Aggregatibacter actinomycetemcomitans", + "Bacterial Toxins", + "Cross-Sectional Studies", + "Exotoxins", + "Female", + "Fusobacterium nucleatum", + "Genotype", + "Humans", + "Male", + "Middle Aged", + "Periodontal Diseases", + "Young Adult" + ], + "raw_abstract": "Aggregatibacter actinomycetemcomitans and Fusobacterium nucleatum are strongly associated with periodontitis, and their evaluations are relevant to understand their role in the etiology and progression of periodontal diseases. In this study, the qualitative and quantitative detection of A.\u00a0actinomycetemcomitans and F.\u00a0nucleatum, as well as their genetic diversity, were evaluated in individuals with gingivitis, chronic periodontitis and periodontally healthy. In addition, the biotyping, serotyping, and prevalence of the ltx and cdt genes in A.\u00a0actinomycetemcomitans were also determined. Subgingival biofilms obtained from gingivitis (70), periodontitis (75) and healthy (95) individuals were analyzed by cultures and PCR. Bacterial typing and presence of ltx and cdt genes in A.\u00a0actinomycetemcomitans were also verified. DNA from A.\u00a0actinomycetemcomitans and F.\u00a0nucleatum was detected respectively, in 65.7% and 57.1% of gingivitis, 80% and 68% of periodontitis, and 57.8% and 37.8% of healthy. A.\u00a0actinomycetemcomitans from gingivitis were biotypes I, II, IV, V, and X, and serotypes a, c, and e. In periodontitis, biotypes II, VI, and X, and serotypes a, b, and c were found. In healthy subjects, biotypes II and X, and serotypes b and c were found. The LTX and ltxA were observed in strains from gingivitis and periodontitis pockets. Subsequently, our data also showed no direct relationship between ltxA gene expression and leukotoxin gene 530-bp presence. On the other hand, cdt gene predominated during the inflammatory disease process. Our results strongly support a role of A.\u00a0actinomycetemcomitans and F.\u00a0nucleatum in advanced stage of periodontal disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28820321", + "title": "Non-Surgical Therapy Reduces Presence of JP2 Clone in Localized Aggressive Periodontitis.", + "year": 2017, + "journal": "Journal of periodontology", + "authors": [ + "Burgess DK", + "Huang H", + "Harrison P", + "Kompotiati T", + "Aukhil I", + "Shaddox LM" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.34096001873804155, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aggregatibacter actinomycetemcomitans", + "Aggressive Periodontitis", + "Amoxicillin", + "Anti-Bacterial Agents", + "Child", + "Child, Preschool", + "Dental Plaque", + "Dental Scaling", + "Drug Therapy, Combination", + "Female", + "Humans", + "Male", + "Metronidazole", + "Periodontal Debridement", + "Polymerase Chain Reaction", + "Root Planing", + "Ultrasonic Surgical Procedures", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Previous studies have provided substantial evidence of the association of Aggregatibacter actinomycetemcomitans, and its highly leukotoxic JP2 genotype, with localized aggressive periodontitis (LAgP). The present study aims to evaluate presence of JP2 in individuals with LAgP after periodontal treatment. METHODS: Sixty African-American patients with LAgP, aged 5 to 25 years, were examined. At baseline, probing depth (PD), clinical attachment level (CAL), bleeding on probing, and plaque index were measured, and subgingival plaque was collected from LAgP diseased and healthy sites for each participant. Patients received whole-mouth ultrasonic debridement, scaling and root planing, and a 7-day prescription of amoxicillin and metronidazole. Participants were reevaluated and resampled and received regular maintenance therapy at 3, 6, and 12 months after treatment. Polymerase chain reaction was used to detect presence of the JP2 genotype before and after treatment. RESULTS: At baseline, the JP2 sequence was identified in 75% of LAgP diseased sites and in 56.67% of healthy sites. At 3, 6, and 12 months after treatment, the number of patients was 40, 31, and 31, respectively, and JP2 detection decreased to 17.5%, 6.45%, and 3.23%, respectively, in diseased sites (P <0.001) and to 2.5%, 3.23%, and 0%, respectively, in healthy sites (P <0.001). Clinical parameters of disease were also significantly reduced after therapy (P <0.001). Additionally, significant correlations were observed between JP2 presence and mean PD (P <0.002) and CAL (P <0.001), after therapy. CONCLUSION: Periodontal therapy was successful in reducing clinical parameters of LAgP and subgingival presence of JP2 in diseased and healthy sites.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39117753", + "title": "Oral microbiota diversity in moderate to severe plaque psoriasis, nail psoriasis and psoriatic arthritis.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Fan W", + "Lei N", + "Zheng Y", + "Liu J", + "Cao X", + "Su T", + "Su Z", + "Lu Y" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.3366524817339176, + "mesh_terms": [ + "Humans", + "Arthritis, Psoriatic", + "Female", + "Male", + "Psoriasis", + "Microbiota", + "Adult", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Mouth", + "Bacteria", + "Nail Diseases", + "Case-Control Studies" + ], + "raw_abstract": "Gaining a comprehensive understanding of the role played by the oral microbiome in moderate to severe plaque psoriasis and its potential implications for disease management and development holds significant importance. With the objective of exploring correlations between the oral microbiota and severe psoriasis, this study involved 72 severe psoriasis patients and 16 healthy individuals, whose clinical manifestations and living habits were carefully recorded. Cutting-edge techniques such as 16S rRNA gene sequencing and bioinformatics analysis were employed to compare the microbial flora, investigating dynamic changes among severe plaque psoriasis patients, psoriatic arthritis patients and healthy individuals. The findings revealed noteworthy patterns including increased levels of Aggregatibacter in the psoriatic arthritis group, accompanied by a decrease in the level of Prevotella. Moreover, the enrichment o Capnocytandophaga (P\u2009=\u20090.009), Campylobacter (P\u2009=\u20090.0022), and Acetobacter (P\u2009=\u20090.0292) was notably more substantial in the psoriasis group compared to the control group, whereas certain bacterial species such as Bacteroides (P\u2009=\u20090.0049), Muribaculaceae (P\u2009=\u20090.0048) demonstrated decreased enrichment. Additionally, the psoriatic arthritis group exhibited significantly higher levels of Ralstonia, Bifidobacterium and Micromonospora. Based on these findings, it can be inferred that individuals with lower levels of Prevotella and higher levels of Corynebacterium may be more susceptible to psoriasis exacerbation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27262209", + "title": "Subgingival microbiota in individuals with severe chronic periodontitis.", + "year": 2018, + "journal": "Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi", + "authors": [ + "Tsai CY", + "Tang CY", + "Tan TS", + "Chen KH", + "Liao KH", + "Liou ML" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.3229689627149441, + "mesh_terms": [ + "Bacteria", + "Base Sequence", + "Biodiversity", + "Chronic Periodontitis", + "Gingiva", + "Humans", + "Microbiota", + "RNA, Ribosomal, 16S", + "Real-Time Polymerase Chain Reaction", + "Sequence Analysis, DNA", + "Taiwan" + ], + "raw_abstract": "BACKGROUND/PURPOSE: Subgingival microorganisms are potentially associated with periodontal diseases. However, the correlation between the variance in the periodontal microbiome and the prevalence and severity of periodontitis remains unclear. The aim of this study was to determine the subgingival microbiota in Taiwanese individuals with severe chronic periodontitis (SP). METHODS: The composition of the subgingival microbiota in healthy and diseased individuals was compared using a 16S rRNA metagenomic approach and quantitative polymerase chain reaction (qPCR). A total of 20 samples, including 10 from healthy individuals and 10 from SP patients, were analyzed. RESULTS: We found high microbial diversity, with an average of 774 classified phylotypes per sample and a total of six bacterial phyla across all samples. Cluster analysis by principal component analysis and heat map showed that the bacterial communities were different in the two groups. Streptococcus dominated across all the healthy samples, whereas Prevotella, Porphyromonas, and Treponema were highly abundant across all diseased samples. At least 13 bacterial genera were conserved among all the samples. Only eight genera, including Lautropia, Parvimonas, Actinomyces, Capnocytophaga, Paludibacter, Streptococcus, Haemophilus, and Corynebacterium, were significantly enriched in the healthy group, and six genera, including Porphyromonas, Treponema, Tannerella, Aggregatibacter, Peptostreptococcus, and Filifactor, were significantly enriched in the diseased group. Furthermore, a trend of abundance of bacteria at the species level measured by qPCR in all samples was consistent with the 16S rRNA metagenomics results. CONCLUSION: This study is the first in Taiwan to provide a picture of the microbiome in SP via 16S rRNA metagenomics.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26392039", + "title": "Periodontal clinical and microbiological characteristics in healthy versus generalized aggressive periodontitis families.", + "year": 2015, + "journal": "Journal of clinical periodontology", + "authors": [ + "Monteiro Mde F", + "Casati MZ", + "Taiete T", + "Vale HF", + "Nociti FH", + "Sallum EA", + "Silv\u00e9rio KG", + "Casarin RC" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.32271383283087446, + "mesh_terms": [ + "Aggregatibacter actinomycetemcomitans", + "Aggressive Periodontitis", + "Bacteroides", + "Case-Control Studies", + "Child", + "Dental Plaque", + "Dental Plaque Index", + "Female", + "Humans", + "Male", + "Periodontal Attachment Loss", + "Periodontal Index", + "Periodontal Pocket", + "Porphyromonas gingivalis" + ], + "raw_abstract": "AIM: Generalized aggressive periodontitis (GAP) is a severe and multifactorial disease in which a familial aggregation and a specific microbiological profile have been suggested. Thus, this case-control study evaluated the clinical and subgingival microbial profile of GAP subjects and their families compared to healthy families. METHODS: Fifteen families with parents presenting periodontal health and 15 with parents with a history of GAP were selected. Each family should have at least one child between 6 and 12\u00a0years old. Plaque index (PI), gingival index (GI), and periodontal probing depth (PPD), as well as Porphyromonas gingivalis, Tannerella forsythia, and Aggregatibacter actinomycetemcomitans (Aa) amounts (by qPCR), were assessed from all subjects. RESULTS: Children of GAP families showed a higher PI, GI, and PPD when compared to children of healthy families (p\u00a0\u2264\u00a00.05). A higher frequency of detection and amounts of Aa was observed in GAP children compared to children of healthy families (p\u00a0\u2264\u00a00.05). Moreover, a significant association between Aa amounts and gingival bleeding was observed in children (p\u00a0\u2264\u00a00.05, r\u00a0=\u00a00.37). CONCLUSION: Children from GAP families have worst clinical conditions, i.e. higher levels of PI, GI, and PPD, a more pathogenic microbiological profile, and the amount of Aa are associated with a higher marginal inflammation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38476115", + "title": "Evaluation of microbiome in primary and permanent dentition in grade C periodontitis in young individuals.", + "year": 2024, + "journal": "Journal of periodontology", + "authors": [ + "Koo SS", + "Fernandes JG", + "Li L", + "Huang H", + "Aukhil I", + "Harrison P", + "Diaz PI", + "Shaddox LM" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.3152671781378518, + "mesh_terms": [ + "Humans", + "Tooth, Deciduous", + "Microbiota", + "Male", + "Female", + "Child", + "Dentition, Permanent", + "Periodontitis", + "Biofilms", + "Aggregatibacter actinomycetemcomitans", + "Adolescent", + "Capnocytophaga", + "Leptotrichia", + "Gingiva", + "Case-Control Studies", + "DNA, Bacterial", + "Child, Preschool" + ], + "raw_abstract": "BACKGROUND: The aim of the present study was to evaluate the subgingival microbiome in patients with grade C molar-incisor pattern periodontitis (C-MIP) affecting the primary or permanent dentitions. METHODS: DNA was isolated from subgingival biofilm samples from diseased and healthy sites from 45 C-MIP patients and subjected to phylogenetic microarray analysis. C-MIP sites were compared between children affected in the primary to those affected in the permanent dentitions. Within-subject differences between C-MIP-affected sites and dentition-matched healthy sites were also evaluated. RESULTS: C-MIP sites of subjects affected in the primary dentition showed partially overlapping but distinct microbial communities from C-MIP permanent dentition sites (p\u00a0<\u00a00.05). Differences were due to increased levels in primary C-MIP sites of certain species of the genera Capnocytophaga and Leptotrichia, while C-MIP permanent dentition sites showed higher prevalence of Filifactor alocis. Aggregatibacter actinomycetemcomitans (Aa) was among species seen in high prevalence and levels in both primary and permanent C-MIP sites. Moreover, both permanent and primary C-MIP sites showed distinct microbial communities when compared to dentition-matched healthy sites in the same subject (p\u00a0<\u00a00.01). CONCLUSIONS: Primary and permanent teeth with C-MIP showed a dysbiotic microbiome, with children affected in the primary dentition showing a distinct profile from those affected in the permanent dentition. However, Aa was enriched in both primary and permanent diseased sites, confirming that this microorganism is implicated in C-MIP in both dentitions.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37451531", + "title": "Multi-omics analyses of serum metabolome, urine metabolome and gut microbiome reveal dysregulated glycerophospholipid metabolism in subacute cadmium-exposed wistar rats.", + "year": 2023, + "journal": "Toxicology", + "authors": [ + "Wu C", + "Fang F", + "Yu Y", + "Wang B", + "Gao H", + "Cui W" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.3070880492648327, + "mesh_terms": [ + "Rats", + "Animals", + "Gastrointestinal Microbiome", + "Rats, Wistar", + "Cadmium", + "Multiomics", + "Metabolome", + "Metabolomics" + ], + "raw_abstract": "Data is limited on intestinal microbiota and metabolites in healthy residents exposed to cadmium (Cd), a population uniquely susceptible to Cd toxicity through contaminated foods. In this study, the 16\u00a0S rRNA gene sequencing, serum metabolomics and urine metabolomics were performed to examine the alterations of gut microbiota and metabolomics profile of wistar rats exposed to Cd. These findings indicated that Cd exposure markedly altered the structure of gut microbial community, reduced significantly microbiome diversity, and identified 5 phyla and 6 genera with significant changes. Specifically, the levels of Pseudoxanthomonas and Anaerovibrio upregulated and that of Akkermansia, Brachyspira, Aggregatibacter and SMB53 reduced in rats treated with Cd. Metabolomics profiles of the urine and serum of Cd-treated rats revealed that the abundance of glycerophospholipid metabolites and their derivatives were markedly altered. Glycerophospholipid metabolic pathways that were markedly enriched in metabolomics in both samples was also significantly predicted in gut microbiota analysis. Further, interaction analysis predicted that there might be a relationship between the differential glycerophospholipid metabolites and affected bacteria genera induced by Cd. These results suggested that subacute Cd could disrupt the intestinal microecologica equilibrium and glycerophospholipid metabolic homeostasis, and also provided potential differential microbiota and glycerophospholipid biomarkers between subacute Cd-exposed rats and healthy rats.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36050830", + "title": "Meta-analysis of caries microbiome studies can improve upon disease prediction outcomes.", + "year": 2022, + "journal": "APMIS : acta pathologica, microbiologica, et immunologica Scandinavica", + "authors": [ + "Butcher MC", + "Short B", + "Veena CLR", + "Bradshaw D", + "Pratten JR", + "McLean W", + "Shaban SMA", + "Ramage G", + "Delaney C" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.3046740633577749, + "mesh_terms": [ + "Humans", + "Dental Caries", + "Dental Caries Susceptibility", + "Microbiota", + "Actinomyces" + ], + "raw_abstract": "As one of the most prevalent infective diseases worldwide, it is crucial that we not only know the constituents of the oral microbiome in dental caries but also understand its functionality. Herein, we present a reproducible meta-analysis to effectively report the key components and the associated functional signature of the oral microbiome in dental caries. Publicly available sequencing data were downloaded from online repositories and subjected to a standardized analysis pipeline before analysis. Meta-analyses identified significant differences in alpha and beta diversities of carious microbiomes when compared to healthy ones. Additionally, machine learning and receiver operator characteristic analysis showed an ability to discriminate between healthy and disease microbiomes. We identified from importance values, as derived from random forest analyses, a group of genera, notably containing Selenomonas, Aggregatibacter, Actinomyces and Treponema, which can be predictive of dental caries. Finally, we propose the most appropriate study design for investigating the microbiome of dental caries by synthesizing the studies, which had the most accurate differentiation based on random forest modelling. In conclusion, we have developed a non-biased, reproducible pipeline, which can be applied to microbiome meta-analyses of multiple diseases, but importantly we have derived from our meta-analysis a key group of organisms that can be used to identify individuals at risk of developing dental caries based on oral microbiome inhabitants.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27888369", + "title": "Prevalence of periodontal pathogens as predictor of the evolution of periodontal status.", + "year": 2017, + "journal": "Odontology", + "authors": [ + "Puig-Silla M", + "Montiel-Company JM", + "Das\u00ed-Fern\u00e1ndez F", + "Almerich-Silla JM" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.30153075877062757, + "mesh_terms": [ + "Adult", + "Aggregatibacter actinomycetemcomitans", + "Chronic Periodontitis", + "Dental Plaque", + "Female", + "Gingivitis", + "Humans", + "Longitudinal Studies", + "Male", + "Middle Aged", + "Polymerase Chain Reaction", + "Porphyromonas gingivalis", + "Prevalence", + "Prospective Studies", + "Tannerella forsythia", + "Treponema denticola" + ], + "raw_abstract": "The aim of this study was to determine the relationship between the prevalence of Porphyromonas gingivalis, its fimA genotypes, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, and Treponema denticola and the evolution of periodontal health. In a longitudinal prospective study, samples of subgingival plaque were taken from 114 patients (37 with chronic periodontitis, 17 with gingivitis, and 60 periodontally healthy) in the course of a full periodontal examination. PCR was employed to determine the presence of the periodontopathogenic bacteria. Four years later, a second examination and sample collection were performed in 90 of these patients (20 with chronic periodontitis, 12 with gingivitis, and 58 periodontally healthy). T. forsythia, P. gingivalis, and T. denticola are the most prevalent bacteria in patients with chronic periodontitis (78.4%, 62.2 y 56.8%, respectively). The P. gingivalis bacterium and its fimA genotypes I, II, and IV showed the highest correlation between the baseline and follow-up assessments. P. gingivalis fimA genotype II and T. forsythia were associated to a significant degree with unfavourable periodontal evolution. Of the variables studied, P. gingivalis fimA genotype II and T. forsythia increase the risk of an unfavourable evolution of periodontal status.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "24529567", + "title": "Aggregatibacter aphrophilus brain abscess secondary to primary tooth extraction: Case report and literature review.", + "year": 2016, + "journal": "Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi", + "authors": [ + "Maraki S", + "Papadakis IS", + "Chronakis E", + "Panagopoulos D", + "Vakis A" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.29804369451882057, + "mesh_terms": [ + "Aggregatibacter aphrophilus", + "Animals", + "Anti-Bacterial Agents", + "Brain Abscess", + "Child", + "Debridement", + "Dogs", + "Humans", + "Male", + "Pasteurellaceae Infections", + "Tooth Extraction", + "Tooth, Deciduous", + "Treatment Outcome" + ], + "raw_abstract": "We report on a rare case of Aggregatibacter aphrophilus brain abscess of odontogenic origin in a 6-year-old previously healthy boy, who had close contact with a pet dog. The poodle was the most likely source of the infecting organism, which subsequently colonized the patient's oral cavity. The abscess was surgically removed and he recovered completely after prolonged antibiotic treatment with meropenem. We also review the relevant medical literature on A. aphrophilus pediatric brain abscesses.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28875948", + "title": "The tongue microbiome in healthy subjects and patients with intra-oral halitosis.", + "year": 2017, + "journal": "Journal of breath research", + "authors": [ + "Seerangaiyan K", + "van Winkelhoff AJ", + "Harmsen HJM", + "Rossen JWA", + "Winkel EG" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.29294589326125386, + "mesh_terms": [ + "Adult", + "Aged", + "Biodiversity", + "Breath Tests", + "Case-Control Studies", + "Demography", + "Female", + "Halitosis", + "Healthy Volunteers", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Mouth", + "Oral Health", + "Phylogeny", + "Species Specificity", + "Tongue", + "Young Adult" + ], + "raw_abstract": "Intra-oral halitosis (IOH) is an unpleasant odor emanating from the oral cavity. It is thought that the microbiota of the dorsal tongue coating plays a crucial role in this condition. The aim of the study was to investigate the composition of the tongue microbiome in subjects with and without IOH. A total of 26 subjects, 16 IOH patients and 10 healthy subjects were recruited based on their organoleptic score and volatile sulfur compound (VSC) measurements. The composition of the tongue microbiome was studied using the 16s amplicon sequencing of the V3-V4 hyper variable region with an Illumina MiSeq. The sequenced data were analyzed using QIIME, and the sequences obtained were distributed across 7 phyla, 27 genera and 825 operational taxonomic units (OTUs). At a higher taxon level, TM7 was associated with IOH patients whereas Gemellaceae was significantly abundant in the healthy subjects. At OTU level, we found several significant OTUs that differentiated the IOH patients from the controls. These included Aggregatibacter (OTU id 4335776), Aggregatibacter segnis (A. segnis), Campylobacter, Capnocytophaga, Clostridiales, Dialister, Leptotrichia, Parvimonas, Peptostreptococcus, Peptococcus, Prevotella, Selenomonas, SR1, Tannerella, TM7-3 and Treponema in the IOH group. In the control group, Aggregatibacter (OTU id 4363066), Haemophilus, Haemophilus parainfluenza (H. parainfluenza), Moryella, Oribacterium, Prevotella, several Streptococcus, Rothia dentocariosa (R. dentocariosa) and OTU from Gemellaceae were significantly abundant. Based on our observation, it was concluded that the bacterial qualitative composition of the IOH and the control group was almost the same, except for the few above-mentioned bacterial species and genera.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35612792", + "title": "Aggregatibacter actinomycetemcomitans: From Basic to Advanced Research.", + "year": 2022, + "journal": "Advances in experimental medicine and biology", + "authors": [ + "Hbibi A", + "Bouziane A", + "Lyoussi B", + "Zouhdi M", + "Benazza D" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.29148633923068945, + "mesh_terms": [ + "Aggregatibacter actinomycetemcomitans", + "Humans", + "Periodontal Diseases", + "Periodontitis", + "Virulence Factors" + ], + "raw_abstract": "Aggregatibacter actinomycetemcomitans is a major periodontal pathogen that was identified firstly in actinomycotic lesions and later in advanced forms of periodontal diseases as well as in oral cavity of healthy subjects. The particular pathogenicity of this specie makes it a target for extensive studies both at fundamental and practical scales. The current advances in experimental and clinical research related to this bacterium focus the light on epidemiologic features, virulence, and invasiveness aspects as well as on identification challenges, bacterial susceptibility, and anti-virulence strategies. The present chapter provide to scientists and periodontal researchers a comprehensive overview on the main advances made in this field with a special focus on epidemiologic dissemination, microbial diagnosis, virulence factors and clinical implementations of such progress.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26121972", + "title": "Periodontal pathogens and tetracycline resistance genes in subgingival biofilm of periodontally healthy and diseased Dominican adults.", + "year": 2016, + "journal": "Clinical oral investigations", + "authors": [ + "Collins JR", + "Arredondo A", + "Roa A", + "Valdez Y", + "Le\u00f3n R", + "Blanc V" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.29086564998570325, + "mesh_terms": [ + "Adult", + "Aged", + "Bacterial Infections", + "Biofilms", + "Case-Control Studies", + "Dominican Republic", + "Female", + "Genotype", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Periodontitis", + "Polymerase Chain Reaction", + "Prevalence", + "Tetracycline Resistance" + ], + "raw_abstract": "OBJECTIVE: The objective of this study was to compare the periodontopathogen prevalence and tetracycline resistance genes in Dominican patients with different periodontal conditions. METHODS: Seventy-seven samples were collected from healthy, gingivitis, chronic (CP) and aggressive (AgP) periodontitis patients. Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, Prevotella intermedia, Parvimonas micra, Eikenella corrodens and Dialister pneumosintes and 11 resistance genes were studied by PCR. P. gingivalis fimA genotype was determined. RESULTS: In healthy patients, P. micra and P. intermedia were the most and least frequently detected, respectively. T. forsythia and E. corrodens appeared in 100% of gingivitis patients. Red complex, D. pneumosintes and E. corrodens were significantly more prevalent in CP compared to healthy patients. F. nucleatum and T. denticola were detected more frequently in AgP. A. actinomycetemcomitans was the most rarely observed in all groups. The fimA II genotype was the most prevalent in periodontitis patients. Seven tetracycline-resistant genes were detected. tet(Q), tet(32) and tet(W) showed the greatest prevalence. tet(32) was significantly more prevalent in CP than in healthy patients. CONCLUSIONS: Red complex bacteria and D. pneumosintes were significantly the most prevalent species among periodontitis patients. T. forsythia was the most frequently detected in this population. To our knowledge, this is the first study describing the tet(32) gene in subgingival biofilm from healthy and periodontally diseased subjects. CLINICAL RELEVANCE: This study contributes to the knowledge on the subgingival microbiota and its resistance genes of a scarcely studied world region. Knowing the prevalence of resistance genes could impact on their clinical prescription and could raise awareness to the appropriate use of antibiotics.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27666672", + "title": "Microbial Characteristics of Peri-Implantitis: A Case-Control Study.", + "year": 2017, + "journal": "Journal of periodontology", + "authors": [ + "de Waal YC", + "Eijsbouts HV", + "Winkel EG", + "van Winkelhoff AJ" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.26127814641461816, + "mesh_terms": [ + "Adult", + "Aged", + "Aged, 80 and over", + "Case-Control Studies", + "Female", + "Fusobacterium nucleatum", + "Humans", + "Male", + "Middle Aged", + "Peri-Implantitis", + "Porphyromonas gingivalis", + "Prevotella intermedia", + "Risk Factors", + "Tannerella forsythia" + ], + "raw_abstract": "BACKGROUND: The aim of this case-control study is to compare oral microbiologic characteristics of patients with healthy peri-implant conditions and patients with peri-implantitis and to explore the influence of various patient- and implant-related factors on microbiologic characteristics. METHODS: Peri-implant submucosal microbial samples were collected from 85 patients with peri-implantitis (cases) and from 69 patients with only implants with healthy peri-implant conditions (controls). Samples were analyzed using culturing techniques. Multivariable logistic regression was used to explore the association of disease status and various patient- and implant-related factors (sex, patient age, smoking, number of remaining teeth, percentage of teeth with bone loss, implant function time, implant surface, and presence of plaque) with microbiologic characteristics. RESULTS: Peri-implant disease status was significantly associated with the submucosal presence of Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi), Tannerella forsythia (Tf), and Fusobacterium nucleatum (Fn). The association with disease status was most obvious for Pi (odds ratio [OR]: 15.1; 95% confidence interval [CI]: 5.1 to 45.3) and Tf (OR: 13.3; 95% CI: 5.4 to 32.5). The prevalence of Aggregatibacter actinomycetemcomitans and Staphylococcus species was very low. CONCLUSIONS: The periodontal pathogens Pg, Pi, Tf, and Fn are associated with peri-implantitis. A. actinomycetemcomitans and Staphylococcus species do not seem to play an important role in peri-implantitis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26477831", + "title": "Differentiation of oral bacteria in in vitro cultures and human saliva by secondary electrospray ionization - mass spectrometry.", + "year": 2015, + "journal": "Scientific reports", + "authors": [ + "Bregy L", + "M\u00fcggler AR", + "Martinez-Lozano Sinues P", + "Garc\u00eda-G\u00f3mez D", + "Suter Y", + "Belibasakis GN", + "Kohler M", + "Schmidlin PR", + "Zenobi R" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.26015584935116465, + "mesh_terms": [ + "Bacteria", + "Biomarkers", + "Humans", + "In Vitro Techniques", + "Metabolomics", + "Mouth", + "Saliva", + "Spectrometry, Mass, Electrospray Ionization" + ], + "raw_abstract": "The detection of bacterial-specific volatile metabolites may be a valuable tool to predict infection. Here we applied a real-time mass spectrometric technique to investigate differences in volatile metabolic profiles of oral bacteria that cause periodontitis. We coupled a secondary electrospray ionization (SESI) source to a commercial high-resolution mass spectrometer to interrogate the headspace from bacterial cultures and human saliva. We identified 120 potential markers characteristic for periodontal pathogens Aggregatibacter actinomycetemcomitans (n\u2009=\u200913), Porphyromonas gingivalis (n\u2009=\u200970), Tanerella forsythia (n\u2009=\u200930) and Treponema denticola (n\u2009=\u20097) in in vitro cultures. In a second proof-of-principle phase, we found 18 (P. gingivalis, T. forsythia and T. denticola) of the 120 in vitro compounds in the saliva from a periodontitis patient with confirmed infection with P. gingivalis, T. forsythia and T. denticola with enhanced ion intensity compared to two healthy controls. In conclusion, this method has the ability to identify individual metabolites of microbial pathogens in a complex medium such as saliva.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36348390", + "title": "The relationship between menopausal syndrome and gut microbes.", + "year": 2022, + "journal": "BMC women's health", + "authors": [ + "Liu Y", + "Zhou Y", + "Mao T", + "Huang Y", + "Liang J", + "Zhu M", + "Yao P", + "Zong Y", + "Lang J", + "Zhang Y" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.25842750316612306, + "mesh_terms": [ + "Acinetobacter", + "Dysbiosis", + "Humans", + "Menopause", + "Follicle Stimulating Hormone", + "Gastrointestinal Microbiome", + "Luteinizing Hormone", + "Female" + ], + "raw_abstract": "BACKGROUND: Gut microbes were closely related to women's health. Previous studies reported that the gut microbes of premenopausal women were different from those of postmenopausal women. However, little was known about the relationship between gut microbiota dysbiosis and menopausal syndrome (MPS). The aim of this study was to explore the relationship between MPS and gut microbes. METHODS: Patients with MPS (P group, n\u2009=\u200977) and healthy women (H group, n\u2009=\u200924) at menopause were recruited in this study. The stool specimen and clinical parameters (demographic data, follicle stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E2), et al) of participants' were collected. We evaluated the differences in gut microbes by 16S ribosomal RNA gene sequencing. We used LEfSe to identify gut microbes with varying abundances in different groups. The Spearman correlation coefficients of clinical parameters and gut microbes were calculated. PICRUSt was used to predict the potential KEGG Ortholog functional profiles of microbial communities. RESULTS: The abundance of 14 species differed substantially between the MPS and menopausal healthy women (LDA significance threshold >\u20092.0) according to LEfSe analysis. Using Spearman's correlation analysis, it was discovered that E2 had a positive correlation with\u00a0Aggregatibacter segnis, Bifidobacterium animalis, Acinetobacter guillouiae (p < 0.05, these three species\u00a0were enriched in menopausal healthy women), while FSH and LH had a negative correlation with them (p < 0.05). KEGG level3 metabolic pathways relevant to cardiovascular disease and carbohydrate metabolism were enriched in the MPS (p < 0.05), according to functional prediction by PICRUST and analyzed by Dunn test. CONCLUSION: There was gut microbiota dysbiosis in MPS, which is reflected in the deficiency of the abundance of Aggregatibacter segnis, Bifidobacterium animalis and Acinetobacter guillouiae related to the level of sex hormones. In MPS individuals, species with altered abundances and unique functional pathways were found.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32061022", + "title": "Aggregatibacter actinomycetemcomitans leukotoxin: From mechanism to targeted anti-toxin therapeutics.", + "year": 2020, + "journal": "Molecular oral microbiology", + "authors": [ + "Krueger E", + "Brown AC" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.25776376160075787, + "mesh_terms": [ + "Aggregatibacter actinomycetemcomitans", + "Exotoxins", + "Humans", + "Lymphocyte Function-Associated Antigen-1", + "Virulence Factors" + ], + "raw_abstract": "Aggregatibacter actinomycetemcomitans is a Gram-negative bacterium associated with localized aggressive periodontitis, as well as other systemic diseases. This organism produces a number of virulence factors, all of which provide some advantage to the bacterium. Several studies have demonstrated that clinical isolates from diseased patients, particularly those of African descent, frequently belong to specific clones of A. actinomycetemcomitans that produce significantly higher amounts of a protein exotoxin belonging to the repeats-in-toxin (RTX) family, leukotoxin (LtxA), whereas isolates from healthy patients harbor minimally leukotoxic strains. This finding suggests that LtxA might play a key role in A. actinomycetemcomitans pathogenicity. Because of this correlation, much work over the past 30\u00a0years has been focused on understanding the mechanisms by which LtxA interacts with and kills host cells. In this article, we review those findings, highlight the remaining open questions, and demonstrate how knowledge of these mechanisms, particularly the toxin's interactions with lymphocyte function-associated antigen-1 (LFA-1) and cholesterol, enables the design of targeted anti-LtxA strategies to prevent/treat disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26252036", + "title": "Microbiologic and Clinical Findings of Implants in Healthy Condition and with Peri-Implantitis.", + "year": 2015, + "journal": "The International journal of oral & maxillofacial implants", + "authors": [ + "Canullo L", + "Pe\u00f1arrocha-Oltra D", + "Covani U", + "Rossetti PH" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.2544247606492554, + "mesh_terms": [ + "Aged", + "Aggregatibacter actinomycetemcomitans", + "Alveolar Process", + "Bacterial Load", + "Bacteroides", + "Bone-Implant Interface", + "Bruxism", + "Campylobacter rectus", + "Candida albicans", + "Cross-Sectional Studies", + "Dental Implants", + "Dental Plaque Index", + "Eikenella corrodens", + "Female", + "Fusobacterium nucleatum", + "Gingiva", + "Humans", + "Male", + "Middle Aged", + "Peptostreptococcus", + "Peri-Implantitis", + "Periodontal Index", + "Periodontal Pocket", + "Porphyromonas gingivalis", + "Prevotella intermedia", + "Radiography", + "Treponema denticola" + ], + "raw_abstract": "PURPOSE: To compare implants in healthy conditions and implants with peri-implantitis with regard to their clinical parameters and the microbiologic composition at the peri-implant sulcus, inside the implant connection, and the gingival sulcus of neighboring teeth. MATERIALS AND METHODS: A cross-sectional study was performed including consecutive patients with implants in healthy conditions and with peri-implantitis. Clinical parameters for which patients were screened included bleeding on probing, pocket depth, and plaque index at six sites. Samples for microbiologic analysis were obtained from three locations: the peri-implant sulcus, inside the implant connection, and the gingival sulcus of neighboring teeth. Quantitative real-time polymerase chain reaction (PCR) was carried out for total counts of 10 microorganisms: Aggregatibacter actinomycetemcomitans, Porphyromona gingivalis, Tanerella forsythia, Tanerella denticola, Prevotela intermedia, Peptostreptococcus micros, Fusobacterium nucleatum, Campylobacter rectus, Eikenella corrodens, and Candida albicans. The response variables were the percentage of positive sites and total bacterial counts. RESULTS: One hundred twenty-two implants in 57 patients were analyzed in the healthy group and 113 implants in 53 patients in the peri-implantitis group. Differences between the groups were statistically significant for bruxism, probing pocket depth, bleeding on probing, and radiographic bone level. Orange complex species (P intermedia, P micros, F nucleatum) were the most prevalent in the three types of sites for both groups, and prevalence values were higher in the peri-implantitis group. Differences in prevalence between groups were more marked inside the connection than in the peri-implant sulcus. Absolute loads of most microbes and total bacterial counts were higher for the peri-implantitis group in the three locations. Again, differences were bigger inside the connection than at the peri-implant sulcus. Significant interactions were found for prevalence and absolute microbial loads between groups and locations, and for the interaction of group \u00d7 location. CONCLUSION: Clinical and microbiologic differences were observed between healthy subjects and those with peri-implantitis. Microbiologic differences between groups were more marked inside the connection than in the peri-implant sulcus. The potential role of the implant connection as a microbial reservoir for peri-implant diseases and in the outcome of their treatment should be confirmed with further studies.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38297252", + "title": "The oral microbiome of a family including Papillon-Lef\u00e8vre-syndrome patients and clinically healthy members.", + "year": 2024, + "journal": "BMC oral health", + "authors": [ + "V\u00e1lyi P", + "Wirth R", + "Min\u00e1rovits J", + "Strang O", + "Mar\u00f3ti G", + "Kov\u00e1cs KL" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.24756170343222256, + "mesh_terms": [ + "Humans", + "Papillon-Lefevre Disease", + "Periodontitis", + "Health Status" + ], + "raw_abstract": "AIMS: The oral microbiota composition of patients diagnosed with Papillon-Lef\u00e8vre-syndrome and treated for several years were compared to those existing in the oral cavity of the clinically healthy family members and a cohort of patients having various stages of chronic periodontitis. MATERIALS AND METHODS: A family with two sisters affected with severe periodontitis and with the typical skin symptoms of Papillon-Lef\u00e8vre-syndrome, and symptomless parents and third sibling were investigated. The Patients received periodontal treatment for several years and their oral microbiome was analysed by amplicon sequencing. Data were evaluated by microbial cluster analysis. RESULTS: The microbiome of the patients with Papillon-Lef\u00e8vre-syndrome was predominated with Aggregatibacter actinomycetemcomitans and associated oral periodontopathogens. Although the clinically healthy family members showed no oral disorder, their microbiome resembled that of subjects having mild periodontitis. CONCLUSIONS: Predominance of A. actinomycetemcomitans in the subgingival microbiome of patients with Papillon-Lef\u00e8vre-syndrome suggests that specific treatment strategies directed against this pathobiont may improve the oral health status of the affected individuals. TRIAL REGISTRATION: The study was conducted in accordance with the Declaration of Helsinki and the ethical permission has been issued by the Human Investigation Review Board of the University of Szeged, Albert Szent-Gy\u00f6rgyi Clinical Centre (Permission No. 63/2017-SZTE). September 19, 2017.\u00a0 https://u-szeged.hu/klinikaikutatas/rkeb-altal-jovahagyott/rkeb-2017 .", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32779013", + "title": "Subgingival microflora in adolescent females with polycystic ovary syndrome and its association with oral hygiene, gingivitis, and selected metabolic and hormonal parameters.", + "year": 2021, + "journal": "Clinical oral investigations", + "authors": [ + "Wendland N", + "Opydo-Szymaczek J", + "Mizgier M", + "Jarz\u0105bek-Bielecka G" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.24584595432706313, + "mesh_terms": [ + "Adolescent", + "Adult", + "Capnocytophaga", + "Female", + "Firmicutes", + "Gingivitis", + "Humans", + "Oral Hygiene", + "Polycystic Ovary Syndrome", + "Young Adult" + ], + "raw_abstract": "OBJECTIVES: Research studies suggest that polycystic ovary syndrome (PCOS) may influence the composition of the oral microflora in women. This study aimed to investigate factors affecting the number of selected periopathogens in a young cohort of females with PCOS and to assess the association between oral hygiene, subgingival microbiome, gingival health, and metabolic and hormonal parameters. MATERIALS AND METHODS: Thirty-two subjects with PCOS and twenty-three healthy controls aged 15-19\u00a0years were examined periodontally by a calibrated dentist. A real-time PCR method was used for the identification of 9 subgingival microorganisms. Subjects with PCOS underwent blood tests for determination of FSH, LH, total testosterone, DHEA-S, estradiol, SHBG, fasting glucose, fasting insulin, and lipid profile. RESULTS: Gingival index (GI), the proportion of bleeding sites (BOP%), probing depth (PD), and plaque index (PLI) did not differ significantly between cases and healthy age-mates. The control group had significantly higher levels of Peptostreptococcus micros and substantially greater percentage of subjects infected by Treponema denticola. Capnocytophaga gingivalis count was positively correlated with the level of estradiol, while the concentration of HDL-C was negatively correlated with the number of Aggregatibacter actinomycetemcomitans and orange complex bacteria. CONCLUSIONS: PCOS in young patients was not associated with higher pathogenicity of subgingival biofilms. CLINICAL RELEVANCE: Further studies are needed to explain the relationship between hormonal and metabolic abnormalities, subgingival microflora, and periodontal health in patients with PCOS.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38884817", + "title": "Oral microbial dysbiosis in patients with oral cavity cancers.", + "year": 2024, + "journal": "Clinical oral investigations", + "authors": [ + "Unlu O", + "Demirci M", + "Paksoy T", + "Eden AB", + "Tansuker HD", + "Dalmizrak A", + "Aktan C", + "Senel F", + "Sunter AV", + "Yigit O", + "Cakir BO", + "Kantarci A" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.23932676383946233, + "mesh_terms": [ + "Humans", + "Female", + "Male", + "Middle Aged", + "Dysbiosis", + "Mouth Neoplasms", + "Saliva", + "Case-Control Studies", + "Surveys and Questionnaires", + "Aged", + "Microbiota", + "Adult", + "RNA, Ribosomal, 16S", + "Oral Health" + ], + "raw_abstract": "OBJECTIVES: The pathogenesis of oral cavity cancers is complex. We tested the hypothesis that oral microbiota dysbiosis is associated with oral cavity cancer. MATERIALS AND METHODS: Patients with primary oral cavity cancer who met the inclusion and exclusion criteria were included in the study. Matching healthy individuals were recruited as controls. Data on socio-demographic and behavioral factors, self-reported periodontal measures and habits, and current dental status were collected using a structured questionnaire and periodontal chartings. In addition to self-reported oral health measures, each participant received a standard and detailed clinical examination. DNA was extracted from saliva samples from patients and healthy controls. Next-generation sequencing was performed by targeting V3-V4 gene regions of the 16\u00a0S rRNA with subsequent bioinformatic analyses. RESULTS: Patients with oral cavity cancers had a lower quality of oral health than healthy controls. Proteobacteria, Aggregatibacter, Haemophilus, and Neisseria decreased, while Firmicutes, Bacteroidetes, Actinobacteria, Lactobacillus, Gemella, and Fusobacteria increased in oral cancer patients. At the species level, C. durum, L. umeaens, N. subflava, A. massiliensis, and V. dispar were significantly lower, while G. haemolysans was significantly increased (p\u2009<\u20090.05). Major periodontopathogens associated with periodontal disease (P. gingivalis and F.nucleatum) increased 6.5- and 2.8-fold, respectively. CONCLUSION: These data suggested that patients with oral cancer had worse oral health conditions and a distinct oral microbiome composition that is affected by personal daily habits and may be associated with the pathogenicity of the disease and interspecies interactions. CLINICAL RELEVANCE: This paper demonstrates the link between oral bacteria and oral cancers, identifying mechanistic interactions between species of oral microbiome.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38485288", + "title": "Association between oral microbiome and breast cancer in the east Asian population: A Mendelian randomization and case-control study.", + "year": 2024, + "journal": "Thoracic cancer", + "authors": [ + "Feng K", + "Ren F", + "Shang Q", + "Wang X", + "Wang X" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.22447477085221693, + "mesh_terms": [ + "Female", + "Humans", + "Breast Neoplasms", + "Case-Control Studies", + "East Asian People", + "Genome-Wide Association Study", + "Mendelian Randomization Analysis", + "Microbiota", + "Mouth" + ], + "raw_abstract": "BACKGROUND: The causal relationship between breast cancer (BC) and the oral microbiome remains unclear. In this case-control study, using two-sample Mendelian randomization (MR), we thoroughly explored the relationship between the oral microbiome and BC in the East Asian population. METHODS: Genetic summary data related to oral microbiota and BC were collected from genome-wide association studies involving participants of East Asian descent. MR estimates were generated by conducting various analyses. Sequencing data from a case-control study were used to verify the validity of these findings. RESULTS: MR analysis revealed that 30 tongue and 37 salivary bacterial species were significantly associated with BC. Interestingly, in both tongue and salivary microbiomes, we observed the causal effect of six genera, namely, Aggregatibacter, Streptococcus, Prevotella, Haemophilus, Lachnospiraceae, Oribacterium, and Solobacterium, on BC. Our case-control study findings suggest differences in specific bacteria between patients with BC and healthy controls. Moreover, sequencing data confirmed the MR analysis results, demonstrating that compared with the healthy control group, the BC group had a higher relative abundance of Pasteurellaceae and Streptococcaceae but a lower relative abundance of Bacteroidaceae. CONCLUSIONS: Our MR analysis suggests that the oral microbiome exerts a causative effect on BC risk, supported by the sequencing data of a case-control study. In the future, studies should be undertaken to comprehensively understand the complex interaction mechanisms between the oral microbiota and BC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35461868", + "title": "Role of salivary glycopatterns for oral microbiota associated with gastric cancer.", + "year": 2022, + "journal": "International journal of biological macromolecules", + "authors": [ + "Shu J", + "Yu H", + "Ren X", + "Wang Y", + "Zhang K", + "Tang Z", + "Dang L", + "Chen W", + "Li B", + "Xie H", + "Li Z" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.22276660905615572, + "mesh_terms": [ + "Dysbiosis", + "Glycoproteins", + "Humans", + "Microbiota", + "RNA, Ribosomal, 16S", + "Saliva", + "Salivary Proteins and Peptides", + "Stomach Neoplasms" + ], + "raw_abstract": "Microbiota in the oral cavity plays an important role in maintaining human health. Our previous studies have revealed significant alterations of salivary glycopatterns in gastric cancer (GC) patients, but it is unclear whether these altered salivary glycopatterns can cause the dysbiosis of oral microbiota. In this study, the oral microbiome of healthy volunteers (HVs) and GC patients were detected. The neoglycoproteins were then synthesized according to the altered glycopatterns in GC patients and used to explore the effects of specific salivary glycopattern against oral microbiota. The results showed that five species were significantly increased (p\u00a0<\u00a00.05) while two species were significantly decreased (p\u00a0<\u00a00.01) in the saliva of GC patients compared with that of HVs. And the fucose-neoglycoproteins (30-100\u00a0\u03bcg/mL) could reduce the adhesion and toxicity of Aggregatibacter segnis (A. segnis) to oral cells (HOEC and CAL-27), change the glycan structures of lipopolysaccharide on the surface of A. segnis, and enhance the capacity of A. segnis to trigger innate immune responses. This study revealed that the changes of salivary protein glycopatterns in GC patients might contribute to the dysbiosis of oral microbiota, and had important implications in developing new carbohydrate drugs to maintain a balanced microbiota in the oral.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28707473", + "title": "Aggregatibacter actinomycetemcomitans Growth in Biofilm versus Planktonic State: Differential Expression of Proteins.", + "year": 2017, + "journal": "Journal of proteome research", + "authors": [ + "Llama-Palacios A", + "Potupa O", + "S\u00e1nchez MC", + "Figuero E", + "Herrera D", + "Sanz M" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.2220697227950478, + "mesh_terms": [ + "Adenylate Kinase", + "Aggregatibacter actinomycetemcomitans", + "Bacterial Outer Membrane Proteins", + "Biofilms", + "Dihydrolipoyllysine-Residue Acetyltransferase", + "Gene Expression Profiling", + "Gene Expression Regulation, Bacterial", + "Gene Ontology", + "Humans", + "Metabolic Networks and Pathways", + "Molecular Chaperones", + "Molecular Sequence Annotation", + "Periodontitis", + "Plankton", + "Two-Dimensional Difference Gel Electrophoresis", + "Virulence Factors" + ], + "raw_abstract": "Aggregatibacter actinomycetemcomitans (Aa) is a pathogenic bacterium residing in the subgingival plaque biofilm strongly associated with the pathogenesis of periodontitis. The aim of this investigation was to study the protein differential expression of Aa when growing on biofilm compared with planktonic state using proteomic analysis by the 2D-DIGE system. Eighty-seven proteins were differentially expressed during biofilm growth (1.5-fold, p < 0.05), with 13 overexpressed and 37 down-expressed. Those repressed were mainly proteins involved in metabolism, biosynthesis, and transport. The overexpressed proteins were outer membrane proteins (OMPs) and highly immunogenic proteins such as YaeT (OMP), FtsZ, OMP39, OMP18/16, the chaperone GroEL, OMPA, adenylate kinase (Adk), and dihydrolipoamide acetyltransferase. The enrichment fractions of the OMPs from biofilm and planktonic states were obtained, and these proteins were analyzed by Western blotting with human serum from a periodontitis patient and one healthy control. These immunogenic proteins overexpressed in the biofilm may represent candidate virulence factors.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39465426", + "title": "Periodontal conditions and salivary microbiota are potential indicators to distinguish silicosis: an exploratory study.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Duan S", + "Shao M", + "Zhang C", + "Zhao J", + "Zhu F", + "Luo N", + "Lei L", + "Zhong T", + "Hu T" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.22153302819674314, + "mesh_terms": [ + "Humans", + "Male", + "Saliva", + "Microbiota", + "Silicosis", + "Cross-Sectional Studies", + "Middle Aged", + "RNA, Ribosomal, 16S", + "China", + "Periodontal Diseases", + "Adult", + "Bacteria", + "Case-Control Studies", + "High-Throughput Nucleotide Sequencing" + ], + "raw_abstract": "BACKGROUND: Silicosis has always been a serious global occupational health problem. Oral microbiota plays important roles in the development of lung disease. However, few studies have investigated the relationship between periodontal conditions, oral bacteria and silicosis disease. METHOD: A single-center and cross-sectional study was conducted in 2019 in Sichuan Province, China, including a small sample of silicosis patient group and healthy control group. Demographic data and periodontal examinations measured by clinical attachment loss (CAL), bleeding on probing (BOP) and periodontal pocket (PD) were collected from each participant. Phenotypic changes were detected by histopathological staining. Next-generation sequencing targeting 16S ribosomal RNA was targeted to decipher the salivary microbiome of the two groups. Random forest, Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression and multivariable logistic regression analysis were conducted to find potential indicators to distinguish silicosis. RESULTS: In general, 29 male healthy controls and 24 male silicosis patients were included. The proportion of CAL\u2009\u2265\u20093\u00a0mm in silicosis group was greater than control group, while the proportion of BOP (+) and PD\u2009\u2265\u20094\u00a0mm was reduced in silicosis group. The \u03b1-smooth muscle actin and fibronectin expression increased in gingiva of patients. The composition of salivary microbiota exhibited significant differences between the two groups, with silicosis patients demonstrating a lower diversity of salivary microbiota. Genus of Aggregatibacter [odds ratio (OR)\u2009=\u20090.000, p\u2009=\u20090.003] and Catonella (OR\u2009=\u20090.000, p\u2009=\u20090.049) were identified as biomarkers to distinguish silicosis. CONCLUSIONS: The silicosis group exhibited worse CAL, improved BOP and PD, which may be related to the gingival fibrosis found in this study. The composition of the oral microbiota underwent significant changes, accompanied by a decrease in diversity, in patients with silicosis. Our study indicates that respirable crystalline silica exposure affects oral health, and alterations of oral microbiota might be implicated in silicosis. We primarily identified Aggregatibacter and Catonella as the potential indicators to distinguish silicosis patients from healthy controls.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27717180", + "title": "Does obesity influence the subgingival microbiota composition in periodontal health and disease?", + "year": 2016, + "journal": "Journal of clinical periodontology", + "authors": [ + "Maciel SS", + "Feres M", + "Gon\u00e7alves TE", + "Zimmermann GS", + "da Silva HD", + "Figueiredo LC", + "Duarte PM" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.21682360926141866, + "mesh_terms": [ + "Aggregatibacter actinomycetemcomitans", + "Bacteroides", + "Dental Plaque", + "Fusobacterium nucleatum", + "Humans", + "Microbiota", + "Obesity", + "Porphyromonas gingivalis", + "Prevotella intermedia" + ], + "raw_abstract": "AIM: To evaluate whether obesity affects the subgingival microbial composition of patients with periodontal health or chronic periodontitis (CP). MATERIALS AND METHODS: Based on periodontal parameters, body mass index and waist-hip ratio, 166 patients were allocated into one of the following groups: Normal weight (NW) patients with periodontal health (n\u00a0=\u00a044), NW patients with CP (n\u00a0=\u00a040), obese patients with periodontal health (n\u00a0=\u00a040) and obese patients with\u00a0CP (n\u00a0=\u00a042). Six subgingival biofilm samples per patient were analysed for\u00a0their\u00a0content of 40 bacterial species using checkerboard DNA-DNA hybridization. RESULTS: Obese patients with CP harboured higher levels and/or higher proportions of several periodontal pathogens than those with NW and CP, including Aggregatibacter actinomycetemcomitans, Eubacterium nodatum, Fusobacterium nucleatum ss vincentii, Parvimonas micra, Prevotella intermedia, Tannerella forsythia, Prevotella melaninogenica and Treponema socranskii. The proportions of most of these pathogens, as well Campylobacter rectus and Eikenella corrodens, were more increased in the diseased sites of the obese patients than in those with NW. Furthermore, the healthy sites of the obese patients, presenting or not CP, also exhibited higher proportions of some of the pathogens than patients with NW. CONCLUSIONS: Obesity is associated with increased levels and proportions of periodontal pathogens, especially in patients with CP.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28383789", + "title": "Salivary microbiome of an urban Indian cohort and patterns linked to subclinical inflammation.", + "year": 2017, + "journal": "Oral diseases", + "authors": [ + "Acharya A", + "Chan Y", + "Kheur S", + "Kheur M", + "Gopalakrishnan D", + "Watt RM", + "Mattheos N" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.21128908568627724, + "mesh_terms": [ + "Adult", + "Aged", + "Asymptomatic Diseases", + "Female", + "Humans", + "India", + "Inflammation", + "Interleukin-1beta", + "Male", + "Microbiota", + "Middle Aged", + "Saliva", + "Urban Population" + ], + "raw_abstract": "OBJECTIVE: To profile salivary microbiomes of an urban-living, healthy Indian cohort and explore associations with proinflammatory status. METHODS: Fifty-one clinically healthy Indian subjects' salivary microbiomes were analyzed using 16S rRNA Illumina MiSeq sequencing. Community distribution was compared with salivary data from the Human Microbiome Project (HMP). Indian subjects were clustered using microbiome-based \"partitioning along medoids\" (PAM), and relationships of interleukin-1 beta levels with community composition were analyzed. RESULTS: Indian subjects presented higher phylogenetic diversity than HMP. Several taxa associated with traditional societies gut microbiomes (Bacteroidales, Paraprevotellaceae, and Spirochaetaceae) were raised. Bifidobacteriaceae and Lactobacillaceae were approximately fourfold greater. A PAM cluster enriched in several Proteobacteria, Actinobacteria, and Bacilli taxa and having almost twofold higher Prevotella to Bacteroides ratio showed significant overrepresentation of subjects within the highest quartile of salivary interleukin-1 beta levels. Abiotrophia, Anaerobacillus, Micrococcus, Aggregatibacter, Halomonas, Propionivivrio, Paracoccus, Mannhemia, unclassified Bradyrhizobiaceae, and Caulobacteraceae were each significant indicators of presence in the highest interleukin-1 beta quartile. 2 OTUs representing Lactobacillus fermentum and Cardiobacterium hominis significantly correlated with interleukin-1 beta levels. CONCLUSION: The salivary microbiome of this urban-dwelling Indian cohort differed significantly from that of a well-studied Western cohort. Specific community patterns were putatively associated with subclinical inflammation levels.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38487975", + "title": "The role of microbiota on rheumatoid arthritis onset.", + "year": 2024, + "journal": "International journal of rheumatic diseases", + "authors": [ + "Ju\u00e1rez-Chairez MF", + "Cid-Gallegos MS", + "Jim\u00e9nez-Mart\u00ednez C", + "Prieto-Contreras LF", + "Bollain-Y-Goytia de-la-Rosa JJ" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.20803588506215975, + "mesh_terms": [ + "Humans", + "Mice", + "Animals", + "Microbiota", + "Arthritis, Rheumatoid", + "Gastrointestinal Microbiome", + "Inflammation", + "Probiotics" + ], + "raw_abstract": "Rheumatoid arthritis (RA) is a chronic autoimmune disease that causes inflammation and pain, which can lead to the loss of normal joint function. Although the exact cause of the disease is not yet fully understood, both environmental factors and genetics may play a role in its development. Moreover, research suggests microbiota contributes to the onset and progression of RA. People with RA show higher quantities of bacteria such as Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Prevotella copri, Proteus mirabilis, and Lactobacillus salivarius compared to healthy individuals. Conversely, studies propose that Lactobacillus casei, a probiotic bacterium with immunomodulatory properties, has beneficial effects for RA in murine and human models. Therefore, this work reviews the potential role of the gut microbiota in the development of RA and explores the feasibility of using probiotic bacteria as a supplementary treatment for this disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31752810", + "title": "Comparative analysis of the oral microbiota between iron-deficiency anaemia (IDA) patients and healthy individuals by high-throughput sequencing.", + "year": 2019, + "journal": "BMC oral health", + "authors": [ + "Xi R", + "Wang R", + "Wang Y", + "Xiang Z", + "Su Z", + "Cao Z", + "Xu X", + "Zheng X", + "Li J" + ], + "bacteria": "Aggregatibacter", + "condition": "healthy", + "relevance_score": 0.206937924009937, + "mesh_terms": [ + "Anemia, Iron-Deficiency", + "China", + "Cross-Sectional Studies", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Iron", + "Microbiota", + "Mouth" + ], + "raw_abstract": "BACKGROUND: The relationship between oral microbiota and IE (infective endocarditis) is well established. Opportunistic pathogens in normal oral flora enter the bloodstream through daily oral cleaning or invasive dental procedures, leading to the occurrence of infective endocarditis. An in vitro iron-deficient condition leads to a drastic community shift in oral microbiota with increasing proportions of taxa related to infective endocarditis. To investigate the relationship among insufficient iron supply, oral microbiota and the risk of IE and to conduct a population amplification study, iron-deficiency anaemia is used as an in vivo model. METHODS: This cross-sectional study enrolled 24 primary iron-deficiency anemia (IDA) patients from 2015.6 to 2016.6 from the hematology department of West China Hospital, Sichuan University, and 24 healthy controls. High-throughput sequencing compared the dental plaque microbiota of 24 IDA (iron-deficiency anaemia) patients and 24 healthy controls. RESULTS: Sequences were classified into 12 phyla, 28 classes, 50 orders, 161 genera and 497 OTUs (the IDA and control groups shared the same 384 OTUs). Iron deficiency leads to lower internal diversity in the oral flora. The abundances of genera Corynebacterium, Neisseria, Cardiobacterium, Capnocytophaga, and Aggregatibacter were significantly higher in healthy controls, while genera Lactococcus, Enterococcus, Lactobacillus, Pseudomonas and Moraxella showed higher proportions in the IDA group (P\u2009<\u20090.05). The relative abundances of genera Lactococcus, Enterococcus, Pseudomonas and Moraxella were significantly negatively correlated with the concentration of serum ferritin (P\u2009<\u20090.05). CONCLUSIONS: Without an increase of oral streptococci, the main pathogen of IE, it is difficult to determine whether IDA can increase the risk of IE. However, the iron-deficient condition did lead to changes in the oral microbiota community structure. The genera that showed higher proportions in the IDA group were frequently reported as antibiotic-resistant. As antibiotics are commonly recommended to prevent IE before dental procedures, this study offers new ideas of personalized prevention of IE.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36615708", + "title": "Probiotic ", + "year": 2022, + "journal": "Nutrients", + "authors": [ + "Shi S", + "Zhang Q", + "Sang Y", + "Ge S", + "Wang Q", + "Wang R", + "He J" + ], + "bacteria": "Epulopiscium", + "condition": "healthy", + "relevance_score": 0.6892467102177692, + "mesh_terms": [ + "Humans", + "Aged", + "Bifidobacterium longum", + "Probiotics", + "Cognition", + "Bifidobacterium", + "Cognitive Dysfunction", + "Double-Blind Method" + ], + "raw_abstract": "Probiotics could improve cognitive functions in patients with neurological disorders such as Alzheimer\u2019s disease, but the effects on cognitive function in healthy older adults without cognitive impairment need further study. The purpose of this study was to investigate the effect of Bifidobacterium longum BB68S (BB68S) on cognitive functions among healthy older adults without cognitive impairment. A randomized, double-blind, placebo-controlled trial was conducted with 60 healthy older adults without cognitive impairment who were divided into probiotic or placebo groups and required to consume either a sachet of probiotic (BB68S, 5 \u00d7 1010 CFU/sachet) or placebo once daily for 8 weeks. The Montreal Cognitive Assessment (MoCA) was used as an inclusion screening tool to screen elderly participants with healthy cognitive function in our study, and the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) was used to assess cognitive function in subjects before and after intervention as an assessment tool. BB68S significantly improved subjects\u2019 cognitive functions (total RBANS score increased by 18.89 points after intervention, p < 0.0001), especially immediate memory, visuospatial/constructional, attention, and delayed memory domains. BB68S intervention increased the relative abundances of beneficial bacteria Lachnospira, Bifidobacterium, Dorea, and Cellulosilyticum, while decreasing those of bacteria related to cognition impairment, such as Collinsella, Parabacteroides, Tyzzerella, Bilophila, unclassified_c_Negativicutes, Epulopiscium, Porphyromonas, and Granulicatella. In conclusion, BB68S could improve cognitive functions in healthy elderly adults without cognitive impairment, along with having beneficial regulatory effects on their gut microbiota. This study supports probiotics as a strategy to promote healthy aging and advances cognitive aging research.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "25533445", + "title": "Dynamics and diversity of the 'Atopobium cluster' in the human faecal microbiota, and phenotypic characterization of 'Atopobium cluster' isolates.", + "year": 2015, + "journal": "Microbiology (Reading, England)", + "authors": [ + "Thorasin T", + "Hoyles L", + "McCartney AL" + ], + "bacteria": "Atopobium", + "condition": "healthy", + "relevance_score": 0.5070024128497554, + "mesh_terms": [ + "Actinobacteria", + "Adult", + "Bacteria", + "Biodiversity", + "DNA, Bacterial", + "DNA, Ribosomal", + "Feces", + "Female", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Molecular Sequence Data", + "Phenotype", + "Phylogeny", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "This study monitored the dynamics and diversity of the human faecal 'Atopobium cluster' over a 3-month period using a polyphasic approach. Fresh faecal samples were collected fortnightly from 13 healthy donors (six males and seven females) aged between 26 and 61 years. FISH was used to enumerate total (EUB338mix) and 'Atopobium cluster' (ATO291) bacteria, with counts ranging between 1.12\u00d710(11) and 9.95\u00d710(11), and 1.03\u00d710(9) and 1.16\u00d710(11) cells (g dry weight faeces)(-1), respectively. The 'Atopobium cluster' population represented 0.2-22\u200a% of the total bacteria, with proportions donor-dependent. Denaturing gradient gel electrophoresis (DGGE) using 'Atopobium cluster'-specific primers demonstrated faecal populations of these bacteria were relatively stable, with bands identified as Collinsella aerofaciens, Collinsella intestinalis/Collinsella stercoris, Collinsella tanakaei, Coriobacteriaceae sp. PEAV3-3, Eggerthella lenta, Gordonibacter pamelaeae, Olsenella profusa, Olsenella uli and Paraeggerthella hongkongensis in the DGGE profiles of individuals. Colony PCR was used to identify 'Atopobium cluster' bacteria isolated from faeces (n\u200a=\u200a224 isolates). 16S rRNA gene sequence analysis of isolates demonstrated Collinsella aerofaciens represented the predominant (88\u200a% of isolates) member of the 'Atopobium cluster' found in human faeces, being found in nine individuals. Eggerthella lenta was identified in three individuals (3.6\u200a% of isolates). Isolates of Collinsella tanakaei, an 'Enorma' sp. and representatives of novel species belonging to the 'Atopobium cluster' were also identified in the study. Phenotypic characterization of the isolates demonstrated their highly saccharolytic nature and heterogeneous phenotypic profiles, and 97\u200a% of the isolates displayed lipase activity.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38782999", + "title": "Uncovering the characteristics of the gut microbiota in patients with ischemic stroke and hemorrhagic stroke.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Chen YZ", + "Huang ZY", + "Zhou WW", + "Li ZY", + "Li XP", + "Chen SS", + "Ma JK" + ], + "bacteria": "Atopobium", + "condition": "healthy", + "relevance_score": 0.3528206515139304, + "mesh_terms": [ + "Gastrointestinal Microbiome", + "Humans", + "Ischemic Stroke", + "Male", + "Hemorrhagic Stroke", + "Female", + "Case-Control Studies", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Aged", + "Bacteria", + "High-Throughput Nucleotide Sequencing" + ], + "raw_abstract": "This study aimed to explore the gut microbiota characteristics of ischemic and hemorrhagic stroke patients. A case-control study was conducted, and high-throughput sequencing of the V4-V5 region of 16S rRNA was used to analyze the differences in gut microbiota. The results showed that Proteobacteria was significantly increased in the ischemic stroke group compared with the healthy control group, while Fusobacteria was significantly increased in the hemorrhagic stroke group. In the ischemic stroke group, Butyricimonas, Alloprevotella, and Escherichia were significantly more abundant than in the healthy control group. In the hemorrhagic stroke group, Atopobium, Hungatella, Eisenbergiella, Butyricimonas, Odonbacter, Lachnociostridium, Alistipes, Parabacteroides, and Fusobacterium were significantly more abundant than in the healthy control group. Additionally, Alloprevotella, Ruminococcus, and Prevotella were significantly more abundant in the ischemic stroke group than in the hemorrhagic stroke group. The gut microbiota of ischemic and hemorrhagic stroke patients has significant diversity characteristics. These results provide new theoretical basis for exploring the prevention and treatment of different types of stroke through gut microbiota research.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34270519", + "title": "\"More Guts Than Brains?\"-The Role of Gut Microbiota in Idiopathic Intracranial Hypertension.", + "year": 2022, + "journal": "Journal of neuro-ophthalmology : the official journal of the North American Neuro-Ophthalmology Society", + "authors": [ + "Berkowitz E", + "Kopelman Y", + "Kadosh D", + "Carasso S", + "Tiosano B", + "Kesler A", + "Geva-Zatorsky N" + ], + "bacteria": "Atopobium", + "condition": "healthy", + "relevance_score": 0.33626742424658496, + "mesh_terms": [ + "Acetazolamide", + "Brain", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Obesity", + "Papilledema", + "Pseudotumor Cerebri" + ], + "raw_abstract": "BACKGROUND: Idiopathic intracranial hypertension syndrome (IIH) is most common among obese women. Weight loss is an important factor in improving papilledema. Over the last decade, growing evidence has identified gut microbiota as a potential factor in the pathophysiology of obesity. Accordingly, we investigated whether the gut microbiome is modified in IIH patients compared with healthy controls, and provide possible new treatment venues. METHODS: Shotgun metagenomic sequencing of the gut microbiome of 25 cases of IIH patients (according to the modified Dandy criteria) and 20 healthy controls. Participants were further stratified according to their body mass index. The total DNA from each sample was extracted using the PureLink Microbiome DNA Purification Kit A29789 (Invitrogen, Thermo Fisher Scientific, US). Library preparation was performed using the Nextera DNA Flex Library Prep Kit. Samples were sequenced on the Illumina Novaseq 6000 device. A list of bacterial species that significantly differed between the IIH patients and healthy controls was produced in addition to species diversity. In addition, patients' cohort alone was analyzed, (excluding the healthy controls), and the effect of acetazolamide treatment on their gut microbiota was analyzed. RESULTS: IIH patients have a lower diversity of bacterial species compared with healthy individuals. These bacteria, that is, Lactobacillus ruminis (L. ruminis) (p<6.95E-08), Atopobium parvulum (p<3.9E-03), Megamonas hypermegale (p<5.61E-03), Ruminococcus gnavus (p<1.29E-02), MEL.A1 (p<3.04E-02), and Streptococcus sp. I-G2 (p<3.04E-02), were previously characterized with beneficial health effects. Moreover, we found that Lactobacillus brevis, a beneficial bacterium as well, is more abundant in acetazolamide treated patients (p<7.07E-06). CONCLUSIONS: Gut microbiota plays a potential role in IIH etiology and therefore, can provide a promising new treatment approach for this disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36241691", + "title": "Profile of gut microbiota and serum metabolites associated with metabolic syndrome in a remote island most afflicted by obesity in Japan.", + "year": 2022, + "journal": "Scientific reports", + "authors": [ + "Uema T", + "Millman JF", + "Okamoto S", + "Nakamura T", + "Yamashiro K", + "Uehara M", + "Honma KI", + "Miyazato M", + "Ashikari A", + "Saito S", + "Maeda S", + "Imamura M", + "Ishida H", + "Matsushita M", + "Nakamura K", + "Masuzaki H" + ], + "bacteria": "Atopobium", + "condition": "healthy", + "relevance_score": 0.33047962826972493, + "mesh_terms": [ + "Body Mass Index", + "Creatine", + "Gastrointestinal Microbiome", + "Glycated Hemoglobin", + "Humans", + "Insulins", + "Japan", + "Metabolic Syndrome", + "Obesity", + "Pyruvic Acid", + "Triglycerides" + ], + "raw_abstract": "Numerous studies have revealed distinct differences in the profiles of gut microbiota between non-obese and obese individuals. To date, however, little is known if any disparities in the community of gut microbiota exist between metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO) subjects. We therefore aimed to comprehensively characterize the gut microbiota and circulating metabolites in serum from both MHO and MUO residing in the remote island, Kumejima, where the prevalence of obesity is one of the highest in Japan, and explored possible correlations between the gut microbiota profile and markers of metabolic syndrome. Results revealed that MUO showed significantly higher levels of genera such as g_Succinivibrio, g_Granulicatella, g_Brachyspira, g_Oribacterium and g_Atopobium in comparison to MHO. Moreover, abundance of g_Succinivibrio, g_Brachyspira and g_Atopobium were positively correlated with value of fasting insulin, HOMA-R, circulating triglycerides, diastolic blood pressure, BMI, body weight, waist circumference and HbA1c. In addition, MUO compared to MHO showed an imbalance of serum metabolites, with a significant elevation in 2-oxoisovaleric acid, pyruvic acid, 2-hydroxybutyric acid, and creatine. Our data highlight unmet needs in precision approaches for the treatment of obesity, targeting the gut microbiota profile and serum metabolites in a distinct population affected by obesity.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34047485", + "title": "Gut microbiota variations in patients diagnosed with major depressive disorder-A systematic review.", + "year": 2021, + "journal": "Brain and behavior", + "authors": [ + "Knudsen JK", + "Bundgaard-Nielsen C", + "Hjerrild S", + "Nielsen RE", + "Leutscher P", + "S\u00f8rensen S" + ], + "bacteria": "Atopobium", + "condition": "healthy", + "relevance_score": 0.3238429202330973, + "mesh_terms": [ + "Bifidobacterium", + "Depressive Disorder, Major", + "Gastrointestinal Microbiome", + "Humans", + "Research Design" + ], + "raw_abstract": "OBJECTIVE: The etiology of major depressive disorder (MDD) is multi-factorial and has been associated with a perturbed gut microbiota. Thus, it is therefore of great importance to determine any variations in gut microbiota in patients with MDD. METHODS: A systematic literature search was conducted including original research articles based on gut microbiota studies performed in patients with MDD. Demographic and clinical characteristics, applied methodology and observed gut microbiota composition were compared between included studies. RESULTS: Seventeen studies were included with a total of 738 patients with MDD and 782 healthy controls using different DNA purification methods, sequencing platforms and data analysis models. Four studies found a reduced \u03b1-diversity in patients with MDD, while gut microbiota compositions clustered separately according to \u03b2-diversity between patients and controls in twelve studies. Additionally, there was an increase in relative abundance of Eggerthella, Atopobium, and Bifidobacterium and a decreased relative abundance of Faecalibacterium in patients with MDD compared with healthy controls. CONCLUSION: Gut microbiota differs significantly when comparing patients with MDD and healthy controls, though inconsistently across studies. The heterogeneity in gut microbiota compositions between the studies may be explained by variations in study design.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35845131", + "title": "The Gut Microbiota and Inflammatory Factors in Pediatric Appendicitis.", + "year": 2022, + "journal": "Disease markers", + "authors": [ + "Bi Y", + "Yang Q", + "Li J", + "Zhao X", + "Yan B", + "Li X", + "Cui H" + ], + "bacteria": "Atopobium", + "condition": "healthy", + "relevance_score": 0.2771491243466065, + "mesh_terms": [ + "Appendicitis", + "Biomarkers", + "Child", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans" + ], + "raw_abstract": "BACKGROUND: The study analyzed gut microflora's composition and investigated the associations between the associations between gut dysbiosis and inflammatory indicators in pediatric patients with acute appendicitis. METHODS: High-throughput sequencing and bioinformatics analysis were used to investigate the composition and diversity of gut microflora in 20 pediatric patients with acute appendicitis and 11 healthy children. Endpoints measured were operational taxonomic units (OTU) of gut microflora. The OTU and its abundance analysis, sample diversity analysis, principal component analysis of samples, differential analysis, and analysis of biomarkers were performed. RESULTS: Overall fecal microbial richness and diversity were similar in patients and controls. Yet richness within the group of Bilophila, Eggerthella, Clostridium, Parvimonas, Megasphaera, Atopobium, Phascolarctobacterium, Adlercreutzia, Barnesiella, Klebsiella, Enterococcus, and Prevotella genera was higher in patients. Adlercreutzia was significantly positively correlated with IL-10, while the three other genera, comprising Klebsiella, Adlercreutzia, and Prevotella, were positively correlated with B cells level. CONCLUSION: Gut microbiome components are significantly different in pediatric patients with acute appendicitis and healthy children. The differential abundance of some genera is correlated with the production of inflammatory markers in appendicitis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30183458", + "title": "El Ni\u00f1o Altered Gut Microbiota of Children: A New Insight on Weather-Gut Interactions and Protective Effects of Probiotic.", + "year": 2019, + "journal": "Journal of medicinal food", + "authors": [ + "Lau ASY", + "Mitsuyama E", + "Odamaki T", + "Xiao JZ", + "Liong MT" + ], + "bacteria": "Atopobium", + "condition": "healthy", + "relevance_score": 0.26068123464267384, + "mesh_terms": [ + "Bacteria", + "Child Health", + "Dysbiosis", + "El Nino-Southern Oscillation", + "Gastrointestinal Microbiome", + "Humans", + "Probiotics", + "Protective Agents", + "Weather" + ], + "raw_abstract": "Changes in weather often trigger a myriad of negative impacts on the environment, which eventually affect human health. During the early months of 2016, Malaysia experienced El Ni\u00f1o, with an extremely dry season of almost zero rainfall. At the same time, an increase of more than twofold in fecal secretary immunoglobulin-A (SIgA) levels of healthy preschool children aged 2-6 years was observed, accompanied by an increase in phylum Bacteroidetes, predominantly attributed to genus Bacteroides and Odoribacter, which also positively correlated with fecal SIgA levels. Here, we present evidence to illustrate the detrimental effects of weather change on a microscopic \"environment,\" the human gut ecosystem. We also discuss the protective effects of probiotic against dysbiosis as induced by weather change. The increase in Bacteroidetes was at an expense of decreased genus Faecalibacterium and Veillonella (phylum Firmicutes), whereas children consuming probiotic had a decrease in genus Collinsella, Atopobium, and Eggerthella (phylum Actinobacteria) instead.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39789755", + "title": "Characteristics and Clinical Significance of Gut Microbiota in Patients With Epstein-Barr Virus-Associated Liver Dysfunction.", + "year": 2025, + "journal": "Microbiology and immunology", + "authors": [ + "Zhan Y", + "Fu Y", + "Dai H", + "Gao H", + "Huang S", + "Chen H", + "Xu J" + ], + "bacteria": "Atopobium", + "condition": "healthy", + "relevance_score": 0.236667447899634, + "mesh_terms": [], + "raw_abstract": "Infectious mononucleosis (IM) is mainly triggered by Epstein-Barr virus (EBV) infection. There are few studies on the role of the gut microbiota in IM and EBV-associated liver dysfunction. The aim of this study was to investigate the characteristics of the gut microbiota in the EBV-associated liver dysfunction and to evaluate the relationship between the severity of gut microbiota dysbiosis and cytokine levels. A case-control study was performed. Individuals meeting the inclusion and exclusion criteria for EBV-induced IM were enrolled and their fecal and blood samples were collected. The V3-V4 region of the 16s rDNA gene of fecal microbiota was sequenced; bioinformatics analysis including \u03b1-diversity, \u03b2-diversity, and linear discriminant analysis (LDA) effect size (LEfSe) was performed; and the correlation between bacteria and clinical indices was analysed. A total of 48 participants completed fecal and blood tests, including 18 IM, 11 EBV-associated liver dysfunction, 12 healthy children and 7 EBV-negative liver dysfunction. The \u03b1-diversity and \u03b2-diversity of the gut microbiota in the EBV-associated liver dysfunction was more than that in IM. The abundance of Granulicatella, Enterococcus, Atopobium and Acinetobacter increased, while the abundance of Prevotella, Sutterella, Collinsella, Desulfovibrio decreased in the EBV-associated liver dysfunction compared with the IM. The abundance of Enterococcus, Atopobium and Acinetobacter correlated positively with the levels of IL-1\u03b2, IL-6, TNF-\u03b1 and CD8", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30778155", + "title": "The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls.", + "year": 2019, + "journal": "Scientific reports", + "authors": [ + "Ata B", + "Yildiz S", + "Turkgeldi E", + "Brocal VP", + "Dinleyici EC", + "Moya A", + "Urman B" + ], + "bacteria": "Atopobium", + "condition": "healthy", + "relevance_score": 0.20526554039446754, + "mesh_terms": [ + "Adult", + "Case-Control Studies", + "Cervix Uteri", + "Endometriosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Metagenome", + "Metagenomics", + "Microbiota", + "Severity of Illness Index", + "Vagina", + "Young Adult" + ], + "raw_abstract": "Dysbiosis in the genital tract or gut microbiome can be associated with endometriosis. We sampled vaginal, cervical and gut microbiota from 14 women with histology proven stage 3/4 endometriosis and 14 healthy controls. The V3 and V4 regions of the 16S rRNA gene were amplified following the 16S Metagenomic Sequencing Library Preparation. Despite overall similar vaginal, cervical and intestinal microbiota composition between stage 3/4 endometriosis group and controls, we observed differences at genus level. The complete absence of Atopobium in the vaginal and cervical microbiota of the stage 3/4 endometriosis group was noteworthy. In the cervical microbiota, Gardnerella, Streptococcus, Escherichia, Shigella, and Ureoplasma, all of which contain potentially pathogenic species, were increased in stage 3/4 endometriosis. More women in the stage 3/4 endometriosis group had Shigella/Escherichia dominant stool microbiome. Further studies can clarify whether the association is causal, and whether dysbiosis leads to endometriosis or endometriosis leads to dysbiosis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37874904", + "title": "Dysregulated Immunity to Clostridioides difficile in IBD Patients Without a History of Recognized Infection.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Cook L", + "Wong MQ", + "Rees WD", + "Schick A", + "Lisko DJ", + "Lunken GR", + "Wang X", + "Peters H", + "Oliveira L", + "Lau T", + "Mah R", + "Bressler B", + "Levings MK", + "Steiner TS" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.5171726436348435, + "mesh_terms": [ + "Humans", + "Male", + "Female", + "Clostridioides difficile", + "Adult", + "Clostridium Infections", + "Case-Control Studies", + "Middle Aged", + "Feces", + "Gastrointestinal Microbiome", + "CD4-Positive T-Lymphocytes", + "Bacterial Toxins", + "Colitis, Ulcerative", + "Th17 Cells", + "Inflammatory Bowel Diseases", + "RNA, Ribosomal, 16S", + "Crohn Disease", + "Integrin beta Chains", + "Young Adult", + "Bacterial Proteins" + ], + "raw_abstract": "BACKGROUND & AIMS: Clostridioides difficile is a toxin-secreting bacteria that is an urgent antimicrobial resistance threat, with approximately 25% of patients developing recurrent infections. Inflammatory bowel disease (IBD) patients are at increased risk of severe, recurrent C. difficile infection. METHODS: To investigate a role for C. difficile infection in IBD pathogenesis, we collected peripheral blood and stool from 20 each of ulcerative colitis patients, Crohn's disease patients, and healthy control subjects. We used a flow cytometric activation induced marker assay to quantify C. difficile toxin-specific CD4+ T cells and 16S ribosomal RNA sequencing to study microbiome diversity. RESULTS: We found IBD patients had significantly increased levels of C. difficile toxin B-specific CD4+ T cells, but not immunoglobulin G or immunoglobulin A, compared with healthy control subjects. Within antigen-specific CD4+ T cells, T helper type 17 cells and cells expressing the gut homing receptor integrin \u03b27 were reduced compared with healthy control subjects, similar to our previous study of non-IBD patients with recurrent C. difficile infection. Stool microbiome analysis revealed that gut homing, toxin-specific CD4+ T cells negatively associated with microbial diversity and, along with T helper type 17 cells, positively associated with bacteria enriched in healthy control subjects. CONCLUSIONS: These data suggest that IBD patients, potentially due to underlying intestinal dysbiosis, experience undiagnosed C. difficile infections that result in impaired toxin-specific immunity. This may contribute to the development of inflammatory T cell responses toward commensal bacteria and provide a rationale for C. difficile testing in IBD patients. Crohn\u2019s disease and ulcerative colitis patients with no history of Clostridioides difficile infection had dysregulated T cell immunity to C. difficile toxin B. This was significantly different from healthy control subjects but similar to non\u2013inflammatory bowel disease patients with recurrent C. difficile infection.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33723543", + "title": "Romanian National Guideline on Translating Fecal Microbiota Transplantation Applications related to Clostridioides difficile Infections into the Local Clinical Practice.", + "year": 2021, + "journal": "Journal of gastrointestinal and liver diseases : JGLD", + "authors": [ + "Gilca-Blanariu GE", + "Stefanescu G", + "Girleanu I", + "Iqbal T", + "Segal J", + "Mullish B", + "Quraishi MN", + "Keller J", + "Molnar T", + "Megraud F", + "Dumitrascu D", + "Manuc M", + "Iancu LS", + "Marica C", + "Gheorghe C", + "Manzoor S", + "Trifan A" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.4622757062715426, + "mesh_terms": [ + "Clostridioides difficile", + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Feces", + "Humans", + "Practice Guidelines as Topic", + "Romania" + ], + "raw_abstract": "Fecal microbiota transplantation involves the infusion of intestinal microorganisms via the transfer of a stool from a healthy individual into a diseased individual, with the intent of restoring normal intestinal flora. Fecal transplant is proposed for the treatment of refractory Clostridioides difficile infection. At present, recurrent Clostridioides difficile infection is the only indication supported by solid scientific evidence. Regulations by healthcare authorities vary among different countries. Considering that Romania does not have an available national guideline to offer standardization, this paper aimed to create a national fecal microbiota transplantation guideline concerning indications, techniques and donor screening, developed by international and local scientific working groups.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34252073", + "title": "Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects.", + "year": 2021, + "journal": "PloS one", + "authors": [ + "Verma S", + "Dutta SK", + "Firnberg E", + "Phillips L", + "Vinayek R", + "Nair PP" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.43586360262441026, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Female", + "Male", + "Clostridium Infections", + "Middle Aged", + "Metagenomics", + "Aged", + "Adult", + "Feces", + "Gastrointestinal Microbiome", + "Clostridioides difficile", + "Recurrence", + "Bacteria", + "Dysbiosis", + "Metagenome" + ], + "raw_abstract": "BACKGROUND: Recurrent Clostridioides diff\u00edcile infection (RCDI) is associated with major bacterial dysbiosis and colitis. Fecal microbiota transplantation (FMT) is a highly effective therapeutic modality for RCDI. While several studies have identified bacterial species associated with resolution of symptoms in patients, characterization of the fecal microbiome at the bacterial strain level in RCDI patients before and after FMT and healthy donors, has been lacking. The aim of this study was to examine the ability of bacterial strains from healthy donors to engraft in the gastrointestinal tract of patients with RCDI following FMT. METHODS: Fecal samples were collected from 22 patients with RCDI before and after FMT and their corresponding healthy donors. Total DNA was extracted from each sample and analyzed by shotgun metagenomic sequencing. The Cosmos-ID analysis platform was used for taxonomic assignment of sequences and calculation of the relative abundance (RA) of bacterial species and strains. From these data, the total number of bacterial strains (BSI), Shannon diversity index, dysbiosis index (DI), and bacterial engraftment factor, were calculated for each strain. FINDINGS: A marked reduction (p<0\u00b70001) in the RA of total and specific bacterial strains, especially from phylum Firmicutes, was observed in RCDI patients prior to FMT. This change was associated with an increase in the DI (p<0\u00b70001) and in pathobiont bacterial strains from phylum Proteobacteria, such as Escherichia coli O157:H7 and Klebsiella pneumoniae UCI 34. BSI was significantly lower in this group of patients as compared to healthy donors and correlated with the Shannon Index. (p<0\u00b70001). Identification and engraftment of bacterial strains from healthy donors revealed a greater diversity and higher relative abundance of short-chain fatty acid (SCFA)-producing bacterial strains, including Lachnospiraceae bacterium 5_1_63FAA_u_t, Dorea formicigenerans ATCC 27755, Anaerostipes hadrusand others, in RCDI patients after FMT. INTERPRETATION: These observations identify a group of SCFA-producing bacterial strains from healthy donors that engraft well in patients with RCDI following FMT and are associated with complete resolution of clinical symptoms and bacterial dysbiosis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34126062", + "title": "Fecal Microbiota Transplantation Influences Procarcinogenic Escherichia coli in Recipient Recurrent Clostridioides difficile Patients.", + "year": 2021, + "journal": "Gastroenterology", + "authors": [ + "Nooij S", + "Ducarmon QR", + "Laros JFJ", + "Zwittink RD", + "Norman JM", + "Smits WK", + "Verspaget HW", + "Keller JJ", + "Terveer EM", + "Kuijper EJ" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.3928596459881143, + "mesh_terms": [ + "Adult", + "Aged", + "Aged, 80 and over", + "Clostridioides difficile", + "Clostridium Infections", + "Dysbiosis", + "Escherichia coli", + "Escherichia coli Proteins", + "Fecal Microbiota Transplantation", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Metagenomics", + "Middle Aged", + "Polyketide Synthases", + "Reinfection", + "Retrospective Studies", + "Time Factors", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND & AIMS: Patients with multiple recurrent Clostridioides difficile infection (rCDI) have a disturbed gut microbiota that can be restored by fecal microbiota transplantation (FMT). Despite extensive screening, healthy feces donors may carry bacteria in their intestinal tract that could have long-term health effects, such as potentially procarcinogenic polyketide synthase-positive (pks METHODS: In a cohort of 49 patients with rCDI treated with FMT and matching donor samples-the largest cohort of its kind, to our knowledge-we retrospectively screened fecal metagenomes for pks RESULTS: The pks island was more prevalent (P\u00a0= .026) and abundant (P < .001) in patients with rCDI (pre-FMT, 27 of 49 [55%]; median, 0.46 reads per kilobase per million [RPKM] pks) than in healthy donors (3 of 8 donors [37.5%], 11 of 38 samples [29%]; median, 0.01 RPKM pks). The pks status of patients post-FMT depended on the pks status of the donor suspension with which the patient was treated (P\u00a0= .046). Particularly, persistence (8 of 9 cases) or clearance (13 of 18) of pks CONCLUSIONS: We conclude that FMT contributes to pks", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31379333", + "title": "The evolution of the use of faecal microbiota transplantation and emerging therapeutic indications.", + "year": 2019, + "journal": "Lancet (London, England)", + "authors": [ + "Allegretti JR", + "Mullish BH", + "Kelly C", + "Fischer M" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.38957366300784124, + "mesh_terms": [ + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Gastrointestinal Microbiome", + "Humans", + "Practice Guidelines as Topic", + "Randomized Controlled Trials as Topic", + "Treatment Outcome" + ], + "raw_abstract": "Developments in high-throughput microbial genomic sequencing and other systems biology techniques have given novel insight into the potential contribution of the gut microbiota to health and disease. As a result, an increasing number of diseases have been characterised by distinctive changes in the composition and functionality of the gut microbiota; however, whether such changes are cause, consequence, or incidental to the disease in question remains largely uncertain. Restoration of the gut microbiota to a premorbid state is a key novel therapeutic approach of interest, and faecal microbiota transplantation-the transfer of prescreened stool from healthy donors into the gastrointestinal tract of patients-is gaining increasing importance in both the clinical and research settings. At present, faecal microbiota transplantation is only recommended in the treatment of recurrent Clostridioides difficile infection, although a large number of trials are ongoing worldwide exploring other potential therapeutic indications.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38175472", + "title": "Fecal Microbiota Transplantation as Emerging Treatment in European Countries 2.0.", + "year": 2024, + "journal": "Advances in experimental medicine and biology", + "authors": [ + "Porcari S", + "Maida M", + "Bibb\u00f2 S", + "McIlroy J", + "Ianiro G", + "Cammarota G" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.3835679594564527, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Feces", + "Anti-Bacterial Agents", + "Cross Infection", + "Inflammatory Bowel Diseases" + ], + "raw_abstract": "Clostridioides difficile infection (CDI) is one of the most common healthcare-associated infections and one of the leading causes of morbidity and mortality in hospitalized patients in the world. Although several antibiotics effectively treat CDI, some individuals may not respond to these drugs and may be cured by transplanting stool from healthy donors. FMT has demonstrated extraordinary cure rates for the cure of CDI recurrences.Moreover, FMT has also been investigated in other disorders associated with the alteration of gut microbiota, such as inflammatory bowel disease (IBD), where the alterations of the gut microbiota ecology have been theorized to play a causative role. Although FMT is currently not recommended to cure IBD patients in clinical practice, several studies have been recently carried out with the ultimate goal to search new therapeutic options to patients.This review summarizes data on the use of FMT for the treatment of both CDI and IBD, with a special attention to highlight studies conducted in European countries.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38841848", + "title": "Current and future microbiome-based therapies in inflammatory bowel disease.", + "year": 2024, + "journal": "Current opinion in gastroenterology", + "authors": [ + "Montrose JA", + "Kurada S", + "Fischer M" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.336654960558467, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Gastrointestinal Microbiome", + "Dysbiosis", + "Inflammatory Bowel Diseases", + "Randomized Controlled Trials as Topic" + ], + "raw_abstract": "PURPOSE OF REVIEW: The role of the microbiome and dysbiosis is increasingly recognized in the pathogenesis of inflammatory bowel disease (IBD). Intestinal microbiota transplant (IMT), previously termed fecal microbiota transplant has demonstrated efficacy in restoring a healthy microbiome and promoting gut health in recurrent Clostridioides difficile infection. Several randomized trials (RCTs) highlighted IMT's potential in treating ulcerative colitis, while smaller studies reported on its application in managing Crohn's disease and pouchitis. RECENT FINDINGS: This review delves into the current understanding of dysbiosis in IBD, highlighting the distinctions in the microbiota of patients with IBD compared to healthy controls. It explores the mechanisms by which IMT can restore a healthy microbiome and provides a focused analysis of recent RCTs using IMT for inducing and maintaining remission in IBD. Lastly, we discuss the current knowledge gaps that limit its widespread use. SUMMARY: The body of evidence supporting the use of IMT in IBD is growing. The lack of a standardized protocol impedes its application beyond clinical trials. Further research is needed to identify patient profile and disease phenotypes that benefit from IMT, to delineate key donor characteristics, optimize the delivery route, dosage, and frequency.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35337386", + "title": "Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation.", + "year": 2022, + "journal": "Microbiome", + "authors": [ + "Podlesny D", + "Arze C", + "D\u00f6rner E", + "Verma S", + "Dutta S", + "Walter J", + "Fricke WF" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.3348096065594099, + "mesh_terms": [ + "Adult", + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Metagenome", + "Metagenomics", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: The understanding of how microbiomes assemble, function, and evolve requires metagenomic tools that can resolve microbiota compositions at the strain level. However, the identification and tracking of microbial strains in fecal metagenomes is challenging and available tools variably classify subspecies lineages, which affects their applicability to infer microbial persistence and transfer. RESULTS: We introduce SameStr, a bioinformatic tool that identifies shared strains in metagenomes by determining single-nucleotide variants (SNV) in species-specific marker genes, which are compared based on a maximum variant profile similarity. We validated SameStr on mock strain populations, available human fecal metagenomes from healthy individuals and newly generated data from recurrent Clostridioides difficile infection (rCDI) patients treated with fecal microbiota transplantation (FMT). SameStr demonstrated enhanced sensitivity to detect shared dominant and subdominant strains in related samples (where strain persistence or transfer would be expected) when compared to other tools, while being robust against false-positive shared strain calls between unrelated samples (where neither strain persistence nor transfer would be expected). We applied SameStr to identify strains that are stably maintained in fecal microbiomes of healthy adults over time (strain persistence) and that successfully engraft in rCDI patients after FMT (strain engraftment). Taxonomy-dependent strain persistence and engraftment frequencies were positively correlated, indicating that a specific core microbiota of intestinal species is adapted to be competitive both in healthy microbiomes and during post-FMT microbiome assembly. We explored other use cases for strain-level microbiota profiling, as a metagenomics quality control measure and to identify individuals based on the persisting core gut microbiota. CONCLUSION: SameStr provides for a robust identification of shared strains in metagenomic sequence data with sufficient specificity and sensitivity to examine strain persistence, transfer, and engraftment in human fecal microbiomes. Our findings identify a persisting healthy adult core gut microbiota, which should be further studied to shed light on microbiota contributions to chronic diseases. Video abstract.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34673840", + "title": "A short chain fatty acid-centric view of Clostridioides difficile pathogenesis.", + "year": 2021, + "journal": "PLoS pathogens", + "authors": [ + "Gregory AL", + "Pensinger DA", + "Hryckowian AJ" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.32861650799630887, + "mesh_terms": [ + "Animals", + "Clostridioides difficile", + "Clostridium Infections", + "Fatty Acids, Volatile", + "Gastrointestinal Microbiome", + "Host-Pathogen Interactions", + "Humans" + ], + "raw_abstract": "Clostridioides difficile is an opportunistic diarrheal pathogen responsible for significant morbidity and mortality worldwide. A disrupted (dysbiotic) gut microbiome, commonly engendered by antibiotic treatment, is the primary risk factor for C. difficile infection, highlighting that C. difficile-microbiome interactions are critical for determining the fitness of this pathogen. Here, we review short chain fatty acids (SCFAs): a major class of metabolites present in the gut, their production by the gut microbiome, and their impacts on the biology of the host and of C. difficile. We use these observations to illustrate a conceptual model whereby C. difficile senses and responds to SCFAs as a marker of a healthy gut and tunes its virulence accordingly in order to maintain dysbiosis. Future work to learn the molecular mechanisms and genetic circuitry underlying the relationships between C. difficile and SCFAs will help to identify precision approaches, distinct from antibiotics and fecal transplant, for mitigating disease caused by C. difficile and will inform similar investigations into other gastrointestinal pathogens.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30849459", + "title": "Epidemiological investigation of Clostridioides difficile colonization in Chinese community infants.", + "year": 2019, + "journal": "Anaerobe", + "authors": [ + "Cui QQ", + "Yang J", + "Niu YN", + "Qiang CX", + "Li ZR", + "Xu KY", + "Li RX", + "Shi DY", + "Wei HL", + "Zhao XZ", + "Wang XM", + "Sun SJ", + "Zhao JH" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.31404933581884664, + "mesh_terms": [ + "Asian People", + "Bacterial Toxins", + "Carrier State", + "China", + "Clostridioides difficile", + "Clostridium Infections", + "Genotype", + "Healthy Volunteers", + "Humans", + "Infant", + "Molecular Epidemiology", + "Polymerase Chain Reaction", + "Prevalence", + "Ribotyping" + ], + "raw_abstract": "Clostridioides difficile is a colonizer of the human gut; asymptomatic colonization has been reported to be more common in infants and is highly variable across regions even with no symptoms of diarrhea or death. Antibiotic treatment strategies might increase the antibiotic resistance of C.\u00a0difficile. We performed a one-point study involving 1098 healthy infants (0-36 months) to address the deficiency of reports on C.\u00a0difficile colonization in Chinese community infants. The C.\u00a0difficile colonization rate was 22.8% (250/1098), and more than half of the strains (55.2%) were toxigenic isolates. Among the 138 toxigenic isolates, 111 were of the A", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38941767", + "title": "Differences in enteric pathogens and intestinal microbiota between diarrheic weaned piglets and healthy penmates.", + "year": 2024, + "journal": "Veterinary microbiology", + "authors": [ + "Garcias B", + "Migura-Garcia L", + "Giler N", + "Mart\u00edn M", + "Darwich L" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.28784491475478535, + "mesh_terms": [ + "Animals", + "Swine", + "Diarrhea", + "Swine Diseases", + "Gastrointestinal Microbiome", + "Weaning", + "Feces", + "Rotavirus", + "Porcine epidemic diarrhea virus", + "Clostridioides difficile", + "Virulence Factors", + "RNA, Ribosomal, 16S", + "Escherichia coli", + "Bacteria" + ], + "raw_abstract": "Postweaning diarrhea (PWD) is a multifactorial disease caused by different aetiological agents, like viruses or bacteria and where the role of the microbiota remains unclear. The aim of this study was to assess differences between healthy and diarrheic weaned pigs concerning the prevalence of pathogens and changes in the intestinal microbiota. Eighteen farms with PWD were selected and 277 fecal samples were collected (152 diarrheic vs 125 healthy). Presence of Rotavirus A (RVA), B (RVB), C (RVC) and Porcine Epidemic Diarrhea Virus (PEDV), virulence factors of Escherichia coli and Clostridioides difficile were analyzed by PCR. Finally, the microbiota composition was also study by 16\u202fS rRNA sequencing on 148 samples (102 diarrheic vs 46 healthy). RVA (53.95\u202f% vs 36\u202f%, p=0.04) and RVB (49.67\u202f% vs 28.8\u202f%, p<0.001) were more frequent in diarrheic animals. Furthermore, RVA viral load was higher in diseased animals. VT2 toxin was significantly associated with diarrhea, whereas other virulence factors were not. Presence of C. difficile and PEDV was almost negligible. Regarding microbiota changes, Fusobacteriota phylum was more frequent in diarrheic samples and Ruminococcaceae family in healthy penmates. During the first week postweaning, Enterobacteriace and Campylobacteria were enriched in animals presenting diarrhea. Furthermore, Lactobacillus was detected in those individuals with no RVA infection. In conclusion, RVA seems to play a primary role in PWD. Classic E. coli virulence factors were not associated with diarrhea, indicating the need for revising their implication in disease. Moreover, Lactobacillus was found frequently in animals negative for RVA, suggesting some protective effect.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36352460", + "title": "Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report.", + "year": 2022, + "journal": "Microbiome", + "authors": [ + "Wei S", + "Jespersen ML", + "Baunwall SMD", + "Myers PN", + "Smith EM", + "Dahlerup JF", + "Rasmussen S", + "Nielsen HB", + "Licht TR", + "Bahl MI", + "Hvas CL" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.28618624907027357, + "mesh_terms": [ + "Adult", + "Female", + "Humans", + "Infant, Newborn", + "Pregnancy", + "Bacteria", + "Clostridioides difficile", + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Feces", + "Recurrence", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Fecal microbiota transplantation (FMT) effectively prevents the recurrence of Clostridioides difficile infection (CDI). Long-term engraftment of donor-specific microbial consortia may occur in the recipient, but potential further transfer to other sites, including the vertical transmission of donor-specific strains to future generations, has not been investigated. Here, we report, for the first time, the cross-generational transmission of specific bacterial strains from an FMT donor to a pregnant patient with CDI and further to her child, born at term, 26 weeks after the FMT treatment. METHODS: A pregnant woman (gestation week 12 + 5) with CDI was treated with FMT via colonoscopy. She gave vaginal birth at term to a healthy baby. Fecal samples were collected from the feces donor, the mother (before FMT, and 1, 8, 15, 22, 26, and 50 weeks after FMT), and the infant (meconium at birth and 3 and 6 months after birth). Fecal samples were profiled by deep metagenomic sequencing for strain-level analysis. The microbial transfer was monitored using single nucleotide variants in metagenomes and further compared to a collection of metagenomic samples from 651 healthy infants and 58 healthy adults. RESULTS: The single FMT procedure led to an uneventful and sustained clinical resolution in the patient, who experienced no further CDI-related symptoms up to 50 weeks after treatment. The gut microbiota of the patient with CDI differed considerably from the healthy donor and was characterized as low in alpha diversity and enriched for several potential pathogens. The FMT successfully normalized the patient's gut microbiota, likely by donor microbiota transfer and engraftment. Importantly, our analysis revealed that some specific strains were transferred from the donor to the patient and then further to the infant, thus demonstrating cross-generational microbial transfer. CONCLUSIONS: The evidence for cross-generational strain transfer following FMT provides novel insights into the dynamics and engraftment of bacterial strains from healthy donors. The data suggests FMT treatment of pregnant women as a potential strategy to introduce beneficial strains or even bacterial consortia to infants, i.e., neonatal seeding. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32652061", + "title": "Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts.", + "year": 2020, + "journal": "Cell host & microbe", + "authors": [ + "Fujimoto K", + "Kimura Y", + "Shimohigoshi M", + "Satoh T", + "Sato S", + "Tremmel G", + "Uematsu M", + "Kawaguchi Y", + "Usui Y", + "Nakano Y", + "Hayashi T", + "Kashima K", + "Yuki Y", + "Yamaguchi K", + "Furukawa Y", + "Kakuta M", + "Akiyama Y", + "Yamaguchi R", + "Crowe SE", + "Ernst PB", + "Miyano S", + "Kiyono H", + "Imoto S", + "Uematsu S" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.27365670500001604, + "mesh_terms": [ + "Animals", + "Anti-Bacterial Agents", + "Bacteriophages", + "Clostridioides difficile", + "Clostridium Infections", + "Disease Models, Animal", + "Endopeptidases", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Genome, Bacterial", + "Genome, Viral", + "Humans", + "Metagenome", + "Mice", + "Mice, Inbred C57BL", + "Phage Therapy", + "Prophages", + "Sequence Analysis, DNA", + "Specific Pathogen-Free Organisms", + "Viral Proteins" + ], + "raw_abstract": "The application of bacteriophages (phages) is proposed as a highly specific therapy for intestinal pathobiont elimination. However, the infectious associations between phages and bacteria in the human intestine, which is essential information for the development of phage therapies, have yet to be fully elucidated. Here, we report the intestinal viral microbiomes (viromes), together with bacterial microbiomes (bacteriomes), in 101 healthy Japanese individuals. Based on the genomic sequences of bacteriomes and viromes from the same fecal samples, the host bacteria-phage associations are illustrated for both temperate and virulent phages. To verify the usefulness of the comprehensive host bacteria-phage information, we screened Clostridioides difficile-specific phages and identified antibacterial enzymes whose activity is confirmed both in\u00a0vitro and in\u00a0vivo. These comprehensive metagenome analyses reveal not only host bacteria-phage associations in the human intestine but also provide vital information for the development of phage therapies against intestinal pathobionts.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37823484", + "title": "Impact of a Purified Microbiome Therapeutic on Abundance of Antimicrobial Resistance Genes in Patients With Recurrent Clostridioides difficile Infection.", + "year": 2024, + "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", + "authors": [ + "Straub TJ", + "Lombardo MJ", + "Bryant JA", + "Diao L", + "Lodise TP", + "Freedberg DE", + "Wortman JR", + "Litcofsky KD", + "Hasson BR", + "McGovern BH", + "Ford CB", + "Henn MR" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.2692314712754844, + "mesh_terms": [ + "Adult", + "Humans", + "Female", + "Aged", + "Male", + "Anti-Bacterial Agents", + "Fecal Microbiota Transplantation", + "Clostridioides difficile", + "Drug Resistance, Bacterial", + "Microbiota", + "Clostridium Infections", + "Bacteria", + "Firmicutes" + ], + "raw_abstract": "BACKGROUND: The gastrointestinal microbiota is an important line of defense against colonization with antimicrobial resistant (AR) bacteria. In this post hoc analysis of the phase 3 ECOSPOR III trial, we assessed impact of a microbiota-based oral therapeutic (fecal microbiota spores, live; VOWST Oral Spores [VOS], formerly SER-109]; Seres Therapeutics) compared with placebo, on AR gene (ARG) abundance in patients with recurrent Clostridioides difficile infection (rCDI). METHODS: Adults with rCDI were randomized to receive VOS or placebo orally for 3 days following standard-of-care antibiotics. ARG and taxonomic profiles were generated using whole metagenomic sequencing of stool at baseline and weeks 1, 2, 8, and 24 posttreatment. RESULTS: Baseline (n = 151) and serial posttreatment stool samples collected through 24 weeks (total N = 472) from 182 patients (59.9% female; mean age: 65.5 years) in ECOSPOR III as well as 68 stool samples obtained at a single time point from a healthy cohort were analyzed. Baseline ARG abundance was similar between arms and significantly elevated versus the healthy cohort. By week 1, there was a greater decline in ARG abundance in VOS versus placebo (P = .003) in association with marked decline of Proteobacteria and repletion of spore-forming Firmicutes, as compared with baseline. We observed abundance of Proteobacteria and non-spore-forming Firmicutes were associated with ARG abundance, while spore-forming Firmicutes abundance was negatively associated. CONCLUSIONS: This proof-of-concept analysis suggests that microbiome remodeling with Firmicutes spores may be a potential novel approach to reduce ARG colonization in the gastrointestinal tract.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33757553", + "title": "16S rRNA sequencing of samples from universal stool bank donors.", + "year": 2021, + "journal": "BMC research notes", + "authors": [ + "Santiago M", + "Olesen SW" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.2637736505317131, + "mesh_terms": [ + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Feces", + "Humans", + "RNA, Ribosomal, 16S", + "Tissue Donors" + ], + "raw_abstract": "OBJECTIVES: Universal stool banks provide stool to physicians for use in treating recurrent Clostridioides difficile infection via fecal microbiota transplantation. Stool donors providing the material are rigorously screened for diseases and disorders with a potential microbiome etiology, and they are likely healthier than the controls in most microbiome datasets. 16S rRNA sequencing was performed on samples from a selection of stool donors at a large stool bank, OpenBiome, to characterize their gut microbial community and to compare samples across different timepoints and sequencing runs. DATA DESCRIPTION: 16S rRNA sequencing was performed on 200 samples derived from 170 unique stool donations from 86 unique donors. Samples were sequenced on 11 different sequencing runs. We are making this data available because rigorously screened, likely very healthy stool donors may be useful for characterizing and understanding microbial community differences across different populations and will help shed light into the how the microbiome community promotes health and disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32346208", + "title": "Faecal microbiota transplantation: indications, evidence and safety.", + "year": 2020, + "journal": "Australian prescriber", + "authors": [ + "Soo WT", + "Bryant RV", + "Costello SP" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.2584993744037282, + "mesh_terms": [], + "raw_abstract": "The human gut contains many species of microorganisms, many of which have a role in maintaining good health. The gut microbiota can be affected by diet, diseases and drugs, especially antibiotics. Faecal microbiota transplantation involves transplanting faecal material from a healthy person to a patient, with the aim of treating disease. It is a recommended treatment option for patients with recurrent or refractory Clostridioides difficile as it has a cure rate over 90%. There is evidence that faecal microbiota transplantation can induce remission in ulcerative colitis, however maintenance of remission data are lacking. For other diseases it currently should not be used outside a clinical trial. Stool donors have to be healthy and are screened for a range of diseases. As faecal material is usually transplanted during colonoscopy, the recipient must have bowel preparation before the procedure. Adverse effects are mainly gastrointestinal and usually resolve in the week following transplantation. There are limited data on long-term safety.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32585148", + "title": "Autologous fecal microbiota transplantation for the treatment of inflammatory bowel disease.", + "year": 2020, + "journal": "Translational research : the journal of laboratory and clinical medicine", + "authors": [ + "Basson AR", + "Zhou Y", + "Seo B", + "Rodriguez-Palacios A", + "Cominelli F" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.2576464855068078, + "mesh_terms": [ + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Humans", + "Inflammatory Bowel Diseases", + "Transplantation, Autologous", + "Treatment Outcome" + ], + "raw_abstract": "The term autologous fecal microbiota transplantation (a-FMT) refers herein to the use of one's feces during a healthy state for later use to restore gut microbial communities after perturbations. Generally, heterologous fecal microbiota transplantation (h-FMT), where feces from a ``healthy\" donor is transplanted into a person with illness, has been used to treat infectious diseases such as recurrent Clostridioides difficile infection (CDI), with cure rates of up to 90%. In humans, due to limited response to medicines, h-FMT has become a hallmark intervention to treat CDI. Extrapolating the benefits from CDI, h-FMT has been attempted in various diseases, including inflammatory bowel disease (IBD), but clinical response has been variable and less effective (ranging between 24% and 50%). Differences in h-FMT clinical response could be because CDI is caused by a Clostridial infection, whereas IBD is a complex, microbiome-driven immunological inflammatory disorder that presents predominantly within the gut wall of genetically-susceptible hosts. FMT response variability could also be due to differences in microbiome composition between donors, recipients, and within individuals, which vary with diet, and environments, across regions. While donor selection has emerged as a key factor in FMT success, the use of heterologous donor stool still places the recipient at risk of exposure to infectious/pathogenic microorganisms. As an implementable solution, herein we review the available literature on a-FMT, and list some considerations on the benefits of a-FMT for IBD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37747018", + "title": "Plant-based dietary index in relation to gut microbiota in Arab women.", + "year": 2023, + "journal": "Medicine", + "authors": [ + "Aljuraiban GS", + "Aljazairy EA", + "Alsahli AS", + "Sabico S", + "Al-Musharaf S" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.25209297672444253, + "mesh_terms": [ + "Humans", + "Female", + "Gastrointestinal Microbiome", + "Arabs", + "Microbiota", + "Anthropometry", + "Bacteroides" + ], + "raw_abstract": "Plant-based foods may influence gut microbiota profiles and contribute to overall human health. However, not all plant-based diets are nutritionally equivalent. We aimed to assess the association between a plant-based dietary index (PDI), specifically unhealthy PDI and healthy PDI (hPDI), and gut microbial composition and diversity in young women in Saudi Arabia. This observational study included 92 healthy women aged 18 to 25 years. Dietary and anthropometric data were collected. Fecal samples were analyzed using a novel whole-genome shotgun sequencing technique. Alpha and beta diversities measured the richness and composition of the gastrointestinal system. Relationships were examined with Pearson correlation, linear regression, and Wilcoxon Rank-Sum tests. Participants with higher PDI had higher levels of Bacteroides_u_s than those with lower PDI. hPDI was positively correlated with Bifidobacterium pseudocatenulatum, Bifidobacterium longum, Oscillibacter, and Lactobacillus acidophilus and inversely correlated with Clostridioides difficile (P\u2005<\u2005.05). Unhealthy plant-based dietary index was inversely correlated with B pseudocatenulatum, B longum, and L acidophilus and positively correlated with C difficile (P\u2005<\u2005.05) and other species of interest. In conclusion, hPDI scores were significantly associated with microbiota species linked with favorable health outcomes, independent of body mass index and gut microbial richness and composition in Arab women. Future studies should investigate the modulating effect of plant-based diets on the species identified in the current study.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37087392", + "title": "The role of faecal microbiota transplantation in chronic noncommunicable disorders.", + "year": 2023, + "journal": "Journal of autoimmunity", + "authors": [ + "Mullish BH", + "Tohumcu E", + "Porcari S", + "Fiorani M", + "Di Tommaso N", + "Gasbarrini A", + "Cammarota G", + "Ponziani FR", + "Ianiro G" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.24958053868884067, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Feces", + "Gastrointestinal Microbiome", + "Microbiota", + "Clostridium Infections", + "Treatment Outcome", + "Chronic Disease" + ], + "raw_abstract": "The gut microbiome plays a key role in influencing several pathways and functions involved in human health, including metabolism, protection against infection, and immune regulation. Perturbation of the gut microbiome is recognised as a pathogenic factor in several gastrointestinal and extraintestinal disorders, and is increasingly considered as a therapeutic target in these conditions. Faecal microbiota transplantation (FMT) is the transfer of the microbiota from healthy screened stool donors into the gut of affected patients, and is a well-established and highly effective treatment for recurrent Clostridioides difficile infection. Despite the mechanisms of efficacy of FMT not being fully understood, it has been investigated in several chronic noncommunicable disorders, with variable results. This review aims to give an overview of mechanisms of efficacy of FMT in chronic noncommunicable disorders, and to paint the current landscape of its investigation in these medical conditions, including inflammatory bowel disease (IBD), chronic liver disorders, and also extraintestinal autoimmune conditions.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34724447", + "title": "Fecal Microbiota Transplantation Commonly Failed in Children With Co-Morbidities.", + "year": 2022, + "journal": "Journal of pediatric gastroenterology and nutrition", + "authors": [ + "Kellermayer R", + "Wu Q", + "Nagy-Szakal D", + "Queliza K", + "Ihekweazu FD", + "Bocchini CE", + "Magee AR", + "Oezguen N", + "Spinler JK", + "Hollister EB", + "Shulman RJ", + "Versalovic J", + "Luna RA", + "Savidge TC" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.2471447763071589, + "mesh_terms": [ + "Child", + "Clostridioides difficile", + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Feces", + "Humans", + "Morbidity", + "Prospective Studies", + "RNA, Ribosomal, 16S", + "Recurrence", + "Treatment Outcome" + ], + "raw_abstract": "OBJECTIVES: Fecal microbiota transplantation (FMT) is arguably the most effective treatment for recurrent Clostridioides difficile infection (rCDI). Clinical reports on pediatric FMT have not systematically evaluated microbiome restoration in patients with co-morbidities. Here, we determined whether FMT recipient age and underlying co-morbidity influenced clinical outcomes and microbiome restoration when treated from shared fecal donor sources. METHODS: Eighteen rCDI patients participating in a single-center, open-label prospective cohort study received fecal preparation from a self-designated (single case) or two universal donors. Twelve age-matched healthy children and four pediatric ulcerative colitis (UC) cases from an independent serial FMT trial, but with a shared fecal donor were examined as controls for microbiome restoration using 16S rRNA gene sequencing of longitudinal fecal specimens. RESULTS: FMT was significantly more effective in rCDI recipients without underlying chronic co-morbidities where fecal microbiome composition in post-transplant responders was restored to levels of healthy children. Microbiome reconstitution was not associated with symptomatic resolution in some rCDI patients who had co-morbidities. Significant elevation in Bacteroidaceae, Bifidobacteriaceae, Lachnospiraceae, Ruminococcaceae, and Erysipelotrichaceae was consistently observed in pediatric rCDI responders, while Enterobacteriaceae decreased, correlating with augmented complex carbohydrate degradation capacity. CONCLUSION: Recipient background disease was a significant risk factor influencing FMT outcomes. Special attention should be taken when considering FMT for pediatric rCDI patients with underlying co-morbidities.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38051631", + "title": "Fecal Pharmacokinetics and Gut Microbiome Effects of Oral Omadacycline Versus Vancomycin in Healthy Volunteers.", + "year": 2024, + "journal": "The Journal of infectious diseases", + "authors": [ + "Jo J", + "Hu C", + "Begum K", + "Wang W", + "Le TM", + "Agyapong S", + "Hanson BM", + "Ayele H", + "Lancaster C", + "Jahangir Alam M", + "Gonzales-Luna AJ", + "Garey KW" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.2467061924307833, + "mesh_terms": [ + "Adult", + "Humans", + "Male", + "Female", + "Vancomycin", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Anti-Bacterial Agents", + "Tetracyclines", + "Clostridium Infections" + ], + "raw_abstract": "BACKGROUND: Clostridioides difficile infection (CDI) is a common healthcare-associated infection with limited treatment options. Omadacycline, an aminomethylcycline tetracycline, has potent in vitro activity against C difficile and a low propensity to cause CDI in clinical trials. We aimed to assess fecal pharmacokinetics and gut microbiome effects of oral omadacycline compared to oral vancomycin in healthy adults. METHODS: This was a phase 1, nonblinded, randomized clinical trial conducted in healthy volunteers aged 18-40 years. Subjects received a 10-day course of omadacycline or vancomycin. Stool samples were collected at baseline, daily during therapy, and at follow-up visits. Omadacycline and vancomycin stool concentrations were assessed, and microbiome changes were compared. RESULTS: Sixteen healthy volunteers with a mean age of 26 (standard deviation [SD], 5) years were enrolled; 62.5% were male, and participants' mean body mass index was 23.5 (SD, 4.0) kg/m2. Omadacycline was well tolerated with no safety signal differences between the 2 antibiotics. A rapid initial increase in fecal concentrations of omadacycline was observed compared to vancomycin, with maximum concentrations achieved within 48 hours. A significant difference in alpha diversity was observed following therapy in both the omadacycline and vancomycin groups (P < .05). Bacterial abundance and beta diversity analysis showed differing microbiome changes in subjects who received omadacycline versus vancomycin. CONCLUSIONS: Subjects given omadacycline had high fecal concentrations with a distinct microbiome profile compared to vancomycin. CLINICAL TRIALS REGISTRATION: NCT06030219.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35906158", + "title": "Study of the gut microbiome in Egyptian patients with active ulcerative colitis.", + "year": 2023, + "journal": "Revista de gastroenterologia de Mexico (English)", + "authors": [ + "Ahmed EA", + "Ahmed SM", + "Zakaria NH", + "Baddour NM", + "Header DA" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.2410936157755144, + "mesh_terms": [], + "raw_abstract": "INTRODUCTION AND AIM: Ulcerative colitis (UC) is characterized by chronic, uncontrolled inflammation of the intestinal mucosa. Gut microbiota dysbiosis was reported to be a factor in intestinal inflammation. The aim of the present study was to study changes in the gut microbiome in Egyptian patients with active UC. MATERIALS AND METHODS: In this cross-sectional study, the gut bacterial microbiome of 21 UC patients and 20 control subjects was analyzed using the quantitative SYBR Green real-time PCR technique, targeting the 16S rRNA gene of selected bacterial phyla/genera and/or species. RESULTS: UC patients showed marked dysbiosis evidenced by a significant decrease in the Firmicutes and F. prausnitzii anti-inflammatory bacteria. The Firmicutes/Bacteroidetes ratio was also lower in the UC cases (1.65), compared with the healthy controls (2.93). In addition, the UC cases showed a statistically significant decrease in Ruminococcus, compared with the control group. However, there were no statistically significant differences between UC patients and the controls, regarding A. muciniphila, Bifidobacterium, Lactobacillus, Bacteroides, and Prevotella. One UC case was positive for the pathogenic bacterium, Clostridioides difficile, with low relative abundance. CONCLUSION: The current study showed differences in the gut microbiome of UC patients, compared with healthy controls. This may help in identifying the gut microbiome and specific bacterial changes that can be targeted for treatment of UC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37678377", + "title": "CE: Current and Emerging Applications of Fecal Microbiota Transplantation.", + "year": 2023, + "journal": "The American journal of nursing", + "authors": [ + "Baker KA", + "Poole C" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.24051901228499956, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Quality of Life", + "Abdominal Pain", + "Anti-Bacterial Agents", + "Dehydration" + ], + "raw_abstract": "Fecal microbiota transplantation (FMT) is a life-changing treatment for people with recurrent Clostridioides difficile infection (rCDI). Frequently acquired in the hospital, CDI can cause serious gastrointestinal symptoms, including persistent watery diarrhea, abdominal pain, and severe dehydration. Antibiotics, the primary treatment, can unfortunately disrupt the gut microbiome and lead to antimicrobial resistance. FMT involves introducing stool from a healthy donor into the affected recipient to strengthen their compromised microbiome. Individuals receiving this treatment have reported remarkable improvement in clinical outcomes and quality of life. In addition to a discussion of rCDI within the context of the gastrointestinal microbiome, this article provides an overview of the FMT procedure, discusses nursing management of individuals undergoing FMT, and highlights emerging applications beyond rCDI. A case scenario is also provided to illustrate a typical trajectory for a patient undergoing FMT.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37572864", + "title": "The role of microbiome-based therapeutics for the reduction and prevention of antimicrobial-resistant organism colonization.", + "year": 2023, + "journal": "Anaerobe", + "authors": [ + "Mansoor AE", + "O'Neil CA", + "Kwon JH" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.23884695240050696, + "mesh_terms": [ + "Humans", + "Feces", + "Microbiota", + "Fecal Microbiota Transplantation", + "Gastrointestinal Microbiome", + "Clostridium Infections" + ], + "raw_abstract": "The gut is host to a diverse array of microbiota that constitute a complex ecological system crucial to human physiology. Disruptors to the normal host microbiota, such as antimicrobials, can cause a loss of species diversity in the gut, reducing its ability to resist colonization by invading pathogens and potentially leading to colonization with antimicrobial resistant organisms (AROs). ARO negatively impact gut health by disrupting the usual heterogeneity of gut microbiota and have the potential to cause systemic disease. In recent years, fecal microbiota transplantation (FMT) has been increasingly explored in the management of specific disease states such as Clostridioides difficile infection (CDI). Promising data from management of CDI has led to considerable interest in understanding the role of therapeutics to restore the gut microbiota to a healthy state. This review aims to discuss key studies that highlight the current landscape, and explore existing clinical evidence, for the use of FMT and microbiome-based therapeutics in combating intestinal colonization with ARO. We also explore potential future directions of such therapeutics and discuss unaddressed needs in this field that merit further investigation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37602713", + "title": "Synthetic microbial consortia for the treatment of Clostridioides difficile infection in mice model.", + "year": 2023, + "journal": "Microbial biotechnology", + "authors": [ + "Liu J", + "Zhu W", + "Lessing DJ", + "Chu W" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.2310467967984093, + "mesh_terms": [], + "raw_abstract": "Clostridioides difficile infection (CDI) as of recent has become a great concern to the impact on human health due to its high hazardous risk and rate of recurrence. Live bacterial therapeutics is a promising method to treat or prevent CDI. Here, a synthetic microbial consortia (SMC) B10 was constructed using probiotic strains with antibacterial and anti-quorum sensing activities, and the therapeutic effect of SMC B10 against C. difficile infection was evaluated in vitro. Compared to the model group, the treatment of SMC B10 significantly increased the survival rate. The clinical signs of mice were significantly ameliorated, especially the cecum injury, while the secretion of pro-inflammatory associated cytokines such as IL-1\u03b1, IL-6, IL-17A and TNF-\u03b1 was reduced, the expression of TLR4 was inhibited, which alleviated the inflammatory response, and the expression of the tight junction protein Claudin-1 was increased, ultimately promoting the recovery of host health. The treatment of B10 restored gut microbiota dysbiosis and led to a healthy intestinal microbiota structure, significantly improved alpha diversity, suppressing potentially harmful bacteria and restoring other core bacterial species. In conclusion, SMC B10 can effectively treat CDI through modulate gut microbiota and attenuate the inflammatory response.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32822584", + "title": "Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease.", + "year": 2020, + "journal": "Cell host & microbe", + "authors": [ + "Bushman FD", + "Conrad M", + "Ren Y", + "Zhao C", + "Gu C", + "Petucci C", + "Kim MS", + "Abbas A", + "Downes KJ", + "Devas N", + "Mattei LM", + "Breton J", + "Kelsen J", + "Marakos S", + "Galgano A", + "Kachelries K", + "Erlichman J", + "Hart JL", + "Moraskie M", + "Kim D", + "Zhang H", + "Hofstaedter CE", + "Wu GD", + "Lewis JD", + "Zackular JP", + "Li H", + "Bittinger K", + "Baldassano R" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.22820231670344768, + "mesh_terms": [ + "Adolescent", + "Biomarkers", + "Caproates", + "Child", + "Clostridioides difficile", + "Clostridium Infections", + "DNA, Bacterial", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Metabolome", + "Metagenomics", + "Taurine" + ], + "raw_abstract": "Children with inflammatory bowel diseases (IBD) are particularly vulnerable to infection with Clostridioides difficile (CDI). IBD and IBD\u00a0+ CDI have overlapping symptoms but respond to distinctive treatments, highlighting the need for diagnostic biomarkers. Here, we studied pediatric patients with IBD and IBD\u00a0+ CDI, comparing longitudinal data on the gut microbiome, metabolome, and other measures. The microbiome is dysbiotic and heterogeneous in both disease states, but the metabolome reveals disease-specific patterns. The IBD group shows increased concentrations of markers of inflammation and tissue damage compared with healthy controls, and metabolic changes associate with susceptibility to CDI. In IBD\u00a0+ CDI, we detect both metabolites associated with inflammation/tissue damage and fermentation products produced by C.\u00a0difficile. The most discriminating metabolite found is isocaproyltaurine, a covalent conjugate of a distinctive C.\u00a0difficile fermentation product (isocaproate) and an amino acid associated with tissue damage (taurine), which may be useful as a joint marker of the two disease processes.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32978424", + "title": "Comparison of gut microbiota in exclusively breast-fed and formula-fed babies: a study of 91 term infants.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Ma J", + "Li Z", + "Zhang W", + "Zhang C", + "Zhang Y", + "Mei H", + "Zhuo N", + "Wang H", + "Wang L", + "Wu D" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.22800512709076773, + "mesh_terms": [ + "Bacteria", + "Breast Feeding", + "DNA, Bacterial", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Infant", + "Infant Formula", + "Infant, Newborn", + "Male", + "Milk, Human", + "Prospective Studies" + ], + "raw_abstract": "To compare gut microbiota of healthy infants that were exclusively breast-fed or formula-fed, we recruited 91 infants, who were assigned into three different groups and fed by breast milk (30 babies), formula A (30 babies) or formula B (31 babies) exclusively for more than 4\u00a0months after birth. Faecal bacterial composition was tested. Among different groups, \u03b1 diversity was lower in breast-fed group than formula-fed groups in 40\u00a0days of age, but increased significantly in 6\u00a0months of age. The Bifidobacterium represented the most predominant genus and Enterobacteriaceae the second in all groups. In 40\u00a0days of age, Bifidobacterium and Bacteroides were significantly higher, while Streptococcus and Enterococcus were significantly lower in breast-fed group than they were in formula A-fed group. Lachnospiraceae was lower in breast-fed than formula B-fed group. Veillonella and Clostridioides were lower in breast-fed than formula-fed groups. In 3\u00a0months of age there were less Lachnospiraceae and Clostridioides in breast-fed group than formula-fed groups. There were also significant differences of microbiota between formula A-fed and formula B-fed groups. Those differences may have impacts on their long-term health.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38419010", + "title": "Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection.", + "year": 2024, + "journal": "Genome medicine", + "authors": [ + "Nooij S", + "Vendrik KEW", + "Zwittink RD", + "Ducarmon QR", + "Keller JJ", + "Kuijper EJ", + "Terveer EM" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.22792802180989125, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Clostridioides difficile", + "Feces", + "Microbiota", + "Clostridium Infections", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Multidrug-resistant (MDR) bacteria are a growing global threat, especially in healthcare facilities. Faecal microbiota transplantation (FMT) is an effective prevention strategy for recurrences of Clostridioides difficile infections and can also be useful for other microbiota-related diseases. METHODS: We study the effect of FMT in patients with multiple recurrent C. difficile infections on colonisation with MDR bacteria and antibiotic resistance genes (ARG) on the short (3\u00a0weeks) and long term (1-3\u00a0years), combining culture methods and faecal metagenomics. RESULTS: Based on MDR culture (n\u2009=\u200987 patients), we notice a decrease of 11.5% in the colonisation rate of MDR bacteria after FMT (20/87 before FMT\u2009=\u200923%, 10/87 3\u00a0weeks after FMT). Metagenomic sequencing of patient stool samples (n\u2009=\u200963) shows a reduction in relative abundances of ARGs in faeces, while the number of different resistance genes in patients remained higher compared to stools of their corresponding healthy donors (n\u2009=\u200911). Furthermore, plasmid predictions in metagenomic data indicate that patients harboured increased levels of resistance plasmids, which appear unaffected by FMT. In the long term (n\u2009=\u200922 patients), the recipients' resistomes are still donor-like, suggesting the effect of FMT may last for years. CONCLUSIONS: Taken together, we hypothesise that FMT restores the gut microbiota to a composition that is closer to the composition of healthy donors, and potential pathogens are either lost or decreased to very low abundances. This process, however, does not end in the days following FMT. It may take months for the gut microbiome to re-establish a balanced state. Even though a reservoir of resistance genes remains, a notable part of which on plasmids, FMT decreases the total load of resistance genes.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33246096", + "title": "Carriage of Clostridioides difficile in healthy infants in the community of Handan, China: A 1-year follow-up study.", + "year": 2021, + "journal": "Anaerobe", + "authors": [ + "Cui QQ", + "Yang J", + "Sun SJ", + "Li ZR", + "Qiang CX", + "Niu YN", + "Li RX", + "Shi DY", + "Wei HL", + "Tian TT", + "Xu KY", + "Wang WG", + "Zhao JH" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.22663806585043278, + "mesh_terms": [ + "Biodiversity", + "Carrier State", + "China", + "Clostridioides difficile", + "Clostridium Infections", + "DNA, Bacterial", + "Feces", + "Feeding Behavior", + "Female", + "Follow-Up Studies", + "Genotype", + "Humans", + "Incidence", + "Infant", + "Infant, Newborn", + "Intestines", + "Male", + "Polymerase Chain Reaction", + "RNA, Ribosomal, 16S", + "Ribotyping" + ], + "raw_abstract": "OBJECTIVE: Clostridioides difficile may colonize healthy infants and young children asymptomatically and for the long-term. C.\u00a0difficile genotypes and the rate and determinants of colonization differ substantially and vary among countries and regions. A 1-year follow-up study was performed to determine the incidence, kinetics and influencing factors of C.\u00a0difficile intestinal colonization. METHODS: Twenty-nine healthy infants (14 girls and 15 boys) living at home with their parents in Handan City were followed by survey from birth to 1 year of age, specifically from October 2014 through December 2015. C.\u00a0difficile isolates were typed by PCR ribotyping and analyzed for the presence of toxin genes. RESULTS: During the follow-up study period in the first year of life, 20 of the 29 total enrolled infants acquired C.\u00a0difficile. A total of 437 fecal samples were obtained, and 111 (25.4%) samples contained C.\u00a0difficile, including 79 (71.2%) toxigenic strains. The toxigenic isolates comprised six PCR ribotypes, and two PCR ribotypes were identified as nontoxigenic strains. CONCLUSION: Our study showed that C.\u00a0difficile colonization increase with age during the 12-month period, and the dominant toxigenic types of C.\u00a0difficile isolates in infants were those involved in long-term colonization. Feeding patterns may affect the dynamic progress of C.\u00a0difficile colonization.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35421353", + "title": "Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers.", + "year": 2022, + "journal": "Cell host & microbe", + "authors": [ + "Dsouza M", + "Menon R", + "Crossette E", + "Bhattarai SK", + "Schneider J", + "Kim YG", + "Reddy S", + "Caballero S", + "Felix C", + "Cornacchione L", + "Hendrickson J", + "Watson AR", + "Minot SS", + "Greenfield N", + "Schopf L", + "Szabady R", + "Patarroyo J", + "Smith W", + "Harrison P", + "Kuijper EJ", + "Kelly CP", + "Olle B", + "Bobilev D", + "Silber JL", + "Bucci V", + "Roberts B", + "Faith J", + "Norman JM" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.22639552035695953, + "mesh_terms": [ + "Clostridioides difficile", + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Healthy Volunteers", + "Humans", + "Microbiota" + ], + "raw_abstract": "Manipulation of the gut microbiota via fecal microbiota transplantation (FMT) has shown clinical promise in diseases such as recurrent Clostridioides difficile infection (rCDI). However, the variable nature of this approach makes it challenging to describe the relationship between fecal strain colonization, corresponding microbiota changes, and clinical efficacy. Live biotherapeutic products (LBPs) consisting of defined consortia of clonal bacterial isolates have been proposed as an alternative therapeutic class because of their promising preclinical results and safety profile. We describe VE303, an LBP comprising 8 commensal Clostridia strains under development for rCDI, and its early clinical development in healthy volunteers (HVs). In a phase 1a/b study in HVs, VE303 is determined to be safe and well-tolerated at all doses tested. VE303 strains optimally colonize HVs if dosed over multiple days after vancomycin pretreatment. VE303 promotes the establishment of a microbiota community known to provide colonization resistance.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36580630", + "title": "Fecal Microbiota Transplantation Across the Lifespan: Balancing Efficacy, Safety, and Innovation.", + "year": 2023, + "journal": "The American journal of gastroenterology", + "authors": [ + "Gulati AS", + "Nicholson MR", + "Khoruts A", + "Kahn SA" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.22597049670303343, + "mesh_terms": [ + "Adult", + "Child", + "Humans", + "Aged", + "Fecal Microbiota Transplantation", + "Longevity", + "Clostridioides difficile", + "Treatment Outcome", + "Feces", + "Clostridium Infections", + "Recurrence" + ], + "raw_abstract": "Fecal microbiota transplantation (FMT) is a rapidly growing therapy aimed at reconstituting the dysbiotic microbiota of a patient with the beneficial stool microbiota of a healthy individual. The efficacy rates of FMT are very robust for recurrent Clostridioides difficile infection in both children and adults. Although complications of FMT have been reported, it is generally believed to be a safe procedure. Novel indications for FMT are being studied, with the hope that ultimately it may be useful for a variety of disorders. As this field continues to grow, however, it is necessary to consider efficacy, safety, and innovation across the lifespan. There are unique concerns regarding FMT as it pertains to children, adults, and the elderly. In this review, we seek to update clinicians, researchers, and regulators on how these factors must be balanced across the lifespan as we move forward with this innovative therapy.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32296918", + "title": "Characterization of Gut Microbiota in Hospitalized Patients with Clostridioides difficile Infection.", + "year": 2020, + "journal": "Current microbiology", + "authors": [ + "Vakili B", + "Fateh A", + "Asadzadeh Aghdaei H", + "Sotoodehnejadnematalahi F", + "Siadat SD" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.2245054083834818, + "mesh_terms": [ + "Adolescent", + "Adult", + "Bacteria", + "Butyrates", + "Case-Control Studies", + "Clostridioides difficile", + "Clostridium Infections", + "Diarrhea", + "Economic Status", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Hospitalization", + "Humans", + "Iran", + "Lactic Acid", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "Clostridioides difficile infection (CDI) is one of the most common causes of nosocomial diarrhea in developed countries and the main cause in healthcare settings. This case-control study was designed to evaluate the composition of the gut microbiota dominant bacterial groups in patients with CDI compared to the healthy control subjects. A total of 100 adult subjects involving 50 inpatients with CDI and 50 healthy persons were enrolled in the study. C. difficile isolates were characterized according to the anaerobic culture and presence of toxin genes with multiplex PCR. An ecological analysis was performed real-time quantitative PCR for bacterial elements. The abundances of Enterococcus spp., Lactobacillus spp., Escherichia coli, C. difficile, and Akkermansia muciniphila were higher in group CDI compared with group HC (P\u2009<\u20090.05). The abundances of Bacteroides spp., Bifidobacterium spp., and Faecalibacterium prausnitzii were lower in group CDI than in group HC (P\u2009<\u20090.05). No significant difference was observed in the copy number of Prevotella genus between the CDI and HC subjects (P-value\u2009=\u20090.087). We observed that economic status and income levels were reduced at patients with CDI, however, there was no significant difference between CDI and HC group results and other variables, such as age, BMI, and educational level. These findings showed a reduction in butyrate-producing bacteria and increase in lactic acid-producing bacteria was seen in CDI status. Overrepresentation of Akkermansia may be a predictive marker for the development of nosocomial diarrhea can result in a worse CDI prognosis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37384665", + "title": "Cytomegalovirus in donors for fecal microbiota transplantation, the phantom menace?", + "year": 2023, + "journal": "PloS one", + "authors": [ + "Galp\u00e9rine T", + "Engelmann I", + "Hantz S", + "Postil D", + "Dewilde A", + "Deplanque D", + "Martin R", + "Labreuche J", + "Lazrek M", + "Somers S", + "Ribot E", + "Alain S" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.21897395781036533, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Cytomegalovirus", + "Cross-Sectional Studies", + "Prospective Studies", + "Antibodies, Viral", + "Cytomegalovirus Infections", + "Immunoglobulin M" + ], + "raw_abstract": "BACKGROUND: Fecal Microbiota Transplantation (FMT) has become the preferred treatment for recurrent Clostridioides difficile Infections (CDI). However, donor screening is a complex process that varies between countries. The primary objective of screening is to prevent the transfer of potential pathogens from the donor to the recipient via feces. Many guidelines recommend Cytomegalovirus (CMV) testing as part of donor screening, but is the risk of CMV transmission well supported by evidence? MATERIALS/METHODS: A French prospective cross-sectional multicenter single-arm study estimated the frequency of detection of CMV in the stool of voluntary healthy donors selected for FMT. All preselected donors were tested for CMV antibodies in blood, and if positive, CMV DNA PCR was performed on whole blood and stool. For samples CMV positive in stool PCR, or case of serological markers positive for IgM, we planned isolation of CMV in cell culture. RESULTS: From June 1, 2016, to July 31, 2017, 500 healthy donors (250 per center) were recruited and 483 included. Of these, 301 were CMV seronegative, and 182 tested positive for CMV IgM and/or IgG. Stool CMV PCR was performed in 162 donors. In two cases, the initial analysis was positive, but below the limit of quantification. Repeated PCR tests using Siemens and Altostar assays were negative. No infectious CMV could be detected in cell culture of these two samples and in the stool of 6 CMV IgM-positive donors. CONCLUSIONS: Our study shows that healthy volunteers with positive CMV serology do not shed CMV DNA in their stool, as detected by PCR or cell culture. This study provides another argument to remove CMV screening for FMT donors.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36289064", + "title": "Functional profile of host microbiome indicates ", + "year": 2022, + "journal": "Gut microbes", + "authors": [ + "Nzabarushimana E", + "Tang H" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.21159579646110452, + "mesh_terms": [ + "Humans", + "Clostridioides difficile", + "Gastrointestinal Microbiome", + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Microbiota", + "Anti-Bacterial Agents", + "Treatment Outcome" + ], + "raw_abstract": "Clostridioides difficile infection (CDI) is a gastro-intestinal (GI) infection that illustrates how perturbations in symbiotic host-microbiome interactions render the GI tract vulnerable to the opportunistic pathogens. CDI also serves as an example of how such perturbations could be reversed via gut microbiota modulation mechanisms, especially fecal microbiota transplantation (FMT). However, microbiome-mediated diagnosis of CDI remains understudied. Here, we evaluated the diagnostic capabilities of the fecal microbiome on the prediction of CDI. We used the metagenomic sequencing data from ten previous studies, encompassing those acquired from CDI patients treated by FMT, CDI-negative patients presenting other intestinal health conditions, and healthy volunteers taking antibiotics. We designed a hybrid species/function profiling approach that determines the abundances of microbial species in the community contributing to its functional profile. These functionally informed taxonomic profiles were then used for classification of the microbial samples. We used logistic regression (LR) models using these features, which showed high prediction accuracy (with an average", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36280324", + "title": "Dysbiosis of human microbiome and infectious diseases.", + "year": 2022, + "journal": "Progress in molecular biology and translational science", + "authors": [ + "Gupta A", + "Singh V", + "Mani I" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.2104969541554066, + "mesh_terms": [ + "Humans", + "Dysbiosis", + "Prebiotics", + "Gastrointestinal Microbiome", + "Microbiota", + "Probiotics", + "Bacteria", + "Communicable Diseases" + ], + "raw_abstract": "Since birth, the human body gets colonized by various communities of symbiotic or commensal microorganisms and they persist till the death of an individual. The human microbiome is comprised of the genomes of microorganisms such as viruses, archaea, eukaryotes, protozoa, and, most remarkably, bacteria. The development of \"omics\" technologies gave way to the Human Microbiome Project (HMP) which aimed at exploring the collection of microbial genes and genomes inhabiting the human body. Eubiosis, i.e., a healthy and balanced composition of such microbes contributes to the metabolic function, protection against pathogens and provides nutrients and energy to the host. Whereas, an imbalance in the diversity of microorganisms, termed dysbiosis, greatly influences the state of health and disease. This chapter summarizes the impact of gut bacteria on the well-being of humans and highlights the protective role played by the human microbiota during bacterial and viral infections. The condition of dysbiosis and how it plays a role in the establishment of various infections and metabolic disorders such as Clostridioides difficile infection (CFI), inflammatory bowel disease (IBD), cancer, periodontitis, and obesity are described in detail. Further, treatments such as fecal transplantation, probiotics, prebiotics, phage therapy, and CRISPR/Cas system, which target gut microbiota during digestive diseases are also discussed.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30969490", + "title": "[Customised infectiology - Fecal microbiota transplantation\u2005: following the ", + "year": 2019, + "journal": "Revue medicale suisse", + "authors": [ + "Galperine TK", + "Guery B" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.20564508261767225, + "mesh_terms": [ + "Clostridioides difficile", + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Humans", + "Switzerland" + ], + "raw_abstract": "Fecal microbiota transplantation (FMT) raised, in the recent years, a growing interest, mostly in Clostridioides difficile infections (CDI). The concept of FMT is quite simple based on the administration of fecal matter from a healthy donor to a patient with a disease related to the gut microbiota imbalance (dysbiosis). Although the theory seems straightforward, the fine mechanisms are multiple and not yet completely understood. In Switzerland, FMT is considered as a drug under the pharmacist responsibility. The only official indication for FMT is multi-recurrent CDI. For practical reasons, most of the FMT are performed with fresh stools, but development of frozen forms and capsules should considerably enhance treatment delivery. Other indications are currently investigated but not yet in the clinical routine. Le microbiote intestinal est devenu depuis plusieurs ann\u00e9es une cible th\u00e9rapeutique, notamment dans les infections \u00e0", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32066975", + "title": "Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota.", + "year": 2020, + "journal": "Nature medicine", + "authors": [ + "Nagao-Kitamoto H", + "Leslie JL", + "Kitamoto S", + "Jin C", + "Thomsson KA", + "Gillilland MG", + "Kuffa P", + "Goto Y", + "Jenq RR", + "Ishii C", + "Hirayama A", + "Seekatz AM", + "Martens EC", + "Eaton KA", + "Kao JY", + "Fukuda S", + "Higgins PDR", + "Karlsson NG", + "Young VB", + "Kamada N" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.2054992704184552, + "mesh_terms": [ + "Animals", + "Bacteria", + "Clostridioides difficile", + "Clostridium Infections", + "Enterocolitis, Pseudomembranous", + "Female", + "Gastrointestinal Microbiome", + "Glycosylation", + "Host Microbial Interactions", + "Humans", + "Interleukins", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Mice, Knockout", + "Veillonellaceae", + "Interleukin-22" + ], + "raw_abstract": "The involvement of host immunity in the gut microbiota-mediated colonization resistance to Clostridioides difficile infection (CDI) is incompletely understood. Here, we show that interleukin (IL)-22, induced by colonization of the gut microbiota, is crucial for the prevention of CDI in human microbiota-associated (HMA) mice. IL-22 signaling in HMA mice regulated host glycosylation, which enabled the growth of succinate-consuming bacteria Phascolarctobacterium spp. within the gut microbiome. Phascolarctobacterium reduced the availability of luminal succinate, a crucial metabolite for the growth of C. difficile, and therefore prevented the growth of C. difficile. IL-22-mediated host N-glycosylation is likely impaired in patients with ulcerative colitis (UC) and renders UC-HMA mice more susceptible to CDI. Transplantation of healthy human-derived microbiota or Phascolarctobacterium reduced luminal succinate levels and restored colonization resistance in UC-HMA mice. IL-22-mediated host glycosylation thus fosters the growth of commensal bacteria that compete with C. difficile for the nutritional niche.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "40013938", + "title": "Advances in Fecal Microbiota Transplantation for Gut Dysbiosis-Related Diseases.", + "year": 2025, + "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", + "authors": [ + "Hou S", + "Yu J", + "Li Y", + "Zhao D", + "Zhang Z" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.20524910687228784, + "mesh_terms": [], + "raw_abstract": "This article provides an overview of the advancements in the application of fecal microbiota transplantation (FMT) in treating diseases related to intestinal dysbiosis. FMT involves the transfer of healthy donor fecal microbiota into the patient's body, aiming to restore the balance of intestinal microbiota and thereby treat a variety of intestinal diseases such as recurrent Clostridioides difficile infection (rCDI), inflammatory bowel disease (IBD), constipation, short bowel syndrome (SBS), and irritable bowel syndrome (IBS). While FMT has shown high efficacy in the treatment of rCDI, further research is needed for its application in other chronic conditions. This article elaborates on the application of FMT in intestinal diseases and the mechanisms of intestinal dysbiosis, as well as discusses key factors influencing the effectiveness of FMT, including donor selection, recipient characteristics, treatment protocols, and methods for assessing microbiota. Additionally, it emphasizes the key to successful FMT. Future research should focus on optimizing the FMT process to ensure long-term safety and explore the potential application of FMT in a broader range of medical conditions.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37161478", + "title": "Emerging applications of phage therapy and fecal virome transplantation for treatment of Clostridioides difficile infection: challenges and perspectives.", + "year": 2023, + "journal": "Gut pathogens", + "authors": [ + "Raeisi H", + "Noori M", + "Azimirad M", + "Mohebbi SR", + "Asadzadeh Aghdaei H", + "Yadegar A", + "Zali MR" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.20395014647621393, + "mesh_terms": [], + "raw_abstract": "Clostridioides difficile, which causes life-threatening diarrheal disease, is considered an urgent threat to healthcare setting worldwide. The current standards of care solely rely on conventional antibiotic treatment, however, there is a risk of promoting recurrent C. difficile infection (rCDI) because of the emergence of antibiotic-resistant strains. Globally, the alarming spread of antibiotic-resistant strains of C. difficile has resulted in a quest for alternative therapeutics. The use of fecal microbiota transplantation (FMT), which involves direct infusion of fecal suspension from a healthy donor into a diseased recipient, has been approved as a highly efficient therapeutic option for patients with rCDI. Bacteriophages or phages are a group of viruses that can infect and destroy bacterial hosts, and are recognized as the dominant viral component of the human gut microbiome. Accumulating data has demonstrated that phages play a vital role in microbial balance of the human gut microbiome. Recently, phage therapy and fecal virome transplantation (FVT) have been introduced as promising alternatives for the treatment of C. difficile\u2009-related infections, in particular drug-resistant CDI. Herein, we review the latest updates on C. difficile-\u2009specific phages, and phage-mediated treatments, and highlight the current and future prospects of phage therapy in the management of CDI.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38726585", + "title": "Clostridioides Difficile: A Concise Review of Best Practices and Updates.", + "year": 2024, + "journal": "Journal of primary care & community health", + "authors": [ + "Yakout A", + "Bi Y", + "Harris DM" + ], + "bacteria": "Clostridioides", + "condition": "healthy", + "relevance_score": 0.20041347301862186, + "mesh_terms": [ + "Humans", + "Clostridium Infections", + "Anti-Bacterial Agents", + "Clostridioides difficile", + "Fecal Microbiota Transplantation", + "Cross Infection", + "Practice Guidelines as Topic", + "Fidaxomicin", + "Metronidazole" + ], + "raw_abstract": "Clostridioides difficile infection (CDI) is one of the most common and severe nosocomial infections worldwide. It can also affect healthy individuals in the community. The incidence of CDI has been on the rise globally for the past decade, necessitating a proactive approach to combat its spread; new strategies are being developed to enhance diagnostic accuracy and optimize treatment outcomes. Implementing the 2-step testing has increased diagnostic specificity, reducing the usage of CD-specific antibiotics with no concomitant increase in surgical complication rates. In 2021, the Infectious Diseases Society of America/Society for Healthcare Epidemiology of America (IDSA/SHEA) shifted its preference for initial treatment to fidaxomicin over vancomycin and metronidazole due to its lower recurrence rate. It also prioritized fidaxomicin for the treatment of recurrent CDI. There are new developments on the frontiers of fecal microbiota therapies, with RBX2660 and SER-109 approved recently by the FDA for prevention, with other microbiome-based therapies in various development and clinical trials. This review offers providers an updated and practical guide for CDI management.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39382754", + "title": "Optimizing antigen preparation for oxalyl-CoA decarboxylase enzyme diagnostic kit and ELISA system cutoff determination.", + "year": 2024, + "journal": "Urolithiasis", + "authors": [ + "Ardestani DK", + "Basiri A", + "Bandehpour M", + "Abdi-Ghavidel A", + "Kazemi B" + ], + "bacteria": "Oxalobacter", + "condition": "healthy", + "relevance_score": 0.36380944051523817, + "mesh_terms": [ + "Enzyme-Linked Immunosorbent Assay", + "Humans", + "Carboxy-Lyases", + "Rabbits", + "Animals", + "Recombinant Proteins", + "Sensitivity and Specificity", + "Kidney Calculi", + "Reagent Kits, Diagnostic", + "Male", + "Escherichia coli", + "Female" + ], + "raw_abstract": "The prevalence of kidney stone disease is increasing globally, with calcium oxalate stones being the most common type. Oxalyl-CoA decarboxylase (OXC), an enzyme produced by the gut bacterium Oxalobacter formigenes, plays a crucial role in oxalate metabolism. Deficiencies in OXC activity can lead to the accumulation of oxalate, contributing to kidney stone formation. This study aimed to develop a reliable diagnostic assay for OXC by optimizing antigen production and establishing a cutoff value for an enzyme-linked immunosorbent assay (ELISA). We cloned, expressed, and purified recombinant OXC protein in Escherichia coli BL21(DE3), and generated specific polyclonal antibodies in rabbits. The ELISA system was optimized and validated using serum samples from 40 healthy individuals and 6 patients with oxalate-related disorders. The cutoff value was determined using the formula (M\u2009+\u20092SD), where (M) is the mean and (SD) is the standard deviation of the healthy sample results. The calculated cutoff value of 0.656750 effectively distinguished between healthy and affected individuals, with a sensitivity of 97.5% and a specificity of 83.3%. These findings provide a valuable tool for the early detection and management of oxalate-related disorders, with significant implications for clinical practice.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31145528", + "title": "Association of intestinal oxalate-degrading bacteria with recurrent calcium kidney stone formation and hyperoxaluria: a case-control study.", + "year": 2020, + "journal": "BJU international", + "authors": [ + "Tavasoli S", + "Alebouyeh M", + "Naji M", + "Shakiba Majd G", + "Shabani Nashtaei M", + "Broumandnia N", + "Basiri A" + ], + "bacteria": "Oxalobacter", + "condition": "healthy", + "relevance_score": 0.32664994978389483, + "mesh_terms": [ + "Adult", + "Bifidobacterium", + "Calcium", + "Carboxy-Lyases", + "Case-Control Studies", + "Cross-Sectional Studies", + "Female", + "Humans", + "Hyperoxaluria", + "Kidney Calculi", + "Lactobacillus", + "Male", + "Middle Aged", + "Oxalates", + "Oxalobacter formigenes", + "Recurrence" + ], + "raw_abstract": "OBJECTIVES: To investigate potential oxalate-degrading bacteria, including Oxalobacter formigenes, Lactobacillus (Lac) and Bifidobacterium (Bif) genera, and Oxalyl-CoA decarboxylase (oxc) encoding Lac (LX) and Bif (BX) species in participants with recurrent calcium kidney stones, and their correlation with 24-h urine oxalate. PARTICIPANTS AND METHODS: Stool and 24-h urine samples were collected from 58 patients with urolithiasis (29 cases with and 29 without hyperoxaluria) and 29 healthy controls. Absolute quantitation and relative abundance of the bacteria were measured by real-time PCR. The relationship between the investigated bacteria and 24-h urine oxalate were assessed statistically. RESULTS: The count per gram of stool and relative abundance of O. formigenes, Lac, Bif, LX and BX and the number of participants carrying O. formigenes, LX and BX bacteria were not significantly different between the groups; however, the relative abundance of O. formigenes in the kidney stone group was lower than in healthy controls (P = 0.035). More healthy controls were O. formigenes-positive compared with participants in the kidney stone group (P = 0.052). The results of the linear regression model, including all study participants, showed that the presence of O. formigenes could decrease 24-h urine oxalate (\u03b2 = -8.4, P = 0.047). Neither Lac and Bif genera nor LX and BX species were correlated with calcium stones or urine oxalate. CONCLUSION: These results emphasize the role of O. formigenes in kidney stone formation and its role in hyperoxaluria, which may be independent of kidney stone disease. Moreover, our results suggest that, although some Lac and Bif strains have oxalate-degrading potential, they may not be among the major oxalate-degrading bacteria of the gut microbiome.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31130222", + "title": "Inhibition of urinary stone disease by a multi-species bacterial network ensures healthy oxalate homeostasis.", + "year": 2019, + "journal": "Kidney international", + "authors": [ + "Miller AW", + "Choy D", + "Penniston KL", + "Lange D" + ], + "bacteria": "Oxalobacter", + "condition": "healthy", + "relevance_score": 0.3222404788075698, + "mesh_terms": [ + "Aged", + "Case-Control Studies", + "DNA, Bacterial", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Hyperoxaluria", + "Male", + "Middle Aged", + "Oxalates", + "Oxalobacter formigenes", + "RNA, Ribosomal, 16S", + "Urinary Calculi" + ], + "raw_abstract": "The incidence of urinary stone disease is rapidly increasing, with oxalate being a primary constituent of approximately 80% of all kidney stones. Despite the high dietary exposure to oxalate by many individuals and its potential nephrotoxicity, mammals do not produce enzymes to metabolize this compound, instead relying in part on bacteria within the gut to reduce oxalate absorption and urinary excretion. While considerable research has focused on isolated species of oxalate-degrading bacteria, particularly those with an absolute requirement for oxalate, recent studies have pointed to broader roles for microbiota both in oxalate metabolism and inhibition of urinary stone disease. Here we examined gut microbiota from patients with and live-in individuals without urinary stone disease to determine if healthy individuals harbored a more extensive microbial network associated with oxalate metabolism. We found a gender-specific association between the gut microbiota composition and urinary stone disease. Bacteria enriched in healthy individuals largely overlapped with those that exhibited a significant, positive correlation with Oxalobacter formigenes, a species presumed to be at the center of an oxalate-metabolizing microbial network. Furthermore, differential abundance analyses identified multiple taxa known to also be stimulated by oxalate in rodent models. Interestingly, the presence of these taxa distinguished patients from healthy individuals better than either the relative abundance or colonization of O.\u00a0formigenes. Thus, our work shows that bacteria stimulated by the presence of oxalate in rodents may, in addition to obligate oxalate users, play a role in the inhibition of urinary stone disease in man.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26292041", + "title": "The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults.", + "year": 2016, + "journal": "The Journal of urology", + "authors": [ + "Barnett C", + "Nazzal L", + "Goldfarb DS", + "Blaser MJ" + ], + "bacteria": "Oxalobacter", + "condition": "healthy", + "relevance_score": 0.2529277774908827, + "mesh_terms": [ + "Adolescent", + "Adult", + "Feces", + "Female", + "Healthy Volunteers", + "Humans", + "Male", + "Metagenome", + "Microbiota", + "Oxalobacter formigenes", + "United States" + ], + "raw_abstract": "PURPOSE: Oxalobacter formigenes, a member of the human colonic microbiota with a major role in net colonic oxalate transport and secretion, is protective against the formation of calcium oxalate kidney stones. We describe the prevalence, relative abundance and stability of O. formigenes in healthy young adults in the United States. MATERIALS AND METHODS: We used HMP (Human Microbiome Project) data on fecal samples from 242 healthy young adults who had 1 to 3 study visits. Samples underwent whole genomic shotgun sequencing and/or 16S rRNA sequencing. Three data sets available from the processed sequence data were studied, including whole genomic shotgun metagenomic analysis by alignment to reference genomes using shotgun community profiling, or MetaPhlAn (http://huttenhower.sph.harvard.edu/metaphlan) or QIIME (http://qiime.org/) analysis of the V1-3 or V3-5 16S sequences. RESULTS: O. formigenes was detected in fecal samples using whole genomic shotgun and 16S rRNA data. Analysis of the whole genomic shotgun data set using shotgun community profiling showed that 29 of 94 subjects (31%) were O. formigenes positive. V1-3 and V3-5 analyses were less sensitive for O. formigenes detection. When present, O. formigenes relative abundance varied over 3 log10 and was normally distributed. All assays agreed in 58 of 66 samples (88%) studied by all 3 methods. Of 14 subjects who were O. formigenes positive at baseline 13 (93%) were positive at the followup visit, indicating the stability of colonization. CONCLUSIONS: O. formigenes appears to be stably present in fewer than half of healthy young adults in the United States. It is most sensitively detected by whole genomic shotgun.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30413731", + "title": "Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease.", + "year": 2018, + "journal": "Scientific reports", + "authors": [ + "Suryavanshi MV", + "Bhute SS", + "Gune RP", + "Shouche YS" + ], + "bacteria": "Oxalobacter", + "condition": "healthy", + "relevance_score": 0.24630766982350402, + "mesh_terms": [ + "Bacteria", + "Calcium Oxalate", + "Case-Control Studies", + "Dysbiosis", + "Gastrointestinal Microbiome", + "Humans", + "Kidney Calculi", + "Metagenomics" + ], + "raw_abstract": "Analyses across all three domains of life are necessary to advance our understanding of taxonomic dysbiosis in human diseases. In the present study, we assessed gut microbiota (eubacteria, archaea, and eukaryotes) of recurrent oxalate kidney stone suffers to explore the extent of trans-domain and functional species dysbiosis inside the gut. Trans-domain taxonomic composition, active oxalate metabolizer and butyrate-producing diversity were explored by utilizing frc-, but-, and buk- functional gene amplicon analysis. Operational taxonomic units (OTUs) level analyses confound with the observation that dysbiosis in gut microbiota is not just limited to eubacteria species, but also to other domains like archaea and eukaryotes. We found that some of healthy eubacterial population retained together with Oxalobacter formigenes and Lactobacillus plantarum colonization in disease condition (p\u2009<\u20090.001 & FDR\u2009=\u20090.05). Interestingly, trans-domain species diversity has been less shared and dysgenic taxa augmentation was found to be higher. Oxalate metabolizing bacterial species (OMBS) and butyrate-producing eubacteria species were found to be decreased in Oxalobacter non-colonizers; and Prevotella and Ruminococcus species which may contribute to oxalate metabolism and butyrate synthesis as well. Our study underscores fact that microbial dysbiosis is not limited to eubacteria only hence suggest the necessity of the trans-domain surveillance in metabolic diseases for intervention studies.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36991009", + "title": "Mendelian randomization analyses reveal causal relationships between the human microbiome and longevity.", + "year": 2023, + "journal": "Scientific reports", + "authors": [ + "Liu X", + "Zou L", + "Nie C", + "Qin Y", + "Tong X", + "Wang J", + "Yang H", + "Xu X", + "Jin X", + "Xiao L", + "Zhang T", + "Min J", + "Zeng Y", + "Jia H", + "Hou Y" + ], + "bacteria": "Oxalobacter", + "condition": "healthy", + "relevance_score": 0.2155727442500768, + "mesh_terms": [ + "Aged, 80 and over", + "Humans", + "Longevity", + "Genome-Wide Association Study", + "Mendelian Randomization Analysis", + "Microbiota", + "Lactobacillus acidophilus" + ], + "raw_abstract": "Although recent studies have revealed the association between the human microbiome especially gut microbiota and longevity, their causality remains unclear. Here, we assess the causal relationships between the human microbiome (gut and oral microbiota) and longevity, by leveraging bidirectional two-sample Mendelian randomization (MR) analyses based on genome-wide association studies (GWAS) summary statistics of the gut and oral microbiome from the 4D-SZ cohort and longevity from the CLHLS cohort. We found that some disease-protected gut microbiota such as Coriobacteriaceae and Oxalobacter as well as the probiotic Lactobacillus amylovorus were related to increased odds of longevity, whereas the other gut microbiota such as colorectal cancer pathogen Fusobacterium nucleatum, Coprococcus, Streptococcus, Lactobacillus, and Neisseria were negatively associated with longevity. The reverse MR analysis further revealed genetically longevous individuals tended to have higher abundances of Prevotella and Paraprevotella but lower abundances of Bacteroides and Fusobacterium species. Few overlaps of gut microbiota-longevity interactions were identified across different populations. We also identified abundant links between the oral microbiome and longevity. The additional analysis suggested that centenarians genetically had a lower gut microbial diversity, but no difference in oral microbiota. Our findings strongly\u00a0implicate\u00a0these\u00a0bacteria\u00a0to\u00a0play\u00a0a\u00a0role\u00a0in\u00a0human\u00a0longevity and underscore the relocation of commensal microbes among different body sites that would need to be monitored for long and healthy life.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39300177", + "title": "Unraveling the role of gut microbiota by fecal microbiota transplantation in rat model of kidney stone disease.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Hunthai S", + "Usawachintachit M", + "Taweevisit M", + "Srisa-Art M", + "Anegkamol W", + "Tosukhowong P", + "Rattanachaisit P", + "Chuaypen N", + "Dissayabutra T" + ], + "bacteria": "Oxalobacter", + "condition": "healthy", + "relevance_score": 0.20842372142854773, + "mesh_terms": [ + "Animals", + "Gastrointestinal Microbiome", + "Fecal Microbiota Transplantation", + "Kidney Calculi", + "Humans", + "Rats", + "Male", + "Rats, Wistar", + "Dysbiosis", + "Disease Models, Animal", + "Feces", + "Female", + "Adult", + "Middle Aged" + ], + "raw_abstract": "Emerging research on the microbiome highlights the significant role of gut health in the development of kidney stones, indicating that an imbalance in gut bacteria or dysbiosis can influence the formation of stones by altering oxalate metabolism and urinary metabolite profiles. In particular, the overabundance of specific bacteria such as Enterococcus and Oxalobacter spp., which are known to affect oxalate absorption, is observed in patients with urolithiasis. This study investigates the effects of gut dysbiosis on urolithiasis through fecal microbiota transplantation (FMT) from patients to rats and its impact on urinary mineral excretion and stone formation. Fecal samples from eight patients with calcium oxalate stones and ten healthy volunteers were collected to assess the gut microbiome. These samples were then transplanted to antibiotic-pretreated Wistar rats for a duration of four weeks. After transplantation, we evaluated changes in the fecal gut microbiome profile, urinary mineral excretion rates, and expression levels of intestinal zonula occluden-1 (ZO-1), SLC26A6 and renal NF-\u03baB. In humans, patients with urolithiasis exhibited increased urinary calcium and oxalate levels, along with decreased citrate excretion and increased urinary supersaturation index. The fecal microbiota showed a notable abundance of Bacteroidota. In rodents, urolithiasis-FMT rats showed urinary disturbances similar to patients, including elevated pH, oxalate level, and supersaturation index, despite negative renal pathology. In addition, a slight elevation in the expression of renal NF-\u03baB, a significant intestinal SLC26A6, and a reduction in ZO-1 expression were observed. The gut microbiome of urolithiasis-FMT rats showed an increased abundance of Bacteroidota, particularly Muribaculaceae, compared to their healthy FMT counterparts. In conclusion, the consistent overabundance of Bacteroidota in both urolithiasis patients and urolithiasis-FMT rats is related to altered intestinal barrier function, hyperoxaluria, and renal inflammation. These findings suggest that gut dysbiosis, characterized by an overgrowth of Bacteroidota, plays a crucial role in the pathogenesis of calcium oxalate urolithiasis, underscoring the potential of targeting the gut microbiota as a therapeutic strategy.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33523001", + "title": "Gut Microbiome Features of Chinese Patients Newly Diagnosed with Alzheimer's Disease or Mild Cognitive Impairment.", + "year": 2021, + "journal": "Journal of Alzheimer's disease : JAD", + "authors": [ + "Guo M", + "Peng J", + "Huang X", + "Xiao L", + "Huang F", + "Zuo Z" + ], + "bacteria": "Ruminiclostridium", + "condition": "healthy", + "relevance_score": 0.38534400667956403, + "mesh_terms": [ + "Aged", + "Aged, 80 and over", + "Alzheimer Disease", + "Asian People", + "Biodiversity", + "China", + "Cognition", + "Cognitive Dysfunction", + "Disease Progression", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Patients with Alzheimer's disease (AD) have gut microbiome alterations compared with healthy controls. However, previous studies often assess AD patients who have been on medications or other interventions for the disease. Also, simultaneous determination of gut microbiome in patients with mild cognitive impairment (MCI) or AD in a study is rare. OBJECTIVE: To determine whether there was a gut microbiome alteration in patients newly diagnosed with AD or MCI and whether the degree of gut microbiome alteration was more severe in patients with AD than patients with MCI. METHODS: Fecal samples of 18 patients with AD, 20 patients with MCI, and 18 age-matched healthy controls were collected in the morning for 16S ribosomal RNA sequencing. No patient had medications or interventions for AD or MCI before the samples were collected. RESULTS: Although there was no difference in the microbial \u03b1-diversity among the three groups, patients with AD or MCI had increased \u03b2-diversity compared with healthy controls. Patients with AD had decreased Bacteroides, Lachnospira, and Ruminiclostridium_9 and increased Prevotella at the genus level compared with healthy controls. The changing direction of these genera in patients with MCI was the same as patients with AD. However, Lachnospira was the only genus whose abundance in patients with MCI was statistically significantly lower than healthy controls. Bacteroides, Lachnospira, and Ruminiclostridium_9 were positively associated with better cognitive functions whereas Prevotella was on the contrary when subjects of all three groups were considered. The negative correlation of Prevotella with cognitive functions remained among patients with MCI. CONCLUSION: Patients newly diagnosed with AD or MCI have gut dysbiosis that includes the decrease of potentially protective microbiome, such as Bacteroides, and the increase of microbiome that can promote inflammation, such as Prevotella. Our results support a novel idea that the degree of gut dysbiosis is worsened with the disease stage from MCI to AD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32997305", + "title": "The effects of cigarettes and alcohol on intestinal microbiota in healthy men.", + "year": 2020, + "journal": "Journal of microbiology (Seoul, Korea)", + "authors": [ + "Lin R", + "Zhang Y", + "Chen L", + "Qi Y", + "He J", + "Hu M", + "Zhang Y", + "Fan L", + "Yang T", + "Wang L", + "Si M", + "Chen S" + ], + "bacteria": "Ruminiclostridium", + "condition": "healthy", + "relevance_score": 0.34666211937389585, + "mesh_terms": [ + "Adult", + "Aged", + "Alcohol Drinking", + "Bacteria", + "Cigarette Smoking", + "Fatty Acids, Volatile", + "Feces", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Male", + "Middle Aged", + "Young Adult" + ], + "raw_abstract": "Human intestinal microbiota is affected by the exogenous microenvironment. This study aimed to determine the effects of cigarettes and alcohol on the gut microbiota of healthy men. In total, 116 healthy male subjects were enrolled and divided into four groups: non-smoking and non-drinking (Group A), smoking only (Group B), drinking only (Group C), and smoking and drinking combined (Group D). Fecal samples were collected and sequenced using 16S rRNA to analyze the microbial composition. Short-chain fatty acid (SCFAs) levels in feces were determined by gas chromatography. We found that cigarette and alcohol consumptions can alter overall composition of gut microbiota in healthy men. The relative abundances of phylum Bacteroidetes and Firmicutes and more than 40 genera were changed with cigarette and alcohol consumptions. SCFAs decreased with smoking and alcohol consumption. Multivariate analysis indicated that when compared with group A, group B/C/D had higher Bacteroides, and lower Phascolarctobacterium, Ruminococcaceae_UCG-002, Ruminococcaceae_UCG-003, and Ruminiclostridium_9 regardless of BMI and age. Additionally, the abundance of Bacteroides was positively correlated with the smoking pack-year (r = 0.207, p < 0.05), the abundance of predicted pathway of bacterial toxins (r = 0.3672, p < 0.001) and the level of carcinoembryonic antigen in host (r = 0.318, p < 0.01). Group D shared similar microbial construction with group B, but exerted differences far from group C with lower abundance of Haemophilus. These results demonstrated that cigarette and alcohol consumption separately affected the intestinal microbiota and function in healthy men; furthermore, the co-occurrence of cigarette and alcohol didn't exacerbate the dysbiosis and cigarette played the predominated role on the alteration.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29353409", + "title": "16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones.", + "year": 2018, + "journal": "Urolithiasis", + "authors": [ + "Tang R", + "Jiang Y", + "Tan A", + "Ye J", + "Xian X", + "Xie Y", + "Wang Q", + "Yao Z", + "Mo Z" + ], + "bacteria": "Ruminiclostridium", + "condition": "healthy", + "relevance_score": 0.33424464292193806, + "mesh_terms": [ + "Biomarkers", + "Case-Control Studies", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Kidney Calculi", + "Male", + "Middle Aged", + "RNA, Bacterial", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "Nephrolithiasis is a common urological disease with high prevalence and recurrence rates. Characterizing gut microbiome profiles of nephrolithiasis patients may provide valuable insights and potential biomarkers for the disease. Therefore, we explored the relation between gut microbiome and nephrolithiasis using 16S ribosomal RNA (rRNA) gene sequencing. 13 patients with multiple kidney stones and 13 matched healthy controls were recruited. A decreasing trend in number of observed species in nephrolithiasis patients was detected, although statistical significance was not reached (p\u2009=\u20090.086). The inter-group variability in community structure by beta diversity analysis showed a clear separation between nephrolithiasis patients and healthy controls. Twenty genera differentiated significantly in relative abundance between nephrolithiasis patients and healthy controls (all p\u2009<\u20090.05). Among the 20 genera, Phascolarctobacterium, Parasutterella, Ruminiclostridium_5, Erysipelatoclostridium, Fusicatenibacter and Dorea were correlated with the concentration of the trace elements in blood, including potassium, sodium, calcium and chlorinum. Characteristic microbiome in nephrolithiasis patients was also identified by linear discriminant analysis effect size (LEfSe). These findings may provide novel and non-invasive potential diagnostic biomarkers for nephrolithiasis, and contribute to prevention and treatment of nephrolithiasis from the perspective of maintaining micro-ecological equilibrium in gut.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35967856", + "title": "Abnormal bile acid metabolism is an important feature of gut microbiota and fecal metabolites in patients with slow transit constipation.", + "year": 2022, + "journal": "Frontiers in cellular and infection microbiology", + "authors": [ + "Fan Y", + "Xu C", + "Xie L", + "Wang Y", + "Zhu S", + "An J", + "Li Y", + "Tian Z", + "Yan Y", + "Yu S", + "Liu H", + "Jia B", + "Wang Y", + "Wang L", + "Yang L", + "Bian Y" + ], + "bacteria": "Ruminiclostridium", + "condition": "healthy", + "relevance_score": 0.30766404261334884, + "mesh_terms": [ + "Bile Acids and Salts", + "Constipation", + "Ecosystem", + "Gastrointestinal Microbiome", + "Humans", + "Lipid Metabolism", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Destructions in the intestinal ecosystem are implicated with changes in slow transit constipation (STC), which is a kind of intractable constipation characterized by colonic motility disorder. In order to deepen the understanding of the structure of the STC gut microbiota and the relationship between the gut microbiota and fecal metabolites, we first used 16S rRNA amplicon sequencing to evaluate the gut microbiota in 30 STC patients and 30 healthy subjects. The \u03b1-diversity of the STC group was changed to a certain degree, and the \u03b2-diversity was significantly different, which indicated that the composition of the gut microbiota of STC patients was inconsistent with healthy subjects. Among them, Bacteroides, Parabacteroides, Desulfovibrionaceae, and Ruminiclostridium were significantly upregulated, while Subdoligranulum was significantly downregulated. The metabolomics showed that different metabolites between the STC and the control group were involved in the process of bile acids and lipid metabolism, including taurocholate, taurochenodeoxycholate, taurine, deoxycholic acid, cyclohexylsulfamate, cholic acid, chenodeoxycholate, arachidonic acid, and 4-pyridoxic acid. We found that the colon histomorphology of STC patients was significantly disrupted, and TGR5 and FXR were significantly downregulated. The differences in metabolites were related to changes in the abundance of specific bacteria and patients' intestinal dysfunction. Analysis of the fecal genomics and metabolomics enabled separation of the STC from controls based on random forest model prediction [STC", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37730588", + "title": "Gut microbiota signature in children with autism spectrum disorder who suffered from chronic gastrointestinal symptoms.", + "year": 2023, + "journal": "BMC pediatrics", + "authors": [ + "Wang H", + "Liu S", + "Xie L", + "Wang J" + ], + "bacteria": "Ruminiclostridium", + "condition": "healthy", + "relevance_score": 0.2545474179029867, + "mesh_terms": [ + "Female", + "Male", + "Child", + "Humans", + "Child, Preschool", + "Gastrointestinal Microbiome", + "Autism Spectrum Disorder", + "Microbiota", + "Anxiety", + "Constipation" + ], + "raw_abstract": "BACKGROUND: Children diagnosed with autism spectrum disorder (ASD) frequently suffer from persistent gastrointestinal symptoms, such as constipation and diarrhea. Various studies have highlighted differences in gut microbiota composition between individuals with ASD and healthy controls of similar ages. However, it's essential to recognize that these disparities may be influenced by cultural practices, dietary habits, and environmental factors. METHODS: In this study, we collected fecal samples from both children diagnosed with ASD (n\u2009=\u200942) and healthy individuals (n\u2009=\u200941) residing in the southeastern coastal region of China. Subsequently, 16\u00a0S rRNA gene sequencing and advanced bioinformatics analyses were conducted to investigate the distinctive features of gut microbial communities within each group. RESULTS: The ASD group consisted of 28 males and 14 females, with a median age of 5.8 years, while the control group included 25 males and 16 females, with a median age of 6.8 years. Among the 83 sequenced fecal samples, a total of 1031 operational taxonomic units (OTUs) were identified. These included 122 unique OTUs specific to the control group and 285 unique OTUs specific to the ASD group. Analyses of \u03b1-diversity and \u03b2-diversity unveiled significant differences in the abundance and composition of gut microbiota between the two groups. It was found that the dominant bacterial taxa in healthy individuals were UBA1819, Flavonifractor, and Bradyrhizobium. In contrast, the ASD group exhibited a prevalence of Streptococcus, Ruminococcus, and Ruminiclostridium. Further analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) showed significant differences in the metabolic functionalities of the gut microbiota between the two groups. Notably, the metabolic pathway related to alpha-linolenic acid (ALA) in the gut microbiota of the ASD group was notably diminished compared to the control group. Conversely, the ASD group demonstrated significantly elevated levels of metabolic pathways involving uncharacterized conserved proteins, aminoglycoside phosphotransferase, and inorganic pyrophosphatase compared to the control group. CONCLUSIONS: Overall, these results confirm that there are significant differences in the gut microbiota structure between children with ASD and healthy controls in the southeast coastal region of China. This underscores the critical significance of delving into clinical interventions capable of mitigating the gastrointestinal and psychological symptoms encountered by children with ASD. A particularly encouraging path for such interventions lies in the realm of fecal microbiota transplantation, a prospect that merits deeper inquiry.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32951067", + "title": "A specific dietary fibre supplementation improves cognitive performance-an exploratory randomised, placebo-controlled, crossover study.", + "year": 2021, + "journal": "Psychopharmacology", + "authors": [ + "Berding K", + "Long-Smith CM", + "Carbia C", + "Bastiaanssen TFS", + "van de Wouw M", + "Wiley N", + "Strain CR", + "Fouhy F", + "Stanton C", + "Cryan JF", + "Dinan TG" + ], + "bacteria": "Ruminiclostridium", + "condition": "healthy", + "relevance_score": 0.20904831840310892, + "mesh_terms": [ + "Adult", + "Cognition", + "Cross-Over Studies", + "Dietary Fiber", + "Double-Blind Method", + "Female", + "Gastrointestinal Microbiome", + "Glucans", + "Humans", + "Male", + "Prebiotics", + "Stress, Psychological", + "Treatment Outcome" + ], + "raw_abstract": "RATIONALE: The impact of the microbiota on the gut-brain axis is increasingly appreciated. A growing body of literature demonstrates that use of dietary fibre and prebiotics can manipulate the microbiota and affect host health. However, the influence on cognition and acute stress response is less well understood. OBJECTIVES: The objective of this study was to investigate the efficacy of a dietary fibre, polydextrose (PDX), in improving cognitive performance and acute stress responses through manipulation of the gut microbiota in a healthy population. METHODS: In this double-blind, randomised, placebo-controlled, crossover design study, 18 healthy female participants received 12.5 g Litesse\u00aeUltra (> 90% PDX polymer) or maltodextrin for 4 weeks. Cognitive performance, mood, acute stress responses, microbiota composition, and inflammatory markers were assessed pre- and post-intervention. RESULTS: PDX improved cognitive flexibility as evidenced by the decrease in the number of errors made in the Intra-Extra Dimensional Set Shift (IED) task. A better performance in sustained attention was observed through higher number of correct responses and rejections in the Rapid Visual Information Processing (RVP) task. Although there was no change in microbial diversity, abundance of Ruminiclostridium 5 significantly increased after PDX supplementation compared with placebo. PDX supplementation attenuated the increase of adhesion receptor CD62L on classical monocytes observed in the placebo group. CONCLUSIONS: Supplementation with the PDX resulted in a modest improvement in cognitive performance. The results indicate that PDX could benefit gut-to-brain communication and modulate behavioural responses.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34755630", + "title": "Sub-chronic low-dose arsenic in rice exposure induces gut microbiome perturbations in mice.", + "year": 2021, + "journal": "Ecotoxicology and environmental safety", + "authors": [ + "Chen F", + "Luo Y", + "Li C", + "Wang J", + "Chen L", + "Zhong X", + "Zhang B", + "Zhu Q", + "Zou R", + "Guo X", + "Zhou Y", + "Guo L" + ], + "bacteria": "Ruminiclostridium", + "condition": "healthy", + "relevance_score": 0.2071250214131883, + "mesh_terms": [ + "Animals", + "Arsenic", + "Arsenicals", + "Gastrointestinal Microbiome", + "Mice", + "Microbiota", + "Oryza" + ], + "raw_abstract": "Long-term consumption of arsenic-contaminated rice has become a public health issue that urgently needs to be addressed. In this study, mice were exposed to arsenic in rice (low dose, 0.91\u00a0mg/kg; medium dose, 9.1\u00a0mg/kg) for 30 days and 60 days, respectively, and the effects on pathological structures of spleen and skin, as well as the structure of the fecal microbiome were examined. The findings revealed dose/time cumulative effects on pathological changes, with even a low dose exposure for 30 days causing destruction of splenic follicular structure and thickening of dermal keratinized and epidermal layers. The Firmicutes/Bacteroidetes ratio in the community and the positive/negative ratio in network links were higher in arsenic groups, suggesting that arsenic resulted in a less healthy and unstable microbiome for the host. Thus lifetime consumption of arsenic in rice may have potential health effects on humans and must be carefully assessed to safeguard human health. Furthermore, in arsenic groups, arsenic-resistant bacteria or arsenic hazards remediation bacteria changed to be the dominant bacteria and acted as the core bacteria in the network modules. Some microbial arsenic transforming genes (arsC, arsR, arsA, ACR3, and aoxB) differed, indicating that the gut microbiome changed to withstand arsenic stress. Furthermore, Faecalibaculum, Lachnospiraceae_NK4A136_group, Angelakisella, Ruminiclostridium, and Desulfovibrionaceae are positively associated with arsenic dosage and may be useful in the early detection of arsenicals.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34982255", + "title": "Arabiibacter massiliensis gen. nov. sp. nov., New Anaerobic Bacterium Isolated from the Human Gut.", + "year": 2022, + "journal": "Current microbiology", + "authors": [ + "Lo CI", + "Traore SI", + "Diop A", + "Bilen M", + "Azhar EI", + "Bibi F", + "Jiman-Fatani A", + "Yasir M", + "Lagier JC", + "Raoult D", + "Fenollar F", + "Fournier PE" + ], + "bacteria": "Paraeggerthella", + "condition": "healthy", + "relevance_score": 0.2584897194375302, + "mesh_terms": [ + "Anaerobiosis", + "Base Composition", + "DNA, Bacterial", + "Feces", + "Female", + "Humans", + "Middle Aged", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Saudi Arabia", + "Sequence Analysis, DNA" + ], + "raw_abstract": "Using microbial culturomics, we were able to isolate strain Marseille-P3078 from a stool sample of a healthy 50-year-old Saudi\u00a0Arabian\u00a0woman. To this end, we used taxonogenomics that combines phenotypic, biochemical and genomic analyses, to describe this bacterium. Cells from strain Marseille-P3078 are anaerobic and Gram-negative rods that are motile and unable to sporulate. Its genome size is 3,377,914-bp-long with a 66.33\u00a0mol% G\u2009+\u2009C content. Based on its phenotypic and genomic features, including a 94.6% 16S rRNA similarity with Paraeggerthella hongkongensis strain JCM 14552, its closest phylogenetic neighbor withstanding in nomenclature, we propose that strain Marseille-P3078T (=\u2009CSUR P3078\u2009=\u2009DSM 104007) is the representative strain of a new genus for which we propose the name Arabiibacter massiliensis gen. nov., sp. nov.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32692360", + "title": "Gut Microbiota in T1DM-Onset Pediatric Patients: Machine-Learning Algorithms to Classify Microorganisms as Disease Linked.", + "year": 2020, + "journal": "The Journal of clinical endocrinology and metabolism", + "authors": [ + "Biassoni R", + "Di Marco E", + "Squillario M", + "Barla A", + "Piccolo G", + "Ugolotti E", + "Gatti C", + "Minuto N", + "Patti G", + "Maghnie M", + "d'Annunzio G" + ], + "bacteria": "Holdemania", + "condition": "healthy", + "relevance_score": 0.40670950945594564, + "mesh_terms": [ + "Adolescent", + "Age of Onset", + "Algorithms", + "Child", + "Child, Preschool", + "Cohort Studies", + "Diabetes Mellitus, Type 1", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Machine Learning", + "Male", + "Metagenome", + "Risk Factors" + ], + "raw_abstract": "AIMS: The purpose of this work is to find the gut microbial fingerprinting of pediatric patients with type 1 diabetes. METHODS: The microbiome of 31 children with type 1 diabetes at onset and of 25 healthy children was determined using multiple polymorphic regions of the 16S ribosomal RNA. We performed machine-learning analyses and metagenome functional analysis to identify significant taxa and their metabolic pathways content. RESULTS: Compared with healthy controls, patients showed a significantly higher relative abundance of the following most important taxa: Bacteroides stercoris, Bacteroides fragilis, Bacteroides intestinalis, Bifidobacterium bifidum, Gammaproteobacteria and its descendants, Holdemania, and Synergistetes and its descendants. On the contrary, the relative abundance of Bacteroides vulgatus, Deltaproteobacteria and its descendants, Parasutterella and the Lactobacillus, Turicibacter genera were significantly lower in patients with respect to healthy controls. The predicted metabolic pathway more associated with type 1 diabetes patients concerns \"carbon metabolism,\" sugar and iron metabolisms in particular. Among the clinical variables considered, standardized body mass index, anti-insulin autoantibodies, glycemia, hemoglobin A1c, Tanner stage, and age at onset emerged as most significant positively or negatively correlated with specific clusters of taxa. CONCLUSIONS: The relative abundance and supervised analyses confirmed the importance of B stercoris in type 1 diabetes patients at onset and showed a relevant role of Synergistetes and its descendants in patients with respect to healthy controls. In general the robustness and coherence of the showed results underline the relevance of studying the microbioma using multiple polymorphic regions, different types of analysis, and different approaches within each analysis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39587126", + "title": "Association between gut microbiota and locomotive syndrome risk in healthy Japanese adults: a cross-sectional study.", + "year": 2024, + "journal": "npj aging", + "authors": [ + "Nishiyama M", + "Nakamura S", + "Matsuki T", + "Narimatsu H" + ], + "bacteria": "Holdemania", + "condition": "healthy", + "relevance_score": 0.38912423345866287, + "mesh_terms": [], + "raw_abstract": "This cross-sectional study examined the association between gut microbiota composition and locomotive syndrome in 568 healthy Japanese adults (36.8% male, median age 58.5 years) using data from the Kanagawa \"ME-BYO\" Prospective Cohort Study. Locomotive syndrome was assessed using the 5-question Geriatric Locomotive Function Scale (GLFS-5). Linear discriminant analysis effect size showed an enrichment of Actinobacteria and depletion of Firmicutes in GLFS-5 positive individuals. Classification tree analysis identified three terminal nodes as GLFS-5 positive, with one node involving Holdemania. Participants aged \u226570.0 and <78.0 years who did not consume probiotic foods and had \u22650.04% relative abundance of Holdemania were classified as at risk for locomotive syndrome. Our findings suggest a potential association between gut microbiota, particularly higher Holdemania abundance, and locomotive syndrome in older adults. This study provides insights into the complex relationship between gut microbiome composition and musculoskeletal health in aging populations. However, the cross-sectional design limits causal inference.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34045537", + "title": "Identification of mucin degraders of the human gut microbiota.", + "year": 2021, + "journal": "Scientific reports", + "authors": [ + "Raimondi S", + "Musmeci E", + "Candeliere F", + "Amaretti A", + "Rossi M" + ], + "bacteria": "Holdemania", + "condition": "healthy", + "relevance_score": 0.2821006428118108, + "mesh_terms": [ + "Clostridium", + "Enterobacteriaceae", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Mucins" + ], + "raw_abstract": "Mucins are large glycoproteins consisting of approximately 80% of hetero-oligosaccharides. Gut mucin degraders of healthy subjects were investigated, through a culture dependent and independent approach. The faeces of five healthy adults were subjected to three steps of anaerobic enrichment in a medium with sole mucins as carbon and nitrogen sources. The bacterial community was compared before and after the enrichment by 16S rRNA gene profiling. Bacteria capable of fermenting sugars, such as Anaerotruncus, Holdemania, and Enterococcaceae likely took advantage of the carbohydrate chains. Escherichia coli and Enterobacteriaceae, Peptococcales, the Coriobacteriale Eggerthella, and a variety of Clostridia such as Oscillospiraceae, Anaerotruncus, and Lachnoclostridium, significantly increased and likely participated to the degradation of the protein backbone of mucin. The affinity of E. coli and Enterobacteriaceae for mucin may facilitate the access to the gut mucosa, promoting gut barrier damage and triggering systemic inflammatory responses. Only three species of strict anaerobes able to grow on mucin were isolated from the enrichments of five different microbiota: Clostridium disporicum, Clostridium tertium, and Paraclostridium benzoelyticum. The limited number of species isolated confirms that in the gut the degradation of these glycoproteins results from cooperation and cross-feeding among several species exhibiting different metabolic capabilities.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30636111", + "title": "Sex Differences in the Gut Microbiota as Potential Determinants of Gender Predisposition to Disease.", + "year": 2019, + "journal": "Molecular nutrition & food research", + "authors": [ + "Santos-Marcos JA", + "Haro C", + "Vega-Rojas A", + "Alcala-Diaz JF", + "Molina-Abril H", + "Leon-Acu\u00f1a A", + "Lopez-Moreno J", + "Landa BB", + "Tena-Sempere M", + "Perez-Martinez P", + "Lopez-Miranda J", + "Perez-Jimenez F", + "Camargo A" + ], + "bacteria": "Holdemania", + "condition": "healthy", + "relevance_score": 0.2645304260472513, + "mesh_terms": [ + "Cholesterol, HDL", + "Diet, Fat-Restricted", + "Diet, Mediterranean", + "Disease Susceptibility", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metabolic Syndrome", + "Middle Aged", + "Sex Factors" + ], + "raw_abstract": "SCOPE: Dysbiosis of gut microbiota is involved in metabolic syndrome (MetS) development, which has a different incidence between men (M) and women (W). The differences in gut microbiota in MetS patients are explored according to gender, and whether consuming two healthy diets, Mediterranean (MED) and low-fat (LF), may, over time, differentially shape the gut microbiota dysbiosis according to gender is evaluated. MATERIALS AND METHODS: All the women from the CORDIOPREV study whose feces samples were available and a similar number of men, matched by the main metabolic variables (N\u00a0=\u00a0246, 123 women and 123 men), and categorized according to the presence or not of MetS are included. Gut microbiota is analyzed at baseline and after 3 years of dietary intervention. RESULTS: Higher abundance of Collinsella, Alistipes, Anaerotruncus, and Phascolarctobacterium genera is observed in MetS-W than in MetS-M, whereas the abundance of Faecalibacterium and Prevotella genera is higher in MetS-M than in MetS-W. Moreover, higher levels of Desulfovibrio, Roseburia, and Holdemania are observed in men than in women after the consumption of the LF diet. CONCLUSION: The results suggest the potential involvement of differences in gut microbiota in the unequal incidence of metabolic diseases between genders, and a sex-dependent effect on shaping the gut microbiota according to diet.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27999162", + "title": "Complete Microbiota Engraftment Is Not Essential for Recovery from Recurrent Clostridium difficile Infection following Fecal Microbiota Transplantation.", + "year": 2016, + "journal": "mBio", + "authors": [ + "Staley C", + "Kelly CR", + "Brandt LJ", + "Khoruts A", + "Sadowsky MJ" + ], + "bacteria": "Holdemania", + "condition": "healthy", + "relevance_score": 0.23969382645243362, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteroidetes", + "Bayes Theorem", + "Clinical Trials as Topic", + "Clostridioides difficile", + "Clostridium Infections", + "Diarrhea", + "Fecal Microbiota Transplantation", + "Feces", + "Female", + "Firmicutes", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Male", + "Middle Aged", + "Recurrence", + "Remission Induction" + ], + "raw_abstract": "UNLABELLED: Bacterial communities from subjects treated for recurrent Clostridium difficile infection (rCDI) by fecal microbiota transplantation (FMT), using either heterologous donor stool samples or autologous stool samples, were characterized by Illumina next-generation sequencing. As previously reported, the success of heterologous FMT (90%) was superior to that of autologous FMT (43%) (P = 0.019), and post-FMT intestinal bacterial communities differed significantly between treatment arms (P < 0.001). Subjects cured by autologous FMT typically had greater abundances of the Clostridium XIVa clade and Holdemania bacteria prior to treatment, and the relative abundances of these groups increased significantly after FMT compared to heterologous FMT and pre-FMT samples. The typical shift to post-FMT, donor-like assemblages, featuring high relative abundances of genera within the Bacteroidetes and Firmicutes phyla, was not observed in the autologous FMT subjects. Autologous FMT patient bacterial communities were significantly different in composition than those for heterologous FMT patients and donors (P < 0.001). The SourceTracker program, which employs a Bayesian algorithm to determine source contributions to sink communities, showed that patients initially treated by heterologous FMT had significantly higher percentages of engraftment (i.e., similarity to donor communities, mean value of 74%) compared to those who suffered recurrence following autologous FMT (1%) (P \u2264 0.013). The findings of this study suggest that complete donor engraftment may be not necessary if functionally critical taxa are present in subjects following antibiotic therapy. IMPORTANCE: This study provides a detailed characterization of fecal bacterial communities in subjects who participated in a previously published randomized clinical trial to treat recurrent C.\u00a0difficile infection (rCDI). Bacterial communities were characterized to determine differences between subjects who received fecal bacteria either from healthy donor stool samples or their own stool samples as \"placebo\" in order to determine which groups of bacteria were most important in achieving a cure. The results of this study suggested that bacteria associated with secondary bile acid metabolism could potentially provide resistance to infection and that complete transfer of healthy donor microorganisms was not necessary to resolve CDI following unsuccessful antibiotic treatment.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31419351", + "title": "Analysis of the gut microbiota in alopecia areata: identification of bacterial biomarkers.", + "year": 2020, + "journal": "Journal of the European Academy of Dermatology and Venereology : JEADV", + "authors": [ + "Moreno-Arrones OM", + "Serrano-Villar S", + "Perez-Brocal V", + "Saceda-Corralo D", + "Morales-Raya C", + "Rodrigues-Barata R", + "Moya A", + "Jaen-Olasolo P", + "Vano-Galvan S" + ], + "bacteria": "Holdemania", + "condition": "healthy", + "relevance_score": 0.20352533499611564, + "mesh_terms": [ + "Adult", + "Alopecia Areata", + "Biomarkers", + "Cross-Sectional Studies", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged" + ], + "raw_abstract": "BACKGROUND: Alopecia areata is a T-cell-mediated autoimmune disease with an unknown etiopathogenesis. Gut microbiota has been revealed as a key modulator of systemic immunity. OBJECTIVE: To determine whether patients affected by alopecia universalis present differences in gut bacteria composition compared with healthy controls and investigate possible bacterial biomarkers of the disease. METHODS: We conducted a cross-sectional study that involved 15 patients affected by alopecia universalis and 15 controls. Gut microbiome of the study subjects was analysed by sequencing the 16SrRNA of stool samples. We searched for bacterial biomarkers of alopecia universalis using the linear discriminant analysis effect size (LEFse) tool. RESULTS: In total, 30 study subjects (46.6% female; mean [SD] age, 40.1 [9.8] years) were enrolled. Neither alpha (Shannon diversity index 5.31\u00a0\u00b1\u00a00.43 vs. 5.03\u00a0\u00b1\u00a00.43, P 0.1) or beta diversity (ADONIS P value: 0.35) of gut microbiota showed statistically significant differences between cases and controls. In patients affected with alopecia, we found an enriched presence (LDA SCORE\u00a0>\u00a02) of Holdemania filiformis, Erysipelotrichacea, Lachnospiraceae, Parabacteroides johnsonii, Clostridiales vadin BB60 group, Bacteroides eggerthii and Parabacteroides distasonis. A predictive model based on the number of bacterial counts of Parabacteroides distasonis and Clostridiales vadin BB60 group correctly predicted disease status in 80% of patients (AUC 0.804 (0.633-0.976), P 0.004). CONCLUSION: Alopecia universalis does not seem to affect broadly gut microbiota structure. Bacterial biomarkers found associated with the disease (Holdemania filiformis, Erysipelotrichacea, Lachnospiraceae, Parabacteroides johnsonii, Eggerthellaceae, Clostridiales vadin BB60 group, Bacteroides eggerthii and Parabacteroides distasonis) should be further studied as they could be involved in its pathophysiology or be used as diagnostic tools.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37173385", + "title": "Influence of grape consumption on the human microbiome.", + "year": 2023, + "journal": "Scientific reports", + "authors": [ + "Dave A", + "Beyo\u011flu D", + "Park EJ", + "Idle JR", + "Pezzuto JM" + ], + "bacteria": "Holdemania", + "condition": "healthy", + "relevance_score": 0.20211715378969128, + "mesh_terms": [ + "Humans", + "Male", + "Female", + "Young Adult", + "Adult", + "Middle Aged", + "Vitis", + "Diet", + "Microbiota", + "Plasma", + "Metabolomics" + ], + "raw_abstract": "Over the years, a substantial body of information has accumulated suggesting dietary consumption of grapes may have a positive influence on human health. Here, we investigate the potential of grapes to modulate the human microbiome. Microbiome composition as well as urinary and plasma metabolites were sequentially assessed in 29 healthy free-living male (age 24-55\u00a0years) and female subjects (age 29-53\u00a0years) following two-weeks of a restricted diet (Day 15), two-weeks of a restricted diet with grape consumption (equivalent to three servings per day) (Day 30), and four-weeks of restricted diet without grape consumption (Day 60). Based on alpha-diversity indices, grape consumption did not alter the overall composition of the microbial community, other than with the female subset based on the Chao index. Similarly, based on beta-diversity analyses, the diversity of species was not significantly altered at the three time points of the study. However, following 2\u00a0weeks of grape consumption, taxonomic abundance was altered (e.g., decreased Holdemania spp. and increased Streptococcus thermophiles), as were various enzyme levels and KEGG pathways. Further, taxonomic, enzyme and pathway shifts were observed 30\u00a0days following the termination of grape consumption, some of which returned to baseline and some of which suggest a delayed effect of grape consumption. Metabolomic analyses supported the functional significance of these alterations wherein, for example, 2'-deoxyribonic acid, glutaconic acid, and 3-hydroxyphenylacetic acid were elevated following grape consumption and returned to baseline following the washout period. Inter-individual variation was observed and exemplified by analysis of a subgroup of the study population showing unique patterns of taxonomic distribution over the study period. The biological ramifications of these dynamics remain to be defined. However, while it seems clear that grape consumption does not perturb the eubiotic state of the microbiome with normal, healthy human subjects, it is likely that shifts in the intricate interactive networks that result from grape consumption have physiological significance of relevance to grape action.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39574251", + "title": "Fecal Microbiota Transplantation Modulates Gut Microbiome Composition and Glial Signaling in Brain and Colon of Rats with Neuropathic Pain: Evidence for Microbiota-Gut-Brain Axis.", + "year": 2024, + "journal": "The Journal of frailty & aging", + "authors": [ + "Shen CL", + "Deshmukh H", + "Santos JM", + "Elmassry MM", + "Presto P", + "Driver Z", + "Bhakta V", + "Yakhnitsa V", + "Kiritoshi T", + "Ji G", + "Lovett J", + "Hamood A", + "Neugebauer V" + ], + "bacteria": "Victivallis", + "condition": "healthy", + "relevance_score": 0.29454732792673566, + "mesh_terms": [ + "Animals", + "Gastrointestinal Microbiome", + "Fecal Microbiota Transplantation", + "Neuralgia", + "Rats", + "Male", + "Brain-Gut Axis", + "Neuroglia", + "Colon", + "Brain", + "Rats, Sprague-Dawley", + "Disease Models, Animal", + "Signal Transduction" + ], + "raw_abstract": "Despite evidence linking the gut microbiome to neuropathic pain (NP), it is not known if altering gut microbiota can alleviate NP via the microbiome-gut-brain axis. This study examined if healthy gut microbiota of sham male rats (Sham+V) and dysbiotic gut microbiota of NP rats (spinal nerve ligation: NP, SNL+V) can be disrupted and restored, respectively, via fecal microbiota transplant (FMT) from the opposite group [Sham+(SNL-FMT) and SNL+(Sham-FMT), respectively]. All groups received FMT daily for two weeks, followed by three weeks without FMT. SNL rats showed higher mechanical hypersensitivity [SNL+V vs. Sham+V] throughout the study. After two weeks, the FMT of healthy gut microbiota decreased mechanical hypersensitivity in SNL rats [SNL+(Sham-FMT) vs. SNL+V]. A temporal shift in microbiome profiles after 2-week FMT treatment was observed in Sham+(SNL-FMT) and SNL+(Sham-FMT) groups, while the microbiome profile shifted back a certain extent after FMT ceased. At the end of study, the Sham+(SNL-FMT) group acquired low abundance of UCG-001, Odoribacter, and Peptococcaceae, and high abundance of UBA1819 and Victivallis. The SNL+(Sham-FMT) group maintained high abundance of Butyricimonas and Escherichia-Shigella. The SNL+(Sham-FMT) group had altered glial and macrophage activation/inflammation markers in the brain/colon than the SNL+V group. Relative to the SNL+V group, the SNL+(Sham-FMT) group had significantly lower gene expressions of GFAP (hypothalamus), IBA-1 (colon), and NF-\u03baB (amygdala/colon), but higher gene expressions of complex I (amygdala/hypothalamus) and claudin-3 (amygdala/hypothalamus/colon). In conclusion, FMT containing healthy microbiota given to SNL rats attenuates mechanical hypersensitivity, modulates microbiota composition, and mitigates downstream glial activation/inflammation markers in a NP model.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37500743", + "title": "Alterations of gut microbiota in biopsy-proven diabetic nephropathy and a long history of diabetes without kidney damage.", + "year": 2023, + "journal": "Scientific reports", + "authors": [ + "Lu X", + "Ma J", + "Li R" + ], + "bacteria": "Eisenbergiella", + "condition": "healthy", + "relevance_score": 0.4565157888106449, + "mesh_terms": [ + "Humans", + "Diabetic Nephropathies", + "Gastrointestinal Microbiome", + "Diabetes Mellitus, Type 2", + "Kidney", + "Bacteria", + "Biopsy" + ], + "raw_abstract": "The gut microbiota is closely related to parenteral noncommunicable diseases through intestinal immunity and plays an important role in the occurrence of diabetes and diabetic nephropathy. The aim of the study was to understand the gut-kidney axis by an analysis of gut microbiota composition among patients with biopsy-proven diabetic nephropathy (DN), patients with type 2 diabetes for more than 10 years without kidney damage (DM), and healthy controls (NC). Thirty-five DN patients, 40 DM patients and 40 healthy subjects matched by age and sex were enrolled between January 2022 and December 2022. Baseline information and clinical parameters were collected. 16S rDNA sequencing was performed to characterize the gut microbiome and identify gut microbes that were differentially abundant between patients and healthy controls. The relationship between the relative abundance of specific bacterial taxa in the gut and clinical phenotype and pathological indicators was evaluated. Substantial differences were found in the richness of the gut microbiota and the variation in the bacterial population among DN patients, DM patients and healthy controls. DM patients could be accurately distinguished from age- and sex-matched healthy controls by variations in g_Clostridium-XVIII (AUC\u2009=\u20090.929), and DN patients could be accurately distinguished from age- and sex-matched healthy controls by variations in g_Gemmiger (AUC\u2009=\u20090.842). DN patients could be accurately distinguished from age- and sex-matched DM patients by variations in g_Flavonifractor or g_Eisenbergiella (AUC\u2009=\u20090.909 and 0.886, respectively). The gut microbiota was also closely related to clinical phenotypes and pathological indicators. The study of gut microbiota composition was explored to determine its relationship to the occurrence of DN and a long history of diabetes without kidney damage. The renal pathological progression of DN may be delayed by regulating changes in the gut microbiota.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38782999", + "title": "Uncovering the characteristics of the gut microbiota in patients with ischemic stroke and hemorrhagic stroke.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Chen YZ", + "Huang ZY", + "Zhou WW", + "Li ZY", + "Li XP", + "Chen SS", + "Ma JK" + ], + "bacteria": "Eisenbergiella", + "condition": "healthy", + "relevance_score": 0.3528206515139304, + "mesh_terms": [ + "Gastrointestinal Microbiome", + "Humans", + "Ischemic Stroke", + "Male", + "Hemorrhagic Stroke", + "Female", + "Case-Control Studies", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Aged", + "Bacteria", + "High-Throughput Nucleotide Sequencing" + ], + "raw_abstract": "This study aimed to explore the gut microbiota characteristics of ischemic and hemorrhagic stroke patients. A case-control study was conducted, and high-throughput sequencing of the V4-V5 region of 16S rRNA was used to analyze the differences in gut microbiota. The results showed that Proteobacteria was significantly increased in the ischemic stroke group compared with the healthy control group, while Fusobacteria was significantly increased in the hemorrhagic stroke group. In the ischemic stroke group, Butyricimonas, Alloprevotella, and Escherichia were significantly more abundant than in the healthy control group. In the hemorrhagic stroke group, Atopobium, Hungatella, Eisenbergiella, Butyricimonas, Odonbacter, Lachnociostridium, Alistipes, Parabacteroides, and Fusobacterium were significantly more abundant than in the healthy control group. Additionally, Alloprevotella, Ruminococcus, and Prevotella were significantly more abundant in the ischemic stroke group than in the hemorrhagic stroke group. The gut microbiota of ischemic and hemorrhagic stroke patients has significant diversity characteristics. These results provide new theoretical basis for exploring the prevention and treatment of different types of stroke through gut microbiota research.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36113426", + "title": "Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course.", + "year": 2022, + "journal": "Cell", + "authors": [], + "bacteria": "Eisenbergiella", + "condition": "healthy", + "relevance_score": 0.3208181431713567, + "mesh_terms": [ + "Fatty Acids, Volatile", + "Gastrointestinal Microbiome", + "Humans", + "Interferon-beta", + "Multiple Sclerosis", + "Phytic Acid", + "Pyruvates" + ], + "raw_abstract": "Changes in gut microbiota have been associated with several diseases. Here, the International Multiple Sclerosis Microbiome Study (iMSMS) studied the gut microbiome of 576 MS patients (36% untreated) and genetically unrelated household healthy controls (1,152 total subjects). We observed a significantly increased proportion of Akkermansia muciniphila, Ruthenibacterium lactatiformans, Hungatella hathewayi, and Eisenbergiella tayi and decreased Faecalibacterium prausnitzii and Blautia species. The phytate degradation pathway was over-represented in untreated MS, while pyruvate-producing carbohydrate metabolism pathways were significantly reduced. Microbiome composition, function, and derived metabolites also differed in response to disease-modifying treatments. The therapeutic activity of interferon-\u03b2 may in part be associated with upregulation of short-chain fatty acid transporters. Distinct microbial networks were observed in untreated MS and healthy controls. These results strongly support specific gut microbiome associations with MS risk, course and progression, and functional changes in response to treatment.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32873292", + "title": "Gut microbial characteristics of adult patients with allergy rhinitis.", + "year": 2020, + "journal": "Microbial cell factories", + "authors": [ + "Zhu L", + "Xu F", + "Wan W", + "Yu B", + "Tang L", + "Yang Y", + "Du Y", + "Chen Z", + "Xu H" + ], + "bacteria": "Eisenbergiella", + "condition": "healthy", + "relevance_score": 0.25404229214013474, + "mesh_terms": [ + "Adult", + "Biodiversity", + "China", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Genome, Bacterial", + "Humans", + "Male", + "Metagenome", + "Quality of Life", + "RNA, Ribosomal, 16S", + "Rhinitis, Allergic", + "Severity of Illness Index", + "Surveys and Questionnaires", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Although recent studies have indicated that intestinal microbiota dweller are involved in the pathogenesis of allergy rhinitis (AR), the influence of gut microbiota on AR adult has not been fully elucidated yet. Hence, we carried out this study to uncover the distinctive bacterial taxa that differentiate allergy rhinitis patients from healthy individuals. Feces samples from thirty three AR patients and thirty one healthy individuals were analyzed by 16S rRNA gene sequencing. RESULTS: Results showed that the bacterial diversity in AR group was significantly higher than that of the non-AR group. Bacterial communities between AR and non-AR group were significantly differentiated as revealed by Principal coordinates analysis (PCoA) and the variation within non-AR were higher than that of the counterpart. Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria and Chloroflexi were the significantly differed phyla taxa and the top significantly distinguished bacterial genus included Prevotella_9, Phascolarctobacterium, Roseburia, Megamonas, Alistipes, Lachnoclostridium and Fusobacterium. The higher network complexity in AR group were dominated by taxa belonging to Firmicutes. The predicted function, alpha linolenic acid metabolism and bacterial invasion of epithelial cells pathway were higher in non-AR group while gonadotropin-releasing hormone (GnRH) signaling pathway, Fc \u03b3-R mediated phagocytosis and endocytosis were higher in AR patients. Although the bacterial diversity between moderate and severe AR patients showed no significant difference, the significant correlation between featured genus and total nasal symptom score or rhinoconjunctivitis quality of life questionnaire, such as Butyricicoccus and Eisenbergiella, revealed the potential to intervene the AR status by means of gut microbiota. CONCLUSIONS: In conclusion, patients with allergy rhinitis had distinguished gut microbiota characteritics in comparison with healthy controls. The results suggest that gut microbiota might play crucial roles in influencing the course and different symptoms of AR. Trial registration ChiCTR, ChiCTR1900028613. Registered 29 December 2019, https://www.chictr.org.cn/showproj.aspx?proj=47650 .", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32508748", + "title": "Characteristics of the Urinary Microbiome From Patients With Gout: A Prospective Study.", + "year": 2020, + "journal": "Frontiers in endocrinology", + "authors": [ + "Ning Y", + "Yang G", + "Chen Y", + "Zhao X", + "Qian H", + "Liu Y", + "Chen S", + "Shi G" + ], + "bacteria": "Finegoldia", + "condition": "healthy", + "relevance_score": 0.343524292826313, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biomarkers", + "Case-Control Studies", + "DNA, Bacterial", + "Follow-Up Studies", + "Gout", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Prognosis", + "Prospective Studies", + "RNA, Ribosomal, 16S", + "Urine" + ], + "raw_abstract": "The role of host microbes in the pathogenesis of several diseases has been established, and altered microbiomes have been related to diseases. However, the variability of the urinary microbiome in individuals with gout has not been evaluated to date. Therefore, we conducted the present prospective study to characterize the urinary microbiome and its potential relation to gout. Urine samples from 30 patients with gout and 30 healthy controls were analyzed by Illumina MiSeq sequencing of the 16S rRNA hypervariable regions, and the microbiomes were compared according to alpha-diversity indices, complexity (beta diversity) with principal component analysis, and composition with linear discriminant analysis effect size. The most significantly different taxa at the phylum and genus levels were identified, and their potential as biomarkers for discriminating gout patients was assessed based on receiver operating characteristic (ROC) curve analysis. Compared with the healthy controls, there was a dramatic decrease in microbial richness and diversity in the urine of gout patients. The phylum Firmicutes and its derivatives (Lactobacillus_iners, Family_XI, and Finegoldia), the phylum Actinobacteria and its derivatives (unidentified_Actinobacteria, Corynebacteriales, Corynebacteriale, Corynebacterium_1, and Corynebacterium_tuberculostearicum), and the genera", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32327694", + "title": "Potential Pathogenic Bacteria in Seminal Microbiota of Patients with Different Types of Dysspermatism.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Yang H", + "Zhang J", + "Xue Z", + "Zhao C", + "Lei L", + "Wen Y", + "Dong Y", + "Yang J", + "Zhang L" + ], + "bacteria": "Finegoldia", + "condition": "healthy", + "relevance_score": 0.3214002956392608, + "mesh_terms": [ + "Adult", + "Asthenozoospermia", + "Bacteria", + "Biodiversity", + "Biomarkers", + "Case-Control Studies", + "Discriminant Analysis", + "Humans", + "Infertility, Male", + "Male", + "Metagenome", + "Microbiota", + "Oligospermia", + "Phylogeny", + "Principal Component Analysis", + "Semen" + ], + "raw_abstract": "Human microbiota play an important role in the health of their human hosts. Recent studies have demonstrated that microbiota exist in seminal plasma. The current study aims to elucidate whether seminal microbiota exist in patients with different types of dysspermatism and whether bacterial biomarkers can be identified for them. A total of 159 study participants were recruited, including 22 patients with oligoasthenospermia, 58 patients with asthenospermia, 8 patients with azoospermia, 13 patients with oligospermia, and 58 matched healthy controls. Seminal microbiota composition was analyzed using 16S rRNA gene-based sequencing. The results showed that the composition of seminal microbiota of patients with dysspermatism differed from those of healthy controls. Comparison of the microbiota composition in semen samples from patients with different types of dysspermatism showed that microbiota in patients with asthenospermia and oligoasthenospermia were distinct from healthy controls in beta diversity (P\u2009<\u20090.05). Characteristic biomarkers, including Ureaplasma, Bacteroides, Anaerococcus, Finegoldia, Lactobacillus and Acinetobacter lwoffii, were identified based on LEfSe analysis. Inferred functional analysis based on seminal microbiome data further indicated the presence of potential pathogenic biomarkers in patients with asthenospermia and oligoasthenospermia. These results provided profiles of seminal microbiota exhibited in different types of dysspermatism, thus providing new insights into their pathogenesis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34364884", + "title": "Altered Skin and Gut Microbiome in Hidradenitis Suppurativa.", + "year": 2022, + "journal": "The Journal of investigative dermatology", + "authors": [ + "McCarthy S", + "Barrett M", + "Kirthi S", + "Pellanda P", + "Vlckova K", + "Tobin AM", + "Murphy M", + "Shanahan F", + "O'Toole PW" + ], + "bacteria": "Finegoldia", + "condition": "healthy", + "relevance_score": 0.22463768739705917, + "mesh_terms": [ + "Adult", + "Aged", + "Case-Control Studies", + "Clostridiales", + "Extracellular Traps", + "Fecal Microbiota Transplantation", + "Feces", + "Female", + "Firmicutes", + "Gastrointestinal Microbiome", + "Hidradenitis Suppurativa", + "Humans", + "Male", + "Middle Aged", + "Skin", + "Young Adult" + ], + "raw_abstract": "Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease characterized by the formation of nodules, abscesses, and fistulae at intertriginous sites. The skin-gut axis is an area of emerging research in inflammatory skin disease and is a potential contributory factor to the pathogenesis of HS. A total of 59 patients with HS provided fecal samples and nasal and skin swabs of affected sites for analysis. A total of 30 healthy controls provided fecal samples, and 20 healthy controls provided nasal and skin swabs. We performed bacterial 16S ribosomal RNA gene amplicon sequencing on total DNA derived from the samples. Microbiome alpha diversity was significantly lower in the fecal, skin, and nasal samples of individuals with HS, which may be secondary to disease biology or related to antibiotic usage. Ruminococcus gnavus was more abundant in the fecal microbiome of individuals with HS, which is also reported in Crohn's disease, suggesting comorbidity due to shared gut microbiota alterations. Finegoldia magna was overabundant in HS skin samples relative to that in the healthy controls. It is possible that local inflammation is driven by F.\u00a0magna by promoting the formation of neutrophil extracellular traps. These alterations in both the gut and skin microbiome in HS warrant further exploration, and therapeutic strategies, including fecal microbiota transplant or bacteriotherapy, could be of benefit.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36557565", + "title": "Microbiome in Male Genital Mucosa (Prepuce, Glans, and Coronal Sulcus): A Systematic Review.", + "year": 2022, + "journal": "Microorganisms", + "authors": [ + "Gon\u00e7alves MFM", + "Fernandes \u00c2R", + "Rodrigues AG", + "Lisboa C" + ], + "bacteria": "Finegoldia", + "condition": "healthy", + "relevance_score": 0.21581993509703956, + "mesh_terms": [], + "raw_abstract": "The human body represents a complex and diverse reservoir of microorganisms. Although the human microbiome remains poorly characterized and understood, it should not be underestimated, since recent studies have highlighted its importance in health. This is especially evident when considering microbiota in the male reproductive system, responsible for men\u2019s fertility and sexual behavior. Therefore, the aim of this systematic review is to provide an overview of the microbial communities of the healthy male genital mucosa and its role in disease. This study was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The search was limited to the English language and studies published until August 2022 that included culture-independent techniques for microbiome characterization in male genital mucosa. Ten articles were included. The bacterial composition of the male genital mucosa consists of several genera including Prevotella, Finegoldia, Peptoniphilus, Staphylococcus, Corynebacterium, and Anaerococcus, suggesting that the male genital microbiome composition shows similarities with the adjacent anatomical sites and is related with sexual intercourse. Moreover, male circumcision appears to influence the penile microbiome. Despite the lack of knowledge on the male genital mucosa microbiome in disease, it was reported that Staphylococcus warneri and Prevotella bivia were associated with balanoposthitis, whereas Enterobacteriaceae, Prevotella, and Fusobacterium were more abundant in male genital lichen sclerosus. The limited data and paucity of prospective controlled studies highlight the need for additional studies and established criteria for sampling methods and the microbiome assay procedure. Such a consensus would foster the knowledge about the composition of the genital microbiome of healthy males and its role in disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "25881534", + "title": "A rarely seen cause for empyema: Leuconostoc mesentero\u0131des.", + "year": 2015, + "journal": "Journal of infection in developing countries", + "authors": [ + "Usta-Atmaca H", + "Akbas F", + "Karagoz Y", + "Piskinpasa ME" + ], + "bacteria": "Leuconostoc", + "condition": "healthy", + "relevance_score": 0.5742213916962715, + "mesh_terms": [ + "Empyema, Pleural", + "Humans", + "Leuconostoc", + "Male", + "Middle Aged", + "Occupational Exposure", + "Radiography, Thoracic", + "Skin Diseases, Bacterial" + ], + "raw_abstract": "Leuconostoc species are Gram-positive, non-motile, vancomycin-resistant bacteria placed within the family of Streptococcaceae. They naturally exist in food and are important in the sauerkraut, milk and wine industries due to their role in fermentation. Infections caused by Leuconostocs are generally reported in immunosuppressed patients with an underlying disease, or in those who were previously treated with vancomycin. Central venous catheter insertion is also a risk factor for introducing bacteria into the body. Although they are resistant to vancomycin, leuconostocs are sensitive to erythromycin and clindamycin. Here, we report a case with pleural empyema due to Leuconostoc mesenteroides in an otherwise healthy person whose occupation is known to be selling pickles.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30683056", + "title": "The respiratory microbiota: new insights into pulmonary tuberculosis.", + "year": 2019, + "journal": "BMC infectious diseases", + "authors": [ + "Eshetie S", + "van Soolingen D" + ], + "bacteria": "Leuconostoc", + "condition": "healthy", + "relevance_score": 0.5677376070120949, + "mesh_terms": [ + "Bacteria", + "Humans", + "Microbiota", + "Respiratory System", + "Tuberculosis, Pulmonary" + ], + "raw_abstract": "BACKGROUND: Previous studies demonstrated that the diversity and composition of respiratory microbiota in TB patients were different from healthy individuals. Therefore, the aim of the present analysis was to estimate the relative proportion of respiratory microbiota at phylum and genus levels among TB cases and healthy controls. METHODS: The PubMed and Google Scholar online databases were searched to retrieve relevant studies for the analysis. The statistical analysis was done using STATA version 11, pooled estimates are presented using graphs. The summary of findings in included studies is also presented in Table 1. RESULTS: The phylum level analysis shows that the pooled proportions of Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Crenarchaeota were determined among tuberculosis patients and healthy controls. In brief, Firmicutes, and Proteobacteria were the most abundant bacterial phyla in both TB cases and healthy controls, composing 39.9 and 22.7% in TB cases and 39.4 and 19.5% in healthy controls, respectively. The genus level analysis noted that Streptococcus (35.01%), Neisseria (27.1%), Prevotella (9.02%) and Veillonella (7.8%) were abundant in TB patients. The Prevotella (36.9%), Gammaproteobacteria (22%), Streptococcus (19.2%) and Haemophilus (15.4%) were largely seen in healthy controls. Interestingly, Veillonella, Rothia, Leuconostoc were unique to TB cases, whereas Lactobacillus, and Gammaproteobacteria, Haemophilus, and Actinobacillus were identified only in healthy controls. CONCLUSION: The composition of the respiratory microbiota in TB patients and healthy controls were quite different. More deep sequencing studies are needed to explore the microbial variation in the respiratory system in connection with TB.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36695274", + "title": "Composition of the gut microbiota in patients with inflammatory bowel disease in Saudi Arabia: A pilot study.", + "year": 2023, + "journal": "Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association", + "authors": [ + "Al-Amrah H", + "Saadah OI", + "Mosli M", + "Annese V", + "Al-Hindi R", + "Edris S", + "Alshehri D", + "Alatawi H", + "Alatawy M", + "Bahieldin A" + ], + "bacteria": "Leuconostoc", + "condition": "healthy", + "relevance_score": 0.5116679814796394, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Pilot Projects", + "Saudi Arabia", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Feces" + ], + "raw_abstract": "CONCLUSIONS: The results of this study provide an overview of the variations in microbiota diversity present in Saudi IBD patients compared to healthy controls. RESULTS: The key finding was three negative bacterial biomarkers, Paraprevotellaceae, the Muribaculaceae families of Bacteroidetes phylum, and the Leuconostocaceae family of Firmicutes phylum, which had a higher relative abundance in healthy individuals compared to IBD patients. It was also found that primary microbiota signatures at certain genera and species levels, including Prevotella copri, Bifidobacterium adolescentis, Ruminococcus callidus, Coprococcus sp., Ruminococcus gnavus, Dorea formicigenerans, Leuconostoc, Dialister, Catenibacterium, Eubacterium biforme, and Lactobacillus mucosae, were absent in almost all IBD patients, while Veillonella dispar was absent in all healthy individuals. METHODS: After obtaining an informed consent, fecal samples were collected from 11 participants with IBD (patients) and 10 healthy individuals (controls). The bacterial components of the microbial population were identified by next-generation sequencing of partial 16S rRNA. Statistically significant dissimilarities were observed between samples for all metrics. BACKGROUND: Inflammatory bowel disease (IBD) is a chronic intestinal inflammatory condition attributed to a complex interaction between imbalances in the gut microbiome, environmental conditions, and a deregulated immune response. The aim of the study was to investigate the composition of the gut microbiome of Saudi patients with IBD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32388491", + "title": "Gut microbiome alterations in patients with wheat-dependent exercise-induced anaphylaxis.", + "year": 2020, + "journal": "International immunopharmacology", + "authors": [ + "Du Z", + "Gao X", + "Yin J" + ], + "bacteria": "Leuconostoc", + "condition": "healthy", + "relevance_score": 0.2681333194622995, + "mesh_terms": [ + "Adolescent", + "Adult", + "Anaphylaxis", + "Bacteria", + "Exercise", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gliadin", + "Glutens", + "Humans", + "Immunoglobulin E", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Triticum", + "Wheat Hypersensitivity", + "Young Adult" + ], + "raw_abstract": "The intestinal microbiota plays a critical role in food allergy development. However, little is known regarding the structure and composition of the intestinal microbiota in patients with wheat-dependent exercise-induced anaphylaxis (WDEIA). We examined the gut microbiota alterations in patients with WDEIA and the microbiota's association with WDEIA. Fecal samples were collected from 25 patients with WDEIA and 25 healthy controls. Environmental exposure factors were obtained, serum total IgE, IgE specific to wheat, gluten, and \u03c9-5 gliadin were measured. Fecal samples were profiled using 16S rRNA gene sequencing. The relative abundances of the bacterial genera Blautia (P\u00a0<\u00a00.05), Erysipelatoclostridium (P\u00a0<\u00a00.01), Akkermansia (P\u00a0<\u00a00.05) and Lachnospiraceae_NK4A136_group (P\u00a0<\u00a00.05) were significantly increased, while those of Lactobacillus (P\u00a0=\u00a00.001) and Dialister (P\u00a0<\u00a00.05) were significantly decreased in subjects with WDEIA. The microbial diversity did not differ between WDEIA patients and healthy controls. IgE specific to \u03c9-5 gliadin was positively associated with the Oscillospira (r\u00a0=\u00a00.48, P\u00a0<\u00a00.05) and negatively associated with Leuconostoc (r\u00a0=\u00a0-0.49, P\u00a0<\u00a00.05). Total IgE levels were significantly negatively correlated with Bifidobacterium (P\u00a0<\u00a00.05). The gut microbiome compositions in WDEIA patients differed from those of healthy controls. We identified a potential association between the gut microbiome and WDEIA development. Our findings may suggest new methods for preventing and treating WDEIA.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34671923", + "title": "Isolation and Identification of Potential Probiotic Bacteria from Human Milk.", + "year": 2023, + "journal": "Probiotics and antimicrobial proteins", + "authors": [ + "Damaceno QS", + "Gallotti B", + "Reis IMM", + "Totte YCP", + "Assis GB", + "Figueiredo HC", + "Silva TF", + "Azevedo V", + "Nicoli JR", + "Martins FS" + ], + "bacteria": "Leuconostoc", + "condition": "healthy", + "relevance_score": 0.22124176803075818, + "mesh_terms": [ + "Infant", + "Female", + "Pregnancy", + "Humans", + "Animals", + "Mice", + "Milk, Human", + "Bifidobacterium", + "Bacteria", + "Colostrum", + "Probiotics" + ], + "raw_abstract": "Breast milk was long considered a sterile environment, but now it is known to harbor many bacteria that will shape the newborn microbiota. The benefits of breastfeeding to newborn health are, on some level, related to the presence of beneficial bacteria in human milk. Therefore, this study aims to investigate and isolate potential probiotics present in human milk that might be associated with improved health in infants, being potential candidates to be used in simulated human milk formula. Milk samples of 24 healthy mothers were collected at three time points: 30\u00a0min (colostrum), 5-9\u00a0days (transitional milk), and 25-30\u00a0days (mature milk) postpartum. Samples were evaluated by culturing, and the isolated bacteria were identified by MALDI-TOF MS and 16S DNA sequencing. In vitro screening for probiotics properties was performed, and the potential probiotics were mono-associated with germ-free mice to evaluate their ability to colonize the gastrointestinal tract. The microorganisms were submitted to the spray-drying process to check their viability for a potential simulated milk formula production. Seventy-seven bacteria were isolated from breast milk pertaining to four bacterial genera (Staphylococcus, Streptococcus, Leuconostoc, and Lacticaseibacillus). Four potential probiotics were selected: Lacticaseibacillus rhamnosus (n\u2009=\u20092) and Leuconostoc mesenteroides (n\u2009=\u20092). Isolates were able to colonize the gastrointestinal tract of germ-free mice and remained viable after the spray-drying process. In conclusion, breast milk harbors a unique microbiota with beneficial microorganisms that will impact the newborn gut colonization, being an essential source of probiotic candidates to be used in a formula of simulated maternal milk.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33646379", + "title": "Diversity and Composition of Gut Bacterial Community in Giant Panda with Anorexia.", + "year": 2021, + "journal": "Current microbiology", + "authors": [ + "Zhao S", + "Li C", + "Zhu T", + "Jin L", + "Deng W", + "Zhao K", + "He Y", + "Li G", + "Xiong Y", + "Li T", + "Li B", + "Huang Y", + "Zhang H", + "Zou L" + ], + "bacteria": "Leuconostoc", + "condition": "healthy", + "relevance_score": 0.21269316898023186, + "mesh_terms": [ + "Animals", + "Anorexia", + "China", + "Feces", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Ursidae" + ], + "raw_abstract": "The giant panda (GP) is the most precious animal in China. Gastrointestinal tract disease, especially associated with dysbiosis of gut microbiota, is the leading cause of death in GPs. Here, we performed 16S rRNA high-throughput sequencing to investigate the gut microbiota of GPs having symptoms of anorexia. Results showed that gut microbiota of GP with anorexia had lower richness (Chao1 index) than the healthy GP. However, no significant differences in alpha diversity were observed. There is a significance in the microbial structure between anorexia and healthy GPs. The abundance of phylum Firmicutes (99.23%\u2009\u00b1\u20097.1%), unidentified genus Clostridiales (24.75%\u2009\u00b1\u20092.5%), was significantly higher in the subadult anorexia group (P\u2009<\u20090.01), and that of the unidentified genus Clostridiales (4.53%\u2009\u00b1\u20091.2%) was also significantly higher in the adult anorexia group (P\u2009<\u20090.01). Weissella and Streptococcus were found to be decreased in both anorexia groups. The decreased abundance of Weissella (0.02%\u2009\u00b1\u20090.0%, 0.08%\u2009\u00b1\u20090.0%) and Streptococcus (73.89%\u2009\u00b1\u20094.3%, 91.15%\u2009\u00b1\u20097.6%) and increase in Clostridium may cause symptoms of anorexia in giant pandas. The correlation analysis indicated that there is a symbiotic relationship among Streptococcus, Leuconostoc, Weissella, and Bacillus which are classified as probiotics (r\u2009>\u20090.6, P\u2009<\u20090.05). Importantly, a negative correlation has been found between Streptococcus and unidentified_Clostridium in two groups (r\u2009>\u20090.6, P\u2009<\u20090.05). Our results suggested that Streptococcus might be used as probiotics to control the growth of Clostridium causing the anorexia.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35439925", + "title": "Amplicon-based sequencing and co-occurence network analysis reveals notable differences of microbial community structure in healthy and dandruff scalps.", + "year": 2022, + "journal": "BMC genomics", + "authors": [ + "Wang L", + "Yu T", + "Zhu Y", + "Luo Y", + "Dong F", + "Lin X", + "Zhao W", + "He Z", + "Hu S", + "Dong Z" + ], + "bacteria": "Pediococcus", + "condition": "healthy", + "relevance_score": 0.4567499838239504, + "mesh_terms": [ + "Bacteria", + "Dandruff", + "Fungi", + "Humans", + "Microbiota", + "Scalp" + ], + "raw_abstract": "BACKGROUND: Dandruff is a chronic, recurring, and common scalp problem that is caused by several etiopathogeneses with complex mechanisms. Management of this condition is typically achieved via antifungal therapies. However, the precise roles played by microbiota in the development of the condition have not been elucidated. Despite their omnipresence on human scalp little is known about the co-occurrence/co-exclusion network of cutaneous microbiota. RESULTS: We characterized the scalp and hair surface bacterial and fungal communities of 95 dandruff-afflicted and healthy individuals residing in China. The degree distributions of co-occurrence/co-exclusion network in fungi-bacteria and bacteria-bacteria were higher in the healthy group (P\u2009<\u20090.0001), whereas the betweenness values are higher in the dandruff group (P\u2009<\u20090.01). Meanwhile, the co-occurrence/co-exclusion network among fungi-fungi and fungi-bacteria showed that compared to the healthy group, the dandruff group had more positive links (P\u2009<\u20090.0001). In addition, we observed that Malassezia slooffiae, Malassezia japonica and Malassezia furfur, were more abundant in the dandruff group than in the healthy group. These microbiota were co-exclusion by either multiple bacterial genera or Malassezia sp. in healthy group. The lactic acid bacteria on the scalp and hair surface, especially the genera Lactobacillus and Lactococcus, exhibit a negative correlation with multiple bacterial genera on the scalp and hair surface. Lactobacillus plantarum and Pediococcus lactis isolated on the healthy human scalp can inhibit the growth of Staphylococcus epidermidis in vitro. CONCLUSIONS: We showed that microbial networks on scalp and hair surface with dandruff were less integrated than their healthy counterparts, with lower node degree and more positive and stronger links which were deemed to be unstable and may be more susceptible to environmental fluctuations. Lactobacillus bacteria have extensive interactions with other bacteria or fungi in the scalp and hair surface micro-ecological network and can be used as targets for improving scalp health.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37821210", + "title": "Comparison of intestinal microbes and metabolites in active VKH versus acute anterior uveitis associated with ankylosing spondylitis.", + "year": 2025, + "journal": "The British journal of ophthalmology", + "authors": [ + "Li M", + "Liu M", + "Wang X", + "Wei H", + "Jin S", + "Liu X" + ], + "bacteria": "Pediococcus", + "condition": "healthy", + "relevance_score": 0.22762929284032468, + "mesh_terms": [ + "Humans", + "Uveitis, Anterior", + "Female", + "Male", + "Adult", + "Gastrointestinal Microbiome", + "Uveomeningoencephalitic Syndrome", + "Middle Aged", + "Spondylitis, Ankylosing", + "Acute Disease", + "Tandem Mass Spectrometry", + "Bacteria", + "Chromatography, Liquid", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: It has been reported that the gut microbiome is involved in the pathogenesis of uveitis, but the specific pathogenic microbes and metabolites in different types of uveitis are still unclear. METHODS: Microbiome and metabolites were detected using 16S ribosomal DNA and LC\u2012MS/MS (liquid chromatography tandem mass spectrometry) in 45 individuals, including 16 patients with Vogt Koyanagi Harada (VKH), 11 patients with acute anterior uveitis (AAU) and 18 healthy controls. RESULT: The diversity of intestinal microbes among the VKH, AAU and control groups was not significantly different. Thirteen specific microbes and 38 metabolites were detected in the VKH group, and 7 metabolites (vanillin, erythro-isoleucine, pyrimidine, 1-aminocyclopropanecarboxylic acid, beta-tocopherol, (-)-gallocatechin and N1-methyl-4-pyridone-3-carboxamide) significantly changed only in patients with VKH, which mainly acted on nicotinamide and nicotinamide metabolism and biotin metabolism (p<0.05). Compared with the VKH group, the AAU group had milder intestinal changes. Only 11 specific microbes and 29 metabolites changed in the AAU group, while these metabolites were not specific (p<0.05). These metabolites mainly acted on arachidonic acid metabolism. In addition, three microbes and two metabolites had the same changes in the VKH and AAU groups (p<0.05). Multiple correlations were found between gut microbes and metabolites in the VKH and AAU groups. Six microbes (Pediococcus, Pseudomonas, Rhodococcus, Photobacterium, Gardnerella and Lawsonia) and two metabolites (pyrimidine and gallocatechin) as biomarkers could effectively distinguish patients with VKH from patients with AAU and healthy individuals, with AUC (area under the curve) values greater than 82%. Four microbes (Lentilactobacillus, Lachnospiraceae_UCG-010, Cetobacterium, Liquorilactobacillus) could distinguish patients with AAU from patients with VKH and healthy controls with AUC>76%. CONCLUSION: Significant differences in intestinal microbes and metabolites suggest their different roles in the pathogenesis of uveitis entities. Changes in the metabolism of certain B vitamins may be involved in the pathogenesis of VKH.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39895074", + "title": "Characteristics of skin microbiome associated with disease severity in systemic sclerosis.", + "year": 2025, + "journal": "Journal of microbiology (Seoul, Korea)", + "authors": [ + "Lee KA", + "Ul-Haq A", + "Seo H", + "Jo S", + "Kim S", + "Song HY", + "Kim HS" + ], + "bacteria": "Pediococcus", + "condition": "healthy", + "relevance_score": 0.2051235305965815, + "mesh_terms": [ + "Humans", + "Scleroderma, Systemic", + "Skin", + "Microbiota", + "Female", + "Middle Aged", + "Male", + "RNA, Ribosomal, 16S", + "Adult", + "Bacteria", + "Severity of Illness Index", + "Aged", + "Biomarkers", + "Metagenomics" + ], + "raw_abstract": "Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (\u2265 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38509359", + "title": "A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche.", + "year": 2024, + "journal": "Nature", + "authors": [ + "Zepeda-Rivera M", + "Minot SS", + "Bouzek H", + "Wu H", + "Blanco-M\u00edguez A", + "Manghi P", + "Jones DS", + "LaCourse KD", + "Wu Y", + "McMahon EF", + "Park SN", + "Lim YK", + "Kempchinsky AG", + "Willis AD", + "Cotton SL", + "Yost SC", + "Sicinska E", + "Kook JK", + "Dewhirst FE", + "Segata N", + "Bullman S", + "Johnston CD" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.7820740557503907, + "mesh_terms": [ + "Animals", + "Humans", + "Mice", + "Adenoma", + "Case-Control Studies", + "Colorectal Neoplasms", + "Feces", + "Fusobacterium nucleatum", + "Gastrointestinal Tract", + "Genome, Bacterial", + "Mouth", + "Female" + ], + "raw_abstract": "Fusobacterium nucleatum (Fn), a bacterium present in the human oral cavity and rarely found in the lower gastrointestinal tract of healthy individuals", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27126270", + "title": "Highly sensitive stool DNA testing of Fusobacterium nucleatum as a marker for detection of colorectal tumours in a Japanese population.", + "year": 2017, + "journal": "Annals of clinical biochemistry", + "authors": [ + "Suehiro Y", + "Sakai K", + "Nishioka M", + "Hashimoto S", + "Takami T", + "Higaki S", + "Shindo Y", + "Hazama S", + "Oka M", + "Nagano H", + "Sakaida I", + "Yamasaki T" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.7372440670102562, + "mesh_terms": [ + "Adenoma", + "Adult", + "Aged", + "Biomarkers, Tumor", + "Carcinoma in Situ", + "Case-Control Studies", + "Colorectal Neoplasms", + "DNA Copy Number Variations", + "DNA, Bacterial", + "Feces", + "Female", + "Fusobacterium Infections", + "Fusobacterium nucleatum", + "Humans", + "Male", + "Middle Aged", + "Neoplasm Grading", + "Neoplasm Staging", + "Polymerase Chain Reaction", + "ROC Curve" + ], + "raw_abstract": "Background Accumulating evidence shows an over-abundance of Fusobacterium nucleatum in colorectal tumour tissues. Although stool DNA testing of Fusobacterium nucleatum might be a potential marker for the detection of colorectal tumours, the difficulty in detecting Fusobacterium nucleatum in stool by conventional methods prevented further explorations. Therefore, we developed a droplet digital polymerase chain reaction (PCR) assay for detecting Fusobacterium nucleatum in stool and investigated its clinical utility in the management of colorectal tumours in a Japanese population. Methods Feces were collected from 60 healthy subjects (control group) and from 11 patients with colorectal non-advanced adenomas (non-advanced adenoma group), 19 patients with colorectal advanced adenoma/carcinoma in situ (advanced adenoma/carcinoma in situ (CIS) group) and 158 patients with colorectal cancer of stages I to IV (colorectal cancer group). Absolute copy numbers of Fusobacterium nucleatum were measured by droplet digital PCR. Results The median copy number of Fusobacterium nucleatum was 17.5 in the control group, 311 in the non-advanced adenoma group, 122 in the advanced adenoma/CIS group, and 317 in the colorectal cancer group. In comparison with that in the control group, the Fusobacterium nucleatum level was significantly higher in the non-advanced adenoma group, the advanced adenoma/CIS group and the colorectal cancer group. Conclusions This study illustrates the potential of stool DNA testing of Fusobacterium nucleatum by droplet digital PCR to detect individuals with colorectal tumours in a Japanese population.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27684872", + "title": "Increased Enterococcus faecalis infection is associated with clinically active Crohn disease.", + "year": 2016, + "journal": "Medicine", + "authors": [ + "Zhou Y", + "Chen H", + "He H", + "Du Y", + "Hu J", + "Li Y", + "Li Y", + "Zhou Y", + "Wang H", + "Chen Y", + "Nie Y" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.6800049936208933, + "mesh_terms": [ + "Adult", + "China", + "Crohn Disease", + "DNA, Bacterial", + "Enterococcus faecalis", + "Feces", + "Female", + "Gram-Positive Bacterial Infections", + "Humans", + "Incidence", + "Male", + "Real-Time Polymerase Chain Reaction", + "Young Adult" + ], + "raw_abstract": "This study was performed to investigate the relationship between the abundance of pathogenic gut microbes in Chinese patients with inflammatory bowel disease (IBD) and disease severity.We collected clinical data and fecal samples from 47 therapy-naive Chinese patients with ulcerative colitis (UC), 67 patients with Crohn disease (CD), and 48 healthy volunteers. Bacteria levels of Fusobacterium species (spp), enterotoxigenic Bacteroides fragilis (B fragilis), enteropathogenic Escherichia coli (E coli), and Enterococcus faecalis (E faecalis) were assessed by quantitative real-time PCR (qRT-PCR). Spearman correlation coefficients were calculated to test associations between bacterial content and clinical parameters.Compared to healthy controls, the levels of both Fusobacterium spp and E faecalis were significantly increased in the feces of patients with IBD (P\u200a<\u200a0.01). B fragilis levels were higher (P\u200a<\u200a0.05) and E faecalis levels lower (P\u200a<\u200a0.05) in patients with CD compared to those with UC. Increased E faecalis colonization in CD associated positively with disease activity (P = 0.015), Crohn disease activity index (CDAI; R = 0.3118, P = 0.0108), and fecal calprotectin (P = 0.016).E faecalis and Fusobacterium spp are significantly enriched in patients with IBD, and increased E faecalis infection is associated with clinically active CD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31730997", + "title": "The gut microbiome in epilepsy.", + "year": 2020, + "journal": "Microbial pathogenesis", + "authors": [ + "\u015eafak B", + "Altunan B", + "Top\u00e7u B", + "Eren Topkaya A" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.6079795136051275, + "mesh_terms": [ + "Adult", + "Autoimmunity", + "Bacteria", + "Central Nervous System", + "DNA, Ribosomal", + "Epilepsy", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Male", + "Middle Aged", + "Proteobacteria", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "The close relationship between epilepsy and autoimmune diseases and the fact that the cause of epilepsy is idiopathic in 60% of cases suggest that intestinal microbiota may play a role in the etiology of epilepsy. In this study, we analyzed and compared the intestinal microbiota composition of patients with idiopathic focal epilepsy (n\u202f=\u202f30) and healthy volunteer group (n\u202f=\u202f10) by 16s ribosomal DNA sequencing. Proteobacteria phylum was found to be higher in patients with epilepsy (25.4%) than in healthy volunteers group (1.5%). The genera of Campylobacter, Delftia, Haemophilus, Lautropia, Neisseria among Proteobacteria phylum were found to be statistically significantly higher in patients with epilepsy than in healthy volunteers (p\u202f<\u202f0.05). Fusobacteria phylum was detected in 10.6% of the patients with epilepsy but not in the healthy volunteer group. The genus of the Fusobacteria phylum was found as Leptotrichia and Fusobacterium. In our study, taxonomic drift and significant differences in the intestinal microbiota of patients with epilepsy according to healthy volunteer group showed that autoimmune mechanisms and inflammation may have a role in the etiology of epilepsy. Our data should be supported by other studies as to the role of the intestinal microbiome in the prevention and treatment of epilepsy.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33970546", + "title": "Gut dysbiosis and clinical phases of pancolitis in patients with ulcerative colitis.", + "year": 2021, + "journal": "MicrobiologyOpen", + "authors": [ + "Maldonado-Arriaga B", + "Sandoval-Jim\u00e9nez S", + "Rodr\u00edguez-Silverio J", + "Lizeth Alcar\u00e1z-Estrada S", + "Cort\u00e9s-Espinosa T", + "P\u00e9rez-Cabeza de Vaca R", + "Licona-Cassani C", + "G\u00e1mez-Valdez JS", + "Shaw J", + "Mondrag\u00f3n-Ter\u00e1n P", + "Hern\u00e1ndez-Cortez C", + "Su\u00e1rez-Cuenca JA", + "Castro-Escarpulli G" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.5059813695425408, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biodiversity", + "Colitis", + "Colitis, Ulcerative", + "DNA, Bacterial", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "RNA, Ribosomal, 16S", + "Severity of Illness Index" + ], + "raw_abstract": "Ulcerative colitis (UC) is a frequent type of inflammatory bowel disease, characterized by periods of remission and exacerbation. Gut dysbiosis may influence pathophysiology and clinical response in UC. The purpose of this study was to evaluate whether gut microbiota is related to the active and remission phases of pancolitis in patients with UC as well as in healthy participants. Fecal samples were obtained from 18 patients with UC and clinical-endoscopic evidenced pancolitis (active phase n\u00a0=\u00a09 and remission phase n\u00a0=\u00a09), as well as 15 healthy participants. After fecal DNA extraction, the 16S rRNA gene was amplified and sequenced (Illumina MiSeq), operational taxonomic units were analyzed with the QIIME software. Gut microbiota composition revealed a higher abundance of the phyla Proteobacteria and Fusobacteria in active pancolitis, as compared with remission and healthy participants. Likewise, a marked abundance of the genus Bilophila and Fusobacteria were present in active pancolitis, whereas a higher abundance of Faecalibacterium characterized both remission and healthy participants. LEfSe analysis showed that the genus\u00a0Roseburia\u00a0and Faecalibacterium were enriched in remission pancolitis, and genera\u00a0Bilophila\u00a0and\u00a0Fusobacterium\u00a0were enriched in active pancolitis. The relative abundance of Fecalibacterium and Roseburia showed a higher correlation with fecal calprotectin, while Bilophila and Fusobacterium showed AUCs (area under the curve) of 0.917 and 0.988 for active vs. remission pancolitis. The results of our study highlight the relation of gut dysbiosis with clinically relevant phases of pancolitis in patients with UC. Particularly, Fecalibacterium, Roseburia, Bilophila, and Fusobacterium were identified as genera highly related to the different clinical phases of pancolitis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39256724", + "title": "Metagenomic analysis of colonic tissue and stool microbiome in patients with colorectal cancer in a South Asian population.", + "year": 2024, + "journal": "BMC cancer", + "authors": [ + "Gamage BD", + "Ranasinghe D", + "Sahankumari A", + "Malavige GN" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.4814349317830098, + "mesh_terms": [ + "Adult", + "Aged", + "Female", + "Humans", + "Male", + "Middle Aged", + "Bacteria", + "Colon", + "Colorectal Neoplasms", + "Feces", + "Gastrointestinal Microbiome", + "Metagenome", + "Metagenomics", + "RNA, Ribosomal, 16S", + "South Asian People" + ], + "raw_abstract": "BACKGROUND: The gut microbiome is thought to play an important role in the development of colorectal cancer (CRC). However, as the gut microbiome varies widely based on diet, we sought to investigate the gut microbiome changes in patients with CRC in a South Asian population. METHODS: The gut microbiome was assessed by 16s metagenomic sequencing targeting the V4 hypervariable region of the bacterial 16S rRNA in stool samples (n\u2009=\u2009112) and colonic tissue (n\u2009=\u200936) in 112 individuals. The cohort comprised of individuals with CRC (n\u2009=\u200924), premalignant lesions (n\u2009=\u200910), healthy individuals (n\u2009=\u200950) and in those with diabetes (n\u2009=\u200928). RESULTS: Overall, the relative abundances of genus Fusobacterium (p\u2009<\u20090.001), Acinetobacter (p\u2009<\u20090.001), Escherichia-Shigella (p\u2009<\u20090.05) were significantly higher in gut tissue, while Romboutsia (p\u2009<\u20090.01) and Prevotella (p\u2009<\u20090.05) were significantly higher in stool samples. Bacteroides and Fusobacterium were the most abundant genera found in stool samples in patients with CRC. Patients with pre-malignant lesions had significantly high abundances of Christensenellaceae, Enterobacteriaceae, Mollicutes and Ruminococcaceae (p\u2009<\u20090.001) compared to patients with CRC, and healthy individuals. Romboutsia was significantly more abundant (p\u2009<\u20090.01) in stool samples in healthy individuals compared to those with CRC and diabetes. CONCLUSION: Despite marked differences in the Sri Lankan diet compared to the typical Western diet, Bacteroides and Fusobacterium species were the most abundant in those with CRC, with Prevotella species, being most abundant in many individuals. We believe these results pave the way for possible dietary interventions for prevention of CRC in the South Asian population.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37029071", + "title": "A comprehensive microbial analysis of pediatric patients with acute appendicitis.", + "year": 2023, + "journal": "Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi", + "authors": [ + "Aiyoshi T", + "Kakihara T", + "Watanabe E", + "Tanaka N", + "Ogata Y", + "Masuoka H", + "Kurokawa R", + "Fujishiro J", + "Masumoto K", + "Suda W" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.476565210841728, + "mesh_terms": [ + "Child", + "Humans", + "Appendicitis", + "RNA, Ribosomal, 16S", + "Appendix", + "Bacteria", + "Feces", + "Acute Disease" + ], + "raw_abstract": "BACKGROUND: Pathogenesis of pediatric acute appendicitis (AA) is yet to be elucidated. Therefore, we performed a comprehensive microbial analysis of saliva, feces, and appendiceal lumen of AA patients using 16S ribosomal RNA (rRNA) gene amplicon sequencing to elucidate the pathogenesis of pediatric AA. METHODS: This study included 33 AA patients and 17 healthy controls (HCs) aged <15\u00a0y. Among the AA patients, 18 had simple appendicitis, and 15 had complicated appendicitis. Salivary and fecal samples were obtained from both groups. The contents of the appendiceal lumen were collected from the AA group. All samples were analyzed using 16S rRNA gene amplicon sequencing. RESULTS: The relative abundance of Fusobacterium was significantly higher in the saliva of AA patients as compared to that in HCs (P\u00a0=\u00a00.011). Bacteroides, Escherichia, Fusobacterium, Coprobacillus, and Flavonifractor were significantly increased in the feces of AA patients, as compared to that in HCs (P\u00a0=\u00a00.020, 0.010, 0.029, 0.031, and 0.002, respectively). In the appendiceal lumen, Bacteroides, Parvimonas, Fusobacterium, and Alloprevotella were the top bacterial genera with an average relative abundance >5% (16.0%, 9.1%, 7.9%, and 6.0%, respectively). CONCLUSIONS: The relative abundance of Fusobacterium was high in the appendiceal lumen of pediatric AA patients. Moreover, the relative abundance of Fusobacterium was significantly higher in the saliva and feces of pediatric AA patients than in those of healthy children. These results suggest that ectopic colonization of oral Fusobacterium in the appendix might play an important role in the pathogenesis of pediatric AA.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29543545", + "title": "Systematic review: Gut microbiota in fecal samples and detection of colorectal neoplasms.", + "year": 2018, + "journal": "Gut microbes", + "authors": [ + "Amitay EL", + "Krilaviciute A", + "Brenner H" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.47223398744397355, + "mesh_terms": [ + "Animals", + "Bacteria", + "Colorectal Neoplasms", + "Feces", + "Gastrointestinal Microbiome", + "Humans" + ], + "raw_abstract": "Colorectal cancer (CRC) is a leading cause of cancer morbidity and mortality. Dysbiosis in the gut microbiota may be associated with CRC. This systematic review focuses on differences in gut microbial community between people diagnosed with CRC or adenoma and healthy individuals using fecal samples, emphasizing non-invasive fecal microbiome models for CRC early diagnosis. Nineteen studies were identified in a systematic literature search of Pubmed, Web of Science and ScienceDirect. Several bacteria were reported to differ in abundance between CRC and adenoma cases and healthy controls, with Fusobacterium the most common. Fecal multi-bacterial predictive models used to distinguish CRC patients from healthy controls had reported areas under the receiver operating curve (AUCs) in external validation populations of 0.68-0.77. Though advanced sequencing techniques could in the future complement current non-invasive methods for CRC early detection, more studies with high statistical power, comparable and reproducible methods and external validation of predictive models are needed.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39023095", + "title": "Metagenomic analysis of the gut virome in patients with irritable bowel syndrome.", + "year": 2024, + "journal": "Journal of medical virology", + "authors": [ + "Zhang P", + "Ma S", + "Guo R", + "Li L", + "Guo X", + "Chang D", + "Li S", + "Zhang H", + "Fu C", + "Yang L", + "Zhang Y", + "Jiang J", + "Wang T", + "Wang J", + "Shi H" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.46125048374753075, + "mesh_terms": [ + "Humans", + "Irritable Bowel Syndrome", + "Virome", + "Gastrointestinal Microbiome", + "Metagenomics", + "Feces", + "Viruses", + "Adult", + "Male", + "Female", + "Middle Aged", + "Bacteria", + "Metagenome" + ], + "raw_abstract": "Irritable bowel syndrome (IBS), a chronic functional gastrointestinal disorder, is recognized for its association with alterations in the gut microbiome and metabolome. This study delves into the largely unexplored domain of the gut virome in IBS patients. We conducted a comprehensive analysis of the fecal metagenomic data set from 277 IBS patients and 84 healthy controls to characterize the gut viral community. Our findings revealed a distinct gut virome in IBS patients compared to healthy individuals, marked by significant variances in between-sample diversity and altered abundances of 127 viral operational taxonomic units (vOTUs). Specifically, 111 vOTUs, predominantly belonging to crAss-like, Siphoviridae, Myoviridae, and Quimbyviridae families, were more abundant in IBS patients, whereas the healthy control group exhibited enrichment of 16 vOTUs from multiple families. We also investigated the interplay between the gut virome and bacteriome, identifying a correlation between IBS-enriched bacteria like Klebsiella pneumoniae, Fusobacterium varium, and Ruminococcus gnavus, and the IBS-associated vOTUs. Furthermore, we assessed the potential of gut viral signatures in predicting IBS, achieving a notable area under the receiver operator characteristic curve (AUC) of 0.834. These findings highlight significant shifts in the viral diversity, taxonomic distribution, and functional composition of the gut virome in IBS patients, suggesting the potential role of the gut virome in IBS pathogenesis and opening new avenues for diagnostic and therapeutic strategies targeting the gut virome in IBS management.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29687353", + "title": "Gut microbiome of Moroccan colorectal cancer patients.", + "year": 2018, + "journal": "Medical microbiology and immunology", + "authors": [ + "Allali I", + "Boukhatem N", + "Bouguenouch L", + "Hardi H", + "Boudouaya HA", + "Cadenas MB", + "Ouldim K", + "Amzazi S", + "Azcarate-Peril MA", + "Ghazal H" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.4543123108960843, + "mesh_terms": [ + "Adult", + "Aged", + "Cluster Analysis", + "Colorectal Neoplasms", + "Cytosol", + "DNA, Bacterial", + "DNA, Ribosomal", + "Dysbiosis", + "Fatty Acids", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenomics", + "Microbiota", + "Middle Aged", + "Morocco", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA", + "Surveys and Questionnaires", + "Young Adult" + ], + "raw_abstract": "Although colorectal cancer is the third leading cause of death in Morocco, there are no studies of the microbiome changes associated with the disease in the Moroccan population. The aim of our study was to compare the stool microbiome of Moroccan cancer patients with healthy individuals. We analyzed the microbiome composition of samples from 11 CRC patients and 12 healthy individuals by 16S rRNA amplicon sequencing. Principal coordinate analysis of samples revealed defined cancer versus healthy clusters. Our findings showed that cancer samples had higher proportions of Firmicutes (T\u2009=\u200950.5%; N\u2009=\u200928.4%; p\u2009=\u20090.04), specifically of Clostridia (T\u2009=\u200948.3%; N\u2009=\u200919.0%; p\u2009=\u20090.002), and Fusobacteria (T\u2009=\u20090.1%; N\u2009=\u20090.0%; p\u2009=\u20090.02), especially of Fusobacteriia (T\u2009=\u20090.1%; N\u2009=\u20090.0%; p\u2009=\u20090.02), while Bacteroidetes were enriched in healthy samples (T\u2009=\u200935.1%; N\u2009=\u200962.8%; p\u2009=\u20090.06), particularly the class Bacteroidia (T\u2009=\u200935.1%; N\u2009=\u200962.6%; p\u2009=\u20090.06). Porphyromonas, Clostridium, Ruminococcus, Selenomonas, and Fusobacterium were significantly overrepresented in diseased patients, similarly to other studies. Predicted functional information showed that bacterial motility proteins, flagellar assembly, and fatty acid biosynthesis metabolism were significantly overrepresented in cancer patients, while amino acid metabolism and glycan biosynthesis were overrepresented in controls. This suggests that involvement of these functional metagenomes is similar and relevant in the carcinogenesis process, independent of the origin of the samples. Results from this study allowed identification of bacterial taxa relevant to the Moroccan population and encourages larger studies to facilitate population-directed therapeutic approaches.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30794590", + "title": "Metagenomic analyses of the gut microbiota associated with colorectal adenoma.", + "year": 2019, + "journal": "PloS one", + "authors": [ + "Saito K", + "Koido S", + "Odamaki T", + "Kajihara M", + "Kato K", + "Horiuchi S", + "Adachi S", + "Arakawa H", + "Yoshida S", + "Akasu T", + "Ito Z", + "Uchiyama K", + "Saruta M", + "Xiao JZ", + "Sato N", + "Ohkusa T" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.4507683831940573, + "mesh_terms": [ + "Adenoma", + "Aged", + "Bacteria", + "Case-Control Studies", + "Colorectal Neoplasms", + "Disease Progression", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenomics", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "Recent studies have suggested an association between certain members of the Fusobacterium genus, especially F. nucleatum, and the progression of advanced colorectal carcinoma (CRC). We assessed such an association of the gut microbiota in Japanese patients with colorectal adenoma (CRA) or intramucosal CRC using colonoscopy aspirates. We analyzed samples from 81 Japanese patients, including 47 CRA and 24 intramucosal CRC patients, and 10 healthy subjects. Metagenomic analysis of the V3-V4 region of the 16S ribosomal RNA gene was performed. The linear discriminant analysis (LDA) effect size (LEfSe) method was used to examine microbial dysbiosis, revealing significant differences in bacterial abundances between the healthy controls and CRA or intramucosal CRC patients. In particular, F. varium was statistically more abundant in patients with CRA and intramucosal CRC than in healthy subjects. Here, we present the metagenomic profile of CRA and intramucosal CRC and demonstrate that F. varium is at least partially involved in the pathogenesis of CRA and intramucosal CRC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30108246", + "title": "The urinary microbiome associated with bladder cancer.", + "year": 2018, + "journal": "Scientific reports", + "authors": [ + "Bu\u010devi\u0107 Popovi\u0107 V", + "\u0160itum M", + "Chow CT", + "Chan LS", + "Roje B", + "Terzi\u0107 J" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.4495805181598435, + "mesh_terms": [ + "Aged", + "Aged, 80 and over", + "Bacteria", + "Case-Control Studies", + "DNA, Bacterial", + "Healthy Volunteers", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Urinary Bladder", + "Urinary Bladder Neoplasms", + "Urine" + ], + "raw_abstract": "Recent findings suggest that human microbiome can influence the development of cancer, but the role of microorganisms in bladder cancer pathogenesis has not been explored yet. The aim of this study was to characterize and compare the urinary microbiome of bladder cancer patients with those of healthy controls. Bacterial communities present in urine specimens collected from 12 male patients diagnosed with bladder cancer, and from 11 healthy, age-matched individuals were analysed using 16S sequencing. Our results show that the most abundant phylum in both groups was Firmicutes, followed by Actinobacteria, Bacteroidetes and Proteobacteria. While microbial diversity and overall microbiome composition were not significantly different between groups, we could identify operational taxonomic units (OTUs) that were more abundant in either group. Among those that were significantly enriched in the bladder cancer group, we identified an OTU belonging to genus Fusobacterium, a possible protumorigenic pathogen. In an independent sample of 42 bladder cancer tissues, 11 had Fusobacterium nucleatum sequences detected by PCR. Three OTUs from genera Veillonella, Streptococcus and Corynebacterium were more abundant in healthy urines. However, due to the limited number of participants additional studies are needed to determine if urinary microbiome is associated with bladder cancer.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33620078", + "title": "The Gastrointestinal Microbiota of the Common Marmoset (Callithrix jacchus).", + "year": 2020, + "journal": "ILAR journal", + "authors": [ + "Sheh A" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.43298100879890683, + "mesh_terms": [ + "Animals", + "Bacteria", + "Callithrix", + "Feces", + "Gastrointestinal Microbiome", + "Prospective Studies" + ], + "raw_abstract": "The microbiota is heavily involved in both health and disease pathogenesis, but defining a normal, healthy microbiota in the common marmoset has been challenging. The aim of this review was to systematically review recent literature involving the gastrointestinal microbiome of common marmosets in health and disease. Twelve sources were included in this review. The gut microbiome composition was reviewed across institutions worldwide, and taxonomic shifts between healthy individuals were described. Unlike the human gut microbiome, which is dominated by Firmicutes and Bacteroidetes, the marmoset gut microbiome shows great plasticity across institutions, with 5 different phyla described as dominant in different healthy cohorts. Genera shared across institutions include Anaerobiospirillum, Bacteroides, Bifidobacterium, Collinsella, Fusobacterium, Megamonas, Megasphaera, Phascolarctobacterium, and Prevotella. Shifts in the abundance of Prevotella or Bifidobacterium or invasion by pathogens like Clostridium perfringens may be associated with disease. Changes in microbial composition have been described in healthy and diseased marmosets, but factors influencing the severe changes in microbial composition have not been established. Multi-institutional, prospective, and longitudinal studies that utilize multiple testing methodologies are required to determine sources of variability in the reporting of marmoset microbiomes. Furthermore, methods of microbial manipulation, whether by diet, enrichment, fecal microbiome transplantation, etc, need to be established to modulate and maintain robust and resilient microbiome communities in marmoset colonies and reduce the incidence of idiopathic gastrointestinal disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28912092", + "title": "Comparison of gut microbiota in adult patients with type 2 diabetes and healthy individuals.", + "year": 2017, + "journal": "Microbial pathogenesis", + "authors": [ + "Sedighi M", + "Razavi S", + "Navab-Moghadam F", + "Khamseh ME", + "Alaei-Shahmiri F", + "Mehrtash A", + "Amirmozafari N" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.41907327937016564, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteria", + "Blood Glucose", + "Case-Control Studies", + "Diabetes Mellitus, Type 2", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Male", + "Middle Aged" + ], + "raw_abstract": "Recent studies indicate that inflammatory reactions leading to the development of type 2 diabetes mellitus (T2DM) may also contribute to variations in the composition of the intestinal microbiota, suggesting a relation between T2DM and bacterial residents in the intestinal tract. This case-control study was designed to evaluate the composition of the gut microbiota dominant bacterial groups in patients with T2DM compared to the healthy people. A total of 36 adult subjects (18 patients diagnosed with T2DM and 18 healthy persons) were included in the study. The intestinal microbiota composition was investigated by quantitative real-time polymerase chain reaction (qPCR) method using bacterial 16S rRNA gene. The quantities of two groups of bacteria were meaningfully different among T2DM patients and healthy individuals. While, the level of Lactobacillus was significantly higher in the patients with T2DM (P value\u00a0<\u00a00.001), Bifidobacterium was significantly more frequent in the healthy people (P value\u00a0<\u00a00.001). The quantities of Prevotella (P value\u00a0=\u00a00.0.08) and Fusobacterium (P value\u00a0=\u00a00.99) genera in faecal samples were not significantly different between the two groups. The significant alterations in dominant faecal bacterial genera found in T2DM patients participating in the current study highlight the link between T2DM disease and compositional variation in intestinal flora. These findings may be valuable for developing approaches to control T2DM by modifying the gut microbiota. More investigations with focus on various taxonomic levels (family, genus and species) of bacteria are necessary to clarify the exact relevance of changes in the gut microbial communities with the progression of T2DM disorder.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35292670", + "title": "Analysis of gut microbiome profiles in common marmosets (Callithrix jacchus) in health and intestinal disease.", + "year": 2022, + "journal": "Scientific reports", + "authors": [ + "Sheh A", + "Artim SC", + "Burns MA", + "Molina-Mora JA", + "Lee MA", + "Dzink-Fox J", + "Muthupalani S", + "Fox JG" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.4128662407104758, + "mesh_terms": [ + "Animals", + "Callithrix", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Prevotella" + ], + "raw_abstract": "Chronic gastrointestinal (GI) diseases are the most common diseases in captive common marmosets. To understand the role of the microbiome in GI diseases, we characterized the gut microbiome of 91 healthy marmosets (303 samples) and 59 marmosets diagnosed with inflammatory bowel disease (IBD) (200 samples). Healthy marmosets exhibited \"humanized,\" Bacteroidetes-dominant microbiomes. After up to 2 years of standardized diet, housing and husbandry, marmoset microbiomes could be classified into four distinct marmoset sources based on Prevotella and Bacteroides levels. Using a random forest (RF) model, marmosets were classified by source with an accuracy of 93% with 100% sensitivity and 95% specificity using abundance data from 4 Prevotellaceae amplicon sequence variants (ASVs), as well as single ASVs from Coprobacter, Parabacteroides, Paraprevotella, Phascolarctobacterium, Oribacterium and Fusobacterium. A single dysbiotic IBD state was not found across all marmoset sources, but IBD was associated with lower alpha diversity and a lower Bacteroides:Prevotella copri ratio within each source. IBD was highest in a Prevotella-dominant cohort, and consistent with Prevotella-linked diseases, pro-inflammatory genes in the jejunum were upregulated. RF analysis of serum biomarkers identified serum calcium, hemoglobin and red blood cell (RBC) counts as potential biomarkers for marmoset IBD. This study characterizes the microbiome of healthy captive common marmosets and demonstrates that source-specific microbiomes can be retained despite standardized diets and husbandry practices. Marmosets with IBD had decreased alpha diversity and a shift in the ratio of Bacteroides:Prevotella copri compared to healthy marmosets.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37777841", + "title": "Gut microbial signatures of patients with primary hepatocellular carcinoma and their healthy first-degree relatives.", + "year": 2023, + "journal": "Journal of applied microbiology", + "authors": [ + "Feng J", + "Wu Y", + "Dai P", + "Wang D", + "Liu L", + "Chai B" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.41200668369630916, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Carcinoma, Hepatocellular", + "RNA, Ribosomal, 16S", + "Liver Neoplasms", + "Bacteria", + "Lactobacillales" + ], + "raw_abstract": "AIMS: The gut microbiome has been recognized as a significant contributor to primary hepatocellular carcinoma (HCC), with mounting evidence indicating associations between bacterial components and cancers of the digestive system. METHODS AND RESULTS: Here, to characterize gut bacterial signature in patients with primary HCC and to assess the diagnostic potential of bacterial taxa for primary HCC, 21 HCC patients and 21 healthy first-degree relatives (control group) were enrolled in this study. Bacterial DNA in the fecal samples was quantified by 16S rRNA gene sequencing. We found that 743 operational taxonomic units (OTUs) were shared between patients with primary HCC and healthy controls. Of these, 197 OTUs were unique to patients with primary HCC, while 95 OTUs were unique to healthy subjects. Additionally, we observed significant differences in the abundance of Ruminococcaceae_UCG-014 and Romboutsia between patients with primary HCC and their healthy first-degree relatives. Besides, the relative abundance of Ruminococcaceae_UCG-014 and Prevotella_9 was positively correlated with physiological indicators including AST, ALT, ALB, or TBIL. Signature bacterial taxa could serve as non-invasive biomarkers, of which Romboutsia and Veillonella were identified as differential taxa in fecal samples from patients with HCC compared to healthy controls. Romboutsia showed a strong association with HCC (AUC\u00a0=\u00a00.802). Additionally, the combination of Romboutsia and Veillonella (AUC\u00a0=\u00a00.812) or the grouping of Fusobacterium, Faccalibacterium, and Peptostreptococcacae together (AUC\u00a0=\u00a00.762) exhibited promising outcomes for the diagnosis of HCC. CONCLUSIONS: The composition of gut microbes in patients with HCC was found to be significantly altered. Differential taxa Romboutsia, Veillonella, and Peptostreptococcacae could be tested for identification of HCC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35129067", + "title": "16S rDNA sequencing analyzes differences in intestinal flora of human immunodeficiency virus (HIV) patients and association with immune activation.", + "year": 2022, + "journal": "Bioengineered", + "authors": [ + "Mingjun Z", + "Fei M", + "Zhousong X", + "Wei X", + "Jian X", + "Yuanxue Y", + "Youfeng S", + "Zhongping C", + "Yiqin L", + "Xiaohong Z", + "Ying C", + "Zhenbing W", + "Zehu D", + "Lanjuan L" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3943967319684413, + "mesh_terms": [ + "CD4-Positive T-Lymphocytes", + "Case-Control Studies", + "Cytokines", + "DNA, Bacterial", + "Feces", + "Gastrointestinal Microbiome", + "HIV Infections", + "Humans", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "To clarify the influence of HIV on the intestinal flora and the interrelationship with CD4 T cells, the present study collected stool specimens from 33 HIV patients and 28\u00a0healthy subjects to compare the differences in the intestinal flora and CD4 T cells in a 16S rDNA-sequencing approach. ELISA was used to detect the expressions of interleukin 2 (IL-2), IL-8, and tumor necrosis factor-\u03b1 (TNF-\u03b1). Meanwhile, correlation analysis with the different bacterial populations in each group was carried out. The results revealed that Alpha diversity indices of the intestinal flora of HIV patients were markedly lower than that of the healthy group (p\u00a0<\u00a00.05). The top five bacterial species in the HIV group were Bacteroides (23.453%), Prevotella (19.237%), Fusobacterium (12.408%), Lachnospira (3.811%), and Escherichia-Shigella (3.126%). Spearman correlation analysis results indicated that Fusobacterium_mortiferum, Fusobacterium, and Gammaproteobacteria were positively correlated with TNF-\u03b1 (p\u00a0<\u00a00.05), whereas Ruminococcaceae, Bacteroidales was negatively correlated with TNF-\u03b1 (p\u00a0<\u00a00.05). Additionally, Agathobacter was positively correlated with contents of IL-2 and IL-8 (p\u00a0<\u00a00.05), whereas Prevotellaceae, and Prevotella were negatively correlated with IL-8 content (p\u00a0<\u00a00.05). Furthermore, the top five strains in the CD4 high group (\u2265350/mm", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39431364", + "title": "Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study.", + "year": 2025, + "journal": "BJOG : an international journal of obstetrics and gynaecology", + "authors": [ + "Hicks C", + "Leonardi M", + "Chua XY", + "Mari-Breedt L", + "Espada M", + "El-Omar EM", + "Condous G", + "El-Assaad F" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.38684329184243843, + "mesh_terms": [ + "Humans", + "Female", + "Endometriosis", + "Adult", + "Prospective Studies", + "Feces", + "Vagina", + "Biomarkers", + "Microbiota", + "Mouth", + "Pilot Projects", + "Case-Control Studies", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: To identify a microbial signature for endometriosis for use as a diagnostic non-invasive biomarker. DESIGN: Prospective cohort pilot study. SETTING: Nepean Hospital and UNSW Microbiome Research Centre, Australia. POPULATION: Sixty-four age- and sex-matched subjects (n\u2009=\u200919 healthy control (HC); n\u2009=\u200924 non-endometriosis (N-ENDO) and n\u2009=\u200921 confirmed endometriosis (ENDO)). All study participants, besides healthy controls, underwent laparoscopic surgical assessment for endometriosis, and histology was performed on excised lesions. METHODS: Oral, stool and, vaginal samples were self-collected at a single time point for healthy controls, and preoperatively for patients undergoing laparoscopy. Samples underwent 16S rRNA amplicon sequencing, followed by bioinformatics analysis. MAIN OUTCOME MEASURES: Compositional differences between cohorts as identified by diversity analyses, and differentially abundant microbial taxa, as identified by LEfSE analysis. RESULTS: The composition of the oral (adjusted p\u2009=\u20090.003), and stool (adjusted p\u2009=\u20090.042) microbiota is different between the three cohorts. Differentially abundant taxa are present within each cohort as identified by LEfSE analysis. Particularly, Fusobacterium was enriched in the oral samples of patients with moderate/severe endometriosis. CONCLUSIONS: Taxonomic and compositional differences were found between the microbiota in the mouth, gut and, vagina of patients with and without endometriosis and healthy controls. Fusobacterium was enriched in patients with moderate/severe endometriosis. Fusobacterium is noted as a key pathogen in periodontal disease, a common comorbidity in endometriosis. These findings suggest a role for the oral, stool and, vaginal microbiome in endometriosis, and present potential for microbial-based treatments and the design of a diagnostic swab.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39836282", + "title": "Evaluation of variations in predominant gut microbiota members in inflammatory bowel disease using real-time PCR.", + "year": 2025, + "journal": "Molecular biology reports", + "authors": [ + "Tasoujlu M", + "Sharifi Y", + "Ghahremani M", + "Alizadeh K", + "Babaie F", + "Hosseiniazar MM" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3748611981985815, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Real-Time Polymerase Chain Reaction", + "Male", + "Adult", + "Female", + "Feces", + "Middle Aged", + "Akkermansia", + "Bifidobacterium", + "Bacteria", + "Case-Control Studies", + "Lactobacillus", + "Enterobacteriaceae" + ], + "raw_abstract": "Inflammatory Bowel Disease (IBD) is a persistent ailment that impacts many individuals worldwide. The interaction between the immune system and gut microbiome is thought to influence IBD development. This study aimed to assess some microbiota in IBD patients compared to healthy individuals. The investigation involved a selected group of twenty patients suffering from IBD and an equal number of healthy participants. Stool specimens were obtained and analyzed for Lactobacillus, Bifidobacterium, Bacteroides, Clostridium leptum, Akkermansia muciniphila, Fusobacterium and Enterobacteriaceae using real-time PCR. The findings indicated significantly higher levels of Bifidobacterium in IBD patients (Pv\u2009=\u20090.009) and lower levels of A. muciniphila (Pv\u2009=\u20090.003) healthy individuals. Other bacteria tested did not show significant differences. The study suggests that the progression of IBD patients could be influenced by the rising of Bifidobacterium and the declining of A. muciniphila. Targeting these bacteria could lead to improved treatments and quality of life for those with IBD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26691472", + "title": "High occurrence of Fusobacterium nucleatum and Clostridium difficile in the intestinal microbiota of colorectal carcinoma patients.", + "year": 2015, + "journal": "Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]", + "authors": [ + "Fukugaiti MH", + "Ignacio A", + "Fernandes MR", + "Ribeiro J\u00fanior U", + "Nakano V", + "Avila-Campos MJ" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.36736435931574757, + "mesh_terms": [ + "Aged", + "Brazil", + "Clostridioides difficile", + "Clostridium Infections", + "Colorectal Neoplasms", + "Female", + "Fusobacterium Infections", + "Fusobacterium nucleatum", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "Real-Time Polymerase Chain Reaction" + ], + "raw_abstract": "Colorectal carcinoma is considered the fourth leading cause of cancer deaths worldwide. Several microorganisms have been associated with carcinogenesis, including Enterococcus spp., Helicobacter pylori, enterotoxigenic Bacteroides fragilis, pathogenic E. coli strains and oral Fusobacterium. Here we qualitatively and quantitatively evaluated the presence of oral and intestinal microorganisms in the fecal microbiota of colorectal cancer patients and healthy controls. Seventeen patients (between 49 and 70 years-old) visiting the Cancer Institute of the Sao Paulo State were selected, 7 of whom were diagnosed with colorectal carcinoma. Bacterial detection was performed by qRT-PCR. Although all of the tested bacteria were detected in the majority of the fecal samples, quantitative differences between the Cancer Group and healthy controls were detected only for F. nucleatum and C. difficile. The three tested oral microorganisms were frequently observed, suggesting a need for furthers studies into a potential role for these bacteria during colorectal carcinoma pathogenesis. Despite the small number of patients included in this study, we were able to detect significantly more F. nucleatum and C. difficile in the Cancer Group patients compared to healthy controls, suggesting a possible role of these bacteria in colon carcinogenesis. This finding should be considered when screening for colorectal cancer.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29040443", + "title": "A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy.", + "year": 2017, + "journal": "FEMS microbiology ecology", + "authors": [ + "AlShawaqfeh MK", + "Wajid B", + "Minamoto Y", + "Markel M", + "Lidbury JA", + "Steiner JM", + "Serpedin E", + "Suchodolski JS" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.36139473290417984, + "mesh_terms": [ + "Algorithms", + "Animals", + "Bacteria", + "Dog Diseases", + "Dogs", + "Dysbiosis", + "Feces", + "Female", + "Inflammatory Bowel Diseases", + "Male", + "Microbiota", + "Real-Time Polymerase Chain Reaction" + ], + "raw_abstract": "Recent studies have identified various bacterial groups that are altered in dogs with chronic inflammatory enteropathies (CE) compared to healthy dogs. The study aim was to use quantitative PCR (qPCR) assays to confirm these findings in a larger number of dogs, and to build a mathematical algorithm to report these microbiota changes as a dysbiosis index (DI). Fecal DNA from 95 healthy dogs and 106 dogs with histologically confirmed CE was analyzed. Samples were grouped into a training set and a validation set. Various mathematical models and combination of qPCR assays were evaluated to find a model with highest discriminatory power. The final qPCR panel consisted of eight bacterial groups: total bacteria, Faecalibacterium, Turicibacter, Escherichia coli, Streptococcus, Blautia, Fusobacterium and Clostridium hiranonis. The qPCR-based DI was built based on the nearest centroid classifier, and reports the degree of dysbiosis in a single numerical value that measures the closeness in the l2 - norm of the test sample to the mean prototype of each class. A negative DI indicates normobiosis, whereas a positive DI indicates dysbiosis. For a threshold of 0, the DI based on the combined dataset achieved 74% sensitivity and 95% specificity to separate healthy and CE dogs.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39289618", + "title": "Improved diagnostic efficiency of CRC subgroups revealed using machine learning based on intestinal microbes.", + "year": 2024, + "journal": "BMC gastroenterology", + "authors": [ + "Liu G", + "Su L", + "Kong C", + "Huang L", + "Zhu X", + "Zhang X", + "Ma Y", + "Wang J" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.35642226549199757, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Colorectal Neoplasms", + "Machine Learning", + "Female", + "Male", + "Middle Aged", + "Case-Control Studies", + "Aged", + "Algorithms", + "Feces" + ], + "raw_abstract": "BACKGROUND: Colorectal cancer (CRC) is a common cancer that causes millions of deaths worldwide each year. At present, numerous studies have confirmed that intestinal microbes play a crucial role in the process of CRC. Additionally, studies have shown that CRC can be divided into several consensus molecular subtypes (CMS) based on tumor gene expression, and CRC microbiomes have been reported related to CMS. However, most previous studies on intestinal microbiome of CRC have only compared patients with healthy controls, without classifying of CRC patients based on intestinal microbial composition. RESULTS: In this study, a CRC cohort including 339 CRC samples and 333 healthy controls was selected as the discovery set, and the CRC samples were divided into two subgroups (234 Subgroup1 and 105 Subgroup2) using PAM clustering algorithm based on the intestinal microbial composition. We found that not only the microbial diversity was significantly different (Shannon index, p-value\u2009<\u20090.05), but also 129 shared genera altered (p-value\u2009<\u20090.05) between the two CRC subgroups, including several marker genera in CRC, such as Fusobacterium and \ufeffBacteroides. A random forest algorithm was used to construct diagnostic models, which showed significantly higher efficiency when the CRC samples were divided into subgroups. Then an independent cohort including 187 CRC samples (divided into 153 Subgroup1 and 34 Subgroup2) and 123 healthy controls was chosen to validate the models, and confirmed the results. CONCLUSIONS: These results indicate that the divided CRC subgroups can improve the efficiency of disease diagnosis, with various microbial composition in the subgroups.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38782999", + "title": "Uncovering the characteristics of the gut microbiota in patients with ischemic stroke and hemorrhagic stroke.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Chen YZ", + "Huang ZY", + "Zhou WW", + "Li ZY", + "Li XP", + "Chen SS", + "Ma JK" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3528206515139304, + "mesh_terms": [ + "Gastrointestinal Microbiome", + "Humans", + "Ischemic Stroke", + "Male", + "Hemorrhagic Stroke", + "Female", + "Case-Control Studies", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Aged", + "Bacteria", + "High-Throughput Nucleotide Sequencing" + ], + "raw_abstract": "This study aimed to explore the gut microbiota characteristics of ischemic and hemorrhagic stroke patients. A case-control study was conducted, and high-throughput sequencing of the V4-V5 region of 16S rRNA was used to analyze the differences in gut microbiota. The results showed that Proteobacteria was significantly increased in the ischemic stroke group compared with the healthy control group, while Fusobacteria was significantly increased in the hemorrhagic stroke group. In the ischemic stroke group, Butyricimonas, Alloprevotella, and Escherichia were significantly more abundant than in the healthy control group. In the hemorrhagic stroke group, Atopobium, Hungatella, Eisenbergiella, Butyricimonas, Odonbacter, Lachnociostridium, Alistipes, Parabacteroides, and Fusobacterium were significantly more abundant than in the healthy control group. Additionally, Alloprevotella, Ruminococcus, and Prevotella were significantly more abundant in the ischemic stroke group than in the hemorrhagic stroke group. The gut microbiota of ischemic and hemorrhagic stroke patients has significant diversity characteristics. These results provide new theoretical basis for exploring the prevention and treatment of different types of stroke through gut microbiota research.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39208963", + "title": "Dysbiosis of the gut microbiota in glioblastoma patients and potential biomarkers for risk assessment.", + "year": 2024, + "journal": "Microbial pathogenesis", + "authors": [ + "Jiang H", + "Yang F", + "Zhang X", + "Fang H", + "Qiu T", + "Li Y", + "Peng A" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3521017874781462, + "mesh_terms": [ + "Humans", + "Glioblastoma", + "Gastrointestinal Microbiome", + "Dysbiosis", + "RNA, Ribosomal, 16S", + "Feces", + "Bacteria", + "Male", + "Middle Aged", + "Risk Assessment", + "Female", + "Biomarkers", + "Adult", + "Aged", + "Case-Control Studies" + ], + "raw_abstract": "BACKGROUND: The significant death rate of glioblastoma is well-known around the world. The link between gut microbiota and glioma is becoming more studied. The goal of this study was to look at the relationships between intestinal flora and glioblastoma, and to provide a new perspective for the diagnosis as well as treatment of glioblastoma. METHODS: Fecal samples from 80 participants with glioblastoma (n\u00a0=\u00a040) and healthy individuals (n\u00a0=\u00a040) in this study were collected as well as analyzed utilizing 16S rRNA gene amplicon sequencing in order to characterize the gut microbial community. RESULTS: Each group has its own microbial community, and the microbial environment of glioblastoma patients had lower richness and evenness. The structure of gut microbiota community in glioblastoma patients showed profound changes, which includes the increase of pathogens in Fusobacteria and Bacteroidetes, and the reduction of probiotic bacteria in Firmicutes, Actinobacteria and Verrucomicrobia. Meanwhile, the significant correlations and clustering of OTUS (operational taxonomic units) in glioblastoma patients were discovered, and a biomarker panel (Fusobacterium, Escherichia/Shigella, Ruminococcus gnavus group, Lachnospira, Akkermansia, Parasutterella) had been used to discriminate the patients with glioblastoma from the healthy subjects (AUC: 0.80). Furthermore, the glioblastoma group exhibited multiple disturbed pathways through KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, particularly in genetic information processing. Moreover, the prediction of phenotypic characteristics of microbiome proposed that the glioblastoma patients might have more Gram-negative bacteria and opportunistic pathogens than the healthy controls. CONCLUSIONS: When compared to healthy people, glioblastoma sufferers have a different host-microbe interaction. Furthermore, certain types of intestinal flora could be regarded as biomarkers and drug targets for the diagnosis as well as treatment of glioblastomas.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32653436", + "title": "Comparison of the fecal microbiomes of healthy and diarrheic captive wild boar.", + "year": 2020, + "journal": "Microbial pathogenesis", + "authors": [ + "Wang B", + "Deng B", + "Yong F", + "Zhou H", + "Qu C", + "Zhou Z" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.34741339315865877, + "mesh_terms": [ + "Animals", + "Feces", + "Microbiota", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Sus scrofa", + "Swine" + ], + "raw_abstract": "Diarrhea caused by Enterotoxigenic Escherichia coli (ETEC) is one of the most common clinical diseases observed in captive wild boars, is usually caused by an imbalance in the gut microbiome, and is responsible for piglets significant mortality. However, little research has been undertaken into the structure and function of the intestinal microbial communities in wild boar with diarrhea influenced by enterotoxigenic E. coli. In this study, fecal samples were collected and 16S-rRNA gene sequencing was used to compare the intestinal microbiome of healthy captive wild boar and wild boar with diarrhea on the same farm. We found that the intestinal microbial diversity of healthy wild boar (HWB) was relatively high, while that of diarrheic wild boar (DWB) was significantly lower. Line Discriminant Analysis Effect Size showed that at the genus level, the abundance of Escherichia-Shigella and Fusobacterium was significantly higher in DWB. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis showed that the expression of genes in pathways including infectious diseases: bacterial, metabolism of amino acids, membrane transport, and signal transduction was significantly higher in DWB. In summary, this study provides a theoretical basis for the design of appropriate means of diarrhea treatment in captive wild boar.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "24811328", + "title": "Microbial mucosal colonic shifts associated with the development of colorectal cancer reveal the presence of different bacterial and archaeal biomarkers.", + "year": 2015, + "journal": "Journal of gastroenterology", + "authors": [ + "Mira-Pascual L", + "Cabrera-Rubio R", + "Ocon S", + "Costales P", + "Parra A", + "Suarez A", + "Moris F", + "Rodrigo L", + "Mira A", + "Collado MC" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3434025563677596, + "mesh_terms": [ + "Adenocarcinoma", + "Adenoma", + "Adolescent", + "Adult", + "Aged", + "Aged, 80 and over", + "Archaea", + "Bacteria", + "Case-Control Studies", + "Colon", + "Colorectal Neoplasms", + "Disease Progression", + "Feces", + "Female", + "Humans", + "Intestinal Mucosa", + "Male", + "Microbiota", + "Middle Aged", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Epidemiological studies demonstrate a link between gastrointestinal cancers and environmental factors such as diet. It has been suggested that environmental cancer risk is determined by the interaction between diet and microbes. Thus, the purpose of this study was to examine the hypothesis that microbiota composition during colorectal cancer (CRC) progression might differ depending on the stage of the disease. METHODS: A total of 28 age-matched and sex-matched subjects, seven with CRC adenocarcinoma, 11 with tubular adenomas and ten healthy subjects with intact colon, were included into the study. Microbiomes from mucosal and fecal samples were analyzed with 16S ribosomal RNA gene pyrosequencing, together with quantitative PCR of specific bacteria and archaea. RESULTS: The principal coordinates analysis clearly separated healthy tissue samples from polyps and tumors, supporting the presence of specific bacterial consortia that are associated with affected sites and that can serve as potential biomarkers of CRC progression. A higher presence of Fusobacterium nucleatum and Enterobacteriaceae was found by qPCR in samples from CRC compared to healthy controls. We observed a correlation between CRC process development and levels of Methanobacteriales (R = 0.537, P = 0.007) and Methanobrevibacterium (R = 0.574, P = 0.03) in fecal samples. CONCLUSION: Differences in microbial and archaeal composition between mucosal samples from healthy and disease tissues were observed in tubular adenoma and adenocarcinoma. In addition, microbiota from mucosal samples represented the underlying dysbiosis, whereas fecal samples seem not to be appropriate to detect shifts in microbial composition. CRC risk is influenced by microbial composition, showing differences according to disease progression step and tumor severity.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34212246", + "title": "Association of gut microbiomes with lung and esophageal cancer: a pilot study.", + "year": 2021, + "journal": "World journal of microbiology & biotechnology", + "authors": [ + "Shen W", + "Tang D", + "Deng Y", + "Li H", + "Wang T", + "Wan P", + "Liu R" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.34044821241623147, + "mesh_terms": [ + "Aged", + "Bacteria", + "Case-Control Studies", + "Esophageal Neoplasms", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Lung Neoplasms", + "Male", + "Middle Aged", + "Pilot Projects" + ], + "raw_abstract": "Gut microbiota, especially human pathogens, has been shown to be involved in the occurrence and development of cancer. Esophageal squamous cell carcinoma and lung cancer are two malignant cancers, and their relationship with gut microbiota is still unclear. Virulence factor database (VFDB) is an integrated and comprehensive online resource for curating information about human pathogens. Here, based on VFDB database, we analyzed the differences of bacteria at genus level in the gut of patients with esophageal squamous cell carcinoma, lung cancer, and healthy controls. We proposed the possible cancer-associated bacteria in gut and put forward their possible effects. Apart from this, principal coordinate analysis (PCoA) and analysis of similarities (ANSOIM) suggested that some bacteria in the gut can be used as potential biomarkers to screen esophageal squamous cell carcinoma and lung cancer, and their effectiveness was preliminary verified. The relative abundance of Klebsiella and Streptococcus can be used to distinguish patients with esophageal squamous cell carcinoma and lung cancer from healthy controls. The absolute abundance of Klebsiella can further distinguish patients with esophageal squamous cell carcinoma from patients with lung cancer. In particular, the relative abundance of Fusobacterium can directly distinguish between patients with esophageal squamous cell carcinoma and healthy controls. Additionally, the absolute abundance of Haemophilus can distinguish lung cancer from healthy controls. Our study provided a new way based on VFDB database to explore the relationship between gut microbiota and cancer, and initially proposed a feasible cancer screening method.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36703031", + "title": "Microbial dynamics with CRC progression: a study of the mucosal microbiota at multiple sites in cancers, adenomatous polyps, and healthy controls.", + "year": 2023, + "journal": "European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology", + "authors": [ + "Senthakumaran T", + "Moen AEF", + "Tann\u00e6s TM", + "Endres A", + "Brackmann SA", + "Rounge TB", + "Bemanian V", + "Tunsj\u00f8 HS" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3280940063730635, + "mesh_terms": [ + "Humans", + "RNA, Ribosomal, 16S", + "Fusobacterium nucleatum", + "Bacteria", + "Carcinogenesis", + "Gastrointestinal Microbiome", + "Adenomatous Polyps", + "Colorectal Neoplasms" + ], + "raw_abstract": "Accumulating evidence has related the gut microbiota to colorectal cancer (CRC). Fusobacterium nucleatum has repeatedly been linked to colorectal tumorigenesis. The aim of this study was to investigate microbial composition in different sampling sites, in order to profile the microbial dynamics with CRC progression. Further, we characterized the tumor-associated F. nucleatum subspecies. Here, we conducted Illumina Miseq next-generation sequencing of the 16S rRNA V4 region in biopsy samples, to investigate microbiota alterations in cancer patients, patients with adenomatous polyp, and healthy controls in Norway. Further, Fusobacterium positive tumor biopsies were subjected to MinION nanopore sequencing of Fusobacterium-specific amplicons to characterize the Fusobacterium species and subspecies. We found enrichment of oral biofilm-associated bacteria, Fusobacterium, Gemella, Parvimonas, Granulicatella, Leptotrichia, Peptostreptococcus, Campylobacter, Selenomonas, Porphyromonas, and Prevotella in cancer patients compared to adenomatous polyp patients and control patients. Higher abundance of amplicon sequence variants (ASVs) classified as Phascolarctobacterium, Bacteroides vulgatus, Bacteroides plebeius, Bacteroides eggerthii, Tyzzerella, Desulfovibrio, Frisingicoccus, Eubacterium coprostanoligenes\u00a0group, and Lachnospiraceae were identified in cancer and adenomatous polyp patients compared to healthy controls. F. nucleatum ssp. animalis was the dominating subspecies. F. nucleatum ssp. nucleatum, F. nucleatum ssp. vincentii, Fusobacterium pseudoperiodonticum, Fusobacterium necrophorum, and Fusobacterium gonidiaformans were identified in five samples. Several biofilm-associated bacteria were enriched at multiple sites in cancer patients. Another group of bacteria was enriched in both cancer and polyps, suggesting that they may have a role in polyp development and possibly early stages of CRC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26839545", + "title": "Quantitative Analysis of Intestinal Flora of Uygur and Han Ethnic Chinese Patients with Ulcerative Colitis.", + "year": 2016, + "journal": "Gastroenterology research and practice", + "authors": [ + "Yao P", + "Cui M", + "Wang H", + "Gao H", + "Wang L", + "Yang T", + "Cheng Y" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3253677638871584, + "mesh_terms": [], + "raw_abstract": "Aim. To study the correlation between intestinal flora and ulcerative colitis by analyzing the abundance of Bacteroides, Fusobacterium, Clostridium, Bifidobacterium spp., and Faecalibacterium prausnitzii in the intestinal of ulcerative colitis (UC) patients and healthy controls with Uygur and Han ethnic. Methods. Bacterial genomic DNA was extracted from fecal samples and analyzed with real-time fluorescence quantitative polymerase chain reaction (PCR) to identify the abundance of Bacteroides, Fusobacterium, Clostridium, Bifidobacterium spp., and Faecalibacterium prausnitzii. Results. The samples from UC patients, Uygur and Han ethnic combined, had higher abundance of Bacteroides (P = 0.026) but lower Clostridium (P = 0.004), Bifidobacterium spp. (P = 0.009), and Faecalibacterium prausnitzii (P = 0.008) than those from healthy controls. Among UC patients, Bacteroides population was raised in acute UC patients (P \u2264 0.05), while the abundance of Clostridium, Bifidobacterium spp., Fusobacterium, and Faecalibacterium prausnitzii decreased (P \u2264 0.05) compared with the remission. In both UC patients group and control group, no difference was observed in the abundance of these 5 bacteria between the Han and the Uygur group. Conclusions. Variations in the abundance of these five bacterial strains in intestines may be associated with the occurrence of UC in Uygur and Han populations; however, these variations were not associated with ethnic difference.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31671166", + "title": "Altered microbiota, fecal lactate, and fecal bile acids in dogs with gastrointestinal disease.", + "year": 2019, + "journal": "PloS one", + "authors": [ + "Blake AB", + "Guard BC", + "Honneffer JB", + "Lidbury JA", + "Steiner JM", + "Suchodolski JS" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3133888065024354, + "mesh_terms": [ + "Animals", + "Bile Acids and Salts", + "Diarrhea", + "Dog Diseases", + "Dogs", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Diseases", + "Gastrointestinal Microbiome", + "Intestinal Diseases", + "Lactic Acid", + "Male", + "Real-Time Polymerase Chain Reaction" + ], + "raw_abstract": "The intestinal microbiota plays an important role in health and disease and produces, through fermentative reactions, several metabolic products, such as lactate, that can affect the host. The microbiota also interacts with and metabolizes compounds produced by the host, such as primary bile acids. Lactate and bile acids (BA) are of particular interest in gastrointestinal diseases because they have been associated with metabolic acidosis and bile acid diarrhea, respectively. The objectives of this study were to validate an enzymatic assay to quantify D-, L-, and total lactate in canine feces, and to characterize fecal lactate and BA concentrations as well as bacterial abundances in healthy dogs and dogs with gastrointestinal diseases. Fecal samples were collected from 34 healthy dogs, 15 dogs with chronic enteropathy (CE), and 36 dogs with exocrine pancreatic insufficiency (EPI). Lactate was quantified with an enzymatic assay, BA with gas chromatography-mass spectrometry, and 11 bacterial groups with qPCR. A fecal lactate reference interval was established from 34 healthy dogs and was 0.7-1.4 mM, 0.3-6.0 mM, and 1.0-7.0 mM for D-, L-, and total lactate, respectively. The assay to measure D-, L-, and total lactate in canine fecal samples was linear, accurate, precise, and reproducible. Significant increases in fecal lactate and decreases in secondary BA concentrations were observed in dogs with CE and dogs with EPI. Dogs with EPI had an increased abundance of Escherichia coli, Lactobacillus, and Bifidobacterium; a decreased abundance of Fusobacterium and Clostridium hiranonis; and a higher Dysbiosis Index when compared to healthy dogs. Further studies are necessary to determine the clinical utility of lactate and BA quantification in canine feces. These metabolites suggest functional alterations of intestinal dysbiosis and may become promising targets for further elucidating the role of the microbiota in health and disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38366793", + "title": "The multispecies microbial cluster of Fusobacterium, Parvimonas, Bacteroides and Faecalibacterium as a precision biomarker for colorectal cancer diagnosis.", + "year": 2024, + "journal": "Molecular oncology", + "authors": [ + "Conde-P\u00e9rez K", + "Aja-Macaya P", + "Buetas E", + "Trigo-Tasende N", + "Nasser-Ali M", + "Rumbo-Feal S", + "Ni\u00f3n P", + "Arribas EM", + "Est\u00e9vez LS", + "Otero-Al\u00e9n B", + "Noguera JF", + "Concha \u00c1", + "Pardi\u00f1as-L\u00f3pez S", + "Carda-Di\u00e9guez M", + "G\u00f3mez-Randulfe I", + "Mart\u00ednez-Lago N", + "Ladra S", + "Aparicio LMA", + "Bou G", + "Mira \u00c1", + "Vallejo JA", + "Poza M" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3130490676603703, + "mesh_terms": [ + "Humans", + "Colorectal Neoplasms", + "Fusobacterium", + "Male", + "Female", + "Bacteroides", + "Middle Aged", + "Feces", + "Biomarkers, Tumor", + "Faecalibacterium", + "Aged", + "RNA, Ribosomal, 16S", + "Gastrointestinal Microbiome", + "Saliva", + "Adult" + ], + "raw_abstract": "The incidence of colorectal cancer (CRC) has increased worldwide, and early diagnosis is crucial to reduce mortality rates. Therefore, new noninvasive biomarkers for CRC are required. Recent studies have revealed an imbalance in the oral and gut microbiomes of patients with CRC, as well as impaired gut vascular barrier function. In the present study, the microbiomes of saliva, crevicular fluid, feces, and non-neoplastic and tumor intestinal tissue samples of 93 CRC patients and 30 healthy individuals without digestive disorders (non-CRC) were analyzed by 16S rRNA metabarcoding procedures. The data revealed that Parvimonas, Fusobacterium, and Bacteroides fragilis were significantly over-represented in stool samples of CRC patients, whereas Faecalibacterium and Blautia were significantly over-abundant in the non-CRC group. Moreover, the tumor samples were enriched in well-known periodontal anaerobes, including Fusobacterium, Parvimonas, Peptostreptococcus, Porphyromonas, and Prevotella. Co-occurrence patterns of these oral microorganisms were observed in the subgingival pocket and in the tumor tissues of CRC patients, where they also correlated with other gut microbes, such as Hungatella. This study provides new evidence that oral pathobionts, normally located in subgingival pockets, can migrate to the colon and probably aggregate with aerobic bacteria, forming synergistic consortia. Furthermore, we suggest that the group composed of Fusobacterium, Parvimonas, Bacteroides, and Faecalibacterium could be used to design an excellent noninvasive fecal test for the early diagnosis of CRC. The combination of these four genera would significantly improve the reliability of a discriminatory test with respect to others that use a single species as a unique CRC biomarker.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33227279", + "title": "Fusobacteriumnucleatum Adheres to Clostridioides difficile via the RadD Adhesin to Enhance Biofilm Formation in Intestinal Mucus.", + "year": 2021, + "journal": "Gastroenterology", + "authors": [ + "Engevik MA", + "Danhof HA", + "Auchtung J", + "Endres BT", + "Ruan W", + "Bass\u00e8res E", + "Engevik AC", + "Wu Q", + "Nicholson M", + "Luna RA", + "Garey KW", + "Crawford SE", + "Estes MK", + "Lux R", + "Yacyshyn MB", + "Yacyshyn B", + "Savidge T", + "Britton RA", + "Versalovic J" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3123383774374259, + "mesh_terms": [ + "Adhesins, Bacterial", + "Bacterial Adhesion", + "Biofilms", + "Bioreactors", + "Clostridioides difficile", + "Clostridium Infections", + "Feces", + "Flagella", + "Fusobacterium nucleatum", + "Gastrointestinal Microbiome", + "HT29 Cells", + "Humans", + "Intestinal Mucosa", + "Mucin-2" + ], + "raw_abstract": "BACKGROUND & AIMS: Although Clostridioides difficile infection (CDI) is known to involve the disruption of the gut microbiota, little is understood regarding how mucus-associated microbes interact with C difficile. We hypothesized that select mucus-associated bacteria would promote C difficile colonization and biofilm formation. METHODS: To create a model of the human intestinal mucus layer and gut microbiota, we used bioreactors inoculated with healthy human feces, treated with clindamycin and infected with C difficile with the addition of human MUC2-coated coverslips. RESULTS: C difficile was found to colonize and form biofilms on MUC2-coated coverslips, and 16S rRNA sequencing showed a unique biofilm profile with substantial cocolonization with Fusobacterium species. Consistent with our bioreactor data, publicly available data sets and patient stool samples showed that a subset of patients with C difficile infection harbored high levels of Fusobacterium species. We observed colocalization of C difficile and F nucleatum in an aggregation assay using adult patients and stool of pediatric patients with inflammatory bowel disease and in tissue sections of patients with CDI. C difficile strains were found to coaggregate with F nucleatum subspecies in\u00a0vitro; an effect that was inhibited by blocking or mutating the adhesin RadD on Fusobacterium and removal of flagella on C difficile. Aggregation was shown to be unique between F nucleatum and C difficile, because other gut commensals did not aggregate with C difficile. Addition of F nucleatum also enhanced C difficile biofilm formation and extracellular polysaccharide production. CONCLUSIONS: Collectively, these data show a unique interaction of between pathogenic C difficile and F nucleatum in the intestinal mucus layer.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36991009", + "title": "Mendelian randomization analyses reveal causal relationships between the human microbiome and longevity.", + "year": 2023, + "journal": "Scientific reports", + "authors": [ + "Liu X", + "Zou L", + "Nie C", + "Qin Y", + "Tong X", + "Wang J", + "Yang H", + "Xu X", + "Jin X", + "Xiao L", + "Zhang T", + "Min J", + "Zeng Y", + "Jia H", + "Hou Y" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.30752074846839883, + "mesh_terms": [ + "Aged, 80 and over", + "Humans", + "Longevity", + "Genome-Wide Association Study", + "Mendelian Randomization Analysis", + "Microbiota", + "Lactobacillus acidophilus" + ], + "raw_abstract": "Although recent studies have revealed the association between the human microbiome especially gut microbiota and longevity, their causality remains unclear. Here, we assess the causal relationships between the human microbiome (gut and oral microbiota) and longevity, by leveraging bidirectional two-sample Mendelian randomization (MR) analyses based on genome-wide association studies (GWAS) summary statistics of the gut and oral microbiome from the 4D-SZ cohort and longevity from the CLHLS cohort. We found that some disease-protected gut microbiota such as Coriobacteriaceae and Oxalobacter as well as the probiotic Lactobacillus amylovorus were related to increased odds of longevity, whereas the other gut microbiota such as colorectal cancer pathogen Fusobacterium nucleatum, Coprococcus, Streptococcus, Lactobacillus, and Neisseria were negatively associated with longevity. The reverse MR analysis further revealed genetically longevous individuals tended to have higher abundances of Prevotella and Paraprevotella but lower abundances of Bacteroides and Fusobacterium species. Few overlaps of gut microbiota-longevity interactions were identified across different populations. We also identified abundant links between the oral microbiome and longevity. The additional analysis suggested that centenarians genetically had a lower gut microbial diversity, but no difference in oral microbiota. Our findings strongly\u00a0implicate\u00a0these\u00a0bacteria\u00a0to\u00a0play\u00a0a\u00a0role\u00a0in\u00a0human\u00a0longevity and underscore the relocation of commensal microbes among different body sites that would need to be monitored for long and healthy life.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30349083", + "title": "Recovery of gut microbiota of healthy adults following antibiotic exposure.", + "year": 2018, + "journal": "Nature microbiology", + "authors": [ + "Palleja A", + "Mikkelsen KH", + "Forslund SK", + "Kashani A", + "Allin KH", + "Nielsen T", + "Hansen TH", + "Liang S", + "Feng Q", + "Zhang C", + "Pyl PT", + "Coelho LP", + "Yang H", + "Wang J", + "Typas A", + "Nielsen MF", + "Nielsen HB", + "Bork P", + "Wang J", + "Vilsb\u00f8ll T", + "Hansen T", + "Knop FK", + "Arumugam M", + "Pedersen O" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3049850533758888, + "mesh_terms": [ + "Adolescent", + "Adult", + "Anti-Bacterial Agents", + "Bacteria", + "Bacterial Physiological Phenomena", + "Biodiversity", + "Drug Resistance, Bacterial", + "Feces", + "Gastrointestinal Microbiome", + "Genes, Bacterial", + "Healthy Volunteers", + "Humans", + "Male", + "Metagenomics", + "Virulence Factors", + "Young Adult" + ], + "raw_abstract": "To minimize the impact of antibiotics, gut microorganisms harbour and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing-based metagenomics, we analysed the partial eradication and subsequent regrowth of the gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 last-resort antibiotics: meropenem, gentamicin and vancomycin. Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and the depletion of Bifidobacterium species and butyrate producers. The gut microbiota of the subjects recovered to near-baseline composition within 1.5 months, although 9 common species, which were present in all subjects before the treatment, remained undetectable in most of the subjects after 180 days. Species that harbour \u03b2-lactam resistance genes were positively selected for during and after the intervention. Harbouring glycopeptide or aminoglycoside resistance genes increased the odds of de novo colonization, however, the former also decreased the odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention and their antibiotics resistance gene carriage modulates their recovery processes.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33789570", + "title": "Bacterial community structure alterations within the colorectal cancer gut microbiome.", + "year": 2021, + "journal": "BMC microbiology", + "authors": [ + "Loftus M", + "Hassouneh SA", + "Yooseph S" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.30450074230992036, + "mesh_terms": [ + "Bacteria", + "Biodiversity", + "Colorectal Neoplasms", + "Feces", + "Gastrointestinal Microbiome", + "Genome, Bacterial", + "High-Throughput Nucleotide Sequencing", + "Humans" + ], + "raw_abstract": "BACKGROUND: Colorectal cancer is a leading cause of cancer-related deaths worldwide. The human gut microbiome has become an active area of research for understanding the initiation, progression, and treatment of colorectal cancer. Despite multiple studies having found significant alterations in the carriage of specific bacteria within the gut microbiome of colorectal cancer patients, no single bacterium has been unequivocally connected to all cases. Whether alterations in species carriages are the cause or outcome of cancer formation is still unclear, but what is clear is that focus should be placed on understanding changes to the bacterial community structure within the cancer-associated gut microbiome. RESULTS: By applying a novel set of analyses on 252 previously published whole-genome shotgun sequenced fecal samples from healthy and late-stage colorectal cancer subjects, we identify taxonomic, functional, and structural changes within the cancer-associated human gut microbiome. Bacterial association networks constructed from these data exhibited widespread differences in the underlying bacterial community structure between healthy and colorectal cancer associated gut microbiomes. Within the cancer-associated ecosystem, bacterial species were found to form associations with other species that are taxonomically and functionally dissimilar to themselves, as well as form modules functionally geared towards potential changes in the tumor-associated ecosystem. Bacterial community profiling of these samples revealed a significant increase in species diversity within the cancer-associated gut microbiome, and an elevated relative abundance of species classified as originating from the oral microbiome including, but not limited to, Fusobacterium nucleatum, Peptostreptococcus stomatis, Gemella morbillorum, and Parvimonas micra. Differential abundance analyses of community functional capabilities revealed an elevation in functions linked to virulence factors and peptide degradation, and a reduction in functions involved in amino-acid biosynthesis within the colorectal cancer gut microbiome. CONCLUSIONS: We utilize whole-genome shotgun sequenced fecal samples provided from a large cohort of late-stage colorectal cancer and healthy subjects to identify a number of potentially important taxonomic, functional, and structural alterations occurring within the colorectal cancer associated gut microbiome. Our analyses indicate that the cancer-associated ecosystem influences bacterial partner selection in the native microbiota, and we highlight specific oral bacteria and their associations as potentially relevant towards aiding tumor progression.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32393255", + "title": "Gut microbiota in early pregnancy among women with Hyperglycaemia vs. Normal blood glucose.", + "year": 2020, + "journal": "BMC pregnancy and childbirth", + "authors": [ + "Gao B", + "Zhong M", + "Shen Q", + "Wu Y", + "Cao M", + "Ju S", + "Chen L" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.3044943292360826, + "mesh_terms": [ + "Adult", + "Blood Glucose", + "Case-Control Studies", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Hyperglycemia", + "Pregnancy", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Recent studies suggest that there is a link between the gut microbiota and glucose metabolism. This study aimed to compare the gut microbiota during early pregnancy of women with hyperglycymia to those with normal blood glucose. METHODS: Gut microbial composition\u2009was\u2009analysed in 22 women with hyperglycaemia and 28 age-matched\u2009healthy\u2009controls during their first prenatal visits (<\u200920\u2009weeks) using\u2009high throughput sequencing\u2009of\u2009the\u2009V3-V4\u2009region\u2009of\u2009the\u200916S\u2009ribosomal\u2009RNA\u2009gene. Hyperglycemia was diagnosed based on the criteria recommended by the International Association of Diabetes and Pregnancy Study Groups in 2010. RESULTS: Women with hyperglycemia in pregnancy (HIP) had significantly lower microbial richness and diversity compared with healthy pregnant women. The proportions of the Firmicutes and Bacteroidetes phyla and the ratio of Firmicutes:Bacteroidetes were not different between the two groups. We observed\u2009that individuals with HIP had an increased\u2009abundance\u2009of Nocardiaceae, Fusobacteriaceae, etc., whereas healthy controls had significantly higher levels of Christensenellaceae, Clostridiales_vadinBB60_group, Coriobacteriaceae, etc. Similarly, levels of the members of the Ruminococcaceae family, including Ruminococcaceae_UCG-014, Ruminococcaceae_UCG-003, and Ruminococcaceae_UCG-002, were significantly reduced in the HIP group and were negatively correlated with HbA1c. HbA1c levels were positively correlated with Bacteroidaceae and Enterobacteriaceae and negatively correlated with Christensenellaceae, etc. CRP was positively correlated with the Bacteroidaceae and Fusobacteriaceae families and the Fusobacterium genus. CONCLUSIONS: Our study revealed that individuals with HIP have gut microbial dysbiosis and that certain bacterial groups are associated with glucose metabolism during pregnancy. Further study is needed to provide new ideas to control glucose by modifying the gut microbiota.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38689063", + "title": "Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development.", + "year": 2024, + "journal": "Nature medicine", + "authors": [ + "Tito RY", + "Verbandt S", + "Aguirre Vazquez M", + "Lahti L", + "Verspecht C", + "Llor\u00e9ns-Rico V", + "Vieira-Silva S", + "Arts J", + "Falony G", + "Dekker E", + "Reumers J", + "Tejpar S", + "Raes J" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2983167629668599, + "mesh_terms": [ + "Humans", + "Colorectal Neoplasms", + "Middle Aged", + "Feces", + "Female", + "Aged", + "Male", + "RNA, Ribosomal, 16S", + "Adult", + "Gastrointestinal Microbiome", + "Aged, 80 and over", + "Young Adult", + "Microbiota", + "Leukocyte L1 Antigen Complex" + ], + "raw_abstract": "Despite substantial progress in cancer microbiome research, recognized confounders and advances in absolute microbiome quantification remain underused; this raises concerns regarding potential spurious associations. Here we study the fecal microbiota of 589 patients at different colorectal cancer (CRC) stages and compare observations with up to 15 published studies (4,439 patients and controls total). Using quantitative microbiome profiling based on 16S ribosomal RNA amplicon sequencing, combined with rigorous confounder control, we identified transit time, fecal calprotectin (intestinal inflammation) and body mass index as primary microbial covariates, superseding variance explained by CRC diagnostic groups. Well-established microbiome CRC targets, such as Fusobacterium nucleatum, did not significantly associate with CRC diagnostic groups (healthy, adenoma and carcinoma) when controlling for these covariates. In contrast, the associations of Anaerococcus vaginalis, Dialister pneumosintes, Parvimonas micra, Peptostreptococcus anaerobius, Porphyromonas asaccharolytica and Prevotella intermedia remained robust, highlighting their future target potential. Finally, control individuals (age 22-80\u2009years, mean 57.7\u2009years, standard deviation 11.3) meeting criteria for colonoscopy (for example, through a positive fecal immunochemical test) but without colonic lesions are enriched for the dysbiotic Bacteroides2 enterotype, emphasizing uncertainties in defining healthy controls in cancer microbiome research. Together, these results indicate the importance of quantitative microbiome profiling and covariate control for biomarker identification in CRC microbiome studies.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36239621", + "title": "The Oral Microbiome in Treatment-Na\u00efve Paediatric IBD Patients Exhibits Dysbiosis Related to Disease Severity that Resolves Following Therapy.", + "year": 2023, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Elmaghrawy K", + "Fleming P", + "Fitzgerald K", + "Cooper S", + "Dominik A", + "Hussey S", + "Moran GP" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.29292418220008304, + "mesh_terms": [ + "Humans", + "Child", + "Dysbiosis", + "Gastrointestinal Microbiome", + "Feces", + "Inflammatory Bowel Diseases", + "Microbiota", + "Patient Acuity" + ], + "raw_abstract": "BACKGROUND: There is a limited literature describing the oral microbiome and its diagnostic potential in paediatric inflammatory bowel disease [IBD]. METHODS: We examined the dorsum tongue microbiome by V1-V2 sequencing in a cohort of 156 treatment-na\u00efve children diagnosed with IBD compared to 102 healthy control children. Microbiome changes over time following treatment were examined in a subset of patients and associations between IBD diagnosis and dysbiosis were explored. RESULTS: Analysis of community structure of the microbiome in tongue samples revealed that IBD samples diverged significantly from healthy control samples [PERMANOVA p\u2005=\u20050.0009] and exhibited a reduced abundance of Clostridia in addition to several major oral genera [Veillonella, Prevotella and Fusobacterium species] with an increased abundance of streptococci. This dysbiosis was more marked in patients with severe disease. Higher levels of the potential pathobionts Klebsiella and Pseudomonas spp. were also associated with IBD. In terms of predicted functions, the IBD oral microbiome was potentially more acidogenic and exhibited reduced capacity for B vitamin biosynthesis. We used a machine learning approach to develop a predictive model of IBD which exhibited a mean-prediction AUC [area under the ROC curve] of 0.762. Finally, we examined a subset of 53 patients following 12 months of therapy and could show resolution of oral dysbiosis as demonstrated by a shift towards a healthy community structure and a significant reduction in oral dysbiosis. CONCLUSION: Oral dysbiosis found in children with IBD is related to disease severity and resolves over time following successful IBD treatment.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35902689", + "title": "Microbial dysbiosis and fecal metabolomic perturbations in Yorkshire Terriers with chronic enteropathy.", + "year": 2022, + "journal": "Scientific reports", + "authors": [ + "Galler AI", + "Suchodolski JS", + "Steiner JM", + "Sung CH", + "Hittmair KM", + "Richter B", + "Burgener IA" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2856353997649171, + "mesh_terms": [ + "Animals", + "Bile Acids and Salts", + "Dog Diseases", + "Dogs", + "Dysbiosis", + "Fatty Acids", + "Feces", + "Inflammatory Bowel Diseases", + "Sterols" + ], + "raw_abstract": "Dysbiosis and perturbations of fecal metabolic profiles have been reported in dogs with inflammatory bowel disease. Currently the incidence of dysbiosis and the fecal metabolomic profile in Yorkshire Terriers with chronic enteropathy (YTE) and the effects of treatment are unknown. This prospective observational study analyzed the dysbiosis index (DI) and fecal bile acid, sterol and fatty acid profiles in 14 Yorkshire Terriers with active YTE, 11 dogs in clinical remission, and 26 healthy Yorkshire Terriers. YTE was associated with dysbiosis and a significant increase in fatty acids (docosanoate, p\u2009=\u20090.002; gondoate, p\u2009=\u20090.026; erucate, p\u2009<\u20090.001; nervonate, p\u2009<\u20090.001; linolenate, p\u2009<\u20090.001), and plant sterols (campesterol, p\u2009<\u20090.001; brassicasterol, p\u2009=\u20090.024). The abundances of Fusobacterium (p\u2009<\u20090.001) and Cl. hiranonis (p\u2009=\u20090.018) and the concentrations of the secondary bile acid ursodeoxycholic acid (p\u2009=\u20090.033) and the plant sterol sitostanol (p\u2009=\u20090.003) were significantly decreased compared to healthy dogs. Dysbiosis, abundances of Fusobacterium, Cl. hiranonis and fecal concentrations of bile acids and sterols did not recover after treatment, while fecal fatty acid concentrations decreased in treated dogs. YTE is associated with dysbiosis and changes in bile acid, fatty acid, and sterol metabolism. These changes only recovered partially despite clinical remission. They might be breed-specific and involved in the pathogenesis of YTE.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33407128", + "title": "Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals.", + "year": 2021, + "journal": "BMC microbiology", + "authors": [ + "Xie Y", + "Sun J", + "Wei L", + "Jiang H", + "Hu C", + "Yang J", + "Huang Y", + "Ruan B", + "Zhu B" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.27945146593191994, + "mesh_terms": [ + "Adult", + "Antiretroviral Therapy, Highly Active", + "Bacteria", + "CD4-CD8 Ratio", + "CD4-Positive T-Lymphocytes", + "CD8-Positive T-Lymphocytes", + "Case-Control Studies", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "HIV Infections", + "Humans", + "Male", + "Metagenomics", + "Middle Aged", + "Phylogeny", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Although gut microbiota dysbiosis has been reported in HIV infected individuals recently, the relationship between the gut microbiota and immune activation in patients with different immune responses to highly active antiretroviral therapy (HAART) is still not well understood. Gut microbiota and immune activation were studied in 36 non-HIV-infected subjects (healthy controls) and 58 HIV-infected individuals, including 28 immunological responders (IR) and 30 immunological non-responders (INR) (\u2265500 and\u2009<\u2009200 CD4+ T-cell counts/\u03bcl after 2\u2009years of HIV-1 viral suppression respectively) without comorbidities. RESULTS: Metagenome sequencing revealed that HIV-infected immunological responders and immunological non-responders could not recover completely from the gut microbiota dysbiosis. At a 97% similarity level, the relative abundances of Fusobacterium, Ruminococcus gnavus and Megamonas were greater, whereas Faecalibacterium, Alistipes, Bifidobacterium, Eubacterium rectale and Roseburia were more depleted in the IR and INR groups than those in the healthy controls. Ruminococcaceae and Alistipes were positively correlated with nadir and current CD4+ T-cell counts, but negatively correlated with CD8\u2009+\u2009CD57+ T-cell counts. Inflammation markers and translocation biomarkers (LPS) levels were positively correlated with the abundances of genera Ruminococcus and Fusobacterium but were negatively correlated with the genus Faecalibacterium. The relative abundances of Escherichia-Shigella and Blautia were significantly higher in the IR than those in the INR group. Escherichia-Shigella were negatively correlated with the CD4/CD8 ratio but positively correlated with the amount of CD8\u2009+\u2009CD57+ T-cells. Roseburia and Blautia were negatively associated with nadir CD4+ T-cell and positively associated with CD8\u2009+\u2009CD57+ T-cell counts. CONCLUSIONS: Gut microbiota dysbiosis may be one of the factors contributing to different immune responses and treatment outcomes to HAART.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29969632", + "title": "Faecal microRNA as a biomarker of the activity and prognosis of inflammatory bowel diseases.", + "year": 2018, + "journal": "Biochemical and biophysical research communications", + "authors": [ + "Ji Y", + "Li X", + "Zhu Y", + "Li N", + "Zhang N", + "Niu M" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.27744473395237135, + "mesh_terms": [ + "Adult", + "Bacteria", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "MicroRNAs", + "Middle Aged", + "Phylogeny", + "Prognosis", + "RNA, Bacterial", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Reasons underlying the individual differences in the clinical manifestations of inflammatory bowel diseases (IBD) and the mechanism by which the host screens the intestinal microbiota remain unclear. The presence of miRNA in faeces might be a potential clue into differences in gut microbiota among these patients. In this study, we analysed the differences in miRNA levels in faecal samples from 117 patients diagnosed with IBD. There was a significant difference in faecal miRNAs between healthy subjects and those with inactive IBD. Further analysis showed that some miRNAs might indicate the severity of IBD activity and prognosis. Sequencing analysis of the 16S RNA V4 region in faecal microbiota in these IBD patients revealed significant differences in the phylogenetic architecture between subjects with active or inactive IBD and between IBD patients and healthy subjects. Finally, in\u00a0vitro studies showed that these differentially expressed miRNAs have different effects on the proliferative activity of the intestinal microorganisms Fusobacterium nucleatum (Fn), Escherichia coli (E.\u00a0coli) and segmental filamentous bacteria (SFB). We observed the dynamic uptake of miRNA by these bacteria using flow cytometry. This study reveals a potential link between faecal miRNA, intestinal microbiota, IBD activity and prognosis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36719965", + "title": "Association Between Diet and Fusobacterium nucleatum in the Feces of Healthy Adults: A Hospital-based Cross-sectional Study.", + "year": 2023, + "journal": "Cancer prevention research (Philadelphia, Pa.)", + "authors": [ + "Narii N", + "Zha L", + "Sobue T", + "Kitamura T", + "Shiba S", + "Mizutani S", + "Yamada T", + "Yachida S" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2766844533221742, + "mesh_terms": [], + "raw_abstract": "UNLABELLED: Fusobacterium nucleatum is involved in the development and progression of colorectal cancer. Although the gut microbiota is influenced by diet, studies on the association between diet and F. nucleatum are limited. We aimed to evaluate the association between various dietary factors and fecal F. nucleatum in healthy adults without a history of colorectal cancer or precancerous lesions. This was a cross-sectional study. Subjects who underwent total colonoscopy at the National Cancer Center Hospital (Tokyo, Japan) were included. Healthy subjects (n = 212) were divided into two groups according to the presence or absence of F. nucleatum in their feces which was calculated from data of whole-genome shotgun sequencing, with the group with F. nucleatum serving as cases and the group without F. nucleatum serving as controls. Multivariable logistic regression analysis adjusted potential confounders was conducted to estimate the associations between dietary intake and nutrients estimated by a validated food frequency questionnaire and the presence of F. nucleatum in the feces. There was a significant inverse association between dairy products and the presence of fecal F. nucleatum [high vs. low; OR, 0.41; 95% confidence interval, 0.17-0.95; Ptrend, 0.039]. These results may have important implications for colorectal cancer prevention through nutritional intervention. PREVENTION RELEVANCE: F. nucleatum is well known as a colorectal cancer-associated bacterium. Dietary habits alter the composition and function of the intestinal microbiota. A high intake of dairy products in healthy adults may reduce F. nucleatum and prevent colorectal cancer.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29926167", + "title": "Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects.", + "year": 2019, + "journal": "Journal of gastroenterology", + "authors": [ + "Takagi T", + "Naito Y", + "Inoue R", + "Kashiwagi S", + "Uchiyama K", + "Mizushima K", + "Tsuchiya S", + "Dohi O", + "Yoshida N", + "Kamada K", + "Ishikawa T", + "Handa O", + "Konishi H", + "Okuda K", + "Tsujimoto Y", + "Ohnogi H", + "Itoh Y" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2762419531536453, + "mesh_terms": [ + "Adult", + "Age Factors", + "Aged", + "Aged, 80 and over", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Japan", + "Male", + "Middle Aged", + "Sex Factors", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Human gut microbiota is involved in host health and disease development. Investigations of age-related and sex-related alterations in gut microbiota are limited, and the association between stool consistency and gut microbiota has not been fully investigated. We investigated gut microbiota differences related to age, sex, and stool consistency in healthy Japanese subjects. METHODS: Two-hundred and seventy-seven healthy Japanese subjects aged 20-89\u00a0years were enrolled. Fecal samples were obtained to analyze the gut microbiome. We evaluated the association between stool consistency [Bristol stool scale (BSS)] and gut microbiota. RESULTS: Although there were significant differences in the microbial structure between males and females, the \u03b1-diversity of gut microbiota showed no difference between males and females or among age groups. There were significant increases in genera Prevotella, Megamonas, Fusobacterium, and Megasphaera and Bifidobacterium, Ruminococcus, and Akkermansia in males and females, respectively. The ratio of hard stools (BSS types 1 and 2) was higher in females; the ratio of loose stools (BSS type 6) was higher in males. No younger male had BSS type 1 or type 2. Fusobacterium in males was significantly higher in the loose consistency group, and Oscillospira was significantly higher in the hard consistency group in males; Campylobacter, SMB53, and Turicibacter were significantly higher in the hard consistency group in females. CONCLUSIONS: Several changes in gut microbiota were associated with age and sex. Stool consistency and gut microbiota associations emphasized the importance of stool consistency assessments to understand intestinal function.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31410749", + "title": "Response of gut microbiota in type 2 diabetes to hypoglycemic agents.", + "year": 2019, + "journal": "Endocrine", + "authors": [ + "Zhang F", + "Wang M", + "Yang J", + "Xu Q", + "Liang C", + "Chen B", + "Zhang J", + "Yang Y", + "Wang H", + "Shang Y", + "Wang Y", + "Mu X", + "Zhu D", + "Zhang C", + "Yao M", + "Zhang L" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.27572511416457773, + "mesh_terms": [ + "Aged", + "Case-Control Studies", + "Diabetes Mellitus, Type 2", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Hyperglycemia", + "Hypoglycemic Agents", + "Male", + "Middle Aged" + ], + "raw_abstract": "PURPOSE: Accumulated evidence has indicated that the gut microbiome affected the pharmacology of anti-diabetic agents, and their metabolic products induced by the agents transformed the structure of gastrointestinal microbiota in return. However, the studies around heredity, ethnicity, or living condition, referring to human microbiome were mostly represented by an occidental pattern partial and rare studies that focused on the effect of several first-line hypoglycemic agents on the gut flora in a single medical center. Therefore, we aimed to explore the interaction between gut microbiome and type 2 diabetes (T2D) or hypoglycemics in Chinese population. METHODS: A total of 130 T2D patients with a specific hypoglycemic treatment and 50 healthy volunteers were enrolled in this study. Gut microbiome compositons were analyzed by 16S ribosomal RNA gene-based sequencing protocol. RESULTS: Hypoglycemic agents contributed to the alteration of specific species in gut bacteria rather than its total diversity. Metformin increased the abundance of Spirochaete, Turicibacter, and Fusobacterium. Insulin also increased Fusobacterium, and \u03b1-glucosidase inhibitors (\u03b1-GIs) contributed to the plentitude of Bifidobacterium and Lactobacillus. Both metformin and insulin improved taurine and hypotaurine metabolism, and \u03b1-GI promoted several amino acid pathways. Although the community of gut microbiota with metformin and insulin showed similarity, significant differences were available in each diabetic group with hypoglycemia. CONCLUSIONS: Gut microbiota is significantly associated with anti-diabetic agents. The gut microbiome and metabolism have shown respective characteristics in different T2D groups, which were also significantly different from the healthy group. This study provides some new insights for identification and exploration of the pathogenesis of T2D.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30029052", + "title": "Altered gut microbiota profile in patients with generalized anxiety disorder.", + "year": 2018, + "journal": "Journal of psychiatric research", + "authors": [ + "Jiang HY", + "Zhang X", + "Yu ZH", + "Zhang Z", + "Deng M", + "Zhao JH", + "Ruan B" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2695057014437089, + "mesh_terms": [ + "Adult", + "Anxiety Disorders", + "Case-Control Studies", + "Cohort Studies", + "Cross-Sectional Studies", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Male", + "Statistics, Nonparametric" + ], + "raw_abstract": "Close relationships have recently been established between gut microbiota and some mental disorders. Here, we performed a systematic comparative analysis of the gut microbiome in patients with generalized anxiety disorder (GAD) and healthy controls (HCs). We first conducted a cross-sectional study of 40 patients with GAD in the active state and 36\u202fHCs. Second, subgroup analysis consisting of 12 antidepressant-naive patients and 22 controls was performed to validate the results. Finally, a prospective study was performed in a subgroup of nine patients with GAD who underwent analysis in the active state of anxiety and in remission. Compared with the HCs, we found markedly decreased microbial richness and diversity, distinct metagenomic composition with reduced short-chain fatty acid (SCFA)-producing bacteria (associated with a healthy status) and overgrowth of bacteria, such as Escherichia-Shigella, Fusobacterium and Ruminococcus gnavus. Unexpectedly, these changes in the genera were not reversed in remissive GAD. This study identified microbiota dysbiosis of gut microbiota in GAD patients, suggesting that targeting the microbiome may be a useful therapeutic and preventive target for GAD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36474311", + "title": "Association between Diet and Fusobacterium nucleatum in the Feces of Healthy Adults: A hospital-based cross-sectional study.", + "year": 2022, + "journal": "Cancer prevention research (Philadelphia, Pa.)", + "authors": [ + "Narii N", + "Zha L", + "Sobue T", + "Kitamura T", + "Shiba S", + "Mizutani S", + "Yamada T", + "Yachida S" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2694382277970283, + "mesh_terms": [], + "raw_abstract": "Fusobacterium nucleatum is involved in the development and progression of colorectal cancer. Although the gut microbiota is influenced by diet, studies on the association between diet and F. nucleatum are limited. We aimed to evaluate the association between various dietary factors and fecal F. nucleatum in healthy adults without a history of colorectal cancer or precancerous lesions. This was a cross-sectional study. Subjects who underwent total colonoscopy at the National Cancer Center Hospital (Tokyo, Japan) were included. Healthy subjects (n = 212) were divided into two groups according to the presence or absence of F. nucleatum in their feces which was calculated from data of whole-genome shotgun sequencing, with the group with F. nucleatum serving as cases and the group without F. nucleatum serving as controls. Multivariable logistic regression analysis adjusted potential confounders was conducted to estimate the associations between dietary intake and nutrients estimated by a validated food frequency questionnaire and the presence of F. nucleatum in the feces. There was a significant inverse association between dairy products and the presence of fecal F. nucleatum (High vs. Low, OR 0.41, 95% CI 0.17-0.95, P for trend 0.039). These results may have important implications for colorectal cancer prevention through nutritional intervention.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36790675", + "title": "Progress of gut microbiome and its metabolomics in early screening of colorectal cancer.", + "year": 2023, + "journal": "Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico", + "authors": [ + "Zhou L", + "Jiang Z", + "Zhang Z", + "Xing J", + "Wang D", + "Tang D" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2588600940987086, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Early Detection of Cancer", + "Metabolomics", + "Microbiota", + "Biomarkers", + "Colorectal Neoplasms" + ], + "raw_abstract": "Gut microbes are widely considered to be closely associated with colorectal cancer (CRC) development. The microbiota is regarded as a potential identifier of CRC, as several studies have found great significant changes in CRC patients' microbiota and metabolic groups. Changes in microbiota, like Fusobacterium nucleatum and Bacteroides fragilis, also alter the metabolic activity of the host, promoting CRC development. In contrast, the metabolome is an intuitive discriminative biomarker as a small molecular bridge to distinguish CRC from healthy individuals due to the direct action of microbes on the host. More diagnostic microbial markers have been found, and the potential discriminatory power of microorganisms in CRC has been investigated through the combined use of biomic genomic metabolomics, bringing new ideas for screening fecal microbial markers. In this paper, we discuss the potential of microorganisms and their metabolites as biomarkers in CRC screening, hoping to provide thoughts and references for non-invasive screening of CRC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37681574", + "title": "Longitudinal effects of oral administration of antimicrobial drugs on fecal microbiota of horses.", + "year": 2023, + "journal": "Journal of veterinary internal medicine", + "authors": [ + "Gomez D", + "Toribio R", + "Caddey B", + "Costa M", + "Vijan S", + "Dembek K" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2569611752326107, + "mesh_terms": [ + "Animals", + "Horses", + "Metronidazole", + "Doxycycline", + "Longitudinal Studies", + "Prospective Studies", + "RNA, Ribosomal, 16S", + "Anti-Infective Agents", + "Microbiota", + "Trimethoprim, Sulfamethoxazole Drug Combination", + "Administration, Oral", + "Diarrhea", + "Erythromycin" + ], + "raw_abstract": "BACKGROUND: Antimicrobial drug-associated diarrhea (AAD) is the most common adverse effect in horses receiving antimicrobials. Little information on how oral administration of antimicrobials alters intestinal microbiota in horses is available. OBJECTIVE: Investigate changes of the fecal microbiota in response to oral administration of antimicrobials. ANIMALS: Twenty healthy horses. METHODS: Prospective, longitudinal study. Horses were randomly assigned to 4 groups comprising 4 horses each: group 1 (metronidazole); group 2 (erythromycin); group 3 (doxycycline); group 4 (sulfadiazine/trimethoprim, SMZ-TMP); and group 5 (control). Antimicrobials were administered for 5\u2009days. Fecal samples were obtained before (day 0) and at 1, 2, 3, 4, 5, 6, and 30\u2009days of the study period. Fecal microbiota was characterized by high throughput sequencing of the V4 region of the 16S rRNA. RESULTS: Horses remained healthy throughout the study. Richness and diversity in doxycycline, erythromycin, and metronidazole, but not SMZ-TMP groups, was significantly lower (P\u2009<\u2009.05) at multiple time points after administration of antimicrobials compared with samples from day 0. Main changes in the microbiota were observed during the time of antimicrobial administration (day 2-5; weighted and unweighted UniFrac PERMANOVA P\u2009<\u2009.05). Administration of erythromycin, doxycycline and, to a lesser extent, metronidazole produced a pronounced alteration in the microbiota compared with day 0 samples by decreasing the abundance of Treponema, Fibrobacter, and Lachnospiraceae and increasing Fusobacterium and Escherichia-Shigella. CONCLUSIONS AND CLINICAL IMPORTANCE: Oral administration of antimicrobials alters the intestinal microbiota of healthy horses resembling horses with dysbiosis, potentially resulting in intestinal inflammation and predisposition to diarrhea.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39761011", + "title": "Association of gut microbiota and gut metabolites and adverse outcomes in biliary atresia: A longitudinal prospective study.", + "year": 2024, + "journal": "Hepatology communications", + "authors": [ + "Jain V", + "Dalby MJ", + "Alexander EC", + "Burford C", + "Acford-Palmer H", + "Serghiou IR", + "Teng NMY", + "Kiu R", + "Gerasimidis K", + "Zafeiropoulou K", + "Logan M", + "Verma A", + "Davenport M", + "Hall LJ", + "Dhawan A" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2555277925583577, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Biliary Atresia", + "Feces", + "Male", + "Female", + "Prospective Studies", + "Infant", + "Longitudinal Studies", + "Portoenterostomy, Hepatic", + "RNA, Ribosomal, 16S", + "Enterococcus", + "Case-Control Studies", + "Infant, Newborn", + "Bifidobacterium" + ], + "raw_abstract": "BACKGROUND: The Kasai portoenterostomy (KPE) aims to re-establish bile flow in biliary atresia (BA); however, BA remains the commonest indication for liver transplantation in pediatrics. Gut microbiota-host interplay is increasingly associated with outcomes in chronic liver disease. This study characterized fecal microbiota and fatty acid metabolites in BA. METHODS: Fecal samples were prospectively collected in newly diagnosed BA infants (n = 55) before and after KPE. Age-matched healthy control (n = 19) and cholestatic control (n = 21) fecal samples were collected. Fecal 16S rRNA gene amplicon sequencing for gut microbiota and gas chromatography for fecal fatty acids was performed. RESULTS: Increased abundance of Enterococcus in pre-KPE BA and cholestatic control infants, compared to healthy infants, was demonstrated. At the early post-KPE time points, increased alpha diversity was revealed in BA versus healthy cohorts. A lower relative abundance of Bifidobacterium and increased Enterococcus, Clostridium, Fusobacterium, and Pseudomonas was seen in infants with BA. Fecal acetate was reduced, and fecal butyrate and propionate were elevated in early post-KPE BA infants. Higher post-KPE alpha diversity was associated with nonfavorable clinical outcomes (6-month jaundice and liver transplantation). A higher relative abundance of post-KPE Streptococcus and Fusobacterium and a lower relative abundance of Dorea, Blautia, and Oscillospira were associated with nonfavorable clinical outcomes. Blautia inversely correlated to liver disease severity, and Bifidobacterium inversely correlated to fibrosis biomarkers. Bifidobacterium abundance was significantly lower in infants experiencing cholangitis within 6 months after KPE. CONCLUSIONS: Increased diversity, enrichment of pathogenic, and depletion of beneficial microbiota early post-KPE are all factors associated with nonfavorable BA outcomes. Manipulation of gut microbiota in the early postsurgical period could provide therapeutic potential.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34937552", + "title": "High frequency of enterotoxigenic Bacteroides fragilis and Enterococcus faecalis in the paraffin-embedded tissues of Iranian colorectal cancer patients.", + "year": 2021, + "journal": "BMC cancer", + "authors": [ + "Khodaverdi N", + "Zeighami H", + "Jalilvand A", + "Haghi F", + "Hesami N" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.255292873711679, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteroides Infections", + "Bacteroides fragilis", + "Case-Control Studies", + "Colon", + "Colorectal Neoplasms", + "DNA, Bacterial", + "Enterococcus faecalis", + "Female", + "Gram-Positive Bacterial Infections", + "Humans", + "Intestinal Mucosa", + "Iran", + "Male", + "Middle Aged", + "Neoplasm Staging", + "Paraffin Embedding", + "Prevalence" + ], + "raw_abstract": "BACKGROUND: The association between specific bacteria and colorectal cancer (CRC) has been proposed. Only a few studies have, however, investigated this relationship directly in colorectal tissue with conflicting results. So, we aimed to quantitate Streptococcus gallolyticus, Fusobacterium spp, Enterococcus faecalis and enterotoxigenic Bacteroides fragilis (ETBF) in formalin-fixed and paraffin-embedded (FFPE) colorectal tissue samples of Iranian CRC patients and healthy controls. METHODS: A total of 80 FFPE colorectal tissue samples of CRC patients (n\u00a0=\u200940) and healthy controls (n\u2009=\u200940) were investigated for the presence and copy number of above bacterial species using quantitative PCR. Relative quantification was determined using \u0394\u0394CT method and expressed as relative fold difference compared to reference gene. RESULTS: Relative abundance and copy number of E. faecalis and ETBF were significantly higher in CRC samples compared to control group. E. faecalis was more prevalent than ETBF in tumor samples. Frequency of ETBF and E. faecalis in late stages (III/IV) of cancer was significantly higher than early stages (I/II). We did not detect a significant difference in abundance of S. gallolyticus and Fusobacterium spp between two groups. CONCLUSION: Our study revealed the higher concentration of E. faecalis and ETBF in FFPE samples of CRC patients than controls. However, additional investigations on fecal and fresh colorectal cancer tissue samples are required to substantiate this correlation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32873292", + "title": "Gut microbial characteristics of adult patients with allergy rhinitis.", + "year": 2020, + "journal": "Microbial cell factories", + "authors": [ + "Zhu L", + "Xu F", + "Wan W", + "Yu B", + "Tang L", + "Yang Y", + "Du Y", + "Chen Z", + "Xu H" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.25404229214013474, + "mesh_terms": [ + "Adult", + "Biodiversity", + "China", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Genome, Bacterial", + "Humans", + "Male", + "Metagenome", + "Quality of Life", + "RNA, Ribosomal, 16S", + "Rhinitis, Allergic", + "Severity of Illness Index", + "Surveys and Questionnaires", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Although recent studies have indicated that intestinal microbiota dweller are involved in the pathogenesis of allergy rhinitis (AR), the influence of gut microbiota on AR adult has not been fully elucidated yet. Hence, we carried out this study to uncover the distinctive bacterial taxa that differentiate allergy rhinitis patients from healthy individuals. Feces samples from thirty three AR patients and thirty one healthy individuals were analyzed by 16S rRNA gene sequencing. RESULTS: Results showed that the bacterial diversity in AR group was significantly higher than that of the non-AR group. Bacterial communities between AR and non-AR group were significantly differentiated as revealed by Principal coordinates analysis (PCoA) and the variation within non-AR were higher than that of the counterpart. Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria and Chloroflexi were the significantly differed phyla taxa and the top significantly distinguished bacterial genus included Prevotella_9, Phascolarctobacterium, Roseburia, Megamonas, Alistipes, Lachnoclostridium and Fusobacterium. The higher network complexity in AR group were dominated by taxa belonging to Firmicutes. The predicted function, alpha linolenic acid metabolism and bacterial invasion of epithelial cells pathway were higher in non-AR group while gonadotropin-releasing hormone (GnRH) signaling pathway, Fc \u03b3-R mediated phagocytosis and endocytosis were higher in AR patients. Although the bacterial diversity between moderate and severe AR patients showed no significant difference, the significant correlation between featured genus and total nasal symptom score or rhinoconjunctivitis quality of life questionnaire, such as Butyricicoccus and Eisenbergiella, revealed the potential to intervene the AR status by means of gut microbiota. CONCLUSIONS: In conclusion, patients with allergy rhinitis had distinguished gut microbiota characteritics in comparison with healthy controls. The results suggest that gut microbiota might play crucial roles in influencing the course and different symptoms of AR. Trial registration ChiCTR, ChiCTR1900028613. Registered 29 December 2019, https://www.chictr.org.cn/showproj.aspx?proj=47650 .", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38831399", + "title": "Characterization of the intestinal microbiota in MSM with HIV infection.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Fu Y", + "Ke S", + "Tang G", + "Guo Q", + "Guo Q", + "Wang Z", + "Leng R", + "Fan Y" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.25378947814480385, + "mesh_terms": [ + "Humans", + "Male", + "Gastrointestinal Microbiome", + "HIV Infections", + "Homosexuality, Male", + "Adult", + "RNA, Ribosomal, 16S", + "Bacteria", + "Feces", + "Middle Aged", + "HIV-1", + "Dysbiosis" + ], + "raw_abstract": "BACKGROUND: HIV-infected persons demonstrate notable disturbances in their intestinal microbiota; however, the impact of intestinal microbiota on HIV susceptibility in men who have sex with men (MSM), as well as the effects of HIV and antiretroviral therapy (ART) on their gut microbiota, remains under active study. Thus, our research focuses on clarifying the distinctions in intestinal microbiota composition among uninfected MSM and non-MSM healthy controls, investigating the alterations in early-stage intestinal microbial communities following HIV infection, and assessing how ART affects the intestinal microbiota. METHODS: This study enrolled four participant groups: uninfected MSM, Recent HIV-1 infection (RHI) MSM, MSM on ART, and non-MSM healthy controls, with 30 individuals in each group. We utilized 16S ribosomal DNA (16S rDNA) amplicon sequencing to analyze fecal microbiota and employed Luminex multiplex assays to measure plasma markers for microbial translocation (LBP, sCD14) and the inflammatory marker CRP. FINDINGS: Comparing uninfected MSM to non-MSM healthy controls, no substantial variances were observed in \u03b1 and \u03b2 diversity. Uninfected MSM had higher average relative abundances of Bacteroidetes, Prevotella, and Alloprevotella, while Bacteroides, Firmicutes, and Faecalibacterium had lower average relative abundances. MSM on ART had lower intestinal microbiota diversity than RHI MSM and uninfected MSM. In MSM on ART, Megasphaera and Fusobacterium increased, while Faecalibacterium and Roseburia decreased at genus level. Additionally, treatment with a non-nucleoside reverse transcriptase inhibitor (NNRTI) led to significant alterations in intestinal microbiota diversity and composition compared to RHI MSM. The random forest model showed that HIV infection biomarkers effectively distinguished between newly diagnosed HIV-infected MSM and HIV-negative MSM, with an ROC AUC of 76.24% (95% CI: 61.17-91.31%). CONCLUSIONS: MSM showed early intestinal microbiota imbalances after new HIV infection. MSM on ART experienced worsened dysbiosis, indicating a combined effect of HIV and ART. NNRTI-based treatment notably changed intestinal microbiota, suggesting a potential direct impact of NNRTI drugs on intestinal microbiota.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33352216", + "title": "Changes in intestinal microbiota and correlation with TLRs in ulcerative colitis in the coastal area of northern China.", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Xu N", + "Bai X", + "Cao X", + "Yue W", + "Jiang W", + "Yu Z" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.25038127020307305, + "mesh_terms": [ + "China", + "Colitis, Ulcerative", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: To investigate the communities of fecal microbiota and the role of Toll-like receptors in patients with ulcerative colitis in the coastal area of northern China. METHODS: Stool samples from 31 patients with ulcerative colitis and 12 healthy individuals were collected. The total bacterial genomic DNA was extracted, and the V3+V4 hypervariable region in the bacterial 16S rRNA gene sequence was amplified by polymerase chain reaction (PCR). High-throughput sequencing analysis was performed on the Illumina Hiseq platform. The expression of TLR2, TLR4, Tollip, PPAR-\u03b3, IL-6, and TNF-\u03b1 in the colonic mucosa was measured by Western blots. RESULTS: The diversity of the fecal microbiota in patients with ulcerative colitis was significantly less than that in healthy control individuals (p\u00a0<\u00a00.05). The proportion of Bacteroidetes was significantly reduced (p\u00a0<\u00a00.01), whereas Proteobacteria was prevalent (p\u00a0<\u00a00.01) in patients with ulcerative colitis. At the genus level, the relative abundance of Streptococcus and Anaerostipes was significantly increased (p\u00a0<\u00a00.05), whereas the proportion of Bacteroides, Lachnospira, Ruminococcus, Phascolarctobacterium, and Coprococcus was significantly decreased in patients with ulcerative colitis (p\u00a0<\u00a00.05). The diversity indexes of fecal microbiota in patients with ulcerative colitis were negatively correlated with disease severity (p\u00a0<\u00a00.05). The relative abundance of Enterobacteriaceae was positively correlated with disease severity, and the relative abundance of Phascolarctobacterium, Anaerostipes, Fusobacterium, Parabacteroides, Oscillospira, and Ochrobactrum were negatively correlated with disease severity. The expression levels of TLR2 and TLR4 in the intestinal mucosa were positively correlated with the relative abundance of Streptococcus and Enterobacteriaceae, respectively (r\u00a0=\u00a00.481, p\u00a0=\u00a00.007; r\u00a0=\u00a00.455, p\u00a0=\u00a00.017). CONCLUSION: There were significant changes in the diversity and composition of the fecal microbiota in patients with ulcerative colitis compared to healthy individuals. The dysbiosis of gut microbiota and correlation with TLRs might play important roles in the pathogenesis and progression of ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28904330", + "title": "Analysis of Mucosa-Associated Microbiota in Colorectal Cancer.", + "year": 2017, + "journal": "Medical science monitor : international medical journal of experimental and clinical research", + "authors": [ + "Xu K", + "Jiang B" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.24268227756596727, + "mesh_terms": [ + "Adenocarcinoma", + "Adenoma", + "Adult", + "Bacteria", + "Biomarkers", + "Case-Control Studies", + "Colon", + "Colonic Neoplasms", + "Colorectal Neoplasms", + "Escherichia coli", + "Female", + "Humans", + "Intestinal Mucosa", + "Male", + "Microbiota", + "Middle Aged", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND The aim of this study was to compare the microbiota community structure, assess differences in intestinal bacterial types, and identify metagenomic biomarkers for disparate stages of colorectal cancer formation. MATERIAL AND METHODS A total of 160 individuals were recruited: 61 cases with non-tumor colon were regarded as the normal group, 47 cases with histology-substantiated colorectal adenomas were regarded as the adenoma group, and 52 cases with invasive adenocarcinomas were regarded as the cancer group. Biopsy on the mucosa was performed on each subject. USEARCH was used to process the sequences data and generate OTUs. Gut mucosal microbiota from healthy controls, adenoma patients, and carcinoma patients were analyzed. RESULTS Principal coordinate analysis of unweighted and weighted UniFrac distance showed a separation in composition of microbiota in the 3 groups. Bacteria with potential tumorigenesis, like Bacteroides fragilis and Fusobacterium, were more common in the carcinoma group, while some SCFA (short chain fatty acids)\u00a0-\u00a0producing microbes were enriched in the normal group. The commensal Escherichia were more abundant in adenoma patients. CONCLUSIONS Our study provides insights into possible function of gut microbiota in diagnosis and treatment of colorectal cancer. Some bacteria, such as Butyricicoccus, E. coli, and Fusobacterium, can be used as potential biomarkers for normal, adenoma, and cancer groups, respectively.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27298564", + "title": "Visceral hypersensitive rats share common dysbiosis features with irritable bowel syndrome patients.", + "year": 2016, + "journal": "World journal of gastroenterology", + "authors": [ + "Zhou XY", + "Li M", + "Li X", + "Long X", + "Zuo XL", + "Hou XH", + "Cong YZ", + "Li YQ" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.23738813696145528, + "mesh_terms": [ + "Animals", + "Clostridium", + "Colon", + "Disease Models, Animal", + "Dysbiosis", + "Electromyography", + "Feces", + "Fusobacteria", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Hyperalgesia", + "Irritable Bowel Syndrome", + "Mechanotransduction, Cellular", + "Pain Perception", + "Phylogeny", + "Pressure", + "Rats, Sprague-Dawley", + "Rectum", + "Reflex, Abdominal", + "Reflex, Abnormal", + "Ribotyping" + ], + "raw_abstract": "AIM: To evaluate gut microbial dysbiosis in two visceral hypersensitive models in comparison with irritable bowel syndrome (IBS) patients and to explore the extent to which these models capture the dysbiosis of IBS patients. METHODS: Visceral hypersensitivity was developed using the maternal separation (MS) rat model and post-inflammatory rat model. The visceral sensitivity of the model groups and control group was evaluated using the abdominal withdraw reflex score and electromyography in response to graded colorectal distention. The 16S ribosomal RNA gene from fecal samples was pyrosequenced and analyzed. The correlation between dysbiosis in the microbiota and visceral hypersensitivity was calculated. Positive findings were compared to sequencing data from a published human IBS cohort. RESULTS: Dysbiosis triggered by neonatal maternal separation was lasting but not static. Both MS and post-inflammatory rat fecal microbiota deviated from that of the control rats to an extent that was larger than the co-housing effect. Two short chain fatty acid producing genera, Fusobacterium and Clostridium XI, were shared by the human IBS cohort and by the maternal separation rats and post-inflammatory rats, respectively, to different extents. Fusobacterium was significantly increased in the MS group, and its abundance positively correlated with the degree of visceral hypersensitivity. Porphyromonadaceae was a protective biomarker for both the rat control group and healthy human controls. CONCLUSION: The dysbiosis MS rat model and the post-inflammatory rat model captured some of the dysbiosis features of IBS patients. Fusobacterium, Clostridium XI and Porphyromonadaceae were identified as targets for future mechanistic research.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38226944", + "title": "Gut microbiota composition may be an indicator of erectile dysfunction.", + "year": 2024, + "journal": "Microbial biotechnology", + "authors": [ + "Qiao Y", + "Chen J", + "Jiang Y", + "Zhang Z", + "Wang H", + "Liu T", + "Yang Z", + "Fu G", + "Chen Y" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.23666102079346935, + "mesh_terms": [ + "Male", + "Humans", + "Gastrointestinal Microbiome", + "Erectile Dysfunction", + "RNA, Ribosomal, 16S", + "Dysbiosis", + "Bifidobacterium" + ], + "raw_abstract": "Erectile Dysfunction (ED) is considered a physical and mental illness. A variety of potential associations between gut microbiota and health or disease have been found. By comparing the gut microbiota of healthy controls and ED patients, our study investigated the relationship between ED and gut microbiota. The results revealed that the ED group exhibited a significantly higher relative abundance of Bacteroides, Fusobacterium, Lachnoclostridium, Escherichia-Shigella and Megamonas, while showing a significantly lower relative abundance of Bifidobacterium compared to the control group. The dysbiosis of gut microbiota played a role in the onset and progression of ED by influencing the gut barrier, cardiovascular system and mental health, which provided a novel perspective on understanding the pathophysiology of ED. What is more, we had identified several key gut microbiota. By combining 16S rRNA sequencing with machine learning techniques, we were able to uncover the significant value and impact of gut microbiota in the early detection of ED.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35658028", + "title": "Detection of Fusobacterium nucleatum DNA in primary care patient stool samples does not predict progression of colorectal neoplasia.", + "year": 2022, + "journal": "PloS one", + "authors": [ + "Aitchison A", + "Pearson JF", + "Purcell RV", + "Frizelle FA", + "Keenan JI" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2354910759181869, + "mesh_terms": [ + "Colonoscopy", + "Colorectal Neoplasms", + "Fusobacterium Infections", + "Fusobacterium nucleatum", + "Humans", + "Occult Blood", + "Primary Health Care" + ], + "raw_abstract": "BACKGROUND: Carriage of certain bacterial species may represent potential biomarkers of colorectal cancer (CRC). Prominent among these is Fusobacterium nucleatum. We explored the association of F. nucleatum DNA in stool samples with the presence of colonic neoplastic lesions in a cohort of primary care patients, and compared our findings with those from an unrelated cohort of colonoscopy patients followed clinically over time. METHODS: Carriage rates of F. nucleatum in stool samples were assessed in 185 patients referred for a faecal immunochemical test (FIT) by their general practitioners (GPs). Comparisons were made with stool samples from 57 patients diagnosed with CRC and 57 age-matched healthy controls, and with tissue samples taken at colonoscopy from 150 patients with a decade of subsequent clinical follow-up. FINDINGS: F. nucleatum DNA was found at a high rate (47.0%) in stool samples from primary care patients, and more often in stool samples from CRC patients (47.4%) than in healthy controls (7.0%), (P = 7.66E-7). No association was found between carriage of F. nucleatum and FIT positivity (P = 0.588). While evidence of stool-associated F. nucleatum DNA was significantly more likely to indicate a lesion in those primary care patients progressed to colonoscopy (P = 0.023), this finding did not extend to the progression of neoplastic lesions in the 150 patients with a decade of follow up. CONCLUSION: The finding of F. nucleatum DNA at similar rates in stool samples from patients diagnosed with CRC and in primary care patients with pre-cancerous lesions supports growing awareness that the presence of these bacteria may be a biomarker for increased risk of disease. However, molecular evidence of F. nucleatum did not predict progression of colonic lesions, which may lessen the utility of this bacterium as a biomarker for increased risk of disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34689777", + "title": "A fecal-based test for the detection of advanced adenoma and colorectal cancer: a case-control and screening cohort study.", + "year": 2021, + "journal": "BMC medicine", + "authors": [ + "Cao LJ", + "Peng XL", + "Xue WQ", + "Zhang R", + "Zhang JB", + "Zhou T", + "Wu ZY", + "Li GR", + "Wang TM", + "He YQ", + "Yang DW", + "Liao Y", + "Tong XT", + "Wang F", + "Chen KX", + "Zhang SH", + "Zhu LQ", + "Ding PR", + "Jia WH" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.23408490062416748, + "mesh_terms": [ + "Adenoma", + "Case-Control Studies", + "Cohort Studies", + "Colorectal Neoplasms", + "Early Detection of Cancer", + "Humans" + ], + "raw_abstract": "BACKGROUND: Colorectal cancer (CRC) is the leading cause of cancer death worldwide. Screening is a confirmed way to reduce the incidence and mortality rates of CRC. This study aimed to identify a fecal-based, noninvasive, and accurate method for detection of colorectal cancer (CRC) and advanced adenoma (AA). METHODS: Through detection in tissue (n = 96) and fecal samples (n = 88) and tested in an independent group of fecal samples (n = 294), the methylated DNA marker ITGA4 and bacterial markers Fusobacterium nucleatum (Fn) and Pepetostreptococcusanaerobius (Pa) were identified from the candidate biomarkers for CRC and AA detection. A prediction score (pd-score) was constructed using the selected markers and fecal immunochemical test (FIT) for distinguishing AA and CRC from healthy subjects by logistic regression method. The diagnostic performance of the pd-score was compared with FIT and validated in the external validation cohort (n = 117) and in a large CRC screening cohort. RESULTS: The pd-score accurately identified AA and CRC from healthy subjects with an area under the curve (AUC) of 0.958, at a specificity of 91.37%; the pd-score showed sensitivities of 95.38% for CRC and 70.83% for AA, respectively. In the external validation cohort, the sensitivities of the pd-score for CRC and AA detection were 94.03% and 80.00%, respectively. When applied in screening, the pd-score identified 100% (11/11) of CRC and 70.83% (17/24) of AA in participants with both colonoscopy results and qualified fecal samples, showing an improvement by 41.19% compared to FIT. CONCLUSIONS: The current study developed a noninvasive and well-validated approach for AA and CRC detection, which could be applied widely as a diagnostic and screening test.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27056397", + "title": "Acute Appendicitis in Children Is Associated With a Local Expansion of Fusobacteria.", + "year": 2016, + "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", + "authors": [ + "Rogers MB", + "Brower-Sinning R", + "Firek B", + "Zhong D", + "Morowitz MJ" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.232362056341027, + "mesh_terms": [ + "Acute Disease", + "Adolescent", + "Adult", + "Appendicitis", + "Appendix", + "Child", + "Child, Preschool", + "Cohort Studies", + "Feces", + "Fusobacteria", + "Gastrointestinal Microbiome", + "Gram-Negative Bacterial Infections", + "Humans" + ], + "raw_abstract": "BACKGROUND: Lumenal obstruction has typically been regarded as the cause of acute appendicitis (AA). Recent evidence including data from \"antibiotics first\" trials suggests that this disease may result from invasion of the appendix by specific pathogens. Small studies have identified an abundance of bacteria from the genus Fusobacterium in appendixes from patients with AA. We aimed to validate these findings in a larger cohort of children with appendicitis in addition to profiling the appendiceal microbiota in a population of children without appendicitis. METHODS: Appendix swabs were collected from children undergoing appendectomy for AA (n = 60), incidental appendectomy for reasons other than appendicitis (n = 18), or ileocecectomy for inflammatory bowel disease (n = 7), in addition to samples from other sites. Bacterial 16S ribosomal RNA gene sequences from each sample were amplified, sequenced, and analyzed with the UPARSE and QIIME programs. RESULTS: We found that the normal human appendix harbors populations of Fusobacteria that are generally absent in fecal samples from healthy adults and children. In patients with AA, Fusobacteria populations proliferate and often persist despite several weeks of broad-spectrum antibiotics prior to surgery. Relative to non-AA samples, AA samples were depleted of sequences from the genus Bacteroides Phylogenetic analysis of sequence data indicates that F. nucleatum, F. necrophorum, and F. varium are the species of Fusobacterium observed in AA samples. CONCLUSIONS: These results indicate that the appendiceal niche harbors distinct microbial populations that likely contribute to the pathogenesis of appendicitis, which may one day be leveraged to improve the diagnosis and/or treatment of patients with AA.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36252516", + "title": "Arsenolipids reduce butyrate levels and influence human gut microbiota in a donor-dependent way.", + "year": 2022, + "journal": "Ecotoxicology and environmental safety", + "authors": [ + "Calatayud M", + "Xiong C", + "Selma-Royo M", + "van de Wiele T" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.23236082462861388, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Butyrates", + "Arsenic", + "RNA, Ribosomal, 16S", + "Ecosystem" + ], + "raw_abstract": "Arsenolipids are organic arsenic species with variable toxicity. Accurate assessment of the risks derived from arsenic-contaminated seafood intake requires studying the interplay between arsenolipids and the human gut microbiota. This research used the in vitro mucosal simulator of the human intestinal microbial ecosystem (M-SHIME) to assess the effect of defined chemical standards of arsenolipids (AsFA 362 and AsHC 332) on a simulated healthy human gut microbiota (n\u00a0=\u00a04). Microbial-derived metabolites were quantified by gas chromatography and microbiota structure was characterized by 16S rRNA gene sequencing. A specific reduction in butyrate production (control=5.28\u00a0\u00b1\u00a00.3\u00a0mM; AsFAs=4.56\u00a0\u00b1\u00a00.4\u00a0mM; AsHC 332=4.4\u202f\u00b1\u202f0.6\u202fmM, n\u00a0=\u00a04 donors), concomitant with a reduction in the abundance of Lachnospiraceae UCG-004 group and the Faecalibacterium genus was observed, albeit in a donor-dependent manner. Furthermore, an increase in Escherichia/Shigella, Proteobacteria and Fusobacterium abundance was observed after arsenolipid treatments, depending on individual microbiota background. These alterations in microbial functionality and microbial community structure suggest a detrimental effect of arsenolipids intake towards the commensal gut microbiome, and consequently, on human health.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34438891", + "title": "Comparison of Gut Microbiota of 96 Healthy Dogs by Individual Traits: Breed, Age, and Body Condition Score.", + "year": 2021, + "journal": "Animals : an open access journal from MDPI", + "authors": [ + "You I", + "Kim MJ" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.23213518389113136, + "mesh_terms": [], + "raw_abstract": "Since dogs are part of many peoples' lives, research and industry related to their health and longevity are becoming a rising topic. Although gut microbiota (GM) is a key contributor to host health, limited information is available for canines. Therefore, this study characterized GM according to individual signatures (e.g., breed, age, and body condition score-BCS) of dogs living in the same environment. Fresh fecal samples from 96 healthy dogs were analyzed by sequencing the V3-V4 region of the 16S rRNA gene. The major microbial phyla were Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, and Actinobacteria. In the comparison by breeds, relative abundance of Fusobacterium was significantly differed. Interestingly,", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37458823", + "title": "The altered composition of gut microbiota and biochemical features as well as dietary patterns in a southern Chinese population with recurrent renal calcium oxalate stones.", + "year": 2023, + "journal": "Urolithiasis", + "authors": [ + "Cao C", + "Jin X", + "Ding Q", + "Zhu J", + "Yang D", + "Fan B" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.23180808157929714, + "mesh_terms": [ + "Humans", + "Kidney Calculi", + "Calcium Oxalate", + "Creatinine", + "Magnesium", + "Gastrointestinal Microbiome", + "East Asian People", + "Phosphates", + "Calcium" + ], + "raw_abstract": "The correlation among gut microbiota, biochemical features, and dietary patterns in recurrent stone formers has been inadequately investigated in the Chinese population. Forty-two patients with calcium oxalate stones (CaOxS group), including 34 recurrent stone formers (RS group), and 40 nonstone healthy subjects (NS group) from Changshu Hospital Affiliated with Soochow University, were prospectively recruited. Food frequency questionnaires were completed by participants, fasting vein blood was extracted, 24-h urine was collected for biochemical detection, and fecal samples were gathered for 16S ribosomal RNA (rRNA) gene sequencing. BMI; serum levels of triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), magnesium, and creatinine; and urine levels of magnesium in stone formers were significantly different from those of controls, and RS patients showed significantly low serum phosphate and high urine phosphate levels. Celery, bamboo shoots, and pickled food were the favored foods of local stone formers. Patients with recurrent stones had altered microbiota composition, with Escherichia, Fusobacterium, and Epulopiscium being the predominant pathogenic genera. The gut microbiota in RS patients had stronger functions in fatty acid and amino acid degradation but weaker functions in their biosynthesis. The pathogenic genera were positively correlated with BMI; serum levels of TGs and creatinine; urine levels of calcium, phosphate, and uric acid (UA); and celery, bamboo shoots, and pickled food intake. The abundance of Escherichia and Fusobacterium and the levels of serum magnesium and creatinine were the most relevant factors associated with stone recurrence and could be validated as biomarkers of recurrence. Our research provides a novel prevention strategy for the recurrence of renal calcium oxalate stones in the Han Chinese population of southern China.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36056757", + "title": "Metagenomic analysis of the fecal microbiome in colorectal cancer patients compared to healthy controls as a function of age.", + "year": 2023, + "journal": "Cancer medicine", + "authors": [ + "Kharofa J", + "Apewokin S", + "Alenghat T", + "Ollberding NJ" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.23098773501396874, + "mesh_terms": [ + "Humans", + "Colorectal Neoplasms", + "Metagenome", + "Metagenomics", + "Fusobacterium nucleatum", + "Carcinogenesis", + "Microbiota" + ], + "raw_abstract": "BACKGROUND AND AIMS: Colorectal cancer (CRC) incidence is increasing in young patients without a clear etiology. Emerging data have implicated the fecal microbiome in CRC carcinogenesis. However, its impact on young onset CRC is poorly defined. METHODS: We performed a meta-analysis of fecal metagenomics sequencing data from n\u00a0=\u2009692 patients with CRC and n\u00a0=\u2009602 healthy controls from eleven studies to evaluate features of the fecal metagenome associated with CRC. We hypothesized that known carcinogenic virulence factors (colibactin, fadA) and species abundance may be differentially enriched in young CRC patients relative to older CRC patients and controls. RESULTS: Summary odds ratios (OR) for CRC were increased with the presence of colibactin (OR 1.92 95% CI 1.08-3.38), fadA (OR 4.57 95% CI 1.63-12.85), and F. nucleatum (OR 6.93 95% CI 3.01-15.96) in meta-analysis models adjusted for age, gender, and body mass index. The OR for CRC for the presence of E.coli was 2.02 (0.92-4.45). An increase in the prevalence of Fusobacterium nucleatum (OR\u00a0=\u00a01.40 [1.18; 1.65]) and Escherichia coli (OR\u00a0=\u00a01.14 [1.02; 1.28]) per 10-year increase in age was observed in models including samples from both CRC and healthy controls. Species relative abundance was differentially enriched in young CRC patients for five species-Intestinimonas butyriciproducens, Holdemania filiformis, Firimicutues bacterium CAG 83, Bilophilia wadsworthia, and Alistipes putredinis. CONCLUSION: In this study, we observed strong associations with CRC status for colibactin, fadA, and Fusobacterium nucleatum with CRC relative to controls. In addition, we identified several microbial species differentially enriched in young colorectal cancer patients. Studies targeting the young CRC patients are warranted to elucidate underlying preclinical mechanisms.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34373464", + "title": "Metagenomic analysis revealed the potential role of gut microbiome in gout.", + "year": 2021, + "journal": "NPJ biofilms and microbiomes", + "authors": [ + "Chu Y", + "Sun S", + "Huang Y", + "Gao Q", + "Xie X", + "Wang P", + "Li J", + "Liang L", + "He X", + "Jiang Y", + "Wang M", + "Yang J", + "Chen X", + "Zhou C", + "Zhao Y", + "Ding F", + "Zhang Y", + "Wu X", + "Bai X", + "Wu J", + "Wei X", + "Chen X", + "Yue Z", + "Fang X", + "Huang Q", + "Wang Z", + "Huang R" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.23063718028416721, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Arthritis", + "Bacteria", + "Butyrates", + "Diabetes Mellitus, Type 2", + "Dysbiosis", + "Fatty Acids, Volatile", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gout", + "Humans", + "Inflammation", + "Male", + "Metabolic Diseases", + "Metagenome", + "Metagenomics", + "Middle Aged", + "Spondylitis, Ankylosing", + "Uric Acid", + "Young Adult" + ], + "raw_abstract": "Emerging evidence indicates an association between gut microbiome and arthritis diseases including gout. However, how and which gut bacteria affect host urate degradation and inflammation in gout remains unclear. Here we performed a metagenome analysis on 307 fecal samples from 102 gout patients and 86 healthy controls. Gout metagenomes significantly differed from those of healthy controls. The relative abundances of Prevotella, Fusobacterium, and Bacteroides were increased in gout, whereas those of Enterobacteriaceae and butyrate-producing species were decreased. Functionally, gout patients had greater abundances for genes in fructose, mannose metabolism and lipid A biosynthesis, and lower for genes in urate degradation and short chain fatty acid production. A three-pronged association between metagenomic species, functions and clinical parameters revealed that decreased abundances of species in Enterobacteriaceae were associated with reduced amino acid metabolism and environmental sensing, which together contribute to increased serum uric acid and C-reactive protein levels in gout. A random forest classifier based on three gut microbial genes showed high predictivity for gout in both discovery and validation cohorts (0.91 and 0.80 accuracy), with high specificity in the context of other chronic disorders. Longitudinal analysis showed that uric-acid-lowering and anti-inflammatory drugs partially restored gut microbiota after 24-week treatment. Comparative analysis with obesity, type 2 diabetes, ankylosing spondylitis and rheumatoid arthritis indicated that gout metagenomes were more similar to those of autoimmune than metabolic diseases. Our results suggest that gut dysbiosis was associated with dysregulated host urate degradation and systemic inflammation and may be used as non-invasive diagnostic markers for gout.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39320604", + "title": "The gut microbiota is altered significantly in primary diffuse large b-cell lymphoma patients and relapse refractory diffuse large b-cell lymphoma patients.", + "year": 2024, + "journal": "Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico", + "authors": [ + "Xu Y", + "Shi C", + "Qian J", + "Yu X", + "Wang S", + "Shao L", + "Yu W" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.22958975544118498, + "mesh_terms": [], + "raw_abstract": "PURPOSE: Studies have shown that the gut microbiota may affect anti-tumor immunity by regulating the host immune system and tumor microenvironment. To date, little is known about whether the gut microbiota underlies the occurrence of diffuse large B-cell lymphoma (DLBCL) and drug resistance. METHODS: In the present study, we compared the gut microbiota structure of fecal samples from 26 patients with primary DLBCL, 28 patients with relapsed and refractory (RR) DLBCL, and 30 healthy people. RESULTS: Notably, Fusobacteria (from phylum to species) was enriched in the primary group. A decrease of Fusobacterium and an increase of Enterococcus were found in the RR group. PICRUSt analysis found that genes related to cytochrome P450 were upregulated in the RR group compared to the primary group, which likely contributes to the occurrence of DLBCL and the formation of drug resistance. CONCLUSIONS: Our study provides further evidence for the relationship between gut microbiota and DLBCL and the formation of drug resistance, highlighting the potential significance of the bacterial variations may be used as new biomarkers of DLBCL.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35312122", + "title": "Gut microbiome: New biomarkers in early screening of colorectal cancer.", + "year": 2022, + "journal": "Journal of clinical laboratory analysis", + "authors": [ + "Zhou P", + "Yang D", + "Sun D", + "Zhou Y" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2292474113773472, + "mesh_terms": [ + "Adenoma", + "Biomarkers", + "Colorectal Neoplasms", + "Early Detection of Cancer", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Reproducibility of Results" + ], + "raw_abstract": "BACKGROUND: Certain \"star intestinal bacteria\" have been found to act as a contributor to the development of colorectal cancer (CRC). Besides, given that the gut microbiome can be detected in a diverse range of samples (stool, tissue, blood, etc), it is categorized into fecal microbiome, blood microbiome, and tissue microbiome. METHODS: To provide an overview of the recent research progress, this review summarizes the characteristics of the gut microbiome in different samples at each stage of CRC and their screening efficiency. RESULTS: The screening models constructed from different sample microbiomes (healthy/colorectal adenoma, healthy/CRC, and colorectal adenoma/CRC) have both strengths and constraints in terms of biomarker reproducibility and area under the receiver-operating characteristic curve (AUC) of the screening models. Many bacteria, such as Bifidobacteria, Fusobacterium nucleatum (F. n), Geotrichum candidum, Porphyromonas asaccharolytica, Escherichia coli, Rhodococcus, Anaerostipes caccae, Enhydrobacter, Lachnoclostridiumsp. m3, Bacteroides clarus, Clostridium hathewayi, Ruminococcaceae, Bacteroides thetaiotaomicron, Culinariside, and enterotoxigenic Bacteroides fragilis (ETBF), show favorable diagnostic efficacy in early screening of colorectal cancer. CONCLUSIONS: This review highlights stool, blood, tissue, and bowel fluid are the main sample sources for biomarkers, each with its own advantages and limitations. Moreover, other samples such as extracellular vesicles and biofilms also should been deserved further attention.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31240835", + "title": "Correlation of diet, microbiota and metabolite networks in inflammatory bowel disease.", + "year": 2019, + "journal": "Journal of digestive diseases", + "authors": [ + "Weng YJ", + "Gan HY", + "Li X", + "Huang Y", + "Li ZC", + "Deng HM", + "Chen SZ", + "Zhou Y", + "Wang LS", + "Han YP", + "Tan YF", + "Song YJ", + "Du ZM", + "Liu YY", + "Wang Y", + "Qin N", + "Bai Y", + "Yang RF", + "Bi YJ", + "Zhi FC" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.22706486040528745, + "mesh_terms": [ + "Adult", + "Biopsy", + "Body Mass Index", + "Case-Control Studies", + "Diet", + "Dysbiosis", + "Feces", + "Female", + "Food Preferences", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Male", + "Metabolic Networks and Pathways", + "Metagenomics", + "Middle Aged", + "Nutrition Assessment", + "Young Adult" + ], + "raw_abstract": "OBJECTIVES: Microbiota dysbiosis in inflammatory bowel disease (IBD) has been widely reported. The gut microbiota connect diet to the metabolism by producing small molecules via diverse metabolic pathways. In this study we aimed to investigate the dietary preferences of IBD patients, and to explore the interactions among gut microbiota composition, dietary components, and metabolites in relation to IBD. METHODS: Dietary preferences of IBD patients (including those with ulcerative colitis [UC] and Crohn's disease [CD]) and health controls were investigated, and their gut microbiota were analyzed using 16S rRNA gene sequencing and metagenomic analyses of fecal and biopsy samples. The metabolite profiles of the samples were then analyzed using gas and liquid chromatography-mass spectrometry analyses. RESULTS: The daily intake of folic acid, niacin, vitamins C and D, calcium, and selenium differed significantly between patients with IBD and healthy controls. A decrease in long-chain (such as arachidic, and oleic acid) and medium-chain fatty acids (sebacic acid and isocaproic acid) as well as bile acid was observed in patients with IBD. Compared with healthy controls, 22 microbial species (including Sulfolobus acidocaldarius, and Clostridium clostridioforme CAG132) in the UC group and 37 microbial species (such as Bacteroides fragilis and Fusobacterium nucleatum) in the CD group were found to be correlated to diet and metabolites. Bacteroides fragilis was enriched in patients with IBD and associated with multi-nutrients, and 21 metabolites including 25-hydroxyvitamin D CONCLUSIONS: This study provides an interaction network to identify key micronutrients, microbiota components and metabolites that contribute to IBD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38183479", + "title": "Potassium sodium hydrogen citrate intervention on gut microbiota and clinical features in uric acid stone patients.", + "year": 2024, + "journal": "Applied microbiology and biotechnology", + "authors": [ + "Cao C", + "Li F", + "Ding Q", + "Jin X", + "Tu W", + "Zhu H", + "Sun M", + "Zhu J", + "Yang D", + "Fan B" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2267707376016375, + "mesh_terms": [ + "Humans", + "Citric Acid", + "Potassium Citrate", + "Sodium Citrate", + "Potassium", + "Uric Acid", + "Gastrointestinal Microbiome", + "Sodium", + "Citrates", + "Bacteroides", + "Butyric Acid" + ], + "raw_abstract": "The high recurrence rate of renal uric acid stone (UAS) poses a significant challenge for urologists, and potassium sodium hydrogen citrate (PSHC) has been proven to be an effective oral dissolution drug. However, no studies have investigated the impact of PSHC on gut microbiota and its metabolites during stone dissolution therapy. We prospectively recruited 37 UAS patients and 40 healthy subjects, of which 12 patients completed a 3-month pharmacological intervention. Fasting vein blood was extracted and mid-stream urine was retained for biochemical testing. Fecal samples were collected for 16S ribosomal RNA (rRNA) gene sequencing and short chain fatty acids (SCFAs) content determination. UAS patients exhibited comorbidities such as obesity, hypertension, gout, and dyslipidemia. The richness and diversity of the gut microbiota were significantly decreased in UAS patients, Bacteroides and Fusobacterium were dominant genera while Subdoligranulum and Bifidobacterium were poorly enriched. After PSHC intervention, there was a significant reduction in stone size accompanied by decreased serum uric acid and increased urinary pH levels. The abundance of pathogenic bacterium Fusobacterium was significantly downregulated following the intervention, whereas there was an upregulation observed in SCFA-producing bacteria Lachnoclostridium and Parasutterella, leading to a significant elevation in butyric acid content. Functions related to fatty acid synthesis and amino acid metabolism within the microbiota showed upregulation following PSHC intervention. The correlation analysis revealed a positive association between stone pathogenic bacteria abundance and clinical factors for stone formation, while a negative correlation with SCFAs contents. Our preliminary study revealed that alterations in gut microbiota and metabolites were the crucial physiological adaptation to PSHC intervention. Targeted regulation of microbiota and SCFA holds promise for enhancing drug therapy efficacy and preventing stone recurrence. KEY POINTS: \u2022 Bacteroides and Fusobacterium were identified as dominant genera for UAS patients \u2022 After PSHC intervention, Fusobacterium decreased and butyric acid content increased \u2022 The microbiota increased capacity for fatty acid synthesis after PSHC intervention.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37260140", + "title": "Disease-associated gut microbiome and critical metabolomic alterations in patients with colorectal cancer.", + "year": 2023, + "journal": "Cancer medicine", + "authors": [ + "Zhang H", + "Jin K", + "Xiong K", + "Jing W", + "Pang Z", + "Feng M", + "Cheng X" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2263097659676364, + "mesh_terms": [ + "Microbiota", + "Gastrointestinal Microbiome", + "Carcinogenesis", + "Bacteria", + "Fusobacterium", + "Humans", + "Colorectal Neoplasms" + ], + "raw_abstract": "BACKGROUND: Gut microbiota plays a significant role in the colorectal cancer (CRC) process. Ectopic colonization of multiple oral bacteria is reportedly associated with CRC pathogenesis and progression, but the details remain unclear. METHODS: We enrolled a cohort of 50 CRC patients and 52 healthy controls from an East China population. Taxonomic and functional analysis of the fecal microbiota were performed using 16S rDNA (50\u2009+\u200952 samples) and shotgun metagenomic sequencing (8\u2009+\u20096 samples), respectively, with particular attention paid to gut-colonized oral bacteria. RESULTS AND CONCLUSIONS: The results showed more detected bacterial species but lower species evenness within the samples from CRC patients. To determine the specific bacteria enriched in each group, we analyzed their possible protective, carcinogenic, or opportunistic roles in the CRC process. Among the ectopic oral bacteria, we observed a significant increase in the abundance of Fusobacterium and decreased abundance of Prevotella and Ruminococcus in the CRC group. Main differences in the functional composition of these two groups were related to energy metabolism and biosynthesis, especially the glycolytic pathway. Furthermore, we validated the colonization of Fusobacterium nucleatum subsp. animalis within CRC tissues and studied its impact on the host intestinal epithelium and tumor cells. With high selectivity for cancerous tissues, this subspecies promoted CRC cell proliferation and induced potential DNA damage.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35724733", + "title": "Altered Mycobiota Signatures and Enriched Pathogenic Aspergillus rambellii Are Associated With Colorectal Cancer Based on Multicohort Fecal Metagenomic Analyses.", + "year": 2022, + "journal": "Gastroenterology", + "authors": [ + "Lin Y", + "Lau HC", + "Liu Y", + "Kang X", + "Wang Y", + "Ting NL", + "Kwong TN", + "Han J", + "Liu W", + "Liu C", + "She J", + "Wong SH", + "Sung JJ", + "Yu J" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.22584848041692202, + "mesh_terms": [ + "Adenoma", + "Animals", + "Aspergillus", + "Bacteria", + "Biomarkers", + "Cell Transformation, Neoplastic", + "Colorectal Neoplasms", + "Feces", + "Humans", + "Metagenome", + "Mice" + ], + "raw_abstract": "BACKGROUND & AIMS: The enteric mycobiota is a major component of the human gut microbiota, but its role in colorectal cancer (CRC) remains largely elusive. We conducted a meta-analysis to uncover the contribution of the fungal mycobiota to CRC. METHODS: We retrieved fecal metagenomic data sets from 7 previous publications and established an additional in-house cohort, totaling 1329 metagenomes (454 with CRC, 350 with adenoma, and 525 healthy individuals). Mycobiota composition and microbial interactions were analyzed. Candidate CRC-enriched fungal species (Aspergillus rambellii) was functionally validated in\u00a0vitro and in\u00a0vivo. RESULTS: Multicohort analysis revealed that the enteric mycobiota was altered in CRC. We identified fungi that were associated with patients with CRC or adenoma from multiple cohorts. Signature CRC-associated fungi included 6 enriched (A rambellii, Cordyceps sp. RAO-2017, Erysiphe pulchra, Moniliophthora perniciosa, Sphaerulina musiva, and Phytophthora capsici) and 1 depleted species (A kawachii). Co-occurrent interactions among CRC-enriched fungi became stronger in CRC compared with adenoma and healthy individuals. Moreover, we reported the transkingdom interactions between enteric fungi and bacteria in CRC progression, of which A rambellii was closely associated with CRC-enriched bacteria Fusobacterium nucleatum. A rambellii promoted CRC cell growth in\u00a0vitro and tumor growth in xenograft mice. We further identified that combined fungal and bacterial biomarkers were more accurate than panels with pure bacterial species to discriminate patients with CRC from healthy individuals (the area under the curve relative change increased by 1.44%-10.60%). CONCLUSIONS: This study reveals enteric mycobiota signatures and pathogenic fungi in stages of colorectal tumorigenesis. Fecal fungi can be used, in addition to bacteria, for noninvasive diagnosis of patients with CRC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39294269", + "title": "Vertical transfer of gut microbiota from dam to neonate calf in the early of life.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Gomes V", + "Hoffmann C", + "Castro-Tard\u00f3n DI", + "Ramos Dos Santos FC", + "Su\u00e1rez-Retamozo S", + "Hurley DJ" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.22452411085590174, + "mesh_terms": [ + "Animals", + "Gastrointestinal Microbiome", + "Animals, Newborn", + "Cattle", + "Female", + "Feces", + "Colostrum", + "RNA, Ribosomal, 16S", + "Bacteria", + "Pregnancy", + "Vagina", + "Meconium" + ], + "raw_abstract": "The aim of this study was to investigate the vertical transfer of microbiota from dams to the offspring. We studied a pair of 20 dams and its offspring. Maternal sources (colostrum, feces and vaginal secretion) and newborn fecal samples were analyzed using 16S rDNA amplicon sequencing on days 1, 3, 7, 14 and 28. Overall, newborns were maintained healthy and did not receive antimicrobial therapy. The Source Tracker analysis indicated that the newborn fecal microbiota was similar to colostrum and vaginal secretion from day 1 up to 7. However, an unknown source (probably from the environment) showed a gradual increase in its similarity with fecal samples from calves measured from day 3 to 28. The most abundant bacteria groups on meconium (day 1) and calf fecal samples on day 3 were Escherichia-Shigella and Clostridium, respectively. On day 7, the predominant genus were Bifidobacterium and Lactobacillus, while Fusobacterium was the most abundant genus on day 14, coinciding with the diarrhea peak. Faecalibacterium showed a gradual increase throughout the neonatal period. Maternal sources contribute to the neonatal microbiota, however other unknown sources (probably environment) had a strong influence on development of the gut microbiota later in the neonate period.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31448571", + "title": "Alterations in the human gut microbiome in anti-N-methyl-D-aspartate receptor encephalitis.", + "year": 2019, + "journal": "Annals of clinical and translational neurology", + "authors": [ + "Gong X", + "Liu X", + "Li C", + "Chen C", + "Lin J", + "Li A", + "An D", + "Zhou D", + "Hong Z" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.22173719238417713, + "mesh_terms": [ + "Adolescent", + "Adult", + "Anti-N-Methyl-D-Aspartate Receptor Encephalitis", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "OBJECTIVE: To explore the diversity and composition of the fecal microbiota in patients with anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis. METHODS: We enrolled 10 patients in the acute stage with na\u00efve treatment, seven patients with relapse, 13 patients without relapse in the remission phase, and 12 paired healthy controls. The fecal microbiota in different groups was compared by 16S ribosomal DNA (rDNA) gene pyrosequencing. RESULTS: Prominent dysbiosis in the gut microbiome of patients with anti-NMDAR encephalitis was found. Our primary findings showed that the overall species richness (alpha diversity indexes) of the microbiota was higher in patients than in controls (P\u00a0<\u00a00.05). Distance-based community analysis revealed that the microbiota differed substantially within all subgroups of patients and controls (P\u00a0<\u00a00.05). The relative abundance of species heatmap showed a tendency toward depletion for some commensal genera, such as Prevotella_6, Bifidobacterium, Faecalibacterium, and other short-chain fatty acid (SCFA)-producing bacteria. Additionally, our results showed that all subgroups had a distinct bacterial species, with an increase in the genus Fusobacterium in the acute phase group and the genera Streptococcus and Parabacteroides in patients with relapse. However, the genus Bacteroides was very abundant in patients without relapse. Although the findings regarding the Firmicutes/Bacteroidetes (F/B) ratios across the four comparison groups were not statistically significant, the F/B ratio gradually increased in patients from the acute phase group (0.87), to the disease remission group with relapse (1.06), to the group without relapse (1.28), to the healthy group (1.63). INTERPRETATION: Patients with anti-NMDAR encephalitis exhibit a substantial alteration in fecal microbiota composition.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36576461", + "title": "Is there a difference in fecal microbiota of children with and without voiding dysfunction?", + "year": 2022, + "journal": "Archivio italiano di urologia, andrologia : organo ufficiale [di] Societa italiana di ecografia urologica e nefrologica", + "authors": [ + "Akarken I", + "Tarhan H", + "\u015eener G", + "Deliktas H", + "Cengiz N", + "\u015eahin H" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.22113219109384186, + "mesh_terms": [ + "Adult", + "Child", + "Urinary Bladder", + "Lower Urinary Tract Symptoms", + "Humans", + "Microbiota", + "Clostridiales" + ], + "raw_abstract": "OBJECTIVE: Voiding dysfunction (VD), which encompasses many urinary symptoms that are not caused by neurological or anatomical anomalies, is a frequently encountered functional urinary bladder disorder in children. It was reported that there was an association between lower urinary tract symptoms and fecal microbiota in adult patients. Therefore, we aimed to investigate the differences in fecal microbiota between children with or without VD. METHODS: Two patient groups, including 30 patients, were compared. Group 1 included patients with VD, while Group 2 consisted of healthy children. All study participants were asked to fill lower urinary tract and voiding dysfunction symptom score forms with the assistance of their parents. Subsequently, uroflowmetry tests and postvoiding residual urine measurements were performed. Fresh stool samples were collected from all children and analyzed by polymerase chain reaction. General bacterial load and presence of Roseburia intestinalis, Clostridium difficile, Fusobacterium nucleatum, and Bacteroides clarus were tested. RESULTS: The two groups were significantly different regarding general bacterial load; the presence of Fusobacterium nucleatum. Clostridium difficile and Bacteroides clarus was not detected in the fresh stool samples of the patients in Group 2; the counts of Roseburia intestinalis were less in Group 1 than in Group 2, although there was no statistically significant difference. There was a negative correlation between symptom scores, general bacterial load, and the presence of Fusobacterium nucleatum. However, there was no correlation between the presence of Roseburia intestinalis and symptom scores. CONCLUSIONS: There is a potential relationship between VD and a deviation in the fecal microbiota in the pediatric population.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29530088", + "title": "Investigations on the interplays between Schistosoma mansoni, praziquantel and the gut microbiome.", + "year": 2018, + "journal": "Parasites & vectors", + "authors": [ + "Schneeberger PHH", + "Coulibaly JT", + "Panic G", + "Daubenberger C", + "Gueuning M", + "Frey JE", + "Keiser J" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.21840810649588657, + "mesh_terms": [ + "Adolescent", + "Animals", + "Anthelmintics", + "Biodiversity", + "Child", + "Child, Preschool", + "Cote d'Ivoire", + "DNA Barcoding, Taxonomic", + "Feces", + "Female", + "Fusobacterium", + "Gastrointestinal Microbiome", + "Host-Parasite Interactions", + "Humans", + "Male", + "Praziquantel", + "RNA, Ribosomal, 16S", + "Schistosoma mansoni", + "Schistosomiasis mansoni", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Schistosomiasis is a neglected tropical disease burdening millions of people. One drug, praziquantel, is currently used for treatment and control. Clinically relevant drug resistance has not yet been described, but there is considerable heterogeneity in treatment outcomes, ranging from cure to only moderate egg reduction rates. The objectives of this study are to investigate potential worm-induced dysbacteriosis of the gut microbiota and to assess whether a specific microbiome profile could influence praziquantel response. METHODS: Using V3 and V4 regions of 16S rRNA genes, we screened the gut microbiota of 34 Schistosoma mansoni infected and uninfected children from C\u00f4te d'Ivoire. From each infected child one pre-treatment, one 24-hour and one 21-day follow-up sample after administering 60 mg/kg praziquantel or placebo, were collected. RESULTS: Overall taxonomic profiling and diversity indicators were found to be close to a \"healthy\" gut structure in all children. Slight overall compositional changes were observed between S. mansoni-infected and non-infected children. Praziquantel treatment was not linked to a major shift in the gut taxonomic profiles, thus reinforcing the good safety profile of the drug by ruling out off-targets effects on the gut microbes.16S rRNA gene of the Fusobacteriales order was significantly more abundant in cured individuals, both at baseline and 24 hours post-treatment. A real-time qPCR confirmed the over-abundance of Fusobacterium spp. in cured children. Fusobacterium spp. abundance could also be correlated with treatment induced S. mansoni egg-reduction. CONCLUSIONS: Our study suggests that neither a S. mansoni infection nor praziquantel administration triggers a significant effect on the microbial composition and that a higher abundance of Fusobacterium spp., before treatment, is associated with higher efficacy of praziquantel in the treatment of S. mansoni infections. TRIAL REGISTRATION: International Standard Randomised Controlled Trial, number ISRCTN15280205 .", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36557565", + "title": "Microbiome in Male Genital Mucosa (Prepuce, Glans, and Coronal Sulcus): A Systematic Review.", + "year": 2022, + "journal": "Microorganisms", + "authors": [ + "Gon\u00e7alves MFM", + "Fernandes \u00c2R", + "Rodrigues AG", + "Lisboa C" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.21581993509703956, + "mesh_terms": [], + "raw_abstract": "The human body represents a complex and diverse reservoir of microorganisms. Although the human microbiome remains poorly characterized and understood, it should not be underestimated, since recent studies have highlighted its importance in health. This is especially evident when considering microbiota in the male reproductive system, responsible for men\u2019s fertility and sexual behavior. Therefore, the aim of this systematic review is to provide an overview of the microbial communities of the healthy male genital mucosa and its role in disease. This study was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The search was limited to the English language and studies published until August 2022 that included culture-independent techniques for microbiome characterization in male genital mucosa. Ten articles were included. The bacterial composition of the male genital mucosa consists of several genera including Prevotella, Finegoldia, Peptoniphilus, Staphylococcus, Corynebacterium, and Anaerococcus, suggesting that the male genital microbiome composition shows similarities with the adjacent anatomical sites and is related with sexual intercourse. Moreover, male circumcision appears to influence the penile microbiome. Despite the lack of knowledge on the male genital mucosa microbiome in disease, it was reported that Staphylococcus warneri and Prevotella bivia were associated with balanoposthitis, whereas Enterobacteriaceae, Prevotella, and Fusobacterium were more abundant in male genital lichen sclerosus. The limited data and paucity of prospective controlled studies highlight the need for additional studies and established criteria for sampling methods and the microbiome assay procedure. Such a consensus would foster the knowledge about the composition of the genital microbiome of healthy males and its role in disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31388884", + "title": "Changes in Gut Microbiota Composition after Bariatric Surgery: a New Balance to Decode.", + "year": 2020, + "journal": "Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract", + "authors": [ + "Palmisano S", + "Campisciano G", + "Silvestri M", + "Guerra M", + "Giuricin M", + "Casagranda B", + "Comar M", + "de Manzini N" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.21327719527422548, + "mesh_terms": [ + "Bariatric Surgery", + "Enterobacteriaceae", + "Fusobacterium", + "Gastrectomy", + "Gastric Bypass", + "Gastrointestinal Microbiome", + "Humans", + "Laparoscopy", + "Longitudinal Studies", + "Obesity, Morbid", + "Prospective Studies", + "Streptococcus", + "Veillonella" + ], + "raw_abstract": "BACKGROUND: Recently, the link between obesity and gut microbiota has become a focus for research. This study shed some light on the modification of postoperative gut microbial composition after bariatric surgery. METHODS: A prospective longitudinal study on healthy lean subjects and patients who underwent bariatric surgery (Roux-en-Y gastric bypass and laparoscopic sleeve gastrectomy) was carried out. Anthropometric and metabolic data, smoking, food preferences data, and stool samples were collected from lean subjects and from obese patients before and 3 and 6\u00a0months after surgery (T0, T3, and T6, respectively). RESULTS: We collected stool samples from 25 obese patients before surgery and 3 and 6\u00a0months thereafter and from 25 normal weight patients. After Roux-en-Y gastric bypass, Yokenella regensburgei (p\u2009<\u20090.05), Fusobacterium varium (p\u2009<\u20090.05), Veillonella dispar/atypica (p\u2009<\u20090.05), and Streptococcus australis/gordonii (p\u2009<\u20090.05) were transiently identified in the gut at T3. Roux-en-Y gastric bypass patients had a permanent increase in Akkermansia muciniphila (p\u2009<\u20090.05), which is associated with healthy metabolism, both at T3 and T6. There were no significant changes in gut microbiota in laparoscopic sleeve gastrectomy patients. CONCLUSIONS: In our study, Roux-en-Y gastric bypass induced major microbial differences and greater weight loss compared with laparoscopic sleeve gastrectomy. Analyzing the microbiota composition, a proliferation of potential pathogens and the onset of beneficial bacteria was observed. The effects of these bacteria on human health are still far from clear. Understanding the mechanisms of action of these bacteria could be the keystone in developing new therapeutic strategies for obesity.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37946238", + "title": "The oral bacterial microbiota facilitates the stratification for ulcerative colitis patients with oral ulcers.", + "year": 2023, + "journal": "Annals of clinical microbiology and antimicrobials", + "authors": [ + "Xu J", + "Zhang Y", + "Fang XH", + "Liu Y", + "Huang YB", + "Ke ZL", + "Wang Y", + "Zhang YF", + "Zhang Y", + "Zhou JH", + "Su HT", + "Chen N", + "Liu YL" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2103888292486434, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Oral Ulcer", + "RNA, Ribosomal, 16S", + "Gastrointestinal Microbiome", + "Microbiota", + "Inflammatory Bowel Diseases", + "Bacteria", + "Feces", + "Mesalamine" + ], + "raw_abstract": "BACKGROUND: Clinically, a large part of inflammatory bowel disease (IBD) patients is complicated by oral lesions. Although previous studies proved oral microbial dysbiosis in IBD patients, the bacterial community in the gastrointestinal (GI) tract of those IBD patients combined with oral ulcers has not been profiled yet. METHODS: In this study, we enrolled four groups of subjects, including healthy controls (CON), oral ulcer patients (OU), and ulcerative colitis patients with (UC_OU) and without (UC) oral ulcers. Bio-samples from three GI niches containing salivary, buccal, and fecal samples, were collected for 16S rRNA V3-V4 region sequencing. Bacterial abundance and related bio-functions were compared, and data showed that the fecal microbiota was more potent than salivary and buccal microbes in shaping the host immune system.\u2009~\u200922 UC and 10 UC_OU 5-aminosalicylate (5-ASA) routine treated patients were followed-up for six months; according to their treatment response (a decrease in the endoscopic Mayo score), they were further sub-grouped as responding and non-responding patients. RESULTS: We found those UC patients complicated with oral ulcers presented weaker treatment response, and three oral bacterial genera, i.e., Fusobacterium, Oribacterium, and Campylobacter, might be connected with treatment responding. Additionally, the salivary microbiome could be an indicator of treatment responding in 5-ASA routine treatment rather than buccal or fecal ones. CONCLUSIONS: The fecal microbiota had a strong effect on the host's immune indices, while the oral bacterial microbiota could help stratification for ulcerative colitis patients with oral ulcers. Additionally, the oral microbiota had the potential role in reflecting the treatment response of UC patients. Three oral bacteria genera (Fusobacterium, Oribacterium, and Campylobacter) might be involved in UC patients with oral ulcers lacking treatment responses, and monitoring oral microbiota may be meaningful in assessing the therapeutic response in UC patients.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33291114", + "title": "The Role of Fusobacterium nucleatum in Colorectal Carcinogenesis.", + "year": 2021, + "journal": "Pathobiology : journal of immunopathology, molecular and cellular biology", + "authors": [ + "Datorre JG", + "de Carvalho AC", + "Guimar\u00e3es DP", + "Reis RM" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2099347662485124, + "mesh_terms": [ + "Animals", + "Carcinogenesis", + "Cell Transformation, Neoplastic", + "Colorectal Neoplasms", + "Disease Progression", + "Dysbiosis", + "Fusobacterium nucleatum", + "Gastrointestinal Microbiome", + "Humans", + "Intestines", + "Mice", + "Risk Factors" + ], + "raw_abstract": "Colorectal cancer (CRC) is one of the most frequent and deadly neoplasms worldwide. Genetic factors, lifestyle habits, and inflammation are important risk factors associated with CRC development. In recent years, growing evidence has supporting the significant role of the intestinal microbiome in CRC carcinogenesis. Disturbances in the healthy microbial balance, known as dysbiosis, are frequently observed in these patients. Pathogenic microorganisms that induce intestinal dysbiosis have become an important target to determine the role of bacterial infection in tumorigenesis. Interestingly, the presence of different bacterial strains, such as Fusobacterium nucleatum, has been detected in tissue and stool from patients with CRC and associated with substantial clinical and molecular features, as well as with patient therapy response. Therefore, understanding how the presence and levels of F. nucleatumstrains in the gut affect the risk of CRC onset and progression may inform suitable candidates for interventions focused on modulation of this bacteria. Here we review new insights into the role of gut microbiota in CRC carcinogenesis and the clinical utility of using the detection of F. nucleatum in different settings such as screening, prognosis, and microbiota modulation as a means to prevent cancer, augment therapies, and reduce adverse effects of treatment.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39400776", + "title": "Impact of bariatric surgery on gut microbiota composition in obese patients compared to healthy controls.", + "year": 2024, + "journal": "AMB Express", + "authors": [ + "Mohammadzadeh N", + "Razavi S", + "Ebrahimipour G" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.20723672126459006, + "mesh_terms": [], + "raw_abstract": "Bariatric surgery is vital for sustainable weight loss and metabolic improvement in obese individuals, but its effects on gut microbiota and their role in these benefits require further investigation. Investigate the temporal changes in gut microbiota in obese patients undergoing bariatric surgery (gastric sleeve gastrectomy or Roux-en-Y Gastric Bypass (RYGB)) compared to healthy controls, aiming to understand their role in weight loss and metabolic health improvement. A case-control study included 30 obese patients aged 65-95 undergoing bariatric surgery, and 18 matched healthy controls. Selection criteria were based on age, race, BMI, history of antibiotics, probiotics, and prebiotics usage. Stool samples were collected at baseline, three months, and six months post-surgery for DNA extraction and quantitative real-time PCR analysis to assess gut microbiota changes. Physical activity and dietary intake were evaluated using standardized questionnaires. Statistical analyses were performed using R. Post-surgery, patients showed significant reductions in weight and BMI, with changes in dietary habits and physical activity. Quantitative real-time PCR analysis revealed substantial alterations in bacterial groups such as Bacteroides and Fusobacterium. However, some groups showed no significant changes, indicating a complex interaction between gut microbiota and bariatric surgery. Notable correlations were found between body weight, BMI, and specific bacterial groups like the C. cluster IV and Lactobacillus, particularly in RYGB patients. Bariatric surgery significantly alters gut microbiota, aiding weight loss and metabolic regulation in obese patients. Understanding these changes is crucial for developing effective obesity management strategies, requiring further research to optimize outcomes.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35662119", + "title": "Intestinal Microflora Changes in Patients with Mild Alzheimer's Disease in a Chinese Cohort.", + "year": 2022, + "journal": "Journal of Alzheimer's disease : JAD", + "authors": [ + "Wang Y", + "Li L", + "Zhao X", + "Sui S", + "Wang Q", + "Shi G", + "Xu H", + "Zhang X", + "He Y", + "Gu J" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.2065108384953541, + "mesh_terms": [ + "Alzheimer Disease", + "China", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Understanding the relationship between Alzheimer's disease (AD) and intestinal flora is still a major scientific topic that continues to advance. OBJECTIVE: To determine characterized changes in the intestinal microbe community of patients with mild AD. METHODS: Comparison of the 16S ribosomal RNA (rRNA) high-throughput sequencing data was obtained from the Illumina MiSeq platform of fecal microorganisms of the patients and healthy controls (HC) which were selected from cohabiting caregivers of AD patients to exclude environmental and dietary factors. RESULTS: We found that the abundance of several bacteria taxa in AD patients was different from that in HC at the genus level, such as Anaerostipes, Mitsuokella, Prevotella, Bosea, Fusobacterium, Anaerotruncus, Clostridium, and Coprobacillus. Interestingly, the abundance of Akkermansia, an emerging probiotic, increased significantly in the AD group compared with that in the HC group. Meanwhile, the quantity of traditional probiotic Bifidobacteria of the AD group also rose. CONCLUSION: These alterations in fecal microbiome of the AD group indicate that patients with mild AD have unique gut microbial characteristics. These specific AD-associated intestinal microbes could serve as novel potential targets for early intervention of AD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38877111", + "title": "Rapid detection of FadA in Fusobacterium nucleatum using the quantitative LAMP colorimetric phenol red method in stool samples from colorectal cancer patients.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Zuraik AA", + "Daboul Y", + "Awama MA", + "Yazigi H", + "Kayasseh MA", + "Georges M" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.20087353797916763, + "mesh_terms": [ + "Humans", + "Colorectal Neoplasms", + "Fusobacterium nucleatum", + "Feces", + "Nucleic Acid Amplification Techniques", + "Colorimetry", + "Male", + "Female", + "Phenolsulfonphthalein", + "Molecular Diagnostic Techniques", + "Middle Aged", + "Aged", + "Fusobacterium Infections", + "Sensitivity and Specificity", + "Adult" + ], + "raw_abstract": "The study aimed to develop a quantitative colorimetric loop-mediated isothermal amplification technique using the phenol red indicator (QLAMP-PhR) for detecting Fusobacterium nucleatum (Fn) levels in colorectal cancer (CRC) patients and healthy individuals. QLAMP-PhR assays were conducted on 251 stool samples specific for the Fn FadA gene. Six primers were synthesized and utilized with master mix reagents, and a phenol red indicator was employed to enhance the QLAMP-PhR technique. A standard quantitative analysis curve was generated using a logarithmic function (absorbance vs. concentration) by serially diluting the copy number of genomic DNA templates (Fn ATCC25586). The CRC group exhibited a significantly higher abundance of Fn compared to the healthy control group (P\u2009<\u20090.001). These findings suggest that the QLAMP-PhR technique effectively identifies Fn specifically by its gene for the key virulence factor FadA. Additionally, ideas for developing a real-time QLAMP-PhR test were presented. Compared to the traditional polymerase chain reaction (PCR) technique, QLAMP-PhR offers several advantages including rapidity, simplicity, specificity, sensitivity, and cost-effectiveness method that can quantitatively screen for Fn presence in normal populations. The QLAMP-PhR method represents a sensitive and specific amplification assay for the rapid detection of the Fn pathogen. To the best of our knowledge, this study is the first to report the application of QLAMP-PhR for detecting FadA in Fn.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37196002", + "title": "Isolation and identification of hyaluronan-degrading bacteria from Japanese fecal microbiota.", + "year": 2023, + "journal": "PloS one", + "authors": [ + "Akazawa H", + "Fukuda I", + "Kaneda H", + "Yoda S", + "Kimura M", + "Nomoto R", + "Ueda S", + "Shirai Y", + "Osawa R" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.20066664434624557, + "mesh_terms": [ + "Humans", + "Hyaluronic Acid", + "East Asian People", + "Bacteria", + "Feces", + "Gastrointestinal Microbiome" + ], + "raw_abstract": "Hyaluronan (HA) is a high-molecular-weight glycosaminoglycan and widely distributed in all connective tissues and organs with diverse biological functions. HA has been increasingly used as dietary supplements targeted to joint and skin health for humans. We here first report isolation of bacteria from human feces that are capable of degrading HA to lower molecular weight HA oligosaccharides (oligo-HAs). The bacteria were successfully isolated via a selective enrichment method, in which the serially diluted feces of healthy Japanese donors were individually incubated in an enrichment medium containing HA, followed by the isolation of candidate strains from streaked HA-containing agar plates and selection of HA-degrading strains by measuring HA using an ELISA. Subsequent genomic and biochemical assays identified the strains as Bacteroides finegoldii, B. caccae, B. thetaiotaomicron, and Fusobacterium mortiferum. Furthermore, our HPLC analysis revealed that the strains degraded HA to oligo-HAs of various lengths. Subsequent quantitative PCR assay targeting the HA degrading bacteria showed that their distribution in the Japanese donors varied. The evidence suggests that dietary HA is degraded by the human gut microbiota with individual variation to oligo-HAs components, which are more absorbable than HA, thereby exerting its beneficial effects.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38970464", + "title": "Detection of colorectal-cancer-associated bacterial taxa in fecal samples using next-generation sequencing and 19 newly established qPCR assays.", + "year": 2025, + "journal": "Molecular oncology", + "authors": [ + "Senthakumaran T", + "Tann\u00e6s TM", + "Moen AEF", + "Brackmann SA", + "Jahanlu D", + "Rounge TB", + "Bemanian V", + "Tunsj\u00f8 HS" + ], + "bacteria": "Fusobacterium", + "condition": "healthy", + "relevance_score": 0.20040861092972392, + "mesh_terms": [ + "Humans", + "Feces", + "Colorectal Neoplasms", + "High-Throughput Nucleotide Sequencing", + "Bacteria", + "Real-Time Polymerase Chain Reaction", + "Female", + "Middle Aged", + "Male", + "Aged", + "RNA, Ribosomal, 16S", + "Adult" + ], + "raw_abstract": "We have previously identified increased levels of distinct bacterial taxa within mucosal biopsies from colorectal cancer (CRC) patients. Following prior research, the aim of this study was to investigate the detection of the same CRC-associated bacteria in fecal samples and to evaluate the suitability of fecal samples as a non-invasive material for the detection of CRC-associated bacteria. Next-generation sequencing (NGS) of the 16S ribosomal RNA (rRNA) V4 region was performed to evaluate the detection of the CRC-associated bacteria in the fecal microbiota of cancer patients, patients with adenomatous polyp and healthy controls. Furthermore, 19 novel species-specific quantitative PCR (qPCR) assays were established to detect the CRC-associated bacteria. Approximately, 75% of the bacterial taxa identified in biopsies were reflected in fecal samples. NGS failed to detect low-abundance CRC-associated taxa in fecal samples, whereas qPCR exhibited high sensitivity and specificity in identifying all targeted taxa. Comparison of fecal microbial composition between the different patient groups showed enrichment of Fusobacterium\u2009nucleatum, Parvimonas\u2009micra, and Gemella\u2009morbillorum in cancer patients. Our findings suggest that low-abundance mucosa-associated bacteria can be detected in fecal samples using sensitive qPCR assays.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32333495", + "title": "High levels of Helicobacter pylori antigens and antibodies in patients with severe acne vulgaris.", + "year": 2020, + "journal": "Journal of cosmetic dermatology", + "authors": [ + "Saleh R", + "Sedky Mahmoud A", + "Moustafa DA", + "Abu El-Hamd M" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.3893911164486102, + "mesh_terms": [ + "Acne Vulgaris", + "Antigens, Bacterial", + "Cross-Sectional Studies", + "Enzyme-Linked Immunosorbent Assay", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans" + ], + "raw_abstract": "BACKGROUND: Helicobacter pylori (H\u00a0pylori) may play a role in the pathogenesis of extra-intestinal disorders including dermatological diseases. AIMS: This study aimed to assess the levels of H\u00a0pylori antigen and antibody in patients with acne vulgaris (AV). METHODS: This cross-sectional study compared the levels of fecal H\u00a0pylori antigen and serum H\u00a0pylori antibody in 100 patients with AV and 100 age and sex-matched healthy volunteers. Patients with AV were classified into mild, moderate, and severe according to the Global Acne Grading Scale. Levels of\u00a0fecal H\u00a0pylori antigen and serum H\u00a0pylori antibodies were assessed using commercially available enzyme-linked immune-sorbent assay. RESULTS: The patients with severe AV had significantly higher levels of fecal H\u00a0pylori antigen as compared to the patients with mild AV, moderate AV, and healthy controls (P\u00a0<\u00a0.001). The patients with severe AV had significantly higher serum H\u00a0pylori antibody as compared to the patients with mild AV, moderate AV, and healthy controls (P\u00a0=\u00a0.001). The levels of fecal H\u00a0pylori antigen and serum H\u00a0pylori antibody in the patients with mild AV were not significantly different from those in the patients with moderate AV (P\u00a0=\u00a0.49 and P\u00a0=\u00a0.05, respectively). CONCLUSION: The patients with severe AV had higher levels of fecal H\u00a0pylori antigen and serum H\u00a0pylori antibody as compared to the patients with mild and moderate AV and with healthy controls. The indicators of H\u00a0pylori infection were positively correlated with the severity and duration of AV.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26691472", + "title": "High occurrence of Fusobacterium nucleatum and Clostridium difficile in the intestinal microbiota of colorectal carcinoma patients.", + "year": 2015, + "journal": "Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]", + "authors": [ + "Fukugaiti MH", + "Ignacio A", + "Fernandes MR", + "Ribeiro J\u00fanior U", + "Nakano V", + "Avila-Campos MJ" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.36736435931574757, + "mesh_terms": [ + "Aged", + "Brazil", + "Clostridioides difficile", + "Clostridium Infections", + "Colorectal Neoplasms", + "Female", + "Fusobacterium Infections", + "Fusobacterium nucleatum", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "Real-Time Polymerase Chain Reaction" + ], + "raw_abstract": "Colorectal carcinoma is considered the fourth leading cause of cancer deaths worldwide. Several microorganisms have been associated with carcinogenesis, including Enterococcus spp., Helicobacter pylori, enterotoxigenic Bacteroides fragilis, pathogenic E. coli strains and oral Fusobacterium. Here we qualitatively and quantitatively evaluated the presence of oral and intestinal microorganisms in the fecal microbiota of colorectal cancer patients and healthy controls. Seventeen patients (between 49 and 70 years-old) visiting the Cancer Institute of the Sao Paulo State were selected, 7 of whom were diagnosed with colorectal carcinoma. Bacterial detection was performed by qRT-PCR. Although all of the tested bacteria were detected in the majority of the fecal samples, quantitative differences between the Cancer Group and healthy controls were detected only for F. nucleatum and C. difficile. The three tested oral microorganisms were frequently observed, suggesting a need for furthers studies into a potential role for these bacteria during colorectal carcinoma pathogenesis. Despite the small number of patients included in this study, we were able to detect significantly more F. nucleatum and C. difficile in the Cancer Group patients compared to healthy controls, suggesting a possible role of these bacteria in colon carcinogenesis. This finding should be considered when screening for colorectal cancer.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32884012", + "title": "Altered gut microbiota correlated with systemic inflammation in children with Kawasaki disease.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Chen J", + "Yue Y", + "Wang L", + "Deng Z", + "Yuan Y", + "Zhao M", + "Yuan Z", + "Tan C", + "Cao Y" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.3633388449117485, + "mesh_terms": [ + "Acinetobacter", + "Child, Preschool", + "Computational Biology", + "Enterococcus", + "Female", + "Gastrointestinal Microbiome", + "Helicobacter", + "Humans", + "Infant", + "Inflammation", + "Lactococcus", + "Male", + "Mucocutaneous Lymph Node Syndrome", + "Polymerase Chain Reaction", + "Staphylococcus" + ], + "raw_abstract": "Kawasaki disease (KD) is a multi-systemic vasculitis of unknown etiology that occurs mainly in children, and the disturbance of gut microbiota is generally believed to cause a hyperimmune reaction triggering KD. The aim of the study was to investigate the alterations in the fecal microbiota and assess its relationship with systemic inflammation. Totally 30 KD children were enrolled and followed up for 6\u00a0months, with another group of 30 age- and sex-matched healthy children as controls. Phylotype profiles of fecal microbial communities were analyzed using 16S rRNA gene sequencing. Serum inflammatory markers were detected by flow cytometer. We showed that KD children exhibited a significant reduction in fecal microbial diversity in the acute phase compared with the healthy controls. Enterococcus, Acinetobacter, Helicobacter, Lactococcus, Staphylococcus and Butyricimonas in acute KD children were significantly higher than the healthy children. Levels of systemic inflammation biomarkers, including IL-2, IL-4, IL-6, IL-10, TNF-\u03b1, and INF-\u03b3, were significantly elevated in the acute KD children. Altered microbiota genera Enterococcus and Helicobacter abundances were shown to be correlated positively with IL-6, which were never previously reported in KD. This study suggested that gut microbiota alteration is closely associated with systemic inflammation, which provides a new perspective on the etiology and pathogenesis of KD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28799681", + "title": "Genomic and clinical evidence uncovers the enterohepatic species Helicobacter valdiviensis as a potential human intestinal pathogen.", + "year": 2017, + "journal": "Helicobacter", + "authors": [ + "Fresia P", + "Jara R", + "Sierra R", + "Ferr\u00e9s I", + "Greif G", + "Iraola G", + "Collado L" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.3379572048635876, + "mesh_terms": [ + "Adult", + "Base Composition", + "Case-Control Studies", + "Child, Preschool", + "Computational Biology", + "Feces", + "Female", + "Gastrointestinal Diseases", + "Helicobacter", + "Helicobacter Infections", + "Humans", + "Incidence", + "Infant", + "Male", + "Mass Screening", + "Middle Aged", + "Phylogeny", + "Polymerase Chain Reaction", + "Retrospective Studies", + "Sequence Analysis, DNA", + "Virulence Factors", + "Whole Genome Sequencing" + ], + "raw_abstract": "BACKGROUND: Helicobacter valdiviensis is a recently described enterohepatic species isolated from wild bird's fecal samples. Currently, its pathogenic potential and clinical significance are unknown mainly due to the lack of whole-genome sequences to compare with other helicobacters and the absence of specific screenings to determine its prevalence in humans. MATERIALS AND METHODS: The species type strain (WBE14 RESULTS: Helicobacter valdiviensis belongs to a monophyletic clade conformed by H.\u00a0canadensis, H.\u00a0pullorum, H.\u00a0winghamensis, H.\u00a0rodentium, and H.\u00a0apodemus. Its predicted genome size is 2\u00a0176\u00a0246\u00a0bp., with 30% of G+C content and 2064 annotated protein-coding genes. The patterns of virulence factors in H.\u00a0valdiviensis were similar to other enterohepatic species, but evidence of horizontal gene transfer from Campylobacter species was detected for key genes like those coding for the CDT subunits. Positive PCR results confirmed the presence of H.\u00a0valdiviensis in 2 of 254 (0.78%) stools of patients with acute diarrhea while not a single sample was positive in healthy individuals. CONCLUSIONS: Horizontal gene transfer has contributed to shape the gene repertory of H.\u00a0valdiviensis, which codes for virulence factors conserved in other pathogens that are well-known human pathogens. Additionally, the detection of H.\u00a0valdiviensisDNA in diarrheic patients supports its role as a potential emergent intestinal pathogen. Further, sampling efforts are needed to uncover the clinical relevance of this species, which should be accomplished by the isolation of H.\u00a0valdiviensis from ill humans and the obtention of whole genomes from clinical isolates.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "25992741", + "title": "The fecal microbiome in cats with diarrhea.", + "year": 2015, + "journal": "PloS one", + "authors": [ + "Suchodolski JS", + "Foster ML", + "Sohail MU", + "Leutenegger C", + "Queen EV", + "Steiner JM", + "Marks SL" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.33563224990060736, + "mesh_terms": [ + "Animals", + "Cat Diseases", + "Cats", + "Diarrhea", + "Feces", + "Microbiota", + "Polymerase Chain Reaction" + ], + "raw_abstract": "Recent studies have revealed that microbes play an important role in the pathogenesis of gastrointestinal (GI) diseases in various animal species, but only limited data is available about the microbiome in cats with GI disease. The aim of this study was to evaluate the fecal microbiome in cats with diarrhea. Fecal samples were obtained from healthy cats (n = 21) and cats with acute (n = 19) or chronic diarrhea (n = 29) and analyzed by sequencing of 16S rRNA genes, and PICRUSt was used to predict the functional gene content of the microbiome. Linear discriminant analysis (LDA) effect size (LEfSe) revealed significant differences in bacterial groups between healthy cats and cats with diarrhea. The order Burkholderiales, the families Enterobacteriaceae, and the genera Streptococcus and Collinsella were significantly increased in diarrheic cats. In contrast the order Campylobacterales, the family Bacteroidaceae, and the genera Megamonas, Helicobacter, and Roseburia were significantly increased in healthy cats. Phylum Bacteroidetes was significantly decreased in cats with chronic diarrhea (>21 days duration), while the class Erysipelotrichi and the genus Lactobacillus were significantly decreased in cats with acute diarrhea. The observed changes in bacterial groups were accompanied by significant differences in functional gene contents: metabolism of fatty acids, biosynthesis of glycosphingolipids, metabolism of biotin, metabolism of tryptophan, and ascorbate and aldarate metabolism, were all significantly (p<0.001) altered in cats with diarrhea. In conclusion, significant differences in the fecal microbiomes between healthy cats and cats with diarrhea were identified. This dysbiosis was accompanied by changes in bacterial functional gene categories. Future studies are warranted to evaluate if these microbial changes correlate with changes in fecal concentrations of microbial metabolites in cats with diarrhea for the identification of potential diagnostic or therapeutic targets.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27532494", + "title": "Stool microbiome reveals diverse bacterial ureases as confounders of oral urea breath testing for Helicobacter pylori and Mycobacterium tuberculosis in Bamako, Mali.", + "year": 2016, + "journal": "Journal of breath research", + "authors": [ + "Maiga M", + "Cohen K", + "Baya B", + "Srikrishna G", + "Siddiqui S", + "Sanogo M", + "Somboro AM", + "Diarra B", + "Diallo MH", + "Mazumdar V", + "Yoder C", + "Orsega S", + "Belson M", + "Kassambara H", + "Goita D", + "Murphy RL", + "Dao S", + "Polis M", + "Diallo S", + "Timmins GS", + "Dodd L", + "Earl AM", + "Bishai WR" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.3030473758245368, + "mesh_terms": [ + "Adult", + "Breath Tests", + "Demography", + "Feces", + "Female", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Male", + "Mali", + "Microbiota", + "Middle Aged", + "Mycobacterium tuberculosis", + "Sensitivity and Specificity", + "Tuberculosis", + "Urea", + "Urease", + "Young Adult" + ], + "raw_abstract": "Detection of bacterial urease activity has been utilized successfully to diagnose Helicobacter pylori (H. pylori). While Mycobacterium tuberculosis (M. tuberculosis) also possesses an active urease, it is unknown whether detection of mycobacterial urease activity by oral urease breath test (UBT) can be exploited as a rapid point of care biomarker for tuberculosis (TB) in humans. We enrolled 34 individuals newly diagnosed with pulmonary TB and 46 healthy subjects in Bamako, Mali and performed oral UBT, mycobacterial sputum culture and H. pylori testing. Oral UBT had a sensitivity and specificity (95% CI) of 70% (46-88%) and 11% (3-26%), respectively, to diagnose culture-confirmed M. tuberculosis disease among patients without H. pylori, and 100% sensitivity (69-100%) and 11% specificity (3-26%) to diagnose H. pylori among patients without pulmonary TB. Stool microbiome analysis of controls without TB or H. pylori but with positive oral UBT detected high levels of non-H. pylori urease producing organisms, which likely explains the low specificity of oral UBT in this setting and in other reports of oral UBT studies in Africa.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33606766", + "title": "Systemic Helicobacter infection and associated mortalities in endangered Grand Cayman blue iguanas (Cyclura lewisi) and introduced green iguanas (Iguana iguana).", + "year": 2021, + "journal": "PloS one", + "authors": [ + "Conley KJ", + "Seimon TA", + "Popescu IS", + "Wellehan JFX", + "Fox JG", + "Shen Z", + "Haakonsson J", + "Seimon A", + "Brown AT", + "King V", + "Burton F", + "Calle PP" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.29857335704455035, + "mesh_terms": [ + "Animals", + "Breeding", + "Endangered Species", + "Helicobacter Infections", + "Iguanas", + "Introduced Species", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "The Blue Iguana Recovery Programme maintains a captive breeding and head-starting program for endangered Grand Cayman blue iguanas (Cyclura lewisi) on Grand Cayman, Cayman Islands. In May 2015, program staff encountered two lethargic wild Grand Cayman blue iguanas within the Queen Elizabeth II Botanic Park (QEIIBP). Spiral-shaped bacteria were identified on peripheral blood smears from both animals, which molecular diagnostics identified as a novel Helicobacter species (provisionary name Helicobacter sp. GCBI1). Between March 2015 and February 2017, 11 Grand Cayman blue iguanas were identified with the infection. Two of these were found dead and nine were treated; five of the nine treated animals survived the initial infection. Phylogenetic analysis of the 16S rRNA gene suggests Helicobacter sp. GCBI1 is most closely related to Helicobacter spp. in chelonians. We developed a Taqman qPCR assay specific for Helicobacter sp. GCBI1 to screen tissue and/or blood samples from clinical cases, fecal and cloacal samples from clinically healthy Grand Cayman blue iguanas, including previously infected and recovered iguanas, and iguanas housed adjacent to clinical cases. Fecal and/or cloacal swab samples were all negative, suggesting that Grand Cayman blue iguanas do not asymptomatically carry this organism nor shed this pathogen per cloaca post infection. Retrospective analysis of a 2014 mortality event affecting green iguanas (Iguana iguana) from a separate Grand Cayman location identified Helicobacter sp. GCBI1 in two of three cases. The source of infection and mode of transmission are yet to be confirmed. Analysis of rainfall data reveal that all infections occurred during a multi-year dry period, and most occurred shortly after the first rains at the end of seasonal drought. Additionally, further screening has identified Helicobacter sp. GCBI1 from choanal swabs of clinically normal green iguanas in the QEIIBP, suggesting they could be asymptomatic carriers and a potential source of the pathogen.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "25838286", + "title": "Persistent and transient Helicobacter pylori infections in early childhood.", + "year": 2015, + "journal": "Clinical infectious diseases : an official publication of the Infectious Diseases Society of America", + "authors": [ + "O'Ryan ML", + "Lucero Y", + "Rabello M", + "Mamani N", + "Salinas AM", + "Pe\u00f1a A", + "Torres-Torreti JP", + "Mej\u00edas A", + "Ramilo O", + "Suarez N", + "Reynolds HE", + "Orellana A", + "Lagomarcino AJ" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.29547725941402786, + "mesh_terms": [ + "Antibodies, Bacterial", + "Antigens, Bacterial", + "Asymptomatic Diseases", + "Bacterial Proteins", + "Child, Preschool", + "Chile", + "Cohort Studies", + "Enzyme-Linked Immunosorbent Assay", + "Feces", + "Gene Expression Profiling", + "Helicobacter Infections", + "Helicobacter pylori", + "Host-Pathogen Interactions", + "Humans", + "Infant", + "Polymerase Chain Reaction", + "Prospective Studies", + "Time Factors" + ], + "raw_abstract": "BACKGROUND: Helicobacter pylori, the main cause of peptic ulcer disease and gastric cancer in adult populations, is generally acquired during the first years of life. Infection can be persistent or transient and bacterial and host factors determining persistence are largely unknown and may prove relevant for future disease. METHODS: Two cohorts of healthy Chilean infants (313 total) were evaluated every 3 months for 18-57 months to determine pathogen- and host-factors associated with persistent and transient infection. RESULTS: One-third had at least one positive stool ELISA by age 3, with 20% overall persistence. Persistent infections were acquired at an earlier age, associated with more household members, decreased duration of breastfeeding, and nonsecretor status compared to transient infections. The cagA positive strains were more common in persistent stools, and nearly 60% of fully characterized persistent stool samples amplified cagA/vacAs1m1. Persistent children were more likely to elicit a serologic immune response, and both infection groups had differential gene expression profiles, including genes associated with cancer suppression when compared to healthy controls. CONCLUSIONS: These results indicate that persistent H. pylori infections acquired early in life are associated with specific host and/or strain profiles possibly associated with future disease occurrence.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38419635", + "title": "The mutual interactions among Helicobacter pylori, chronic gastritis, and the gut microbiota: a population-based study in Jinjiang, Fujian.", + "year": 2024, + "journal": "Frontiers in microbiology", + "authors": [ + "Li H", + "Hu Y", + "Huang Y", + "Ding S", + "Zhu L", + "Li X", + "Lan M", + "Huang W", + "Lin X" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.26386767029228203, + "mesh_terms": [], + "raw_abstract": "OBJECTIVES: Helicobacter pylori ( PARTICIPANTS: Enrollment involved sequencing the 16S rRNA gene in fecal samples from 176 cases, adhering to stringent inclusion and exclusion criteria. For our study, we included healthy volunteers (Normal), individuals with chronic non-atrophic gastritis (CNAG), and those with CAG from Fujian, China. The aim was to assess gut microbiome dysbiosis based on various histopathological features. QIIME and LEfSe analyses were performed. There were 176 cases, comprising 126 individuals who tested negative for RESULTS: When merging the outcomes from 16S rRNA gene sequencing results, there were no notable variations in alpha diversity among the following groups: Normal, CNAG, and CAG; OLGIM I and OLGIM II; and CONCLUSION: The study uncovered notable distinctions in the characteristics of gut microbiota among the following groups: Normal, CNAG, and CAG; OLGIM I and OLGIM II; and Hp (+) and Hp (-) groups. Through the analysis of", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35188047", + "title": "Helicobacter pylori infection in migraine headache: a true association or an innocent bystander?", + "year": 2023, + "journal": "The International journal of neuroscience", + "authors": [ + "Hassan A", + "Mehany D", + "Eldin HG", + "Abdelghaffar M", + "Abdelbaky HA", + "Kamal YS", + "Hussein M" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.2596843245425669, + "mesh_terms": [ + "Humans", + "Helicobacter Infections", + "Helicobacter pylori", + "Dyspepsia", + "Flatulence", + "Case-Control Studies", + "Migraine Disorders", + "Pain" + ], + "raw_abstract": "Much concern was directed towards the relationship between migraine and Helicobacter pylori (H. pylori) infection. Some researchers reported a strong association. Meanwhile, others have indicated totally negative results. The aim of this work was to clarify the association between migraine headaches and both H. pylori infection and Gastrointestinal (GIT) symptoms and to study their impact on the frequency and severity of migraine headache attacks. This is a case control study conducted on 77 migraine patients and 77 healthy controls. History was taken from the included patients regarding the frequency of migraine headache attacks/month and GIT symptoms including dyspepsia, flatulence, weight loss, and epigastric pain. Migraine Disability Assessment Test (MIDAS) and Visual Analogue Scale (VAS) were used for assessment of migraine severity. Helicobacter pylori was detected in the stool of the included patients and controls. There was a significantly higher prevalence of infection with H. pylori in migraine patients [77.9% (", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39276224", + "title": "Helicobacter pylori and acne vulgaris: is there a relationship?", + "year": 2024, + "journal": "Archives of dermatological research", + "authors": [ + "Afify AA", + "Saleh HMA", + "Hussein AF" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.2590270143341729, + "mesh_terms": [ + "Humans", + "Helicobacter pylori", + "Acne Vulgaris", + "Male", + "Helicobacter Infections", + "Female", + "Case-Control Studies", + "Adult", + "Antibodies, Bacterial", + "Young Adult", + "Severity of Illness Index", + "Feces", + "Adolescent", + "Antigens, Bacterial", + "Middle Aged" + ], + "raw_abstract": "BACKGROUND: Helicobacter pylori (H. pylori) is a gastric Gram-negative, spiral-shaped microaerophilic pathogen. H. pylori may play a potential pathogenic role in extra-intestinal diseases such as hepatobiliary, respiratory, and dermatological disorders. The latter included chronic urticaria, psoriasis and rosacea. The first report in literature on the relationship between H. pylori and acne vulgaris (AV), found association between severe AV and H. pylori infection. There are very limited data in AV patients addressing the impact of H. pylori infection on various severities. In this context, the aim of the present work was to determine the association of H. Pylori infection among AV patients and correlate it with the disease severity. METHODS: This case-control study included 45 Patients with AV and 45 age and sex matched healthy volunteers as a control group. H. pylori antigen in stool and serum H. pylori antibody IgG using commercially available ELISA kits was tested in all included subjects. RESULTS: The percentage of participants with a positive H. pylori antigen in stool and positive H. pylori antibody in serum in the whole study population was 35/90 (38. 9%) and 41/90 (45. 6%). On comparing between the percentages of positive H. pylori antigen in stool and positive H. pylori antibody in serum between the patients with AV and healthy controls, a highly statistically significant difference was found between the two groups (P\u2009<\u20090.001, P\u2009=\u20090.006). On comparing between the percentages of positive H. pylori antigen in stool and positive H. pylori antibody in serum in the patients with different grades of acne severity and healthy controls, the rate of positive H. pylori antigen in stool and positive H. pylori Ab in serum was significantly associated with severity of acne comparing with healthy controls (p\u2009<\u20090. 001). CONCLUSION: The rate of H. pylori infection in patients with AV is high so it may influence the pathogenesis of this skin disease. Patients with severe AV had higher rates of H. pylori antigen in stool and H. pylori antibody in serum as compared to the patients with mild AV and healthy controls.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36168945", + "title": "Microbial gut evaluation in an angolan paediatric population with sickle cell disease.", + "year": 2022, + "journal": "Journal of cellular and molecular medicine", + "authors": [ + "Delgadinho M", + "Ginete C", + "Santos B", + "Mendes J", + "Miranda A", + "Vasconcelos J", + "Brito M" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.24144178659905305, + "mesh_terms": [ + "Child", + "Humans", + "Aged", + "Child, Preschool", + "Adolescent", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Microbiota", + "Bacteria", + "Anemia, Sickle Cell" + ], + "raw_abstract": "Sickle cell disease (SCD) is one of the most common genetic conditions worldwide. It can contribute up to 90% of under-5 mortality in sub-Saharan Africa. Clinical manifestations are very heterogeneous, and the intestinal microbiome appears to be crucial in the modulation of inflammation, cell adhesion and induction of aged neutrophils, the main interveners of recurrent vaso-occlusive crisis. Enterocyte injury, increased permeability, altered microbial composition and bacterial overgrowth have all been documented as microbial and pathophysiologic changes in the gut microbiome of SCD patients in recent studies. Our aim was to sequence the bacterial 16S rRNA gene in order to characterize the gut microbiome of Angolan children with SCA and healthy siblings as a control. A total of 72 stool samples were obtained from children between 3 and 14\u2009years old. Our data showed that the two groups exhibit some notable differences in microbiota relative abundance at different classification levels. Children with SCA have a higher number of the phylum Actinobacteria. As for the genus level, Clostridium cluster XI bacteria was more prevalent in the SCA children, whereas the siblings had a higher abundance of Blautia, Aestuariispira, Campylobacter, Helicobacter, Polaribacter and Anaerorhabdus. In this study, we have presented the first microbiota analysis in an Angolan paediatric population with SCD and provided a detailed view of the microbial differences between patients and healthy controls. There is still much to learn before fully relying on the therapeutic approaches for gut modulation, which is why more research in this field is crucial to making this a reality.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33278617", + "title": "Helicobacter pylori, clinical, laboratory, and noninvasive biomarkers suggestive of gastric damage in healthy school-aged children: A case-control study.", + "year": 2021, + "journal": "International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases", + "authors": [ + "Lucero Y", + "Lagomarcino AJ", + "Torres JP", + "Roessler P", + "Mamani N", + "George S", + "Huerta N", + "Gonzalez M", + "O'Ryan M" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.22220628062366266, + "mesh_terms": [ + "Aged", + "Biomarkers", + "Case-Control Studies", + "Child", + "Child, Preschool", + "Chile", + "Feces", + "Female", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Male", + "Middle Aged", + "Pepsinogen A", + "Pepsinogen C", + "Stomach", + "Stomach Diseases" + ], + "raw_abstract": "BACKGROUND: Helicobacter pylori is acquired largely in early childhood, but its association with symptoms and indirect biomarkers of gastric damage in apparently healthy children remains controversial. We aimed to relate persistent H. pylori infection in apparently healthy school-aged children with clinical, laboratory, and noninvasive biomarkers suggestive of gastric damage using a case-control design. MATERIALS AND METHODS: We followed up 83 children aged 4-5 years with persistent H. pylori infection determined by stool antigen detection and/or a urea breath test and 80 noninfected matched controls from a low-income to middle-income, periurban city in Chile for at least 3 years. Monitoring included clinical visits every 4 months and annual assessment by a pediatric gastroenterologist. A blood sample was obtained to determine laboratory parameters potentially associated with gastric damage (hemogram and serum iron and ferritin levels), biomarkers of inflammation (cytokines, pepsinogens I and II, and tissue inhibitor metalloproteinase 1), and expression of cancer-related genes KLK1, BTG3, and SLC5A8. RESULTS: Persistently infected children had higher frequency of epigastric pain on physical examination (40% versus 16%; P\u2009=\u20090.001), especially from 8 to 10 years of age. No differences in anthropometric measurements or iron-deficiency parameters were found. Persistent infection was associated with higher levels of pepsinogen II (median 12.7 ng/mL versus 9.0 ng/mL; P\u2009<\u20090.001); no difference was observed in other biomarkers or gene expression profiles. CONCLUSIONS: H. pylori infection in apparently asymptomatic school-aged children is associated with an increase in clinical symptoms and in the level of one significant biomarker, pepsinogen II, suggesting early gastric involvement.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28579087", + "title": "The protective role of Helicobacter pylori neutrophil-activating protein in childhood asthma.", + "year": 2017, + "journal": "Allergologia et immunopathologia", + "authors": [ + "Karakullukcu A", + "Tokman HB", + "Nepesov S", + "Demirci M", + "Saribas S", + "Vehid S", + "Caliskan R", + "Taner Z", + "Cokugras H", + "Ziver T", + "Demiryas S", + "Kocazeybek B" + ], + "bacteria": "Helicobacter", + "condition": "healthy", + "relevance_score": 0.20476111202724512, + "mesh_terms": [ + "Asthma", + "Bacterial Proteins", + "Child", + "Child, Preschool", + "DNA, Bacterial", + "Feces", + "Female", + "Gene Expression Regulation, Bacterial", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Hygiene Hypothesis", + "Male", + "RNA, Ribosomal, 16S", + "Sex Factors" + ], + "raw_abstract": "BACKGROUND: Helicobacter pylori quantity and HP-NAP gene expression were evaluated in the faeces of healthy and asthmatic children. METHODS: H. pylori DNAs and RNAs were isolated from the stool samples of 92 asthmatic children (AC; 3-8 years) and 88 healthy controls (HC). Quantitative PCR was used to determine the quantity of H. pylori and HP-NAP expression relative to the 16S rRNA (reference gene). Gene expression was analysed using the delta delta-Ct method. RESULTS: H. pylori DNA was detected in the stool samples of 18 (20.4%) of the 88 HC (p<0.0001, OR=0.79) and none of AC. No meaningful statistical differences were found between individuals with positive and negative family histories for asthma in AC and HC (p>0.05). H. pylori quantity was higher in seven of 18 H. pylori-positive samples, but HP-NAP expression levels were low in four of these seven samples. Based on a multivariate logistic regression analysis of these three variables together, only males displayed a significant difference based on gender differences (p<0.02) and it was determined that, based on the OR value of 0.46 and the 95% CI range of 0.241-0.888, male gender was an independent protective factor in asthma. CONCLUSIONS: HP-NAP levels vary to the relative concentrations of bacteria in the stationary or late logarithmic phases. Different napA expression levels may be caused by different endogenous napA gene expression or different environmental conditions.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26597167", + "title": "The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism.", + "year": 2016, + "journal": "Food & function", + "authors": [ + "Selma MV", + "Romo-Vaquero M", + "Garc\u00eda-Villalba R", + "Gonz\u00e1lez-Sarr\u00edas A", + "Tom\u00e1s-Barber\u00e1n FA", + "Esp\u00edn JC" + ], + "bacteria": "Gordonibacter", + "condition": "healthy", + "relevance_score": 0.5529616131613352, + "mesh_terms": [ + "Actinobacteria", + "Adult", + "Bacteria", + "Biodiversity", + "Coumarins", + "Ellagic Acid", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "Obesity", + "Overweight" + ], + "raw_abstract": "We recently identified three metabotypes (0, A and B) that depend on the metabolic profile of urolithins produced from polyphenol ellagic acid (EA). The gut microbiota and Gordonibacter spp. recently were identified as species able to produce urolithins. A higher percentage of metabotype B was found in patients with metabolic syndrome or colorectal cancer in comparison with healthy individuals. The aim of the present study was to analyse differences in EA metabolism between healthy overweight-obese and normoweight individuals and evaluate the role of gut microbial composition including Gordonibacter. Although the three metabotypes were confirmed in both groups, metabotype B prevailed in overweight-obese (31%) versus normoweight (20%) individuals while metabotype A was higher in normoweight (70%) than the overweight-obese group (57%). This suggests that weight gain favours the growth of bacteria capable of producing urolithin B and/or isourolithin A with respect to urolithin A-producing bacteria. Gordonibacter spp. levels were not significantly different between normoweight and overweight-obese groups but higher Gordonibacter levels were found in metabotype A individuals than in those with metabotype B. Other bacterial species have been reported to show a much closer relationship to obesity and dysbiosis than Gordonibacter. However, Gordonibacter levels are negatively correlated with metabotype B, which prevails in metabolic syndrome and colorectal cancer. This is the first report that links overweight and obesity with an alteration in the catabolism of EA, and where the correlation of Gordonibacter to this alteration is shown. Future investigation of Gordonibacter and urolithin metabotypes as potential biomarkers or therapeutic targets of obesity-related diseases is warranted.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29583112", + "title": "Ellagibacter isourolithinifaciens gen. nov., sp. nov., a new member of the family Eggerthellaceae, isolated from human gut.", + "year": 2018, + "journal": "International journal of systematic and evolutionary microbiology", + "authors": [ + "Beltr\u00e1n D", + "Romo-Vaquero M", + "Esp\u00edn JC", + "Tom\u00e1s-Barber\u00e1n FA", + "Selma MV" + ], + "bacteria": "Gordonibacter", + "condition": "healthy", + "relevance_score": 0.31240125800715646, + "mesh_terms": [ + "Actinobacteria", + "Adult", + "Bacterial Typing Techniques", + "Base Composition", + "DNA, Bacterial", + "Diaminopimelic Acid", + "Fatty Acids", + "Feces", + "Gastrointestinal Tract", + "Glycolipids", + "Humans", + "Male", + "Peptidoglycan", + "Phospholipids", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA", + "Vitamin K 2" + ], + "raw_abstract": "Urolithins are gut microbial metabolites that exert health benefits in vivo and are generated from ellagic acid (EA) and ellagitannin-containing foods such as strawberries, pomegranates and walnuts. Gordonibacter species produce some intermediary urolithins but the micro-organisms responsible for the transformation of EA into the final and more bioactive urolithins, such as urolithin A and isourolithin A, are unknown. We report here a new bacterium, capable of metabolizing EA into isourolithin A, isolated from healthy human faeces and characterized by determining phenotypic, biochemical and molecular methods. Strain CEBAS 4A belongs to the Eggerthellaceae family and differed from other genera of this family, both phylogenetically and phenotypically. Based on 16S rRNA gene sequence similarity, the strain was related to Enterorhabdus musicola DSM 19490", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36941248", + "title": "The gut microbiome in social anxiety disorder: evidence of altered composition and function.", + "year": 2023, + "journal": "Translational psychiatry", + "authors": [ + "Butler MI", + "Bastiaanssen TFS", + "Long-Smith C", + "Morkl S", + "Berding K", + "Ritz NL", + "Strain C", + "Patangia D", + "Patel S", + "Stanton C", + "O'Mahony SM", + "Cryan JF", + "Clarke G", + "Dinan TG" + ], + "bacteria": "Gordonibacter", + "condition": "healthy", + "relevance_score": 0.307411559444327, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Autism Spectrum Disorder", + "Phobia, Social", + "Microbiota", + "Schizophrenia" + ], + "raw_abstract": "The microbiome-gut-brain axis plays a role in anxiety, the stress response and social development, and is of growing interest in neuropsychiatric conditions. The gut microbiota shows compositional alterations in a variety of psychiatric disorders including depression, generalised anxiety disorder (GAD), autism spectrum disorder (ASD) and schizophrenia but studies investigating the gut microbiome in social anxiety disorder (SAD) are very limited. Using whole-genome shotgun analysis of 49 faecal samples (31 cases and 18 sex- and age-matched controls), we analysed compositional and functional differences in the gut microbiome of patients with SAD in comparison to healthy controls. Overall microbiota composition, as measured by beta-diversity, was found to be different between the SAD and control groups and several taxonomic differences were seen at a genus- and species-level. The relative abundance of the genera Anaeromassillibacillus and Gordonibacter were elevated in SAD, while Parasuterella was enriched in healthy controls. At a species-level, Anaeromassilibacillus sp An250 was found to be more abundant in SAD patients while Parasutterella excrementihominis was higher in controls. No differences were seen in alpha diversity. In relation to functional differences, the gut metabolic module 'aspartate degradation I' was elevated in SAD patients. In conclusion, the gut microbiome of patients with SAD differs in composition and function to that of healthy controls. Larger, longitudinal studies are warranted to validate these preliminary results and explore the clinical implications of these microbiome changes.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35142786", + "title": "Enriched and Decreased Intestinal Microbes in Active VKH Patients.", + "year": 2022, + "journal": "Investigative ophthalmology & visual science", + "authors": [ + "Li M", + "Yang L", + "Cao J", + "Liu T", + "Liu X" + ], + "bacteria": "Gordonibacter", + "condition": "healthy", + "relevance_score": 0.224843575271723, + "mesh_terms": [ + "Actinobacteria", + "Adult", + "Case-Control Studies", + "Clostridiales", + "DNA, Bacterial", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Genotyping Techniques", + "Healthy Volunteers", + "Humans", + "Male", + "Middle Aged", + "Pseudomonas", + "RNA, Ribosomal, 16S", + "Scleritis", + "Uveomeningoencephalitic Syndrome" + ], + "raw_abstract": "PURPOSE: To determine the possible microbiome related to Vogt-Koyanagi-Harada (VKH) disease in comparison to patients with noninfectious anterior scleritis and healthy people. METHODS: Fecal samples were extracted from 42 individuals, including 11 patients with active VKH, 11 healthy people, and 20 patients with noninfectious anterior scleritis. We amplified the V3 to V4 16S ribosomal DNA (rDNA) region to obtain the target sequence. Then, the target sequence was amplified by polymerase chain reaction. The obtained target sequences were sequenced by high-throughput 16S rDNA analysis. RESULTS: At the genus level, there were three enriched (Stomatobaculum, Pseudomonas, Lachnoanaerobaculum) and two depleted (Gordonibacter, Slackia) microbes that were detected only in patients with VKH. There were 10 enriched and 12 depleted microbes that were observed in both patients with VKH disease and noninfectious anterior scleritis (P < 0.05). The interactions of these microbes were graphed. Tyzzerella and Eggerthella were the nodes of interaction between these microorganisms, which were regulated by both positive and negative aspects, but the expression level in patients with active VKH was upregulated. CONCLUSIONS: Special or nonspecial enrichment and decreased intestinal microbes were observed in patients with active VKH. The action mechanism of these microbes needs further study.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38331564", + "title": "The semen microbiome of miniature pony stallions.", + "year": 2024, + "journal": "Reproduction, fertility, and development", + "authors": [ + "Cooke CG", + "Gibb Z", + "Grupen CG", + "Schemann K", + "Deshpande N", + "Harnett JE" + ], + "bacteria": "Fastidiosipila", + "condition": "healthy", + "relevance_score": 0.2284597326055187, + "mesh_terms": [ + "Female", + "Male", + "Horses", + "Humans", + "Animals", + "Semen", + "RNA, Ribosomal, 16S", + "Microbiota", + "Fertility" + ], + "raw_abstract": "CONTEXT: Little is known about the microbial composition of stallion semen. AIMS: To describe the microbiota detected in equine semen of healthy miniature pony stallions. METHODS: Semen specimens were collected using a Missouri artificial vagina at a single time point. PacBio (Pacific Biosciences) genomic DNA sequencing of the 16S rRNA gene was performed on these specimens, following which next-generation microbiome bioinformatics platform QIIME2 was used to process fastq files and analyse the amplicon data. The data were categorised into genus, family, class, order and phylum. KEY RESULTS: Firmicutes and Bacteroidetes phyla predominated (76%), followed by Proteobacteria (15%). Bacteroidales, Clostridiales and Cardiobacteriales predominated the microbial rank of order (86%). Class was mainly composed of Bacteroidia, Clostridia and Gammaproteobacteria (87%), while family was mainly composed of Porphyromonadaceae , Family_XI and Cardiobacteriaceae (62%). At the level of genus, 80% of the abundance was composed of seven genera, namely Porphyromonas, Suttonella, Peptoniphilus, Fastidiosipila, Ezakiella, Petrimonas and an unknown taxon. CONCLUSIONS: The findings indicate that specific microbiota may be characteristic of healthy miniature pony stallions' semen with some inter-individual variations observed. IMPLICATIONS: Larger equine studies involving fertile and infertile subjects could be informed by this study and could explore the relationship of the semen microbiome to male fertility.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37587110", + "title": "Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome.", + "year": 2023, + "journal": "NPJ science of food", + "authors": [ + "Walsh LH", + "Walsh AM", + "Garcia-Perez I", + "Crispie F", + "Costabile A", + "Ellis R", + "Finlayson J", + "Finnegan LA", + "Claesson MJ", + "Holmes E", + "Cotter PD" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.31556533080837273, + "mesh_terms": [], + "raw_abstract": "It has been established that the human gut microbiota is central to health, and, consequently, there has been a growing desire to positively modulate its composition and/or function through, for example, the use of fermented foods, prebiotics or probiotics. Here, we compare the relative impact of the daily consumption of an inulin-enriched diet (n\u2009=\u200910), a commercial probiotic-containing fermented milk product (FMP) (n\u2009=\u200910), or a traditional kefir FMP (n\u2009=\u20099), over a 28-day period on the gut microbiome and urine metabolome of healthy human adults. None of the treatments resulted in significant changes to clinical parameters or biomarkers tested. However, shotgun metagenomic analysis revealed that kefir consumption resulted in a significant change in taxonomy, in the form of an increased abundance of the sub-dominant FMP-associated species Lactococcus raffinolactis, which further corresponded to shifts in the urine metabolome. Overall, our results indicated that daily consumption of a single portion of kefir alone resulted in detectable changes to the gut microbiota and metabolome of consumers.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32884012", + "title": "Altered gut microbiota correlated with systemic inflammation in children with Kawasaki disease.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Chen J", + "Yue Y", + "Wang L", + "Deng Z", + "Yuan Y", + "Zhao M", + "Yuan Z", + "Tan C", + "Cao Y" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.2894806313455323, + "mesh_terms": [ + "Acinetobacter", + "Child, Preschool", + "Computational Biology", + "Enterococcus", + "Female", + "Gastrointestinal Microbiome", + "Helicobacter", + "Humans", + "Infant", + "Inflammation", + "Lactococcus", + "Male", + "Mucocutaneous Lymph Node Syndrome", + "Polymerase Chain Reaction", + "Staphylococcus" + ], + "raw_abstract": "Kawasaki disease (KD) is a multi-systemic vasculitis of unknown etiology that occurs mainly in children, and the disturbance of gut microbiota is generally believed to cause a hyperimmune reaction triggering KD. The aim of the study was to investigate the alterations in the fecal microbiota and assess its relationship with systemic inflammation. Totally 30 KD children were enrolled and followed up for 6\u00a0months, with another group of 30 age- and sex-matched healthy children as controls. Phylotype profiles of fecal microbial communities were analyzed using 16S rRNA gene sequencing. Serum inflammatory markers were detected by flow cytometer. We showed that KD children exhibited a significant reduction in fecal microbial diversity in the acute phase compared with the healthy controls. Enterococcus, Acinetobacter, Helicobacter, Lactococcus, Staphylococcus and Butyricimonas in acute KD children were significantly higher than the healthy children. Levels of systemic inflammation biomarkers, including IL-2, IL-4, IL-6, IL-10, TNF-\u03b1, and INF-\u03b3, were significantly elevated in the acute KD children. Altered microbiota genera Enterococcus and Helicobacter abundances were shown to be correlated positively with IL-6, which were never previously reported in KD. This study suggested that gut microbiota alteration is closely associated with systemic inflammation, which provides a new perspective on the etiology and pathogenesis of KD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26460205", + "title": "Relationship Between Microbiota of the Colonic Mucosa vs Feces and Symptoms, Colonic Transit, and Methane Production in Female Patients With Chronic Constipation.", + "year": 2016, + "journal": "Gastroenterology", + "authors": [ + "Parthasarathy G", + "Chen J", + "Chen X", + "Chia N", + "O'Connor HM", + "Wolf PG", + "Gaskins HR", + "Bharucha AE" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.28277005045995335, + "mesh_terms": [ + "Adult", + "Algorithms", + "Bacteria", + "Breath Tests", + "Case-Control Studies", + "Chronic Disease", + "Colon", + "Constipation", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Transit", + "Humans", + "Intestinal Mucosa", + "Methane", + "Middle Aged", + "Multivariate Analysis", + "Nonlinear Dynamics", + "Phylogeny", + "Ribotyping" + ], + "raw_abstract": "BACKGROUND & AIMS: In fecal samples from patients with chronic constipation, the microbiota differs from that of healthy subjects. However, the profiles of fecal microbiota only partially replicate those of the mucosal microbiota. It is not clear whether these differences are caused by variations in diet or colonic transit, or are associated with methane production (measured by breath tests). We compared the colonic mucosal and fecal microbiota in patients with chronic constipation and in healthy subjects to investigate the relationships between microbiota and other parameters. METHODS: Sigmoid colonic mucosal and fecal microbiota samples were collected from 25 healthy women (controls) and 25 women with chronic constipation and evaluated by 16S ribosomal RNA gene sequencing (average, 49,186 reads/sample). We assessed associations between microbiota (overall composition and operational taxonomic units) and demographic variables, diet, constipation status, colonic transit, and methane production (measured in breath samples after oral lactulose intake). RESULTS: Fourteen patients with chronic constipation had slow colonic transit. The profile of the colonic mucosal microbiota differed between constipated patients and controls (P < .05). The overall composition of the colonic mucosal microbiota was associated with constipation, independent of colonic transit (P < .05), and discriminated between patients with constipation and controls with 94% accuracy. Genera from Bacteroidetes were more abundant in the colonic mucosal microbiota of patients with constipation. The profile of the fecal microbiota was associated with colonic transit before adjusting for constipation, age, body mass index, and diet; genera from Firmicutes (Faecalibacterium, Lactococcus, and Roseburia) correlated with faster colonic transit. Methane production was associated with the composition of the fecal microbiota, but not with constipation or colonic transit. CONCLUSIONS: After adjusting for diet and colonic transit, the profile of the microbiota in the colonic mucosa could discriminate patients with constipation from healthy individuals. The profile of the fecal microbiota was associated with colonic transit and methane production (measured in breath), but not constipation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28951355", + "title": "[High-throughput sequencing for analysis of structural change of intestinal microbiota in patients with colorectal adenoma].", + "year": 2017, + "journal": "Nan fang yi ke da xue xue bao = Journal of Southern Medical University", + "authors": [ + "Lu YY", + "Zeng Y", + "Hu GY", + "Wang XP" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.2777273830194432, + "mesh_terms": [], + "raw_abstract": "OBJECTIVE: To investigate the taxonomic richness and diversity of gut microbiota in patients with colorectal adenoma and elucidate the role of gut microorganisms in precancerous lesions in the colon and rectum. METHOD: Adenomatous tissues from 31 patients with colorectal adenoma and normal intestinal mucosal tissues from 20 healthy control subjects were collected through colonoscopy. The total bacterial genomic DNA was extracted, and the V RESULTS: Patients with colorectal adenomas had a higher alpha diversity and richness indices compared to the healthy controls (P<0.01). The mucosal microbiota in colorectal adenoma tissue showed a distinctive structural difference from that in normal intestinal mucosal tissues. At the phylum level, a large decrease in Firmicutes with concomitant relative expansion of Proteobacteria was observed in patients with colorectal adenomas, resulting in a significant decrease in the Firmicutes/Bacteroidetes ratio (P<0.01). At the genus level, Lactococcus and Pseudomonas were enriched whereas Enterococcus, Bacillus, and Solibacillus were reduced obviously in the preneoplastic tissues (P<0.01). We also found a similar gut microbiome composition between low-grade and high-grade intraepithelial neoplasia; the ratio of Escherichia-Shigella tended to increase in high-grade intraepithelial neoplasia, but this change was not statistically significant (P%0.28). CONCLUSION: Significant changes in the structure of the intestinal flora occur in patients with colorectal adenomas, indicating that the association of dysbiosis of the gut microbiota with the occurrence of a pro-oncogenic microenvironment. \u76ee\u7684: \u63a2\u8ba8\u7ed3\u76f4\u80a0\u764c\u53d1\u5c55\u65e9\u671f\u80a0\u9053\u83cc\u7fa4\u7684\u53d8\u5316\u89c4\u5f8b\u3002 \u65b9\u6cd5: \u901a\u8fc7\u7ed3\u80a0\u955c\u6d3b\u68c0\u6536\u96c631\u4f8b\u7ed3\u80a0\u817a\u7624\u60a3\u8005\u7684\u817a\u7624\u7ec4\u7ec7\u4ee5\u53ca20\u4f8b\u5065\u5eb7\u5fd7\u613f\u8005\u7684\u80a0\u9053\u9ecf\u819c\uff0c\u63d0\u53d6\u57fa\u56e0\u7ec4DNA\uff0c\u5bf9\u7ec6\u83cc16SrRNA\u57fa\u56e0\u5e8f\u5217V \u7ed3\u679c: \u7ed3\u80a0\u817a\u7624\u60a3\u8005\u7684\u80a0\u9053\u9ecf\u819c\u83cc\u7fa4\u591a\u6837\u6027\u6bd4\u5065\u5eb7\u5bf9\u7167\u4eba\u7fa4\u663e\u8457\u589e\u9ad8( \u7ed3\u8bba: \u7ed3\u80a0\u817a\u7624\u60a3\u8005\u80a0\u9053\u83cc\u7fa4\u591a\u6837\u6027\u548c\u6784\u6210\u4e0e\u6b63\u5e38\u5065\u5eb7\u4eba\u5b58\u5728\u660e\u663e\u5dee\u5f02\uff0c\u817a\u7624\u60a3\u8005\u9ecf\u819c\u83cc\u7fa4\u7ed3\u6784\u53d1\u751f\u660e\u663e\u5931\u8861\uff0c\u5f62\u6210\u4e86\u6613\u4e8e\u80bf\u7624\u751f\u957f\u7684\u80a0\u9053\u5fae\u751f\u6001\u73af\u5883\u3002", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32910902", + "title": "Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization.", + "year": 2020, + "journal": "Cell host & microbe", + "authors": [ + "Zuo T", + "Sun Y", + "Wan Y", + "Yeoh YK", + "Zhang F", + "Cheung CP", + "Chen N", + "Luo J", + "Wang W", + "Sung JJY", + "Chan PKS", + "Wang K", + "Chan FKL", + "Miao Y", + "Ng SC" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.2711699926342849, + "mesh_terms": [ + "Adult", + "Bacteria", + "Bacteriophages", + "Biodiversity", + "China", + "DNA, Viral", + "Diet", + "Ethnicity", + "Feces", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Geography", + "Humans", + "Lactococcus", + "Urbanization", + "Virome" + ], + "raw_abstract": "The human-gut-DNA virome is highly diverse and individual specific, but little is known of its variation at a population level. Here, we report the fecal DNA virome of 930 healthy adult subjects from two regions in China (Hong Kong and Yunnan) spanning six ethnicities (Han, Zang, Miao, Bai, Dai, and Hani), and including urban and rural residents for each ethnicity. Twenty host factors were found to significantly correlate with the human-gut virome variation, with geography carrying the strongest impact and ethnicity-distinct diets associating with certain viral species. Urbanization enhances interindividual dissimilarities between gut viromes, with the duration of urban residence associating with multiple bacteriophages, including Lactobacillus phage and Lactococcus phage. Overall, the gut virome presents more heterogeneity relative to the bacterial microbiome across the examined Chinese populations. This study highlights population-based variations and the importance of host and environmental factors in shaping the DNA virome in the human gut.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33125401", + "title": "Baseline gut microbiome composition predicts metformin therapy short-term efficacy in newly diagnosed type 2 diabetes patients.", + "year": 2020, + "journal": "PloS one", + "authors": [ + "Elbere I", + "Silamikelis I", + "Dindune II", + "Kalnina I", + "Ustinova M", + "Zaharenko L", + "Silamikele L", + "Rovite V", + "Gudra D", + "Konrade I", + "Sokolovska J", + "Pirags V", + "Klovins J" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.262289789308794, + "mesh_terms": [ + "Adult", + "Bacteroidetes", + "Diabetes Mellitus, Type 2", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Lactococcus lactis", + "Longitudinal Studies", + "Male", + "Metformin", + "Microbiota", + "Prevotella", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The study was conducted to investigate the effects of metformin treatment on the human gut microbiome's taxonomic and functional profile in the Latvian population, and to evaluate the correlation of these changes with therapeutic efficacy and tolerance. METHODS: In this longitudinal observational study, stool samples for shotgun metagenomic sequencing-based analysis were collected in two cohorts. The first cohort included 35 healthy nondiabetic individuals (metformin dose 2x850mg/day) at three time-points during metformin administration. The second cohort was composed of 50 newly-diagnosed type 2 diabetes patients (metformin dose-determined by an endocrinologist) at two concordant times. Patients were defined as Responders if their HbA1c levels during three months of metformin therapy had decreased by \u226512.6 mmol/mol (1%), while in Non-responders HbA1c were decreased by <12.6 mmol/mol (1%). RESULTS: Metformin reduced the alpha diversity of microbiota in healthy controls (p = 0.02) but not in T2D patients. At the species level, reduction in the abundance of Clostridium bartlettii and Barnesiella intestinihominis, as well as an increase in the abundance of Parabacteroides distasonis and Oscillibacter unclassified overlapped between both study groups. A large number of group-specific changes in taxonomic and functional profiles was observed. We identified an increased abundance of Prevotella copri (FDR = 0.01) in the Non-Responders subgroup, and enrichment of Enterococcus faecium, Lactococcus lactis, Odoribacter, and Dialister at baseline in the Responders group. Various taxonomic units were associated with the observed incidence of side effects in both cohorts. CONCLUSIONS: Metformin effects are different in T2D patients and healthy individuals. Therapy induced changes in the composition of gut microbiome revealed possible mediators of observed short-term therapeutic effects. The baseline composition of the gut microbiome may influence metformin therapy efficacy and tolerance in T2D patients and could be used as a powerful prediction tool.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27194068", + "title": "Mucosal adherent bacterial dysbiosis in patients with colorectal adenomas.", + "year": 2016, + "journal": "Scientific reports", + "authors": [ + "Lu Y", + "Chen J", + "Zheng J", + "Hu G", + "Wang J", + "Huang C", + "Lou L", + "Wang X", + "Zeng Y" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.24665147513221786, + "mesh_terms": [ + "Adenoma", + "Adult", + "Aged", + "Bacteria", + "Bacterial Adhesion", + "Biopsy", + "Colon", + "Dysbiosis", + "Female", + "Humans", + "Male", + "Middle Aged", + "Phylogeny", + "Pretectal Region", + "RNA, Bacterial", + "RNA, Ribosomal, 16S", + "Sequence Analysis, RNA" + ], + "raw_abstract": "Recent reports have suggested that the gut microbiota is involved in the progression of colorectal cancer (CRC). The composition of gut microbiota in CRC precursors has not been adequately described. To characterize the structure of adherent microbiota in this disease, we conducted pyrosequencing-based analysis of 16S rRNA genes to determine the bacterial profile of normal colons (healthy controls) and colorectal adenomas (CRC precursors). Adenoma mucosal biopsy samples and adjacent normal colonic mucosa from 31 patients with adenomas and 20 healthy volunteers were profiled using the Illumina MiSeq platform. Principal coordinate analysis (PCoA) showed structural segregation between colorectal adenomatous tissue and control tissue. Alpha diversity estimations revealed higher microbiota diversity in samples from patients with adenomas. Taxonomic analysis illustrated that abundance of eight phyla (Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Chloroflexi, Cyanobacteria, Candidate-division TM7, and Tenericutes) was significantly different. In addition, Lactococcus and Pseudomonas were enriched in preneoplastic tissue, whereas Enterococcus, Bacillus, and Solibacillus were reduced. However, both PCoA and cluster tree analyses showed similar microbiota structure between adenomatous and adjacent non-adenoma tissues. These present findings provide preliminary experimental evidence supporting that colorectal preneoplastic lesion may be the most important factor leading to alterations in bacterial community composition.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34398307", + "title": "Contrasting gut microbiota in captive Eurasian otters (Lutra lutra) by age.", + "year": 2021, + "journal": "Archives of microbiology", + "authors": [ + "Okamoto Y", + "Ichinohe N", + "Woo C", + "Han SY", + "Kim HH", + "Ito S", + "Nakamura C", + "Kumura J", + "Nagaoka K", + "Yamamoto N" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.24620623500248273, + "mesh_terms": [ + "Animals", + "Endangered Species", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Otters", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Understanding the gut microbiota characteristics of endangered species such as the Eurasian otter (Lutra lutra), especially in their early stages of life, could be essential for improving their management and ex situ conservation strategies. Here, we analyzed the gut microbiota diversity, composition, and function of captive Eurasian otters at different ages using high-throughput 16S rRNA gene sequencing. We found that: (1) Clostridiaceae was abundant in all age stages; (2) Lactococcus in cubs is thought to predominate for digesting milk; (3) bacteria associated with amino acid metabolism increase with age, while bacteria associated with carbohydrate metabolism decrease with age, which is likely due to decrease in dietary carbohydrate content (e.g., milk) and increase in dietary protein contents (e.g., fishes) with age; and (4) fish-related bacteria were detected in feces of healthy adults and juveniles. Overall, the gut microbiota of captive Eurasian otters was taxonomically and functionally different by age, which is thought to be attributed to the difference in the diet in their life stages. This study provided baseline information regarding the gut microbiota of Eurasian otters for the first time and contributes to improvement in their management in captivity.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29340896", + "title": "Analysis of fecal microbiota in patients with functional constipation undergoing treatment with synbiotics.", + "year": 2018, + "journal": "European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology", + "authors": [ + "Huang LS", + "Kong C", + "Gao RY", + "Yan X", + "Yu HJ", + "Wen B", + "Zhu Q", + "Shen TY", + "Sun ZL", + "Qin HL" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.24364654613148962, + "mesh_terms": [ + "Aged", + "Case-Control Studies", + "Constipation", + "DNA, Bacterial", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "RNA, Ribosomal, 16S", + "Synbiotics" + ], + "raw_abstract": "This study was performed to identify changes to microbial composition after treatment with synbiotics in patients with functional constipation and to define the key microbiota in the pathogenesis of functional constipation. Fecal samples from 53 patients diagnosed with chronic functional constipation according to the Rome III criteria were analyzed using 16S rRNA sequencing. After treatment with synbiotics for 1\u00a0month, fecal samples were collected from 36 patients; after a total of 3\u00a0months, fecal samples were collected from 15 patients. The outcomes were compared with the intestinal microbiota profiles of 53 healthy community volunteers. The microbiota in the constipation group differed from that in the treatment group and healthy group. After synbiotic treatment for 1 and 3\u00a0months, the abundance of Escherichia/Shigella decreased, whereas that of Prevotella_9 and Lactococcus increased. Comparison of the microbiota among the three groups showed that Prevotella_9 was the characteristic bacteria that decreased in the constipation group and increased in the treatment group. Synbiotic treatment can improve the microbiota in patients with constipation. Identification of the key bacterial genus is important to reveal the mechanism and provide a reliable theoretical basis of synbiotic treatment. It will also promote relevant research of microbiota treatment and individualized treatments.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30768688", + "title": "The Alternate Consumption of Quercetin and Alliin in the Traditional Asian Diet Reshaped Microbiota and Altered Gene Expression of Colonic Epithelial Cells in Rats.", + "year": 2019, + "journal": "Journal of food science", + "authors": [ + "Yu J", + "Guo H", + "Xie J", + "Luo J", + "Li Y", + "Liu L", + "Ou S", + "Zhang G", + "Peng X" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.22593126227913893, + "mesh_terms": [ + "Animals", + "Bacteria", + "Colon", + "Cysteine", + "Diet", + "Epithelial Cells", + "Feces", + "Gastrointestinal Microbiome", + "Gene Expression Regulation", + "Intestinal Mucosa", + "Male", + "Quercetin", + "RNA, Ribosomal, 16S", + "Rats" + ], + "raw_abstract": "The diet of traditional Asian is similar to the Mediterranean that was considered as a healthy dietary pattern. The report was scarce on whether different plant-derived components with similar anti-oxidative and anti-inflammatory function such as quercetin and alliin in traditional Asian diet consumed in an alternate style cooperatively affect health including the growth of host and the status of the gut microbiota and colonic epithelial immunity. In the present study, the effects of alternate consumption of quercetin and alliin on host health judging by the profile of gut microbiota and gene expression of colonic epithelial cells were investigated with the Illumina MiSeq sequencing (16S rRNA genes) and Illumina HiSeq (RNA-seq) technique, respectively. The results showed that the alternate consumption significantly increased the rat body weight and reshaped the gut microbiota composition. At the phylum level, it significantly increased the relative abundance of fecal Firmicutes and Cyanobacteria but decreased that of Bacteroidetes (P < 0.05) and increased the relative abundance of Candidatus Arthromitus, Lactococcus, Geobacillus, and Ruminococcus at the genus level that benefits the host's health. The alternate consumption of quercetin and alliin also altered 13 genes expression involved in the KEGG pathways of complement and coagulation cascades and hematopoietic cell lineage to improve the gut immunity. Therefore, the alternate consumption of quercetin and alliin in traditional Asian diet can contribute beneficial metabolic effects by optimizing gut microbiota and altering the immunologic function of colonic epithelial cells, resulting in its potential to improve the sub-health status.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35013099", + "title": "A pilot exploration of multi-omics research of gut microbiome in major depressive disorders.", + "year": 2022, + "journal": "Translational psychiatry", + "authors": [ + "Zhao H", + "Jin K", + "Jiang C", + "Pan F", + "Wu J", + "Luan H", + "Zhao Z", + "Chen J", + "Mou T", + "Wang Z", + "Lu J", + "Lu S", + "Hu S", + "Xu Y", + "Huang M" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.2233864938355151, + "mesh_terms": [ + "Brain", + "Depressive Disorder, Major", + "Gastrointestinal Microbiome", + "Gray Matter", + "Humans", + "Microbiota" + ], + "raw_abstract": "The pathophysiology of major depressive disorder (MDD) remains obscure. Recently, the microbiota-gut-brain (MGB) axis's role in MDD has an increasing attention. However, the specific mechanism of the multi-level effects of gut microbiota on host metabolism, immunity, and brain structure is unclear. Multi-omics approaches based on the analysis of different body fluids and tissues using a variety of analytical platforms have the potential to provide a deeper understanding of MGB axis disorders. Therefore, the data of metagenomics, metabolomic, inflammatory factors, and MRI scanning are collected from the two groups including 24 drug-na\u00efve MDD patients and 26 healthy controls (HCs). Then, the correlation analysis is performed in all omics. The results confirmed that there are many markedly altered differences, such as elevated Actinobacteria abundance, plasma IL-1\u03b2 concentration, lipid, vitamin, and carbohydrate metabolism disorder, and diminished grey matter volume (GMV) of inferior frontal gyrus (IFG) in the MDD patients. Notably, three kinds of discriminative bacteria, Ruminococcus bromii, Lactococcus chungangensis, and Streptococcus gallolyticus have an extensive correlation with metabolome, immunology, GMV, and clinical symptoms. All three microbiota are closely related to IL-1\u03b2 and lipids (as an example, phosphoethanolamine (PEA)). Besides, Lactococcus chungangensis is negatively related to the GMV of left IFG. Overall, this study demonstrate that the effects of gut microbiome exert in MDD is multifactorial.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32199523", + "title": "Microbiota Stability and Gastrointestinal Tolerance in Response to a High-Protein Diet with and without a Prebiotic, Probiotic, and Synbiotic: A Randomized, Double-Blind, Placebo-Controlled Trial in Older Women.", + "year": 2020, + "journal": "Journal of the Academy of Nutrition and Dietetics", + "authors": [ + "Ford AL", + "Nagulesapillai V", + "Piano A", + "Auger J", + "Girard SA", + "Christman M", + "Tompkins TA", + "Dahl WJ" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.22112021492653067, + "mesh_terms": [ + "Aged", + "Cross-Over Studies", + "Diet, High-Protein", + "Double-Blind Method", + "Elder Nutritional Physiological Phenomena", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Healthy Volunteers", + "Humans", + "Prebiotics", + "Probiotics", + "Synbiotics" + ], + "raw_abstract": "BACKGROUND: Higher protein intakes may help reduce sarcopenia and facilitate recovery from illness and injury in older adults. However, high-protein diets (HPDs) including animal-sourced foods may negatively perturb the microbiota, and provision of probiotics and prebiotics may mitigate these effects. OBJECTIVE: The aim of this study was to examine the effects of HPD, with and without a probiotic and/or prebiotic, on gut microbiota and wellness in older women. DESIGN: We conducted an 18-week, double-blind, placebo-controlled, crossover study. PARTICIPANTS/SETTING: Participants were healthy, older women (mean age\u00b1standard deviation=73.7\u00b15.6 years; n=26) recruited from Florida. INTERVENTION: Participants received a weight-maintenance HPD for 2-week periods and the following, in random order: HPD alone (1.5 to 2.2 g/kg/day protein); HPD plus multistrain probiotic formulation (1.54\u00d710 MAIN OUTCOME MEASURES: Microbiota composition and probiotic strain recovery were measured. STATISTICAL ANALYSES: Microbiota composition was analyzed by Wilcoxon signed-rank test and t test. Secondary outcomes were analyzing using generalized linear mixed models. RESULTS: The microbiota profile demonstrated relative stability with the HPD; representation of Lactobacillus, Lactococcus, and Streptococcus were enhanced, whereas butyrate producers, Roseburia and Anaerostipes, were suppressed. Lactococcus was suppressed with synbiotic vs other HPD periods. Recovery was confirmed for all probiotic strains. Indicators of wellness were unchanged, with the exception of a minimal increase in gastrointestinal distress with inulin. Fat-free mass increased from baseline to study end. CONCLUSIONS: An HPD adhering to the recommended acceptable macronutrient distribution ranges maintains wellness in healthy older women and exerts minor perturbations to the microbiome profile, a group that may benefit from a higher protein intake. ClinicalTrials.gov ID: NCT #02445560.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37742216", + "title": "Effects of commercial and traditional kefir supplementation on apparent total tract macronutrient digestibility and the fecal characteristics, metabolites, and microbiota of healthy adult dogs.", + "year": 2023, + "journal": "Journal of animal science", + "authors": [ + "Metras BN", + "Oba PM", + "Miller MJ", + "Swanson KS" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.2125615316867641, + "mesh_terms": [ + "Humans", + "Dogs", + "Animals", + "Kefir", + "Digestion", + "Feces", + "Nutrients", + "Diet", + "Microbiota", + "Dietary Supplements", + "Immunoglobulin A", + "Animal Feed" + ], + "raw_abstract": "Kefir is a fermented dairy beverage that has been consumed by humans for centuries, but poorly studied in pets. The objective of this study was to determine the effects of commercial or traditional kefir supplementation on apparent total tract macronutrient digestibility (ATTD) and fecal characteristics, microbiota populations, and metabolite and immunoglobulin (Ig) A concentrations of healthy adult dogs. Twelve healthy adult dogs (5.67\u2005\u00b1\u20051.72 yr, 7.27\u2005\u00b1\u20051.15 kg) were used in a replicated 3\u2005\u00d7\u20053 Latin square design (n\u2005=\u200512/group). All dogs were fed a commercial diet and allotted to 1 of 3 treatments (60 mL/d): 2% reduced-fat milk treated with lactase [CNTL; 4.57E\u2005+\u200503 lactic acid bacteria (LAB) colony-forming units (CFU)/mL], commercial kefir (C-Kefir; 6.95E\u2005+\u200504 LAB CFU/mL), or traditional kefir brewed daily from 2% reduced-fat milk and kefir grains (T-Kefir; 1.79E\u2005+\u200509 LAB CFU/mL). The experiment was composed of three 28-d periods, with each consisting of a 22-d transition phase, a 5-d fecal collection phase, and 1 d for blood collection. Fecal samples were collected for determination of ATTD and fecal pH, dry matter, microbiota, and metabolite, and IgA concentrations. Data were analyzed using the Mixed Models procedure of SAS 9.4. The main effects of treatment were tested, with significance set at P\u2005\u2264\u20050.05 and trends set at P\u2005\u2264\u20050.10. Kefir products differed in microbial density and profile, but fecal microbiota populations were weakly impacted. Bacterial alpha diversity tended to be greater (P\u2005=\u20050.10) in dogs fed T-Kefir than those fed CNTL. Bacterial beta diversity analysis identified a difference (P\u2005<\u20050.0004) between dogs-fed CNTL and those fed C-Kefir. Dogs-fed C-Kefir tended to have a greater (P\u2005=\u20050.06) relative abundance of Fusobacteriota than those fed CNTL or T-Kefir. Dogs-fed T-Kefir had a greater (P\u2005<\u20050.0001) relative abundance of Lactococcus than those fed CNTL or C-Kefir. Dogs-fed T-Kefir also tended to have a lower (P\u2005=\u20050.09) relative abundance of Escherichia Shigella and greater (P\u2005=\u20050.09) relative abundance of Candidatus stoquefichus than dogs-fed CNTL or C-Kefir. Dogs-fed C-Kefir tended to have lower (P\u2005=\u20050.08) fecal valerate concentrations than those fed CNTL or T-Kefir. All other measures were unaffected by kefir treatments. Our results suggest that kefir supplementation had minor effects on the fecal microbiota populations and fecal metabolite concentrations of healthy adult dogs without impacting ATTD, fecal characteristics, or fecal IgA concentrations. Kefir is a fermented dairy beverage that has been consumed by humans for centuries, but poorly studied in pets. Our objective was to determine the effects of commercial or traditional kefir supplementation on apparent total tract macronutrient digestibility and fecal characteristics, microbiota populations, and metabolite and immunoglobulin A concentrations of healthy adult dogs. Using a replicated Latin square design, milk (control; CNTL), commercial kefir (C-Kefir), and traditional kefir (T-Kefir) treatments were tested. Kefir products differed in microbial density and profile, but fecal microbiota populations were weakly impacted. Bacterial alpha diversity tended to be greater in T-Kefir than CNTL. Bacterial beta diversity analysis identified differences between CNTL and C-Kefir. Dogs-fed C-Kefir tended to have greater relative abundance of Fusobacteriota than those fed CNTL or T-Kefir. Dogs-fed T-Kefir had a greater relative abundance of Lactococcus than those fed CNTL or C-Kefir. Dogs-fed T-Kefir tended to have a lower relative abundance of Escherichia-Shigella and greater relative abundance of Candidatus stoquefichus than dogs-fed CNTL or C-Kefir. Dogs-fed C-Kefir tended to have lower fecal valerate than those fed CNTL or T-Kefir. Our results suggest that kefir supplementation had minor effects on the fecal microbiota and metabolites of healthy adult dogs.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30018338", + "title": "Parkinson's disease and bacteriophages as its overlooked contributors.", + "year": 2018, + "journal": "Scientific reports", + "authors": [ + "Tetz G", + "Brown SM", + "Hao Y", + "Tetz V" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.2089493357378648, + "mesh_terms": [ + "Bacteria", + "Bacteriophages", + "Case-Control Studies", + "DNA, Bacterial", + "DNA, Viral", + "Dopamine", + "Feces", + "Humans", + "Microbiota", + "Parkinson Disease", + "Principal Component Analysis" + ], + "raw_abstract": "Recent studies suggest that alterations in the gut phagobiota may contribute to pathophysiological processes in mammals; however, the association of bacteriophage community structure with Parkinson's disease (PD) has not been yet characterized. Towards this end, we used a published dataset to analyse bacteriophage composition and determine the phage/bacteria ratio in faecal samples from drug-naive PD patients and healthy participants. Our analyses revealed significant alterations in the representation of certain bacteriophages in the phagobiota of PD patients. We identified shifts of the phage/bacteria ratio in lactic acid bacteria known to produce dopamine and regulate intestinal permeability, which are major factors implicated in PD pathogenesis. Furthermore, we observed the depletion of Lactococcus spp. in the PD group, which was most likely due to the increase of lytic c2-like and 936-like lactococcal phages frequently present in dairy products. Our findings add bacteriophages to the list of possible factors associated with the development of PD, suggesting that gut phagobiota composition may serve as a diagnostic tool as well as a target for therapeutic intervention, which should be confirmed in further studies. Our results open a discussion on the role of environmental phages and phagobiota composition in health and disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35689701", + "title": "Features of the gut prokaryotic virome of Japanese patients with Crohn's disease.", + "year": 2022, + "journal": "Journal of gastroenterology", + "authors": [ + "Imai T", + "Inoue R", + "Nishida A", + "Yokota Y", + "Morishima S", + "Kawahara M", + "Kusada H", + "Tamaki H", + "Andoh A" + ], + "bacteria": "Lactococcus", + "condition": "healthy", + "relevance_score": 0.20021960081514537, + "mesh_terms": [ + "Bacteria", + "Crohn Disease", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Japan", + "RNA, Ribosomal, 16S", + "Virome" + ], + "raw_abstract": "BACKGROUND/AIMS: The gut virome is mainly composed of bacteriophages and influences gut homeostasis and pathogenic conditions. In this study, we analyzed the gut prokaryotic virome in Japanese patients with Crohn's disease (CD). MATERIALS/METHODS: We collected 19 fecal samples from CD patients and 16 samples from healthy controls. The gut bacteriome was analyzed by 16S rRNA gene sequencing and the virome was profiled by shotgun metagenomic sequencing. RESULTS: Despite no differences in richness and evenness, there was a significant difference in the overall structure of the gut virome between CD patients and controls (P\u2009=\u20090.013). CrAssphage and Staphylococcus virus, belonging to the order Caudovirales, were dominant in the gut virome of controls and CD patients. The abundance of crAssphage was significantly greater in CD patients than controls (P\u2009=\u20090.021). Lactococcus, Enterococcus and Lactobacillus phages were present only in CD patients, while Xanthomonas and Escherichia phages were unique to the controls. In the gut bacteriome of CD patients, richness and evenness were significantly lower, and a significant difference in the overall structure was observed between groups (P\u2009=\u20090.014). The gut bacteriome of CD patients was characterized by a decrease of the genera Faecalibacterium, Roseburia, and Ruminococcus and an increase of the family Enterobacteriaceae. There were more significant correlations between viruses and bacteria in CD patients than controls. CONCLUSIONS: The gut virome of CD patients was distinct from that of healthy controls in a Japanese population. An altered gut virome may be one of the factors associated with the bacterial dysbiosis of CD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34045537", + "title": "Identification of mucin degraders of the human gut microbiota.", + "year": 2021, + "journal": "Scientific reports", + "authors": [ + "Raimondi S", + "Musmeci E", + "Candeliere F", + "Amaretti A", + "Rossi M" + ], + "bacteria": "Paraclostridium", + "condition": "healthy", + "relevance_score": 0.2821006428118108, + "mesh_terms": [ + "Clostridium", + "Enterobacteriaceae", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Mucins" + ], + "raw_abstract": "Mucins are large glycoproteins consisting of approximately 80% of hetero-oligosaccharides. Gut mucin degraders of healthy subjects were investigated, through a culture dependent and independent approach. The faeces of five healthy adults were subjected to three steps of anaerobic enrichment in a medium with sole mucins as carbon and nitrogen sources. The bacterial community was compared before and after the enrichment by 16S rRNA gene profiling. Bacteria capable of fermenting sugars, such as Anaerotruncus, Holdemania, and Enterococcaceae likely took advantage of the carbohydrate chains. Escherichia coli and Enterobacteriaceae, Peptococcales, the Coriobacteriale Eggerthella, and a variety of Clostridia such as Oscillospiraceae, Anaerotruncus, and Lachnoclostridium, significantly increased and likely participated to the degradation of the protein backbone of mucin. The affinity of E. coli and Enterobacteriaceae for mucin may facilitate the access to the gut mucosa, promoting gut barrier damage and triggering systemic inflammatory responses. Only three species of strict anaerobes able to grow on mucin were isolated from the enrichments of five different microbiota: Clostridium disporicum, Clostridium tertium, and Paraclostridium benzoelyticum. The limited number of species isolated confirms that in the gut the degradation of these glycoproteins results from cooperation and cross-feeding among several species exhibiting different metabolic capabilities.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28536926", + "title": "Structural changes of gut microbiota in Parkinson's disease and its correlation with clinical features.", + "year": 2017, + "journal": "Science China. Life sciences", + "authors": [ + "Li W", + "Wu X", + "Hu X", + "Wang T", + "Liang S", + "Duan Y", + "Jin F", + "Qin B" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.5687008720147798, + "mesh_terms": [ + "Aged", + "Bacteria", + "Brain", + "DNA, Bacterial", + "Disease Progression", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Host-Pathogen Interactions", + "Humans", + "Male", + "Metagenome", + "Parkinson Disease", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "The aim of this study was to compare the structure of gut microbiota in Parkinson's disease (PD) patients and healthy controls; and to explore correlations between gut microbiota and PD clinical features. We analyzed fecal bacterial composition of 24 PD patients and 14 healthy volunteers by using 16S rRNA sequencing. There were significant differences between PD and healthy controls, as well as among different PD stages. The putative cellulose degrading bacteria from the genera Blautia (P=0.018), Faecalibacterium (P=0.048) and Ruminococcus (P=0.019) were significantly decreased in PD compared to healthy controls. The putative pathobionts from the genera Escherichia-Shigella (P=0.038), Streptococcus (P=0.01), Proteus (P=0.022), and Enterococcus (P=0.006) were significantly increased in PD subjects. Correlation analysis indicated that disease severity and PD duration negatively correlated with the putative cellulose degraders, and positively correlated with the putative pathobionts. The results suggest that structural changes of gut microbiota in PD are characterized by the decreases of putative cellulose degraders and the increases of putative pathobionts, which may potentially reduce the production of short chain fatty acids, and produce more endotoxins and neurotoxins; and these changes is potentially associated with the development of PD pathology.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35751044", + "title": "Longitudinal alterations of the gut mycobiota and microbiota on COVID-19 severity.", + "year": 2022, + "journal": "BMC infectious diseases", + "authors": [ + "Maeda Y", + "Motooka D", + "Kawasaki T", + "Oki H", + "Noda Y", + "Adachi Y", + "Niitsu T", + "Okamoto S", + "Tanaka K", + "Fukushima K", + "Amiya S", + "Hara R", + "Oguro-Igashira E", + "Matsuki T", + "Hirata H", + "Takeda Y", + "Kida H", + "Kumanogoh A", + "Nakamura S", + "Takeda K" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.5287296697038254, + "mesh_terms": [ + "COVID-19", + "Enterococcus", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Microbiota", + "SARS-CoV-2" + ], + "raw_abstract": "BACKGROUND: The impact of SARS-CoV-2 infection on the gut fungal (mycobiota) and bacterial (microbiota) communities has been elucidated individually. This study analyzed both gut mycobiota and microbiota and their correlation in the COVID-19 patients with severe and mild conditions and follow-up to monitor their alterations after recovery. METHODS: We analyzed the gut mycobiota and microbiota by bacterial 16S and fungal ITS1 metagenomic sequencing of 40 severe patients, 38 mild patients, and 30 healthy individuals and reanalyzed those of 10 patients with severe COVID-19 approximately 6\u00a0months after discharge. RESULTS: The mycobiota of the severe and mild groups showed lower diversity than the healthy group, and in some, characteristic patterns dominated by a single fungal species, Candida albicans, were detected. Lower microbial diversity in the severe group was observed, but no differences in its diversity or community structure were detected between the mild and healthy groups. The microbiota of the severe group was characterized by an increase in Enterococcus and Lactobacillus, and a decrease in Faecalibacterium and Bacteroides. The abundance of Candida was positively correlated with that of Enterococcus in patients with COVID-19. After the recovery of severe patients, alteration of the microbiota remained, but the mycobiota recovered its diversity comparable to that of mild and healthy groups. CONCLUSION: In mild cases, the microbiota is stable during SARS-CoV-2 infection, but in severe cases, alterations persist for 6\u00a0months after recovery.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36519210", + "title": "The fecal bacterial microbiota of healthy and sick newborn foals.", + "year": 2023, + "journal": "Journal of veterinary internal medicine", + "authors": [ + "Gomez DE", + "Wong D", + "MacNicol J", + "Dembek K" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.5069420562169177, + "mesh_terms": [ + "Pregnancy", + "Female", + "Animals", + "Horses", + "Animals, Newborn", + "Case-Control Studies", + "Feces", + "Microbiota", + "Bacteria", + "Horse Diseases", + "Bacteremia" + ], + "raw_abstract": "BACKGROUND: The fecal bacterial microbiota of normal foals and foals with enterocolitis has been characterized using next-generation sequencing technology; however, there are no reports investigating the gut microbiota in foals hospitalized for other perinatal diseases. OBJECTIVE: To describe and compare the fecal bacterial microbiota in healthy and sick foals using next-generation sequencing techniques. ANIMALS: Hospitalized (17) and healthy foals (21). METHODS: Case-control study. Fecal samples were collected from healthy and sick foals on admission. Sick foals were further divided into sick nonseptic (SNS, n\u00a0=\u00a09) and septic (n\u00a0=\u00a08) foals. After extraction of DNA, the V4 region of the 16\u2009S rRNA gene was amplified using a PCR assay, and the final product was sequenced with an Illumina MiSeq. RESULTS: Diversity was significantly lower in healthy than sick foals (P\u2009<\u2009.05). The bacterial membership (Jaccard index) and structure (Yue & Clayton index) of the fecal microbiota of healthy, septic, and SNS foals were similar (AMOVA, P\u2009>\u2009.05). Bacterial membership (AMOVA, P\u00a0=\u00a0.06) and structure (AMOVA, P\u00a0=\u00a0.33) were not different between healthy and sick foals. Enterobacteriaceae, Enterococcus, and Streptococcus were among the 5 more abundant taxa identified in both groups. CONCLUSION AND CLINICAL IMPORTANCE: Higher fecal microbiota diversity in sick than healthy foals might suggest a high exposure to environmental microorganisms or an unstable colonic microbiota. The presence of microorganisms causing bacteremia in foals in a high relative abundance in the feces of foals suggests the intestine might play an essential role in the causation of bacteremia in foals.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37715414", + "title": "Changes of Gut Microbiota in Maintenance Hemodialysis Patients and Their Impact on Patient's Microinflammation Status.", + "year": 2023, + "journal": "Cellular and molecular biology (Noisy-le-Grand, France)", + "authors": [ + "Zhang X", + "Wang Y", + "Yin Y", + "Sun B", + "Chen G", + "Chen F" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.49075848475601125, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "C-Reactive Protein", + "Interleukin-6", + "Tumor Necrosis Factor-alpha", + "Enterococcus", + "Enterococcus faecalis", + "Escherichia coli", + "Inflammation", + "Lactobacillus", + "Renal Dialysis", + "Renal Insufficiency, Chronic" + ], + "raw_abstract": "This study was to investigate the changes in gut microbiota in maintenance hemodialysis patients and analyze their impact on patient's microinflammation status. For this purpose, thirty-nine chronic kidney disease (CKD) maintenance hemodialysis patients admitted to our hospital from March 2019 to March 2022 were selected as the experimental group, and 40 healthy individuals with examination results during the same period were selected as the control group. The levels of gut microbiota (Lactobacillus, Bifidobacterium, Escherichia coli, and Enterococcus faecalis) and microinflammation indicators [interleukin-6 (IL-6), tumor necrosis factor \u03b1 (TNF-\u03b1), and high-sensitivity C-reactive protein (hs-CRP)] were measured in both groups. The relationship between changes in gut microbiota and microinflammation in maintenance hemodialysis CKD patients was analyzed. Results showed that the levels of Lactobacillus and Bifidobacterium in the experimental group were significantly lower than those in the control group (all, P<0.05), while the levels of Escherichia coli and Enterococcus faecalis in the experimental group were significantly higher than those in the control group (all, P<0.05). The IL-6, TNF-\u03b1, and hs-CRP levels in the experimental group were significantly higher than those in the control group (all, P<0.05). Using microinflammation indicators as dependent variables and microbiota indicators as independent variables for stepwise regression analysis, the results showed that the levels of Lactobacillus were negatively correlated with IL-6 and TNF-\u03b1 levels in patients (r=-0.358, -0.942, P<0.05); the levels of Bifidobacterium were negatively correlated with IL-6, TNF-\u03b1, and hs-CRP levels in patients (r=-0.394, -0.211, -0.547, P<0.05); the levels of Escherichia coli were positively correlated with IL-6 and TNF-\u03b1 levels in patients (r=0.221, 0.268, P<0.05); the levels of Enterococcus faecalis were positively correlated with IL-6 and hs-CRP levels in patients (r=0.253, 0.378, P<0.05). In conclusion, patients with maintenance hemodialysis for CKD commonly exhibit gut microbiota dysbiosis and varying degrees of low-grade inflammation. Compared to healthy individuals, maintenance hemodialysis patients with CKD have lower levels of Bifidobacterium and Lactobacillus and higher levels of Escherichia coli and Enterococcus in their gut. Bifidobacterium, Lactobacillus, Escherichia coli, and Enterococcus all have a certain impact on the low-grade inflammation status of patients with maintenance hemodialysis for CKD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33009628", + "title": "Assessment of oncogenic role of intestinal microbiota in colorectal cancer patients.", + "year": 2021, + "journal": "Journal of gastrointestinal cancer", + "authors": [ + "D'asheesh TA", + "Hussen BM", + "Al-Marzoqi AH", + "Ghasemian A" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.4610255526380761, + "mesh_terms": [ + "Adult", + "Aged", + "Carcinogenesis", + "Colorectal Neoplasms", + "Escherichia", + "Feces", + "Female", + "Humans", + "Iran", + "Lactobacillus acidophilus", + "Lactobacillus plantarum", + "Male", + "Microbiota", + "Middle Aged", + "Risk Factors", + "Surveys and Questionnaires", + "Young Adult" + ], + "raw_abstract": "INTRODUCTION: The direct association between some microbial species and cancers, such as in colorectal cancer (CRC), has been disclosed. OBJECTIVE: The aim of this study was to evaluate the changes in intestinal microbiota in subjects with CRC compared with healthy group. METHODS: Three-hundred fecal specimens were gathered from patients with CRC and 300 from healthy individuals during March 2014 to October 2019 from two hospitals in Tehran. The informed consent form and the questionnaire were completed by the patients. Following the identification of Lactobaccilus acidophilus (L. acidophilus), Lactobacillus palntarom (L. palntarom), and Enterococcus faecalis (E. faecalis), the number of bacteria was determined using quantitative real-time PCR (qPCR). RESULTS: The patients' age range was 20-76 years (mean: 55.34 \u00b1 3.66). The qPCR clarified that number of E. faecalis was 2.2-fold higher in patients with CRC compared to healthy population (p = 0.0013). Additionally, the number of L. acidophilus and L. plantarom was 3.4-fold (p < 0.0001) and 4.8-fold (p < 0.0001) higher in healthy population. CONCLUSION: The inhibitory effect of intestinal microflora against the CRC development was proposed by observation of the changes in intestinal microbiota and determining their composition in subjects with CRC compared with that of healthy individuals. Microbiota was considered as a goal for the prevention and treatment of CRC. The relationship between microbiota and human health would be known deeper; this knowledge provides insights into the management of intestinal microbiota and therapeutics.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27684872", + "title": "Increased Enterococcus faecalis infection is associated with clinically active Crohn disease.", + "year": 2016, + "journal": "Medicine", + "authors": [ + "Zhou Y", + "Chen H", + "He H", + "Du Y", + "Hu J", + "Li Y", + "Li Y", + "Zhou Y", + "Wang H", + "Chen Y", + "Nie Y" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.46008605363871424, + "mesh_terms": [ + "Adult", + "China", + "Crohn Disease", + "DNA, Bacterial", + "Enterococcus faecalis", + "Feces", + "Female", + "Gram-Positive Bacterial Infections", + "Humans", + "Incidence", + "Male", + "Real-Time Polymerase Chain Reaction", + "Young Adult" + ], + "raw_abstract": "This study was performed to investigate the relationship between the abundance of pathogenic gut microbes in Chinese patients with inflammatory bowel disease (IBD) and disease severity.We collected clinical data and fecal samples from 47 therapy-naive Chinese patients with ulcerative colitis (UC), 67 patients with Crohn disease (CD), and 48 healthy volunteers. Bacteria levels of Fusobacterium species (spp), enterotoxigenic Bacteroides fragilis (B fragilis), enteropathogenic Escherichia coli (E coli), and Enterococcus faecalis (E faecalis) were assessed by quantitative real-time PCR (qRT-PCR). Spearman correlation coefficients were calculated to test associations between bacterial content and clinical parameters.Compared to healthy controls, the levels of both Fusobacterium spp and E faecalis were significantly increased in the feces of patients with IBD (P\u200a<\u200a0.01). B fragilis levels were higher (P\u200a<\u200a0.05) and E faecalis levels lower (P\u200a<\u200a0.05) in patients with CD compared to those with UC. Increased E faecalis colonization in CD associated positively with disease activity (P = 0.015), Crohn disease activity index (CDAI; R = 0.3118, P = 0.0108), and fecal calprotectin (P = 0.016).E faecalis and Fusobacterium spp are significantly enriched in patients with IBD, and increased E faecalis infection is associated with clinically active CD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33993646", + "title": "Profiling of gut microbial dysbiosis in adults with myeloid leukemia.", + "year": 2021, + "journal": "FEBS open bio", + "authors": [ + "Yu D", + "Yu X", + "Ye A", + "Xu C", + "Li X", + "Geng W", + "Zhu L" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.45547371611798626, + "mesh_terms": [ + "Adult", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Leukemia, Myeloid", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Dysregulation of gut microbiota is implicated in the pathogenesis of various diseases, including metabolic diseases, inflammatory diseases, and cancer. To date, the link between gut microbiota and myeloid leukemia (ML) remains largely unelucidated. Herein, a total of 29 patients with acute myeloid leukemia (AML), 17 patients with chronic myeloid leukemia (CML), and 33 healthy subjects were enrolled, and gut microbiota were profiled via Illumina sequencing of the 16S rRNA. We evaluated the correlation between ML and gut microbiota. The microbial \u03b1-diversity and \u03b2-diversity exhibited significant differences between ML patients and healthy controls (HCs). Compared to healthy subjects, we found that at the phylum level, the relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi was increased, while that of Tenericutes was decreased. Correspondingly, at the genus level in ML, Streptococcus were increased, especially in AML patients, while Megamonas (P\u00a0=\u00a00.02), Lachnospiraceae NC2004 group, and Prevotella 9 (P\u00a0=\u00a00.007) were decreased. Moreover, ML-enriched species, including Sphingomonas, Lysobacyer, Helicobacter, Lactobacillus, Enterococcus, and Clostridium\u00a0sensu\u00a0stricto 1, were identified. Our results indicate that the gut microbiota was altered in ML patients compared to that of healthy subjects, which could contribute to the elucidation of microbiota-related pathogenesis of ML, and the development of novel therapeutic strategies in the treatment of ML.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31460576", + "title": "INVESTIGATION OF ENTEROCOCCUS FAECALIS POPULATION IN PATIENTS WITH POLYP AND COLORECTAL CANCER IN COMPARISON OF HEALTHY INDIVIDUALS.", + "year": 2019, + "journal": "Arquivos de gastroenterologia", + "authors": [ + "Geravand M", + "Fallah P", + "Yaghoobi MH", + "Soleimanifar F", + "Farid M", + "Zinatizadeh N", + "Yaslianifard S" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.40769319870269244, + "mesh_terms": [ + "Aged", + "Case-Control Studies", + "Colonic Polyps", + "Colorectal Neoplasms", + "DNA, Bacterial", + "Enterococcus faecalis", + "Feces", + "Female", + "Humans", + "Male", + "Middle Aged", + "Real-Time Polymerase Chain Reaction" + ], + "raw_abstract": "BACKGROUND: Colorectal cancer is one of the most commonly diagnosed cancers around the world. One of the factors involved in the development of colorectal cancer is the changes in the normal flora of the intestine. OBJECTIVE: In this study, the mean copy number of Enterococcus faecalis in people with polyps and people with colorectal cancer has been evaluated in comparison with healthy controls. METHODS: In this study, 25 patients with colorectal cancer and 28 patients with intestinal polyps were selected and stool specimens were taken. In addition, 24 healthy individuals were selected as control group. Extraction of bacterial DNA from the stool sample were performed. The molecular methods of PCR for confirmation of standard strain and absolute Real Time PCR (qRT-PCR) method were used to evaluate the number of Enterococcus faecalis in the studied groups. RESULTS: The results of this study indicate that the mean copy number of Enterococcus faecalis in patients with colorectal cancer was 11.2x109 per gram of stool, and in patients with polyps was 9.4x108 per gram of stool. In healthy people, this number was 9x108 per gram of stool. There was a significant difference between the implicit copy numbers in the three groups. (P<0.05). CONCLUSION: Enterococcus faecalis in faecal flora of people with colorectal cancer was significantly higher than those with polyps and healthy people. This could potentially signify the ability of this bacterium to induce colorectal cancer. More studies are needed to prove this theory.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32487494", + "title": "Development of the gut microbiota in early life: The impact of cystic fibrosis and antibiotic treatment.", + "year": 2020, + "journal": "Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society", + "authors": [ + "Kristensen M", + "Prevaes SMPJ", + "Kalkman G", + "Tramper-Stranders GA", + "Hasrat R", + "de Winter-de Groot KM", + "Janssens HM", + "Tiddens HA", + "van Westreenen M", + "Sanders EAM", + "Arets B", + "Keijser B", + "van der Ent CK", + "Bogaert D" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.4070363873512231, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Bacteria", + "Cystic Fibrosis", + "Cystic Fibrosis Transmembrane Conductance Regulator", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Infant", + "Intestinal Mucosa", + "Male", + "Netherlands", + "RNA, Ribosomal, 16S", + "Sequence Analysis, RNA" + ], + "raw_abstract": "OBJECTIVES: Patients with Cystic Fibrosis (CF) suffer from pancreatic insufficiency, lipid malabsorption and gastrointestinal complaints, next to progressive pulmonary disease. Altered mucosal homoeostasis due to malfunctioning chloride channels results in an adapted microbial composition of the gastrointestinal and the respiratory tract. Additionally, antibiotic treatment has the potential to distort resident microbial communities dramatically. This study aims to investigate early life development of the gut microbial community composition of children with CF compared to healthy infants and to study the independent effects of antibiotics taking into account other clinical and lifestyle factors. STUDY DESIGN: Faecal samples from 20 infants with CF and 45 healthy infants were collected regularly during the first 18 months of life and microbial composition was determined using 16S rRNA based sequencing. RESULTS: We observed significant differences in the overall microbiota composition between infants with CF and healthy infants (p<0.001). Akkermansia and Anaerostipes were significantly more abundant in control infants, whereas Streptococci and E. coli were significantly more abundant in infants with CF, also after correction for several clinical factors (p<0.05). Antibiotic use in infants with CF was associated with a lower alpha diversity, a reduced abundance of Bifidobacterium and Bacteroides, and a higher abundance of Enterococcus. CONCLUSION: Microbial development of the gut is different in infants with CF compared to healthy infants from the first months of life on, and further deviates over time, in part as a result of antibiotic treatment. The resulting dysbiosis may have significant functional consequences for the microbial ecosystem in CF patients.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35971252", + "title": "Faecal carriage of enterococci harbouring oxazolidinone resistance genes among healthy humans in the community in Switzerland.", + "year": 2022, + "journal": "The Journal of antimicrobial chemotherapy", + "authors": [ + "N\u00fcesch-Inderbinen M", + "Biggel M", + "Zurfluh K", + "Treier A", + "Stephan R" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.4069406250637591, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Drug Resistance, Bacterial", + "Enterococcus", + "Enterococcus faecalis", + "Enterococcus faecium", + "Gram-Positive Bacterial Infections", + "Humans", + "Linezolid", + "Oxazolidinones", + "Switzerland" + ], + "raw_abstract": "OBJECTIVES: This study aimed to investigate the faecal carriage of enterococci harbouring oxazolidinone resistance genes among healthy humans in Switzerland and to genetically characterize the isolates. METHODS: A total of 399 stool samples from healthy individuals employed in different food-processing plants were cultured on a selective medium containing 10\u2005mg/L florfenicol. Resulting enterococci were screened by PCR for the presence of cfr, optrA and poxtA. A hybrid approach combining short-read and long-read WGS was used to analyse the genetic context of the cfr, optrA and poxtA genes. RESULTS: Enterococcus faecalis (n\u200a=\u200a6), Enterococcus faecium (n\u200a=\u200a6), Enterococcus gallinarum (n\u200a=\u200a1) and Enterococcus hirae (n\u200a=\u200a2) were detected in 15/399 (3.8%) of the faecal samples. They carried cfr\u200a+\u200apoxtA, optrA, optrA\u200a+\u200apoxtA or poxtA. Four E. faecalis harbouring optrA and one E. faecium carrying poxtA were resistant to linezolid (8\u2005mg/L). In most optrA-positive isolates, the genetic environments of optrA were highly variable, but often resembled previously described platforms. In most poxtA-positive isolates, the poxtA gene was flanked on both sides by IS1216E elements and located on medium-sized plasmids. CONCLUSIONS: Faecal carriage of Enterococcus spp. harbouring cfr, optrA and poxtA in healthy humans associated with the food-production industry demonstrates the possibility of spread of oxazolidinone resistance genes into the community. Given the importance of linezolid as a last-resort antibiotic for the treatment of serious infections caused by Gram-positive pathogens, the detection of the oxazolidinone resistance determinants in enterococci from healthy humans is of concern for public health.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33684236", + "title": "Breast milk contains probiotics with anti-infantile diarrhoea effects that may protect infants as they change to solid foods.", + "year": 2021, + "journal": "Environmental microbiology", + "authors": [ + "Niu H", + "Zhou X", + "Zhang X", + "Liu T", + "Wu Y", + "Lyu L", + "Liang C", + "Chen S", + "Gong P", + "Zhang J", + "Han X", + "Jiang S", + "Zhang L" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.393313842428608, + "mesh_terms": [ + "Animals", + "Breast Feeding", + "Feces", + "Female", + "Humans", + "Lactobacillus", + "Microbiota", + "Milk, Human", + "Probiotics", + "Rats" + ], + "raw_abstract": "Infants often experience complementary food-induced diarrhoea (CFID), which occurs when infants switch from breast milk to solid foods. The relative abundances of Prevotella and Rothia were higher in stools of infants with CFID, while the relative abundances of Enterococcus and Escherichia were higher in healthy infants. The abundance of Lactobacillus spp. normally found in breast milk fed to infants with CFID was significantly reduced, and Enterococcus spp. were less abundant when diarrhoea occurred. Furthermore, Lactobacillus and Enterococcus were present as shared bacteria in both mother and infant, and they were considered potential anti-CFID probiotics as their relative abundances in breast milk were negatively correlated to infant CFID. Kyoto encyclopedia of genes and genomes (KEGG) functional analysis showed that the function of amino acid metabolism differed between infants with CFID and healthy infants. Therefore, CFID might be related to the decomposition of proteins in food supplements. The screening revealed seven hydrolytic casein and five hydrolytic casein and rice protein isolates from 320 suspected Lactobacillus and Enterococcus isolates. The animal experiments demonstrated that a mixture of five isolates effectively hydrolysed the casein and rice protein and prevented diarrhoea in young rats. Thus, the occurrence of CFID was found to be closely related to the intestinal and breast milk microbiota, and bacteria that could assist in the digestion of cereal proteins were involved in CFID.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29419918", + "title": "Isolation of vancomycin-resistant Enterococcus from apparently healthy human animal attendants, cattle and cattle wastes in Tanzania.", + "year": 2018, + "journal": "Journal of applied microbiology", + "authors": [ + "Madoshi BP", + "Mtambo MMA", + "Muhairwa AP", + "Lupindu AM", + "Olsen JE" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.3886271943181617, + "mesh_terms": [ + "Animals", + "Cattle", + "Enterococcus", + "Enterococcus faecalis", + "Enterococcus faecium", + "Feces", + "Healthy Volunteers", + "Humans", + "Phenotype", + "Prevalence", + "Tanzania", + "Vancomycin Resistance" + ], + "raw_abstract": "AIM: The study aimed to isolate and characterize Enterococcus species from apparently healthy waste attendants, cattle and cattle waste in Tanzania. Emphasis was given to antimicrobial resistance and in particular occurrence of vancomycin (VA)-resistant enterococci. METHODS AND RESULTS: Faecal samples were collected from healthy cattle, cattle waste attendants and cattle house wastes, and isolation of Enterococcus species was performed using Slanetz Bartley agar. Isolates were characterized with regard to species, antimicrobial susceptibility and presence of VA resistance genes. Enterococcus faecalis was the most prevalent species from all sources of isolation (43\u00b75%), followed by Enterococcus faecium (38\u00b74%). Isolates of E. faecium showed a higher number of phenotypic antimicrobial resistance than isolates of E. faecalis. Fifty-eight isolates, which showed resistance or intermediate resistance to VA by disc diffusion test, were analysed for VA-resistant Enterococcus (VRE) by PCR. The vanA gene was detected in 14 isolates of E. faecium and 12 isolates of E. faecalis, while vanB was detected in three isolates. No isolates were found to carry vanC1-gene. CONCLUSION: VRE was detected in both human and cattle samples, despite no known use of antimicrobial agents that can select for VRE in livestock in Tanzania. Enterococcus faecalis was the most commonly isolated species from cattle and humans. SIGNIFICANCE AND IMPACT OF THE STUDY: The study provides information on the prevalence of VRE in human and nonhuman samples in Tanzania calling for further studies on the origin of VRE in such isolates, since no selection mechanism in Tanzania are known.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31494301", + "title": "Intestinal microbiota dysbiosis in children with recurrent respiratory tract infections.", + "year": 2019, + "journal": "Microbial pathogenesis", + "authors": [ + "Li L", + "Wang F", + "Liu Y", + "Gu F" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.38248791602646115, + "mesh_terms": [ + "Bacteria", + "Child", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenomics", + "ROC Curve", + "Recurrence", + "Respiratory Tract Infections" + ], + "raw_abstract": "BACKGROUND: The impact of the gut microbiota on recurrent respiratory tract infection (RRTI) remains to be fully elucidated. METHODS: To characterize the gut microbiota in patients with RRTI, fecal samples from 26 patients with RRTI and 23 healthy volunteers were profiled using the Illumina MiSeq platform. Beta diversity (Principal Component Analysis (PCA), Principal Co-ordinates Analysis (PCoA), Non-metric multidimensional scaling (NMDS)) analysis showed that the bacterial community structure segregated differently between the RRTI and control groups. RESULTS: Results from alpha diversity analysis revealed lower microbiota diversity in samples from RRTI patients than in normal controls. Taxonomic analysis illustrated that the abundance of six phyla (Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, Tenericutes) and four genera (Enterococcus, Faecalibacterium, Bifidobacterium, Eubacterium were significantly different between these two groups. In addition, Enterococcus (P\u202f<\u202f0.001) was more enriched in the RRTI group, whereas the abundances of Eubacterium (P\u202f<\u202f0.001), Faecalibacterium (0.01\u202f<\u202fP\u202f<\u202f0.05) and Bifidobacterium (0.01\u202f<\u202fP\u202f<\u202f0.05) were reduced in the RRTI group compared to those in the normal control group. The performance of the model was assessed using ROC analysis, and Enterococcus, Eubacterium and Bifidobacterium achieved AUC values of 0.860, 0.820, and 0.689, respectively. CONCLUSIONS: These results provide fundamental evidence in support of intestinal microbiota dysbiosis in children with RRTI.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30527539", + "title": "Altered host-gut microbes symbiosis in severely malnourished anorexia nervosa (AN) patients undergoing enteral nutrition: An explicative factor of functional intestinal disorders?", + "year": 2019, + "journal": "Clinical nutrition (Edinburgh, Scotland)", + "authors": [ + "Hanachi M", + "Manichanh C", + "Schoenenberger A", + "Pascal V", + "Levenez F", + "Courn\u00e8de N", + "Dor\u00e9 J", + "Melchior JC" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.3776174008095917, + "mesh_terms": [ + "Adult", + "Anorexia Nervosa", + "Case-Control Studies", + "Dysbiosis", + "Enteral Nutrition", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Diseases", + "Male", + "Malnutrition", + "Middle Aged", + "Symbiosis", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Functional intestinal disorders (FIDs) are frequently observed in patients with anorexia nervosa (AN). Relationship between FIDs and a potential gut microbiota dysbiosis has been poorly explored. OBJECTIVE: We aimed to determine an association between FIDs severity and dysbiosis of the intestinal microbiota in a severely malnourished patient population with AN undergoing enteral nutrition. DESIGN: Faecal microbiota of AN (DSM IVr criteria) female inpatients were collected and compared to healthy controls based on 16S rRNA profiling. The severity of FIDs was evaluated in patients and healthy controls using Francis Score. RESULTS: Thirty-three patients (BMI: 11,7\u00a0\u00b1\u00a01,5; Age: 32\u00a0\u00b1\u00a012) and 22 healthy controls (BMI: 21\u00a0\u00b1\u00a02; age: 36\u00a0\u00b1\u00a012) were included. A marked dysbiosis was identified in AN patients compared to healthy controls (p\u00a0=\u00a00.03). Some potentially pathogenic bacterial genera (Klebsiella, Salmonella) were more abundant in AN patients whereas, other bacterial symbionts (Eubacterium and Roseburia) involved in immune balance were significantly less abundant in patients than controls. Severity of FIDs was strongly correlated with several microbial genera (r\u00a0=\u00a0-0.581 for an unknown genus belonging to Peptostreptococcaceae family; r\u00a0=\u00a00.392 for Dialister, r\u00a0=\u00a00.444 for Robinsoniella and r\u00a0=\u00a00.488 for Enterococcus). Other associations between dysbiosis, clinical and biological characteristics were identified including severity of undernutrition (BMI). CONCLUSION: Observed gut microbiota dysbiosis in malnourished patients with anorexia nervosa is correlated with the severity of FIDs and other metabolic disturbances, which strongly suggests an altered host-microbe symbiosis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32884012", + "title": "Altered gut microbiota correlated with systemic inflammation in children with Kawasaki disease.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Chen J", + "Yue Y", + "Wang L", + "Deng Z", + "Yuan Y", + "Zhao M", + "Yuan Z", + "Tan C", + "Cao Y" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.3633388449117485, + "mesh_terms": [ + "Acinetobacter", + "Child, Preschool", + "Computational Biology", + "Enterococcus", + "Female", + "Gastrointestinal Microbiome", + "Helicobacter", + "Humans", + "Infant", + "Inflammation", + "Lactococcus", + "Male", + "Mucocutaneous Lymph Node Syndrome", + "Polymerase Chain Reaction", + "Staphylococcus" + ], + "raw_abstract": "Kawasaki disease (KD) is a multi-systemic vasculitis of unknown etiology that occurs mainly in children, and the disturbance of gut microbiota is generally believed to cause a hyperimmune reaction triggering KD. The aim of the study was to investigate the alterations in the fecal microbiota and assess its relationship with systemic inflammation. Totally 30 KD children were enrolled and followed up for 6\u00a0months, with another group of 30 age- and sex-matched healthy children as controls. Phylotype profiles of fecal microbial communities were analyzed using 16S rRNA gene sequencing. Serum inflammatory markers were detected by flow cytometer. We showed that KD children exhibited a significant reduction in fecal microbial diversity in the acute phase compared with the healthy controls. Enterococcus, Acinetobacter, Helicobacter, Lactococcus, Staphylococcus and Butyricimonas in acute KD children were significantly higher than the healthy children. Levels of systemic inflammation biomarkers, including IL-2, IL-4, IL-6, IL-10, TNF-\u03b1, and INF-\u03b3, were significantly elevated in the acute KD children. Altered microbiota genera Enterococcus and Helicobacter abundances were shown to be correlated positively with IL-6, which were never previously reported in KD. This study suggested that gut microbiota alteration is closely associated with systemic inflammation, which provides a new perspective on the etiology and pathogenesis of KD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29458413", + "title": "Gut microbiota trajectory in early life may predict development of celiac disease.", + "year": 2018, + "journal": "Microbiome", + "authors": [ + "Olivares M", + "Walker AW", + "Capilla A", + "Ben\u00edtez-P\u00e1ez A", + "Palau F", + "Parkhill J", + "Castillejo G", + "Sanz Y" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.358660726324112, + "mesh_terms": [ + "Bifidobacterium", + "Case-Control Studies", + "Celiac Disease", + "Child, Preschool", + "Enterococcus", + "Feces", + "Female", + "Firmicutes", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Infant", + "Infant, Newborn", + "Male", + "Prospective Studies", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: To investigate whether alterations in the developing intestinal microbiota and immune markers precede celiac disease (CD) onset in infants at familial risk of developing the disease. METHODS: A nested case-control study was carried out as part of a larger prospective cohort study, which included healthy full-term newborns (>\u2009200) with at least one first relative with biopsy-verified CD. The present study includes cases of CD (n\u2009=\u200910) and the best-matched controls (n\u2009=\u200910) who did not develop the disease after 5-year follow-up. Fecal microbiota, assessed by high-throughput 16S rRNA gene amplicon sequencing, and immune parameters were profiled at 4 and 6\u00a0months of age and related to CD onset. RESULTS: The microbiota of infants who remained healthy showed an increase in bacterial diversity over time, characterized by increases in Firmicutes families, but not those who developed CD. Infants who subsequently developed CD showed a significant reduction in sIgA levels over time, while those who remained healthy showed increases in TNF-\u03b1 correlated to Bifidobacterium spp. An increased relative abundance of Bifidobacterium longum was associated with control children while increased proportions of Bifidobacterium breve and Enterococcus spp. were associated with CD development. CONCLUSION: The findings suggest that alterations in the early trajectory of gut microbiota in infants at CD risk could influence the immune maturation process and predispose to CD, although larger population studies are warranted to confirm this hypothesis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39127664", + "title": "Distinct enterotypes and dysbiosis: unraveling gut microbiota in pulmonary and critical care medicine inpatients.", + "year": 2024, + "journal": "Respiratory research", + "authors": [ + "Li N", + "Tan G", + "Xie Z", + "Chen W", + "Yang Z", + "Wang Z", + "Liu S", + "He M" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.3520044522403799, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Male", + "Dysbiosis", + "Female", + "Middle Aged", + "Aged", + "Critical Care", + "Inpatients", + "Adult", + "Feces" + ], + "raw_abstract": "BACKGROUND: The gut-lung axis, pivotal for respiratory health, is inadequately explored in pulmonary and critical care medicine (PCCM) inpatients. METHODS: Examining PCCM inpatients from three medical university-affiliated hospitals, we conducted 16S ribosomal RNA sequencing on stool samples (inpatients, n\u2009=\u2009374; healthy controls, n\u2009=\u2009105). We conducted statistical analyses to examine the gut microbiota composition in PCCM inpatients, comparing it to that of healthy controls. Additionally, we explored the associations between gut microbiota composition and various clinical factors, including age, white blood cell count, neutrophil count, platelet count, albumin level, hemoglobin level, length of hospital stay, and medical costs. RESULTS: PCCM inpatients exhibited lower gut microbiota diversity than healthy controls. Principal Coordinates Analysis revealed marked overall microbiota structure differences. Four enterotypes, including the exclusive Enterococcaceae enterotype in inpatients, were identified. Although no distinctions were found at the phylum level, 15 bacterial families exhibited varying abundances. Specifically, the inpatient population from PCCM showed a significantly higher abundance of Enterococcaceae, Lactobacillaceae, Erysipelatoclostridiaceae, Clostridiaceae, and Tannerellaceae. Using random forest analyses, we calculated the areas under the receiver operating characteristic curves (AUCs) to be 0.75 (95% CIs 0.69-0.80) for distinguishing healthy individuals from inpatients. The four most abundant genera retained in the classifier were Blautia, Subdoligranulum, Enterococcus, and Klebsiella. CONCLUSIONS: Evidence of gut microbiota dysbiosis in PCCM inpatients underscores the gut-lung axis's significance, promising further avenues in respiratory health research.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36124625", + "title": "Intestinal Microflora Characteristics of Antheraea pernyi (Lepidoptera: Saturniidae) Larvae With Vomit Disease.", + "year": 2022, + "journal": "Journal of economic entomology", + "authors": [ + "Jia S", + "Zhang J", + "Li X", + "He Y", + "Yu T", + "Zhao C", + "Song C" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.34752106610451333, + "mesh_terms": [ + "Animals", + "Larva", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Moths", + "Silk", + "Bacteria" + ], + "raw_abstract": "Antheraea pernyi Gu\u00e9rin-M\u00e9neville (Lepidoptera: Saturniidae) is of high economic value as a source of silk, food, and bioactive substances with medicinal properties. A. pernyi larvae are prone to A. pernyi vomit disease (AVD), which results in substantial economic losses during cultivation; however, the relationship between AVD and A. pernyi gut microbiota remains unclear. Here, we investigated the bacterial community in the midgut and feces of A. pernyi larvae with and without AVD using 16S rRNA gene sequencing with Illumina MiSeq technology. Compared with healthy larvae, intestinal bacterial diversity and community richness increased and decreased in larvae with mild and severe AVD, respectively. In addition, the proportion of gut Enterobacter Hormaeche and Edwards(Enterobacteriales: Enterobacteriaceae) and Enterococcus Thiercelin and Jouhaud (Lactobacillales: Enterococcaceae) was higher and lower, respectively, in larvae with mild AVD than those in healthy larvae. A. pernyi vomit disease infection significantly increased the genera with abundance <1%. In the gut of larvae with severe AVD, the proportion of Turicibacter Bosshard et al. (Erysipelotrichales: Turicibacteraceae) increased significantly to 81.53-99.92%, whereas that of Enterobacter decreased compared with healthy larvae. However, the diversity of fecal bacteria was similar between healthy larvae and those with mild AVD. Overall, the findings demonstrate that intestinal microflora in A. pernyi larvae are altered by AVD infection and may cause secondary bacterial infection. This is the first report of the presence of Turicibacter in the intestinal tract of lepidopterans.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32018061", + "title": "Enterococcus: A Predictor of Ravaged Microbiota and Poor Prognosis after Allogeneic Hematopoietic Stem Cell Transplantation.", + "year": 2020, + "journal": "Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation", + "authors": [ + "Kusakabe S", + "Fukushima K", + "Yokota T", + "Hino A", + "Fujita J", + "Motooka D", + "Nakamura S", + "Shibayama H", + "Kanakura Y" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.34323145718517817, + "mesh_terms": [ + "Enterococcus", + "Gastrointestinal Microbiome", + "Hematopoietic Stem Cell Transplantation", + "Humans", + "Microbiota", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Intestinal flora plays an essential role in regulating immune responses. Changes in the gut flora are associated with poor prognosis after allogeneic hematopoietic stem cell transplantation (HSCT). We aimed to investigate the impact of diverse intestinal flora on survival after allogeneic HSCT. Using next-generation sequencing of the bacterial 16S ribosomal RNA (rRNA) gene, we found that the intestinal microbiota of patients undergoing allogeneic HSCT differed significantly from that of healthy controls. Furthermore, dysbiosis persisted for at least 1 year after transplantation. Interestingly, increased abundance of the genus Enterococcus detected by 16S rRNA sequencing as early as 1 month after transplantation was correlated with poor survival (overall survival at 2 years post-HSCT, 83.9% for patients with <1% relative abundance of Enterococcus and 47.6% for those with \u22651% relative abundance of Enterococcus), which was undetectable by conventional standard stool culture. These findings suggest that detection of Enterococcus by 16S rRNA analysis reflects compromised intestinal flora and may be a promising prognostic indicator.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30349083", + "title": "Recovery of gut microbiota of healthy adults following antibiotic exposure.", + "year": 2018, + "journal": "Nature microbiology", + "authors": [ + "Palleja A", + "Mikkelsen KH", + "Forslund SK", + "Kashani A", + "Allin KH", + "Nielsen T", + "Hansen TH", + "Liang S", + "Feng Q", + "Zhang C", + "Pyl PT", + "Coelho LP", + "Yang H", + "Wang J", + "Typas A", + "Nielsen MF", + "Nielsen HB", + "Bork P", + "Wang J", + "Vilsb\u00f8ll T", + "Hansen T", + "Knop FK", + "Arumugam M", + "Pedersen O" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.3049850533758888, + "mesh_terms": [ + "Adolescent", + "Adult", + "Anti-Bacterial Agents", + "Bacteria", + "Bacterial Physiological Phenomena", + "Biodiversity", + "Drug Resistance, Bacterial", + "Feces", + "Gastrointestinal Microbiome", + "Genes, Bacterial", + "Healthy Volunteers", + "Humans", + "Male", + "Metagenomics", + "Virulence Factors", + "Young Adult" + ], + "raw_abstract": "To minimize the impact of antibiotics, gut microorganisms harbour and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing-based metagenomics, we analysed the partial eradication and subsequent regrowth of the gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 last-resort antibiotics: meropenem, gentamicin and vancomycin. Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and the depletion of Bifidobacterium species and butyrate producers. The gut microbiota of the subjects recovered to near-baseline composition within 1.5 months, although 9 common species, which were present in all subjects before the treatment, remained undetectable in most of the subjects after 180 days. Species that harbour \u03b2-lactam resistance genes were positively selected for during and after the intervention. Harbouring glycopeptide or aminoglycoside resistance genes increased the odds of de novo colonization, however, the former also decreased the odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention and their antibiotics resistance gene carriage modulates their recovery processes.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39174731", + "title": "Gut Microbiome in Children with Congenital Heart Disease After Cardiopulmonary Bypass Surgery (GuMiBear Study).", + "year": 2024, + "journal": "Pediatric cardiology", + "authors": [ + "Koc F", + "Magner C", + "Murphy K", + "Kelleher ST", + "Tan MH", + "O'Toole M", + "Jenkins D", + "Boyle J", + "Lavelle M", + "Maguire N", + "Ross PR", + "Stanton C", + "McMahon CJ" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.3049679026650182, + "mesh_terms": [], + "raw_abstract": "The gut microbiome of infants with congenital heart disease (CHD) undergoing cardiopulmonary bypass surgery (CPB) is at risk of profound alteration. The aim of this study was to examine the gut microbiome pre- and post-bypass surgery to explore potential implications of altered gut biodiversity.\u00a0A prospective cohort study involving infants with CHD who underwent CPB\u00a0was performed. Faecal samples were collected from infants alongside the collection of demographic and clinical data in order to examine gut microbiome changes before and after surgery. 16S rRNA sequencing analysis was performed on DNA isolated from stool samples to determine changes in gut microbiome composition. Thirty-three patients were recruited, with samples from thirteen of these available for final analysis. Compared with healthy, matched controls, at a genus level, pre-operative samples for infants with CHD demonstrated a higher relative abundance of Escherichia-Shigella (31% vs 2-6%) and a lower relative abundance of Bifidobacterium (13% vs 40-60%). In post-operative samples, the relative abundance of Escherichia-Shigella (35%), Enterococcus (11%), Akkermansia (6%), and Staphylococcus (5%) were higher than pre-op samples. One infant developed post-operative necrotising-enterocolitis (NEC). They displayed a marked abundance of the Enterococcus (93%) genus pre-operatively. This study demonstrates that infants with CHD have an altered gut\u00a0microbiome when compared with healthy controls and there might be a possible link between an abundance of virulent species and NEC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26663491", + "title": "Alterations in the gut microbiotas of children with food sensitization in early life.", + "year": 2016, + "journal": "Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology", + "authors": [ + "Chen CC", + "Chen KJ", + "Kong MS", + "Chang HJ", + "Huang JL" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.304292199106004, + "mesh_terms": [ + "Bacteria", + "Case-Control Studies", + "Child, Preschool", + "Feces", + "Female", + "Food", + "Food Hypersensitivity", + "Gastrointestinal Microbiome", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Infant", + "Male", + "Polymerase Chain Reaction", + "Time Factors" + ], + "raw_abstract": "BACKGROUND: We hypothesized that food sensitization (FS) in children could be linked to specific gut microbiota. The aim of our study is to quantify and evaluate differences in gut microbiota composition between children with FS and healthy controls. METHODS: A case-control study of 23 children with FS and 22 healthy children was performed. Individual microbial diversity and composition were analyzed via parallel barcoded 454 pyrosequencing targeting the 16S rRNA gene hypervariable V3-V5 regions. RESULTS: The children with FS exhibited lower diversity of both the total microbiota (p = 0.01) and the bacterial phylum Bacteroidetes (p = 0.02). In these children, the number of Bacteroidetes bacteria was significantly decreased and that of Firmicutes were significantly increased compared with the healthy children. At the genus level, we observed significant increases in the numbers of Sphingomonas, Sutterella, Bifidobacterium, Collinsella, Clostridium sensu stricto, Clostridium IV, Enterococcus, Lactobacillus, Roseburia, Faecalibacterium, Ruminococcus, Subdoligranulum, and Akkermansia in the FS group. We also found significant decreases in the numbers of Bacteroides, Parabacteroides, Prevotella, Alistipes, Streptococcus, and Veillonella in this group. Furthermore, linear discriminant analysis (LDA) coupled with effect size measurements revealed the most differentially abundant taxa (increased abundances of Clostridium IV and Subdoligranulum and decreased abundances of Bacteroides and Veillonella), which could be used to identify FS. CONCLUSIONS: Our results showed that FS is associated with compositional changes in the gut microbiota. These findings could be useful for developing strategies to control the development of FS or atopy by modifying the gut microbiota.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "25931253", + "title": "Dysbiosis of Intestinal Microbiota Associated With Inflammation Involved in the Progression of Acute Pancreatitis.", + "year": 2015, + "journal": "Pancreas", + "authors": [ + "Tan C", + "Ling Z", + "Huang Y", + "Cao Y", + "Liu Q", + "Cai T", + "Yuan H", + "Liu C", + "Li Y", + "Xu K" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.30395463900074615, + "mesh_terms": [ + "Acute Disease", + "Adult", + "Bacteria", + "Biomarkers", + "Case-Control Studies", + "China", + "Cytokines", + "DNA, Bacterial", + "Denaturing Gradient Gel Electrophoresis", + "Disease Progression", + "Dysbiosis", + "Endotoxins", + "Feces", + "Female", + "Host-Pathogen Interactions", + "Humans", + "Inflammation Mediators", + "Intestines", + "Male", + "Microbiota", + "Middle Aged", + "Multiple Organ Failure", + "Pancreatitis", + "Predictive Value of Tests", + "Prospective Studies", + "Real-Time Polymerase Chain Reaction", + "Risk Factors", + "Severity of Illness Index" + ], + "raw_abstract": "OBJECTIVES: To evaluate alterations of the intestinal bacteria and its associations with the inflammation in acute pancreatitis (AP). METHODS: A multihospital prospective clinical study was conducted, and a total of 108 participants were enrolled in our study, including 44 with severe AP (SAP), 32 with mild AP (MAP), and 32 healthy volunteers. The structure of intestinal microbiota, 10 predominant bacteria, plasma endotoxin, and serum cytokines were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis, real-time quantitative polymerase chain reaction, Limulus amebocyte lysate tests, and enzyme-linked immunosorbent assays, respectively. RESULTS: Dramatic alterations in the predominant fecal microbiota were observed in most of both MAP and SAP patients. In addition, the rates of the multiorgan failures and infectious complications in the patients with SAP with altered intestinal microbiota were significantly higher than in those whose intestinal microbiota remained unaltered. Enterococcus increased and Bifidobacterium decreased in the patients with SAP compared to the patients with MAP. Serum IL-6 were positively correlated with Enterobacteriaceae and Enterococcus and negatively correlated with Bifidobacterium, whereas plasma endotoxin positively correlated with Enterococcus (P < 0.05). CONCLUSIONS: The intestinal bacteria most frequently altered in both the patients with MAP and those with SAP significantly correlated with inflammation, which indicated that the intestinal microbiota may be involved in the progression of AP.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31132360", + "title": "Dr. Jekyll and Mr. Hide: How Enterococcus faecalis Subverts the Host Immune Response to Cause Infection.", + "year": 2019, + "journal": "Journal of molecular biology", + "authors": [ + "Kao PHN", + "Kline KA" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2999403374747695, + "mesh_terms": [ + "Adaptive Immunity", + "Blood", + "Enterococcus faecalis", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Heart", + "Humans", + "Immune System", + "Immunity, Innate", + "Urinary Tract" + ], + "raw_abstract": "Enterococcus faecalis, a ubiquitous member of the healthy human gut microbiota, is also a common opportunistic pathogen and leading cause of nosocomial infections. This tenacious microbe is well adapted to infect and persist in multiple niches within the mammalian host and can rapidly tune its metabolism to respond to new environments, enabling infection in sites including the gastrointestinal tract, urinary tract, wounded epithelium, heart, and blood. In order to withstand and persist in the face of host immune responses, E. faecalis has an arsenal of strategies to suppress, evade, or inactivate innate and adaptive immune mechanisms. In this review, we present the variety of ways E. faecalis modulates the immune response, enabling this otherwise innocuous gut commensal to transition and persist as a pathogen.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36271677", + "title": "Fecal microbiota of horses with colitis and its association with laminitis and survival during hospitalization.", + "year": 2022, + "journal": "Journal of veterinary internal medicine", + "authors": [ + "Ayoub C", + "Arroyo LG", + "MacNicol JL", + "Renaud D", + "Weese JS", + "Gomez DE" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2989770122235919, + "mesh_terms": [ + "Horses", + "Animals", + "Case-Control Studies", + "Feces", + "Microbiota", + "Colitis", + "Streptococcus", + "Hospitalization", + "Horse Diseases" + ], + "raw_abstract": "BACKGROUND: The association of microbiota with clinical outcomes and the taxa associated with colitis in horses remains generally unknown. OBJECTIVES: Describe the fecal microbiota of horses with colitis and investigate the association of the fecal microbiota with the development of laminitis and survival. ANIMALS: Thirty-six healthy and 55 colitis horses subdivided into laminitis (n\u00a0=\u00a015) and non-laminitis (n\u00a0=\u00a039, 1 horse with chronic laminitis was removed from this comparison) and survivors (n\u00a0=\u00a027) and nonsurvivors (n\u00a0=\u00a028). METHODS: Unmatched case-control study. The Illumina MiSeq platform targeting the V4 region of the 16S ribosomal RNA gene was used to assess the microbiota. RESULTS: The community membership (Jaccard index) and structure (Yue and Clayton index) were different (analysis of molecular variance [AMOVA]; P\u2009<\u2009.001) between healthy and colitis horses. The linear discriminant analysis effect size (LEfSe; linear discriminant analysis [LDA] >3; P\u2009<\u2009.05) and random forest analyses found Enterobacteriaceae, Lactobacillus, Streptococcus, and Enterococcus enriched in colitis horses, whereas Treponema, Faecalibacterium, Ruminococcaceae, and Lachnospiraceae were enriched in healthy horses. The community membership and structure of colitis horses with or without laminitis was (AMOVA; P\u2009>\u2009.05). Enterobacteriaceae, Streptococcus, and Lactobacillus were enriched in horses with laminitis (LDA >\u20093; P\u2009<\u2009.05). The community membership (AMOVA; P\u00a0=\u00a0.008) of surviving and nonsurviving horses was different. Nonsurviving horses had an enrichment of Enterobacteriaceae, Pseudomonas, Streptococcus, and Enterococcus (LDA >3; P\u2009<\u2009.05). CONCLUSION AND CLINICAL IMPORTANCE: Differences in the microbiota of horses with colitis that survive or do not survive are minor and, similarly, the microbiota differences in horses with colitis that do or do not develop laminitis are minor.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26490635", + "title": "Influence of H7N9 virus infection and associated treatment on human gut microbiota.", + "year": 2015, + "journal": "Scientific reports", + "authors": [ + "Qin N", + "Zheng B", + "Yao J", + "Guo L", + "Zuo J", + "Wu L", + "Zhou J", + "Liu L", + "Guo J", + "Ni S", + "Li A", + "Zhu Y", + "Liang W", + "Xiao Y", + "Ehrlich SD", + "Li L" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.29634167323942157, + "mesh_terms": [ + "Adult", + "Aged", + "Aged, 80 and over", + "Clostridium", + "Enterococcus faecium", + "Escherichia coli", + "Female", + "Gastrointestinal Microbiome", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Influenza A Virus, H7N9 Subtype", + "Influenza, Human", + "Male", + "Metagenomics", + "Middle Aged" + ], + "raw_abstract": "Between March and June, 2013, forty H7N9 patients were hospitalized in our hospital. Next-generation sequencing technologies have been used to sequence the fecal DNA samples of the patient, the within sample diversity analysis, enterotyping, functional gene and metagenomic species analysis have been carried on both the patients and healthy controls. The influence of associated treatment in H7N9 infected patients is dramatic and was firstly revealed in species level due to deep sequencing technology. We found that most of the MetaGenomic Species (MGS) enriched in the control samples were Roseburia inulinivorans DSM 16841, butyrate producing bacterium SS3/4 and most of MGS enriched in the H7N9 patients were Clostridium sp. 7 2 43FAA and Enterococcus faecium. It was concluded that H7N9 viral infection and antibiotic administration have a significant effect on the microbiota community with decreased diversity and overgrowth of the bacteria such as Escherichia coli and Enterococcus faecium. Enterotype analysis showed that the communities were unstable. Treatment including antivirals, probiotics and antibiotics helps to improve the microbiota diversity and the abundance of beneficial bacteria in the gut.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30594615", + "title": "Characterization of novel exopolysaccharide of Enterococcus faecium WEFA23 from infant and demonstration of its in vitro biological properties.", + "year": 2019, + "journal": "International journal of biological macromolecules", + "authors": [ + "Jia K", + "Tao X", + "Liu Z", + "Zhan H", + "He W", + "Zhang Z", + "Zeng Z", + "Wei H" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.29122239329814203, + "mesh_terms": [ + "Bacterial Adhesion", + "Biphenyl Compounds", + "Enterococcus faecium", + "Feces", + "HT29 Cells", + "Humans", + "Infant", + "Listeria monocytogenes", + "Molecular Weight", + "Monosaccharides", + "Picrates", + "Polysaccharides, Bacterial" + ], + "raw_abstract": "In this study exopolysaccharide (EPS) of Enterococcus faecium WEFA23 from healthy infant's feces was yielded as high as 130\u202fmg/L by fermentation. By purification the EPS was further fractioned into A23-1, A23-2, A23-3 and A23-4 on HiTrap Q HP and Superdex G-200 column. As the major purified fractions, A23-2 and A23-4 were analyzed for the preliminary structures and investigated for the biological properties in vitro. The molecular weight of A23-2 and A23-4 was 2.50\u202f\u00d7\u202f10", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29410448", + "title": "Intestinal microbiota development and gestational age in preterm neonates.", + "year": 2018, + "journal": "Scientific reports", + "authors": [ + "Korpela K", + "Blakstad EW", + "Moltu SJ", + "Str\u00f8mmen K", + "Nakstad B", + "R\u00f8nnestad AE", + "Br\u00e6kke K", + "Iversen PO", + "Drevon CA", + "de Vos W" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.29005199289683786, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Bifidobacterium", + "Breast Feeding", + "Enterobacter", + "Enterococcus", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gestational Age", + "Humans", + "Infant", + "Infant, Newborn", + "Infant, Premature", + "Infant, Very Low Birth Weight", + "Male", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA", + "Staphylococcus" + ], + "raw_abstract": "The intestinal microbiota is an important contributor to the health of preterm infants, and may be destabilized by a number of environmental factors and treatment modalities. How to promote the development of a healthy microbiota in preterm infants is largely unknown. We collected fecal samples from 45 breastfed preterm very low birth weight (birth weight\u2009<\u20091500\u2009g) infants from birth until 60 days postnatal age to characterize the intestinal microbiota development during the first weeks of life in preterm infants. Fecal microbiota composition was determined by 16S rRNA amplicon sequencing. The main driver of microbiota development was gestational age; antibiotic use had strong but temporary effects and birth mode had little influence. Microbiota development proceeded in four phases indicated by the dominance of Staphylococcus, Enterococcus, Enterobacter, and finally Bifidobacterium. The Enterococcus phase was only observed among the extremely premature infants and appeared to delay the microbiota succession. The results indicate that hospitalized preterm infants receiving breast milk may develop a normal microbiota resembling that of term infants.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30076974", + "title": "Faecal carriage of optrA-positive enterococci in asymptomatic healthy humans in Hangzhou, China.", + "year": 2019, + "journal": "Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases", + "authors": [ + "Cai J", + "Schwarz S", + "Chi D", + "Wang Z", + "Zhang R", + "Wang Y" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2893681928589351, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Aged, 80 and over", + "Anti-Bacterial Agents", + "Bacterial Proteins", + "Carrier State", + "Child", + "Child, Preschool", + "China", + "Drug Resistance, Bacterial", + "Enterococcus faecalis", + "Enterococcus faecium", + "Feces", + "Female", + "Genetic Variation", + "Gram-Positive Bacterial Infections", + "Humans", + "Infant", + "Infant, Newborn", + "Linezolid", + "Male", + "Microbial Sensitivity Tests", + "Middle Aged", + "Polymerase Chain Reaction", + "Sequence Analysis, DNA", + "Whole Genome Sequencing", + "Young Adult" + ], + "raw_abstract": "OBJECTIVES: To investigate the faecal carriage of optrA-positive enterococci among asymptomatic healthy humans in Hangzhou, China, and to characterize the genetic context of optrA. METHODS: A total of 3458 stool samples from healthy individuals were collected and cultured on a selective medium containing 10 mg/L florfenicol and resulting enterococci were screened for the presence of optrA by PCR. OptrA variants were determined by amino acid sequence comparison with the original OptrA from Enterococcus faecalis E349. Whole genome sequencing and PCR mapping were performed to obtain and analyse the genetic environment of optrA. RESULTS: Similar optrA carriage rates (\u223c3.5%) were detected in samples from adults (55/1558) and children (66/1900). Linezolid resistance rates for E.\u00a0faecalis, Enterococcus faecium and other Enterococcus species were 58.5% (38/65), 42.3% (11/26) and 0% (0/31), respectively. Nineteen OptrA variants exhibiting different linezolid MICs were identified. Isolates carrying wild-type OptrA and variants RDK, KLDP, KD, D, RDKP, and EDP generally demonstrated linezolid MICs \u22658 mg/L. The OptrA variants, with fexA upstream and erm(A) downstream, were flanked by IS1216E at one or both ends. The fexA-optrA(wild-type) was located downstream of a Tn554 transposon, and was inserted into the radC gene. The EDM variant was detected in 31/73 enterococci with linezolid MICs \u22644 mg/L. Despite the variable genetic context, Tn558-araC-optrA(EDM)-erm(A)-met was the most common gene array. CONCLUSIONS: This study revealed a correlation between linezolid MIC, genetic context and OptrA variant. Intestinal colonization of healthy individuals by optrA-positive enterococci is a concern, and active epidemiological surveillance of optrA is warranted.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36517872", + "title": "Gut microbiota in the early stage of Crohn's disease has unique characteristics.", + "year": 2022, + "journal": "Gut pathogens", + "authors": [ + "Ma X", + "Lu X", + "Zhang W", + "Yang L", + "Wang D", + "Xu J", + "Jia Y", + "Wang X", + "Xie H", + "Li S", + "Zhang M", + "He Y", + "Jin P", + "Sheng J" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2890082668524287, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Emerging evidence suggests that gut microbiota plays a predominant role in Crohn's disease (CD). However, the microbiome alterations in the early stage of CD patients still remain unclear. The present study aimed to identify dysbacteriosis in patients with early CD and explore specific gut bacteria related to the progression of CD. METHODS: This study was nested within a longitudinal prospective Chinese CD cohort, and it included 18 early CD patients, 22 advanced CD patients and 30 healthy controls. The microbiota communities were investigated using high-throughput Illumina HiSeq sequencing targeting the V3-V4 region of 16S ribosomal DNA (rDNA) gene. The relationship between the gut microbiota and clinical characteristics of CD was analyzed. RESULTS: Differential microbiota compositions were observed in CD samples (including early and advanced CD samples) and healthy controls samples. Notably, Lachnospiracea_incertae_sedis and Parabacteroides were enriched in the early CD patients, Escherichia/Shigella, Enterococcus and Proteus were enriched in the advanced CD patients, and Roseburia, Gemmiger, Coprococcus, Ruminococcus 2, Butyricicoccus, Dorea, Fusicatenibacter, Anaerostipes, Clostridium IV were enriched in the healthy controls [LDA score (log10)\u2009>\u20092]. Furthermore, Kruskal-Wallis Rank sum test results showed that Blautia, Clostridium IV, Coprococcus, Dorea, Fusicatenibacter continued to significantly decrease in early and advanced CD patients, and Escherichia/Shigella and Proteus continued to significantly increase compared with healthy controls (P\u2009<\u20090.05). The PICRUSt analysis identified 16 remarkably different metabolic pathways [LDA score (log10)\u2009>\u20092]. Some genera were significantly correlated with various clinical parameters, such as fecal calprotectin, erythrocyte sedimentation rate, C-reactive protein, gland reduce, goblet cells decreased, clinical symptoms (P\u2009<\u20090.05). CONCLUSIONS: Dysbacteriosis occurs in the early stage of CD and is associated with the progression of CD. This data provides a foundation that furthers the understanding of the role of gut microbiota in CD's pathogenesis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36284437", + "title": "Gut bacterial profiles in Parkinson's disease: A systematic review.", + "year": 2023, + "journal": "CNS neuroscience & therapeutics", + "authors": [ + "Li Z", + "Liang H", + "Hu Y", + "Lu L", + "Zheng C", + "Fan Y", + "Wu B", + "Zou T", + "Luo X", + "Zhang X", + "Zeng Y", + "Liu Z", + "Zhou Z", + "Yue Z", + "Ren Y", + "Li Z", + "Su Q", + "Xu P" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.286105978536533, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "Parkinson Disease", + "Gastrointestinal Microbiome", + "Bacteria", + "Feces", + "Fatty Acids, Volatile" + ], + "raw_abstract": "INTRODUCTION: Recent advances have highlighted the relationships between gut dysbiosis and Parkinson's disease (PD). Microbiota transplantation from PD patients to mice can induce increased alpha-synuclein-mediated motor deficits. Human studies have identified differences in the gut microbiota of PD patients compared to healthy controls. We undertook a systematic review to evaluate the available evidence for the involvement of gut bacteria in the etiology of PD. METHODS: The PubMed databank, the China National Knowledge Infrastructure databank, and Wanfang Data were searched from inception until June 2021 to identify human case-control studies that investigated relationships between PD and microbiota quantified from feces. We evaluated the resulting studies focusing on bacterial taxa that were different between PD patients and healthy controls. RESULTS: Twenty-six studies were found in which 53 microbial families and 98 genera exhibited differences between patients with PD and healthy controls. The genera identified by more than two studies as increased in PD were Bifidobacterium, Alistipes, Christensenella, Enterococcus, Oscillospira, Bilophila, Desulfovibrio, Escherichia/Shigella, and Akkermansia, while Prevotella, Blautia, Faecalibacterium, Fusicatenibacter, and Haemophilus had three or more reports of being lower in PD patients. More than one report demonstrated that Bacteroides, Odoribacter, Parabacteroides, Butyricicoccus, Butyrivibrio, Clostridium, Coprococcus, Lachnospira, Lactobacillus, Megasphaera, Phascolarctobacterium, Roseburia, Ruminococcus, Streptococcus, and Klebsiella were altered in both directions. CONCLUSION: Our review shows that the involvement of the gut microbiome in the etiology of PD may involve alterations of short-chain fatty acids (SCFAs)-producing bacteria and an increase in putative gut pathobionts. SCFAs-producing bacteria may vary above or below an \"optimal range,\" causing imbalances. Considering that Bifidobacterium, Lactobacillus, and Akkermansia are beneficial for human health, increased Bifidobacterium and Lactobacillus in the PD gut microbiome may be associated with PD medications, especially COMT inhibitors, while a high level of Akkermansia may be associated with aging.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31994568", + "title": "A pregnancy complication-dependent change in SIgA-targeted microbiota during third trimester.", + "year": 2020, + "journal": "Food & function", + "authors": [ + "Cui M", + "Qi C", + "Yang L", + "Zhang M", + "Wang H", + "She G", + "Yu R", + "Miao T", + "Sun J" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2847864048631231, + "mesh_terms": [ + "Adult", + "Diabetes, Gestational", + "Diet", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Hypertension, Pregnancy-Induced", + "Immunoglobulin A, Secretory", + "Pregnancy", + "Probiotics" + ], + "raw_abstract": "Gut microbiota play a crucial role in metabolic dysfunction during gestation, which might be prevented by using probiotics. This study compared the composition of the gut microbiota in healthy and complicated pregnancies, for screening and isolating healthy pregnancy-derived probiotics. According to the principal component analysis of secretory immunoglobulin A (SIgA)-coated microbiota in the gut, third-trimester volunteers can be divided into three groups: AHd (n = 29), GDMd (n = 37), and GHd (n = 25), dominated by asymptomatic healthy donors (62.07%), gestational diabetes mellitus (GDM) donors (40.54%), and gestational hypertension (GH) donors (40%), respectively. There was a significant difference in \u03b2-diversity (p < 0.01) and \u03b1-diversity (p < 0.05) among the three groups. At the phylum level, the Firmicutes of the GHd group were significantly lower than those of the AHd group (p = 0.039), while Bacteroidetes (p = 0.005) and Proteobacteria (p = 0.002) of the GHd group were more dominant than those of the AHd group. At the genus level, the linear discriminant analysis effect size showed that SIgA-targeted Enterococcus was the dominant taxonomic biomarker of the AHd group, and the GHd group was enriched with Escherichia and Streptococcus. The GDMd and GHd groups had higher faecal calprotectin, serum lipopolysaccharide, zonulin, and GLYCAM-1 levels. We conclude that the occurrence of complications in the third trimester may be related to intestinal barrier injury associated with disorders of the intestinal SIgA-targeted microbiota; gut barrier injury triggers inflammation in pregnant women. SIgA-targeted L. reuteri showed a significant correlation with low inflammatory response and may be a potential probiotic candidate for preventing pregnancy complications.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37853925", + "title": "Gut microbiota changes in patients with hypertension: A systematic review and meta-analysis.", + "year": 2023, + "journal": "Journal of clinical hypertension (Greenwich, Conn.)", + "authors": [ + "Cai M", + "Lin L", + "Jiang F", + "Peng Y", + "Li S", + "Chen L", + "Lin Y" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2807175629857556, + "mesh_terms": [ + "Humans", + "Hypertension", + "Gastrointestinal Microbiome" + ], + "raw_abstract": "Hypertension is a major public health issue worldwide. The imbalance of gut microbiota is thought to play an important role in the pathogenesis of hypertension. The authors conducted the systematic review and meta-analysis to clarify the relationship between gut microbiota and hypertension through conducting an electronic search in six databases. Our meta-analysis included 19 studies and the results showed that compared with healthy controls, Shannon significantly decreased in hypertension [SMD\u00a0=\u00a0-0.13, 95%CI (-0.22, -0.04), p\u00a0=\u00a0.007]; however, Simpson [SMD\u00a0=\u00a0-0.01, 95%CI (-0.14, 0.12), p\u00a0=\u00a0.87], ACE [SMD\u00a0=\u00a00.18, 95%CI (-0.06, 0.43), p\u00a0=\u00a0.14], and Chao1 [SMD\u00a0=\u00a00.11, 95%CI (-0.01, 0.23), p\u00a0=\u00a0.08] did not differ significantly between hypertension and healthy controls. The F/B ratio significantly increased in hypertension [SMD\u00a0=\u00a00.84, 95%CI (0.10, 1.58), p\u00a0=\u00a0.03]. In addition, Shannon index was negatively correlated with hypertension [r\u00a0=\u00a0-0.12, 95%CI (-0.19, -0.05)], but had no significant correlation with SBP [r\u00a0=\u00a00.10, 95%CI (-0.19, 0.37)] and DBP [r\u00a0=\u00a0-0.39, 95%CI (-0.73, 0.12)]. At the phylum level, the relative abundance of Firmicutes [SMD\u00a0=\u00a0-0.01, 95%CI (-0.37, 0.34), p\u00a0=\u00a0.94], Bacteroidetes [SMD\u00a0=\u00a0-0.15, 95%CI (-0.44, 0.14), p\u00a0=\u00a0.30], Proteobacteria [SMD\u00a0=\u00a00.25, 95%CI (-0.01, 0.51), p\u00a0=\u00a0.06], and Actinobacteria [SMD\u00a0=\u00a00.21, 95%CI (-0.11, 0.53), p\u00a0=\u00a0.21] did not differ significantly between hypertension and healthy controls. At the genus level, compared with healthy controls, the relative abundance of Faecalibacterium decreased significantly [SMD = -0.16, 95%CI (-0.28, -0.04), p = .01], while the Streptococcus [SMD = 0.20, 95%CI (0.08, 0.32), p = .001] and Enterococcus [SMD = 0.20, 95%CI (0.08, 0.33), p = .002] significantly increased in hypertension. Available evidence suggests that hypertensive patients may have an imbalance of gut microbiota. However, it still needs further validation by large sample size studies of high quality.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35845131", + "title": "The Gut Microbiota and Inflammatory Factors in Pediatric Appendicitis.", + "year": 2022, + "journal": "Disease markers", + "authors": [ + "Bi Y", + "Yang Q", + "Li J", + "Zhao X", + "Yan B", + "Li X", + "Cui H" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.27714912434660655, + "mesh_terms": [ + "Appendicitis", + "Biomarkers", + "Child", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans" + ], + "raw_abstract": "BACKGROUND: The study analyzed gut microflora's composition and investigated the associations between the associations between gut dysbiosis and inflammatory indicators in pediatric patients with acute appendicitis. METHODS: High-throughput sequencing and bioinformatics analysis were used to investigate the composition and diversity of gut microflora in 20 pediatric patients with acute appendicitis and 11 healthy children. Endpoints measured were operational taxonomic units (OTU) of gut microflora. The OTU and its abundance analysis, sample diversity analysis, principal component analysis of samples, differential analysis, and analysis of biomarkers were performed. RESULTS: Overall fecal microbial richness and diversity were similar in patients and controls. Yet richness within the group of Bilophila, Eggerthella, Clostridium, Parvimonas, Megasphaera, Atopobium, Phascolarctobacterium, Adlercreutzia, Barnesiella, Klebsiella, Enterococcus, and Prevotella genera was higher in patients. Adlercreutzia was significantly positively correlated with IL-10, while the three other genera, comprising Klebsiella, Adlercreutzia, and Prevotella, were positively correlated with B cells level. CONCLUSION: Gut microbiome components are significantly different in pediatric patients with acute appendicitis and healthy children. The differential abundance of some genera is correlated with the production of inflammatory markers in appendicitis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32058024", + "title": "The distribution characteristics of intestinal microbiota in children with community-acquired pneumonia under five\u00a0Years of age.", + "year": 2020, + "journal": "Microbial pathogenesis", + "authors": [ + "Ren X", + "Gamallat Y", + "Liu D", + "Zhu Y", + "Meyiah A", + "Yan C", + "Shang D", + "Xin Y" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.27370802947704215, + "mesh_terms": [], + "raw_abstract": "Pneumonia is the leading cause of morbidity and mortality in children under five years of age worldwide. Over the past decades, studies have shown that the upper respiratory pathogens are closely related to the occurrence of pneumonia. However, the co-occurrence of gut microbiome dysbiosis may have clinical manifestation in the prognosis of childhood pneumonia. The aim of the present study is to investigate the differences in gut microbial communities between children's diagnosed community-acquired pneumonia (CAP) under five compared to healthy controls in Inner Mongolia. Fecal samples were collected from children with CAP and healthy controls (<5 years old) and the genomic microbiome 16S rRNA was amplified using the hypervariable V4 region and subjected to MiSeq Illumina sequencing, and then analyzed for microbiota composition and phenotype. Finally functional profiling was performed by KEGG pathways analyses. Our results revealed a gut microbiota dysbiosis in children with CAP. Distinct gut microbiome composition and structure were associated with childhood CAP between two age categories compared to healthy controls. In addition, the phylogenic phenotype's prediction was found to be significantly different between the groups. The prominent genera in age group of 0-3 were Bifidobacterium and Enterococcus. On the contrary, Escherichia-Shigella, Prevotella, Faecalibacterium and Enterobacter were remarkably decreased in most of the fecal samples from CAP patients in age group of 0-3 compared to the control. At the genus level, the CAP children in the age group of 4-5 showed an increase in the abundance of Escherichia/Shigella, Bifidobacterium, Streptococcus and Psychrobacter and, a decrease in the abundance of Faecalibacterium, Bacteroides, Lachnospiraceae and Ruminococcus compared with the matched healthy controls. Moreover, CAP children in both age groups exhibited distinct profiles in the KEGG functional analysis. Our data revealed that the gut microbiota differ between CAP patients and health children and certain gut microbial species are associated with CAP. Further research to identify specific microbial species which may contribute to the development CAP are merited. In addition, rectification of microbiota dysbiosis may provide supplemental benefits for treatment of the childhood CAP.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39621250", + "title": "Gut Microbiota Dysbiosis Facilitates Susceptibility to Bloodstream Infection.", + "year": 2024, + "journal": "Journal of microbiology (Seoul, Korea)", + "authors": [ + "Lin X", + "Lin C", + "Li X", + "Yao F", + "Guo X", + "Wang M", + "Zeng M", + "Yuan Y", + "Xie Q", + "Huang X", + "Jiao X" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.27066692170623335, + "mesh_terms": [ + "Humans", + "Dysbiosis", + "Gastrointestinal Microbiome", + "Male", + "Female", + "RNA, Ribosomal, 16S", + "Middle Aged", + "Feces", + "Bacteria", + "Aged", + "Adult", + "Bacteremia", + "Disease Susceptibility", + "DNA, Bacterial" + ], + "raw_abstract": "To study the role of intestinal flora in the development of bloodstream infections (BSIs). 42 patients and 19 healthy controls (HCs) were screened into the study and their intestinal flora was measured by 16S rRNA gene sequencing. The bacterial diversity was significantly lower in the BSI group compared with that in the HCs (P\u2009<\u20090.001), and beta diversity was significantly differentiated between the two groups (PERMANOVA, P\u2009=\u20090.001). The four keystone species [Roseburia, Faecalibacterium, Prevotella, and Enterococcus (LDA\u2009>\u20094)] differed significantly between the two groups. Dysbiosis of fecal microbial ecology is a common condition present in patients with BSI. The proliferation of certain pathogens or reduction of SCFA-producing bacteria would cause susceptibility to BSI.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39113137", + "title": "Effect of \u03b2-lactam antibiotics on the gut microbiota of term neonates.", + "year": 2024, + "journal": "Annals of clinical microbiology and antimicrobials", + "authors": [ + "Gu H", + "Tao E", + "Fan Y", + "Long G", + "Jia X", + "Yuan T", + "Chen L", + "Shu X", + "Zheng W", + "Jiang M" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2697828818388973, + "mesh_terms": [ + "Female", + "Humans", + "Infant, Newborn", + "Male", + "Bacteria", + "beta Lactam Antibiotics", + "Feces", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "\u03b2-Lactam antibiotics are a class of antibiotics commonly used to treat bacterial infections. However, the effects of \u03b2-lactam antibiotics on term neonatal intestinal flora have not been fully elucidated. Hospitalized full-term newborns receiving \u03b2-lactam antibiotics formed the antibiotic group (n\u2009=\u200967), while those without antibiotic treatment comprised the non-antibiotic group (n\u2009=\u200947). A healthy group included healthy full-term newborns (n\u2009=\u200916). Stool samples were collected for 16\u00a0S rDNA sequencing to analyze gut microbiota variations. Further investigation was carried out within the \u03b2-lactam antibiotic group, exploring the effects of antibiotic use on the newborns' gut microbiota in relation to the duration and type of antibiotic administration, delivery method, and feeding practices. The antibiotic group exhibited significant difference of microbial community composition compared to the other groups. Genera like Klebsiella, Enterococcus, Streptococcus, Alistipes, and Aeromonas were enriched, while Escherichia-Shigella, Clostridium sensu stricto 1, Bifidobacterium, and Parabacteroides were reduced. Klebsiella negatively correlated with Escherichia-Shigella, positively with Enterobacter, while Escherichia-Shigella negatively correlated with Enterococcus and Streptococcus. Regardless of neonatal age, \u03b2-lactam antibiotics induced an elevated abundance of Klebsiella and Enterococcus. The impact on gut microbiota varied with the duration and type of antibiotic (cefotaxime or ampicillin/sulbactam). Compared to vaginal delivery, cesarean delivery after \u03b2-lactam treatment heightened the abundance of Klebsiella, Enterobacteriaceae_Unclassified, Lactobacillales_Unclassified, and Pectobacterium. Feeding patterns minimally influenced \u03b2-lactam-induced alterations. In conclusion, \u03b2-lactam antibiotic treatment for neonatal pneumonia and sepsis markedly disrupted intestinal microbiota, favoring Klebsiella, Enterococcus, Streptococcus, Alistipes, and Aeromonas. The impact of \u03b2-lactam varied by duration, type, and delivery method, emphasizing heightened disruptions post-cesarean delivery.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31735171", + "title": "Characterization of gut microbiota in children with pulmonary tuberculosis.", + "year": 2019, + "journal": "BMC pediatrics", + "authors": [ + "Li W", + "Zhu Y", + "Liao Q", + "Wang Z", + "Wan C" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.26487689408327847, + "mesh_terms": [ + "Adolescent", + "Case-Control Studies", + "Child", + "Child, Preschool", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Infant", + "Male", + "Tuberculosis, Pulmonary" + ], + "raw_abstract": "BACKGROUND: Gut microbiota plays a critical role in many important physiological processes and is linked with various pulmonary infectious diseases. The relationship between pulmonary tuberculosis (PTB) and gut microbiota has been poorly studied. The present study aimed to characterize gut microbiota in pediatric patients with PTB. METHODS: A case-controlled study was executed for the characterization of gut microbiota in pediatric PTB patients. Fecal samples were collected from the PTB patients and healthy controls upon admission. In addition, a one-month follow-up assessment was performed to investigate alterations in the gut microbiota post anti-tuberculosis treatment. 16SrDNA sequencing analysis of fecal DNA was completed on the Illumina MiSeq platform. RESULTS: Compared with healthy controls, the gut microbiota of pediatric patients with PTB was characterized by decreased microbial diversity. PTB patients further presented an up-regulation of the pro-inflammatory bacteria Prevotella, the opportunistic pathogen Enterococcus, as well as a reduction of beneficial bacteria including Ruminococcaceae, Bifidobacteriaceae and prausnitzii. One-month after anti-tuberculosis therapy, the richness of gut microbiota in PTB patients was distinctly depleted. CONCLUSIONS: The gut microbiota of pediatric patients with PTB was significantly distinct from healthy controls. Additionally, the richness of gut microbiota in PTB patients decreased after one-month anti-tuberculosis treatment. It is hypothesized that the homeostasis of gut microbiota in PTB patients may affect the pathogenies of PTB by de-regulation of the hosts' immune status through the gut-lung axis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39347930", + "title": "Gram-Negative Colonization and Bacterial Translocation Drive Neonatal Sepsis in the Indian Setting.", + "year": 2024, + "journal": "Journal of epidemiology and global health", + "authors": [ + "Iqbal F", + "Barche A", + "Shenoy PA", + "Lewis LES", + "Purkayastha J", + "Vandana KE" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.26248711522154206, + "mesh_terms": [ + "Humans", + "Infant, Newborn", + "India", + "Neonatal Sepsis", + "Gastrointestinal Microbiome", + "Prospective Studies", + "Female", + "Male", + "Bacterial Translocation", + "Gram-Negative Bacteria", + "Intensive Care Units, Neonatal", + "Feces", + "Infant, Premature", + "Gram-Negative Bacterial Infections" + ], + "raw_abstract": "BACKGROUND: The gut microbiota, comprising billions of microorganisms, plays a pivotal role in health and disease. This study aims to investigate the effect of sepsis on gut microbiome of neonates admitted to the Neonatal Intensive Care Unit. METHODS: A prospective cohort study was carried out in the NICU of tertiary care hospital in Karnataka, India, from January 2021 to September 2023. Preterm neonates with birth weight\u2009<\u20091500\u00a0g and gestational age\u2009<\u200937 weeks were recruited, excluding those with congenital gastrointestinal anomalies, necrotizing enterocolitis, or blood culture-negative infections. The study population was divided into three groups: healthy neonates (Group A), neonates with drug-sensitive GNB sepsis (Group B), and neonates with pan drug-resistant GNB sepsis (Group C). Stool samples were collected aseptically, snapped in liquid nitrogen, and stored at -80\u2070C for extraction of DNA and microbiome analysis. RESULTS: The gut microbiota of healthy neonates (Group A) was dominated by Proteobacteria (24.04%), Actinobacteria (27.13%), Firmicutes (12.74%), and Bacteroidetes (3%). Predominant genera included Bifidobacterium (55.17%), Enterobacter (12.55%), Enterococcus (50.69%), Streptococcus (7.92%), and Bacteroides (3.58%).Groups B and C, the microbiota exhibited higher Proteobacteria abundance (57.16% and 66.58%, respectively) and reduced diversity of beneficial bacteria. Notably, the presence of sepsis was associated with an increase in pathogenic bacteria and a decrease in beneficial commensal bacteria. CONCLUSION: Neonates with sepsis exhibited significant gut microbiome dysbiosis, characterized by increased Proteobacteria and reduced beneficial bacteria diversity. These findings highlight the potential of microbiome profiling as a diagnostic tool and underscore the importance of gut microbiota modulation in managing neonatal sepsis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33125401", + "title": "Baseline gut microbiome composition predicts metformin therapy short-term efficacy in newly diagnosed type 2 diabetes patients.", + "year": 2020, + "journal": "PloS one", + "authors": [ + "Elbere I", + "Silamikelis I", + "Dindune II", + "Kalnina I", + "Ustinova M", + "Zaharenko L", + "Silamikele L", + "Rovite V", + "Gudra D", + "Konrade I", + "Sokolovska J", + "Pirags V", + "Klovins J" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.262289789308794, + "mesh_terms": [ + "Adult", + "Bacteroidetes", + "Diabetes Mellitus, Type 2", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Lactococcus lactis", + "Longitudinal Studies", + "Male", + "Metformin", + "Microbiota", + "Prevotella", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The study was conducted to investigate the effects of metformin treatment on the human gut microbiome's taxonomic and functional profile in the Latvian population, and to evaluate the correlation of these changes with therapeutic efficacy and tolerance. METHODS: In this longitudinal observational study, stool samples for shotgun metagenomic sequencing-based analysis were collected in two cohorts. The first cohort included 35 healthy nondiabetic individuals (metformin dose 2x850mg/day) at three time-points during metformin administration. The second cohort was composed of 50 newly-diagnosed type 2 diabetes patients (metformin dose-determined by an endocrinologist) at two concordant times. Patients were defined as Responders if their HbA1c levels during three months of metformin therapy had decreased by \u226512.6 mmol/mol (1%), while in Non-responders HbA1c were decreased by <12.6 mmol/mol (1%). RESULTS: Metformin reduced the alpha diversity of microbiota in healthy controls (p = 0.02) but not in T2D patients. At the species level, reduction in the abundance of Clostridium bartlettii and Barnesiella intestinihominis, as well as an increase in the abundance of Parabacteroides distasonis and Oscillibacter unclassified overlapped between both study groups. A large number of group-specific changes in taxonomic and functional profiles was observed. We identified an increased abundance of Prevotella copri (FDR = 0.01) in the Non-Responders subgroup, and enrichment of Enterococcus faecium, Lactococcus lactis, Odoribacter, and Dialister at baseline in the Responders group. Various taxonomic units were associated with the observed incidence of side effects in both cohorts. CONCLUSIONS: Metformin effects are different in T2D patients and healthy individuals. Therapy induced changes in the composition of gut microbiome revealed possible mediators of observed short-term therapeutic effects. The baseline composition of the gut microbiome may influence metformin therapy efficacy and tolerance in T2D patients and could be used as a powerful prediction tool.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38431763", + "title": "Clostridium butyricum MIYAIRI 588 contributes to the maintenance of intestinal microbiota diversity early after haematopoietic cell transplantation.", + "year": 2024, + "journal": "Bone marrow transplantation", + "authors": [ + "Fukushima K", + "Kudo H", + "Oka K", + "Hayashi A", + "Onizuka M", + "Kusakabe S", + "Hino A", + "Takahashi M", + "Takeda K", + "Mori M", + "Ando K", + "Hosen N" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.26189356209688924, + "mesh_terms": [ + "Humans", + "Hematopoietic Stem Cell Transplantation", + "Gastrointestinal Microbiome", + "Clostridium butyricum", + "Male", + "Female", + "Middle Aged", + "Adult", + "Retrospective Studies", + "Graft vs Host Disease", + "Aged" + ], + "raw_abstract": "In patients undergoing haematopoietic stem-cell transplantation (HSCT), the intestinal microbiota plays an important role in prognosis, transplant outcome, and complications such as graft-versus-host disease (GVHD). Our prior research revealed that patients undergoing HSCT substantially differed from healthy controls. In this retrospective study, we showed that administering Clostridium butyricum MIYAIRI 588 (CBM588) as a live biotherapeutic agent is associated with maintaining intestinal microbiota in the early post-HSCT period. Alpha diversity, which reflects species richness, declined considerably in patients who did not receive CBM588, whereas it remained consistent in those who received CBM588. In addition, \u03b2-diversity analysis revealed that CBM588 did not alter the gut microbiota structure at 7-21 days post-HSCT. Patients who developed GVHD showed structural changes in their microbiota from the pre-transplant period, which was noticeable on day 14 before developing GVHD. Enterococcus was significantly prevalent in patients with GVHD after HSCT, and the population of Bacteroides was maintained from the pre-HSCT period through to the post-HSCT period. Patients who received CBM588 exhibited a contrasting trend, with lower relative abundances of both genera Enterococcus and Bacteroides. These results suggest that preoperative treatment with CBM588 could potentially be beneficial in maintaining intestinal microbiota balance.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35678794", + "title": "Bifidobacteria Was Decreased in Adult Patients With Irritable Bowel Syndrome Based on PCR and Bacterial Culture: A Systematic Review and Meta-Analysis.", + "year": 2022, + "journal": "The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology", + "authors": [ + "Bu Z", + "Ye X", + "Huang B", + "Liu R", + "Peng L" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.26050258130537957, + "mesh_terms": [ + "Adult", + "Bifidobacterium", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Irritable Bowel Syndrome", + "Polymerase Chain Reaction" + ], + "raw_abstract": "The causes of irritable bowel syndrome remain unknown. Studies and meta-analyses revealed that intestinal microbiota disturbance was one of the causes of irritable bowel syndrome, but the results remained controversial. Therefore, we performed a systematic review and meta-analysis to identify the association between them. We performed a systematic meta-analysis of case-control studies from January 2000 to December 2020 to compare fecal microbes based on polymerase chain reaction and bacterial cul- ture between adult irritable bowel syndrome patients and healthy controls. The standardized mean difference value and a 95% CI were calculated. Two professional researchers used Newcastle-Ottawa Scale to reassess selected literature and extract high- quality studies. Six studies were included in our analysis. When all eligible studies were pooled into the meta-analysis, compared with healthy controls, the standardized mean differences of Bifidobacteria (standardized mean difference = -1.01, 95% CI =: -2.01 to -0.01) in irritable bowel syndrome patients decreased significantly, whereas the standardized mean differences of Enterococcus, Enterobacter, Lactobacillus, Bacteroides, and Escherichia coli did not change significantly in irritable bowel syndrome patients. However, heterogeneity was significant to perform sensitivity analysis and stratified analysis in all these special intestinal microbes. In summary, this study indicated that only Bifidobacteria was decreased in irritable bowel syndrome patients compared with healthy controls using Newcastle-Ottawa Scale standards to extract high-quality literature. Future studies are warranted to further dem- onstrate the relationship between them.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38519184", + "title": "Food additives impair gut microbiota from healthy individuals and IBD patients in a colonic in vitro fermentation model.", + "year": 2024, + "journal": "Food research international (Ottawa, Ont.)", + "authors": [ + "Gonza I", + "Goya-Jorge E", + "Douny C", + "Boutaleb S", + "Taminiau B", + "Daube G", + "Scippo ML", + "Louis E", + "Delcenserie V" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.25686453169917933, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Fermentation", + "Food Additives", + "Ecosystem", + "Polysorbates", + "Inflammatory Bowel Diseases", + "Fibrosis", + "Inflammation" + ], + "raw_abstract": "Intestinal fibrosis is a long-term complication of inflammatory bowel diseases (IBD). Changes in microbial populations have been linked with the onset of fibrosis and some food additives are known to promote intestinal inflammation facilitating fibrosis induction. In this study, we investigated how polysorbate 80, sucralose, titanium dioxide, sodium nitrite and maltodextrin affect the gut microbiota and the metabolic activity in healthy and IBD donors (patients in remission and with a flare of IBD). The Simulator of the Human Intestinal Microbial Ecosystem (SHIME\u00ae) with a static (batch) configuration was used to evaluate the effects of food additives on the human intestinal microbiota. Polysorbate 80 and sucralose decreased butyrate-producing bacteria such as Roseburia and Faecalibacterium prausnitzii. Both compounds, also increased bacterial species positively correlated with intestinal inflammation and fibrosis (i.e.: Enterococcus, Veillonella and Mucispirillum schaedleri), especially in donors in remission of IBD. Additionally, polysorbate 80 induced a lower activity of the aryl hydrocarbon receptor (AhR) in the three groups of donors, which can affect the intestinal homeostasis. Maltodextrin, despite increasing short-chain fatty acids production, promoted the growth of Ruminococcus genus, correlated with higher risk of fibrosis, and decreased Oscillospira which is negatively associated with fibrosis. Our findings unveil crucial insights into the potential deleterious effects of polysorbate 80, sucralose and maltodextrin on human gut microbiota in healthy and, to a greater extent, in IBD patients.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36581858", + "title": "Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health.", + "year": 2022, + "journal": "Microbiome", + "authors": [ + "Huang Y", + "Lu W", + "Zeng M", + "Hu X", + "Su Z", + "Liu Y", + "Liu Z", + "Yuan J", + "Li L", + "Zhang X", + "Huang L", + "Hu W", + "Wang X", + "Li S", + "Zhang H" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.24910851564205164, + "mesh_terms": [ + "Infant, Newborn", + "Humans", + "Gastrointestinal Microbiome", + "Multiomics", + "Inflammation", + "Bacteria", + "Heart Defects, Congenital", + "Dysbiosis" + ], + "raw_abstract": "BACKGROUND: The early life gut microbiome is crucial in maintaining host metabolic and immune homeostasis. Though neonates with critical congenital heart disease (CCHD) are at substantial risks of malnutrition and immune imbalance, the microbial links to CCHD pathophysiology remain poorly understood. In this study, we aimed to investigate the gut microbiome in neonates with CCHD in association with metabolomic traits. Moreover, we explored the clinical implications of the host-microbe interactions in CCHD. METHODS: Deep metagenomic sequencing and metabolomic profiling of paired fecal samples from 45 neonates with CCHD and 50 healthy controls were performed. The characteristics of gut microbiome were investigated in three dimensions (microbial abundance, functionality, and genetic variation). An in-depth analysis of gut virome was conducted to elucidate the ecological interaction between gut viral and bacterial communities. Correlations between multilevel microbial features and fecal metabolites were determined using integrated association analysis. Finally, we conducted a subgroup analysis to examine whether the interactions between gut microbiota and metabolites could mediate inflammatory responses and poor surgical prognosis. RESULTS: Gut microbiota dysbiosis was observed in neonates with CCHD, characterized by the depletion of Bifidobacterium and overgrowth of Enterococcus, which was highly correlated with metabolomic perturbations. Genetic variations of Bifidobacterium and Enterococcus orchestrate the metabolomic perturbations in CCHD. A temperate core virome represented by Siphoviridae was identified to be implicated in shaping the gut bacterial composition by modifying microbial adaptation. The overgrowth of Enterococcus was correlated with systemic inflammation and poor surgical prognosis in subgroup analysis. Mediation analysis indicated that the overgrowth of Enterococcus could mediate gut barrier impairment and inflammatory responses in CCHD. CONCLUSIONS: We demonstrate for the first time that an aberrant gut microbiome associated with metabolomic perturbations is implicated in immune imbalance and adverse clinical outcomes in neonates with CCHD. Our data support the importance of reconstituting optimal gut microbiome in maintaining host metabolic and immunological homeostasis in CCHD. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36978107", + "title": "Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis.", + "year": 2023, + "journal": "Critical care (London, England)", + "authors": [ + "Sun S", + "Wang D", + "Dong D", + "Xu L", + "Xie M", + "Wang Y", + "Ni T", + "Jiang W", + "Zhu X", + "Ning N", + "Sun Q", + "Zhao S", + "Li M", + "Chen P", + "Yu M", + "Li J", + "Chen E", + "Zhao B", + "Peng Y", + "Mao E" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.24770414502568683, + "mesh_terms": [ + "Animals", + "Rats", + "Gastrointestinal Microbiome", + "Metabolome", + "Metabolomics", + "Microbiota", + "Sepsis", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: The gut microbiome plays a pivotal role in the progression of sepsis. However, the specific mechanism of gut microbiota and its metabolites involved in the process of sepsis remains elusive, which limits its translational application. METHOD: In this study, we used a combination of the microbiome and untargeted metabolomics to analyze stool samples from patients with sepsis enrolled at admission, then microbiota, metabolites, and potential signaling pathways that might play important roles in disease outcome were screened out. Finally, the above results were validated by the microbiome and transcriptomics analysis in an animal model of sepsis. RESULTS: Patients with sepsis showed destruction of symbiotic flora and elevated abundance of Enterococcus, which were validated in animal experiments. Additionally, patients with a high burden of Bacteroides, especially B. vulgatus, had higher Acute Physiology and Chronic Health Evaluation II scores and longer stays in the intensive care unit. The intestinal transcriptome in CLP rats illustrated that Enterococcus and Bacteroides had divergent profiles of correlation with differentially expressed genes, indicating distinctly different roles for these bacteria in sepsis. Furthermore, patients with sepsis exhibited disturbances in gut amino acid metabolism compared with healthy controls; namely, tryptophan metabolism was tightly related to an altered microbiota and the severity of sepsis. CONCLUSION: Alterations in microbial and metabolic features in the gut corresponded with the progression of sepsis. Our findings may help to predict the clinical outcome of patients in the early stage of sepsis and provide a translational basis for exploring new therapies.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33871395", + "title": "Fecal microbiota profile in patients with inflammatory bowel disease in Taiwan.", + "year": 2021, + "journal": "Journal of the Chinese Medical Association : JCMA", + "authors": [ + "Chang TE", + "Luo JC", + "Yang UC", + "Huang YH", + "Hou MC", + "Lee FY" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.24559223002049818, + "mesh_terms": [ + "Adult", + "Cross-Sectional Studies", + "Feces", + "Female", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Microbiota", + "Middle Aged", + "Taiwan" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with complicated interaction between immune, gut microbiota, and environmental factors in a genetically vulnerable host. Dysbiosis is often seen in patients with IBD. We aimed to investigate the fecal microbiota in patients with IBD and compared them with a control group in Taiwan. METHODS: In this cross-sectional study, we investigated fecal microbiota in 20 patients with IBD and 48 healthy controls. Fecal samples from both IBD patients and controls were analyzed by the next-generation sequencing method and relevant software. RESULTS: The IBD group showed lower bacterial richness and diversity compared with the control group. The principal coordinate analysis also revealed the significant structural differences between the IBD group and the control group. These findings were consistent whether the analysis was based on an operational taxonomic unit or amplicon sequence variant. However, no significant difference was found when comparing the composition of fecal microbiota between ulcerative colitis (UC) and Crohn's disease (CD). Further analysis showed that Lactobacillus, Enterococcus, and Bifidobacterium were dominant in the IBD group, whereas Faecalibacterium and Subdoligranulum were dominant in the control group at the genus level. When comparing UC, CD, and control group, Lactobacillus, Bifidobacterium, and Enterococcus were identified as dominant genera in the UC group. Fusobacterium and Escherichia_Shigella were dominant in the CD group. CONCLUSION: Compared with the healthy control, the IBD group showed dysbiosis with a significant decrease in both richness and diversity of gut microbiota.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34931007", + "title": "Commercial microbiota test revealed differences in the composition of intestinal microorganisms between children with autism spectrum disorders and neurotypical peers.", + "year": 2021, + "journal": "Scientific reports", + "authors": [ + "Jendraszak M", + "Ga\u0142\u0119cka M", + "Kotwicka M", + "Regdos A", + "Pazgrat-Patan M", + "Andrusiewicz M" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.24403676947746217, + "mesh_terms": [ + "Akkermansia", + "Autism Spectrum Disorder", + "Bacteroides", + "Body Mass Index", + "Child", + "Child, Preschool", + "Enterococcus", + "Escherichia coli", + "Faecalibacterium", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Hypersensitivity", + "Inflammation", + "Intestines", + "Klebsiella", + "Male", + "Microbiology", + "Microbiota", + "Principal Component Analysis", + "Probiotics" + ], + "raw_abstract": "The early-life modifications of intestinal microbiota may impact children's subsequent emotional and cognitive development. Studies show that some bacteria species in gut microbiota, and the lack of others, may play a key role in autism spectrum disorders (ASD) development. Fecal samples were obtained from three groups of children: 16 healthy, 24 with allergies (ALG), and 33 with ASD (probiotics and non-probiotics users). The analysis was carried out according to the KyberKompakt Pro protocol. We observed a significantly higher level of Klebsiella spp. in the healthy children from the non-probiotics group, considering three groups. In the same group, Bifidobacterium spp. the level was lower in ASD compared to neurotypical individuals. In healthy children who did not use probiotics, strong positive correlations were observed in E. coli and Enterococcus spp. and Bacteroides and Klebsiella spp., and a negative correlation for Akkermansia muciniphila with both Klebsiella spp. and Bacteroides spp. In the ASD group who take probiotics, a strongly negative correlation was observed in Lactobacillus spp., and both Faecalibacterium prausnitzii and Akkermansia muciniphila levels. In the ALG group, the strongest, negative correlation was found between Enterococcus spp. and Lactobacillus spp. as in Akkermansia muciniphila and Bifidobacterium spp. The simple commercial test revealed minor differences in the composition of intestinal microorganisms between children with autism spectrum disorders and neurotypical peers.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39588509", + "title": "Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation.", + "year": 2024, + "journal": "Frontiers in cellular and infection microbiology", + "authors": [ + "Zhang A", + "Chen S", + "Zhu Y", + "Wu M", + "Lu B", + "Zhou X", + "Zhu Y", + "Xu X", + "Liu H", + "Zhu F", + "Lin R" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.24201715561760903, + "mesh_terms": [ + "Humans", + "Constipation", + "Gastrointestinal Microbiome", + "Renal Dialysis", + "Feces", + "Male", + "RNA, Ribosomal, 16S", + "Middle Aged", + "Female", + "Bacteria", + "Aged", + "Adult" + ], + "raw_abstract": "BACKGROUND: Constipation is a common symptom in maintenance hemodialysis patients and greatly affects the quality of survival of hemodialysis patients. Fecal microbiota transplantation and probiotics are feasible treatments for functional constipation, but there is still a gap in the research on the characteristics of gut flora in patients with maintenance hemodialysis combined with constipation. The aim of this study is to clarify the characteristics of the intestinal flora and its changes in maintenance hemodialysis patients with constipation. METHODS: Fecal samples were collected from 45 participants, containing 15 in the maintenance hemodialysis constipation group,15 in the maintenance hemodialysis non-constipation group and 15 in the healthy control group. These samples were analyzed using 16S rRNA gene sequencing. The feature of the intestinal microbiome of maintenance hemodialysis constipation group and the microbiome differences among the three groups were elucidated by species annotation analysis, \u03b1-diversity analysis, \u03b2-diversity analysis, species difference analysis, and predictive functional analysis. RESULTS: The alpha diversity analysis indicated that maintenance hemodialysis constipation group was less diverse and homogeneous than maintenance hemodialysis non-constipation group and healthy control group. At the genus level, the top ten dominant genera in maintenance hemodialysis constipation group patients were Enterococcus, Escherichia-Shigella, Bacteroides, Streptococcus, Bifidobacterium, Ruminococcus_gnavus_group, Lachnospiraceae_unclassified, Faecalibacterium, Akkermansia and UCG-002. Compared with non-constipation group, the Enterococcus, Rhizobiales_unclassified, Filomicrobium, Eggerthella, Allobaculum, Prevotella_7, Gordonibacter, Mitochondria_unclassified, Lachnoanaerobaculum were significantly higher in constipation group (p<0.05). Compared with non-constipation group, the Kineothrix, Rhodopirellula, Weissella were significantly lower in constipation group (p<0.05). The predictive functional analysis revealed that compared with non-constipation group, constipation group was significantly enriched in pathways associated with pyruate metabolism, flavonoid biosynthesis. CONCLUSIONS: This study describes for the first time the intestinal microbiome characteristics of maintenance hemodialysis patients with constipation. The results of this study suggest that there is a difference in the intestinal flora between maintenance hemodialysis patients with constipation and maintenance hemodialysis patients without constipation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35025938", + "title": "Respiratory tract infections and gut microbiome modifications: A systematic review.", + "year": 2022, + "journal": "PloS one", + "authors": [ + "Woodall CA", + "McGeoch LJ", + "Hay AD", + "Hammond A" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2418498479928903, + "mesh_terms": [ + "Animals", + "Bacteria", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Respiratory Tract Infections" + ], + "raw_abstract": "Respiratory tract infections (RTIs) are extremely common and can cause gastrointestinal tract symptoms and changes to the gut microbiota, yet these effects are poorly understood. We conducted a systematic review to evaluate the reported evidence of gut microbiome alterations in patients with a RTI compared to healthy controls (PROSPERO: CRD42019138853). We systematically searched Medline, Embase, Web of Science, Cochrane and the Clinical Trial Database for studies published between January 2015 and June 2021. Studies were eligible for inclusion if they were human cohorts describing the gut microbiome in patients with an RTI compared to healthy controls and the infection was caused by a viral or bacterial pathogen. Dual data screening and extraction with narrative synthesis was performed. We identified 1,593 articles and assessed 11 full texts for inclusion. Included studies (some nested) reported gut microbiome changes in the context of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (n = 5), influenza (H1N1 and H7N9) (n = 2), Tuberculosis (TB) (n = 4), Community-Acquired Pneumonia CAP (n = 2) and recurrent RTIs (rRTI) (n = 1) infections. We found studies of patients with an RTI compared to controls reported a decrease in gut microbiome diversity (Shannon) of 1.45 units (95% CI, 0.15-2.50 [p, <0.0001]) and a lower abundance of taxa (p, 0.0086). Meta-analysis of the Shannon value showed considerable heterogeneity between studies (I2, 94.42). Unbiased analysis displayed as a funnel plot revealed a depletion of Lachnospiraceae, Ruminococcaceae and Ruminococcus and enrichment of Enterococcus. There was an important absence in the lack of cohort studies reporting gut microbiome changes and high heterogeneity between studies may be explained by variations in microbiome methods and confounder effects. Further human cohort studies are needed to understand RTI-induced gut microbiome changes to better understand interplay between microbes and respiratory health.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33077095", + "title": "Antimicrobial-Resistant Enterococcus faecium and Enterococcus faecalis Isolated From Healthy Thoroughbred Racehorses in Japan.", + "year": 2020, + "journal": "Journal of equine veterinary science", + "authors": [ + "Sukmawinata E", + "Sato W", + "Uemura R", + "Kanda T", + "Kusano K", + "Kambayashi Y", + "Sato T", + "Ishikawa Y", + "Toya R", + "Sueyoshi M" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.24090237768829956, + "mesh_terms": [ + "Animals", + "Anti-Bacterial Agents", + "Anti-Infective Agents", + "Enterococcus faecalis", + "Enterococcus faecium", + "Horses", + "Japan" + ], + "raw_abstract": "In this study, the occurrence of antimicrobial-resistant (AMR) enterococci was evaluated in Thoroughbred (TB) racehorses in Japan. Fecal samples were collected from 212 healthy TB racehorses at the Miho and Ritto Training Centers of the Japan Racing Association from March 2017 to August 2018. Isolation and identification were performed by enterococcus selective medium and confirmed to the species using MALDI-TOF MS. Enterococcus faecium and E.\u00a0faecalis isolates were subjected to antimicrobial susceptibility test against 11 antimicrobials by minimum inhibitory concentration based on recommendation from Clinical and Laboratory Standards Institute guidelines. Among 583 enterococcus isolates, E.\u00a0faecium and E.\u00a0faecalis were identified for 48.2% (281/583) and 7.4% (43/583), respectively. One isolate that was representing E.\u00a0faecium (153 isolates) and E.\u00a0faecalis (31 isolates) from each sample was selected for antimicrobial susceptibility test. The highest rate of resistance for E.\u00a0faecium isolates was observed against enrofloxacin (57.5%; 88/153), followed by streptomycin (32.0%; 49/153), kanamycin (18.3%; 28/153), gentamycin (5.9%; 9/153), erythromycin (5.9%; 9/153), and oxytetracycline (4.6%; 7/153). For E.\u00a0faecium isolates, the highest resistance was observed against streptomycin (90.3%; 28/31), followed by kanamycin (41.9%; 13/31), gentamycin (29.0%; 9/31), lincomycin (9.7%; 3/31), oxytetracycline (6.5%; 2/31), erythromycin (6.5%; 2/31), tylosin (6.5%; 2/31), enrofloxacin (6.5%; 2/31), and chloramphenicol (3.2%; 1/31). The results indicated that enrofloxacin and aminoglycosides were highly resistant among tested antimicrobials. Continuous monitoring studies are useful to increase the awareness of the potential for AMR bacteria to arise from imprudent use of antimicrobials in TB racehorses in Japan.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27976593", + "title": "Antimicrobial resistance in Enterococcus strains isolated from healthy domestic dogs.", + "year": 2017, + "journal": "Acta microbiologica et immunologica Hungarica", + "authors": [ + "Bertelloni F", + "Salvadori C", + "Lotti G", + "Cerri D", + "Ebani VV" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.24047625846537835, + "mesh_terms": [ + "Animals", + "Anti-Bacterial Agents", + "Dogs", + "Drug Resistance, Bacterial", + "Enterococcus", + "Feces", + "Microbial Sensitivity Tests" + ], + "raw_abstract": "Enterococci are opportunistic bacteria that cause severe infections in animals and humans, capable to acquire, express, and transfer antimicrobial resistance. Susceptibility to 21 antimicrobial agents was tested by the disk diffusion method in 222 Enterococcus spp. strains isolated from the fecal samples of 287 healthy domestic dogs. Vancomycin and ampicillin minimum inhibitory concentrations (MICs) and high-level aminoglycoside resistance (HLAR) tests were also performed. Isolates showed resistance mainly to streptomycin (88.7%), neomycin (80.6%), and tetracycline (69.4%). Forty-two (18.9%) isolates showed an HLAR to streptomycin and 15 (6.7%) to gentamicin. Vancomycin and ampicillin MIC values showed 1 and 18 resistant strains, respectively. One hundred and thirty-six (61.2%) strains were classified as multidrug resistant and six (2.7%) strains as possibly extensively drug-resistant bacteria. Enterococcus faecium and Enterococcus faecalis were the most prevalent antimicrobial resistant species. Companion animals, which often live in close contact with their owners and share the same environment, represent a serious source of enterococci resistant to several antibiotics; for this reason, they may be a hazard for public health by providing a conduit for the entrance of resistance genes into the community.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26400889", + "title": "Prebiotic properties of potato starch dextrins.", + "year": 2015, + "journal": "Postepy higieny i medycyny doswiadczalnej (Online)", + "authors": [ + "Barczy\u0144ska R", + "\u015ali\u017cewska K", + "Libudzisz Z", + "Kapu\u015bniak K", + "Kapu\u015bniak J" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.23790130146976857, + "mesh_terms": [ + "Dextrins", + "Dietary Fiber", + "Feces", + "Gastrointestinal Microbiome", + "Intestines", + "Prebiotics", + "Solanum tuberosum" + ], + "raw_abstract": "The objective of the present study was to compare the prebiotic properties of starch dextrins, that is, resistant dextrins obtained from potato starch in the process of simultaneous thermolysis and chemical modification, which were selected based on previous research. Both prepared dextrins met the definition criterion of dietary fiber and also the basic prebiotic criterion - they were not degraded by the digestive enzymes of the initial sections of the gastrointestinal tract. The growth of probiotic lactobacilli and bifidobacteria, as well as Escherichia coli, Enterococcus, Bacteroides, and Clostridium strains isolated from feces of healthy people, showed that both studied dextrins were utilized as a source of assimilable carbon and energy by the strains. Furthermore, better growth (higher numbers of cells) counts of probiotic bacteria than those of fecal isolates indicated that the studied resistant dextrins showed a selective effect. Both dextrins might be considered as substances with prebiotic properties due to their chemical and physical properties and selectivity towards the studied probiotic bacterial strains.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "25918444", + "title": "The human gut resistome.", + "year": 2015, + "journal": "Philosophical transactions of the Royal Society of London. Series B, Biological sciences", + "authors": [ + "van Schaik W" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.23456983340693963, + "mesh_terms": [ + "Disease Reservoirs", + "Drug Resistance, Microbial", + "Gastrointestinal Microbiome", + "Gene Transfer, Horizontal", + "Genes, Bacterial", + "Humans", + "Metagenomics" + ], + "raw_abstract": "In recent decades, the emergence and spread of antibiotic resistance among bacterial pathogens has become a major threat to public health. Bacteria can acquire antibiotic resistance genes by the mobilization and transfer of resistance genes from a donor strain. The human gut contains a densely populated microbial ecosystem, termed the gut microbiota, which offers ample opportunities for the horizontal transfer of genetic material, including antibiotic resistance genes. Recent technological advances allow microbiota-wide studies into the diversity and dynamics of the antibiotic resistance genes that are harboured by the gut microbiota ('the gut resistome'). Genes conferring resistance to antibiotics are ubiquitously present among the gut microbiota of humans and most resistance genes are harboured by strictly anaerobic gut commensals. The horizontal transfer of genetic material, including antibiotic resistance genes, through conjugation and transduction is a frequent event in the gut microbiota, but mostly involves non-pathogenic gut commensals as these dominate the microbiota of healthy individuals. Resistance gene transfer from commensals to gut-dwelling opportunistic pathogens appears to be a relatively rare event but may contribute to the emergence of multi-drug resistant strains, as is illustrated by the vancomycin resistance determinants that are shared by anaerobic gut commensals and the nosocomial pathogen Enterococcus faecium.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39897957", + "title": "A systematic review on gut microbiota in type 2 diabetes mellitus.", + "year": 2024, + "journal": "Frontiers in endocrinology", + "authors": [ + "Chong S", + "Lin M", + "Chong D", + "Jensen S", + "Lau NS" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.23351276071024285, + "mesh_terms": [ + "Diabetes Mellitus, Type 2", + "Humans", + "Gastrointestinal Microbiome", + "Dysbiosis" + ], + "raw_abstract": "AIMS/HYPOTHESIS: The gut microbiota play crucial roles in the digestion and degradation of nutrients, synthesis of biological agents, development of the immune system, and maintenance of gastrointestinal integrity. Gut dysbiosis is thought to be associated with type 2 diabetes mellitus (T2DM), one of the world's fastest growing diseases. The aim of this systematic review is to identify differences in the composition and diversity of the gut microbiota in individuals with T2DM. METHODS: A systematic search was conducted to identify studies reporting on the difference in gut microbiota composition between individuals with T2DM and healthy controls. Relevant studies were evaluated, and their characteristics and results were extracted using a standardized data extraction form. The studies were assessed for risk of bias and their findings were reported narratively. RESULTS: 58 observational studies published between 2010 and 2024 were included. Beta diversity was commonly reported to be different between individuals with T2DM and healthy individuals. Genera Lactobacillus, Escherichia-Shigella, Enterococcus, Subdoligranulum and Fusobacteria were found to be positively associated; while Akkermansia, Bifidobacterium, Bacteroides, Roseburia, Faecalibacteirum and Prevotella were found to be negatively associated with T2DM. CONCLUSIONS: This systematic review demonstrates a strong association between T2DM and gut dysbiosis, as evidenced by differential microbial abundances and altered diversity indices. Among these taxa, SYSTEMATIC REVIEW REGISTRATION: https://www.crd.york.ac.uk/prospero/, identifier CRD42023459937.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39761011", + "title": "Association of gut microbiota and gut metabolites and adverse outcomes in biliary atresia: A longitudinal prospective study.", + "year": 2024, + "journal": "Hepatology communications", + "authors": [ + "Jain V", + "Dalby MJ", + "Alexander EC", + "Burford C", + "Acford-Palmer H", + "Serghiou IR", + "Teng NMY", + "Kiu R", + "Gerasimidis K", + "Zafeiropoulou K", + "Logan M", + "Verma A", + "Davenport M", + "Hall LJ", + "Dhawan A" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.23302779255835773, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Biliary Atresia", + "Feces", + "Male", + "Female", + "Prospective Studies", + "Infant", + "Longitudinal Studies", + "Portoenterostomy, Hepatic", + "RNA, Ribosomal, 16S", + "Enterococcus", + "Case-Control Studies", + "Infant, Newborn", + "Bifidobacterium" + ], + "raw_abstract": "BACKGROUND: The Kasai portoenterostomy (KPE) aims to re-establish bile flow in biliary atresia (BA); however, BA remains the commonest indication for liver transplantation in pediatrics. Gut microbiota-host interplay is increasingly associated with outcomes in chronic liver disease. This study characterized fecal microbiota and fatty acid metabolites in BA. METHODS: Fecal samples were prospectively collected in newly diagnosed BA infants (n = 55) before and after KPE. Age-matched healthy control (n = 19) and cholestatic control (n = 21) fecal samples were collected. Fecal 16S rRNA gene amplicon sequencing for gut microbiota and gas chromatography for fecal fatty acids was performed. RESULTS: Increased abundance of Enterococcus in pre-KPE BA and cholestatic control infants, compared to healthy infants, was demonstrated. At the early post-KPE time points, increased alpha diversity was revealed in BA versus healthy cohorts. A lower relative abundance of Bifidobacterium and increased Enterococcus, Clostridium, Fusobacterium, and Pseudomonas was seen in infants with BA. Fecal acetate was reduced, and fecal butyrate and propionate were elevated in early post-KPE BA infants. Higher post-KPE alpha diversity was associated with nonfavorable clinical outcomes (6-month jaundice and liver transplantation). A higher relative abundance of post-KPE Streptococcus and Fusobacterium and a lower relative abundance of Dorea, Blautia, and Oscillospira were associated with nonfavorable clinical outcomes. Blautia inversely correlated to liver disease severity, and Bifidobacterium inversely correlated to fibrosis biomarkers. Bifidobacterium abundance was significantly lower in infants experiencing cholangitis within 6 months after KPE. CONCLUSIONS: Increased diversity, enrichment of pathogenic, and depletion of beneficial microbiota early post-KPE are all factors associated with nonfavorable BA outcomes. Manipulation of gut microbiota in the early postsurgical period could provide therapeutic potential.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35716285", + "title": "Dissemination of Quinupristin-Dalfopristin and Linezolid resistance genes among hospital environmental and healthy volunteer fecal isolates of Enterococcus faecalis and Enterococcus faecium.", + "year": 2022, + "journal": "Molecular biology reports", + "authors": [ + "Boodaghi Malidareh E", + "Ahanjan M", + "Asgharzadeh Marghmalek S", + "Goli HR" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2312407073455741, + "mesh_terms": [ + "Agar", + "Anti-Bacterial Agents", + "Drug Resistance, Bacterial", + "Enterococcus", + "Enterococcus faecalis", + "Enterococcus faecium", + "Healthy Volunteers", + "Hospitals", + "Humans", + "Linezolid", + "Microbial Sensitivity Tests", + "Virginiamycin" + ], + "raw_abstract": "BACKGROUND: Streptogramins and linezolid are important in the treatment of infections caused by vancomycin-resistant enterococci. PURPOSE: Then, we aimed to evaluate the resistance rates against these drugs and the prevalence of genes involved in hospital environmental and fecal normal-flora isolates of Enterococcus faecalis and Enterococcus faecium. METHODS AND RESULTS: The strains were isolated from the stool samples and hospital environments by culturing on M-Enterococcus (ME) agar, and identified by phenotypic and genotypic microbiological tests. The disk agar diffusion method was used to identify the antimicrobial susceptibility pattern of the isolates. The genomic DNA extraction was done by the alkaline lysis method, and the PCR test was used to detect the resistance genes. A total of 145 enterococci isolates were taken, from which 84 (57.9%) isolates were detected as E. faecalis and 61 (42.06%) isolates were E. faecium. Moreover, 70 (83.33), 4 (4.76%), 1 (1.19%), and 40 (47.61%) isolates of E. faecalis and 20 (32.78%), 1 (1.63%), 4 (6.55%), and 26 (42.62%) E. faecium isolates were resistant against quinupristin-dalfopristin, linezolid, vancomycin, and erythromycin, respectively. Also, 112 (77.24%), 50 (34.48%), 39 (26.89%), 27 (18.62%), 19 (13.1%), 4 (2.75%), and 1 (0.68%) isolates were contained LsaA, vatD, vgbB, vatE, cfr, lsaE and optrA genes, respectively. None of the isolates carried the vgbA gene. CONCLUSIONS: High-level streptogramin resistance rate and high prevalence of resistance genes in enterococci isolated from the stool of healthy persons and the hospital environment indicates the importance of possible transmission of resistance genes from these isolates to clinical ones.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31295581", + "title": "Faecal carriage of high-level aminoglycoside-resistant and ampicillin-resistant Enterococcus species in healthy Iranian children.", + "year": 2020, + "journal": "Journal of global antimicrobial resistance", + "authors": [ + "Jannati E", + "Amirmozaffari N", + "Saadatmand S", + "Arzanlou M" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.22999153690175553, + "mesh_terms": [ + "Adolescent", + "Aminoglycosides", + "Ampicillin", + "Anti-Bacterial Agents", + "Carrier State", + "Drug Resistance, Bacterial", + "Enterococcus", + "Enterococcus faecalis", + "Enterococcus faecium", + "Feces", + "Female", + "Healthy Volunteers", + "Humans", + "Iran", + "Male", + "Microbial Sensitivity Tests", + "Sex Characteristics", + "Virulence Factors" + ], + "raw_abstract": "OBJECTIVES: High-level aminoglycoside, ampicillin and vancomycin resistance and virulence genes among enterococcal isolates collected from healthy middle-school children in Ardabil, Iran, during 2016 were investigated. METHODS: Totally, 305 faecal specimens were collected. Isolates underwent antimicrobial susceptibility testing, virulence gene detection and molecular typing. RESULTS: Totally, 409 enterococcal isolates were collected, comprising Enterococcus faecium (235; 57.5%), Enterococcus faecalis (56; 13.7%) and other Enterococcus spp. (118; 28.9%). Overall, 71 (17.4%), 11 (2.7%) and 10 (2.4%) isolates were identified as high-level streptomycin-resistant (HLSR), high-level gentamicin-resistant (HLGR) and ampicillin-resistant (AR), respectively. Among HLSR isolates, 40 (56.3%), 5 (7.0%) and 26 (36.6%) were E. faecium, E. faecalis and other Enterococcus spp., respectively. Among HLGR isolates 4 (36.4%) and 7 (63.6%) and among AR isolates 7 (70.0%) and 3 (30.0%) were E. faecium and other Enterococcus spp., respectively. Accordingly, 21.6%, 3.6% and 3.3% of subjects were colonised with HLSR, HLGR and AR Enterococcus spp. Carriage of HLGR, HLSR and AR isolates was associated with prior antibiotic consumption (P\u22640.05). Additionally, male sex and antacid consumption were associated with AR enterococcal carriage. Moreover, 69 (97.2%), 10 (90.9%) and 9 (90.0%) of HLSR, HLGR and AR isolates were multidrug-resistant, respectively. No vancomycin-resistant enterococci were detected. ERIC-PCR revealed high genetic diversity among isolates. gelE and asa1 were major virulence genes both in E. faecalis and E. faecium. Presence of gelE was associated with HLSR and HLGR phenotypes (P\u22640.05). CONCLUSION: Community intestinal carriage of HLSR enterococci was high; however, carriage of HLGR and AR enterococci was low.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34311015", + "title": "Comparative analysis of fecal microbiota composition diversity in Tibetan piglets suffering from diarrheagenic Escherichia coli (DEC).", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Qi M", + "Cao Z", + "Shang P", + "Zhang H", + "Hussain R", + "Mehmood K", + "Chang Z", + "Wu Q", + "Dong H" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.22934203246983903, + "mesh_terms": [ + "Animals", + "Escherichia coli", + "Feces", + "Microbiota", + "RNA, Ribosomal, 16S", + "Swine", + "Tibet" + ], + "raw_abstract": "This study was ascertained to investigate the adverse effects of pathogenic E. coli on gut microbiota of Tibetan piglets with history of yellow and white dysentery. For this purpose, a total of 18 fecal samples were collected from infected and healthy Tibetan piglets for 16S rRNA gene amplification and sequencing of V3-V4 region. Results showed that Firmicutes, Bacteroidia Fusobacteriota, Proteobacteria and Actinobacteriota were the predominant bacteria in Tibetan piglets at the level of phylum classification. Results on classification at family level showed that Lactobacillus, Bacteroidota, Fusobacteriota and Enterobacteriaceae were the dominant bacteria. Results on classification of bacteria at phylum level compared with normal piglets indicated that Bacteroidota, Actinobacteriota, Euryarchaota and Spirochaetota in fecal microbial community in Tibetan piglets showing yellow dysenteric and diarrhea group were significantly decreased (P\u00a0\u2264\u00a00.05). Compared with the feces of healthy Tibetan piglets, the abundance of Escherichia-Shigella, Lactobacillus and Enterococcus increased significantly in feces of Tibetan piglets having yellow dysentery and white dysentery. Moreover, results exhibited that the Proteobacteria and Fusobacteriota were significantly increased (P\u00a0\u2264\u00a00.05) suggesting dominant microbial community. Results revealed that E. coli induced different pathological alterations in intestine including damage to intestinal epithelial cells, infiltration of inflammatory cells, presence of red blood cells in spaces of tissues, hemorrhages and necrosis of intestinal villi in piglets with history of yellow dysentery. This study for the first time reported the composition, characteristics, and differences of the fecal microflora diversity of Tibetan piglets with yellow and white dysentery in Qinghai-Tibet Plateau, which can provide a suitable support for effective control of diarrhoeal disease in these animals.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37676050", + "title": "Identification of microbial markers associated with lung cancer based on multi-cohort 16\u2009s rRNA analyses: A systematic review and meta-analysis.", + "year": 2023, + "journal": "Cancer medicine", + "authors": [ + "Han W", + "Wang N", + "Han M", + "Liu X", + "Sun T", + "Xu J" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.22869791204529194, + "mesh_terms": [ + "Humans", + "Lung Neoplasms", + "Gastrointestinal Microbiome", + "Microbiota", + "Databases, Factual", + "Biomarkers" + ], + "raw_abstract": "BACKGROUND: The relationship between commensal microbiota and lung cancer (LC) has been studied extensively. However, developing replicable microbiological markers for early LC diagnosis across multiple populations has remained challenging. Current studies are limited to a single region, single LC subtype, and small sample size. Therefore, we aimed to perform the first large-scale meta-analysis for identifying micro biomarkers for LC screening by integrating gut and respiratory samples from multiple studies and building a machine-learning classifier. METHODS: In total, 712 gut and 393 respiratory samples were assessed via 16\u2009s rRNA amplicon sequencing. After identifying the taxa of differential biomarkers, we established random forest models to distinguish between LC populations and normal controls. We validated the robustness and specificity of the model using external cohorts. Moreover, we also used the KEGG database for the predictive analysis of colony-related functions. RESULTS: The \u03b1 and \u03b2 diversity indices indicated that LC patients' gut microbiota (GM) and lung microbiota (LM) differed significantly from those of the healthy population. Linear discriminant analysis (LDA) of effect size (LEfSe) helped us identify the top-ranked biomarkers, Enterococcus, Lactobacillus, and Escherichia, in two microbial niches. The area under the curve values of the diagnostic model for the two sites were 0.81 and 0.90, respectively. KEGG enrichment analysis also revealed significant differences in microbiota-associated functions between cancer-affected and healthy individuals that were primarily associated with metabolic disturbances. CONCLUSIONS: GM and LM profiles were significantly altered in LC patients, compared to healthy individuals. We identified the taxa of biomarkers at the two loci and constructed accurate diagnostic models. This study demonstrates the effectiveness of LC-specific microbiological markers in multiple populations and contributes to the early diagnosis and screening of LC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35889029", + "title": "Profile of the Gut Microbiome Containing Carbapenem-Resistant Enterobacteriaceae in ICU Patients.", + "year": 2022, + "journal": "Microorganisms", + "authors": [ + "Sindi AA", + "Alsayed SM", + "Abushoshah I", + "Bokhary DH", + "Tashkandy NR" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.22591425641222077, + "mesh_terms": [], + "raw_abstract": "Carbapenem-resistant Enterobacteriaceae (CRE) is a risk to public health worldwide and causes epidemic outbreaks in hospitals. The identification of alterations in the gut microbial profile can potentially serve as an early diagnostic tool to prevent harmful bacterial colonization. The purpose of this study was to characterize the gut microbiota profile of CRE-positive stool samples using 16S rRNA gene sequencing and to compare it with that of healthy control groups at King AbdulAziz University Hospital. Our results demonstrate that compared to the control group samples, the CRE-positive and CRE-negative group samples were less diverse and were dominated by a few operational taxonomic clusters of Enterococcus, Sphingomonas, and Staphylococcus. An analysis of samples from CRE-positive patients revealed Pseudomonas as the most abundant taxon. The existence of Pseudomonas in clinical samples undoubtedly indicates the development of resistance to a variety of antimicrobial drugs, with a less diverse microbiota. In our study, we found that the co-occurrence patterns of Klebsiella, Parabacteroides, Proteus and Pseudomonas differed between the CRE-negative and control stool groups.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28786749", + "title": "Specificities of the intestinal microbiota in patients with inflammatory bowel disease and Clostridium difficile infection.", + "year": 2018, + "journal": "Gut microbes", + "authors": [ + "Sokol H", + "Jegou S", + "McQuitty C", + "Straub M", + "Leducq V", + "Landman C", + "Kirchgesner J", + "Le Gall G", + "Bourrier A", + "Nion-Larmurier I", + "Cosnes J", + "Seksik P", + "Richard ML", + "Beaugerie L" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.22558777628858215, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biodiversity", + "Clostridium Infections", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestines", + "Male", + "Middle Aged", + "Species Specificity", + "Young Adult" + ], + "raw_abstract": "Clostridium difficile infection (CDI) is a common complication in inflammatory bowel disease (IBD) and has been associated with poor IBD outcome. Intestinal microbiota composition in IBD patients with CDI has not been specifically evaluated to date. The fecal microbiota of 56 IBD patients, including 8 in flare with concomitant CDI, 24 in flare without CDI, and 24 in remission, as well as 24 healthy subjects, was studied using 16S sequencing. Analysis was performed using the Qiime pipeline. Compared to IBD patients without CDI, IBD patients with CDI had more pronounced dysbiosis with higher levels of Ruminococcus gnavus and Enterococcus operational taxonomic units (OTUs) and lower levels of Blautia and Dorea OTUs. Correlation network analysis suggested a disrupted ecosystem in IBD patients in flare, particularly in those with CDI. In patients with IBD, CDI is associated with a more pronounced intestinal dysbiosis with specific alterations in intestinal microorganisms.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39859243", + "title": "A Systematic Review of Microbiota in Cirrhosis: A Change Towards a More Pathogenic Predisposition.", + "year": 2025, + "journal": "International journal of molecular sciences", + "authors": [ + "Xirouchakis E", + "Pelekanos A", + "Xirouchakis S", + "Kranidioti H", + "Manolakopoulos S" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.22539887946067608, + "mesh_terms": [ + "Humans", + "Liver Cirrhosis", + "Gastrointestinal Microbiome", + "Dysbiosis", + "Bacteria", + "Hepatic Encephalopathy", + "Liver Neoplasms", + "Disease Susceptibility", + "Carcinoma, Hepatocellular" + ], + "raw_abstract": "The microbiome of the human intestine is a regulator of health that modulates immune response and plays an important role in metabolism. The diversity, and abundance of microbiota communities in the gut have been shown to change in cirrhosis and its complications. We aimed to review the current knowledge regarding microbiota alterations in cirrhosis, its potential differences according to etiology, and its role in the development of cirrhosis complications. A systematic search of the online bibliographic database up to July 2024 was performed. Randomized controlled trials and observational and cohort studies that included a total or at least a cohort of cirrhotic adult patients were enlisted for data extraction and analysis. A total of 73 publications were included for data extraction. Alpha diversity was found to decrease in cirrhotic patients in 30/38 (78%) of the studies, while beta diversity in 20/22 (90%) presented significant differences between healthy and cirrhotic groups. Proteobacteria significantly increased in 20/27 (74%) studies, followed by Actinobacteria and Fusobacteria, while 22/25 (88%) studies found either a reduction in cirrhotic patients or increased abundance in healthy controls for Firmicutes and Bacteroidetes. The most abundant genera in hepatic encephalopathy groups were pathobionts such as Enterococcus and Streptococcus, followed by Vellionella and Escherichia. Heterogeneity was found among studies regarding Alpha diversity in hepatocellular carcinoma (HCC) as it was decreased in three studies, indifferent in five, and increased in three studies in comparison to cirrhotic non-HCC patients. The dysbiosis of the gut microbiota is associated with cirrhosis and the development of complications such as hepatic encephalopathy and hepatocellular carcinoma.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32296918", + "title": "Characterization of Gut Microbiota in Hospitalized Patients with Clostridioides difficile Infection.", + "year": 2020, + "journal": "Current microbiology", + "authors": [ + "Vakili B", + "Fateh A", + "Asadzadeh Aghdaei H", + "Sotoodehnejadnematalahi F", + "Siadat SD" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2245054083834818, + "mesh_terms": [ + "Adolescent", + "Adult", + "Bacteria", + "Butyrates", + "Case-Control Studies", + "Clostridioides difficile", + "Clostridium Infections", + "Diarrhea", + "Economic Status", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Hospitalization", + "Humans", + "Iran", + "Lactic Acid", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "Clostridioides difficile infection (CDI) is one of the most common causes of nosocomial diarrhea in developed countries and the main cause in healthcare settings. This case-control study was designed to evaluate the composition of the gut microbiota dominant bacterial groups in patients with CDI compared to the healthy control subjects. A total of 100 adult subjects involving 50 inpatients with CDI and 50 healthy persons were enrolled in the study. C. difficile isolates were characterized according to the anaerobic culture and presence of toxin genes with multiplex PCR. An ecological analysis was performed real-time quantitative PCR for bacterial elements. The abundances of Enterococcus spp., Lactobacillus spp., Escherichia coli, C. difficile, and Akkermansia muciniphila were higher in group CDI compared with group HC (P\u2009<\u20090.05). The abundances of Bacteroides spp., Bifidobacterium spp., and Faecalibacterium prausnitzii were lower in group CDI than in group HC (P\u2009<\u20090.05). No significant difference was observed in the copy number of Prevotella genus between the CDI and HC subjects (P-value\u2009=\u20090.087). We observed that economic status and income levels were reduced at patients with CDI, however, there was no significant difference between CDI and HC group results and other variables, such as age, BMI, and educational level. These findings showed a reduction in butyrate-producing bacteria and increase in lactic acid-producing bacteria was seen in CDI status. Overrepresentation of Akkermansia may be a predictive marker for the development of nosocomial diarrhea can result in a worse CDI prognosis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27300149", + "title": "Alterations of gut microbiota in patients with irritable bowel syndrome: A systematic review and meta-analysis.", + "year": 2017, + "journal": "Journal of gastroenterology and hepatology", + "authors": [ + "Zhuang X", + "Xiong L", + "Li L", + "Li M", + "Chen M" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2168135780254471, + "mesh_terms": [ + "Bacterial Load", + "Bifidobacterium", + "Case-Control Studies", + "Databases, Bibliographic", + "Enterobacter", + "Escherichia coli", + "Gastrointestinal Microbiome", + "Humans", + "Irritable Bowel Syndrome", + "Lactobacillus" + ], + "raw_abstract": "BACKGROUND AND AIMS: Alterations of gut microbiota were assumed to be the etiology and pathogenesis of irritable bowel syndrome (IBS) in some studies. However, alterations of gut microbiota in IBS patients had not been systematically assessed with a meta-analysis. We performed a mate-analysis to explore and compare the alterations of gut microbiota in IBS patients from China and other regions around the world. METHODS: Case-control studies detecting gut microbiota in IBS patients were identified through English and Chinese databases. The standardized mean difference (SMD) with 95% confidence interval (CI) of bacterial counts was calculated. RESULTS: Ten studies from China and seven studies from other regions around the world were included in our study. As compared with healthy controls, the SMDs of Bifidobacteria, Lactobacillus, Escherichia Coli, and Enterobacter in Chinese IBS patients were -1.42 (CI: -2.10, -0.75), -0.91 (95% CI: -1.31, -0.52), 0.83 (95% CI: 0.26, 1.40), and 0.57 (95% CI: 0.33, 0.82), respectively. But the SMDs of Bacteroides and Enterococcus were found no significant differences in Chinese IBS patients. However, the SMDs of Bifidobacteria and Bacteroides in IBS patients from other regions were -0.76 (CI: -1.43, -0.09) and 1.17 (CI: 0.00, 2.35), while the SMDs of Lactobacillus, E. Coli, Enterobacter, and Enterococcus were found no significant differences. CONCLUSIONS: There were alterations of gut microbiota in IBS patients, and it implied that alterations of gut microbiota might be involved in the pathogenesis of IBS. However, the species-specific alterations of gut microbiota were different between IBS patients from China and other regions.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35634439", + "title": "Correlation between Intestinal Microflora in Irritable Bowel Syndrome and Severity.", + "year": 2022, + "journal": "Disease markers", + "authors": [ + "Ji M", + "Huang H", + "Lan X" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.21362236399701626, + "mesh_terms": [ + "Bifidobacterium", + "Biomarkers", + "Gastrointestinal Microbiome", + "Humans", + "Irritable Bowel Syndrome", + "Lactic Acid", + "Lactobacillus" + ], + "raw_abstract": "BACKGROUND: Irritable bowel syndrome (IBS) is a common chronic functional gastrointestinal disease accompanied by changes in intestinal microecology. This study investigated the relationship between gut microbiota and disease severity in patients with irritable bowel syndrome (IBS). METHODS: An observational study was performed on 60 IBS patients (study group) and 20 healthy controls admitted to our hospital from January 2013 to December 2014. Fecal samples were taken after admission to measure intestinal flora including Bifidobacterium, Lactobacillus, Enterobacter, and Enterococcus, and patient blood was collected to determine serum D-lactate and diamine oxidase (DAO) levels. The gut microbiota and serum markers of the two groups were analyzed. The correlation of gut microbiota index levels and serum markers with disease severity, as well as the correlation between gut microbiota index levels and serum markers, were analyzed. RESULTS: The levels of intestinal CONCLUSION: Intestinal flora, D-lactate, and DAO were abnormal in IBS patients, and intestinal flora was closely correlated with disease severity, D-lactate, and DAO levels.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29411528", + "title": "Alterations in the gut microbiota of patients with acquired immune deficiency syndrome.", + "year": 2018, + "journal": "Journal of cellular and molecular medicine", + "authors": [ + "Zhou Y", + "Ou Z", + "Tang X", + "Zhou Y", + "Xu H", + "Wang X", + "Li K", + "He J", + "Du Y", + "Wang H", + "Chen Y", + "Nie Y" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2130130329631479, + "mesh_terms": [ + "Acquired Immunodeficiency Syndrome", + "Adult", + "Antiretroviral Therapy, Highly Active", + "China", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "HIV", + "HIV Infections", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Acquired immune deficiency syndrome (AIDS), caused by infection with human immunodeficiency virus (HIV), is associated with gastrointestinal disease, systemic immune activation and changes in the gut microbiota. Here, we aim to investigate the gut microbiota patterns of HIV-infected individuals and HIV-uninfected individuals in populations from South China. We enrolled 33 patients with HIV (14 participants treated with highly active antiretroviral therapy [HAART] for more than 3 months; the remaining 19 individuals had not received treatment) and 35 healthy controls (HC) for a cross-sectional comparison of gut microbiota using stool samples. Gut microbial communities were profiled by sequencing the bacterial 16S rRNA genes. Dysbiosis was more common among patients with AIDS compared with healthy individuals. Dysbiosis was characterized by decreased \u03b1-diversity, low mean counts of Bacteroidetes, Faecalibacterium, Prevotella, Bacteroides vulgatus, Dialister and Roseburia inulnivorans, and high mean counts of Proteobacteria, Enterococcus, Streptococcus, Lactobacillus, Lachnociostridium, Ruminococcus gnavus and Streptococcus vestibularis. Increased abundance of Bacilli was observed in homosexual patients. Proteobacteria were higher among heterosexual patients with HIV infections. Tenericutes were higher among patients with history of intravenous drug abuse. Restoration of gut microbiota diversity and a significant increase in abundance of Faecalibacterium, Blautia and Bacteroides were found in patients receiving HAART compared to those who did not receive. HIV infection-associated dysbiosis is characterized by decreased levels of \u03b1-diversity and Bacteroidetes, increased levels of Proteobacteria and the alterations of gut microbiota correlate with the route of HIV transmission. The imbalanced faecal microbiota of HIV infection is partially restored after therapy.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26727418", + "title": "Characterization of bacterial isolates from the microbiota of mothers' breast milk and their infants.", + "year": 2015, + "journal": "Gut microbes", + "authors": [ + "Kozak K", + "Charbonneau D", + "Sanozky-Dawes R", + "Klaenhammer T" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.21209424798139243, + "mesh_terms": [ + "Bacteria", + "Bacterial Adhesion", + "Bacteriocins", + "Bifidobacterium", + "Caco-2 Cells", + "Feces", + "Female", + "Gastrointestinal Tract", + "Humans", + "Infant", + "Lactobacillus", + "Microbial Sensitivity Tests", + "Microbiota", + "Milk, Human", + "Mothers", + "Probiotics" + ], + "raw_abstract": "This investigation assessed the potential of isolating novel probiotics from mothers and their infants. A subset of 21 isolates among 126 unique bacteria from breast milk and infant stools from 15 mother-infant pairs were examined for simulated GI transit survival, adherence to Caco-2 cells, bacteriocin production, and lack of antibiotic resistance. Of the 21 selected isolates a Lactobacillus crispatus isolate and 3 Lactobacillus gasseri isolates demonstrated good profiles of in vitro GI transit tolerance and Caco-2 cell adherence. Bacteriocin production was observed only by L. gasseri and Enterococcus faecalis isolates. Antibiotic resistance was widespread, although not universal, among isolates from infants. Highly similar isolates (\u2265 97% similarity by barcode match) of Bifidobacterium longum subsp. infantis (1 match), Lactobacillus fermentum (2 matches), Lactobacillus gasseri (6 matches), and Enterococcus faecalis (1 match) were isolated from 5 infant-mother pairs. Antibiotic resistance profiles between these isolate matches were similar, except in one case where the L. gasseri isolate from the infant exhibited resistance to erythromycin and tetracycline, not observed in matching mother isolate. In a second case, L. gasseri isolates differed in resistance to ampicillin, chloramphenicol and vancomycin between the mother and infant. In this study, gram positive bacteria isolated from mothers' breast milk as well as their infants exhibited diversity in GI transit survival and acid inhibition of pathogens, but demonstrated limited ability to produce bacteriocins. Mothers and their infants offer the potential for identification of probiotics; however, even in the early stages of development, healthy infants contain isolates with antibiotic resistance.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30427066", + "title": "The gut microbiota of hand, foot and mouth disease patients demonstrates down-regulated butyrate-producing bacteria and up-regulated inflammation-inducing bacteria.", + "year": 2019, + "journal": "Acta paediatrica (Oslo, Norway : 1992)", + "authors": [ + "Li W", + "Zhu Y", + "Li Y", + "Shu M", + "Wen Y", + "Gao X", + "Wan C" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.21196392460987412, + "mesh_terms": [ + "Bacteria", + "Butyrates", + "Child, Preschool", + "Cross-Sectional Studies", + "Down-Regulation", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Hand, Foot and Mouth Disease", + "Humans", + "Inflammation", + "Male", + "Up-Regulation" + ], + "raw_abstract": "AIM: This study explored the gut microbiota of children with hand, foot and mouth disease (HFMD). METHODS: We enrolled 15 cases with HFMD admitted to the West China Second Hospital, Sichuan University, China, from July to September 2016 at a median age of three years. The controls were 15 healthy children of a similar age who underwent routine health examinations at the hospital during the same period. Gut microbiota was analysed using high throughput 16S ribosomal deoxyribonucleic acid\u00a0sequencing. RESULTS: The gut microbiota in the HFMD patients was distinct from the controls. Compared with the controls, the composition of gut microbiota in the HFMD cases represented a reduction of two butyrate-producing bacteria, Ruminococcus (0.73\u00a0\u00b1\u00a01.28 versus 7.78\u00a0\u00b1\u00a020.01, p\u00a0=\u00a00.026) and Roseburia (0.67\u00a0\u00b1\u00a01.69 versus 1.61\u00a0\u00b1\u00a03.27, p\u00a0=\u00a00.024) and an up-regulation of Escherichia (5.26\u00a0\u00b1\u00a010.50 versus 1.59\u00a0\u00b1\u00a05.90,p\u00a0<\u00a00.01) and Enterococcus (4.12\u00a0\u00b1\u00a012.49 versus 0.12\u00a0\u00b1\u00a00.41, p\u00a0=\u00a00.015). CONCLUSION: The dysbiosis of gut microbiota of the HFMD cases included a reduction of butyrate-producing bacteria and an up-regulation of inflammation-inducing bacteria. These may have impaired the intestinal biological mucosal barrier and host immune functions, promoting the invasion of the enterovirus.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29194468", + "title": "Characteristics of Faecal Microbiota in Paediatric Crohn's Disease and Their Dynamic Changes During Infliximab Therapy.", + "year": 2018, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Wang Y", + "Gao X", + "Ghozlane A", + "Hu H", + "Li X", + "Xiao Y", + "Li D", + "Yu G", + "Zhang T" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.21057632259001555, + "mesh_terms": [ + "Adolescent", + "Bacteroidetes", + "Burkholderiales", + "Case-Control Studies", + "Child", + "Child, Preschool", + "Clostridiales", + "Crohn Disease", + "Dysbiosis", + "Enterococcus", + "Faecalibacterium", + "Fatty Acids, Volatile", + "Feces", + "Female", + "Gastrointestinal Agents", + "Gastrointestinal Microbiome", + "Humans", + "Infliximab", + "Male", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Crohn's disease [CD] is known to be associated with gut microbial dysbiosis. Infliximab [IFX] is increasingly used to treat paediatric CD; however, it is not clear how the gut microbiota is modified during IFX treatment. The aim of this study was to characterise the faecal microbiota community composition in paediatric CD patients and to assess its dynamic changes during IFX therapy. METHODS: A 16S rRNA sequencing approach was applied to determine the compositions of microbial communities in faecal samples. The composition and function of the faecal microbiota were compared between CD patients and healthy controls. RESULTS: Characteristics of faecal microbiome composition in paediatric CD patients before IFX treatment were represented by a lower biodiversity, a gain in Enterococcus, and a significant loss in multiple short-chain fatty acid [SCFA]-producing bacteria, including Anaerostipes, Blautia, Coprococcus, Faecalibacterium, Lachnospira, Odoribacter, Roseburia, Ruminococcus, and Sutterella. Additionally, alterations were observed in metabolic functions of the gut microbial community in CD. IFX treatment increased the biodiversity of gut microbiota and shifted its composition as well as its functional capabilities in the paediatric CD patients toward a healthy status. However, multiple SCFA-producing taxa were not significantly expanded. The sustained response of paediatric CD patients to IFX was associated with abundance of SCFA-producing bacteria. CONCLUSIONS: A lower biodiversity with alterations in the composition and function of faecal microbial community, characterising gut microbial dysbiosis, was observed in Chinese paediatric CD patients. IFX diminished the CD-associated gut microbial dysbiosis but was deficient in increasing certain SCFA-producing taxa.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36677307", + "title": "Gluten Degradation by the Gut Microbiota of Ulcerative Colitis Patients.", + "year": 2022, + "journal": "Microorganisms", + "authors": [ + "Harringer EOS", + "Durack J", + "Piceno Y", + "Andersen V", + "Lynch SV" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.20955122925881114, + "mesh_terms": [], + "raw_abstract": "Several studies have reported improved disease symptomatology in ulcerative colitis (UC) patients consuming a gluten free diet. This observation coupled with diversity depletion in the gut microbiota of UC patients led us to hypothesize that UC-associated enteric microbes differentially metabolize dietary gluten to produce immunogenic products that promote inflammation. Gluten concentration in stool was determined using gluten-specific ELISA, and gluten intake was assessed by food frequency questionnaire (FFQ) in UC (n = 12) and healthy controls (HC; n = 13). Gluten-metabolizing bacteria were isolated on minimal media supplemented with 1% gluten from UC and HC and identified by 16S rRNA profiling. Cell-free culture media from gluten metabolizing gut bacterial isolates was assessed for immunogenicity in vitro using HT29 colonocytes. Compared to HC, UC patients did not consume gluten differently (Mann\u2212Whitney; p > 0.10) and exhibited equivalent levels of gluten in their feces (Mann\u2212Whitney; p = 0.163). The profile of gluten-degrading bacteria isolated from UC stool was distinct (Chi-square; p \u2264 0.0001). Compared with Enterococcus isolates, products of gluten degradation by Bacillus strains induced higher IL8 and lower occludin (Mann\u2212Whitney; p = 0.002 and p = 0.059, respectively) gene expression in colonocytes irrespective of whether they originated from UC or healthy gut. Members of HC and UC microbiota exhibit gluten-degrading ability, metabolites of which influence genes involved in inflammation and barrier function in enteric colonocyte cultures. Preliminary findings of this study warrant further investigations into the mechanisms by which gut microbiota contribute to UC pathogenesis through gluten degradation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39300177", + "title": "Unraveling the role of gut microbiota by fecal microbiota transplantation in rat model of kidney stone disease.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Hunthai S", + "Usawachintachit M", + "Taweevisit M", + "Srisa-Art M", + "Anegkamol W", + "Tosukhowong P", + "Rattanachaisit P", + "Chuaypen N", + "Dissayabutra T" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.20842372142854773, + "mesh_terms": [ + "Animals", + "Gastrointestinal Microbiome", + "Fecal Microbiota Transplantation", + "Kidney Calculi", + "Humans", + "Rats", + "Male", + "Rats, Wistar", + "Dysbiosis", + "Disease Models, Animal", + "Feces", + "Female", + "Adult", + "Middle Aged" + ], + "raw_abstract": "Emerging research on the microbiome highlights the significant role of gut health in the development of kidney stones, indicating that an imbalance in gut bacteria or dysbiosis can influence the formation of stones by altering oxalate metabolism and urinary metabolite profiles. In particular, the overabundance of specific bacteria such as Enterococcus and Oxalobacter spp., which are known to affect oxalate absorption, is observed in patients with urolithiasis. This study investigates the effects of gut dysbiosis on urolithiasis through fecal microbiota transplantation (FMT) from patients to rats and its impact on urinary mineral excretion and stone formation. Fecal samples from eight patients with calcium oxalate stones and ten healthy volunteers were collected to assess the gut microbiome. These samples were then transplanted to antibiotic-pretreated Wistar rats for a duration of four weeks. After transplantation, we evaluated changes in the fecal gut microbiome profile, urinary mineral excretion rates, and expression levels of intestinal zonula occluden-1 (ZO-1), SLC26A6 and renal NF-\u03baB. In humans, patients with urolithiasis exhibited increased urinary calcium and oxalate levels, along with decreased citrate excretion and increased urinary supersaturation index. The fecal microbiota showed a notable abundance of Bacteroidota. In rodents, urolithiasis-FMT rats showed urinary disturbances similar to patients, including elevated pH, oxalate level, and supersaturation index, despite negative renal pathology. In addition, a slight elevation in the expression of renal NF-\u03baB, a significant intestinal SLC26A6, and a reduction in ZO-1 expression were observed. The gut microbiome of urolithiasis-FMT rats showed an increased abundance of Bacteroidota, particularly Muribaculaceae, compared to their healthy FMT counterparts. In conclusion, the consistent overabundance of Bacteroidota in both urolithiasis patients and urolithiasis-FMT rats is related to altered intestinal barrier function, hyperoxaluria, and renal inflammation. These findings suggest that gut dysbiosis, characterized by an overgrowth of Bacteroidota, plays a crucial role in the pathogenesis of calcium oxalate urolithiasis, underscoring the potential of targeting the gut microbiota as a therapeutic strategy.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35622224", + "title": "Dynamic colonization of gut microbiota and its influencing factors among the breast-feeding infants during the first two years of life.", + "year": 2022, + "journal": "Journal of microbiology (Seoul, Korea)", + "authors": [ + "Li P", + "Chang X", + "Chen X", + "Tang T", + "Liu Y", + "Shang Y", + "Qi K" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.2041901168485065, + "mesh_terms": [ + "Adult", + "Bacteria", + "Bifidobacterium", + "Breast Feeding", + "Feces", + "Female", + "Firmicutes", + "Gastrointestinal Microbiome", + "Humans", + "Infant", + "Infant, Newborn", + "Pregnancy", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "The maturation of infant gut microbiota has lifelong implications on health, which has been proposed as the major events during the first year of life. However, little is known about their dynamic colonization and influencing elements among the first two-year infancy as well as into the adulthood. So based on the 16S rRNA sequencing data among 30 healthy breast-feeding mother-infant pairs with normal ranges of growth and development indicators from birth to two years old, the dynamic colonization of gut microbiota and its influencing factors were discussed using this birth cohort. Among these, we identified that the diversity of gut microbiota was significantly increased from six-month to two-year subgroups. The significantly dynamic trends of gut microbiota at the phylum (genus) level were that the percents of Firmicutes (Faecalibacterium, Blautia, Enterococcus, Subdoligranulum, Agathobacter, unidentified_Erysipelotrichaceae, Staphylococcus, unidentified_Ruminococcaceae, and Fusicatenibacter), Bacteroidetes and Verrucomicrobia were increased, while Actinobacteria (Bifidobacterium) and Proteobacteria (unidentified-Enterobacteriaceae and Klebsiella) were decreased with the increased ages from six months to two years old, which might simultaneously modulate the host pathways, such as the higher percents of chemoheterotrophy and fermentation, and lower percentages of nitrate_reduction, aerobic_chemoheterotrophy and so on. Furthermore, there were significant associations between maternal (milk microbiota, pre-pregnancy BMI, BMI increment during the pregnancy)/infant characteristics (BMI at birth and BMI gain), and the compositions of gut microbiota. However, no differences of gut microbiota were shown between the different sex and productive mode subgroups. Overall, the colonization of gut microbiota is significantly matured into the adulthood with the increased ages to two-years old and regulated by the above maternal/infant characteristics, which will provide a new direction for the host-gut microbiota interplay during the first two years of life.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37099394", + "title": "The role of Klebsiella populations in preterm infants.", + "year": 2023, + "journal": "Biochemical Society transactions", + "authors": [ + "McCartney AL", + "Hoyles L" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.20373269201307392, + "mesh_terms": [ + "Infant", + "Infant, Newborn", + "Humans", + "Infant, Premature", + "Retrospective Studies", + "Klebsiella", + "Feces", + "Sepsis", + "Bacteria" + ], + "raw_abstract": "The preterm infant microbiota is dominated by Enterobacteriaceae (Escherichia, Klebsiella or Enterobacter spp.), Enterococcus and Staphylococcus spp. Recent work has demonstrated the development of this microbiota is predictable and driven by simple microbe-microbe interactions. Because of their systemic immaturity, including an underdeveloped immune system, preterm infants are susceptible to a range of infections. Numerous retrospective studies have examined the association of the preterm gut microbiota with diseases such as necrotizing enterocolitis (NEC), early-onset sepsis and late-onset sepsis. To date, no single bacterium has been associated with infection in these infants, but a Klebsiella/Enterococcus-dominated faecal microbiota is associated with an increased risk of developing NEC. Staphylococci aid and enterococci inhibit establishment/maintenance of gastrointestinal Klebsiella populations in preterm infants, though the mechanisms underlying these interactions are poorly understood. Klebsiella spp. recovered from healthy and sick preterm infants display similar antimicrobial resistance and virulence profiles, giving no clues as to why some infants develop potentially life-threatening diseases while others do not. The identification of cytotoxin-producing Klebsiella oxytoca sensu lato in the gut microbiota of some preterm infants has led to the suggestion that these bacteria may contribute to NEC in a subset of neonates. This mini review highlights current knowledge on Klebsiella spp. contributing to the preterm gut microbiota and provides insights into areas of research that warrant further attention.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37932698", + "title": "Safety assessment of Enterococcus lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species.", + "year": 2023, + "journal": "BMC genomics", + "authors": [ + "Ahmed NA", + "Khattab RA", + "Ragab YM", + "Hassan M" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.20187015207932932, + "mesh_terms": [ + "Humans", + "Caco-2 Cells", + "Microbial Sensitivity Tests", + "Enterococcus", + "Anti-Bacterial Agents", + "Probiotics", + "Genomics", + "Enterococcus faecium" + ], + "raw_abstract": "BACKGROUND: The gut microbiota is considered a rich source for potential novel probiotics. Enterococcus genus is a normal component of a healthy gut microbiota, suggesting its vital role. Nosocomial infections caused mainly by E. facalis and E. faecium have been attributed to the plasticity of the Enterococcus genomes. In this study, we assessed the probiotic and safety characteristics of two E. lactis strains isolated from the human gut microbiota using in-vitro and in silico approaches. Additionally, the safety of the E. lactis species was evaluated using comparative genomics analysis. RESULTS: The two E. lactis strains 10NA and 50NA showed resistance to bile salts and acid tolerance with antibacterial activity against Escherichia coli, Salmonella typhi, and Clostridioides difficile. For safety assays, the two strains did not display any type of hemolysis on blood agar, and the survival of Caco-2 cells was not significantly different (P-value\u2009>\u20090.05) compared to the control using cell free supernatants at 100% (v/v), 50% (v/v), 10% (v/v), and 5% (v/v) concentrations. Regarding antibiotic susceptibility, both strains were sensitive to vancomycin, tetracycline, and chloramphenicol. Comprehensive whole-genome analysis revealed no concerning associations between virulence or antibiotic resistance genes and any of the identified mobile genetic elements. Comparative genome analysis with closely related E. faecium species genomes revealed the distinctive genomic safety of the E. lactis species. CONCLUSIONS: Our two E. lactis strains showed promising probiotic properties in-vitro. Their genomes were devoid of any transferable antibiotic resistance genes. In silico comparative analysis confirmed the safety of the E. lactis species. These results suggest that E. lactis species could be a potential source for safer Enterococcus probiotic supplements.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29901916", + "title": "Screening of Potential Probiotic Lactic Acid Bacteria with Anticancer Properties.", + "year": 2016, + "journal": "Journal of the Medical Association of Thailand = Chotmaihet thangphaet", + "authors": [ + "Chimchang J", + "Theparee T", + "Wongein S", + "Trivirot T", + "Tanasupawa S", + "Taweechotipatr M", + "Wongsatayanon B" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.20174258372950352, + "mesh_terms": [ + "Animals", + "Anticarcinogenic Agents", + "Caco-2 Cells", + "Chlorocebus aethiops", + "Feces", + "Humans", + "Infant, Newborn", + "Lactobacillales", + "Probiotics", + "U937 Cells", + "Vero Cells" + ], + "raw_abstract": "BACKGROUND: Probiotics have shown to reduce cancer recurrence and side effects in colorectal cancer patients. OBJECTIVE: To isolate the lactic acid bacteria from Thai healthy newborn feces and screen good probiotics with anticancer properties. MATERIAL AND METHOD: Lactic acid bacteria were isolated from newborn feces and selected for the cytotoxicity property against human cancer cell lines by MTT assay and probiotics property by acid and bile tolerance tests. RESULTS: Among 200 lactic acid bacteria isolated, 3 and 1 isolates significantly demonstrated strong and moderate antiproliferative effect against Caco-2 cells, respectively. Likewise, 4 and 5 isolates showed significant strong and moderate inhibitory effect on U937 cells, respectively. Seven candidate strains did not displayed cytotoxic to normal cells (Vero), except MSMC 112-2. All candidates showed good probiotics properties in resistance to acidic condition (pH 2-4) and to 1-4% bile concentrations, except MSMC105-3 showed intolerance at 4% bile concentration. The nucleotide sequence homology showed that MSMC95-4, MSMC104-2, MSMC111-2, MSMC112-2 and MSMC215-1 strains belong to Enterococcus faecalis (99.4%, 98.8%, 99.5%, 98.7 and 98.9%, respectively), MSMC105-3 is Lactobacillus salivarius (99.1%) and MSMC171-1 is Enterococcus faecium (99.3%). CONCLUSION: The authors have isolated lactic acid bacteria which have anticancer and good probiotics properties.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33302682", + "title": "The gut microbiome can be used to predict the gastrointestinal response and efficacy of lung cancer patients undergoing chemotherapy.", + "year": 2020, + "journal": "Annals of palliative medicine", + "authors": [ + "Zhang M", + "Zhou H", + "Xu S", + "Liu D", + "Cheng Y", + "Gao B", + "Li X", + "Chen J" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.20118049857404988, + "mesh_terms": [ + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Lung Neoplasms" + ], + "raw_abstract": "BACKGROUND: Lung cancer has the highest incidence and mortality rate of any cancer worldwide. Platinum-based combination chemotherapy is still the standard treatment for advanced lung cancer. However, the clinical efficacy of this treatment can be affected by its adverse reactions, especially gastrointestinal mucositis. The adverse reactions often lead to delayed and reduced medication. The role played by gut microbiome in the treatment of cancer is becoming clearer, and evidence suggests that regulation of the gut microbiome may affect the response to multiple types of cancer treatment. METHODS: Sixty lung cancer patients who received chemotherapy for the first time and 17 healthy subjects were enrolled in this study. A metagenomic analysis of 137 fecal samples was performed using next-generation sequencing technology. RESULTS: The relative abundance of Eubacterium, Ruminococcus, and Faecalibacterium was higher in the lung cancer patients than in the healthy subjects; however, the relative abundance of Prevotella, Streptococcus, Enterococcus, and Roseburia showed the opposite result. The relative abundance of each gut microbiome changed significantly during chemotherapy. At the phylum level, the relative abundance of Firmicutes and Euryarchaeota was dramatically increased after chemotherapy. Lung cancer patients with a higher relative abundance of a particular bacterial genus, such as Prevotella, Megamonas, Streptococcus, Faecalibacterium, Roseburia, Parabacteroides, Coprococcus, Oscillibacter, Dorea, or Chlamydia, at baseline were more likely to experience gastrointestinal reactions. These results show that the intestinal flora can play a role in predicting the effect of chemotherapy in lung cancer patients. CONCLUSIONS: The gut microbiome of patients with lung cancer differs from those of healthy people. The results of this study suggest that Ruminococcus and Eubacterium may be related to the occurrence and development of lung cancer. The gut microbiome of lung cancer patients changes significantly after treatment with cytotoxic drugs, which may be associated with the gastrointestinal reaction caused by chemotherapy. The gut microbiome also can be used to predict the efficacy of chemotherapy in lung cancer patients.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39026313", + "title": "Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease.", + "year": 2024, + "journal": "Microbiome", + "authors": [ + "Tian X", + "Li S", + "Wang C", + "Zhang Y", + "Feng X", + "Yan Q", + "Guo R", + "Wu F", + "Wu C", + "Wang Y", + "Huo X", + "Ma X" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.20092758046360001, + "mesh_terms": [ + "Humans", + "Virome", + "Gastrointestinal Microbiome", + "Animals", + "Feces", + "Mice", + "Inflammatory Bowel Diseases", + "Female", + "Male", + "Adult", + "Middle Aged", + "Crohn Disease", + "Bacteriophages", + "Colitis, Ulcerative", + "Bacteria", + "China", + "Fecal Microbiota Transplantation", + "Case-Control Studies", + "Viruses" + ], + "raw_abstract": "BACKGROUND: The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS: In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella\u00a0species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS: Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27207975", + "title": "Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD.", + "year": 2016, + "journal": "Gut", + "authors": [ + "Sabino J", + "Vieira-Silva S", + "Machiels K", + "Joossens M", + "Falony G", + "Ballet V", + "Ferrante M", + "Van Assche G", + "Van der Merwe S", + "Vermeire S", + "Raes J" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.20055257882529484, + "mesh_terms": [ + "Adult", + "Aged", + "Alkaline Phosphatase", + "Biopsy", + "Cholagogues and Choleretics", + "Cholangitis, Sclerosing", + "Colonoscopy", + "Dysbiosis", + "Enterococcus", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "Severity of Illness Index", + "Statistics as Topic", + "Ursodeoxycholic Acid" + ], + "raw_abstract": "OBJECTIVE: Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease often leading to end-stage liver disease. Its pathogenesis remains largely unknown, although frequent concomitant IBD hints towards common factors underlying gut and bile duct inflammation. Considering the mounting evidence on the involvement of the intestinal microbiota in initiating and determining IBD phenotype, we investigated intestinal microbiota composition in patients with PSC. DESIGN: Stool samples were collected from 147 individuals (52 patients with PSC, 52 age, gender and body mass index-matched healthy volunteers, 13 UC and 30 patients with Crohn's disease). An independent validation cohort of 14 PSC and 14 matched controls was recruited. 16S rDNA sequencing of faecal DNA was performed (Illumina MiSeq). RESULTS: The microbiota of patients with PSC was characterised by decreased microbiota diversity, and a significant overrepresentation of Enterococcus (p=3.76e-05), Fusobacterium (p=3.76e-05) and Lactobacillus (p=0.0002) genera. This dysbiosis was present in patients with PSC with and without concomitant IBD and was distinct from IBD, and independent of treatment with ursodeoxycholic acid. A decision tree based on abundances of these three genera allowed reliable classification in the validation cohort. In particular, one operational taxonomic unit belonging to the Enterococcus genus was associated with increased levels of serum alkaline phosphatase (p=0.048), a marker of disease severity. CONCLUSIONS: We here present the first report of PSC-associated faecal dysbiosis, independent from IBD signatures, suggesting the intestinal microbiota could be a contributing factor in PSC pathogenesis. Further studies are needed to confirm these findings and assess causality.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38871760", + "title": "Study on intestinal parasitic infections and gut microbiota in cancer patients at a tertiary teaching hospital in Malaysia.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Siti Farah Norasyikeen SO", + "Ngui R", + "Syaza Zafirah AR", + "Md Zoqratt MZH", + "Eng WWH", + "Ayub Q", + "Amin Nordin S", + "Narcisse Mary Sither Joseph V", + "Musa S", + "Lim YAL" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.20049267319878203, + "mesh_terms": [ + "Humans", + "Malaysia", + "Gastrointestinal Microbiome", + "Male", + "Female", + "Middle Aged", + "Intestinal Diseases, Parasitic", + "Adult", + "Neoplasms", + "Aged", + "Feces", + "Tertiary Care Centers", + "Hospitals, Teaching", + "Prevalence", + "Cryptosporidium", + "Entamoeba", + "Microsporidia", + "Coinfection", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Intestinal parasitic infections (IPIs) can lead to significant morbidity and mortality in cancer patients. While they are unlikely to cause severe disease and are self-limiting in healthy individuals, cancer patients are especially susceptible to opportunistic parasitic infections. The gut microbiota plays a crucial role in various aspects of health, including immune regulation and metabolic processes. Parasites occupy the same environment as bacteria in the gut. Recent research suggests intestinal parasites can disrupt the normal balance of the gut microbiota. However, there is limited understanding of this co-infection dynamic among cancer patients in Malaysia. A study was conducted to determine the prevalence and relationship between intestinal parasites and gut microbiota composition in cancer patients. Stool samples from 134 cancer patients undergoing active treatment or newly diagnosed were collected and examined for the presence of intestinal parasites and gut microbiota composition. The study also involved 17 healthy individuals for comparison and control. Sequencing with 16S RNA at the V3-V4 region was used to determine the gut microbial composition between infected and non-infected cancer patients and healthy control subjects. The overall prevalence of IPIs among cancer patients was found to be 32.8%. Microsporidia spp. Accounted for the highest percentage at 20.1%, followed by Entamoeba spp. (3.7%), Cryptosporidium spp. (3.0%), Cyclospora spp. (2.2%), and Ascaris lumbricoides (0.8%). None of the health control subjects tested positive for intestinal parasites. The sequencing data analysis revealed that the gut microbiota diversity and composition were significantly different in cancer patients than in healthy controls (p\u2009<\u20090.001). A significant dissimilarity was observed in the bacterial composition between parasite-infected and non-infected patients based on Bray-Curtis (p\u2009=\u20090.041) and Jaccard (p\u2009=\u20090.021) measurements. Bacteria from the genus Enterococcus were enriched in the parasite-infected groups, while Faecalibacterium prausnitzii reduced compared to non-infected and control groups. Further analysis between different IPIs and non-infected individuals demonstrated a noteworthy variation in Entamoeba-infected (unweighted UniFrac: p\u2009=\u20090.008), Cryptosporidium-infected (Bray-Curtis: p\u2009=\u20090.034) and microsporidia-infected (unweighted: p\u2009=\u20090.026; weighted: p\u2009=\u20090.019; Jaccard: p\u2009=\u20090.031) samples. No significant dissimilarity was observed between Cyclospora-infected groups and non-infected groups. Specifically, patients infected with Cryptosporidium and Entamoeba showed increased obligate anaerobic bacteria. Clostridiales were enriched with Entamoeba infections, whereas those from Coriobacteriales decreased. Bacteroidales and Clostridium were found in higher abundance in the gut microbiota with Cryptosporidium infection, while Bacillales decreased. Additionally, bacteria from the genus Enterococcus were enriched in microsporidia-infected patients. In contrast, bacteria from the Clostridiales order, Faecalibacterium, Parabacteroides, Collinsella, Ruminococcus, and Sporosarcina decreased compared to the non-infected groups. These findings underscore the importance of understanding and managing the interactions between intestinal parasites and gut microbiota for improved outcomes in cancer patients.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35689701", + "title": "Features of the gut prokaryotic virome of Japanese patients with Crohn's disease.", + "year": 2022, + "journal": "Journal of gastroenterology", + "authors": [ + "Imai T", + "Inoue R", + "Nishida A", + "Yokota Y", + "Morishima S", + "Kawahara M", + "Kusada H", + "Tamaki H", + "Andoh A" + ], + "bacteria": "Enterococcus", + "condition": "healthy", + "relevance_score": 0.20021960081514537, + "mesh_terms": [ + "Bacteria", + "Crohn Disease", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Japan", + "RNA, Ribosomal, 16S", + "Virome" + ], + "raw_abstract": "BACKGROUND/AIMS: The gut virome is mainly composed of bacteriophages and influences gut homeostasis and pathogenic conditions. In this study, we analyzed the gut prokaryotic virome in Japanese patients with Crohn's disease (CD). MATERIALS/METHODS: We collected 19 fecal samples from CD patients and 16 samples from healthy controls. The gut bacteriome was analyzed by 16S rRNA gene sequencing and the virome was profiled by shotgun metagenomic sequencing. RESULTS: Despite no differences in richness and evenness, there was a significant difference in the overall structure of the gut virome between CD patients and controls (P\u2009=\u20090.013). CrAssphage and Staphylococcus virus, belonging to the order Caudovirales, were dominant in the gut virome of controls and CD patients. The abundance of crAssphage was significantly greater in CD patients than controls (P\u2009=\u20090.021). Lactococcus, Enterococcus and Lactobacillus phages were present only in CD patients, while Xanthomonas and Escherichia phages were unique to the controls. In the gut bacteriome of CD patients, richness and evenness were significantly lower, and a significant difference in the overall structure was observed between groups (P\u2009=\u20090.014). The gut bacteriome of CD patients was characterized by a decrease of the genera Faecalibacterium, Roseburia, and Ruminococcus and an increase of the family Enterobacteriaceae. There were more significant correlations between viruses and bacteria in CD patients than controls. CONCLUSIONS: The gut virome of CD patients was distinct from that of healthy controls in a Japanese population. An altered gut virome may be one of the factors associated with the bacterial dysbiosis of CD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32944794", + "title": "Dynamic changes of the fecal bacterial community in dairy cows during early lactation.", + "year": 2020, + "journal": "AMB Express", + "authors": [ + "Huang S", + "Ji S", + "Wang F", + "Huang J", + "Alugongo GM", + "Li S" + ], + "bacteria": "UCG-005", + "condition": "healthy", + "relevance_score": 0.28523063492645584, + "mesh_terms": [], + "raw_abstract": "The dynamics of the community structure and composition of the dairy cow fecal bacterial communities during early lactation is unclear, therefore this study was conducted to characterize the fecal bacterial communities in dairy cows during early lactation using 16S rRNA gene sequencing. Feces were sampled from 20 healthy fresh Holstein dairy cows on day 1 (Fresh1d group) and day 14 (Fresh14d group) after calving. After calving, cows were fed the same fresh diet. The dominant phyla Firmicutes and Proteobacteria were decreased (P\u2009\u2264\u20090.01) with lactating progress and phyla Bacteroidetes were increased (P\u2009=\u20090.008) with lactating progress and dietary transition. At family level, the predominant families were Ruminococcaceae (35.23%), Lachnospiraceae (11.46%), Rikenellaceae (10.44%) and Prevotellaceae (6.89%). A total of 14 genera were different between fecal samples from Fresh1d and Fresh14d, included the predominant genera, such as Ruminococcaceae_UCG-005 (P\u2009=\u20090.008), Rikenellaceae_RC9_gut_group (P\u2009=\u20090.043) and Christensenellaceae_R-7_group (P\u2009=\u20090.008). All fecal bacterial communities shared members of the genera Ruminococcaceae_UCG-005, Bacteroides and Rikenellaceae_RC9_gut_group. These findings help to improve our understanding of the composition and structure of the fecal microbial community in fresh cows and may provide insight into bacterial adaptation time and dietary in lactating cows.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32951160", + "title": "Alterations of gut microbiota composition in post-finasteride patients: a pilot study.", + "year": 2021, + "journal": "Journal of endocrinological investigation", + "authors": [ + "Borgo F", + "Macandog AD", + "Diviccaro S", + "Falvo E", + "Giatti S", + "Cavaletti G", + "Melcangi RC" + ], + "bacteria": "UCG-005", + "condition": "healthy", + "relevance_score": 0.2378025500572424, + "mesh_terms": [ + "5-alpha Reductase Inhibitors", + "Alopecia", + "Biodiversity", + "Cognitive Dysfunction", + "Correlation of Data", + "Depression", + "Drug-Related Side Effects and Adverse Reactions", + "Finasteride", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "Physical Functional Performance", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA", + "Sexual Dysfunction, Physiological" + ], + "raw_abstract": "PURPOSE: Post-finasteride syndrome (PFS) has been reported in a subset of patients treated with finasteride (an inhibitor of the enzyme 5alpha-reductase) for androgenetic alopecia. These patients showed, despite the suspension of the treatment, a variety of persistent symptoms, like sexual dysfunction and cognitive and psychological disorders, including depression. A growing body of literature highlights the relevance of the gut microbiota-brain axis in human health and disease. For instance, alterations in gut microbiota composition have been reported in patients with major depressive disorder. Therefore, we have here analyzed the gut microbiota composition in PFS patients in comparison with a healthy cohort. METHODS: Fecal microbiota of 23 PFS patients was analyzed by 16S rRNA gene sequencing and compared with that reported in ten healthy male subjects. RESULTS: Sexual dysfunction, psychological and cognitive complaints, muscular problems, and physical alterations symptoms were reported in more than half of the PFS patients at the moment of sample collection. The quality sequence check revealed a low library depth for two fecal samples. Therefore, the gut microbiota analyses were conducted on 21 patients. The \u03b1-diversity was significantly lower in PFS group, showing a reduction of richness and diversity of gut microbiota structure. Moreover, when visualizing \u03b2-diversity, a clustering effect was found in the gut microbiota of a subset of PFS subjects, which was also characterized by a reduction in Faecalibacterium spp. and Ruminococcaceae UCG-005, while Alloprevotella and Odoribacter spp were increased compared to healthy control. CONCLUSION: Gut microbiota population is altered in PFS patients, suggesting that it might represent a diagnostic marker and a possible therapeutic target for this syndrome.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34016947", + "title": "Probiotics-induced changes in gut microbial composition and its effects on cognitive performance after stress: exploratory analyses.", + "year": 2021, + "journal": "Translational psychiatry", + "authors": [ + "Bloemendaal M", + "Szopinska-Tokov J", + "Belzer C", + "Boverhoff D", + "Papalini S", + "Michels F", + "van Hemert S", + "Arias Vasquez A", + "Aarts E" + ], + "bacteria": "UCG-005", + "condition": "healthy", + "relevance_score": 0.22603393382237233, + "mesh_terms": [ + "Bacteria", + "Cognition", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Probiotics", + "Stress, Psychological", + "Young Adult" + ], + "raw_abstract": "Stress negatively affects cognitive performance. Probiotics remediate somatic and behavioral stress responses, hypothetically by acting on the gut microbiota. Here, in exploratory analyses, we assessed gut microbial alterations after 28-days supplementation of multi-strain probiotics (EcologicBarrier consisting of Lactobacilli, Lactococci, and Bifidobacteria in healthy, female subjects (probiotics group n\u2009=\u200927, placebo group n\u2009=\u200929). In an identical pre-session and post-session, subjects performed a working memory task before and after an acute stress intervention. Global gut microbial beta diversity changed over time, but we were not able to detect differences between intervention groups. At the taxonomic level, Time by Intervention interactions were not significant after multiple comparison correction; the relative abundance of eight genera in the probiotics group was higher (uncorrected) relative to the placebo group: Butyricimonas, Parabacteroides, Alistipes, Christensenellaceae_R-7_group, Family_XIII_AD3011_group, Ruminococcaceae_UCG-003, Ruminococcaceae_UCG-005, and Ruminococcaceae_UCG-010. In a second analysis step, association analyses were done only within this selection of microbial genera, revealing the probiotics-induced change in genus Ruminococcaceae_UCG-003 was significantly associated with probiotics' effect on stress-induced working memory changes (r", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35292670", + "title": "Analysis of gut microbiome profiles in common marmosets (Callithrix jacchus) in health and intestinal disease.", + "year": 2022, + "journal": "Scientific reports", + "authors": [ + "Sheh A", + "Artim SC", + "Burns MA", + "Molina-Mora JA", + "Lee MA", + "Dzink-Fox J", + "Muthupalani S", + "Fox JG" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.4128662407104758, + "mesh_terms": [ + "Animals", + "Callithrix", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Prevotella" + ], + "raw_abstract": "Chronic gastrointestinal (GI) diseases are the most common diseases in captive common marmosets. To understand the role of the microbiome in GI diseases, we characterized the gut microbiome of 91 healthy marmosets (303 samples) and 59 marmosets diagnosed with inflammatory bowel disease (IBD) (200 samples). Healthy marmosets exhibited \"humanized,\" Bacteroidetes-dominant microbiomes. After up to 2 years of standardized diet, housing and husbandry, marmoset microbiomes could be classified into four distinct marmoset sources based on Prevotella and Bacteroides levels. Using a random forest (RF) model, marmosets were classified by source with an accuracy of 93% with 100% sensitivity and 95% specificity using abundance data from 4 Prevotellaceae amplicon sequence variants (ASVs), as well as single ASVs from Coprobacter, Parabacteroides, Paraprevotella, Phascolarctobacterium, Oribacterium and Fusobacterium. A single dysbiotic IBD state was not found across all marmoset sources, but IBD was associated with lower alpha diversity and a lower Bacteroides:Prevotella copri ratio within each source. IBD was highest in a Prevotella-dominant cohort, and consistent with Prevotella-linked diseases, pro-inflammatory genes in the jejunum were upregulated. RF analysis of serum biomarkers identified serum calcium, hemoglobin and red blood cell (RBC) counts as potential biomarkers for marmoset IBD. This study characterizes the microbiome of healthy captive common marmosets and demonstrates that source-specific microbiomes can be retained despite standardized diets and husbandry practices. Marmosets with IBD had decreased alpha diversity and a shift in the ratio of Bacteroides:Prevotella copri compared to healthy marmosets.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37565923", + "title": "Intestinal flora in the constipation patients before versus after lactulose intervention.", + "year": 2023, + "journal": "Medicine", + "authors": [ + "Ma J", + "Ma H", + "Zheng S", + "Yu X", + "Wang K", + "Wang J", + "Pan Y", + "Yao J" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.3737999984163164, + "mesh_terms": [ + "Humans", + "Lactulose", + "Gastrointestinal Microbiome", + "Constipation", + "Feces", + "Bacteria" + ], + "raw_abstract": "This study aimed to investigate the characteristics of intestinal flora in patients with chronic functional constipation before and after lactulose intervention. Twenty-nine patients with constipation in the treatment group received oral lactulose (15\u2009mL/d) for a month. Twenty healthy subjects served as controls. Stool specimens were collected before and after lactulose treatment. Fecal bacteria were examined by 16SrRNA gene sequencing and bioinformatics analysis. After lactulose treatment, most bacteria in the constipation group, including Bifidobacteria, Bacillus cereus, Prevotella, Bacillus, Anaerostipes, Oribacterium, and Mogibacterium increased as compared to those in the healthy control group. Anaerotruncus declined in the healthy control group after lactulose treatment. Our study shows lactulose can increase the abundance of probiotics, optimize the intestinal microenvironment, and alleviate constipation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27605161", + "title": "Deep sequencing reveals microbiota dysbiosis of tongue coat in patients with liver carcinoma.", + "year": 2016, + "journal": "Scientific reports", + "authors": [ + "Lu H", + "Ren Z", + "Li A", + "Zhang H", + "Jiang J", + "Xu S", + "Luo Q", + "Zhou K", + "Sun X", + "Zheng S", + "Li L" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.3350232892672001, + "mesh_terms": [ + "Carcinoma", + "Dysbiosis", + "Female", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Liver", + "Liver Neoplasms", + "Male", + "Microbiota", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Tongue" + ], + "raw_abstract": "Liver carcinoma (LC) is a common malignancy worldwide, associated with high morbidity and mortality. Characterizing microbiome profiles of tongue coat may provide useful insights and potential diagnostic marker for LC patients. Herein, we are the first time to investigate tongue coat microbiome of LC patients with cirrhosis based on 16S ribosomal RNA (rRNA) gene sequencing. After strict inclusion and exclusion criteria, 35 early LC patients with cirrhosis and 25 matched healthy subjects were enrolled. Microbiome diversity of tongue coat in LC patients was significantly increased shown by Shannon, Simpson and Chao 1 indexes. Microbiome on tongue coat was significantly distinguished LC patients from healthy subjects by principal component analysis. Tongue coat microbial profiles represented 38 operational taxonomic units assigned to 23 different genera, distinguishing LC patients. Linear discriminant analysis (LDA) effect size (LEfSe) reveals significant microbial dysbiosis of tongue coats in LC patients. Strikingly, Oribacterium and Fusobacterium could distinguish LC patients from healthy subjects. LEfSe outputs show microbial gene functions related to categories of nickel/iron_transport, amino_acid_transport, energy produced system and metabolism between LC patients and healthy subjects. These findings firstly identify microbiota dysbiosis of tongue coat in LC patients, may providing novel and non-invasive potential diagnostic biomarker of LC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34225130", + "title": "Oral microbiome in Proliferative Verrucous Leukoplakia exhibits loss of diversity and enrichment of pathogens.", + "year": 2021, + "journal": "Oral oncology", + "authors": [ + "Herreros-Pomares A", + "Llorens C", + "Soriano B", + "Zhang F", + "Gallach S", + "Bagan L", + "Murillo J", + "Jantus-Lewintre E", + "Bagan J" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.32612946434240714, + "mesh_terms": [ + "Biopsy", + "Cell Transformation, Neoplastic", + "Humans", + "Leukoplakia, Oral", + "Microbiota", + "Mouth", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVES: Oral microbiome plays an important role in oral diseases. Among them, proliferative verrucous leucoplakia (PVL) is an uncommon form of progressive multifocal leukoplakia with a worryingly rate of malignant transformation. Here, we aimed to characterize the oral microbiome of PVL patients and compare it with those of healthy controls. MATERIAL AND METHODS: Oral biopsies from ten PVL patients and five healthy individuals were obtained and used to compare their microbial communities. The sequence of the V3-V4 region of 16S rRNA gene was used as the taxonomic basis to estimate and analyze the composition and diversity of bacterial populations present in the samples. RESULTS: Our results show that the oral microbial composition and diversity are significantly different among PVL patients and healthy donors. The average number of observed operational taxonomic units (OTUs) was higher for healthy donors than for PVL, proving a loss of diversity in PVL. Several OTUs were found to be more abundant in either group. Among those that were significantly enriched in PVL patients, potential protumorigenic pathogens like Oribacterium sp. oral taxon 108, Campylobacter jejuni, uncultured Eubacterium sp., Tannerella, and Porphyromonas were identified. CONCLUSION: Oral microbiome dysbiosis was found in patients suffering from PVL. To the best of our knowledge, this is the first study investigating the oral microbiome alterations in PVL and, due to the limited number of participants, additional studies are needed. Oral microbiota-based biomarkers may be helpful in predicting the risks for the development of PVL.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39801018", + "title": "Pharyngeal Microbiome in Atopic Dermatitis: A 16S rRNA Sequencing Study.", + "year": 2025, + "journal": "Experimental dermatology", + "authors": [ + "Zhang T", + "Shi J", + "Li X", + "Liu H", + "Wei Y", + "Li H" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.3254229237530251, + "mesh_terms": [ + "Humans", + "Dermatitis, Atopic", + "RNA, Ribosomal, 16S", + "Male", + "Female", + "Adult", + "Microbiota", + "Pharynx", + "Young Adult", + "Case-Control Studies", + "Bacteria", + "Middle Aged", + "Adolescent", + "Phylogeny" + ], + "raw_abstract": "While recent studies have demonstrated the involvement of the skin and gut microbiome in the pathogenesis of atopic dermatitis (AD), the influence of pharyngeal microbiota on AD remains unclear. This study aims to explore disparities in the composition of pharyngeal flora among AD patients and their potential role in the pathogenesis of AD. Between March and May 2023, 30 patients with AD at the outpatient department of Jiangsu Provincial Traditional Chinese Medicine Hospital were recruited, along with 20 healthy subjects, underwent 16S rRNA sequencing on pharyngeal swabs. Pharyngeal taxonomic biomarkers of AD were identified using linear discriminant analysis effect size (LEfSe), and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) was employed to predict potential functional metabolic pathways of bacteria with differential abundance. Significant variations were observed in the microbiota composition between the two study groups. The Pharynx of AD patients exhibited a notably higher relative abundance of Granulicatella, Pseudomonas, and Acinetobacter compared to healthy volunteers. Conversely, the relative abundance of Prevotella, Porphyromonas, Campylobacter, Lactobacillaceae, Treponema, Megasphaera, Selenomonas, and Oribacterium was lower in AD patients. According to the metabolic functional enrichment annotations predicted by PICRUSt2, bacteria with differential abundance may be involved in the pathogenesis of AD through two metabolic pathways, namely chondroitin sulfate degradation and chitin derivatives degradation. AD patients displayed distinctive microbiota profiles compared to healthy controls. These findings imply a pivotal role of pharyngeal microbiota in the pathogenesis of AD, offering novel perspectives for AD treatment strategies.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32623494", + "title": "A comparative study of microbial community and functions of type 2 diabetes mellitus patients with obesity and healthy people.", + "year": 2020, + "journal": "Applied microbiology and biotechnology", + "authors": [ + "Wang TY", + "Zhang XQ", + "Chen AL", + "Zhang J", + "Lv BH", + "Ma MH", + "Lian J", + "Wu YX", + "Zhou YT", + "Ma CC", + "Dong RJ", + "Ge DY", + "Gao SH", + "Jiang GJ" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.3052586213059582, + "mesh_terms": [ + "Adult", + "Bacteria", + "Computational Biology", + "Diabetes Mellitus, Type 2", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Male", + "Metagenome", + "Metagenomics", + "Middle Aged", + "Obesity" + ], + "raw_abstract": "The gut microbiota is crucial in the pathogenesis of type 2 diabetes mellitus (T2DM). However, the metabolism of T2DM patients is not well-understood. We aimed to identify the differences on composition and function of gut microbiota between T2DM patients with obesity and healthy people. In this study, 6 T2DM patients with obesity and 6 healthy volunteers were recruited, and metagenomic approach and bioinformatics analysis methods were used to understand the composition of the gut microbiota and the metabolic network. We found a decrease in the abundance of Firmicutes, Oribacterium, and Paenibacillus; this may be attributed to a possible mechanism and biological basis of T2DM; moreover, we identified three critical bacterial taxa, Bacteroides plebeius, Phascolarctobacterium sp. CAG207, and the order Acidaminococcales that can potentially be used for T2DM treatment. We also revealed the composition of the microbiota through functional annotation based on multiple databases and found that carbohydrate metabolism contributed greatly to the pathogenesis of T2DM. This study helps in elucidating the different metabolic roles of microbes in T2DM patients with obesity.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29259328", + "title": "Disordered oropharyngeal microbial communities in H7N9 patients with or without secondary bacterial lung infection.", + "year": 2017, + "journal": "Emerging microbes & infections", + "authors": [ + "Lu HF", + "Li A", + "Zhang T", + "Ren ZG", + "He KX", + "Zhang H", + "Yang JZ", + "Luo QX", + "Zhou K", + "Chen CL", + "Chen XL", + "Wu ZW", + "Li LJ" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.29924600358411435, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteria", + "Bacterial Infections", + "Bacterial Physiological Phenomena", + "Coinfection", + "Female", + "Humans", + "Influenza A Virus, H7N9 Subtype", + "Influenza, Human", + "Lung Diseases", + "Male", + "Middle Aged", + "Oropharynx", + "Phylogeny" + ], + "raw_abstract": "Secondary bacterial lung infection (SBLI) is a serious complication in patients with H7N9 virus infection, and increases disease severity. The oropharyngeal (OP) microbiome helps prevent colonisation of respiratory pathogens. We aimed to investigate the OP microbiome of H7N9 patients with/without secondary bacterial pneumonia using 16S rRNA gene sequencing. OP swab samples were collected from 51 H7N9 patients (21 with SBLI and 30 without) and 30 matched healthy controls (HCs) and used for comparative composition, diversity and richness analyses of microbial communities. Principal coordinates analysis successfully distinguished between the OP microbiomes of H7N9 patients and healthy subjects, and the OP microbiome diversity of patients with SBLI was significantly increased. There was significant dysbiosis of the OP microbiome in H7N9 patients, with an abundance of Leptotrichia, Oribacterium, Streptococcus, Atopobium, Eubacterium, Solobacterium and Rothia species in patients with SBLI, and Filifactor, Megasphaera and Leptotrichia species in patients without SBLI, when compared with HCs. Importantly, Haemophilus and Bacteroides species were enriched in HCs. These findings revealed dysbiosis of the OP microbiota in H7N9 patients, and identified OP microbial risk indicators of SBLI, suggesting that the OP microbiome could provide novel and non-invasive diagnostic biomarkers for early microbiota-targeted prophylactic therapies for SBLI prevention.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39387425", + "title": "Characterization of lingual microbiota in pediatric geographic tongue.", + "year": 2024, + "journal": "The Turkish journal of pediatrics", + "authors": [ + "You Y", + "He Y", + "Huang P" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.2828841113174845, + "mesh_terms": [ + "Humans", + "Male", + "Female", + "Microbiota", + "Child", + "Glossitis, Benign Migratory", + "Tongue", + "Child, Preschool", + "RNA, Ribosomal, 16S", + "Case-Control Studies" + ], + "raw_abstract": "BACKGROUND: Geographic tongue is an oral mucosal lesion affecting the tongue. The association between geographic tongue and the mucosal microbiota in children remains unclear. METHOD: To characterize the feature of lingual microbiota in pediatric geographic tongue, lingual swabs were collected from lesion sites and healthy sites of 25 patients with geographic tongue (14 males and 11 females; age 5.21 \u00b12.94 years) and 19 controls (10 males and 9 females; age 5.31\u00b12.82 years). DNA was extracted and the 16S rRNA was amplificated, sequenced and analyzed. RESULTS: The lingual microbiota composition was significantly different between children with geographic tongue and the healthy cohort; Streptobacillus was reduced in geographic tongue, while Catonella, Bacillus and Oribacterium were overrepresented. When the lesions and the normal mucosa were compared, an increased abundance of Prevotella oris was observed. CONCLUSION: Our results provided new insight into the association between oral microbiota and pediatric geographic tongue.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32920149", + "title": "Oral microbial community analysis of the patients in the progression of liver cancer.", + "year": 2020, + "journal": "Microbial pathogenesis", + "authors": [ + "Li D", + "Xi W", + "Zhang Z", + "Ren L", + "Deng C", + "Chen J", + "Sun C", + "Zhang N", + "Xu J" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.2626953301984139, + "mesh_terms": [ + "Humans", + "Liver Neoplasms", + "Microbiota", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Saliva" + ], + "raw_abstract": "Liver disease has been reported to associate with oral microbiota. This study aimed to identify the salivary microbial structure in liver disease patients and determine whether the disease progression influence the bacterial composition. 16S rDNA high-throughput sequencing and bioinformatic analysis were used to examine oral bacterial diversity in the different status of hepatitis patients including 6 patients with Hepatitis B (Y), 6 patients with Hepatitis B Cirrhosis (YY) and 6 patients with liver cancer (C), and 6 healthy controls (T). Phylogenetic analysis revealed that the genera of Streptococcus, Prevotella, Actinomyces, Veillonella and Neisseria are predominant genus in the saliva of Y, YY, C patients and T group. Lautropia, Abiotrophia and Veillonella were enriched in Y patients, while Treponema, Selenomonas and Oribacterium were also existed in YY patients. Haemophilus, Porphyromonas and Filifactor had high abundance in C patients. The genera of Moryella, Leptotrichia, Lactobacillus, Dialister, Serratia, Enterococcus and Actinobacillus were decreased in all patient samples compared with healthy control samples which may be used for treatment of liver disease. Diversity analyses showed decreased diversity of salivary bacterial communities was discovered in the progress of the liver disease. These findings identified the oral microbiota dysbiosis in liver disease, which may providing available information and possible diagnostic biomarkers for liver patients.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29615776", + "title": "Dysbiosis of the salivary microbiota in pediatric-onset primary sclerosing cholangitis and its potential as a biomarker.", + "year": 2018, + "journal": "Scientific reports", + "authors": [ + "Iwasawa K", + "Suda W", + "Tsunoda T", + "Oikawa-Kawamoto M", + "Umetsu S", + "Takayasu L", + "Inui A", + "Fujisawa T", + "Morita H", + "Sogo T", + "Hattori M" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.255189596239146, + "mesh_terms": [ + "Adolescent", + "Biomarkers", + "Case-Control Studies", + "Child", + "Cholangitis, Sclerosing", + "Dysbiosis", + "Female", + "Humans", + "Male", + "Phenotype", + "RNA, Ribosomal, 16S", + "Saliva" + ], + "raw_abstract": "Primary sclerosing cholangitis (PSC) is a liver disease known for its frequent concurrence with inflammatory bowel disease. Dysbiosis of the gut microbiota in PSC was reported in several studies, but the microbiological features of the salivary microbiota in PSC have not been established. Here we compared the salivary microbial communities of 24 pediatric-onset PSC patients, 16 age-matched ulcerative colitis (UC) patients, and 24 healthy controls (HCs) by analyzing the bacterial 16S rRNA gene sequence data. The species-richness (\u03b1-diversity) showed no significant between-group differences, whereas the overall salivary microbiota structure (\u03b2-diversity) showed significant differences among the three groups. Taxonomic assignment revealed that the PSC salivary microbiota were characterized by significant decreases in the abundance of Rothia and Haemophilus compared to the HC group, and significantly decreased Haemophilus and increased Oribacterium compared to the UC group. By combining the genera selected by the random forest algorithm in machine learning, followed by confirmation with 10-fold cross-validation, we were able to distinguish the PSC group from the HC group with the area under the curve (AUC) of 0.7423, and from the UC group with the AUC of 0.8756. Our results indicate the potential of salivary microbiota as biomarkers for a noninvasive diagnosis of PSC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36241691", + "title": "Profile of gut microbiota and serum metabolites associated with metabolic syndrome in a remote island most afflicted by obesity in Japan.", + "year": 2022, + "journal": "Scientific reports", + "authors": [ + "Uema T", + "Millman JF", + "Okamoto S", + "Nakamura T", + "Yamashiro K", + "Uehara M", + "Honma KI", + "Miyazato M", + "Ashikari A", + "Saito S", + "Maeda S", + "Imamura M", + "Ishida H", + "Matsushita M", + "Nakamura K", + "Masuzaki H" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.22762248541258207, + "mesh_terms": [ + "Body Mass Index", + "Creatine", + "Gastrointestinal Microbiome", + "Glycated Hemoglobin", + "Humans", + "Insulins", + "Japan", + "Metabolic Syndrome", + "Obesity", + "Pyruvic Acid", + "Triglycerides" + ], + "raw_abstract": "Numerous studies have revealed distinct differences in the profiles of gut microbiota between non-obese and obese individuals. To date, however, little is known if any disparities in the community of gut microbiota exist between metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO) subjects. We therefore aimed to comprehensively characterize the gut microbiota and circulating metabolites in serum from both MHO and MUO residing in the remote island, Kumejima, where the prevalence of obesity is one of the highest in Japan, and explored possible correlations between the gut microbiota profile and markers of metabolic syndrome. Results revealed that MUO showed significantly higher levels of genera such as g_Succinivibrio, g_Granulicatella, g_Brachyspira, g_Oribacterium and g_Atopobium in comparison to MHO. Moreover, abundance of g_Succinivibrio, g_Brachyspira and g_Atopobium were positively correlated with value of fasting insulin, HOMA-R, circulating triglycerides, diastolic blood pressure, BMI, body weight, waist circumference and HbA1c. In addition, MUO compared to MHO showed an imbalance of serum metabolites, with a significant elevation in 2-oxoisovaleric acid, pyruvic acid, 2-hydroxybutyric acid, and creatine. Our data highlight unmet needs in precision approaches for the treatment of obesity, targeting the gut microbiota profile and serum metabolites in a distinct population affected by obesity.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38485288", + "title": "Association between oral microbiome and breast cancer in the east Asian population: A Mendelian randomization and case-control study.", + "year": 2024, + "journal": "Thoracic cancer", + "authors": [ + "Feng K", + "Ren F", + "Shang Q", + "Wang X", + "Wang X" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.22447477085221693, + "mesh_terms": [ + "Female", + "Humans", + "Breast Neoplasms", + "Case-Control Studies", + "East Asian People", + "Genome-Wide Association Study", + "Mendelian Randomization Analysis", + "Microbiota", + "Mouth" + ], + "raw_abstract": "BACKGROUND: The causal relationship between breast cancer (BC) and the oral microbiome remains unclear. In this case-control study, using two-sample Mendelian randomization (MR), we thoroughly explored the relationship between the oral microbiome and BC in the East Asian population. METHODS: Genetic summary data related to oral microbiota and BC were collected from genome-wide association studies involving participants of East Asian descent. MR estimates were generated by conducting various analyses. Sequencing data from a case-control study were used to verify the validity of these findings. RESULTS: MR analysis revealed that 30 tongue and 37 salivary bacterial species were significantly associated with BC. Interestingly, in both tongue and salivary microbiomes, we observed the causal effect of six genera, namely, Aggregatibacter, Streptococcus, Prevotella, Haemophilus, Lachnospiraceae, Oribacterium, and Solobacterium, on BC. Our case-control study findings suggest differences in specific bacteria between patients with BC and healthy controls. Moreover, sequencing data confirmed the MR analysis results, demonstrating that compared with the healthy control group, the BC group had a higher relative abundance of Pasteurellaceae and Streptococcaceae but a lower relative abundance of Bacteroidaceae. CONCLUSIONS: Our MR analysis suggests that the oral microbiome exerts a causative effect on BC risk, supported by the sequencing data of a case-control study. In the future, studies should be undertaken to comprehensively understand the complex interaction mechanisms between the oral microbiota and BC.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28875948", + "title": "The tongue microbiome in healthy subjects and patients with intra-oral halitosis.", + "year": 2017, + "journal": "Journal of breath research", + "authors": [ + "Seerangaiyan K", + "van Winkelhoff AJ", + "Harmsen HJM", + "Rossen JWA", + "Winkel EG" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.22368664315890577, + "mesh_terms": [ + "Adult", + "Aged", + "Biodiversity", + "Breath Tests", + "Case-Control Studies", + "Demography", + "Female", + "Halitosis", + "Healthy Volunteers", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Mouth", + "Oral Health", + "Phylogeny", + "Species Specificity", + "Tongue", + "Young Adult" + ], + "raw_abstract": "Intra-oral halitosis (IOH) is an unpleasant odor emanating from the oral cavity. It is thought that the microbiota of the dorsal tongue coating plays a crucial role in this condition. The aim of the study was to investigate the composition of the tongue microbiome in subjects with and without IOH. A total of 26 subjects, 16 IOH patients and 10 healthy subjects were recruited based on their organoleptic score and volatile sulfur compound (VSC) measurements. The composition of the tongue microbiome was studied using the 16s amplicon sequencing of the V3-V4 hyper variable region with an Illumina MiSeq. The sequenced data were analyzed using QIIME, and the sequences obtained were distributed across 7 phyla, 27 genera and 825 operational taxonomic units (OTUs). At a higher taxon level, TM7 was associated with IOH patients whereas Gemellaceae was significantly abundant in the healthy subjects. At OTU level, we found several significant OTUs that differentiated the IOH patients from the controls. These included Aggregatibacter (OTU id 4335776), Aggregatibacter segnis (A. segnis), Campylobacter, Capnocytophaga, Clostridiales, Dialister, Leptotrichia, Parvimonas, Peptostreptococcus, Peptococcus, Prevotella, Selenomonas, SR1, Tannerella, TM7-3 and Treponema in the IOH group. In the control group, Aggregatibacter (OTU id 4363066), Haemophilus, Haemophilus parainfluenza (H. parainfluenza), Moryella, Oribacterium, Prevotella, several Streptococcus, Rothia dentocariosa (R. dentocariosa) and OTU from Gemellaceae were significantly abundant. Based on our observation, it was concluded that the bacterial qualitative composition of the IOH and the control group was almost the same, except for the few above-mentioned bacterial species and genera.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37946238", + "title": "The oral bacterial microbiota facilitates the stratification for ulcerative colitis patients with oral ulcers.", + "year": 2023, + "journal": "Annals of clinical microbiology and antimicrobials", + "authors": [ + "Xu J", + "Zhang Y", + "Fang XH", + "Liu Y", + "Huang YB", + "Ke ZL", + "Wang Y", + "Zhang YF", + "Zhang Y", + "Zhou JH", + "Su HT", + "Chen N", + "Liu YL" + ], + "bacteria": "Oribacterium", + "condition": "healthy", + "relevance_score": 0.2103888292486434, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Oral Ulcer", + "RNA, Ribosomal, 16S", + "Gastrointestinal Microbiome", + "Microbiota", + "Inflammatory Bowel Diseases", + "Bacteria", + "Feces", + "Mesalamine" + ], + "raw_abstract": "BACKGROUND: Clinically, a large part of inflammatory bowel disease (IBD) patients is complicated by oral lesions. Although previous studies proved oral microbial dysbiosis in IBD patients, the bacterial community in the gastrointestinal (GI) tract of those IBD patients combined with oral ulcers has not been profiled yet. METHODS: In this study, we enrolled four groups of subjects, including healthy controls (CON), oral ulcer patients (OU), and ulcerative colitis patients with (UC_OU) and without (UC) oral ulcers. Bio-samples from three GI niches containing salivary, buccal, and fecal samples, were collected for 16S rRNA V3-V4 region sequencing. Bacterial abundance and related bio-functions were compared, and data showed that the fecal microbiota was more potent than salivary and buccal microbes in shaping the host immune system.\u2009~\u200922 UC and 10 UC_OU 5-aminosalicylate (5-ASA) routine treated patients were followed-up for six months; according to their treatment response (a decrease in the endoscopic Mayo score), they were further sub-grouped as responding and non-responding patients. RESULTS: We found those UC patients complicated with oral ulcers presented weaker treatment response, and three oral bacterial genera, i.e., Fusobacterium, Oribacterium, and Campylobacter, might be connected with treatment responding. Additionally, the salivary microbiome could be an indicator of treatment responding in 5-ASA routine treatment rather than buccal or fecal ones. CONCLUSIONS: The fecal microbiota had a strong effect on the host's immune indices, while the oral bacterial microbiota could help stratification for ulcerative colitis patients with oral ulcers. Additionally, the oral microbiota had the potential role in reflecting the treatment response of UC patients. Three oral bacteria genera (Fusobacterium, Oribacterium, and Campylobacter) might be involved in UC patients with oral ulcers lacking treatment responses, and monitoring oral microbiota may be meaningful in assessing the therapeutic response in UC patients.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31496126", + "title": "Longitudinal development of the gut microbiota in healthy and diarrheic piglets induced by age-related dietary changes.", + "year": 2019, + "journal": "MicrobiologyOpen", + "authors": [ + "Yang Q", + "Huang X", + "Wang P", + "Yan Z", + "Sun W", + "Zhao S", + "Gun S" + ], + "bacteria": "Bulleidia", + "condition": "healthy", + "relevance_score": 0.40634704240973435, + "mesh_terms": [ + "Age Factors", + "Animal Feed", + "Animals", + "Biodiversity", + "Biomarkers", + "Computational Biology", + "Diarrhea", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Male", + "Metagenomics", + "RNA, Ribosomal, 16S", + "Swine", + "Symbiosis", + "Weaning" + ], + "raw_abstract": "Diarrhea is one of the most common enteric diseases in young piglets. Diverse factors such as an unstable gut microenvironment, immature intestinal immune system, early supplementary feeding, and weaning often induce dysfunction of gut microbiota, thus leading to a continuing high incidence of diarrhea in piglets. However, few studies have characterized the gut microbiota of diarrheic piglets following changes in diet and during the development of intestinal physiology. In this study, we used 16S rRNA gene sequencing to analyze the dynamic establishment of fecal microbiota in six healthy piglets in response to age-related changes in the diet: sow-reared, early supplementary creep-feeding (sow-reared\u00a0+\u00a0starter diet), and weaning (solid nursery diet). We compared the gut microbiota of these six healthy piglets with those of diarrheic piglets during each of the three dietary stages (n\u00a0=\u00a010 sow-reared, n\u00a0=\u00a010 early supplementary creep-feeding, and n\u00a0=\u00a05 weaning). We found that weaning (solid nursery feeding) was the primary factor leading to dynamic colonization by microbiota in healthy piglets, and diarrhea primarily affected the microbial communities of piglets before weaning. Healthy piglets showed a continuous decrease in Lactobacillus and Escherichia, as well as a gradual increase in Prevotella with the transition to solid food. An altered relationship between Prevotella and Escherichia may be the main cause of diarrhea in preweaned piglets, whereas reduced numbers of Bacteroides, Ruminococcus, Bulleidia, and Treponema that are responsible for the digestion and utilization of solid feeds may be related to the onset of postweaning piglet diarrhea. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional analysis indicated that a reduction in genes involved in carbohydrate metabolism induced by intestinal dysbacteriosis in diarrheic piglets was one of the major causes of diarrhea at the three dietary stages. These findings provide insights into developing an intervention strategy for better management of diarrhea in piglets.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34090383", + "title": "Association between premature ovarian insufficiency and gut microbiota.", + "year": 2021, + "journal": "BMC pregnancy and childbirth", + "authors": [ + "Wu J", + "Zhuo Y", + "Liu Y", + "Chen Y", + "Ning Y", + "Yao J" + ], + "bacteria": "Bulleidia", + "condition": "healthy", + "relevance_score": 0.27200219832503353, + "mesh_terms": [ + "Adult", + "Case-Control Studies", + "Estradiol", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Primary Ovarian Insufficiency", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Premature ovarian insufficiency (POI) is characterized by impairment of ovarian function on a continuum before the age of 40\u2009years. POI is affected by multiple factors. Considering new insights from recent gut microbiome studies, this study aimed to investigate the relationship between gut microbial community structure and POI. METHODS: Subjects were recruited at the Shenzhen Maternity & Child Healthcare Hospital. Fecal microbial community profiles of healthy women (n\u2009=\u200918), women with POI (n\u2009=\u200935) were analyzed using 16S rRNA gene sequencing based on Illumina NovaSeq platform. RESULTS: Compared to the controls, the serum levels of FSH, LH, T and FSH/LH ratio significantly increased in women with POI, whereas E2 and AMH decreased significantly. Higher weighted UniFrac value was observed in POI women compared with healthy women. Phylum Firmicutes, genera Bulleidia and Faecalibacterium were more abundant in healthy women, while phylum Bacteroidetes, genera Butyricimonas, Dorea, Lachnobacterium and Sutterella enriched significantly in women with POI. Moreover, these alterations of the gut microbiome in women with POI were closely related to FSH, LH, E2, AMH level and FSH/LH ratio. CONCLUSIONS: Women with POI had altered microbial profiles in their gut microbiome, which were associated with serum hormones levels. These results will shed a new light on the pathogenesis and treatment for POI.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32692651", + "title": "Microbial biodiversity in the throats of pulmonary tuberculosis patients and tuberculin skin test (TST) positive and negative healthy individuals in Malaysia.", + "year": 2020, + "journal": "Tuberculosis (Edinburgh, Scotland)", + "authors": [ + "Semail N", + "Suraiya S", + "Calero R", + "Mirabal M", + "Carrillo H", + "Ezzeddin Kamil MH", + "Sarmiento ME", + "Acosta A", + "Norazmi MN" + ], + "bacteria": "Bulleidia", + "condition": "healthy", + "relevance_score": 0.22951460949823996, + "mesh_terms": [ + "Bacteria", + "Case-Control Studies", + "Humans", + "Malaysia", + "Microbiota", + "Pharynx", + "Predictive Value of Tests", + "Ribotyping", + "Tuberculin Test", + "Tuberculosis, Pulmonary" + ], + "raw_abstract": "The purpose of this study was to investigate the composition of throat microbiota in pulmonary tuberculosis patients (PTB) in comparison to healthy tuberculin skin test positive (TSTp) and negative (TSTn) individuals. Throat swabs samples were collected, and the microbiota was characterized. Richer operational taxonomic units (OTUs) were present in PTB group, compared to TSTp and TSTn. Regarding alpha diversity analysis there was a higher community diversity in TSTn compared to TSTp. Beta diversity analysis showed different species composition in TSTp compared to TSTn and PTB. There was higher presence of Firmicutes in PTB and TSTn compared to TSTp group at phylum level. At the genus level, Leuconostoc and Enterococcus were higher in TSTn compared to TSTp and Pediococcus, Chryseobacterium, Bifidobacterium, Butyrivibrio, and Bulleidia were higher in PTB compared to TSTn. Streptococcus was higher in TSTn compared to PTB and Lactobacillus in PTB compared to TSTp. At species level, Streptococcus sobrinus and Bulleidia moorei were higher in PTB compared to TSTn individuals, while Lactobacillus salivarius was higher in PTB compared to TSTp. The differences in the microbiome composition could influence the resistance/susceptibility to Mtb infection.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38643725", + "title": "The relationship between the gut microbiota and oxidative stress in the cognitive function of schizophrenia: A pilot study in China.", + "year": 2024, + "journal": "Schizophrenia research", + "authors": [ + "Li H", + "Huang Y", + "Liang L", + "Li H", + "Li S", + "Feng Y", + "Feng S", + "Wu K", + "Wu F" + ], + "bacteria": "Bulleidia", + "condition": "healthy", + "relevance_score": 0.21036488439215228, + "mesh_terms": [ + "Humans", + "Schizophrenia", + "Gastrointestinal Microbiome", + "Male", + "Female", + "Oxidative Stress", + "Adult", + "Pilot Projects", + "China", + "Cognitive Dysfunction", + "Superoxide Dismutase", + "Middle Aged", + "Young Adult", + "Machine Learning" + ], + "raw_abstract": "Cognitive impairment is a core symptom of schizophrenia. The gut microbiota (GM) and oxidative stress may play important roles in the pathophysiological mechanisms of cognitive impairment. This study aimed to explore the relationship between GM and oxidative stress in the cognitive function of schizophrenia. GM obtained by 16S RNA sequencing and serum superoxide dismutase (SOD) levels from schizophrenia patients (N\u00a0=\u00a068) and healthy controls (HCs, N\u00a0=\u00a072) were analyzed. All psychiatric symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS). Cognitive function was assessed using the MATRICS Consensus Cognitive Battery (MCCB). Correlation analysis was used to explore the relationship between GM, SOD, and cognitive function. Machine learning models were used to identify potential biomarkers. Compared to HCs, the relative abundances of Collinsella, undefined Ruminococcus, Lactobacillus, Eubacterium, Mogibacterium, Desulfovibrio, Bulleidia, Succinivibrio, Corynebacterium, and Atopobium were higher in patients with schizophrenia, but Faecalibacterium, Anaerostipes, Turicibacter, and Ruminococcus were lower. In patients with schizophrenia, the positive factor, general factor, and total score of MCCB positively correlated with Lactobacillus, Collinsella, and Lactobacillus, respectively; SOD negatively correlated with Eubacterium, Collinsella, Lactobacillus, Corynebacterium, Bulleidia, Mogibacterium, and Succinivibrio, but positively correlated with Faecalibacterium, Ruminococcus, and MCCB verbal learning index scores; Faecalibacterium and Turicibacter were positively correlated with MCCB visual learning index scores and speed of processing index scores, respectively. Our findings revealed a correlation between SOD and GM and confirmed that cognitive dysfunction in patients with schizophrenia involves abnormal SOD levels and GM changes.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32912596", + "title": "Gut microbiota changes in patients with autism spectrum disorders.", + "year": 2020, + "journal": "Journal of psychiatric research", + "authors": [ + "Ding X", + "Xu Y", + "Zhang X", + "Zhang L", + "Duan G", + "Song C", + "Li Z", + "Yang Y", + "Wang Y", + "Wang X", + "Zhu C" + ], + "bacteria": "Caproiciproducens", + "condition": "healthy", + "relevance_score": 0.21405224001523118, + "mesh_terms": [ + "Autism Spectrum Disorder", + "Bacteria", + "Biomarkers", + "Child", + "Gastrointestinal Microbiome", + "Humans", + "Microbiota" + ], + "raw_abstract": "Autism spectrum disorder (ASD) has a high incidence of intestinal comorbidity, indicating a strong association with gut microbiota. The purpose of this study was to characterize gut microbiota profiles in children with ASD. Seventy-seven children with ASD [33 with mild ASD and 44 with severe ASD according to the Childhood Autism Rating Scale score] and 50 age-matched healthy children were enrolled. Compared with children in the healthy control (HC) group, those in the ASD group showed higher biomass, richness, and biodiversity of gut microbiota, and an altered microbial community structure. At the genus level, there was a significant increase in the relative abundance of unidentified Lachnospiraceae, Clostridiales, Erysipelotrichaceae, Dorea, Collinsella, and Lachnoclostridium, whereas Bacteroides, Faecalibacterium, Parasutterella, and Paraprevotella were significantly lower in the ASD group than in the control group. The presence of unidentified Erysipelotrichaceae, Faecalibacterium, and Lachnospiraceae was positively correlated with ASD severity. Notably, three microbial markers (Faecalitalea, Caproiciproducens and Collinsella) were identified in a random forest model with an area under the curve (AUC) of 0.94 for differentiation between HCs and ASD patients. Furthermore, the validation model was consistent with the discovery set (AUC\u00a0=\u00a00.98, 95% CI: 97.9%-100%). The training and testing sets were more effective when the number of bacteria was increased. In addition, the functional properties (such as galactose metabolism, glycosyltransferase activity, and glutathione metabolism) displayed significant differences between the ASD and HC groups. The current study provides evidence for the relationship between gut microbiota and ASD, with the findings suggesting that gut microbiota could contribute to symptomology. Thus, modulation of gut microbiota may be a new therapeutic strategy for ASD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30918225", + "title": "Next-generation sequencing analysis of bacterial flora in bovine protothecal mastitic milk and feces.", + "year": 2019, + "journal": "The Journal of veterinary medical science", + "authors": [ + "Miura A", + "Kurumisawa T", + "Kano R", + "Ito T", + "Suzuki K", + "Kamata H" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.5846128659360795, + "mesh_terms": [ + "Animals", + "Cattle", + "Feces", + "Female", + "High-Throughput Nucleotide Sequencing", + "Mastitis, Bovine", + "RNA, Bacterial", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "The aim of the present study was to evaluate the bacterial flora in the udder and intestinal environments in cows with and without protothecal mastitis. We used next-generation sequencing (NGS) analysis to identify 16S rRNA genes from bacterial flora present in 13 milk and 13 fecal samples from protothecal mastitic and healthy dairy cows in the Aichi region of Japan. Sequences associated with 5 species (Calothrix desertica, Corynebacterium simulans, Corynebacterium striatum, Empedobacter falsenii, and Rothia endophytica) showed the highest prevalence in samples of milk and feces from animals with protothecal mastitis. This range of species differed from those detected in the milk and feces from healthy cows.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28038686", + "title": "The developing hypopharyngeal microbiota in early life.", + "year": 2016, + "journal": "Microbiome", + "authors": [ + "Mortensen MS", + "Brejnrod AD", + "Roggenbuck M", + "Abu Al-Soud W", + "Balle C", + "Krogfelt KA", + "Stokholm J", + "Thorsen J", + "Waage J", + "Rasmussen MA", + "Bisgaard H", + "S\u00f8rensen SJ" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.509278040171133, + "mesh_terms": [ + "Bacteria", + "Base Sequence", + "DNA, Bacterial", + "Female", + "Humans", + "Hypopharynx", + "Infant", + "Infant, Newborn", + "Male", + "Microbiota", + "Prospective Studies", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "BACKGROUND: The airways of healthy humans harbor a distinct microbial community. Perturbations in the microbial community have been associated with disease, yet little is known about the formation and development of a healthy airway microbiota in early life. Our goal was to understand the establishment of the airway microbiota within the first 3\u00a0months of life. We investigated the hypopharyngeal microbiota in the unselected COPSAC RESULTS: Our analysis shows that majority of the hypopharyngeal microbiota of healthy infants belong to each individual's core microbiota and we demonstrate five distinct community pneumotypes. Four of these pneumotypes are dominated by the genera Staphylococcus, Streptococcus, Moraxella, and Corynebacterium, respectively. Furthermore, we show temporal pneumotype changes suggesting a rapid development towards maturation of the hypopharyngeal microbiota and a significant effect from older siblings. Despite an overall common trajectory towards maturation, individual infants' microbiota are more similar to their own, than to others, over time. CONCLUSIONS: Our findings demonstrate a consolidation of the population of indigenous bacteria in healthy airways and indicate distinct trajectories in the early development of the hypopharyngeal microbiota.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34882352", + "title": "Etiological significance of Corynebacterium spp. in the development of diseases of the respiratory tract.", + "year": 2021, + "journal": "Klinicheskaia laboratornaia diagnostika", + "authors": [ + "Kharseeva GG", + "Mangutov EO", + "Alutina EL", + "But OM", + "Pakhomova AE" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.46242267626776135, + "mesh_terms": [ + "Anti-Bacterial Agents", + "COVID-19", + "Corynebacterium", + "Corynebacterium Infections", + "Humans", + "Respiratory System", + "SARS-CoV-2" + ], + "raw_abstract": "Corynebacterium spp. It is associated with inflammatory diseases of the respiratory tract (tracheitis, pharyngitis, rhinosinusitis, bronchitis, pneumonia, etc.). C. pseudodiphtheriticum can be the causative agent of bacterial coinfection in patients with a new coronavirus infection (COVID-19). The aim is to determine the pathogenic properties and resistance to antimicrobial drugs of Corynebacterium spp. strains to establish their etiological significance in the development of inflammatory diseases of the respiratory tract. Strains of Corynebacterium spp. isolated from patients with inflammatory diseases of the respiratory tract (43 pcs.) and practically healthy individuals (29 pcs.). Isolates were identified by mass spectrometric method (MALDI-TOF MS), their cytopathic effect in CHO-K1 cell culture, hemolytic, urease activity, antimicrobial drug resistance were determined. Strains of Corynebacterium spp. isolated from patients in the amount of 105 CFU/ml or more, practically healthy - 104 CFU/ml or less. Isolates of Corynebacterium spp. patients had a more pronounced cytopathic effect (83.7\u00b111.1%) and were more often resistant to antimicrobial drugs than those isolated from practically healthy. To establish the etiological significance of Corynebacterium spp. isolates. in the development of inflammatory diseases of the respiratory tract, it is advisable to determine their amount in biological material (105 CFU/ml or more), the cytopathic effect on CHO-K1 cell culture, as well as the presence of multiple resistance to antimicrobial drugs. Differences in the characteristics of Corynebacterium spp. isolates. from patients with respiratory tract pathology and practically healthy individuals are associated with the strain, not the species, of corynebacteria.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39342108", + "title": "Whole genome sequencing and characterization of Corynebacterium isolated from the healthy and dry eye ocular surface.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Naqvi M", + "Utheim TP", + "Charnock C" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.4591417227677345, + "mesh_terms": [ + "Corynebacterium", + "Whole Genome Sequencing", + "Humans", + "Genome, Bacterial", + "Dry Eye Syndromes", + "Corynebacterium Infections", + "Phylogeny", + "Microbial Sensitivity Tests", + "Anti-Bacterial Agents", + "Eye", + "Female" + ], + "raw_abstract": "BACKGROUND: The purpose of this study was to characterize Corynebacterium isolated from the ocular surface of dry eye disease patients and healthy controls. We aimed to investigate the pathogenic potential of these isolates in relation to ocular surface health. To this end, we performed whole genome sequencing in combination with biochemical, enzymatic, and antibiotic susceptibility tests. In addition, we employed deferred growth inhibition assays to examine how Corynebacterium isolates may impact the growth of potentially competing microorganisms including the ocular pathogens Pseudomonas aeruginosa and Staphylococcus aureus, as well as other Corynebacterium present on the eye. RESULTS: The 23 isolates were found to belong to 8 different species of Corynebacterium with genomes ranging from 2.12 mega base pairs in a novel Corynebacterium sp. to 2.65 mega base pairs in C. bovis. Whole genome sequencing revealed the presence of a range of antimicrobial targets present in all isolates. Pangenome analysis showed the presence of 516 core genes and that the pangenome is open. Phenotypic characterization showed variously urease, lipase, mucinase, protease and DNase activity in some isolates. Attention was\u00a0particularly drawn to a potentially new or novel Corynebacterium species which had the smallest genome, and which produced a range of hydrolytic enzymes. Strikingly the isolate inhibited in vitro the growth of a range of possible pathogenic bacteria as well as other Corynebacterium isolates. The majority of Corynebacterium species included in this study did not seem to possess canonical pathogenic activity. CONCLUSIONS: This study is the first reported genomic and biochemical characterization of ocular Corynebacterium. A number of potential virulence factors were identified which may have direct relevance for ocular health and contribute to the finding of our previous report on the ocular microbiome, where it was shown that DNA libraries were often dominated by members of this genus. Particularly interesting in this regard was the observation that some Corynebacterium, particularly new or novel Corynebacterium sp. can inhibit the growth of other ocular Corynebacterium as well as known pathogens of the eye.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37700874", + "title": "Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing.", + "year": 2023, + "journal": "Journal of asthma and allergy", + "authors": [ + "Wan J", + "Song J", + "Lv Q", + "Zhang H", + "Xiang Q", + "Dai H", + "Zheng H", + "Lin X", + "Zhang W" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.4092405953598793, + "mesh_terms": [], + "raw_abstract": "PURPOSE: Recent studies had shown that gut microbiota played a significant role in the development of the immune system and may affect the course of airway allergic disease. We conducted this study to determine unique gut microbial associated with allergic disease in children by shotgun gene sequencing. METHODS: We collected fecal samples from children with allergic asthma (n = 23) and allergic rhinitis (n = 18), and healthy control (n = 19). The gut microbiota of specimens was analyzed by high-throughput metagenomic shotgun gene sequencing. RESULTS: The intestinal microbiota of children with allergic asthma and allergic rhinitis was characterized by increased microbial richness and diversity. Simpson and Shannon were significantly elevated in children with allergic asthma. Principal coordinates analysis (PCoA) showed that the gut microbial communities cluster patterns of children with asthma or rhinitis were significantly different from those of healthy controls. However, no significant difference was found between asthma group and rhinitis group At the phylum level, higher relative abundance of Firmicutes was found in the allergic rhinitis group and allergic asthma group, while the level of Bacteroidetes was significantly lower. At the genus level, Corynebacterium, Streptococcus, Dorea, Actinomyces, Bifidobacterium, Blautia, and Rothia were significantly enriched in the allergic asthma group. Finally, a random forest classifier model selected 16 general signatures to discriminate the allergic asthma group from the healthy control group. CONCLUSION: In conclusion, children in the allergic rhinitis group and allergic asthma group had altered gut microbiomes in comparison with the healthy control group. Compared to healthy children, the gut microbiome in children with allergic diseases has higher pro-inflammatory potential and increased production of pro-inflammatory molecules.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37301777", + "title": "The potential roles of gut microbiome in anal fistula.", + "year": 2023, + "journal": "AMB Express", + "authors": [ + "Cai P", + "Rong H", + "Zhu Q", + "Dai X", + "Zhao J" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.40424638520995, + "mesh_terms": [], + "raw_abstract": "Anal fistula is a common proctological disease, but the thorough mechanisms of the anal fistula formation are still unclear. An increasing number of studies have revealed the crucial role of gut microbiota in intestinal diseases. We used 16S rRNA gene sequencing to analyze the intestinal microbiome in order to determine whether there are differences in the microbiome between anal fistula patients and healthy individuals. The microbiome samples were extracted by repeatedly wiping the rectal wall with intestinal swab. Before this operation, the whole intestine of all participants was irrigated and the score of the Boston bowel preparation scale reached 9. The biodiversity of gut microbiome of rectum revealed significant difference between anal fistula patients and healthy individuals. 36 discriminative taxa were identified by LEfSe analysis between two groups. At the phylum level, Synergistetes was enriched in anal fistula patients, while Proteobacteria was higher in healthy individuals. We also found that at the genus level, Blautia, Faecalibacterium, Ruminococcus, Coprococcus, Bacteroides, Clostridium, Megamonas and Anaerotruncus were highly enriched in anal fistula patients, while the microbiome of healthy individuals was enriched with Peptoniphilus and Corynebacterium. Spearman correlations showed the extensive and close association among genera and species. Finally, a diagnostic prediction model was constructed by random forest classifier, and the area under curve (AUC) reached 0.990. This study gave an important hint for analyzing gut microbiome of rectum in anal fistula patient.Keypoints.We use the 16S rRNA gene sequencing to test the microbiome samples extracted from the intestinal swab. This is the first study to explore the gut microbiome of rectum using this workflow. We also found the distinct gut microbiome of rectum differences between anal fistula patients and healthy individuals.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28481057", + "title": "Mapping and comparing bacterial microbiota in the sinonasal cavity of healthy, allergic rhinitis, and chronic rhinosinusitis subjects.", + "year": 2017, + "journal": "International forum of allergy & rhinology", + "authors": [ + "Lal D", + "Keim P", + "Delisle J", + "Barker B", + "Rank MA", + "Chia N", + "Schupp JM", + "Gillece JD", + "Cope EK" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.3924765612720713, + "mesh_terms": [ + "Adult", + "Aged", + "Aged, 80 and over", + "Bacteria", + "Female", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Nasal Cavity", + "RNA, Bacterial", + "RNA, Ribosomal, 16S", + "Rhinitis", + "Sinusitis", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The role of microbiota in sinonasal inflammation can be further understood by targeted sampling of healthy and diseased subjects. We compared the microbiota of the middle meatus (MM) and inferior meatus (IM) in healthy, allergic rhinitis (AR), and chronic rhinosinusitis (CRS) subjects to characterize intrasubject, intersubject, and intergroup differences. METHODS: Subjects were recruited in the office, and characterized into healthy, AR, and CRS groups. Endoscopically-guided swab samples were obtained from the MM and IM bilaterally. Bacterial microbiota were characterized by sequencing the V3-V4 region of the 16S ribosomal RNA (rRNA) gene. RESULTS: Intersubject microbiome analyses were conducted in 65 subjects: 8 healthy, 11 AR, and 46 CRS (25 CRS with nasal polyps [CRSwNP]; 21 CRS without nasal polyps [CRSsNP]). Intrasubject analyses were conducted for 48 individuals (4 controls, 11 AR, 8 CRSwNP, and 15 CRSwNP). There was considerable intersubject microbiota variability, but intrasubject profiles were similar (p = 0.001, nonparametric t test). Intrasubject bacterial diversity was significantly reduced in MM of CRSsNP subjects compared to IM samples (p = 0.022, nonparametric t test). CRSsNP MM samples were enriched in Streptococcus, Haemophilus, and Fusobacterium spp. but exhibited loss of diversity compared to healthy, CRSwNP, and AR subject-samples (p < 0.05; nonparametric t test). CRSwNP patients were enriched in Staphylococcus, Alloiococcus, and Corynebacterium spp. CONCLUSION: This study presents the sinonasal microbiome profile in one of the larger populations of non-CRS and CRS subjects, and is the first office-based cohort in the literature. In contrast to healthy, AR, and CRSwNP subjects, CRSsNP MM samples exhibited decreased microbiome diversity and anaerobic enrichment. CRSsNP MM samples had reduced diversity compared to same-subject IM samples, a novel finding.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "25027172", + "title": "Non-toxigenic penicillin-resistant cutaneous C. diphtheriae infection: a case report and review of the literature.", + "year": 2015, + "journal": "Journal of infection and public health", + "authors": [ + "FitzGerald RP", + "Rosser AJ", + "Perera DN" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.39040389212316, + "mesh_terms": [ + "Adolescent", + "Anti-Bacterial Agents", + "Corynebacterium diphtheriae", + "Diphtheria", + "Female", + "Humans", + "Penicillin Resistance", + "Penicillins", + "Skin Diseases, Bacterial" + ], + "raw_abstract": "Here, we report a case of non-toxigenic Corynebacterium diphtheriae in a previously healthy 14-year-old girl that was acquired in Ethiopia and presented locally. This is the first clinical case of penicillin-resistant C. diphtheriae in the UK. This is significant finding because penicillin is the recommended first-line agent for the prophylaxis against and treatment of C. diphtheriae in patients who are not allergic to penicillin.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33084948", + "title": "Taxonomic profiling and functional characterization of the healthy human oral bacterial microbiome from the north Indian urban sub-population.", + "year": 2021, + "journal": "Archives of microbiology", + "authors": [ + "Verma D", + "Srivastava A", + "Garg PK", + "Akhter Y", + "Dubey AK", + "Mishra S", + "Deo SVS" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.38165800523304444, + "mesh_terms": [ + "Adolescent", + "Adult", + "Bacteria", + "Female", + "High-Throughput Nucleotide Sequencing", + "Humans", + "India", + "Male", + "Metagenome", + "Microbiota", + "Middle Aged", + "Mouth", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Poor oral health has broad consequences that can be seen at personal as well as societal levels, especially in developing countries like India. We have limited information on the healthy oral cavity's inhabitant microorganisms that play a crucial role in overall oral health. In a comprehensive culture-independent approach, the bacterial composition of healthy human oral cavities was determined from a sub-population of northern India. During this study, 20 mouthwash-derived metagenomes were explored for identifying bacterial diversity using the 16S rRNA hypervariable V3 region with the MiSeq Illumina platform. On the taxonomy assignment of operational taxonomic units (OTUs), 20 assigned phyla and 162 genera were recovered among the participants. The mean relative abundance revealed that Streptococcus was the dominant genera among the participants. However, at inter-individual analysis, Neisseria and Haemophilus exhibited first-order dominance among five and three healthy individuals, respectively. Correlation studies indicate that Streptococcus shares a strong relationship with Rothia, Corynebacterium, Prevotella, and Veillonella, whereas it was negatively correlated with Neisseria, Aggregatibacter, Porphyromonas, and Fusobacteria like Gram-negative bacteria. Bacterial diversity showed insignificant differences at the level of age and gender within and between the participants. The results support several of the major findings of previous reports on the healthy oral microbiome of the Indian population, however, the present investigation further illustrates that demographic region leaves an impact on overall bacterial composition. The study will assist in a better understanding of the oral microbiome from region-specific Indian population that was otherwise highly under-represented.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28538949", + "title": "The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls.", + "year": 2017, + "journal": "JAMA dermatology", + "authors": [ + "Ring HC", + "Thorsen J", + "Saunte DM", + "Lilje B", + "Bay L", + "Riis PT", + "Larsen N", + "Andersen LO", + "Nielsen HV", + "Miller IM", + "Bjarnsholt T", + "Fuursted K", + "Jemec GB" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.38165520379599105, + "mesh_terms": [ + "Adult", + "Bacteria", + "Case-Control Studies", + "DNA, Bacterial", + "Female", + "Hidradenitis Suppurativa", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Sequence Analysis, DNA", + "Skin" + ], + "raw_abstract": "IMPORTANCE: Although the pathogenesis of hidradenitis suppurativa (HS) remains enigmatic, several factors point to potential involvement of the cutaneous microbiome. Insight into the cutaneous microbiome in HS using next-generation sequencing may provide novel data on the microbiological diversity of the skin. OBJECTIVE: To investigate the follicular skin microbiome in patients with HS and in healthy controls. DESIGN, SETTING, AND PARTICIPANTS: This case-control study obtained punch biopsy specimens from patients with HS (lesional and nonlesional) and healthy controls between October 1, 2014, and August 1, 2016. Data were analyzed from March to November 2016. Patients with HS were recruited from the Department of Dermatology, Zealand University Hospital, Roskilde, Denmark. Biopsy specimens were analyzed at the Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark. None of the participants received any antibiotics (systemic or topical therapy) within 1 month before the study. In patients with HS, biopsy specimens were obtained from lesional skin (axilla or groin) and nonlesional skin. Only nodules containing at least 1 visible hair follicle were biopsied. Biopsy specimens from healthy controls were obtained from the axilla only. MAIN OUTCOMES AND MEASURES: The different microbiomes were investigated using next-generation sequencing targeting 16S and 18S ribosomal RNA. RESULTS: The skin microbiome was characterized in 30 patients with HS (mean [SD] age, 46.9 [14.0] years; 19 [63% female]) and 24 healthy controls (mean [SD] age, 32.2 [12.0] years; 13 [54% female]). The next-generation sequencing data provided a previously unreported (to our knowledge) characterization of the skin microbiome in HS. The study demonstrated that the microbiome in HS differs significantly from that in healthy controls in lesional and nonlesional skin. Overall, the following 5 microbiome types were identified: Corynebacterium species (type I), Acinetobacter and Moraxella species (type II), Staphylococcus epidermidis (type III), Porphyromonas and Peptoniphilus species (type IV), and Propionibacterium acnes (type V). In lesional skin, microbiome types consisted predominantly of type I or type IV. Microbiome type IV was not detected in healthy controls. Several taxa, including Propionibacterium, showed a significantly higher relative abundance in healthy controls vs HS skin, indicating that Propionibacterium may be part of the pathogenesis in HS. CONCLUSIONS AND RELEVANCE: The study findings suggest a link between a dysbiotic cutaneous microbiome and HS.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31228520", + "title": "Psoriatic lesions are characterized by higher bacterial load and imbalance between Cutibacterium and Corynebacterium.", + "year": 2020, + "journal": "Journal of the American Academy of Dermatology", + "authors": [ + "Quan C", + "Chen XY", + "Li X", + "Xue F", + "Chen LH", + "Liu N", + "Wang B", + "Wang LQ", + "Wang XP", + "Yang H", + "Zheng J" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.3790496763717843, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Bacterial Load", + "Corynebacterium", + "DNA, Bacterial", + "Female", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Propionibacterium", + "Psoriasis", + "RNA, Ribosomal, 16S", + "Severity of Illness Index", + "Skin", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Several studies have found that the microbiota of psoriatic lesions is different from that of healthy skin. OBJECTIVE: To characterize the microbiota of lesional and unaffected skin in patients with psoriasis and controls and investigate the correlation between cutaneous microbiota and clinical features of psoriasis. METHODS: Using quantitative polymerase chain reaction and 16S rRNA sequencing, we assayed the profiles of cutaneous microbiota in controls, unaffected skin, and psoriatic lesions. We also investigated the correlation of psoriasis-associated taxa with clinical characteristics. RESULTS: High bacterial load was identified in the psoriatic lesions compared with unaffected skin and controls. There was an imbalance between Cutibacterium (also known as Propionibacterium) and Corynebacterium in psoriatic skin. Lesions showed a higher proportion of Corynebacterium and a lower proportion of Cutibacterium compared with unaffected skin and controls. Corynebacterium was correlated with the severity of local lesions, whereas Cutibacterium showed correlation with the abnormity of skin capacitance. LIMITATIONS: We did not conduct a longitudinal study. CONCLUSIONS: Psoriatic lesions are characterized by higher bacterial load and imbalance between Cutibacterium and Corynebacterium.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36583787", + "title": "Nasal Microbiome in COVID-19: A Potential Role of Corynebacterium in Anosmia.", + "year": 2022, + "journal": "Current microbiology", + "authors": [ + "Nardelli C", + "Scaglione GL", + "Testa D", + "Setaro M", + "Russo F", + "Di Domenico C", + "Atripaldi L", + "Zollo M", + "Corrado F", + "Salvatore P", + "Pinchera B", + "Gentile I", + "Capoluongo E" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.34549276127518647, + "mesh_terms": [ + "Humans", + "Anosmia", + "RNA, Ribosomal, 16S", + "COVID-19", + "SARS-CoV-2", + "Microbiota", + "Bacteria", + "Corynebacterium", + "Actinobacteria" + ], + "raw_abstract": "The evolution and the development of the symptoms of Coronavirus disease 19 (COVID-19) are due to different factors, where the microbiome plays a relevant role. The possible relationships between the gut, lung, nasopharyngeal, and oral microbiome with COVID-19 have been investigated. We analyzed the nasal microbiome of both positive and negative SARS-CoV-2 individuals, showing differences in terms of bacterial composition in this niche of respiratory tract. The microbiota solution A (Arrow Diagnostics) was used to cover the hypervariable V1-V3 regions of the bacterial 16S rRNA gene. MicrobAT Suite and MicrobiomeAnalyst program were used to identify the operational taxonomic units (OTUs) and to perform the statistical analysis, respectively. The main taxa identified in nasal microbiome of COVID-19 patients and in Healthy Control subjects belonged to three distinct phyla: Proteobacteria (HC\u2009=\u200914%, Cov19\u2009=\u200935.8%), Firmicutes (HC\u2009=\u200928.8%, Cov19\u2009=\u200930.6%), and Actinobacteria (HC\u2009=\u200956.7%, Cov19\u2009=\u200914.4%) with a relative abundance\u2009>\u20091% in all groups. A significant reduction of Actinobacteria in Cov19 group compared to controls (P\u2009<\u20090.001, FDR\u2009=\u20090.01) was found. The significant reduction of Actinobacteria was identified in all taxonomic levels down to the genus (P\u2009<\u20090.01) using the ANOVA test. Indeed, a significantly reduced relative abundance of Corynebacterium was found in the patients compared to healthy controls (P\u2009=\u20090.001). Reduced abundance of Corynebacterium has been widely associated with anosmia, a common symptom of COVID-19 as suffered from our patients. Contrastingly, the Corynebacterium genus was highly represented in the nasal mucosa of healthy subjects. Further investigations on larger cohorts are necessary to establish functional relationships between nasal microbiota content and clinical features of COVID-19.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32508748", + "title": "Characteristics of the Urinary Microbiome From Patients With Gout: A Prospective Study.", + "year": 2020, + "journal": "Frontiers in endocrinology", + "authors": [ + "Ning Y", + "Yang G", + "Chen Y", + "Zhao X", + "Qian H", + "Liu Y", + "Chen S", + "Shi G" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.3410218952310593, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biomarkers", + "Case-Control Studies", + "DNA, Bacterial", + "Follow-Up Studies", + "Gout", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Prognosis", + "Prospective Studies", + "RNA, Ribosomal, 16S", + "Urine" + ], + "raw_abstract": "The role of host microbes in the pathogenesis of several diseases has been established, and altered microbiomes have been related to diseases. However, the variability of the urinary microbiome in individuals with gout has not been evaluated to date. Therefore, we conducted the present prospective study to characterize the urinary microbiome and its potential relation to gout. Urine samples from 30 patients with gout and 30 healthy controls were analyzed by Illumina MiSeq sequencing of the 16S rRNA hypervariable regions, and the microbiomes were compared according to alpha-diversity indices, complexity (beta diversity) with principal component analysis, and composition with linear discriminant analysis effect size. The most significantly different taxa at the phylum and genus levels were identified, and their potential as biomarkers for discriminating gout patients was assessed based on receiver operating characteristic (ROC) curve analysis. Compared with the healthy controls, there was a dramatic decrease in microbial richness and diversity in the urine of gout patients. The phylum Firmicutes and its derivatives (Lactobacillus_iners, Family_XI, and Finegoldia), the phylum Actinobacteria and its derivatives (unidentified_Actinobacteria, Corynebacteriales, Corynebacteriale, Corynebacterium_1, and Corynebacterium_tuberculostearicum), and the genera", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32053729", + "title": "The Microbiome of the Meibum and Ocular Surface in Healthy Subjects.", + "year": 2020, + "journal": "Investigative ophthalmology & visual science", + "authors": [ + "Suzuki T", + "Sutani T", + "Nakai H", + "Shirahige K", + "Kinoshita S" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.34033516486082244, + "mesh_terms": [ + "Adult", + "Aged", + "Eyelids", + "Female", + "Healthy Volunteers", + "Humans", + "Lacrimal Apparatus", + "Male", + "Meibomian Glands", + "Microbiota", + "Middle Aged", + "Young Adult" + ], + "raw_abstract": "PURPOSE: The purpose of this study was to investigate the microbiome in the meibum, conjunctival sac, and eyelid skin in young and elderly healthy subjects, and analyze the effect that age, sex, and region have on microbiome composition. METHODS: This study involved 36 healthy subjects (young-age subjects: 9 men/9 women, age range: 20-35 years; elderly age subjects: 9 men/9 women, age range: 60-70 years). In all subjects, lower-eyelid meibum, lower conjunctival sac, and lower-eyelid skin specimens were collected from one eye, and then stored at -20\u00b0C. Taxonomic composition of the microbiome was obtained via 16S rRNA gene sequencing, and then analyzed. RESULTS: The meibum microbiome showed a high \u03b1-diversity (within-community diversity), particularly in the young subjects. However, in approximately 30% of the elderly subjects, a low-diversity microbiome dominated by Corynebacterium sp. or Neisseriaceae was observed. In the young subjects, the microbiome of the meibum resembled that of the conjunctival-sac, yet in the elderly subjects, the microbiome of the conjunctival-sac became more similar to that of the eyelid skin. The eyelid-skin microbiome was relatively simple, and was typically dominated by Propionibacterium acnes in the young subjects, or by Corynebacterium sp. or Neisseriaceae in the elderly subjects. In both age groups, no significant difference was seen between the men and women in regard to the meibum, conjunctival-sac, and eyelid-skin microbiome. CONCLUSIONS: Our findings confirmed that the meibum of healthy adult-age subjects harbors highly diverse microbiota, and revealed that the meibum microbiome, especially the decrease of its diversity, alters with aging and may affect the homeostasis of the ocular surface.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36099461", + "title": "Corynebacterium spp.: relationship of pathogenic properties and antimicrobial resistance.", + "year": 2022, + "journal": "Klinicheskaia laboratornaia diagnostika", + "authors": [ + "Mangutov EO", + "Alieva AA", + "Kharseeva GG", + "Voronina NA", + "Alekseeva LP", + "Evdokimova VV", + "Yakusheva OA", + "Popivnenko MD" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.33812219440010977, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Anti-Infective Agents", + "Corynebacterium", + "Corynebacterium Infections", + "Drug Resistance, Bacterial", + "Humans" + ], + "raw_abstract": "Corynebacterium spp. are part of the human microbiome, but can cause the development of inflammatory diseases of various localization. Purpose - to evaluate the relationship between pathogenic properties and resistance to antimicrobial drugs (AMD) of Corynebacterium spp. from patients with inflammatory diseases of the respiratory tract. Strains of Corynebacterium spp. isolated from patients with inflammatory diseases of the respiratory tract (99 pcs.) and practically healthy individuals (33 pcs.). Isolates were identified by mass spectrometric method (MALDI-ToFMS), their adhesive and invasive activity on Hep-2 cells, cytopathic effect (CPE) in CHO-K1 cell culture, and resistance to antimicrobial drugs (AMD) were determined. Indicators of adhesion (3.65\u00b10.679(CFU\u00b1m)x102/ml), invasion (1.72\u00b10.230 (CFU\u00b1m)x102/ml), cytotoxicity (69.1\u00b13.8% of dead CHO-K1 cells ) Corynebasterium spp. strains isolated from patients are higher (p\u22640.05) than similar indicators in practically healthy people. 90.9% of isolates from patients had resistance to AMD, in most cases (57.6\u00b14.9%) resistance to only one AMP was noted, less often to two (25.2\u00b14.3%), three or more (8.08\u00b12.7%). According to the results of correlation-regression analysis, pathogenic properties (adhesiveness, invasiveness, cytotoxicity) of Corynebacterium spp. strains isolated from patients are in close direct relationship with resistance to AMD. This indicates the importance of identifying strains of non-diphtheria corynebacteria resistant to AMDs, which, under the influence of developing resistance to AMDs, can increase their pathogenic potential, moving from commensalism to parasitism.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34687837", + "title": "Ocular microbial diversity, community structure, and function at high altitude.", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Li Z", + "Xiang Y", + "Wang Y", + "Wan W", + "Ye Z", + "Zheng S", + "Chen Y", + "Xiong L", + "Zhu L", + "Ji Y", + "Hu K" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.33328083124197255, + "mesh_terms": [ + "Altitude", + "Bacteria", + "Conjunctiva", + "Humans", + "Microbiota", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "PURPOSE: To investigate the composition and function of ocular surface microbiome in healthy people from different altitudes. METHODS: Thirty-two healthy people living in a high altitude region and 30 sex- and age-matched individuals living in a low altitude region were enrolled. Samples were collected from the lower conjunctival sac of one randomly chosen eye for each participant. 16S rRNA sequencing was conducted to study the bacterial community composition and predict gene function using PICRUSt software. RESULTS: Microbial diversity and richness was significantly decreased in samples from highlanders as calculated by Abundance-based Coverage Estimator (ACE) index, Chao1 index, and observed-species index (all p\u00a0<\u00a00.01). Principle coordinate analysis (PCoA) suggested significantly distinct clustering of the conjunctival sac bacterial communities between two groups (p\u00a0=\u00a00.03), especially the dominant genera. The relative abundances of Corynebacterium, Staphylococcus, and Anaerococcus were significantly enriched in highlanders, while those of Pseudomonas and Massilia were significantly decreased as compared with lowlanders (p\u00a0<\u00a00.01). In the functional annotation analysis, we found that 74 gene pathways, mainly in metabolism, differed in abundance. Pathways related to immune system diseases and infectious diseases were also enriched in highlanders. CONCLUSION: The composition and function of ocular surface microbiome in highlanders were distinct from those of lowlanders and our study may provide a reference catalog of the healthy conjunctival microbiome in highlanders.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30108246", + "title": "The urinary microbiome associated with bladder cancer.", + "year": 2018, + "journal": "Scientific reports", + "authors": [ + "Bu\u010devi\u0107 Popovi\u0107 V", + "\u0160itum M", + "Chow CT", + "Chan LS", + "Roje B", + "Terzi\u0107 J" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.3273964067017618, + "mesh_terms": [ + "Aged", + "Aged, 80 and over", + "Bacteria", + "Case-Control Studies", + "DNA, Bacterial", + "Healthy Volunteers", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Urinary Bladder", + "Urinary Bladder Neoplasms", + "Urine" + ], + "raw_abstract": "Recent findings suggest that human microbiome can influence the development of cancer, but the role of microorganisms in bladder cancer pathogenesis has not been explored yet. The aim of this study was to characterize and compare the urinary microbiome of bladder cancer patients with those of healthy controls. Bacterial communities present in urine specimens collected from 12 male patients diagnosed with bladder cancer, and from 11 healthy, age-matched individuals were analysed using 16S sequencing. Our results show that the most abundant phylum in both groups was Firmicutes, followed by Actinobacteria, Bacteroidetes and Proteobacteria. While microbial diversity and overall microbiome composition were not significantly different between groups, we could identify operational taxonomic units (OTUs) that were more abundant in either group. Among those that were significantly enriched in the bladder cancer group, we identified an OTU belonging to genus Fusobacterium, a possible protumorigenic pathogen. In an independent sample of 42 bladder cancer tissues, 11 had Fusobacterium nucleatum sequences detected by PCR. Three OTUs from genera Veillonella, Streptococcus and Corynebacterium were more abundant in healthy urines. However, due to the limited number of participants additional studies are needed to determine if urinary microbiome is associated with bladder cancer.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29216202", + "title": "Composition and variation of respiratory microbiota in healthy military personnel.", + "year": 2017, + "journal": "PloS one", + "authors": [ + "Hang J", + "Zavaljevski N", + "Yang Y", + "Desai V", + "Ruck RC", + "Macareo LR", + "Jarman RG", + "Reifman J", + "Kuschner RA", + "Keiser PB" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.30019240842092926, + "mesh_terms": [ + "Corynebacterium", + "DNA, Ribosomal", + "Female", + "Humans", + "Male", + "Microbiota", + "Military Personnel", + "Nasal Cavity", + "Nasopharynx", + "Propionibacterium", + "RNA, Ribosomal, 16S", + "Respiratory System", + "Staphylococcus" + ], + "raw_abstract": "Certain occupational and geographical exposures have been associated with an increased risk of lung disease. As a baseline for future studies, we sought to characterize the upper respiratory microbiomes of healthy military personnel in a garrison environment. Nasal, oropharyngeal, and nasopharyngeal swabs were collected from 50 healthy active duty volunteers eight times over the course of one year (1107 swabs, completion rate = 92.25%) and subjected to pyrosequencing of the V1-V3 region of 16S rDNA. Respiratory bacterial taxa were characterized at the genus level, using QIIME 1.8 and the Ribosomal Database Project classifier. High levels of Staphylococcus, Corynebacterium, and Propionibacterium were observed among both nasal and nasopharyngeal microbiota, comprising more than 75% of all operational taxonomical units (OTUs). In contrast, Streptococcus was the sole dominant bacterial genus (approximately 50% of all OTUs) in the oropharynx. The average bacterial diversity was greater in the oropharynx than in the nasal or nasopharyngeal region at all time points. Diversity analysis indicated a significant overlap between nasal and nasopharyngeal samples, whereas oropharyngeal samples formed a cluster distinct from these two regions. The study produced a large set of pyrosequencing data on the V1-V3 region of bacterial 16S rDNA for the respiratory microbiomes of healthy active duty Service Members. Pre-processing of sequencing reads showed good data quality. The derived microbiome profiles were consistent both internally and with previous reports, suggesting their utility for further analyses and association studies based on sequence and demographic data.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36728960", + "title": "Perturbations of the ocular surface microbiome and their effect on host immune function.", + "year": 2023, + "journal": "Current opinion in ophthalmology", + "authors": [ + "Chang CJ", + "Winn BJ" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.29561172792034923, + "mesh_terms": [ + "Animals", + "Humans", + "Inflammation", + "Contact Lenses", + "Microbiota", + "Immunity" + ], + "raw_abstract": "PURPOSE OF REVIEW: Current literature describing the ocular surface microbiome and host immunity are reviewed alongside experiments studying perturbations of the microbiome to explore the hypothesis that disruption of a healthy microbiome may predispose the ocular surface to inflammation and infection. RECENT FINDINGS: The ocular surface of healthy subjects is colonized by stable, pauci-microbial communities that are tolerant to the host immune response and are dominated by the genera Corynebacterium , Propionibacterium , and Staphylococcus . In animal studies, commensal microbes on the ocular surface interact with toll-like receptors to regulate the immune system through immune cell and inflammatory cytokine production, promoting homeostasis and protecting against infection. Contact lens wear, lens wash solutions, and preserved topical medications can disrupt the native microbiome and alter the relative diversity and composition of microbes on the ocular surface. SUMMARY: The ocular surface microbiome confers protection against pathogenic colonization and immune dysregulation. Disruption of this microbiome by exogenous factors may alter the resistance of the ocular surface to infection. Further study of the relationships between human ocular surface microbiome and the local immune response are needed.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38820284", + "title": "Bacterial and fungal communities in chronic rhinosinusitis with nasal polyps.", + "year": 2024, + "journal": "PloS one", + "authors": [ + "Uzuno\u011flu E", + "Kalkanc\u0131 A", + "K\u0131l\u0131\u00e7 E", + "K\u0131z\u0131l Y", + "Aydil U", + "Diker KS", + "Uslu SS" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.2931634313088901, + "mesh_terms": [ + "Humans", + "Sinusitis", + "Nasal Polyps", + "Female", + "Male", + "Adult", + "Chronic Disease", + "Middle Aged", + "Bacteria", + "Rhinitis", + "Fungi", + "RNA, Ribosomal, 16S", + "Microbiota", + "Case-Control Studies", + "Rhinosinusitis" + ], + "raw_abstract": "OBJECTIVE: Multiple inflammatory mechanisms dynamically interact in the development of chronic rhinosinusitis with nasal polyps (CRSwNP). Disruption of the relationship between host and environmental factors on the mucosal surface leads to the development of inflammation. Microorganisms constitute the most important part of environmental factors. METHODS: 28 volunteers (18 CRSwNP patients and 10 healthy individuals) were included in the study. Eight patients were recurrent nasal polyposis cases, and the remaining were primary cases. Swab samples were taken from the middle meatus under endoscopic examination from all participants. After DNA extraction, a library was created with the Swift Amplicon 16S + ITS kit and sequenced with Illumina Miseq. Sequence analysis was performed using QIIME, UNITE v8.2 database for ITS and Silva v138 for 16S rRNA. RESULTS: The predominant bacteria in all groups were Firmicutes, Proteobacteria, Actinobacteria as phyla and Staphylococcus, Corynebacterium, Sphingomonas as genera. Comparison of bacterial communities of CRSwNP patients and control group highlighted Corynebacterium, as the differentiating taxa for control group and Streptococcus, Moraxella, Rothia, Micrococcus, Gemella, and Prevotella for CRSwNP patients. The predominant fungal genus in all groups was Malassezia. Staphylococcus; showed a statistically significant negative correlation with Dolosigranulum. Corynebacterium had a positive correlation with Anaerococcus, and a negative correlation with Neisseria, Prevotella, Fusobacterium and Peptostreptococcus. CONCLUSION: Nasal microbiome of CRSwNP patients shows greater inter-individual variation than the control group. Corynebacterium is less abundant in patients with CRSwNP compared to the control group. Malassezia is the predominant fungus in the nasal cavity and paranasal sinuses and correlates positively with the abundance of Corynebacterium.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37026304", + "title": "Ocular conjunctival microbiome profiling in dry eye disease: A case control pilot study.", + "year": 2023, + "journal": "Indian journal of ophthalmology", + "authors": [ + "Gupta N", + "Chhibber-Goel J", + "Gupta Y", + "Mukherjee S", + "Maitra A", + "Sharma A", + "Tandon R" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.2700429478277723, + "mesh_terms": [ + "Humans", + "Pilot Projects", + "Conjunctiva", + "Dry Eye Syndromes", + "Microbiota", + "Bacteria", + "Tears", + "Case-Control Studies" + ], + "raw_abstract": "PURPOSE: Keratoconjunctivitis sicca (KCS) or dry eye disease (DED) is a multifactorial disease that results in discomfort, visual disturbance, and tear film instability with potential damage to the ocular surface. A pilot study was undertaken to determine if there were any major substantial differences in the ocular microbiome in DED patients versus healthy controls. METHODS: The bacterial communities residing in the conjunctiva of patients with DED (n = 4) and healthy controls (n = 4) were assessed by 16S ribosomal RNA (rRNA) gene sequencing of the V4-V5 region. RESULTS: The phyla Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were most dominant and accounted for 97% and 94.5% of all bacterial sequences in patients and controls, respectively. At the genus level, 27 bacterial genera were found with more than two-fold difference between patients and controls. Four of these - Acinetobacter, Corynebacterium, Lactobacillus, and Pseudomonas spp. - dominated the ocular microbiome of all subjects, but were proportionately lower in DED (16.5%) compared to controls (37.7%). Several bacterial genera were found to be unique in DED (34) and controls (24). CONCLUSION: This pilot study is an attempt to profile the ocular microbiome in patients with DED that demonstrated a higher concentration of microbial DNA compared to controls, with Firmicutes phyla dominating the bacterial population in patients with DED.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37757827", + "title": "Expanded microbiome niches of RAG-deficient patients.", + "year": 2023, + "journal": "Cell reports. Medicine", + "authors": [ + "Blaustein RA", + "Shen Z", + "Kashaf SS", + "Lee-Lin S", + "Conlan S", + "Bosticardo M", + "Delmonte OM", + "Holmes CJ", + "Taylor ME", + "Banania G", + "Nagao K", + "Dimitrova D", + "Kanakry JA", + "Su H", + "Holland SM", + "Bergerson JRE", + "Freeman AF", + "Notarangelo LD", + "Kong HH", + "Segre JA" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.2633522053384454, + "mesh_terms": [ + "Humans", + "Microbiota", + "Gastrointestinal Microbiome", + "Skin", + "Metagenome" + ], + "raw_abstract": "The complex interplay between microbiota and immunity is important to human health. To explore how altered adaptive immunity influences the microbiome, we characterize skin, nares, and gut microbiota of patients with recombination-activating gene (RAG) deficiency-a rare genetically defined inborn error of immunity (IEI) that results in a broad spectrum of clinical phenotypes. Integrating de novo assembly of metagenomes from RAG-deficient patients with reference genome catalogs provides an expansive multi-kingdom view of microbial diversity. RAG-deficient patient microbiomes exhibit inter-individual variation, including expansion of opportunistic pathogens (e.g., Corynebacterium bovis, Haemophilus influenzae), and a relative loss of body site specificity. We identify 35 and 27 bacterial species derived from skin/nares and gut microbiomes, respectively, which are distinct to RAG-deficient patients compared to healthy individuals. Underscoring IEI patients as potential reservoirs for viral persistence and evolution, we further characterize the colonization of eukaryotic RNA viruses (e.g., Coronavirus 229E, Norovirus GII) in this patient population.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29969843", + "title": "Cariogenic microbiome and microbiota of the early primary dentition: A contemporary overview.", + "year": 2019, + "journal": "Oral diseases", + "authors": [ + "Fakhruddin KS", + "Ngo HC", + "Samaranayake LP" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.261617221217892, + "mesh_terms": [ + "Bacteria", + "Child", + "Child, Preschool", + "Dental Caries", + "Dental Plaque", + "Humans", + "Infant", + "Microbiota", + "Saliva", + "Sequence Analysis, DNA", + "Tooth", + "Tooth, Deciduous" + ], + "raw_abstract": "Recent advances in the field of molecular microbiology provide an unprecedented opportunity to decipher the vast diversity of the oral microbiome in health and disease. Here, we provide a contemporary overview of the oral microbiome and the microbiota of early childhood caries (ECC) with particular reference to newer analytical techniques. A MEDLINE search revealed a total of 20 metagenomic studies describing cariogenic microbiomes of ECC, 10 of which also detailed the healthy microbiomes. In addition, seven studies on site-specific microbiomes, focusing on acidogenic and aciduric microbiota of deep-dentinal lesions, were also reviewed. These studies evaluated plaque and saliva of children aged 1.5-11\u00a0years, in cohorts of 12-485 individuals. These studies reveal a very rich and diverse microbial communities, with hundreds of different phylotypes and microbial species, including novel species and phyla such as Scardovia wiggsiae, Slackia exigua, Granulicatella elegans, Firmicutes in the plaque biofilms of children with ECC. On the contrary, bacteria such as Streptococcus cristatus, S.\u00a0gordonii, S.\u00a0sanguinis, Corynebacterium matruchotii, and Neisseria flavescens were common in plaque biofilm of noncarious, healthy, tooth surfaces in subjects with caries. The review illustrates the immense complexity and the diversity of the human oral microbiota of the cariogenic plaque microbiome in ECC, and the daunting prospect of its demystification.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28175925", + "title": "Skin Microbiome in Small- and Large-plaque Parapsoriasis.", + "year": 2017, + "journal": "Acta dermato-venereologica", + "authors": [ + "Salava A", + "Pereira P", + "Aho V", + "V\u00e4kev\u00e4 L", + "Paulin L", + "Auvinen P", + "Ranki A", + "Lauerma A" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.25944075743981043, + "mesh_terms": [ + "Adult", + "Aged", + "Aged, 80 and over", + "Bacteria", + "Case-Control Studies", + "Female", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Parapsoriasis", + "Ribotyping", + "Skin" + ], + "raw_abstract": "Staphylococcal enterotoxins have been shown to promote lymphoma-associated immune dysregulation. This study examined changes in the skin microbiome of parapsoriasis compared with intact skin. Swab microbiome specimens were taken of the parapsoriasis lesions of 13 patients. Control samples were taken from contralateral healthy sides of the body. Microbiotas were characterized by sequencing the V1-V3 region of the 16S ribosomal RNA bacterial genes on the Illumina MiSeq platform. The most common genera in the microbiome data were Propionibacterium (27.13%), Corynebacterium (21.20%) and Staphylococcus (4.63%). Out of the Staphylococcus sequences, 39.6% represented S. epidermidis, with the rest including S. hominis, S. capitis and unidentified species. No significant differences were observed between the patients' parapsoriasis and contralateral healthy skin or between large- and small-plaque parapsoriasis. Notable interpersonal variation was demonstrated. These results suggest that parapsoriasis is not associated with significant alterations in the cutaneous bacterial microbiome.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37997887", + "title": "Infectious disease for the rhinologist.", + "year": 2024, + "journal": "Current opinion in otolaryngology & head and neck surgery", + "authors": [ + "Png LH", + "Ng DHL", + "Teo NWY" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.25894224092588236, + "mesh_terms": [ + "Humans", + "Pandemics", + "Paranasal Sinuses", + "Sinusitis", + "Chronic Disease", + "COVID-19", + "Communicable Diseases", + "Rhinitis" + ], + "raw_abstract": "PURPOSE OF REVIEW: The purpose of this review is to summarize the recent literature relating to viral, fungal and bacterial infections and their interactions within the sinonasal tract in the past 18 months. RECENT FINDINGS: Coronavirus disease 2019 (COVID-19)-associated olfactory dysfunction (OD) is variant dependent. Magnetic resonance imaging studies have found greater olfactory cleft opacification and higher olfactory bulb volume in post-COVID-19 OD. Olfactory training remains the mainstay of treatment, while platelet-rich plasma injections and ultramicronized palmitoylethanolamide and luteolin combination oral supplementation have shown early promise.Consensus statements on paranasal sinus fungal balls and acute invasive fungal sinusitis have been released.Studies on the nasal microbiome have reported Staphylococcus and Corynebacterium as the most abundant genera, with higher levels of Staphylococcus and Corynebacterium being found in patients with chronic rhinosinusitis (CRS) and healthy individuals respectively. However, there is conflicting evidence on the significance of biodiversity of the nasal microbiome found in CRS versus healthy patients. SUMMARY: While the peak of the COVID-19 pandemic is behind us, its sequelae continue to pose treatment challenges. Further studies in OD have implications in managing the condition, beyond those afflicted post-COVID-19 infection. Similarly, more research is needed in studying the nasal microbiome and its implications in the development and treatment of CRS.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28852195", + "title": "Temporal Stability and Composition of the Ocular Surface Microbiome.", + "year": 2017, + "journal": "Scientific reports", + "authors": [ + "Ozkan J", + "Nielsen S", + "Diez-Vives C", + "Coroneo M", + "Thomas T", + "Willcox M" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.2588876118902885, + "mesh_terms": [ + "Adult", + "Conjunctiva", + "Eyelids", + "Female", + "Humans", + "Male", + "Metagenome", + "Metagenomics", + "Microbiota", + "Middle Aged", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "To determine if there is a core ocular surface microbiome and whether there are microbial community changes over time, the conjunctiva of 45 healthy subjects were sampled at three time points over three months and processed using culture-dependent and -independent methods. Contaminant taxa were removed using a linear regression model using taxa abundances in negative controls as predictor of taxa abundances in subject samples. Both cultured cell counts and sequencing indicated low microbial biomass on the ocular surface. No cultured species was found in all subjects at all times or in all subjects at any one time. After removal of contaminant taxa identified in negative controls using a statistical model, the most commonly detected taxon was Corynebacterium (11.1%). No taxa were found in all subjects at all times or in all subjects in any one time, but there were 26 taxa present in at least one or more subjects at all times including Corynebacterium and Streptococcus. The ocular surface contains a low diversity of microorganisms. Using culture dependent and independent methods, the ocular surface does not appear to support a substantial core microbiome. However, consistently present taxa could be observed within individuals suggesting the possibility of individual-specific core microbiomes.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36241544", + "title": "Characterization of the nasopharyngeal microbiome in patients with Kawasaki disease.", + "year": 2022, + "journal": "Anales de pediatria", + "authors": [ + "S\u00e1nchez-Manubens J", + "Henares D", + "Mu\u00f1oz-Almagro C", + "Brotons de Los Reyes P", + "Timoneda N", + "Ant\u00f3n J" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.24737941417385445, + "mesh_terms": [ + "Child", + "Humans", + "RNA, Ribosomal, 16S", + "Case-Control Studies", + "Mucocutaneous Lymph Node Syndrome", + "Nasopharynx", + "Microbiota", + "Corynebacterium" + ], + "raw_abstract": "INTRODUCTION: The aetiology of Kawasaki disease (KD) remains unknown. Several studies have linked the human microbiome with some diseases. However, there are limited studies on the role of the respiratory microbiome in KD. The aim of our study was to make a more thorough analysis of the causes and processes that increase the susceptibility to KD. METHODS: Case-control study comparing the respiratory microbiome of KD patients with that of healthy children. The V3-V4 region of the 16S rRNA bacterial gene and 16 respiratory viruses were analysed by real-time polimerase-chain reaction. We used the Ribosomal Database Project (RDP) version 11.5 (taxonomic assignment). RESULTS: The initial sample included 11 cases and 11 controls matched for age, sex and seasonality. One of the cases was excluded to poor sample quality. The final analysis included 10 cases and 10 controls. In the case group, the analysis detected Haemophilus, Moraxella, Streptococcus and Corynebacterium species (27.62%, 19.71%, 25.28%, 11.86%, respectively). In the control group, it found Haemophilus, Streptococcus, Moraxella, and Dolosigranulum species (38.59%, 23.71%, 16.08, 8.93%, respectively). We found a higher relative abundance of Corynebacterium in patients with KD (11.86% vs. 1.55%; P\u202f=\u202f0.004). CONCLUSIONS: To our knowledge, this is the first study that has found differences in the composition of the respiratory microbiome between patients with KD and healthy controls. The relative abundance of Corynebacterium spp. was greater in the KD group. This study shows differences in the microbiome between cases and controls, which suggests that the microbiome may play a role in facilitating the development of KD.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "24939571", + "title": "The HLA-DQ2 genotype selects for early intestinal microbiota composition in infants at high risk of developing coeliac disease.", + "year": 2015, + "journal": "Gut", + "authors": [ + "Olivares M", + "Neef A", + "Castillejo G", + "Palma GD", + "Varea V", + "Capilla A", + "Palau F", + "Nova E", + "Marcos A", + "Polanco I", + "Ribes-Koninckx C", + "Ortigosa L", + "Izquierdo L", + "Sanz Y" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.23991188542475606, + "mesh_terms": [ + "Celiac Disease", + "Clostridium", + "Feces", + "Female", + "Genetic Markers", + "Genotype", + "HLA-DQ Antigens", + "Haplotypes", + "Humans", + "Infant", + "Intestines", + "Male", + "Microbiota", + "Prospective Studies", + "Real-Time Polymerase Chain Reaction", + "Risk Factors" + ], + "raw_abstract": "OBJECTIVE: Intestinal dysbiosis has been associated with coeliac disease (CD), but whether the alterations are cause or consequence of the disease is unknown. This study investigated whether the human leukocyte antigen (HLA)-DQ2 genotype is an independent factor influencing the early gut microbiota composition of healthy infants at family risk of CD. DESIGN: As part of a larger prospective study, a subset (n=22) of exclusively breastfed and vaginally delivered infants with either high genetic risk (HLA-DQ2 carriers) or low genetic risk (non-HLA-DQ2/8 carriers) of developing CD were selected from a cohort of healthy infants with at least one first-degree relative with CD. Infant faecal microbiota was analysed by 16S rRNA gene pyrosequencing and real time quantitative PCR. RESULTS: Infants with a high genetic risk had significantly higher proportions of Firmicutes and Proteobacteria and lower proportions of Actinobacteria compared with low-risk infants. At genus level, high-risk infants had significantly less Bifidobacterium and unclassified Bifidobacteriaceae proportions and more Corynebacterium, Gemella, Clostridium sensu stricto, unclassified Clostridiaceae, unclassified Enterobacteriaceae and Raoultella proportions. Quantitative real time PCR also revealed lower numbers of Bifidobacterium species in infants with high genetic risk than in those with low genetic risk. In high-risk infants negative correlations were identified between Bifidobacterium species and several genera of Proteobacteria (Escherichia/Shigella) and Firmicutes (Clostridium). CONCLUSIONS: The genotype of infants at family risk of developing CD, carrying the HLA-DQ2 haplotypes, influences the early gut microbiota composition. This finding suggests that a specific disease-biased host genotype may also select for the first gut colonisers and could contribute to determining disease risk.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32472074", + "title": "Station and train surface microbiomes of Mexico City's metro (subway/underground).", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Hern\u00e1ndez AM", + "Vargas-Robles D", + "Alcaraz LD", + "Peimbert M" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.23033472489751913, + "mesh_terms": [ + "Bacteria", + "DNA, Bacterial", + "DNA, Ribosomal", + "Environmental Microbiology", + "Equipment Contamination", + "Humans", + "Mexico", + "Microbiota", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Railroads", + "Sequence Analysis, DNA", + "Transportation", + "Urban Renewal" + ], + "raw_abstract": "The metro is one of the more representative urban transportation systems of Mexico City, and it transports approximately 4.5 million commuters every day. Large crowds promote the exchange of microbes between humans. In this study, we determined the bacterial diversity profile of the Mexico City metro by massive sequencing of the 16S rRNA gene. We identified a total of 50,174 operational taxonomic units (OTUs) and 1058 genera. The metro microbiome was dominated by the phylum Actinobacteria and by the genera Cutibacterium (15%) (C. acnes 13%), Corynebacterium (13%), Streptococcus (9%), and Staphylococcus (5%) (S. epidermidis; 4%), reflecting the microbe composition of healthy human skin. The metro likely microbial sources were skin, dust, saliva, and vaginal, with no fecal contribution detected. A total of 420 bacterial genera were universal to the twelve metro lines tested, and those genera contributed to 99.10% of the abundance. The annual 1.6 billion ridership makes this public transport a main hub for microbe-host-environment interactions. Finally, this study shows that the microbial composition of the Mexico City metro comes from a mixture of environmental and human sources and that commuters are exposed to healthy composition of the human microbiota.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "34381083", + "title": "Taxonomic profiling of skin microbiome and correlation with clinical skin parameters in healthy Koreans.", + "year": 2021, + "journal": "Scientific reports", + "authors": [ + "Kim JH", + "Son SM", + "Park H", + "Kim BK", + "Choi IS", + "Kim H", + "Huh CS" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.21965112367911338, + "mesh_terms": [ + "Adult", + "Age Factors", + "Aged", + "Asian People", + "Bacteria", + "DNA Barcoding, Taxonomic", + "Face", + "Female", + "Healthy Volunteers", + "Humans", + "Male", + "Metagenomics", + "Middle Aged", + "Skin", + "Water Loss, Insensible", + "Young Adult" + ], + "raw_abstract": "The interest in skin microbiome differences by ethnicity, age, and gender is increasing. Compared to other ethnic groups, studies on the skin microbiome of Koreans remains insufficient; we investigated facial skin microbiome characteristics according to gender and age among Koreans. Fifty-one healthy participants were recruited, the facial skin characteristics of each donor were investigated, their skin bacterial DNA was isolated and metagenomic analysis was performed. The donors were divided into two groups for age and sex each to analyze their skin microbiomes. Moreover, we investigated the correlation between the skin microbiome and clinical characteristics. The alpha diversity of the skin microbiome was significantly higher in the elderly, and beta diversity was significantly different according to age. The comparative skin microbials showed that the genus Lawsonella was more abundant in the younger age group, and Enhydrobacter was predominant in the older age group. Staphylococcus and Corynebacterium were more abundant in males, while Lactobacillus was more abundant in females. Lawsonella had a negative correlation with skin moisture and brown spots. Staphylococcus and Corynebacterium both had negative correlations with the number of UV spots and positive correlations with transepidermal water loss (TEWL). Furthermore, Staphylococcus aureus had a negative correlation with skin moisture parameters.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36557565", + "title": "Microbiome in Male Genital Mucosa (Prepuce, Glans, and Coronal Sulcus): A Systematic Review.", + "year": 2022, + "journal": "Microorganisms", + "authors": [ + "Gon\u00e7alves MFM", + "Fernandes \u00c2R", + "Rodrigues AG", + "Lisboa C" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.21581993509703956, + "mesh_terms": [], + "raw_abstract": "The human body represents a complex and diverse reservoir of microorganisms. Although the human microbiome remains poorly characterized and understood, it should not be underestimated, since recent studies have highlighted its importance in health. This is especially evident when considering microbiota in the male reproductive system, responsible for men\u2019s fertility and sexual behavior. Therefore, the aim of this systematic review is to provide an overview of the microbial communities of the healthy male genital mucosa and its role in disease. This study was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The search was limited to the English language and studies published until August 2022 that included culture-independent techniques for microbiome characterization in male genital mucosa. Ten articles were included. The bacterial composition of the male genital mucosa consists of several genera including Prevotella, Finegoldia, Peptoniphilus, Staphylococcus, Corynebacterium, and Anaerococcus, suggesting that the male genital microbiome composition shows similarities with the adjacent anatomical sites and is related with sexual intercourse. Moreover, male circumcision appears to influence the penile microbiome. Despite the lack of knowledge on the male genital mucosa microbiome in disease, it was reported that Staphylococcus warneri and Prevotella bivia were associated with balanoposthitis, whereas Enterobacteriaceae, Prevotella, and Fusobacterium were more abundant in male genital lichen sclerosus. The limited data and paucity of prospective controlled studies highlight the need for additional studies and established criteria for sampling methods and the microbiome assay procedure. Such a consensus would foster the knowledge about the composition of the genital microbiome of healthy males and its role in disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38643725", + "title": "The relationship between the gut microbiota and oxidative stress in the cognitive function of schizophrenia: A pilot study in China.", + "year": 2024, + "journal": "Schizophrenia research", + "authors": [ + "Li H", + "Huang Y", + "Liang L", + "Li H", + "Li S", + "Feng Y", + "Feng S", + "Wu K", + "Wu F" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.21036488439215228, + "mesh_terms": [ + "Humans", + "Schizophrenia", + "Gastrointestinal Microbiome", + "Male", + "Female", + "Oxidative Stress", + "Adult", + "Pilot Projects", + "China", + "Cognitive Dysfunction", + "Superoxide Dismutase", + "Middle Aged", + "Young Adult", + "Machine Learning" + ], + "raw_abstract": "Cognitive impairment is a core symptom of schizophrenia. The gut microbiota (GM) and oxidative stress may play important roles in the pathophysiological mechanisms of cognitive impairment. This study aimed to explore the relationship between GM and oxidative stress in the cognitive function of schizophrenia. GM obtained by 16S RNA sequencing and serum superoxide dismutase (SOD) levels from schizophrenia patients (N\u00a0=\u00a068) and healthy controls (HCs, N\u00a0=\u00a072) were analyzed. All psychiatric symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS). Cognitive function was assessed using the MATRICS Consensus Cognitive Battery (MCCB). Correlation analysis was used to explore the relationship between GM, SOD, and cognitive function. Machine learning models were used to identify potential biomarkers. Compared to HCs, the relative abundances of Collinsella, undefined Ruminococcus, Lactobacillus, Eubacterium, Mogibacterium, Desulfovibrio, Bulleidia, Succinivibrio, Corynebacterium, and Atopobium were higher in patients with schizophrenia, but Faecalibacterium, Anaerostipes, Turicibacter, and Ruminococcus were lower. In patients with schizophrenia, the positive factor, general factor, and total score of MCCB positively correlated with Lactobacillus, Collinsella, and Lactobacillus, respectively; SOD negatively correlated with Eubacterium, Collinsella, Lactobacillus, Corynebacterium, Bulleidia, Mogibacterium, and Succinivibrio, but positively correlated with Faecalibacterium, Ruminococcus, and MCCB verbal learning index scores; Faecalibacterium and Turicibacter were positively correlated with MCCB visual learning index scores and speed of processing index scores, respectively. Our findings revealed a correlation between SOD and GM and confirmed that cognitive dysfunction in patients with schizophrenia involves abnormal SOD levels and GM changes.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31842923", + "title": "Oral health and plaque microbial profile in juvenile idiopathic arthritis.", + "year": 2019, + "journal": "Pediatric rheumatology online journal", + "authors": [ + "Grevich S", + "Lee P", + "Leroux B", + "Ringold S", + "Darveau R", + "Henstorf G", + "Berg J", + "Kim A", + "Velan E", + "Kelly J", + "Baltuck C", + "Reeves A", + "Leahey H", + "Hager K", + "Brittnacher M", + "Hayden H", + "Miller S", + "McLean J", + "Stevens A" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.20340598208841254, + "mesh_terms": [ + "Adolescent", + "Arthritis, Juvenile", + "Case-Control Studies", + "Child", + "Cross-Sectional Studies", + "Dental Plaque", + "Female", + "Humans", + "Male", + "Microbiota", + "Mouth", + "Oral Health", + "Periodontitis", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: The oral microbiota has been implicated in the pathogenesis of rheumatoid arthritis through activation of mucosal immunity. This study tested for associations between oral health, microbial communities and juvenile idiopathic arthritis (JIA). METHODS: A cross-sectional exploratory study of subjects aged 10-18\u2009years with oligoarticular, extended oligoarticular and polyarticular JIA was conducted. Control groups included pediatric dental clinic patients and healthy volunteers. The primary aim was to test for an association between dental health indices and JIA; the secondary aim was to characterize the microbial profile of supragingival plaque using 16S rRNA gene sequencing. RESULTS: The study included 85 patients with JIA, 62 dental patients and 11 healthy child controls. JIA patients overall had significantly more gingival inflammation compared to dental patients, as evidenced by bleeding on probing of the gingiva, the most specific sign of active inflammation (p\u2009=\u20090.02). Overall, however, there was a trend towards better dental hygiene in the JIA patients compared to dental patients, based on indices for plaque, decay, and periodontitis. In the JIA patients, plaque microbiota analysis revealed bacteria belonging to genera Haemophilus or Kingella elevated, and Corynebacterium underrepresented. In poly JIA, bacteria belonging to the genus Porphyromonas was overrepresented and Prevotella was underrepresented. CONCLUSION: Increased gingival inflammation in JIA was independent of general oral health, and thus cannot be attributed to poor dental hygiene secondary to disability. The variation of microbial profile in JIA patients could indicate a possible link between gingivitis and synovial inflammation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38508974", + "title": "High \u03b1-diversity of skin microbiome and mycobiome in Japanese patients with vitiligo.", + "year": 2024, + "journal": "Journal of dermatological science", + "authors": [ + "Kuroda Y", + "Yang L", + "Shibata T", + "Hayashi M", + "Araki Y", + "Nishida M", + "Namiki T", + "Makino T", + "Shimizu T", + "Suzuki T", + "Sayo T", + "Takahashi Y", + "Tsuruta D", + "Katayama I" + ], + "bacteria": "Corynebacterium", + "condition": "healthy", + "relevance_score": 0.20035724378615175, + "mesh_terms": [ + "Adult", + "Female", + "Humans", + "Male", + "Middle Aged", + "Young Adult", + "Back", + "Case-Control Studies", + "Corynebacterium", + "East Asian People", + "Forehead", + "Japan", + "Malassezia", + "Microbiota", + "Mycobiome", + "RNA, Ribosomal, 16S", + "Skin", + "Staphylococcus", + "Vitiligo" + ], + "raw_abstract": "BACKGROUND: Vitiligo is an acquired pigmentary disorder characterized by depigmented patches on the skin that majorly impact patients' quality of life. Although its etiology involves genetic and environmental factors, the role of microorganisms as environmental factors in vitiligo pathology remains under-researched. OBJECTIVES: Our study explored the presence of characteristic bacterial and fungal flora in vitiligo-affected skin and investigated their potential roles in vitiligo pathogenesis. METHODS: We sequenced bacterial 16S rRNA and the fungal ITS1 region from skin swabs collected at frequently affected sites, namely the forehead and back, of patients with vitiligo. We analyzed bacterial and fungal flora in lesional and non-lesional areas of patients with vitiligo compared with corresponding sites in age- and sex-matched healthy subjects. RESULTS: Our findings revealed elevated \u03b1-diversity in both bacterial and fungal flora within vitiligo lesions compared with healthy controls. Notably, bacterial flora exhibited a distinctive composition in patients with vitiligo, and the proportional representation of Enterococcus was inversely correlated with the degree of vitiligo progression. Gammaproteobacteria, Staphylococcus spp., and Corynebacterium spp. were more abundant in vitiligo patients, with notable Staphylococcus spp. prevalence during the stable phase on the forehead. Conversely, the proportion of Malassezia sympodialis was lower and that of Malassezia globosa was higher in the progressive phase on the back of vitiligo patients. CONCLUSION: Our study identified some characteristic bacterial and fungal groups associated with vitiligo activity and prognosis, highlighting the potential roles of microorganisms in pathogenesis and offering insights into personalized disease-management approaches.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31553956", + "title": "Relationship of tongue coating microbiome on volatile sulfur compounds in healthy and halitosis adults.", + "year": 2019, + "journal": "Journal of breath research", + "authors": [ + "Ye W", + "Zhang Y", + "He M", + "Zhu C", + "Feng XP" + ], + "bacteria": "Stomatobaculum", + "condition": "healthy", + "relevance_score": 0.3340865918449593, + "mesh_terms": [ + "Adult", + "Biodiversity", + "Breath Tests", + "Case-Control Studies", + "Female", + "Halitosis", + "Healthy Volunteers", + "Humans", + "Male", + "Microbiota", + "Sulfur Compounds", + "Tongue", + "Volatile Organic Compounds" + ], + "raw_abstract": "AIM: This study aims to assess the microbiome variations related to intraoral halitosis and its relationship with volatile sulfur compounds (VSCs) among periodontally healthy Chinese adults. MATERIAL AND METHODS: Tongue coating samples were collected from 28 periodontally healthy subjects (16 subjects with halitosis and 12 subjects without halitosis) who fulfilled the selection criteria. The organoleptic score (OS) was used to evaluate the halitosis status. The characterization of associated microbial communities was performed using 16S rRNA gene pyrosequencing and metagenomics methods. RESULTS: A wide range of microbial communities, including 13 phyla, 23 classes, 37 orders, 134 genera, 266 species and 349 operational taxonomic units (OTUs), were detected. The Shannon index values were significantly higher in the halitosis group. Genera, such as Prevotella, Alloprevotella, Leptotrichia, Peptostreptococcus and Stomatobaculum, exhibited significantly higher relative percentages in halitosis samples, when compared to healthy samples. Peptostreptococcus, Alloprevotella, Eubacterium nodatum and Stomatobaculum exhibited significantly positive correlations with the total number of VSCs. Prevotella, Peptostreptococcus, Eubacterium nodatum and Alloprevotella were correlated with increased H CONCLUSION: Microbial diversity was higher in the halitosis group than in the control group, and several bacteria were significantly correlated to halitosis. Furthermore, there were correlations between tongue bacterial composition structure and VSC gases. Tongue coating microbiota can offer important clues in the investigation of the pathogenesis and treatment of halitosis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35142786", + "title": "Enriched and Decreased Intestinal Microbes in Active VKH Patients.", + "year": 2022, + "journal": "Investigative ophthalmology & visual science", + "authors": [ + "Li M", + "Yang L", + "Cao J", + "Liu T", + "Liu X" + ], + "bacteria": "Stomatobaculum", + "condition": "healthy", + "relevance_score": 0.224843575271723, + "mesh_terms": [ + "Actinobacteria", + "Adult", + "Case-Control Studies", + "Clostridiales", + "DNA, Bacterial", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Genotyping Techniques", + "Healthy Volunteers", + "Humans", + "Male", + "Middle Aged", + "Pseudomonas", + "RNA, Ribosomal, 16S", + "Scleritis", + "Uveomeningoencephalitic Syndrome" + ], + "raw_abstract": "PURPOSE: To determine the possible microbiome related to Vogt-Koyanagi-Harada (VKH) disease in comparison to patients with noninfectious anterior scleritis and healthy people. METHODS: Fecal samples were extracted from 42 individuals, including 11 patients with active VKH, 11 healthy people, and 20 patients with noninfectious anterior scleritis. We amplified the V3 to V4 16S ribosomal DNA (rDNA) region to obtain the target sequence. Then, the target sequence was amplified by polymerase chain reaction. The obtained target sequences were sequenced by high-throughput 16S rDNA analysis. RESULTS: At the genus level, there were three enriched (Stomatobaculum, Pseudomonas, Lachnoanaerobaculum) and two depleted (Gordonibacter, Slackia) microbes that were detected only in patients with VKH. There were 10 enriched and 12 depleted microbes that were observed in both patients with VKH disease and noninfectious anterior scleritis (P < 0.05). The interactions of these microbes were graphed. Tyzzerella and Eggerthella were the nodes of interaction between these microorganisms, which were regulated by both positive and negative aspects, but the expression level in patients with active VKH was upregulated. CONCLUSIONS: Special or nonspecial enrichment and decreased intestinal microbes were observed in patients with active VKH. The action mechanism of these microbes needs further study.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27939319", + "title": "Ability of Lactobacillus kefiri LKF01 (DSM32079) to colonize the intestinal environment and modify the gut microbiota composition of healthy individuals.", + "year": 2017, + "journal": "Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver", + "authors": [ + "Toscano M", + "De Grandi R", + "Miniello VL", + "Mattina R", + "Drago L" + ], + "bacteria": "Barnesiella", + "condition": "healthy", + "relevance_score": 0.3069090256069083, + "mesh_terms": [ + "Adult", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Intestines", + "Lactobacillus", + "Male", + "Microbial Sensitivity Tests", + "Middle Aged", + "Probiotics" + ], + "raw_abstract": "BACKGROUND: Probiotics have been observed to positively influence the host's health, but to date few data about the ability of probiotics to modify the gut microbiota composition exist. AIMS: To evaluate the ability of Lactobacillus kefiri LKF01 DSM32079 (LKEF) to colonize the intestinal environment of healthy subjects and modify the gut microbiota composition. METHODS: Twenty Italian healthy volunteers were randomized in pre-prandial and post-prandial groups. Changes in the gut microbiota composition were detected by using a Next Generation Sequencing technology (Ion Torrent Personal Genome Machine). RESULTS: L. kefiri was recovered in the feces of all volunteers after one month of probiotic administration, while it was detected only in three subjects belonging to the pre-prandial group and in two subjects belonging to the post-prandial group one month after the end of probiotic consumption. After one month of probiotic oral intake we observed a reduction of Bilophila, Butyricicomonas, Flavonifractor, Oscillibacter and Prevotella. Interestingly, after the end of probiotic administration Bacteroides, Barnesiella, Butyricicomonas, Clostridium, Haemophilus, Oscillibacter, Salmonella, Streptococcus, Subdoligranolum, and Veillonella were significantly reduced if compared to baseline samples. CONCLUSION: L. kefiri LKF01 showed a strong ability to modulate the gut microbiota composition, leading to a significant reduction of several bacterial genera directly involved in the onset of pro-inflammatory response and gastrointestinal diseases.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32062786", + "title": "Role of preoperative gut microbiota on colorectal anastomotic leakage: preliminary results.", + "year": 2020, + "journal": "Updates in surgery", + "authors": [ + "Palmisano S", + "Campisciano G", + "Iacuzzo C", + "Bonadio L", + "Zucca A", + "Cosola D", + "Comar M", + "de Manzini N" + ], + "bacteria": "Barnesiella", + "condition": "healthy", + "relevance_score": 0.2935711595422666, + "mesh_terms": [ + "Adult", + "Aged", + "Aged, 80 and over", + "Anastomotic Leak", + "Colorectal Neoplasms", + "Digestive System Surgical Procedures", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Healthy Volunteers", + "Host Microbial Interactions", + "Humans", + "Male", + "Middle Aged", + "Neoadjuvant Therapy", + "Postoperative Complications", + "Preoperative Period", + "Risk Factors", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The dysbiosis is defined as a disturbed symbiotic relationship between microbiota and the host and can cause a pro-inflammatory imbalance impairing the healing process at anastomotic level. The aim of this study is to detect, in fecal samples collected in the preoperative time, a peculiar microbiota composition that could predict the onset of colorectal anastomotic leakage. MATERIALS AND METHODS: We compared gut microbiota of healthy patients (Group A) and patients with colorectal cancer eligible for surgery (Group B). Group B was divided into patients who developed anastomotic leak (Group BL) and patients who had uneventful recovery (Group BNL). Stool samples were collected before surgery and after neoadjuvant treatment. RESULTS: We analyzed stool samples from 48 patients, 27 belonging to Group A and 21 to Group B. In Group B, five patients developed anastomotic leakage (Group BL). Compared to healthy subjects, Group B showed a moderate increase of Bacteroidetes and Proteobacteria, a moderate reduction of Firmicutes and Actinobacteria, and a statistically significant reduction of Faecalibacterium prausnitzii. Group BL patients showed an array of bacterial species which promoted dysbiosis, such as Acinetobacter lwoffii and Hafnia alvei. Group BNL patients showed that bacterial species like Faecalibacterium prausnitzii and Barnesiella intestinihominis have a protective function. CONCLUSIONS: The bacterial flora in subjects with colorectal cancer is statistically different compared to healthy patients. The presence of preoperative aggressive bacteria and the lack of protective strains has strengthened the hypothesis that a peculiar microbiota composition could represent a risk factor for the occurrence of anastomotic leakage.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35845131", + "title": "The Gut Microbiota and Inflammatory Factors in Pediatric Appendicitis.", + "year": 2022, + "journal": "Disease markers", + "authors": [ + "Bi Y", + "Yang Q", + "Li J", + "Zhao X", + "Yan B", + "Li X", + "Cui H" + ], + "bacteria": "Barnesiella", + "condition": "healthy", + "relevance_score": 0.27714912434660655, + "mesh_terms": [ + "Appendicitis", + "Biomarkers", + "Child", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans" + ], + "raw_abstract": "BACKGROUND: The study analyzed gut microflora's composition and investigated the associations between the associations between gut dysbiosis and inflammatory indicators in pediatric patients with acute appendicitis. METHODS: High-throughput sequencing and bioinformatics analysis were used to investigate the composition and diversity of gut microflora in 20 pediatric patients with acute appendicitis and 11 healthy children. Endpoints measured were operational taxonomic units (OTU) of gut microflora. The OTU and its abundance analysis, sample diversity analysis, principal component analysis of samples, differential analysis, and analysis of biomarkers were performed. RESULTS: Overall fecal microbial richness and diversity were similar in patients and controls. Yet richness within the group of Bilophila, Eggerthella, Clostridium, Parvimonas, Megasphaera, Atopobium, Phascolarctobacterium, Adlercreutzia, Barnesiella, Klebsiella, Enterococcus, and Prevotella genera was higher in patients. Adlercreutzia was significantly positively correlated with IL-10, while the three other genera, comprising Klebsiella, Adlercreutzia, and Prevotella, were positively correlated with B cells level. CONCLUSION: Gut microbiome components are significantly different in pediatric patients with acute appendicitis and healthy children. The differential abundance of some genera is correlated with the production of inflammatory markers in appendicitis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33125401", + "title": "Baseline gut microbiome composition predicts metformin therapy short-term efficacy in newly diagnosed type 2 diabetes patients.", + "year": 2020, + "journal": "PloS one", + "authors": [ + "Elbere I", + "Silamikelis I", + "Dindune II", + "Kalnina I", + "Ustinova M", + "Zaharenko L", + "Silamikele L", + "Rovite V", + "Gudra D", + "Konrade I", + "Sokolovska J", + "Pirags V", + "Klovins J" + ], + "bacteria": "Barnesiella", + "condition": "healthy", + "relevance_score": 0.262289789308794, + "mesh_terms": [ + "Adult", + "Bacteroidetes", + "Diabetes Mellitus, Type 2", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Lactococcus lactis", + "Longitudinal Studies", + "Male", + "Metformin", + "Microbiota", + "Prevotella", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The study was conducted to investigate the effects of metformin treatment on the human gut microbiome's taxonomic and functional profile in the Latvian population, and to evaluate the correlation of these changes with therapeutic efficacy and tolerance. METHODS: In this longitudinal observational study, stool samples for shotgun metagenomic sequencing-based analysis were collected in two cohorts. The first cohort included 35 healthy nondiabetic individuals (metformin dose 2x850mg/day) at three time-points during metformin administration. The second cohort was composed of 50 newly-diagnosed type 2 diabetes patients (metformin dose-determined by an endocrinologist) at two concordant times. Patients were defined as Responders if their HbA1c levels during three months of metformin therapy had decreased by \u226512.6 mmol/mol (1%), while in Non-responders HbA1c were decreased by <12.6 mmol/mol (1%). RESULTS: Metformin reduced the alpha diversity of microbiota in healthy controls (p = 0.02) but not in T2D patients. At the species level, reduction in the abundance of Clostridium bartlettii and Barnesiella intestinihominis, as well as an increase in the abundance of Parabacteroides distasonis and Oscillibacter unclassified overlapped between both study groups. A large number of group-specific changes in taxonomic and functional profiles was observed. We identified an increased abundance of Prevotella copri (FDR = 0.01) in the Non-Responders subgroup, and enrichment of Enterococcus faecium, Lactococcus lactis, Odoribacter, and Dialister at baseline in the Responders group. Various taxonomic units were associated with the observed incidence of side effects in both cohorts. CONCLUSIONS: Metformin effects are different in T2D patients and healthy individuals. Therapy induced changes in the composition of gut microbiome revealed possible mediators of observed short-term therapeutic effects. The baseline composition of the gut microbiome may influence metformin therapy efficacy and tolerance in T2D patients and could be used as a powerful prediction tool.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31315765", + "title": "[Correlation between gut microbiota and behavior symptoms in children with autism spectrum disorder].", + "year": 2019, + "journal": "Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics", + "authors": [ + "Zhao RH", + "Zheng PY", + "Liu SM", + "Tang YC", + "Li EY", + "Sun ZY", + "Jiang MM" + ], + "bacteria": "Barnesiella", + "condition": "healthy", + "relevance_score": 0.25945384526388166, + "mesh_terms": [ + "Autism Spectrum Disorder", + "Bacteria", + "Child", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: To investigate the composition of gut microbiota and its correlation with the severity of behavior symptoms in children with autism spectrum disorder (ASD). METHODS: A total of 30 children with ASD were enrolled as the ASD group, and 20 healthy children matched for age and sex were enrolled as the healthy control group. Related clinical data were analyzed. The V3-V4 hypervariable regions of the bacterial 16S rRNA gene in fecal samples were sequenced. The severity of behavior symptoms in children with ASD was assessed using the autism behavior checklist. The Spearman's correlation analysis was used to investigate the correlation between gut microbiota and the severity of behavior symptoms in children with ASD. RESULTS: There was a significant difference in the composition of gut microbiota between the two groups. Compared with the healthy control group, the ASD group had significant reductions in Shannon index and Shannoneven index (P<0.05), as well as a significant reduction in the percentage of Firmicutes and a significant increase in the percentage of Acidobacteria in feces (P<0.05). In the ASD group, the dominant bacteria were Megamonas, Megasphaera, and Barnesiella, while in the healthy control group, the dominant bacteria were Eubacterium_rectale_group, Ezakiella, and Streptococcus. In the children with ASD, the abundance of Megamonas was positively correlated with the scores of health/physical/behavior and language communication (P<0.05). CONCLUSIONS: The development of ASD and the severity of behavior symptoms are closely associated with the composition of gut microbiota. \u76ee\u7684: \u63a2\u7d22\u5b64\u72ec\u75c7\u8c31\u7cfb\u969c\u788d(ASD)\u513f\u7ae5\u80a0\u9053\u83cc\u7fa4\u7684\u6784\u6210\u53ca\u5176\u4e0e\u884c\u4e3a\u75c7\u72b6\u4e25\u91cd\u7a0b\u5ea6\u4e4b\u95f4\u7684\u5173\u7cfb\u3002 \u65b9\u6cd5: \u9009\u53d630\u540dASD\u513f\u7ae5\u4e3aASD\u7ec4\uff0c20\u540d\u5e74\u9f84\u3001\u6027\u522b\u4e0e\u4e4b\u5339\u914d\u7684\u5065\u5eb7\u513f\u7ae5\u4e3a\u5065\u5eb7\u5bf9\u7167\u7ec4\uff0c\u7edf\u8ba1\u4e24\u7ec4\u76f8\u5173\u57fa\u672c\u4fe1\u606f\u3002\u5bf9\u4e24\u7ec4\u513f\u7ae5\u7caa\u4fbf\u6837\u672c\u4e2d\u7ec6\u83cc16S rRNA\u57fa\u56e0\u7684V3-V4\u9ad8\u53d8\u533a\u8fdb\u884c\u6d4b\u5e8f\uff0c\u5e76\u91c7\u7528\u5b64\u72ec\u75c7\u6cbb\u7597\u8bc4\u4f30\u91cf\u8868\u8bc4\u4f30ASD\u513f\u7ae5\u884c\u4e3a\u75c7\u72b6\u7684\u4e25\u91cd\u7a0b\u5ea6\u3002\u5e94\u7528Spearman\u79e9\u76f8\u5173\u5206\u6790ASD\u513f\u7ae5\u80a0\u9053\u83cc\u7fa4\u4e0e\u884c\u4e3a\u75c7\u72b6\u4e25\u91cd\u7a0b\u5ea6\u7684\u76f8\u5173\u6027\u3002 \u7ed3\u679c: \u7814\u7a76\u8868\u660e\u4e24\u7ec4\u513f\u7ae5\u80a0\u9053\u5fae\u751f\u6001\u83cc\u7fa4\u7ed3\u6784\u5b58\u5728\u663e\u8457\u5dee\u5f02\u3002\u4e0e\u5065\u5eb7\u5bf9\u7167\u7ec4\u76f8\u6bd4\uff0cASD\u7ec4\u513f\u7ae5\u03b1\u591a\u6837\u6027\u6307\u6570(Shannon\u548cShannoneven)\u663e\u8457\u964d\u4f4e( \u7ed3\u8bba: ASD\u7684\u53d1\u5c55\u53ca\u5176\u884c\u4e3a\u75c7\u72b6\u7684\u4e25\u91cd\u7a0b\u5ea6\u4e0e\u80a0\u9053\u83cc\u7fa4\u7ed3\u6784\u5bc6\u5207\u76f8\u5173\u3002", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27222719", + "title": "Isolation of new species \"Peptoniphilus phoceensis\" from human gut.", + "year": 2016, + "journal": "New microbes and new infections", + "authors": [ + "Mourembou G", + "Traore SI", + "Rathored J", + "Khelaifia S", + "Lagier JC", + "Michelle C", + "Raoult D", + "Million M" + ], + "bacteria": "Peptoniphilus", + "condition": "healthy", + "relevance_score": 0.5835584709820811, + "mesh_terms": [], + "raw_abstract": "Taxonogenomics coupled with culturomics leads to descriptions of new bacteria. Thanks to this strategy, we report the main characteristics of \"Peptoniphilus phoceensis\" strain SIT15, a new bacterium isolated from a stool sample of a 1-year-old healthy Senegalese boy.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33452946", + "title": "Characteristics of the vaginal microbiomes in prepubertal girls with and without vulvovaginitis.", + "year": 2021, + "journal": "European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology", + "authors": [ + "Xiaoming W", + "Jing L", + "Yuchen P", + "Huili L", + "Miao Z", + "Jing S" + ], + "bacteria": "Peptoniphilus", + "condition": "healthy", + "relevance_score": 0.5756048985114303, + "mesh_terms": [ + "Bacteria", + "Child", + "Child, Preschool", + "Female", + "Humans", + "Microbiota", + "Phylogeny", + "Vagina", + "Vulvovaginitis" + ], + "raw_abstract": "The present study focused on the characteristics of the vaginal microbiomes in prepubertal girls with and without vulvovaginitis. We collected 24 vaginal samples and 16 fecal samples from 10 girls aged 3-9 years with vulvovaginitis and 16 healthy girls of the same age. The samples were divided into three groups: fecal swabs from healthy controls (HF), vaginal swabs from healthy controls (HVS), and vaginal swabs from girls with vulvovaginitis (VVS). Sequencing of the V3-V4 region of the 16S rDNA gene was performed with the NovaSeq PE250 platform to reveal the vaginal microbial community structure in healthy prepubertal girls and vulvovaginitis-associated microbiota. The intestinal microbiomes of healthy children were also analyzed for comparison. This study revealed that the healthy vaginal tract in prepubertal girls was dominated by Prevotella, Porphyromonas, Ezakiella, and Peptoniphilus species, with a high diversity of microbiota. The vulvovaginitis-associated microbiota were dominated by Streptococcus, Prevotella, Haemophilus, and Granulicatella, with lower diversity than that in healthy girls. Furthermore, the compositions of the vaginal and intestinal microbiomes were completely different. ANOSIM, MRPP, Adonis, and AMOVA were used to analyze the beta diversity, and the results showed that there were significant differences in the microbial communities among the three groups. Lactobacillus deficiency and high bacterial diversity were characteristics of the vaginal microbiome in healthy prepubertal girls; this is inconsistent with that in reproductive-age women. The vulvovaginitis-associated vaginal microbiota differed dramatically from normal microbiota, and the main causative agents were not fecal in origin.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37301777", + "title": "The potential roles of gut microbiome in anal fistula.", + "year": 2023, + "journal": "AMB Express", + "authors": [ + "Cai P", + "Rong H", + "Zhu Q", + "Dai X", + "Zhao J" + ], + "bacteria": "Peptoniphilus", + "condition": "healthy", + "relevance_score": 0.40424638520995, + "mesh_terms": [], + "raw_abstract": "Anal fistula is a common proctological disease, but the thorough mechanisms of the anal fistula formation are still unclear. An increasing number of studies have revealed the crucial role of gut microbiota in intestinal diseases. We used 16S rRNA gene sequencing to analyze the intestinal microbiome in order to determine whether there are differences in the microbiome between anal fistula patients and healthy individuals. The microbiome samples were extracted by repeatedly wiping the rectal wall with intestinal swab. Before this operation, the whole intestine of all participants was irrigated and the score of the Boston bowel preparation scale reached 9. The biodiversity of gut microbiome of rectum revealed significant difference between anal fistula patients and healthy individuals. 36 discriminative taxa were identified by LEfSe analysis between two groups. At the phylum level, Synergistetes was enriched in anal fistula patients, while Proteobacteria was higher in healthy individuals. We also found that at the genus level, Blautia, Faecalibacterium, Ruminococcus, Coprococcus, Bacteroides, Clostridium, Megamonas and Anaerotruncus were highly enriched in anal fistula patients, while the microbiome of healthy individuals was enriched with Peptoniphilus and Corynebacterium. Spearman correlations showed the extensive and close association among genera and species. Finally, a diagnostic prediction model was constructed by random forest classifier, and the area under curve (AUC) reached 0.990. This study gave an important hint for analyzing gut microbiome of rectum in anal fistula patient.Keypoints.We use the 16S rRNA gene sequencing to test the microbiome samples extracted from the intestinal swab. This is the first study to explore the gut microbiome of rectum using this workflow. We also found the distinct gut microbiome of rectum differences between anal fistula patients and healthy individuals.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35857142", + "title": "Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., isolated from humans.", + "year": 2022, + "journal": "Archives of microbiology", + "authors": [ + "Mbaye B", + "Lo CI", + "Dione N", + "Benabdelkader S", + "Tidjani Alou M", + "Brahimi S", + "Armstrong N", + "Alibar S", + "Raoult D", + "Moal V", + "Million M", + "Fournier PE", + "Fenollar F" + ], + "bacteria": "Peptoniphilus", + "condition": "healthy", + "relevance_score": 0.38179129667535133, + "mesh_terms": [ + "Bacteria, Anaerobic", + "Bacterial Typing Techniques", + "Clostridiales", + "DNA, Bacterial", + "Fatty Acids", + "Gram-Positive Bacteria", + "Humans", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "Strains Marseille-P3761 and Marseille-P3195 are representatives of two bacterial species isolated from human specimens. Strain Marseille-P3761 was isolated from the stool of a healthy volunteer, while strain Marseille-P3915 was cultivated from the urine of a kidney transplant recipient. Both strains are anaerobic Gram-positive coccoid bacteria. Both are catalase-negative and oxidase-negative and grow optimally at 37\u00a0\u00b0C in anaerobic conditions. They also metabolize carbohydrates, such as galactose, glucose, fructose, and glycerol. The major fatty acids were hexadecanoic acid for both strains. The highest digital DNA-DNA hybridization (dDDH) values of Marseille-P3761 and Marseille-P3195 strains when compared to their closest phylogenetic relatives were 52.3% and 56.4%, respectively. Strains Marseille-P3761 and Marseille-P3195 shared an OrthoANI value of 83.5% which was the highest value found with Peptoniphilus species studied here. The morphological, biochemical, phenotypic and genomic characteristics strongly support that these strains are new members of the Peptoniphilus genus. Thus, we suggest that Peptoniphilus coli sp. nov., and Peptoniphilus urinae sp. nov., are new species for which strains Marseille-P3761 (CSUR P3761\u2009=\u2009CCUG 71,569) and Marseille-P3195 (CSUR P3195\u2009=\u2009DSM 103,468) are their type strains, respectively of two new Peptoniphilus species, for which we propose the names Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov., respectively.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28538949", + "title": "The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls.", + "year": 2017, + "journal": "JAMA dermatology", + "authors": [ + "Ring HC", + "Thorsen J", + "Saunte DM", + "Lilje B", + "Bay L", + "Riis PT", + "Larsen N", + "Andersen LO", + "Nielsen HV", + "Miller IM", + "Bjarnsholt T", + "Fuursted K", + "Jemec GB" + ], + "bacteria": "Peptoniphilus", + "condition": "healthy", + "relevance_score": 0.38165520379599105, + "mesh_terms": [ + "Adult", + "Bacteria", + "Case-Control Studies", + "DNA, Bacterial", + "Female", + "Hidradenitis Suppurativa", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Sequence Analysis, DNA", + "Skin" + ], + "raw_abstract": "IMPORTANCE: Although the pathogenesis of hidradenitis suppurativa (HS) remains enigmatic, several factors point to potential involvement of the cutaneous microbiome. Insight into the cutaneous microbiome in HS using next-generation sequencing may provide novel data on the microbiological diversity of the skin. OBJECTIVE: To investigate the follicular skin microbiome in patients with HS and in healthy controls. DESIGN, SETTING, AND PARTICIPANTS: This case-control study obtained punch biopsy specimens from patients with HS (lesional and nonlesional) and healthy controls between October 1, 2014, and August 1, 2016. Data were analyzed from March to November 2016. Patients with HS were recruited from the Department of Dermatology, Zealand University Hospital, Roskilde, Denmark. Biopsy specimens were analyzed at the Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark. None of the participants received any antibiotics (systemic or topical therapy) within 1 month before the study. In patients with HS, biopsy specimens were obtained from lesional skin (axilla or groin) and nonlesional skin. Only nodules containing at least 1 visible hair follicle were biopsied. Biopsy specimens from healthy controls were obtained from the axilla only. MAIN OUTCOMES AND MEASURES: The different microbiomes were investigated using next-generation sequencing targeting 16S and 18S ribosomal RNA. RESULTS: The skin microbiome was characterized in 30 patients with HS (mean [SD] age, 46.9 [14.0] years; 19 [63% female]) and 24 healthy controls (mean [SD] age, 32.2 [12.0] years; 13 [54% female]). The next-generation sequencing data provided a previously unreported (to our knowledge) characterization of the skin microbiome in HS. The study demonstrated that the microbiome in HS differs significantly from that in healthy controls in lesional and nonlesional skin. Overall, the following 5 microbiome types were identified: Corynebacterium species (type I), Acinetobacter and Moraxella species (type II), Staphylococcus epidermidis (type III), Porphyromonas and Peptoniphilus species (type IV), and Propionibacterium acnes (type V). In lesional skin, microbiome types consisted predominantly of type I or type IV. Microbiome type IV was not detected in healthy controls. Several taxa, including Propionibacterium, showed a significantly higher relative abundance in healthy controls vs HS skin, indicating that Propionibacterium may be part of the pathogenesis in HS. CONCLUSIONS AND RELEVANCE: The study findings suggest a link between a dysbiotic cutaneous microbiome and HS.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38331564", + "title": "The semen microbiome of miniature pony stallions.", + "year": 2024, + "journal": "Reproduction, fertility, and development", + "authors": [ + "Cooke CG", + "Gibb Z", + "Grupen CG", + "Schemann K", + "Deshpande N", + "Harnett JE" + ], + "bacteria": "Peptoniphilus", + "condition": "healthy", + "relevance_score": 0.2284597326055187, + "mesh_terms": [ + "Female", + "Male", + "Horses", + "Humans", + "Animals", + "Semen", + "RNA, Ribosomal, 16S", + "Microbiota", + "Fertility" + ], + "raw_abstract": "CONTEXT: Little is known about the microbial composition of stallion semen. AIMS: To describe the microbiota detected in equine semen of healthy miniature pony stallions. METHODS: Semen specimens were collected using a Missouri artificial vagina at a single time point. PacBio (Pacific Biosciences) genomic DNA sequencing of the 16S rRNA gene was performed on these specimens, following which next-generation microbiome bioinformatics platform QIIME2 was used to process fastq files and analyse the amplicon data. The data were categorised into genus, family, class, order and phylum. KEY RESULTS: Firmicutes and Bacteroidetes phyla predominated (76%), followed by Proteobacteria (15%). Bacteroidales, Clostridiales and Cardiobacteriales predominated the microbial rank of order (86%). Class was mainly composed of Bacteroidia, Clostridia and Gammaproteobacteria (87%), while family was mainly composed of Porphyromonadaceae , Family_XI and Cardiobacteriaceae (62%). At the level of genus, 80% of the abundance was composed of seven genera, namely Porphyromonas, Suttonella, Peptoniphilus, Fastidiosipila, Ezakiella, Petrimonas and an unknown taxon. CONCLUSIONS: The findings indicate that specific microbiota may be characteristic of healthy miniature pony stallions' semen with some inter-individual variations observed. IMPLICATIONS: Larger equine studies involving fertile and infertile subjects could be informed by this study and could explore the relationship of the semen microbiome to male fertility.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36557565", + "title": "Microbiome in Male Genital Mucosa (Prepuce, Glans, and Coronal Sulcus): A Systematic Review.", + "year": 2022, + "journal": "Microorganisms", + "authors": [ + "Gon\u00e7alves MFM", + "Fernandes \u00c2R", + "Rodrigues AG", + "Lisboa C" + ], + "bacteria": "Peptoniphilus", + "condition": "healthy", + "relevance_score": 0.21581993509703956, + "mesh_terms": [], + "raw_abstract": "The human body represents a complex and diverse reservoir of microorganisms. Although the human microbiome remains poorly characterized and understood, it should not be underestimated, since recent studies have highlighted its importance in health. This is especially evident when considering microbiota in the male reproductive system, responsible for men\u2019s fertility and sexual behavior. Therefore, the aim of this systematic review is to provide an overview of the microbial communities of the healthy male genital mucosa and its role in disease. This study was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The search was limited to the English language and studies published until August 2022 that included culture-independent techniques for microbiome characterization in male genital mucosa. Ten articles were included. The bacterial composition of the male genital mucosa consists of several genera including Prevotella, Finegoldia, Peptoniphilus, Staphylococcus, Corynebacterium, and Anaerococcus, suggesting that the male genital microbiome composition shows similarities with the adjacent anatomical sites and is related with sexual intercourse. Moreover, male circumcision appears to influence the penile microbiome. Despite the lack of knowledge on the male genital mucosa microbiome in disease, it was reported that Staphylococcus warneri and Prevotella bivia were associated with balanoposthitis, whereas Enterobacteriaceae, Prevotella, and Fusobacterium were more abundant in male genital lichen sclerosus. The limited data and paucity of prospective controlled studies highlight the need for additional studies and established criteria for sampling methods and the microbiome assay procedure. Such a consensus would foster the knowledge about the composition of the genital microbiome of healthy males and its role in disease.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35608350", + "title": "Peripheral Blood Microbiome Analysis via Noninvasive Prenatal Testing Reveals the Complexity of Circulating Microbial Cell-Free DNA.", + "year": 2022, + "journal": "Microbiology spectrum", + "authors": [ + "Tong X", + "Yu X", + "Du Y", + "Su F", + "Liu Y", + "Li H", + "Liu Y", + "Mu K", + "Liu Q", + "Li H", + "Zhu J", + "Xu H", + "Xiao F", + "Li Y" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.5209765451152358, + "mesh_terms": [ + "Cell-Free Nucleic Acids", + "Epstein-Barr Virus Infections", + "Female", + "Herpesvirus 4, Human", + "Humans", + "Microbiota", + "Noninvasive Prenatal Testing", + "Pregnancy", + "Retrospective Studies" + ], + "raw_abstract": "While circulating cell-free DNA (cfDNA) is becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a microbial cfDNA baseline in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Because noninvasive prenatal testing (NIPT) shares many similarities with the sequencing protocol of metagenomics, we utilized the standard low-pass whole-genome-sequencing-based NIPT to establish a microbial cfDNA baseline in healthy people. Sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening were retrospectively collected and reanalyzed for microbiome DNA screening. It was found that more than 95% of exogenous cfDNA was from bacteria, 3% from eukaryotes, and 0.4% from viruses, indicating the gut/environment origins of many microorganisms. Overall and regional abundance patterns were well illustrated, with huge regional diversity and complexity, and unique interspecies and symbiotic relationships were observed for TORCH organisms (Toxoplasma gondii, others [Treponema pallidum {causing syphilis}, hepatitis B virus {HBV}, and human parvovirus B19 {HPV-B19}], rubella virus, cytomegalovirus [CMV], and herpes simplex virus [HSV]) and another common virus, Epstein-Barr virus (EBV). To sum up, our study revealed the complexity of the baseline circulating microbial cfDNA and showed that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "25781328", + "title": "Altered microbiomes in bovine digital dermatitis lesions, and the gut as a pathogen reservoir.", + "year": 2015, + "journal": "PloS one", + "authors": [ + "Zinicola M", + "Lima F", + "Lima S", + "Machado V", + "Gomez M", + "D\u00f6pfer D", + "Guard C", + "Bicalho R" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.5171262775510418, + "mesh_terms": [ + "Animals", + "Cattle", + "Digital Dermatitis", + "Intestines", + "Microbiota", + "Treponema" + ], + "raw_abstract": "Bovine digital dermatitis (DD) is the most important infectious disease associated with lameness in cattle worldwide. Since the disease was first described in 1974, a series of Treponema species concurrent with other microbes have been identified in DD lesions, suggesting a polymicrobial etiology. However, the pathogenesis of DD and the source of the causative microbes remain unclear. Here we characterized the microbiomes of healthy skin and skin lesions in dairy cows affected with different stages of DD and investigated the gut microbiome as a potential reservoir for microbes associated with this disease. Discriminant analysis revealed that the microbiomes of healthy skin, active DD lesions (ulcerative and chronic ulcerative) and inactive DD lesions (healing and chronic proliferative) are completely distinct. Treponema denticola, Treponema maltophilum, Treponema medium, Treponema putidum, Treponema phagedenis and Treponema paraluiscuniculi were all found to be present in greater relative abundance in active DD lesions when compared with healthy skin and inactive DD lesions, and these same Treponema species were nearly ubiquitously present in rumen and fecal microbiomes. The relative abundance of Candidatus Amoebophilus asiaticus, a bacterium not previously reported in DD lesions, was increased in both active and inactive lesions when compared with healthy skin. In conclusion, our data support the concept that DD is a polymicrobial disease, with active DD lesions having a markedly distinct microbiome dominated by T. denticola, T. maltophilum, T. medium, T. putidum, T. phagedenis and T. paraluiscuniculi. Furthermore, these Treponema species are nearly ubiquitously found in rumen and fecal microbiomes, suggesting that the gut is an important reservoir of microbes involved in DD pathogenesis. Additionally, the bacterium Candidatus Amoebophilus asiaticus was highly abundant in active and inactive DD lesions.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36034695", + "title": "Saliva microbiome changes in thyroid cancer and thyroid nodules patients.", + "year": 2022, + "journal": "Frontiers in cellular and infection microbiology", + "authors": [ + "Jiao J", + "Zheng Y", + "Zhang Q", + "Xia D", + "Zhang L", + "Ma N" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.5132117897958779, + "mesh_terms": [ + "Animals", + "Cats", + "Humans", + "Microbiota", + "RNA, Ribosomal, 16S", + "Saliva", + "Thyroid Neoplasms", + "Thyroid Nodule" + ], + "raw_abstract": "OBJECTIVE: Thyroid disease has been reported to associate with gut microbiota, but the effects of thyroid cancer and thyroid nodules on the oral microbiota are still largely unknown. This study aimed to identify the variation in salivary microbiota and their potential association with thyroid cancer and thyroid nodules. METHODS: We used 16S rRNA high-throughput sequencing to examine the salivary microbiota of thyroid cancer patients (n = 14), thyroid nodules patients (n = 9), and healthy controls (n = 15). RESULTS: The alpha-diversity indices Chao1 and ACE were found to be relatively higher in patients with thyroid cancer and thyroid nodules compared to healthy controls. The beta diversity in both the thyroid cancer and thyroid nodules groups was divergent from the healthy control group. The genera Alloprevotella, Anaeroglobus, Acinetobacter, unclassified Bacteroidales, and unclassified Cyanobacteriales were significantly enriched in the thyroid cancer group compared with the healthy control group. In contrast, the microbiome of the healthy controls was mainly composed of the genera Haemophilus, Lautropia, Allorhizobium Neorhizobium Pararhizobium Rhizobium, Escherichia Shigella, and unclassified Rhodobacteraceae. The thyroid nodules group was dominated by genre uncultured Candidatus Saccharibacteria bacterium, unclassified Clostridiales bacterium feline oral taxon 148, Treponema, unclassified Prevotellaceae, Mobiluncus, and Acholeplasma. In contrast, the genera unclassified Rhodobacteraceae and Aggregatibacter dominated the healthy control group. The study also found that clinical indicators were correlated with the saliva microbiome. CONCLUSION: The salivary microbiota variation may be connected with thyroid cancer and thyroid nodules.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35613350", + "title": "Microbiological and molecular identification of the anaerobic component of the oral microbiota in patients with cancer of the oropharyngeal region.", + "year": 2022, + "journal": "Klinicheskaia laboratornaia diagnostika", + "authors": [ + "Bagirova NS", + "Grigorievskaya ZV", + "Tereshchenko IV", + "Petukhova IN", + "Kazimov AE", + "Vinnikova VD", + "Vershinskaya VA" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.41304318447144395, + "mesh_terms": [ + "Aggregatibacter actinomycetemcomitans", + "Anaerobiosis", + "Humans", + "Microbiota", + "Oropharyngeal Neoplasms", + "Porphyromonas gingivalis", + "Prevotella intermedia", + "Treponema denticola" + ], + "raw_abstract": "A research objective - to study tumor tissues of primary and recurrent patients with cancer of the oropharyngeal region for the frequency of occurrence of four types of anaerobic periodontogens and their associations by two methods: real-time PCR and cultural. There is speculation that bacteria can influence the pathogenesis of cancer. A comparative assessment of the content of four anaerobic periodontogens (Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythensis, Treponema denticola) in the tumor tissue and in the healthy tissue of the oral mucosa of patients with oropharyngeal cancer was carried out. It was found that the identification of odontopathogens by the real-time PCR method is much more informative than the traditional culture method, with the exception of P. intermedia, for the identification of which the traditional culture method was more effective. In 33.3% of patients, both primary and secondary, the composition of microorganisms was the same in both healthy and tumor tissue. In 20% of primary patients and in 13.3% of repeat patients, no associations of microorganisms included in the study were found in healthy tissue. Associations of 4 bacteria were recorded only in tumor tissue in both primary and repeated patients, and in repeated patients - statistically significantly more often. In 53.3% of repeat patients, associations of 4 bacteria were recorded in tumor tissue, whereas in primary patients, only in one case. P. gingivalis from tumor tissue in repeat patients was statistically significantly more often than in primary patients. T. forsythensis in primary patients was found statistically significantly more often in healthy tissues than in repeat patients, in which T. forsythensis was found statistically significantly more often from tumor tissue than in healthy tissue). T. denticola in healthy tissue was detected in both primary and repeated patients in isolated cases. T. denticola in tumor tissue was found statistically significantly more frequently in both primary and repeated patients compared to healthy tissue. P. gingivalis, T. forsythensis, and T. denticola should perhaps be considered risk indicators indicating the level of significance of their associations with oropharyngeal cancer.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31496126", + "title": "Longitudinal development of the gut microbiota in healthy and diarrheic piglets induced by age-related dietary changes.", + "year": 2019, + "journal": "MicrobiologyOpen", + "authors": [ + "Yang Q", + "Huang X", + "Wang P", + "Yan Z", + "Sun W", + "Zhao S", + "Gun S" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.40634704240973435, + "mesh_terms": [ + "Age Factors", + "Animal Feed", + "Animals", + "Biodiversity", + "Biomarkers", + "Computational Biology", + "Diarrhea", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Male", + "Metagenomics", + "RNA, Ribosomal, 16S", + "Swine", + "Symbiosis", + "Weaning" + ], + "raw_abstract": "Diarrhea is one of the most common enteric diseases in young piglets. Diverse factors such as an unstable gut microenvironment, immature intestinal immune system, early supplementary feeding, and weaning often induce dysfunction of gut microbiota, thus leading to a continuing high incidence of diarrhea in piglets. However, few studies have characterized the gut microbiota of diarrheic piglets following changes in diet and during the development of intestinal physiology. In this study, we used 16S rRNA gene sequencing to analyze the dynamic establishment of fecal microbiota in six healthy piglets in response to age-related changes in the diet: sow-reared, early supplementary creep-feeding (sow-reared\u00a0+\u00a0starter diet), and weaning (solid nursery diet). We compared the gut microbiota of these six healthy piglets with those of diarrheic piglets during each of the three dietary stages (n\u00a0=\u00a010 sow-reared, n\u00a0=\u00a010 early supplementary creep-feeding, and n\u00a0=\u00a05 weaning). We found that weaning (solid nursery feeding) was the primary factor leading to dynamic colonization by microbiota in healthy piglets, and diarrhea primarily affected the microbial communities of piglets before weaning. Healthy piglets showed a continuous decrease in Lactobacillus and Escherichia, as well as a gradual increase in Prevotella with the transition to solid food. An altered relationship between Prevotella and Escherichia may be the main cause of diarrhea in preweaned piglets, whereas reduced numbers of Bacteroides, Ruminococcus, Bulleidia, and Treponema that are responsible for the digestion and utilization of solid feeds may be related to the onset of postweaning piglet diarrhea. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional analysis indicated that a reduction in genes involved in carbohydrate metabolism induced by intestinal dysbacteriosis in diarrheic piglets was one of the major causes of diarrhea at the three dietary stages. These findings provide insights into developing an intervention strategy for better management of diarrhea in piglets.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37179393", + "title": "Integrated microbiome-metabolome-genome axis data of Laiwu and Lulai pigs.", + "year": 2023, + "journal": "Scientific data", + "authors": [ + "Lai X", + "Zhang Z", + "Zhang Z", + "Liu S", + "Bai C", + "Chen Z", + "Qadri QR", + "Fang Y", + "Wang Z", + "Pan Y", + "Wang Q" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.392490331208087, + "mesh_terms": [ + "Animals", + "Genome", + "Lipid Metabolism", + "Metabolome", + "Microbiota", + "Obesity", + "Swine" + ], + "raw_abstract": "Excessive fat deposition can trigger metabolic diseases, and it is crucial to identify factors that can break the link between fat deposition and metabolic diseases. Healthy obese Laiwu pigs (LW) are high in fat content but resistant to metabolic diseases. In this study, we compared the fecal microbiome, fecal and blood metabolome, and genome of LW and Lulai pigs (LU) to identify factors that can block the link between fat deposition and metabolic diseases. Our results show significant differences in Spirochetes and Treponema, which are involved in carbohydrate metabolism, between LW and LU. The fecal and blood metabolome composition was similar, and some anti-metabolic disease components of blood metabolites were different between the two breeds of pigs. The predicted differential RNA is mainly enriched in lipid metabolism and glucose metabolism, which is consistent with the functions of differential microbiota and metabolites. The down-regulated gene RGP1 is strongly negatively correlated with Treponema. Our omics data would provide valuable resources for further scientific research on healthy obesity in both human and porcine.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "28808698", + "title": "Subgingival Microbiome of Gingivitis in Chinese Undergraduates.", + "year": 2017, + "journal": "The Chinese journal of dental research", + "authors": [ + "Deng K", + "Ouyang XY", + "Chu Y", + "Zhang Q" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.37380481348046884, + "mesh_terms": [ + "Adolescent", + "Asian People", + "Bacteroidetes", + "Capnocytophaga", + "Case-Control Studies", + "China", + "Female", + "Gingivitis", + "Humans", + "Male", + "Microbiota", + "Porphyromonas", + "Porphyromonas endodontalis", + "Porphyromonas gingivalis", + "Prevotella intermedia", + "Principal Component Analysis", + "RNA, Ribosomal, 16S", + "Treponema", + "Young Adult" + ], + "raw_abstract": "OBJECTIVE: To analyse the microbiome composition of health and gingivitis in Chinese undergraduates with high-throughput sequencing. METHODS: Sequencing of 16S rRNA gene amplicons was performed with the MiSeq system to compare subgingival bacterial communities from 54 subjects with gingivitis and 12 periodontally healthy controls. RESULTS: A total of 1,967,372 sequences representing 14 phyla, 104 genera, and 96 species were detected. Analysis of similarities (Anosim) test and Principal Component Analysis (PCA) showed significantly different community profiles between the health control and the subjects with gingivitis. Alpha-diversity metrics were significantly higher in the subgingival plaque of the subjects with gingivitis compared with that of the healthy control. Overall, the relative abundance of 35 genera and 46 species were significantly different between the two groups, among them 28 genera and 45 species showed higher relative abundance in the subjects with gingivitis, whereas seven genera and one species showed a higher relative abundance in the healthy control. The genera Porphyromonas, Treponema, and Tannerella showed higher relative abundance in the subjects with gingivitis, while the genera Capnocytophaga showed higher proportions in health controls. Porphyromonas gingivalis, Prevotella intermedia and Porphyromonas endodontalis had higher relative abundance in gingivitis. Among them, Porphyromonas gingivalis was most abundant. CONCLUSION: Our results revealed significantly different microbial community composition and structures of subgingival plaque between subjects with gingivitis and healthy controls. Subjects with gingivitis showed greater taxonomic diversity compared with periodontally healthy subjects. The proportion of Porphyromonas, especially Porphyromonas gingivalis, may be associated with gingivitis subjects aged between 18 and 21 years old in China. Adults with gingivitis in this age group may have a higher risk of developing periodontitis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36058504", + "title": "Fecal Microbiota Comparison Between Healthy Teaching Horses and Client-Owned Horses.", + "year": 2022, + "journal": "Journal of equine veterinary science", + "authors": [ + "Ayoub C", + "Arroyo LG", + "Renaud D", + "Weese JS", + "Gomez DE" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.35842252366706956, + "mesh_terms": [ + "Horses", + "Animals", + "RNA, Ribosomal, 16S", + "Feces", + "Microbiota", + "Gastrointestinal Microbiome", + "Ontario" + ], + "raw_abstract": "The objective of this study was to compare the fecal microbiota of two healthy teaching horse herds with that of client-owned horses from the same geographic areas. The fecal microbiota of client-owned horses from Ontario Canada (n\u00a0=\u00a015) and Florida, USA (n\u00a0=\u00a011) was compared with that teaching horses from the University of Guelph, Ontario, Canada (n\u00a0=\u00a010) and the University of Florida, Florida, USA (n\u00a0=\u00a015). The fecal microbiota was characterized by sequencing of bacterial DNA using the V4 hypervariable region of the 16S rRNA gene. The diversity (inverse Simpson index) of the fecal microbiota was significantly higher in teaching than client owned horses from the same geographical area (P < .05). The community membership (Jaccard Index) and structure (Yue and Clayton index) of teaching horses was also significantly different from that of client owned horses from the same geographical area (AMOVA P < .001). The bacterial membership and structure of the fecal microbiota of Ontario and Florida teaching horses were significantly different, while the bacterial membership, but not the structure of Ontario and Florida client owned horses was significantly different (AMOVA P < .001). In all four groups of healthy horses, Lachnospiraceae, Ruminococcaceae, Bacteroidales, Clostridiales, and Treponema were detected in high relative abundance. The fecal microbiota of healthy horses from teaching herds kept in the same environment with identical management practices differs significantly from that of horses housed in different facilities with dissimilar management practices. Our results suggest an effect of the environment and management practices on the gastrointestinal microbiota. Researchers should attempt to include healthy horses from the same farm with similar management as control groups when comparing with diseased horses.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29098426", + "title": "Improvement in cardiometabolic risk markers following a multifunctional diet is associated with gut microbial taxa in healthy overweight and obese subjects.", + "year": 2018, + "journal": "European journal of nutrition", + "authors": [ + "Marungruang N", + "Tovar J", + "Bj\u00f6rck I", + "H\u00e5llenius FF" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.3092869726146825, + "mesh_terms": [ + "Aged", + "Bacteria", + "Biomarkers", + "Body Mass Index", + "Cardiovascular Diseases", + "Cholesterol", + "Diet", + "Dietary Fiber", + "Gastrointestinal Microbiome", + "Humans", + "Metabolic Syndrome", + "Middle Aged", + "Obesity", + "Overweight", + "RNA, Ribosomal, 16S", + "Risk Factors", + "Triglycerides" + ], + "raw_abstract": "PURPOSE: A multifunctional diet (MFD) targeting subclinical inflammation was developed as a tool to decrease risk factors for cardiometabolic disease in healthy \"at-risk\" individuals (BMI 25-33\u00a0kg/m METHODS: Cardiometabolic at-risk individuals (n\u2009=\u200947), between 51 and 72\u00a0years old and with a BMI of 25-33\u00a0kg/m RESULTS: The 8-week intervention with MFD did not significantly alter the gut microbiota composition at phylum or genus taxonomic levels, while LEfSE analysis identified increased abundance of Prevotella copri in the MFD group as compared to the control group. Treponema correlated positively with blood pressure. In contrast, Faecalibacterium showed a negative association with blood pressure, while Bilophila appeared to associate with a negative blood lipid profile. CONCLUSIONS: Taken together, results from the present study may be used in the further development of effective dietary concepts capable of reducing cardiometabolic risk markers in humans through a targeted modulation of the gut microbial community. TRIAL REGISTRATION NUMBER: Clinical Trials.gov NCT02148653.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "31696592", + "title": "Gingival crevicular fluid levels of SLIT3 are increased in periodontal disease.", + "year": 2020, + "journal": "Oral diseases", + "authors": [ + "Zhong W", + "Peng Y", + "Yue E", + "Huang B", + "Zhang W", + "Zhao Z", + "Jiang J", + "Wang Q", + "Zhao H" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.29653201464905626, + "mesh_terms": [ + "Adult", + "Animals", + "Dental Plaque", + "Female", + "Gingival Crevicular Fluid", + "Humans", + "Male", + "Membrane Proteins", + "Mice", + "Osteoprotegerin", + "Periodontitis", + "Periodontium", + "Porphyromonas gingivalis", + "RANK Ligand", + "RAW 264.7 Cells", + "Rats", + "Rats, Sprague-Dawley", + "Tannerella forsythia", + "Treponema denticola" + ], + "raw_abstract": "This study aims to investigate the levels of SLIT3 in gingival crevicular fluid (GCF) of healthy and periodontal disease subjects, and their correlations to periodontal disease. A total of 45 periodontal patients and 45 periodontally healthy volunteers were enrolled. The clinical parameters, radiographic bone loss and the levels of SLIT3, receptor activator of NF-\u03baB ligand (RANKL) and osteoprotegerin (OPG) in GCF were measured. The prevalences of Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia in subgingival plaque were also analyzed. The expression of SLIT3 and RANKL was detected in the periodontium of experimental periodontitis in rats and lipopolysaccharide (LPS)-induced mouse macrophage. The total amounts and concentrations of SLIT3 and RANKL were significantly higher in periodontitis than those in healthy, while the level of OPG was significantly lower (p\u00a0<\u00a0.05). Significant positive correlations were observed between the level of GCF SLIT3 and clinical attachment level and radiographic bone loss (p\u00a0<\u00a0.05). There existed a significant positive correlation between SLIT3 and RANKL (p\u00a0<\u00a0.05). Increased expression of SLIT3 and RANKL was observed in the periodontium of periodontal rats. SLIT3 expression was induced by LPS stimulation in macrophages. These results suggest that SLIT3 may act as a diagnostic indicator of periodontal disease and should be further investigated.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38135044", + "title": "Quantifying and mapping digital dermatitis-associated bacteria in lesion and nonlesion body sites and dairy farm environment.", + "year": 2024, + "journal": "Journal of dairy science", + "authors": [ + "Dias AP", + "Orsel K", + "De Buck J" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.2699417128450095, + "mesh_terms": [ + "Cattle", + "Female", + "Animals", + "Digital Dermatitis", + "Cross-Sectional Studies", + "Farms", + "Treponema", + "Bacteria", + "Skin Diseases", + "Cattle Diseases" + ], + "raw_abstract": "The source of infection of digital dermatitis (DD), an infectious lameness condition, is still uncertain. In this cross-sectional study, we aimed to identify potential reservoirs of DD bacteria in dairy cattle body sites with different stages of the disease and farm environments. We collected skin swabs from 85 dairy cows from 5 herds, 3 with and 2 without DD, from foot, hock, and udder cleft skin (with lesions or not), saliva, urine, and feces. We also obtained environmental samples. Real-time quantitative PCR targeted Treponema phagedenis, Treponema medium, Treponema pedis, Porphyromonas levii, Bacteroides pyogenes, Fusobacterium necrophorum, and Fusobacterium mortiferum. Digital dermatitis-associated Treponema spp. were exclusively detected in DD-affected herds in DD-foot and other skin lesions, healthy skin, saliva, and environmental samples. In contrast, the non-Treponema spp. were found in samples from both DD-negative and affected herds. As expected, DD lesions had higher bacterial loads than healthy skin. Interestingly, similar counts were observed in udder cleft lesions, indicating a potential opportunistic behavior on compromised skin. None of the targeted species were detected in fecal samples, but P. levii, B. pyogenes, and F. necrophorum were detected in urine. All 7 species were detected in saliva, although in low quantities. No associations were observed between the presence of each bacterial species in DD lesions and urine; however, there was an association between the presence of DD-Treponema spp. in lesions and saliva, hock, and udder skin. Feces and urine do not seem to be a DD bacteria primary source, but saliva and other skin lesions may play a role. Longitudinal studies would improve our understanding of DD-associated bacteria's transient or persistent presence in these sites. Investigating the sources of DD-associated bacteria will guide future interventions to minimize bacterial shedding and transmission, ultimately more effectively reducing bacterial load, transmission, and sources of infection in dairy herds.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37681574", + "title": "Longitudinal effects of oral administration of antimicrobial drugs on fecal microbiota of horses.", + "year": 2023, + "journal": "Journal of veterinary internal medicine", + "authors": [ + "Gomez D", + "Toribio R", + "Caddey B", + "Costa M", + "Vijan S", + "Dembek K" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.2569611752326107, + "mesh_terms": [ + "Animals", + "Horses", + "Metronidazole", + "Doxycycline", + "Longitudinal Studies", + "Prospective Studies", + "RNA, Ribosomal, 16S", + "Anti-Infective Agents", + "Microbiota", + "Trimethoprim, Sulfamethoxazole Drug Combination", + "Administration, Oral", + "Diarrhea", + "Erythromycin" + ], + "raw_abstract": "BACKGROUND: Antimicrobial drug-associated diarrhea (AAD) is the most common adverse effect in horses receiving antimicrobials. Little information on how oral administration of antimicrobials alters intestinal microbiota in horses is available. OBJECTIVE: Investigate changes of the fecal microbiota in response to oral administration of antimicrobials. ANIMALS: Twenty healthy horses. METHODS: Prospective, longitudinal study. Horses were randomly assigned to 4 groups comprising 4 horses each: group 1 (metronidazole); group 2 (erythromycin); group 3 (doxycycline); group 4 (sulfadiazine/trimethoprim, SMZ-TMP); and group 5 (control). Antimicrobials were administered for 5\u2009days. Fecal samples were obtained before (day 0) and at 1, 2, 3, 4, 5, 6, and 30\u2009days of the study period. Fecal microbiota was characterized by high throughput sequencing of the V4 region of the 16S rRNA. RESULTS: Horses remained healthy throughout the study. Richness and diversity in doxycycline, erythromycin, and metronidazole, but not SMZ-TMP groups, was significantly lower (P\u2009<\u2009.05) at multiple time points after administration of antimicrobials compared with samples from day 0. Main changes in the microbiota were observed during the time of antimicrobial administration (day 2-5; weighted and unweighted UniFrac PERMANOVA P\u2009<\u2009.05). Administration of erythromycin, doxycycline and, to a lesser extent, metronidazole produced a pronounced alteration in the microbiota compared with day 0 samples by decreasing the abundance of Treponema, Fibrobacter, and Lachnospiraceae and increasing Fusobacterium and Escherichia-Shigella. CONCLUSIONS AND CLINICAL IMPORTANCE: Oral administration of antimicrobials alters the intestinal microbiota of healthy horses resembling horses with dysbiosis, potentially resulting in intestinal inflammation and predisposition to diarrhea.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32844406", + "title": "Microbiome changes in young periodontitis patients treated with adjunctive metronidazole and amoxicillin.", + "year": 2021, + "journal": "Journal of periodontology", + "authors": [ + "Feres M", + "Retamal-Valdes B", + "Fermiano D", + "Faveri M", + "Figueiredo LC", + "Mayer MPA", + "Lee JJ", + "Bittinger K", + "Teles F" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.24530770521796535, + "mesh_terms": [ + "Amoxicillin", + "Bacteria", + "Dental Plaque", + "Humans", + "Metronidazole", + "Microbiota", + "Periodontitis", + "RNA, Ribosomal, 16S", + "Treponema" + ], + "raw_abstract": "BACKGROUND: To our knowledge, to date, no studies have comprehensively assessed the changes occurring in the subgingival microbiome of young patients with periodontitis treated by means of mechanical and antibiotic therapy. Thus, this study aimed to use next-generation sequencing to evaluate the subgingival microbial composition of young patients with severe periodontitis treated with scaling and root planing and systemic metronidazole and amoxicillin. METHODS: Subgingival samples from healthy individuals and shallow and deep sites from periodontitis patients were individually collected at baseline and 90 days post-treatment. The samples were analyzed using 16S rRNA-gene sequencing (MiSeq-Illumina) and QIIME pipeline. Differences between groups for the microbiological data were determined using principal coordinate analysis (PCoA), linear mixed models, and the PERMANOVA test. RESULTS: One hundred samples were collected from 10 periodontitis patients and seven healthy individuals. PCoA analysis revealed significant partitioning between pre-and post-treatment samples. No major differences in the composition of the subgingival microbiota were observed between shallow and deep sites, at baseline or at 90-days post-treatment, and the microbiome of both site categories after treatment moved closer in similarity to that observed in periodontal health. Treatment significantly improved all clinical parameters and reduced the relative abundance of classical periodontal pathogens and of Fretibacterium fastidiosum, Eubacterium saphenum, Porphyromonas endodontalis, Treponema medium, Synergistetes, TM7, and Treponema spp, and increased that of Actinomyces, Rothia, Haemophilus, Corynebacterium, and Streptococci spp. CONCLUSION: Mechanical treatment associated with metronidazole and amoxicillin promoted a beneficial change in the microbiome of young individuals with severe periodontitis.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "36271677", + "title": "Fecal microbiota of horses with colitis and its association with laminitis and survival during hospitalization.", + "year": 2022, + "journal": "Journal of veterinary internal medicine", + "authors": [ + "Ayoub C", + "Arroyo LG", + "MacNicol JL", + "Renaud D", + "Weese JS", + "Gomez DE" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.23749411157799832, + "mesh_terms": [ + "Horses", + "Animals", + "Case-Control Studies", + "Feces", + "Microbiota", + "Colitis", + "Streptococcus", + "Hospitalization", + "Horse Diseases" + ], + "raw_abstract": "BACKGROUND: The association of microbiota with clinical outcomes and the taxa associated with colitis in horses remains generally unknown. OBJECTIVES: Describe the fecal microbiota of horses with colitis and investigate the association of the fecal microbiota with the development of laminitis and survival. ANIMALS: Thirty-six healthy and 55 colitis horses subdivided into laminitis (n\u00a0=\u00a015) and non-laminitis (n\u00a0=\u00a039, 1 horse with chronic laminitis was removed from this comparison) and survivors (n\u00a0=\u00a027) and nonsurvivors (n\u00a0=\u00a028). METHODS: Unmatched case-control study. The Illumina MiSeq platform targeting the V4 region of the 16S ribosomal RNA gene was used to assess the microbiota. RESULTS: The community membership (Jaccard index) and structure (Yue and Clayton index) were different (analysis of molecular variance [AMOVA]; P\u2009<\u2009.001) between healthy and colitis horses. The linear discriminant analysis effect size (LEfSe; linear discriminant analysis [LDA] >3; P\u2009<\u2009.05) and random forest analyses found Enterobacteriaceae, Lactobacillus, Streptococcus, and Enterococcus enriched in colitis horses, whereas Treponema, Faecalibacterium, Ruminococcaceae, and Lachnospiraceae were enriched in healthy horses. The community membership and structure of colitis horses with or without laminitis was (AMOVA; P\u2009>\u2009.05). Enterobacteriaceae, Streptococcus, and Lactobacillus were enriched in horses with laminitis (LDA >\u20093; P\u2009<\u2009.05). The community membership (AMOVA; P\u00a0=\u00a0.008) of surviving and nonsurviving horses was different. Nonsurviving horses had an enrichment of Enterobacteriaceae, Pseudomonas, Streptococcus, and Enterococcus (LDA >3; P\u2009<\u2009.05). CONCLUSION AND CLINICAL IMPORTANCE: Differences in the microbiota of horses with colitis that survive or do not survive are minor and, similarly, the microbiota differences in horses with colitis that do or do not develop laminitis are minor.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37770990", + "title": "Immune-mediated hematological disease in dogs is associated with alterations of the fecal microbiota: a pilot study.", + "year": 2023, + "journal": "Animal microbiome", + "authors": [ + "Liu PY", + "Xia D", + "McGonigle K", + "Carroll AB", + "Chiango J", + "Scavello H", + "Martins R", + "Mehta S", + "Krespan E", + "Lunde E", + "LeVine D", + "Fellman CL", + "Goggs R", + "Beiting DP", + "Garden OA" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.23292192642193135, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: The dog is the most popular companion animal and is a valuable large animal model for several human diseases. Canine immune-mediated hematological diseases, including immune-mediated hemolytic anemia (IMHA) and immune thrombocytopenia (ITP), share many features in common with autoimmune hematological diseases of humans. The gut microbiome has been linked to systemic illness, but few studies have evaluated its association with immune-mediated hematological disease. To address this knowledge gap, 16S rRNA gene sequencing was used to profile the fecal microbiota of dogs with spontaneous IMHA and ITP at presentation and following successful treatment. In total, 21 affected and 13 healthy control dogs were included in the study. RESULTS: IMHA/ITP is associated with remodeling of fecal microbiota, marked by decreased relative abundance of the spirochete Treponema spp., increased relative abundance of the pathobionts Clostridium septicum and Escherichia coli, and increased overall microbial diversity. Logistic regression analysis demonstrated that Treponema spp. were associated with decreased risk of IMHA/ITP (odds ratio [OR] 0.24-0.34), while Ruminococcaceae UCG-009 and Christensenellaceae R-7 group were associated with increased risk of disease (OR\u2009=\u20096.84 [95% CI 2-32.74] and 8.36 [95% CI 1.85-71.88] respectively). CONCLUSIONS: This study demonstrates an association of immune-mediated hematological diseases in dogs with fecal dysbiosis, and points to specific bacterial genera as biomarkers of disease. Microbes identified as positive or negative risk factors for IMHA/ITP represent an area for future research as potential targets for new diagnostic assays and/or therapeutic applications.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35787909", + "title": "Increased occurrence of Treponema spp. and double-species infections in patients with Alzheimer's disease.", + "year": 2022, + "journal": "The Science of the total environment", + "authors": [ + "Nemergut M", + "Batkova T", + "Vigasova D", + "Bartos M", + "Hlozankova M", + "Schenkmayerova A", + "Liskova B", + "Sheardova K", + "Vyhnalek M", + "Hort J", + "Lacz\u00f3 J", + "Kovacova I", + "Sitina M", + "Matej R", + "Jancalek R", + "Marek M", + "Damborsky J" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.2302579391502567, + "mesh_terms": [ + "Alzheimer Disease", + "Case-Control Studies", + "Herpesvirus 6, Human", + "Humans", + "Treponema", + "Treponemal Infections" + ], + "raw_abstract": "Although the link between microbial infections and Alzheimer's disease (AD) has been demonstrated in multiple studies, the involvement of pathogens in the development of AD remains unclear. Here, we investigated the frequency of the 10 most commonly cited viral (HSV-1, EBV, HHV-6, HHV-7, and CMV) and bacterial (Chlamydia pneumoniae, Helicobacter pylori, Borrelia burgdorferi, Porphyromonas gingivalis, and Treponema spp.) pathogens in serum, cerebrospinal fluid (CSF) and brain tissues of AD patients. We have used an in-house multiplex PCR kit for simultaneous detection of five bacterial and five viral pathogens in serum and CSF samples from 50 AD patients and 53 healthy controls (CTRL). We observed a significantly higher frequency rate of AD patients who tested positive for Treponema spp. compared to controls (AD: 62.2\u202f%; CTRL: 30.3\u202f%; p-value\u202f=\u202f0.007). Furthermore, we confirmed a significantly higher occurrence of cases with two or more simultaneous infections in AD patients compared to controls (AD: 24\u202f%; CTRL 7.5\u202f%; p-value\u202f=\u202f0.029). The studied pathogens were detected with comparable frequency in serum and CSF. In contrast, Borrelia burgdorferi, human herpesvirus 7, and human cytomegalovirus were not detected in any of the studied samples. This study provides further evidence of the association between microbial infections and AD and shows that paralleled analysis of multiple sample specimens provides complementary information and is advisable for future studies.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35863030", + "title": "Taxonomic and Functional Shifts in the Perinatal Gut Microbiome of Rhesus Macaques.", + "year": 2022, + "journal": "Microbiology spectrum", + "authors": [ + "Rhoades NS", + "Cinco IR", + "Hendrickson SM", + "Slifka MK", + "Messaoudi I" + ], + "bacteria": "Treponema", + "condition": "healthy", + "relevance_score": 0.21430323435835952, + "mesh_terms": [ + "Adult", + "Animals", + "Butyrates", + "Feces", + "Female", + "Folic Acid", + "Gastrointestinal Microbiome", + "Humans", + "Infant, Newborn", + "Macaca mulatta", + "Pregnancy", + "RNA, Ribosomal, 16S", + "Starch" + ], + "raw_abstract": "Pregnancy and the postpartum period result in some of the most dramatic metabolic, hormonal, and physiological changes that can be experienced by an otherwise healthy adult. The timing and magnitude of these changes is key for both maternal and fetal health. One of the factors believed to critically modulate these physiological changes is the maternal gut microbiome. However, the dynamic changes in this community during the perinatal period remain understudied. Clinical studies can be complicated by confounding variables like diet and other drivers of heterogeneity in the human microbiome. Therefore, in this study, we conducted a longitudinal analysis of the fecal microbiome obtained during the pregnancy and postpartum periods in 26 captive rhesus macaques using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Shifts at both the taxonomic and functional potential level were detected when comparing pregnancy to postpartum samples. Taxonomically, Alloprevotella, Actinobacillus, and Anaerovibrio were enriched in the gut microbiome during pregnancy, while Treponema,", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35931488", + "title": "Discrepancies among healthy, subclinical mastitic, and clinical mastitic cows in fecal microbiome and metabolome and serum metabolome.", + "year": 2022, + "journal": "Journal of dairy science", + "authors": [ + "Wang Y", + "Nan X", + "Zhao Y", + "Jiang L", + "Wang H", + "Zhang F", + "Hua D", + "Liu J", + "Yang L", + "Yao J", + "Xiong B" + ], + "bacteria": "Prevotellaceae_UCG-003", + "condition": "healthy", + "relevance_score": 0.3112328215749314, + "mesh_terms": [ + "Animals", + "Cattle", + "Cattle Diseases", + "Feces", + "Female", + "Health Status", + "Mastitis, Bovine", + "Metabolome", + "Microbiota", + "Milk" + ], + "raw_abstract": "Mastitis is generally considered a local inflammatory disease caused by the invasion of exogenous pathogens and resulting in the dysbiosis of microbiota and metabolites in milk. However, the entero-mammary pathway theory may establish a possible link between some endogenous gut bacteria and the occurrence and development of mastitis. In the current study, we attempted to investigate differences in the gut microbiota profile and metabolite composition in gut and serum from healthy cows and those with subclinical mastitis and clinical mastitis. Compared with those of healthy cows, the microbial community diversities in the feces of cows with subclinical mastitis (SM) and clinical mastitis (CM) were lower. Lower abundance of Bifidobacterium, Romboutsia, Lachnospiraceae_NK3A20_group, Coprococcus, Prevotellaceae_UCG-003, Ruminococcus, and Alistipes, and higher abundance of the phylum Proteobacteria and the genera Escherichia-Shigella and Streptococcus were observed in CM cows. Klebsiella and Paeniclostridium were significantly enriched in the feces of SM cows. Several similarities were observed in feces and serum metabolites in mastitic cows. Higher levels of proinflammatory lipid products (20-trihydroxy-leukotriene-B4, 13,14-dihydro-15-keto-PGE", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29567328", + "title": "Literature-based safety assessment of an agriculture- and animal-associated microorganism: Weissella confusa.", + "year": 2018, + "journal": "Regulatory toxicology and pharmacology : RTP", + "authors": [ + "Sturino JM" + ], + "bacteria": "Weissella", + "condition": "healthy", + "relevance_score": 0.6291288803316527, + "mesh_terms": [ + "Agriculture", + "Animal Feed", + "Animals", + "Anti-Bacterial Agents", + "Drug Resistance, Bacterial", + "Food Microbiology", + "Food Safety", + "Humans", + "Microbiota", + "Weissella" + ], + "raw_abstract": "Although Weissella confusa was established as a species over 25 years ago, it has been understudied until very recently. Several independent observations have driven the recent interest in this important microorganism. First, this Leuconostoc-like species of Lactic Acid Bacteria is associated with agricultural environments, many spontaneous food fermentations-especially carbohydrate-rich vegetable fermentations-and silage. Second, Weissella confusa are members of the autochthonous microbiota of healthy humans and livestock. Third, Weissella confusa-in a strain-specific fashion-are postulated to be good candidates for the development of novel direct-fed microbial products. Fourth, Weissella confusa-in a strain-specific fashion-have been described as opportunistic pathogens-especially in immunocompromised individuals. Last, a distantly related species (Weissella ceti) is the etiologic agent of weissellosis, a disease that affects farmed fish that are important for commercial aquaculture. The purpose of this literature-based safety assessment is to consolidate findings from primary research related to Weissella confusa and its natural associations with and effects on animals, humans, and their agricultural environments. Based on these assessments, it is reasonable to conclude that many Weissella confusa are safe for use in direct-fed microbial products for poultry.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33646379", + "title": "Diversity and Composition of Gut Bacterial Community in Giant Panda with Anorexia.", + "year": 2021, + "journal": "Current microbiology", + "authors": [ + "Zhao S", + "Li C", + "Zhu T", + "Jin L", + "Deng W", + "Zhao K", + "He Y", + "Li G", + "Xiong Y", + "Li T", + "Li B", + "Huang Y", + "Zhang H", + "Zou L" + ], + "bacteria": "Weissella", + "condition": "healthy", + "relevance_score": 0.33675038767255694, + "mesh_terms": [ + "Animals", + "Anorexia", + "China", + "Feces", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Ursidae" + ], + "raw_abstract": "The giant panda (GP) is the most precious animal in China. Gastrointestinal tract disease, especially associated with dysbiosis of gut microbiota, is the leading cause of death in GPs. Here, we performed 16S rRNA high-throughput sequencing to investigate the gut microbiota of GPs having symptoms of anorexia. Results showed that gut microbiota of GP with anorexia had lower richness (Chao1 index) than the healthy GP. However, no significant differences in alpha diversity were observed. There is a significance in the microbial structure between anorexia and healthy GPs. The abundance of phylum Firmicutes (99.23%\u2009\u00b1\u20097.1%), unidentified genus Clostridiales (24.75%\u2009\u00b1\u20092.5%), was significantly higher in the subadult anorexia group (P\u2009<\u20090.01), and that of the unidentified genus Clostridiales (4.53%\u2009\u00b1\u20091.2%) was also significantly higher in the adult anorexia group (P\u2009<\u20090.01). Weissella and Streptococcus were found to be decreased in both anorexia groups. The decreased abundance of Weissella (0.02%\u2009\u00b1\u20090.0%, 0.08%\u2009\u00b1\u20090.0%) and Streptococcus (73.89%\u2009\u00b1\u20094.3%, 91.15%\u2009\u00b1\u20097.6%) and increase in Clostridium may cause symptoms of anorexia in giant pandas. The correlation analysis indicated that there is a symbiotic relationship among Streptococcus, Leuconostoc, Weissella, and Bacillus which are classified as probiotics (r\u2009>\u20090.6, P\u2009<\u20090.05). Importantly, a negative correlation has been found between Streptococcus and unidentified_Clostridium in two groups (r\u2009>\u20090.6, P\u2009<\u20090.05). Our results suggested that Streptococcus might be used as probiotics to control the growth of Clostridium causing the anorexia.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "27572508", + "title": "Intestinal Lactobacillus community structure and its correlation with diet of Southern Chinese elderly subjects.", + "year": 2016, + "journal": "Journal of microbiology (Seoul, Korea)", + "authors": [ + "Pan Y", + "Wang F", + "Sun DW", + "Li Q" + ], + "bacteria": "Weissella", + "condition": "healthy", + "relevance_score": 0.2669634372623612, + "mesh_terms": [ + "Aged, 80 and over", + "Biodiversity", + "China", + "DNA, Bacterial", + "Diet", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestines", + "Lactobacillus", + "Male", + "Phylogeny", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "This study aimed to investigate the relationship between the intestinal Lactobacillus species and diet of elderly subjects in a longevity area in Southern China. Healthy elderly subjects ranging from 80 to 99 years old were respectively selected from the regions of Bama and Nanning, Guangxi, China. The nested polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) technology was used to analyze the intestinal Lactobacillus community structure. Results showed that Weissella confusa, L. mucosae, L. crispatus, L. salivarius, and L. delbrueckii were the representative Lactobacillus of elderly subjects. Among them, L. crispatus and L. delbrueckii were the dominant Lactobacillus of all species. In comparison to Nanning elderly subjects, the detection frequencies of W. confusa and L. salivarius were significantly increased in Bama elderly subjects (P < 0.01), whereas L. mucosae was significantly decreased (P < 0.01). Interestingly, it was also found that there were 4 kinds of representative Lactobacillus, which were significantly correlated with dietary fiber. W. confusa (P < 0.01) and L. salivarius (P < 0.05) were significantly positively correlated with the intake of dietary fiber, while L. mucosae (P < 0.01) and L. crispatus (P < 0.05) were significantly negatively correlated with the intake of dietary fiber, respectively. Results confirmed that different diets had obvious effects on the intestinal Lactobacillus community structure of elderly subjects in Southern China, which may provide a certain theoretical basis for the elderly's healthy food strategic design and probiotics product development.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32610159", + "title": "Isolation and preliminary screening of potentially probiotic Weissella confusa strains from healthy human feces by culturomics.", + "year": 2020, + "journal": "Microbial pathogenesis", + "authors": [ + "Wang W", + "Liu W", + "Chu W" + ], + "bacteria": "Weissella", + "condition": "healthy", + "relevance_score": 0.25739398434313326, + "mesh_terms": [ + "Feces", + "Humans", + "Probiotics", + "RNA, Ribosomal, 16S", + "Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization", + "Weissella" + ], + "raw_abstract": "PURPOSE: The objective of this study was to isolate and identify strains of bacteria from feces of healthy human and screen potential probiotic candidate by using culturomics method combined with the matrix-assisted laser desorption/ionization-time of flight mass spectrum (MALDI-TOF MS) and 16S rRNA gene sequencing. METHODS AND RESULTS: 31 strains were isolated and purified from human feces by culturomics method, and identified by MALDI-TOF MS and 16S rRNA gene sequencing. Then the obtained strains were tested for haemolytic activity, antibiotic susceptibility, acid and bile salts tolerance, antimicrobial activity, morphological and physiological characteristics. Three potential probiotic candidate strains named YM5Y, YM5S1 and YM5S2 were selected and identified as Weissella confusa. CONCLUSION: Our results suggest the culturomics approach could be used to isolate and screen human fecal strains which could eventually be used for the development of novel probiotics. In addition, the isolated strains of W. confusa can act as potential probiotics and should be explored further for their potential application.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38036594", + "title": "The anticancer mechanisms of exopolysaccharide from Weissella cibaria D-2 on colorectal cancer via apoptosis induction.", + "year": 2023, + "journal": "Scientific reports", + "authors": [ + "Du Y", + "Liu L", + "Yan W", + "Li Y", + "Li Y", + "Cui K", + "Yu P", + "Gu Z", + "Zhang W", + "Feng J", + "Li Z", + "Tang H", + "Du Y", + "Zhao H" + ], + "bacteria": "Weissella", + "condition": "healthy", + "relevance_score": 0.25666024402461657, + "mesh_terms": [ + "Infant", + "Humans", + "Polysaccharides, Bacterial", + "Weissella", + "Apoptosis", + "Colorectal Neoplasms" + ], + "raw_abstract": "Exopolysaccharide (EPS) from Weissella cibaria has been devoted to the study of food industry. However, the anticancer activity of W. cibaria derived EPS has not yet been investigated. In this study, we obtained the EPS from W. cibaria D-2 isolated from the feces of healthy infants and found that D-2-EPS, a homopolysaccharide with porous web like\u00a0structure, could effectively inhibit the proliferation, migration, invasion and induce cell cycle arrest in G0/G1 phase of colorectal cancer (CRC) cells. In HT-29 tumor xenografts, D-2-EPS significantly retarded tumor growth without obvious cytotoxicity to normal organs. Furthermore, we revealed that D-2-EPS promoted the apoptosis of CRC cells by increasing the levels of Fas, FasL and activating Caspase-8/Caspase-3, indicating that D-2-EPS might induce apoptosis through the extrinsic Fas/FasL pathway. Taken together, the D-2-EPS has the potential to be developed as a nutraceutical or drug to prevent and treat colorectal cancer.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37700874", + "title": "Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing.", + "year": 2023, + "journal": "Journal of asthma and allergy", + "authors": [ + "Wan J", + "Song J", + "Lv Q", + "Zhang H", + "Xiang Q", + "Dai H", + "Zheng H", + "Lin X", + "Zhang W" + ], + "bacteria": "Actinomyces", + "condition": "healthy", + "relevance_score": 0.4092405953598793, + "mesh_terms": [], + "raw_abstract": "PURPOSE: Recent studies had shown that gut microbiota played a significant role in the development of the immune system and may affect the course of airway allergic disease. We conducted this study to determine unique gut microbial associated with allergic disease in children by shotgun gene sequencing. METHODS: We collected fecal samples from children with allergic asthma (n = 23) and allergic rhinitis (n = 18), and healthy control (n = 19). The gut microbiota of specimens was analyzed by high-throughput metagenomic shotgun gene sequencing. RESULTS: The intestinal microbiota of children with allergic asthma and allergic rhinitis was characterized by increased microbial richness and diversity. Simpson and Shannon were significantly elevated in children with allergic asthma. Principal coordinates analysis (PCoA) showed that the gut microbial communities cluster patterns of children with asthma or rhinitis were significantly different from those of healthy controls. However, no significant difference was found between asthma group and rhinitis group At the phylum level, higher relative abundance of Firmicutes was found in the allergic rhinitis group and allergic asthma group, while the level of Bacteroidetes was significantly lower. At the genus level, Corynebacterium, Streptococcus, Dorea, Actinomyces, Bifidobacterium, Blautia, and Rothia were significantly enriched in the allergic asthma group. Finally, a random forest classifier model selected 16 general signatures to discriminate the allergic asthma group from the healthy control group. CONCLUSION: In conclusion, children in the allergic rhinitis group and allergic asthma group had altered gut microbiomes in comparison with the healthy control group. Compared to healthy children, the gut microbiome in children with allergic diseases has higher pro-inflammatory potential and increased production of pro-inflammatory molecules.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "26789999", + "title": "Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease.", + "year": 2016, + "journal": "Digestion", + "authors": [ + "Takahashi K", + "Nishida A", + "Fujimoto T", + "Fujii M", + "Shioya M", + "Imaeda H", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Andoh A" + ], + "bacteria": "Actinomyces", + "condition": "healthy", + "relevance_score": 0.3393860353782703, + "mesh_terms": [ + "Actinomyces", + "Adult", + "Bacteroides", + "Bifidobacterium", + "Butyrates", + "Case-Control Studies", + "Clostridium", + "Crohn Disease", + "DNA, Bacterial", + "DNA, Ribosomal", + "Dysbiosis", + "Eubacterium", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "RNA, Ribosomal, 16S", + "Real-Time Polymerase Chain Reaction", + "Ruminococcus", + "Sequence Analysis, DNA", + "Sequence Analysis, RNA" + ], + "raw_abstract": "BACKGROUND: The global alteration of the gut microbial community (dysbiosis) plays an important role in the pathogenesis of inflammatory bowel diseases (IBDs). However, bacterial species that characterize dysbiosis in IBD remain unclear. In this study, we assessed the alteration of the fecal microbiota profile in patients with Crohn's disease (CD) using 16S rRNA sequencing. SUMMARY: Fecal samples from 10 inactive CD patients and 10 healthy individuals were subjected to 16S rRNA sequencing. The V3-V4 hypervariable regions of 16S rRNA were sequenced by the Illumina MiSeq\u2122II system. The average of 62,201 reads per CD sample was significantly lower than the average of 73,716 reads per control sample. The genera Bacteroides, Eubacterium, Faecalibacterium and Ruminococcus significantly decreased in CD patients as compared to healthy controls. In contrast, the genera Actinomyces and Bifidobacterium significantly increased in CD patients. At the species level, butyrate-producing bacterial species, such as Blautia faecis, Roseburia inulinivorans, Ruminococcus torques, Clostridium lavalense, Bacteroides uniformis and Faecalibacterium prausnitzii were significantly reduced in CD patients as compared to healthy individuals (p < 0.05). These results of 16S rRNA sequencing were confirmed in additional CD patients (n = 68) and in healthy controls (n = 46) using quantitative PCR. The abundance of Roseburia inulinivorans and Ruminococcus torques was significantly lower in C-reactive protein (CRP)-positive CD patients as compared to CRP-negative CD patients (p < 0.05). KEY MESSAGE: The dysbiosis of CD patients is characterized by reduced abundance of multiple butyrate-producing bacteria species.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37382280", + "title": "Characteristics of Gut Microbiota in Patients with Erectile Dysfunction: A Chinese Pilot Study.", + "year": 2024, + "journal": "The world journal of men's health", + "authors": [ + "Kang J", + "Wang Q", + "Wang S", + "Pan Y", + "Niu S", + "Li X", + "Liu L", + "Liu X" + ], + "bacteria": "Actinomyces", + "condition": "healthy", + "relevance_score": 0.3182770756379131, + "mesh_terms": [], + "raw_abstract": "PURPOSE: Little is known about the role of gut microbiota in the pathogenesis of erectile dysfunction (ED). We performed a study to compare taxonomic profiles of gut microbiota of ED and healthy males. MATERIALS AND METHODS: A total of 43 ED patients and 16 healthy controls were enrolled in the study. The 5-item version of the International Index of Erectile Function (IIEF-5) with a cutoff value of 21 was used to evaluate erectile function. All participants underwent nocturnal penile tumescence and rigidity test. Samples of stool were sequenced to determine the gut microbiota. RESULTS: We identified a distinct beta diversity of gut microbiome in ED patients by unweighted UniFrac analysis (R\u00b2=0.026, p=0.036). Linear discriminant analysis effect size (LEfse) analysis showed Actinomyces was significantly enriched, whereas CONCLUSIONS: This pilot study identified evident alterations in the gut microbiome composition of ED patients and found", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "37071621", + "title": "Seasonal variations in gut microbiota and disease course in patients with inflammatory bowel disease.", + "year": 2023, + "journal": "PloS one", + "authors": [ + "Tani M", + "Shinzaki S", + "Asakura A", + "Tashiro T", + "Amano T", + "Otake-Kasamoto Y", + "Yoshihara T", + "Yoshii S", + "Tsujii Y", + "Hayashi Y", + "Inoue T", + "Motooka D", + "Nakamura S", + "Iijima H", + "Takehara T" + ], + "bacteria": "Actinomyces", + "condition": "healthy", + "relevance_score": 0.31205892791853385, + "mesh_terms": [ + "Humans", + "Seasons", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Crohn Disease", + "Bacteria", + "Disease Progression", + "Feces" + ], + "raw_abstract": "BACKGROUND AND AIM: Environmental factors are associated with onset and course of inflammatory bowel disease (IBD). Our previous study by about 1,100 IBD patients revealed half of the patients experienced seasonal exacerbation of disease. We investigated the seasonality of fecal microbiota composition of IBD patients. METHODS: Fecal samples were consecutively collected in each season from IBD outpatients and healthy controls between November 2015 and April 2019. Participants who were treated with full elemental diet or antibiotics within 6 months or had ostomates were excluded. Bacterial profiles were analyzed by 16S rRNA sequencing, and the changes between the diseases and seasons were compared. RESULTS: A total of 188 fecal samples were analyzed from 47 participants comprising 19 Crohn's disease (CD) patients, 20 ulcerative colitis (UC) patients, and 8 healthy controls (HC). In CD patients, the phylum Actinobacteria and TM7 were both significantly more abundant in autumn than in spring and winter, but not in UC patients and HC. Moreover, the genera Actinomyces, a member of Actinobacteria, and c_TM7-3;o_;f_;g_ (TM7-3), that of TM7, were significantly more abundant in autumn than in spring, and the abundance of Actinomyces was significantly correlated with that of TM7-3 throughout the year in CD patients, but not in UC patients and HC. CD patients with high abundance of TM7-3 in the autumn required significantly fewer therapeutic intervention than those without seasonal fluctuation. CONCLUSIONS: Oral commensals Actinomyces and its symbiont TM7-3 were correlatively fluctuated in the feces of CD patients by season, which could affect the disease course.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39085949", + "title": "Meta-analysis identifies common gut microbiota associated with multiple sclerosis.", + "year": 2024, + "journal": "Genome medicine", + "authors": [ + "Lin Q", + "Dorsett Y", + "Mirza A", + "Tremlett H", + "Piccio L", + "Longbrake EE", + "Choileain SN", + "Hafler DA", + "Cox LM", + "Weiner HL", + "Yamamura T", + "Chen K", + "Wu Y", + "Zhou Y" + ], + "bacteria": "Actinomyces", + "condition": "healthy", + "relevance_score": 0.29628159373464663, + "mesh_terms": [ + "Humans", + "Multiple Sclerosis", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Bacteria", + "Adult", + "Male", + "Female", + "Case-Control Studies" + ], + "raw_abstract": "BACKGROUND: Previous studies have identified a diverse group of microbial taxa that differ between patients with multiple sclerosis (MS) and the healthy population. However, interpreting findings on MS-associated microbiota is challenging, as there is no true consensus. It is unclear whether there is gut microbiota commonly altered in MS across studies. METHODS: To answer this, we performed a meta-analysis based on the 16S rRNA gene sequencing data from seven geographically and technically diverse studies comprising a total of 524 adult subjects (257 MS and 267 healthy controls). Analysis was conducted for each individual study after reprocessing the data and also by combining all data together. The blocked Wilcoxon rank-sum test and linear mixed-effects regression were used to identify differences in microbial composition and diversity between MS and healthy controls. Network analysis was conducted to identify bacterial correlations. A leave-one-out sensitivity analysis was performed to ensure the robustness of the findings. RESULTS: The microbiome community structure was significantly different between studies. Re-analysis of data from individual studies revealed a lower relative abundance of Prevotella in MS across studies, compared to controls. Meta-analysis found that although alpha and beta diversity did not differ between MS and controls, a higher abundance of Actinomyces and a lower abundance of Faecalibacterium were reproducibly associated with MS. Additionally, network analysis revealed that the recognized negative Bacteroides-Prevotella correlation in controls was disrupted in patients with MS. CONCLUSIONS: Our meta-analysis identified common gut microbiota associated with MS across geographically and technically diverse studies.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39787116", + "title": "The gut microbiota-SCFA-inflammation axis in patients with AECOPD.", + "year": 2025, + "journal": "PloS one", + "authors": [ + "Zhu H", + "Wu C", + "Wu H", + "Liu J", + "Ye W", + "Zhao T", + "Li Z" + ], + "bacteria": "Actinomyces", + "condition": "healthy", + "relevance_score": 0.29059208842920076, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Pulmonary Disease, Chronic Obstructive", + "Male", + "Female", + "Aged", + "Inflammation", + "Middle Aged", + "Fatty Acids, Volatile", + "Case-Control Studies", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVES: The aim of the study was to explore the alteration of microbiota and SCFA in gut and inflammation in acute exacerbation chronic obstructive pulmonary disease (AECOPD) patients, and to test the hypothesis that a disorder of gut microbiota will lead to the alteration of SCFA, which will aggravate inflammation in AECOPD patients. METHODS AND RESULTS: 24 patients with AECOPD and 18 healthy volunteers were included in the study. Gut microbiota were analyzed by 16S rDNA and serum was used to detect levels of inflammatory factors by ELISA. Fatty acid concentrations were determined in lumen via gas chromatography-mass spectrometry. The richness and diversity of gut microbiota were decreased in AECOPD patients. \u03b2-diversity analysis revealed differences between AECOPD patients and healthy controls. p_Bacteroidetes, g_Paraprevotella, g_Ruminococcus2, g_Parasutterella, o_Rhodospirillales, and g_Romboutsia in the healthy controls and p_Firmicutes, o_Actinomycetales, f_Actinomycetadeae, g_Actinomyces, g_Mogibacterium, f_Veillonellaceae, f_Enterococcaceae, and g_Enterococcus in AECOPD patients were the most abundant microbiota. SCFA levels were decreased in patients with AECOPD. In addition, the results demonstrated that except for a reduction in IL-6, there was no change in inflammatory markers in AECOPD patients. CONCLUSION: In AECOPD patients, the gut microbiota-SCFA-inflammation axis is augmented, with decreased diversity and abundance of gut microbiota, leading to a reduction in SCFA and an imbalance of inflammation.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33124578", + "title": "Intestinal microbiota composition of patients with Beh\u00e7et's disease: differences between eye, mucocutaneous and vascular involvement. The Rheuma-BIOTA study.", + "year": 2020, + "journal": "Clinical and experimental rheumatology", + "authors": [ + "Yasar Bilge NS", + "P\u00e9rez Brocal V", + "Kasifoglu T", + "Bilge U", + "Kasifoglu N", + "Moya A", + "Dinleyici EC" + ], + "bacteria": "Actinomyces", + "condition": "healthy", + "relevance_score": 0.27484843161521166, + "mesh_terms": [ + "Adult", + "Behcet Syndrome", + "Gastrointestinal Microbiome", + "Humans", + "Prospective Studies" + ], + "raw_abstract": "OBJECTIVES: Changes in microbiota composition affect the aetiology and patho-genesis of chronic diseases, including Beh\u00e7et's disease (BD). However, no studies have analysed the potential gut microbiota changes among different clinical forms of BD. This study evaluated the intestinal microbiota composition of patients with BD and healthy controls and also compared differences between patients with BD with respect to eye, mucocutaneous, and vascular involvement. METHODS: In this prospective cohort study, 27 patients diagnosed with BD according to the International Study Group criteria and 10 age- and sex-matched healthy controls were included. Detailed intestinal microbiota analysis was performed. RESULTS: There were no differences between the BD group and the control group in terms of alpha and beta microbial diversity and abundance indices (p>0.05). Actinomyces, Libanicoccus, Collinsella, Eggerthella, Enetrohabdus, Catenibacterium, and Enterobacter were significantly higher in the BD group than in the control group. In addition, Bacteroides, Cricetibacter, Alistipes, Lachnospira, Dielma, Akkermansia, Sutterella, Anaerofilum, Ruminococcease-UCG007, Acetanaerobacterium, and Copropaacter were lower in the BD group than in the control group. When we compared three different system involvement (eye, mucocutaneous, and vascular), the linear discriminant analysis effective size revealed a difference for the following genera: Lachnospiraceae NK4A136 in the uveitis group; Dialister, Intestinomonas, and Marvinbryantia in the mucocutaneous group; and Gemella in the vascular group. CONCLUSIONS: The composition of intestinal microbiota was significantly different in patients with BD compared with healthy adults. Ours is the first study to show differences in microbiota composition in isolated mucocutaneous, eye, and vascular involvement. These findings should be evaluated in a larger series.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30081953", + "title": "Breast cancer in postmenopausal women is associated with an altered gut metagenome.", + "year": 2018, + "journal": "Microbiome", + "authors": [ + "Zhu J", + "Liao M", + "Yao Z", + "Liang W", + "Li Q", + "Liu J", + "Yang H", + "Ji Y", + "Wei W", + "Tan A", + "Liang S", + "Chen Y", + "Lin H", + "Zhu X", + "Huang S", + "Tian J", + "Tang R", + "Wang Q", + "Mo Z" + ], + "bacteria": "Actinomyces", + "condition": "healthy", + "relevance_score": 0.2748269007645083, + "mesh_terms": [ + "Adult", + "Bacteria", + "Bacterial Proteins", + "Breast Neoplasms", + "C-Reactive Protein", + "Case-Control Studies", + "Estradiol", + "Female", + "Gastrointestinal Microbiome", + "Gene Regulatory Networks", + "Humans", + "Metagenomics", + "Middle Aged", + "Phylogeny", + "Postmenopause", + "Premenopause" + ], + "raw_abstract": "BACKGROUND: Increasing evidence suggests that gut microbiota play a role in the pathogenesis of breast cancer. The composition and functional capacity of gut microbiota associated with breast cancer have not been studied systematically. METHODS: We performed a comprehensive shotgun metagenomic analysis of 18 premenopausal breast cancer patients, 25 premenopausal healthy controls, 44 postmenopausal breast cancer patients, and 46 postmenopausal healthy controls. RESULTS: Microbial diversity was higher in breast cancer patients than in controls. Relative species abundance in gut microbiota did not differ significantly between premenopausal breast cancer patients and premenopausal controls. In contrast, relative abundance of 45 species differed significantly between postmenopausal patients and postmenopausal controls: 38 species were enriched in postmenopausal patients, including Escherichia coli, Klebsiella sp_1_1_55, Prevotella amnii, Enterococcus gallinarum, Actinomyces sp. HPA0247, Shewanella putrefaciens, and Erwinia amylovora, and 7 species were less abundant in postmenopausal patients, including Eubacterium eligens and Lactobacillus vaginalis. Acinetobacter radioresistens and Enterococcus gallinarum were positively but weakly associated with expression of high-sensitivity C-reactive protein; Shewanella putrefaciens and Erwinia amylovora were positively but weakly associated with estradiol levels. Actinomyces sp. HPA0247 negatively but weakly correlated with CD3 CONCLUSION: The composition and functions of the gut microbial community differ between postmenopausal breast cancer patients and healthy controls. The gut microbiota may regulate or respond to host immunity and metabolic balance. Thus, while cause and effect cannot be determined, there is a reproducible change in the microbiota of treatment-naive patients relative to matched controls.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "29482338", + "title": "Effect of Bacillus subtilis C-3102 on loose stools in healthy volunteers.", + "year": 2018, + "journal": "Beneficial microbes", + "authors": [ + "Hatanaka M", + "Yamamoto K", + "Suzuki N", + "Iio S", + "Takara T", + "Morita H", + "Takimoto T", + "Nakamura T" + ], + "bacteria": "Actinomyces", + "condition": "healthy", + "relevance_score": 0.2656681067013936, + "mesh_terms": [ + "Administration, Oral", + "Antidiarrheals", + "Bacillus subtilis", + "Double-Blind Method", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Placebos", + "Probiotics", + "Tablets" + ], + "raw_abstract": "Ingestion of Bacillus subtilis C-3102 spores (C-3102) has relieved the symptoms of diarrhoea in piglets and changed the composition of gut microbiota in humans. Recently, it was suggested that the composition of the human gut microbiota affects stool consistency. In this study, a double-blind, randomised, placebo-controlled trial was conducted to assess the preventive effects of chronic diarrhoea in healthy volunteers with loose stools by ingestion of C-3102. The results showed that oral doses of C-3102 tablets significantly decreased the Bristol Stool Scale score and stool frequency, and also significantly improved abdominal sounds. With regard to gut microbiota, the relative abundance of Lachnospira, Actinomyces and SMB53 were significantly changed. This study shows that C-3102 could be effective for treating loose stools (Trial registration: UMIN000022583, http://tinyurl.com/ya4refqn ).", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "32144305", + "title": "The association between breastmilk oligosaccharides and faecal microbiota in healthy breastfed infants at two, six, and twelve weeks of age.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Borewicz K", + "Gu F", + "Saccenti E", + "Hechler C", + "Beijers R", + "de Weerth C", + "van Leeuwen SS", + "Schols HA", + "Smidt H" + ], + "bacteria": "Actinomyces", + "condition": "healthy", + "relevance_score": 0.25508255612443803, + "mesh_terms": [ + "Breast Feeding", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Infant", + "Infant, Newborn", + "Lactation", + "Male", + "Milk, Human", + "Mothers", + "Oligosaccharides" + ], + "raw_abstract": "Several factors affect gut microbiota development in early life, among which breastfeeding plays a key role. We followed 24 mother-infant pairs to investigate the associations between concentrations of selected human milk oligosaccharides (HMOs) in breastmilk, infant faeces, and the faecal microbiota composition in healthy, breastfed infants at two, six and 12 weeks of age. Lactation duration had a significant effect on breastmilk HMO content, which decreased with time, except for 3-fucosyllactose (3FL) and Lacto-N-fucopentaose III (LNFP III). We confirmed that microbiota composition was strongly influenced by infant age and was associated with mode of delivery and breastmilk LNFP III concentration at two weeks, with infant sex, delivery mode, and concentrations of 3'sialyllactose (3'SL) in milk at six weeks, and infant sex and Lacto-N-hexaose (LNH) in milk at 12 weeks of age. Correlations between levels of individual breastmilk HMOs and relative abundance of OTUs found in infant faeces, including the most predominant Bifidobacterium OTUs, were weak and varied with age. The faecal concentration of HMOs decreased with age and were strongly and negatively correlated with relative abundance of OTUs within genera Bifidobacterium, Parabacteroides, Escherichia-Shigella, Bacteroides, Actinomyces, Veillonella, Lachnospiraceae Incertae Sedis, and Erysipelotrichaceae Incertae Sedis, indicating the likely importance of these taxa for HMO metabolism in vivo.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "33648648", + "title": "The faecal metabolome in COVID-19 patients is altered and associated with clinical features and gut microbes.", + "year": 2021, + "journal": "Analytica chimica acta", + "authors": [ + "Lv L", + "Jiang H", + "Chen Y", + "Gu S", + "Xia J", + "Zhang H", + "Lu Y", + "Yan R", + "Li L" + ], + "bacteria": "Actinomyces", + "condition": "healthy", + "relevance_score": 0.2419216026430759, + "mesh_terms": [ + "Adult", + "Bacteria", + "COVID-19", + "Cohort Studies", + "Dysbiosis", + "Feces", + "Female", + "Fungi", + "Gas Chromatography-Mass Spectrometry", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metabolome", + "Middle Aged", + "SARS-CoV-2" + ], + "raw_abstract": "Although SARS-CoV-2 can invade the intestine, though its effect on digestion and absorption is not fully understood. In the present study, 56 COVID-19 patients and 47 age- and sex-matched healthy subjects were divided into a discovery cohort and a validation cohort. Blood, faeces and clinical information were collected from the patients in the hospital and at discharge. The faecal metabolome was analysed using gas chromatography-mass spectrometry, and Spearman's correlation analyses of clinical features, the serum metabolome, and the faecal micro- and mycobiota were conducted. The results showed that, the faeces of COVID-19 patients were enriched with important nutrients that should be metabolized or absorbed, such as sucrose and 2-palmitoyl-glycerol; diet-related components that cannot be synthesized by humans, such as 1,5-anhydroglucitol and D-pinitol; and harmful metabolites, such as oxalate, were also detected. In contrast, purine metabolites such as deoxyinosine and hypoxanthine, low-water-soluble long-chain fatty alcohols/acids such as behenic acid, compounds rarely occurring in nature such as D-allose and D-arabinose, and microbe-related compounds such as 2,4-di-tert-butylphenol were depleted in the faeces of COVID-19 patients. Moreover, these metabolites significantly correlated with altered serum metabolites such as oxalate and gut microbesincluding Ruminococcaceae, Actinomyces, Sphingomonas and Aspergillus. Although levels of several faecal metabolites, such as sucrose, 1,5-anhydroglucitol and D-pinitol, of discharged patients were not different from those of healthy controls (HCs), those of oxalate and 2-palmitoyl-glycerol did differ. Therefore, alterations in the faecal metabolome of COVID-19 patients may reflect malnutrition and intestinal inflammation and warrant greater attention. The results of present study provide new insights into the pathogenesis and treatment of COVID-19.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "38331300", + "title": "Alterations in the diversity, composition and function of the gut microbiota in Uyghur individuals with sarcopenia.", + "year": 2024, + "journal": "Experimental gerontology", + "authors": [ + "Zhang Q", + "Li X", + "Huang T", + "Zhang S", + "Teng K", + "Rousitemu N", + "Lan T", + "Wen Y" + ], + "bacteria": "Allisonella", + "condition": "healthy", + "relevance_score": 0.2732731009592868, + "mesh_terms": [ + "Humans", + "Sarcopenia", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Aging", + "Bacteroidetes" + ], + "raw_abstract": "BACKGROUND: Research on the gut microbiota has emerged as a new direction for understanding pathophysiologic changes in diseases associated with aging, such as sarcopenia. Several studies have shown that there are differences in the gut microbiota between individuals with sarcopenia and without sarcopenia. However, these differences are not consistent across regions and ethnic groups, and additional research is needed. METHODS: In this study, we collected fresh fecal samples from 31 Uyghur individuals with sarcopenia and 31 healthy controls. We used 16S rRNA sequencing to obtain fecal base sequences and analyzed the diversity, composition and function of the gut microbiota. RESULTS: There was no significant difference in alpha diversity between the sarcopenia group and the healthy control group (P\u00a0>\u00a00.05). There was a significant difference in beta diversity between the groups (P\u00a0<\u00a00.05). In the sarcopenia group, the abundances of Alloprevotella, un_f_Prevotellaceae, Anaerovibrio, Prevotellaceae_NK3B31_group, Mitsuokella, Prevotella and Allisonella were lower than those in the heathy control group, and the abundances of Flavobacteriales, Flavobacteriaceae, Catenibacterium, Romboutsia, Erysipelotrichaceae_UCG-003, GCA-900066575, Lachnospiraceae_FCS020_group, and un_f_Flavobacteriaceae were higher than those in the heathy control group. Linear discriminant analysis effect size (LEfSe) revealed that the microbial species in the control group that were significantly different from those in the sarcopenia group were concentrated in the genus Alloprevotella, while the species in the sarcopenia group were concentrated in the genus Catenibacterium. Functional prediction analysis revealed that D-alanine, glycine, serine, and threonine metabolism and transcription machinery, among others, were enriched in the sarcopenia group, which indicated that metabolic pathways related to amino acid metabolism and nutrient transport may be regulated to varying degrees in the pathophysiological context of sarcopenia. CONCLUSIONS: There were significant differences in the composition and function of the gut microbiota between Xinjiang Uyghur sarcopenia individuals and healthy individuals. These findings might aid in the development of probiotics or microbial-based therapies for sarcopenia in Uyhur individuals.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30592383", + "title": "Microbiome Analytics of the Gut Microbiota in Patients With Juvenile Idiopathic Arthritis: A Longitudinal Observational Cohort Study.", + "year": 2019, + "journal": "Arthritis & rheumatology (Hoboken, N.J.)", + "authors": [ + "van Dijkhuizen EHP", + "Del Chierico F", + "Malattia C", + "Russo A", + "Pires Marafon D", + "Ter Haar NM", + "Magni-Manzoni S", + "Vastert SJ", + "Dallapiccola B", + "Prakken B", + "Martini A", + "De Benedetti F", + "Putignani L" + ], + "bacteria": "Allobaculum", + "condition": "healthy", + "relevance_score": 0.47809853377310574, + "mesh_terms": [ + "Arthritis, Juvenile", + "Case-Control Studies", + "Child", + "Child, Preschool", + "Cohort Studies", + "Comorbidity", + "Dysbiosis", + "Faecalibacterium prausnitzii", + "Female", + "Firmicutes", + "Gastrointestinal Microbiome", + "Humans", + "Italy", + "Logistic Models", + "Longitudinal Studies", + "Male", + "Metagenomics", + "Netherlands", + "RNA, Ribosomal, 16S", + "Severity of Illness Index" + ], + "raw_abstract": "OBJECTIVE: To assess the composition of gut microbiota in Italian and Dutch patients with juvenile idiopathic arthritis (JIA) at baseline, with inactive disease, and with persistent activity compared to healthy controls. METHODS: In a multicenter, prospective, observational cohort study, fecal samples were collected at baseline from 78 Italian and 21 Dutch treatment-naive JIA patients with <6 months of disease duration and compared to 107 geographically matched samples from healthy children. Forty-four follow-up samples from patients with inactive disease and 25 follow-up samples from patients with persistent activity were analyzed. Gut microbiota composition was determined by 16S ribosomal RNA-based metagenomics. Alpha- and \u03b2-diversity were computed, and log ratios of relative abundance were compared between patients and healthy controls using random forest models and logistic regression. RESULTS: Baseline samples from Italian patients showed reduced richness compared to healthy controls (P < 0.001). Random forest models distinguished between Italian patient baseline samples and healthy controls and suggested differences between Dutch patient samples and healthy controls (areas under the curve >0.99 and 0.71, respectively). The operational taxonomic units (OTUs) of Erysipelotrichaceae (increased in patients), Allobaculum (decreased in patients), and Faecalibacterium prausnitzii (increased in patients) showed different relative abundance in Italian patient baseline samples compared to controls after controlling for multiple comparisons. Some OTUs differed between Dutch patient samples and healthy controls, but no evidence remained after controlling for multiple comparisons. No differences were found in paired analysis between Italian patient baseline and inactive disease samples. CONCLUSION: Our findings show evidence for dysbiosis in JIA patients. Only patient/control status, age, and geographic origin appear to be drivers of the microbiota profiles, regardless of disease activity stage, inflammation, and markers of autoimmunity.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "39169196", + "title": "Characterization of faecal microbiota and serum inflammatory markers in dogs diagnosed with chronic enteropathy or small-cell lymphoma: a pilot study.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Kaga C", + "Kakiyama S", + "Hokkyo A", + "Ogata Y", + "Shibata J", + "Nagahara T", + "Nakazawa M", + "Nakagawa T", + "Tsujimoto H", + "Chambers JK", + "Uchida K", + "Matsumoto S", + "Kobayashi T", + "Tomiyasu H", + "Mizusawa N" + ], + "bacteria": "Allobaculum", + "condition": "healthy", + "relevance_score": 0.27538894636512634, + "mesh_terms": [ + "Dogs", + "Animals", + "Pilot Projects", + "Feces", + "Dog Diseases", + "Gastrointestinal Microbiome", + "Male", + "Female", + "Biomarkers", + "Intestinal Diseases", + "Chronic Disease", + "Inflammatory Bowel Diseases", + "Case-Control Studies" + ], + "raw_abstract": "Dogs diagnosed with chronic enteropathy (CE) or small-cell lymphoma (SCL) exhibit marked differences in faecal microbiota and organic acid profiles compared with healthy dogs, as well as immune abnormalities in intestinal mucosal tissue. However, few studies have analysed trace organic acids, such as succinic acid, which have been suggested to be associated with IBD in humans. Therefore, in this study, we compared the faecal microbiota and organic acid profiles as well as serum inflammatory markers between dogs with disease (n\u2009=\u200911; 6 with CE and 5 with SCL) and healthy controls (n\u2009=\u200916). We also performed machine learning and correlation analysis to obtain more detailed insights into the characteristics of affected dogs. These results revealed that dogs with CE and SCL had lower levels of Erysipelotrichaceae (e.g. Turicibacter and Allobaculum), exhibited abnormalities in the succinic acid metabolism (i.e. succinic acid accumulation and decreased levels of Phascolarctobacterium as succinic acid-utilising bacteria) and increased levels of pathobiont bacteria such as Escherichia-Shigella. Additionally, the presence of Dubosiella was significantly negatively correlated with Canine Inflammatory Bowel Disease Activity Index scores. These findings are expected to aid the development of microbiome-based medications and/or supplements, although further verification is needed.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30101990", + "title": "Gut microbiota alterations in moderate to severe acne vulgaris patients.", + "year": 2018, + "journal": "The Journal of dermatology", + "authors": [ + "Yan HM", + "Zhao HJ", + "Guo DY", + "Zhu PQ", + "Zhang CL", + "Jiang W" + ], + "bacteria": "Allobaculum", + "condition": "healthy", + "relevance_score": 0.2506740633577749, + "mesh_terms": [ + "Acne Vulgaris", + "Adolescent", + "Adult", + "Bacteria", + "Case-Control Studies", + "DNA, Bacterial", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Male", + "RNA, Bacterial", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA", + "Severity of Illness Index", + "Young Adult" + ], + "raw_abstract": "Acne vulgaris is a chronic inflammatory dermatosis affecting approximately 85% of adolescents. There are many factors contributing to the development of this ailment. A recent study indicated that gut microbiota takes part in the pathogenesis of acne. We aimed to investigate the link between acne vulgaris and gut microbiota. A total of 31 moderate to severe acne vulgaris patients and 31 healthy controls were enrolled. We collected their feces, and gut microbiota was evaluated by the hypervariable regions of 16S rRNA genes through high-throughput sequencing. We identified links between acne vulgaris and changes of gut microbiota. At the phylum level, Actinobacteria (0.89% in acne patients and 2.84% in normal controls, P = 0.004) was decreased and Proteobacteria (8.35% in acne patients and 7.01% in normal controls, P = 0.031) was increased. At the genus level, Bifidobacterium, Butyricicoccus, Coprobacillus, Lactobacillus and Allobaculum were all decreased. The observed difference in genera between acne patients and healthy controls provides a new insight into the link between gut microbiota changes and acne vulgaris risk.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "30256506", + "title": "Chronic nonbacterial prostate inflammation in a rat model is associated with changes of gut microbiota that can be modified with a galactoglucomannan-rich hemicellulose extract in the diet.", + "year": 2019, + "journal": "BJU international", + "authors": [ + "Konkol Y", + "Keskitalo A", + "Vuorikoski H", + "Pietil\u00e4 S", + "Elo LL", + "Munukka E", + "Bernoulli J", + "Tuomela J" + ], + "bacteria": "Allobaculum", + "condition": "healthy", + "relevance_score": 0.2080806089146485, + "mesh_terms": [ + "Animals", + "Disease Models, Animal", + "Feces", + "Gastrointestinal Microbiome", + "Inflammation", + "Male", + "Mannans", + "Polysaccharides", + "Prostate", + "Prostatic Diseases", + "Rats", + "Rats, Wistar" + ], + "raw_abstract": "OBJECTIVES: To investigate dietary effects on the gut microbiota composition in a rat model of nonbacterial chronic prostate inflammation (CPI). MATERIALS AND METHODS: Nonbacterial CPI was induced in the Wistar rat strain with subcutaneous testosterone and 17\u03b2-oestradiol (E RESULTS: The microbial biodiversity was significantly different between the treatment groups. In the rats with CPI, there was a significant increase in gut microbial populations Rikenellaceae, Odoribacter, Clostridiaceae, Allobaculum and Peptococcaceae compared with healthy rats. Conversely, levels of Bacteroides uniformis, Lactobacillus and Lachnospiraceae were decreased in rats with CPI. SCFA butyric-, valeric- and caproic-acid concentrations were also decreased in the faecal samples of the rats with CPI. In contrast, acetic acid concentrations and serum LBP were significantly elevated in CPI rats compared with healthy ones. Amongst rats with CPI, treatment with the GGM extract significantly reduced the abundance of Odoribacter and Clostridiaceae levels, and increased the B. uniformis levels compared with CPI rats drinking tap water only. In addition, GGM significantly increased the levels of butyric acid and caproic acid, and reduced the levels of LBP in serum. CONCLUSIONS: Hormone-induced nonbacterial CPI in rats is associated with specific changes in gut microbiota and secondary changes in SCFAs and LPS due to gut microbiota alteration. Our results further suggest that fermentable compounds may have a beneficial effect on CPI.", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "35931488", + "title": "Discrepancies among healthy, subclinical mastitic, and clinical mastitic cows in fecal microbiome and metabolome and serum metabolome.", + "year": 2022, + "journal": "Journal of dairy science", + "authors": [ + "Wang Y", + "Nan X", + "Zhao Y", + "Jiang L", + "Wang H", + "Zhang F", + "Hua D", + "Liu J", + "Yang L", + "Yao J", + "Xiong B" + ], + "bacteria": "Paeniclostridium", + "condition": "healthy", + "relevance_score": 0.3074192925989778, + "mesh_terms": [ + "Animals", + "Cattle", + "Cattle Diseases", + "Feces", + "Female", + "Health Status", + "Mastitis, Bovine", + "Metabolome", + "Microbiota", + "Milk" + ], + "raw_abstract": "Mastitis is generally considered a local inflammatory disease caused by the invasion of exogenous pathogens and resulting in the dysbiosis of microbiota and metabolites in milk. However, the entero-mammary pathway theory may establish a possible link between some endogenous gut bacteria and the occurrence and development of mastitis. In the current study, we attempted to investigate differences in the gut microbiota profile and metabolite composition in gut and serum from healthy cows and those with subclinical mastitis and clinical mastitis. Compared with those of healthy cows, the microbial community diversities in the feces of cows with subclinical mastitis (SM) and clinical mastitis (CM) were lower. Lower abundance of Bifidobacterium, Romboutsia, Lachnospiraceae_NK3A20_group, Coprococcus, Prevotellaceae_UCG-003, Ruminococcus, and Alistipes, and higher abundance of the phylum Proteobacteria and the genera Escherichia-Shigella and Streptococcus were observed in CM cows. Klebsiella and Paeniclostridium were significantly enriched in the feces of SM cows. Several similarities were observed in feces and serum metabolites in mastitic cows. Higher levels of proinflammatory lipid products (20-trihydroxy-leukotriene-B4, 13,14-dihydro-15-keto-PGE", + "condition_dir": "microbiome-uc-ibd/healthy" + }, + { + "pmid": "25567118", + "title": "Geographical patterns of the standing and active human gut microbiome in health and IBD.", + "year": 2016, + "journal": "Gut", + "authors": [ + "Rehman A", + "Rausch P", + "Wang J", + "Skieceviciene J", + "Kiudelis G", + "Bhagalia K", + "Amarapurkar D", + "Kupcinskas L", + "Schreiber S", + "Rosenstiel P", + "Baines JF", + "Ott S" + ], + "bacteria": "Papillibacter", + "condition": "ulcerative colitis", + "relevance_score": 0.39139528774962323, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Aged, 80 and over", + "Clostridium", + "Female", + "Germany", + "Humans", + "India", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Lithuania", + "Male", + "Microbiota", + "Middle Aged", + "RNA, Ribosomal", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "OBJECTIVE: A global increase of IBD has been reported, especially in countries that previously had low incidence rates. Also, the knowledge of the human gut microbiome is steadily increasing, however, limited information regarding its variation on a global scale is available. In the light of the microbial involvement in IBDs, we aimed to (1) identify shared and distinct IBD-associated mucosal microbiota patterns from different geographical regions including Europe (Germany, Lithuania) and South Asia (India) and (2) determine whether profiling based on 16S rRNA transcripts provides additional resolution, both of which may hold important clinical relevance. DESIGN: In this study, we analyse a set of 89 mucosal biopsies sampled from individuals of German, Lithuanian and Indian origins, using bacterial community profiling of a roughly equal number of healthy controls, patients with Crohn's disease and UC from each location, and analyse 16S rDNA and rRNA as proxies for standing and active microbial community structure, respectively. RESULTS: We find pronounced population-specific as well as general disease patterns in the major phyla and patterns of diversity, which differ between the standing and active communities. The geographical origin of samples dominates the patterns of \u03b2 diversity with locally restricted disease clusters and more pronounced effects in the active microbial communities. However, two genera belonging to the Clostridium leptum subgroup, Faecalibacteria and Papillibacter, display consistent patterns with respect to disease status and may thus serve as reliable 'microbiomarkers'. CONCLUSIONS: These analyses reveal important interactions of patients' geographical origin and disease in the interpretation of disease-associated changes in microbial communities and highlight the added value of analysing communities on both the 16S rRNA gene (DNA) and transcript (RNA) level.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29204849", + "title": "Human intestinal spirochetosis mimicking ulcerative colitis.", + "year": 2018, + "journal": "Clinical journal of gastroenterology", + "authors": [ + "Nishii S", + "Higashiyama M", + "Ogata S", + "Komoto S", + "Ito S", + "Mizoguchi A", + "Terada H", + "Furuhashi H", + "Takajo T", + "Shirakabe K", + "Watanabe C", + "Tomita K", + "Nagao S", + "Miura S", + "Hokari R" + ], + "bacteria": "Brachyspira", + "condition": "ulcerative colitis", + "relevance_score": 0.6124719425677797, + "mesh_terms": [ + "Aged", + "Anti-Infective Agents", + "Brachyspira", + "Colitis", + "Colitis, Ulcerative", + "Colonoscopy", + "Diagnosis, Differential", + "Diarrhea", + "Female", + "Gram-Negative Bacterial Infections", + "Humans", + "Metronidazole" + ], + "raw_abstract": "Human intestinal spirochetosis (HIS) is a colorectal infection caused by the Brachyspira species of intestinal spirochetes, whose pathogenicity in humans remains unclear owing to the lack of or mild symptoms. We monitored the 5-year clinical course of a woman diagnosed with HIS in whom ulcerative colitis (UC) had been suspected. Following a positive fecal occult blood test, she underwent a colonoscopic examination at a local clinic where she was diagnosed with \"right-sided\" UC concomitant with incidentally detected HIS, and was referred to our hospital. Colonoscopic, histopathological, and cytological examination revealed localized erosive colitis in the ascending and the right transverse colon concomitant with HIS resembling skip lesions of UC. Initially, we chose the wait-and-watch approach; however, she gradually developed bloody diarrhea. Metronidazole improved her abdominal symptoms, as well as her colonoscopic and histopathological findings, suggesting that HIS was responsible for her colorectal inflammation. This case reveals (1) a possible pro-inflammatory role of HIS, (2) difficulties in diagnosing HIS in chronic proctocolitis, and (3) a possible inclusion of some HIS cases in \"UC\". HIS could mimic UC and might be included in differential diagnoses for UC. Antibiotic administration is necessary following the detection of HIS, particularly in patients demonstrating an atypical presentation of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Mitsuokella", + "condition": "ulcerative colitis", + "relevance_score": 0.47549133808592103, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36725284", + "title": "Functional analysis of metalloenzymes from human gut microbiota and their role in ulcerative colitis.", + "year": 2023, + "journal": "Journal of applied microbiology", + "authors": [ + "Shinde PB", + "Mohite SV", + "Yadav A", + "Singh MK", + "Kedia S", + "Ahuja V", + "Sharma KK" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.7625698689981166, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "AIM: Metalloenzymes produced by gut microbiota play an essential role in various physiological processes, and maintains homeostasis of gastrointestinal tract. Our study includes functional analysis of microbial metalloenzymes using metagenomics and metatranscriptomics data from Inflammatory Bowel Disease Multiomics Database. METHODS AND RESULTS: The distance matrix calculated by using metalloenzymes data produced significant results for bacterial taxonomy, with higher variance compared to HMP analysis in both Western and Indian population. Differential gene expression analysis revealed altered expression of ulcerative colitis (UC)-associated enzymes, increased folds changes in Prevotella and Megamonas transcripts; whereas, low transcripts of Alistipes genera. Further, docking and simulation studies performed on screened UC-associated enzymes revealed changes in catalytic efficiency and ligand interacting residues. CONCLUSION: The \u03b2-diversity using microbes containing metalloenzymes suggests considering small group of specific genes or enzymes for understanding the diversity between UC and healthy individuals. The docking and differential gene expression analysis collectively indicate the probable role of metalloenzymes and few UC-associated enzymes in the severity of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30102706", + "title": "Variability of core microbiota in newly diagnosed treatment-na\u00efve paediatric inflammatory bowel disease patients.", + "year": 2018, + "journal": "PloS one", + "authors": [ + "de Meij TGJ", + "de Groot EFJ", + "Peeters CFW", + "de Boer NKH", + "Kneepkens CMF", + "Eck A", + "Benninga MA", + "Savelkoul PHM", + "van Bodegraven AA", + "Budding AE" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.7383613409778521, + "mesh_terms": [ + "Adolescent", + "Case-Control Studies", + "Child", + "Child, Preschool", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Individuality", + "Inflammatory Bowel Diseases", + "Male" + ], + "raw_abstract": "BACKGROUND & AIMS: Intestinal microbiota is considered to play a crucial role in the aetiology of inflammatory bowel disease (IBD). We aimed to describe faecal microbiota composition and dynamics in a large cohort of children with de novo (na\u00efve) IBD, in comparison to healthy paediatric controls (HC). METHODS: In this prospective study, performed at two tertiary centres, faecal samples from newly diagnosed, treatment-na\u00efve paediatric IBD patients were collected prior to bowel cleansing for colonoscopy (t0) and 1, 3 and 6 weeks and 3 months after initiation of therapy. The microbial profiles of Crohn's disease (CD) and Ulcerative colitis (UC) patients were compared with HC and linked to therapeutic response. Microbiota composition was analysed by IS-pro technology. RESULTS: Microbial profiles of 104 new IBD-patients (63 CD, 41 UC, median age 14.0 years) were compared to 61 HC (median 7.8 years). IBD was mainly characterised by decreased abundance of Alistipes finegoldii and Alistipes putredinis, which characterize a healthy state microbial core. The classifier including these core species as predictors achieved an AUC of the ROC curve of .87. Core bacteria tended to regain abundance during treatment, but did not reach healthy levels. CONCLUSION: Faecal microbiota profiles of children with de novo CD and UC can be discriminated from HC with high accuracy, mainly driven by a decreased abundance of species shaping the microbial core in the healthy state. Paediatric IBD can therefore be characterized by decreased abundance of certain bacterial species reflecting the healthy state rather than by the introduction of pathogens.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38608475", + "title": "Turtle peptide and its derivative peptide ameliorated DSS-induced ulcerative colitis by inhibiting inflammation and modulating the composition of the gut microbiota.", + "year": 2024, + "journal": "International immunopharmacology", + "authors": [ + "Guo HX", + "Wang BB", + "Wu HY", + "Feng HY", + "Zhang HY", + "Gao W", + "Yuan B" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.7362113372008529, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Dextran Sulfate", + "Mice", + "Peptides", + "Anti-Inflammatory Agents", + "Turtles", + "Male", + "Mice, Inbred C57BL", + "Toll-Like Receptor 4", + "NF-kappa B", + "Disease Models, Animal", + "Intestinal Mucosa", + "Colon", + "Humans", + "Oxidative Stress", + "Signal Transduction" + ], + "raw_abstract": "Ulcerative colitis (UC) is a recurrent intestinal disease with an increasing incidence worldwide that seriously affects the life of patients. Turtle peptide (TP) is a bioactive peptide extracted from turtles that has anti-inflammatory, antioxidant and anti-aging properties. However, studies investigating the effect of TP on the progression of UC are lacking. The aim of this study was to investigate effects and underlying mechanisms of TP and its derivative peptide GPAGPIGPV (GP-9) in alleviating UC in mice. The results showed that 500\u00a0mg/kg TP treatment significantly ameliorated colitis symptoms and oxidative stress in UC mice. TP alleviated intestinal barrier damage in UC mice by promoting mucosal repair and increasing the expression of tight junction proteins (ZO1, occludin and claudin-1). TP also modulated the composition of the gut microbiota by increasing the abundance of the beneficial bacteria Anaerotignum, Prevotellaceae_UCG-001, Alistipes, and Lachno-spiraceae_NK4A136_group and decreasing the abundance of the harmful bacteria Prevotella_9 and Parasutterella. Furthermore, we characterized the peptide composition of TP and found that GP-9 ameliorated the symptoms of dextran sodium sulfate (DSS)-induced colitis in mice by inhibiting the TLR4/NF-\u03baB signaling pathway. In conclusion, TP and its derivative peptides ameliorated DSS-induced ulcerative colitis by inhibiting the expression of inflammatory factors and modulating the composition of the intestinal microbiota; this study provides a theoretical basis for the application of TP and its derivative peptides for their anti-inflammatory activity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39150994", + "title": "The Composition of the Fecal and Mucosa-adherent Microbiota Varies Based on Age and Disease Activity in Ulcerative Colitis.", + "year": 2025, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Malham M", + "Vestergaard MV", + "Bataillon T", + "Villesen P", + "Dempfle A", + "Bang C", + "Engsbro AL", + "Jakobsen C", + "Franke A", + "Wewer V", + "Thingholm LB", + "Petersen AM" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.7177144463997426, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Feces", + "Prospective Studies", + "Female", + "Male", + "Adult", + "Longitudinal Studies", + "Gastrointestinal Microbiome", + "Child", + "Adolescent", + "Intestinal Mucosa", + "RNA, Ribosomal, 16S", + "Young Adult", + "Middle Aged", + "Age Factors" + ], + "raw_abstract": "BACKGROUND: Pediatric-onset ulcerative colitis (pUC) represents a more aggressive disease phenotype compared with adult-onset UC. We hypothesized that this difference can, in part, be explained by the composition of the microbiota. METHODS: In a prospective, longitudinal study, we included pediatric (N\u2005=\u200530) and adult (N\u2005=\u200530) patients with newly or previously (>1 year) diagnosed UC. We analyzed the microbiota composition in the mucosa-adherent microbiota at baseline, using 16S rRNA gene sequencing, and the fecal microbiota at baseline and at 3-month intervals, using shotgun metagenomics. RESULTS: For fecal samples, the bacterial composition differed between pUC and aUC in newly diagnosed patients (\u03b2-diversity, Bray Curtis: R2\u2005=\u20050.08, P\u2005=\u2005.02). In colon biopsies, microbial diversity was higher in aUC compared with pUC (\u03b1-diversity, Shannon: estimated difference 0.54, P\u2005=\u2005.006). In the mucosa-adherent microbiota, Alistipes finegoldii was negatively associated with disease activity in pUC while being positively associated in aUC (estimate: -0.255 and 0.098, P\u2005=\u2005.003 and P\u2005=\u2005.02 in pUC and aUC, respectively). Finally, we showed reduced stability of the fecal microbiota in pediatric patients, evidenced by a different composition of the fecal microbiota in newly and previously diagnosed pUC, a pattern not found in adults. CONCLUSIONS: Our results indicate that pediatric UC patients have a more unstable fecal microbiota and a lower \u03b1 diversity than adult patients and that the microbiota composition differs between aUC and pUC patients. These findings offer some explanation for the observed differences between pUC and aUC and indicate that individualized approaches are needed if microbiota modifications are to be used in the future treatment of UC. In a prospective study, we found substantial differences in the mucosa-adherent and fecal microbiota between patients with pediatric and adult-onset ulcerative colitis. These differences offer some explanation for the severe phenotype reported in pediatric-onset ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36759757", + "title": "Integrating the serum proteomic and fecal metaproteomic to analyze the impacts of overweight/obesity on IBD: a pilot investigation.", + "year": 2023, + "journal": "Clinical proteomics", + "authors": [ + "Yan P", + "Sun Y", + "Luo J", + "Liu X", + "Wu J", + "Miao Y" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.7128360828961658, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) encompasses a group of chronic relapsing disorders which include ulcerative colitis (UC) and Crohn's disease (CD). The incidences of IBD and overweight/obesity are increasing in parallel. Here, we investigated alterations in proteomic in serum and metaproteomic in feces of IBD patients with overweight/obesity and aimed to explore the effect of overweight/ obesity on IBD and the underlying mechanism. METHODS: This prospective observational study (n\u2009=\u200964) comprised 26 health control subjects (HC, 13 with overweight/obesity) and 38 IBD patients (19 with overweight/obesity) at a tertiary hospital. Overweight/obesity was evaluated by body mass index (BMI) and defined as a BMI greater than 24\u00a0kg/m RESULTS: UC and CD presented similar serum molecular profiles but distinct gut microbiota. UC and CD serum exhibited higher levels of cytoskeleton organization- associated and inflammatory response-related proteins than the HC serum. Compared the serum proteome of UC and CD without overweight/obesity, inflammatory response-associated proteins were dramatically decreased in UC and CD with overweight/obesity. Fecal metaproteome identified 66 species in the feces. Among them, Parasutterella excrementihominis was increased in CD compared with that in HC. UC group had a significant enrichment of Moniliophthora roreri, but had dramatically decreased abundances of Alistipes indistinctus, Clostridium methylpentosum, Bacteroides vulgatus, and Schizochytrium aggregatum. In addition, overweight/obesity could improve the microbial diversity of UC. Specifically, the UC patients with overweight/obesity had increased abundance of some probiotics in contrast to those without overweight/obesity, including Parabacteroides distasonis, Alistipes indistincus, and Ruminococcus bromii. CONCLUSION: This study provided high-quality multi-omics data of IBD serum and fecal samples, which enabled deciphering the molecular bases of clinical phenotypes of IBD, revealing the impacts of microbiota on IBD, and emphasizing the important role of overweight/obesity in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39574001", + "title": "Changes in amino acid concentrations and the gut microbiota composition are implicated in the mucosal healing of ulcerative colitis and can be used as noninvasive diagnostic biomarkers.", + "year": 2024, + "journal": "Clinical proteomics", + "authors": [ + "Wu J", + "Li M", + "Zhou C", + "Rong J", + "Zhang F", + "Wen Y", + "Qu J", + "Wu R", + "Miao Y", + "Niu J" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.6679002620268726, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Mucosal healing is the therapeutic target for ulcerative colitis (UC). While amino acids (AAs) and the gut microbiota are known to be involved in the pathogenesis of UC, their specific roles in mucosal healing have not been fully defined. OBJECTIVES: To longitudinally assess the changes in AA concentrations and the gut microbiota composition in the context of mucosal healing in UC patients, with the aim of identifying new biomarkers with predictive value for mucosal healing in UC patients and providing a new theoretical basis for dietary therapy. METHODS: A total of 15 UC patients with infliximab-induced mucosal healing were enrolled. Serum and fecal AA concentrations before and after mucosal healing were determined via targeted metabolomics. A receiver operating characteristic (ROC) curve was plotted to evaluate the value of different AAs in predicting mucosal healing in UC patients. The changes in the composition of the fecal gut microbiota were analyzed via metagenomics, and bioinformatics was used to analyze the functional genes and metabolic pathways associated with different bacterial species. Spearman correlation analyses of fecal AAs with significantly different concentrations and the differentially abundant bacterial species before and after mucosal healing were performed. RESULTS: 1. The fecal concentrations of alanine, aspartic acid, glutamic acid, glutamine, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine were significantly decreased after mucosal healing. The serum concentrations of alanine, cysteine and valine significantly increased, whereas that of aspartic acid significantly decreased. Glutamic acid, leucine, lysine, methionine and threonine could accurately predict mucosal healing in UC patients, and the area under the curve (AUC) was >\u20090.9. After combining the 5 amino acids, the AUC reached 0.96. 2. There were significant differences in the gut microbiota composition before and after mucosal healing in UC, characterized by an increase in the abundance of beneficial microbiota (Faecalibacterium prausnitzii and Bacteroides fragilis) and a decrease in the abundance of harmful microbiota (Enterococcus faecalis). LEfSe analysis identified 57 species that could predict mucosal healing, and the AUC was 0.7846. 3. Amino acid metabolic pathways were enriched in samples after mucosal healing, was associated with the abundance of multiple species, such as Faecalibacterium prausnitzi, Bacteroides fragilis, Bacteroides vulgatus and Alistipes putredinis. 4. The fecal concentrations of several AAs were negatively correlated with the abundance of a variety of beneficial strains, such as Bacteroides fragilis, uncultured Clostridium sp., Firmicutes bacterium CAG:103, Adlercreutzia equolifaciens, Coprococcus comes and positively correlated with the abundance of several harmful strains, such as Citrobacter freundii, Enterococcus faecalis, Klebsiella aerogenes, Salmonella enterica. CONCLUSION: Altered concentrations of amino acids and their associations with the gut microbiota are implicated in the mucosal healing of UC patients and can serve as noninvasive diagnostic biomarkers.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37951857", + "title": "Diagnosis of Crohn's disease and ulcerative colitis using the microbiome.", + "year": 2023, + "journal": "BMC microbiology", + "authors": [ + "Kang DY", + "Park JL", + "Yeo MK", + "Kang SB", + "Kim JM", + "Kim JS", + "Kim SY" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.6658978930739262, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Crohn Disease", + "Inflammatory Bowel Diseases", + "Gastrointestinal Microbiome", + "Bacteria", + "Biomarkers" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is a multifactorial chronic inflammatory disease resulting from dysregulation of the mucosal immune response and gut microbiota. Crohn's disease (CD) and ulcerative colitis (UC) are difficult to distinguish, and differential diagnosis is essential for establishing a long-term treatment plan for patients. Furthermore, the abundance of mucosal bacteria is associated with the severity of the disease. This study aimed to differentiate and diagnose these two diseases using the microbiome and identify specific biomarkers associated with disease activity. RESULTS: Differences in the abundance and composition of the microbiome between IBD patients and healthy controls (HC) were observed. Compared to HC, the diversity of the gut microbiome in patients with IBD decreased; the diversity of the gut microbiome in patients with CD was significantly lower. Sixty-eight microbiota members (28 for CD and 40 for UC) associated with these diseases were identified. Additionally, as the disease progressed through different stages, the diversity of the bacteria decreased. The abundances of Alistipes shahii and Pseudodesulfovibrio aespoeensis were negatively correlated with the severity of CD, whereas the abundance of Polynucleobacter wianus was positively correlated. The severity of UC was negatively correlated with the abundance of A. shahii, Porphyromonas asaccharolytica and Akkermansia muciniphilla, while it was positively correlated with the abundance of Pantoea candidatus pantoea carbekii. A regularized logistic regression model was used for the differential diagnosis of the two diseases. The area under the curve (AUC) was used to examine the performance of the model. The model discriminated UC and CD at an AUC of 0.873 (train set), 0.778 (test set), and 0.633 (validation set) and an area under the precision-recall curve (PRAUC) of 0.888 (train set), 0.806 (test set), and 0.474 (validation set). CONCLUSIONS: Based on fecal whole-metagenome shotgun (WMS) sequencing, CD and UC were diagnosed using a machine-learning predictive model. Microbiome biomarkers associated with disease activity (UC and CD) are also proposed.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38347087", + "title": "Microbial butyrate capacity is reduced in inflamed mucosa in patients with ulcerative colitis.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Jangi S", + "Moyer J", + "Sandlow S", + "Fu M", + "Chen H", + "Shum A", + "Hsia K", + "Cersosimo L", + "Yeliseyev V", + "Zhao N", + "Bry L", + "Michaud DS" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.6416246832663991, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Butyrates", + "Colon", + "Biopsy", + "Intestinal Mucosa", + "Bacteria" + ], + "raw_abstract": "Reduced butyrate-production capacity has been reported in fecal microbial communities in patients with active ulcerative colitis. However, the butyrate-production capacity of the mucosal microbiome from active vs quiescent mucosa in ulcerative colitis has been unexplored. We sought to determine the diversity and relative abundance of mucosal bacterial and fungal communities from endoscopically active vs quiescent mucosa in patients with UC, and aimed to predict contributions of mucosal microbial communities to butyrate synthesis. Systematic, segmental right- and left-sided biopsies were obtained from endoscopically active (n\u2009=\u200913) or quiescent (n\u2009=\u200917) colonic mucosa, among 15 patients with pan-colonic ulcerative colitis. Dietary fiber intake of patients was performed using the validated five-item FiberScreen questionnaire. Amplicon sequencing of mucosal bacteria and fungi was performed. The diversity and relative abundance of mucosal bacterial and fungal taxa were quantified, and predicted contributions to butyrate synthesis were ascertained. Bacterial alpha and beta diversity were similar between active vs quiescent mucosa. Butyrogenic taxa were significantly increased in quiescence, including Butyricimonas, Subdoligranulum, and Alistipes. Predicted butyrate kinase activity was significantly and concomitantly increased in quiescent mucosa. Fiber intake was positively correlated with butyrogenic microbes. Compared to mucosal bacterial prevalence, mucosal fungi were detected in low prevalence. Butyrogenic microbes are relatively increased in quiescent mucosa in ulcerative colitis, and may be related to increased fiber intake during quiescence. Manipulation of the mucosal microbiome towards butyrate-producing bacteria may be associated with endoscopic quiescence.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29126267", + "title": "Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis.", + "year": 2017, + "journal": "FEMS microbiology ecology", + "authors": [ + "Mancabelli L", + "Milani C", + "Lugli GA", + "Turroni F", + "Cocconi D", + "van Sinderen D", + "Ventura M" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.6374957297651715, + "mesh_terms": [ + "Bacteria", + "Biodiversity", + "Biomarkers", + "Colitis, Ulcerative", + "Crohn Disease", + "Enterocolitis, Pseudomembranous", + "Gastrointestinal Microbiome", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Intestines", + "Polymerase Chain Reaction", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Intestinal diseases, such as Crohn's disease (CD), ulcerative colitis (UC) and pseudomembranous colitis (CDI), are among the most common diseases in humans and may lead to more serious pathologies, e.g. colorectal cancer (CRC). Next generation sequencing has in recent years allowed the identification of correlations between intestinal bacteria and diseases, although the formulation of universal gut microbial biomarkers for such diseases is only in its infancy. In the current study, we selected and reanalyzed a total of 3048 public datasets obtained from 16S rRNA profiling of individuals affected by CD, UC, CDI and CRC. This meta-analysis revealed possible biases in the reconstruction of the gut microbiota composition due to the use of different primer pairs employed for PCR of 16S rRNA gene fragments. Notably, this approach also identified common features of individuals affected by gut diseases (DS), including lower biodiversity compared to control subjects. Moreover, potential universal intestinal disease microbial biomarkers were identified through cross-disease comparisons. In detail, CTRL showed high abundance of the genera Barnesiella, Ruminococcaceae UCG-005, Alistipes, Christensenellaceae R-7 group and unclassified member of Lachnospiraceae family, while DS exhibited high abundance of Lactobacillus, unclassified member of Erysipelotrichaceae family and Streptococcus genera.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39126385", + "title": "Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis.", + "year": 2025, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Jangi S", + "Zhao N", + "Hsia K", + "Park YS", + "Michaud DS", + "Yoon H" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.5805885116520583, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Male", + "Adult", + "Female", + "Prospective Studies", + "Middle Aged", + "Clostridiales", + "Candida", + "Republic of Korea", + "Feces" + ], + "raw_abstract": "BACKGROUND AND AIMS: While there is increasing interest in microbiome-directed therapies for patients with ulcerative colitis (UC), the identification of microbial targets remains elusive, underlining the need for novel approaches. METHODS: Utilizing metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation, we used a tree-based dichotomous approach to assemble distinct clusters of species-level bacterial co-abundance groups (CAGs). We evaluated the abundance of bacterial CAGs and fungal taxa during remission (n\u2005=\u2005166) and activity (n\u2005=\u200546). We examined if the bacterial CAGs identified in our cohorts were conserved in 2 healthy cohorts and a Korean UC cohort. RESULTS: CAG3 and CAG8, dominated by bacteria from the family Lachnospiraceae, were associated with remission. Low abundance of CAG8 and elevated abundance of Candida genus were predictive of active UC. Constituents from CAG8 were influential hub species of the remission-associated microbial UC network, including Ruminococcus gnavus, Erysipelatoclostridium ramosum, Blautia, and Dorea species. These hub species interactions were preserved in 2 healthy cohorts and were partially recapitulated in a Korean UC cohort. CAG8 abundance correlated with the secondary bile acid production pathway. Bacterial CAGs did not correlate with Candida; however, Bifidobacterium adolescentis and Alistipes putredinis were negatively associated with Candida. CONCLUSIONS: Lachnospiraceae-dominated bacterial CAGs were associated with remission in UC, with key bacterial interactions within the CAG also observed in 2 healthy cohorts and a Korean UC cohort. Bacterial CAG-based analyses may aid in designing candidate consortia for microbiome-based therapeutics.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38733623", + "title": "Anti-inflammatory Effects of Bacteroidota Strains Derived From Outstanding Donors of Fecal Microbiota Transplantation for the Treatment of Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Ishikawa D", + "Zhang X", + "Nomura K", + "Shibuya T", + "Hojo M", + "Yamashita M", + "Koizumi S", + "Yamazaki F", + "Iwamoto S", + "Saito M", + "Kunigo K", + "Nakano R", + "Honma N", + "Urakawa I", + "Nagahara A" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.5482200599936418, + "mesh_terms": [ + "Fecal Microbiota Transplantation", + "Colitis, Ulcerative", + "Animals", + "Mice", + "Humans", + "Feces", + "Interleukin-10", + "Disease Models, Animal", + "Male", + "Bacteroidetes", + "Female", + "Gastrointestinal Microbiome", + "Mice, Inbred C57BL", + "RNA, Ribosomal, 16S", + "Dextran Sulfate", + "Anti-Inflammatory Agents" + ], + "raw_abstract": "BACKGROUND: The proportion of certain Bacteroidota species decreased in patients with ulcerative colitis, and the recovery of Bacteroidota is associated with the efficacy of fecal microbiota transplantation therapy. We hypothesized that certain Bacteroidota may advance ulcerative colitis treatment. Accordingly, we aimed to evaluate the anti-inflammatory effects of Bacteroidota strains isolated from donors. METHODS: Donors with proven efficacy of fecal microbiota transplantation for ulcerative colitis were selected, and Bacteroidota strains were isolated from their stools. The immune function of Bacteroidota isolates was evaluated through in vitro and in vivo studies. RESULTS: Twenty-four Bacteroidota strains were isolated and identified. Using an in vitro interleukin (IL)-10 induction assay, we identified 4 Bacteroidota strains with remarkable IL-10-induction activity. Of these, an Alistipes putredinis strain exhibited anti-inflammatory effects in a mouse model of colitis induced by sodium dextran sulfate and oxazolone. However, 16S rRNA gene-based sequencing analysis of A. putredinis cultures in the in vivo study revealed unexpected Veillonella strain contamination. A second in vitro study confirmed that the coculture exhibited an even more potent IL-10-inducing activity. Furthermore, the production of A. putredinis-induced IL-10 was likely mediated via toll-like receptor 2 signaling. CONCLUSIONS: This study demonstrated that A. putredinis, a representative Bacteroidota species, exhibits anti-inflammatory effects in vivo and in vitro; however, the effects of other Bacteroidota species remain unexplored. Our fecal microbiota transplantation-based reverse translation approach using promising bacterial species may represent a breakthrough in microbiome drug development for controlling dysbiosis during ulcerative colitis. We isolated Bacteroidota species from the feces of donors who were effectively cured of UC with fecal microbiota transplantation and proved the anti-inflammatory effects of Bacteroidota species, especially Alistipes putredinis, through cell experiments and in vivo experiments.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37095601", + "title": "A Mediterranean Diet Pattern Improves Intestinal Inflammation Concomitant with Reshaping of the Bacteriome in Ulcerative Colitis: A Randomised Controlled Trial.", + "year": 2023, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Haskey N", + "Estaki M", + "Ye J", + "Shim RK", + "Singh S", + "Dieleman LA", + "Jacobson K", + "Gibson DL" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.5345849190962763, + "mesh_terms": [ + "Adult", + "Humans", + "Female", + "Middle Aged", + "Male", + "Colitis, Ulcerative", + "Diet, Mediterranean", + "Prospective Studies", + "RNA, Ribosomal, 16S", + "Canada", + "Inflammation", + "Feces", + "Butyric Acid", + "Leukocyte L1 Antigen Complex" + ], + "raw_abstract": "BACKGROUND AND AIMS: Dietary patterns are important in managing ulcerative colitis [UC], given their influence on gut microbiome-host symbiosis and inflammation. We investigated whether the Mediterranean Diet Pattern [MDP] vs the Canadian Habitual Diet Pattern [CHD] would affect disease activity, inflammation, and the gut microbiome in patients with quiescent UC. METHODS: We performed a prospective, randomised, controlled trial in adults [65% female; median age 47 years] with quiescent UC in an outpatient setting from 2017 to 2021. Participants were randomised to an MDP [n\u2005=\u200515] or CHD [n\u2005=\u200513] for 12 weeks. Disease activity [Simple Clinical Colitis Activity Index] and faecal calprotectin [FC] were measured at baseline and week 12. Stool samples were analysed by 16S rRNA gene amplicon sequencing. RESULTS: The diet was well tolerated by the MDP group. At week 12, 75% [9/12] of participants in the CHD had an FC\u2005>100 \u03bcg/g, vs 20% [3/15] of participants in the MDP group. The MDP group had higher levels of total faecal short chain fatty acids [SCFAs] [p\u2005=\u20050.01], acetic acid [p\u2005=\u20050.03], and butyric acid [p\u2005=\u20050.03] compared with the CHD. Furthermore, the MDP induced alterations in microbial species associated with a protective role in colitis [Alistipes finegoldii and Flavonifractor plautii], as well as the production of SCFAs [Ruminococcus bromii]. CONCLUSIONS: An MDP induces gut microbiome alterations associated with the maintenance of clinical remission and reduced FC in patients with quiescent UC. The data support that the MDP is a sustainable diet pattern that could be recommended as a maintenance diet and adjunctive therapy for UC patients in clinical remission. ClinicalTrials.gov no: NCT0305371.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35151255", + "title": "Gut microbiome alterations in colitis rats after moxibustion at bilateral Tianshu acupoints.", + "year": 2022, + "journal": "BMC gastroenterology", + "authors": [ + "Qi Q", + "Liu YN", + "Lv SY", + "Wu HG", + "Zhang LS", + "Cao Z", + "Liu HR", + "Wang XM", + "Wu LY" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.4767693447749241, + "mesh_terms": [ + "Acupuncture Points", + "Animals", + "Colitis", + "Colitis, Ulcerative", + "Dextran Sulfate", + "Disease Models, Animal", + "Gastrointestinal Microbiome", + "Male", + "Moxibustion", + "Rats" + ], + "raw_abstract": "BACKGROUND: The pathogenesis of ulcerative colitis (UC) is closely related to the gut microbiota. Moxibustion has been used to improve the inflammation and gastrointestinal dysfunctions in gastrointestinal\u00a0disorders such as UC. In this study, we investigated whether moxibustion could improve the gut microbial dysbiosis induced by dextran sulphate sodium. METHODS: Twenty-five male rats were randomly assigned into five groups. The UC rat model was established by administering DSS solution. The rats in the moxibustion and normal rats with moxibustion groups were treated with moxibustion at Tianshu (bilateral, ST25) points, and the mesalazine group rats were treated with mesalazine once daily for 7 consecutive days. Disease activity index (DAI) and haematoxylin and eosin staining were used to evaluate the effect of moxibustion. Gut microbiota profiling was conducted by metagenomic high throughput sequencing technology. The gut microbiota composition, diversity and function were analyzed and compared using metagenomics methodologies. RESULTS: The DAI scores and histopathology scores in the moxibustion and mesalazine groups were significantly decreased compared with the UC group (P\u2009<\u20090.01). Moxibustion treatment increased abundance levels of Bacteroidetes, Actinobacteria, Ascomycota, Synergistetes and decreased abundance of Firmicutes, Proteobacteria. At the genus level, the abundance of Bacteroides, Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2, were increased and Bacteroides_bacterium_H3, Parabacteroides, Porphyromonas, Alistipes, Parasutterella were decreased in the UC group in comparsion with those in the NG group. Moxibustion increased the abundance of Bacteroides and Bacteroides_bacterium_H3 and decreased Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2. In UC group, the specie Bacteroides_massiliensis was negatively (P\u2009<\u20090.05) correlated with IL-23, Bacteroides_eggerthii_CAG109 and Bacteroides_eggerthii were negatively (P\u2009<\u20090.05) correlated with TGF-\u03b2. And the species Prevotella_sp_CAG1031 and Bacteroides_bacterium_H2 were significant positively (P\u2009<\u20090.05) correlated with IL-23. In addition, compare with the normal group, genes involved in certain metabolic pathways, such as energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, were under-represented in the UC group, and these changes in the metabolic pathways could be reversed by moxibustion treatment and mesalazine treatment. CONCLUSIONS: Our findings suggest that moxibustion treatment may protect the host from mucosal inflammation by modulating the intestinal microbiota community.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29311644", + "title": "Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.", + "year": 2018, + "journal": "Nature microbiology", + "authors": [ + "Schirmer M", + "Franzosa EA", + "Lloyd-Price J", + "McIver LJ", + "Schwager R", + "Poon TW", + "Ananthakrishnan AN", + "Andrews E", + "Barron G", + "Lake K", + "Prasad M", + "Sauk J", + "Stevens B", + "Wilson RG", + "Braun J", + "Denson LA", + "Kugathasan S", + "McGovern DPB", + "Vlamakis H", + "Xavier RJ", + "Huttenhower C" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.45259503835603765, + "mesh_terms": [ + "Adolescent", + "Adult", + "Child", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gene Expression Profiling", + "Humans", + "Inflammatory Bowel Diseases", + "Longitudinal Studies", + "Male", + "Metagenomics", + "Phenotype", + "Transcription, Genetic", + "Young Adult" + ], + "raw_abstract": "Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period. Here, we present the first results based on 78 paired faecal metagenomes\u00a0and\u00a0metatranscriptomes, and 222 additional metagenomes from 59 patients with Crohn's disease, 34 with ulcerative colitis and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, although many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microorganisms per host (for example, by Faecalibacterium prausnitzii). Thus, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Furthermore, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (for example, Dialister invisus). Last, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways that were predominantly expressed by different organisms in patients with IBD (for example, Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypical changes that are complementary to those linked to metagenomic abundances. The study's results highlight the strength of analysing both the activity and the presence of gut microorganisms to provide insight into the role of the microbiome in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32048723", + "title": "Aging Increases the Severity of Colitis and the Related Changes to the Gut Barrier and Gut Microbiota in Humans and Mice.", + "year": 2020, + "journal": "The journals of gerontology. Series A, Biological sciences and medical sciences", + "authors": [ + "Liu A", + "Lv H", + "Wang H", + "Yang H", + "Li Y", + "Qian J" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.42065181675976, + "mesh_terms": [ + "Adult", + "Age Factors", + "Aged", + "Aging", + "Animals", + "Cadherins", + "Case-Control Studies", + "Colitis, Ulcerative", + "Disease Models, Animal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Middle Aged", + "Occludin", + "Severity of Illness Index" + ], + "raw_abstract": "This study aims to compare intestinal mucosal barrier function in older and young ulcerative colitis (UC) patients and the healthy population, and to explore the possible mechanisms through which aging increases the severity of colitis in mice. The old healthy group showed discontinued tight junction (TJ) strand. The E-cadherin and occludin protein expressions in the colonic tissue of the old healthy subjects were lower than those in the younger healthy people. The protein expressions of E-cadherin and occludin were lower in the old UC patients than in the younger UC patients. In mice, disease activity indexes induced by inflammatory stimulus differed as a function of age. Weight loss level, histological scores, and expression of proinflammatory factors were higher in the dextran sulfate sodium (DSS)-induced group of aged mice than in the young DSS-induced mice. Compared with the results observed in the young DSS-induced mice, the protein expressions of E-cadherin and occludin in the aged DSS-induced mice were lower. Furthermore, significant differences were observed in the composition of the gut microbiota between the young and aged mice. In the aged mice, the fraction of beneficial bacteria (Lactobacillus) was lower before the DSS treatment, while the fraction of the harmful bacteria (Turicibacter, Parasutterella) was higher than that observed in the young mice. After the DSS treatment in the aged mice, the fraction of beneficial bacteria (Odoribacter and Alistipes) was lower, while the fraction of harmful bacteria (Turicibacter) was higher than in the young mice. We demonstrate that the aging of the human colon is characterized by an impairment of the intestinal barrier. Aging leads to more severe disease following DSS challenge. Age-related deterioration of gastrointestinal barrier function and gut microbial dysbiosis may be involved in the pathogenesis of colitis in the aged mice.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36327509", + "title": "In vitro fermentation characteristics of the dietary fiber in bamboo (Phyllostachys edulis) shoots and its regulatory effects on the intestinal microbiota and metabolites.", + "year": 2023, + "journal": "Food chemistry", + "authors": [ + "Wu W", + "Li Q", + "Chen H", + "Fang X", + "Niu B", + "Liu R", + "Mu H", + "Gao H" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.33098025404675113, + "mesh_terms": [ + "Animals", + "Mice", + "Gastrointestinal Microbiome", + "Dextran Sulfate", + "Fermentation", + "Dietary Fiber", + "Colitis, Ulcerative", + "Colon", + "Poaceae", + "Disease Models, Animal", + "Colitis", + "Mice, Inbred C57BL" + ], + "raw_abstract": "The effects of bamboo (Phyllostachys edulis) shoot dietary fiber (BSDF-1) on ulcerative colitis (UC) are unclear. Therefore, we performed an in vitro glycolysis study of intestinal microbiota samples, based on 16S rDNA sequencing and determining the metabolites in non-targeted colonic fecal fermentation broth. After a 48\u00a0h fermentation, the pH of the fermentation broth decreased significantly (p\u00a0<\u00a00.05) with the dextran sulfate sodium group (referred to here as the Mod group). The carbohydrate utilization rate was 26.59\u00a0%, and the total short-chain fatty acid content was 16.46\u00a0\u00b1\u00a00.71\u00a0mmol/L. The abundances of Alistipes and Lactobacillus increased after BDSF-1 fermentation, whereas those of Escherichia-Shigella, Enterococcus, and Proteus significantly decreased. BSDF-1 altered the levels of 17 metabolites in the Mod group after fermentation for 48\u00a0h, which reduced the cadaverine increasing induced by DSS. These results indicate that BSDF-1 can regulate the metabolism of the intestinal microbiota and the host, suggesting its use as a promising therapeutic strategy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37208257", + "title": "Gut microbial signatures and their functions in Behcet's uveitis and Vogt-Koyanagi-Harada disease.", + "year": 2023, + "journal": "Journal of autoimmunity", + "authors": [ + "Wang Q", + "Wu S", + "Ye X", + "Tan S", + "Huang F", + "Su G", + "Kijlstra A", + "Yang P" + ], + "bacteria": "Alistipes", + "condition": "ulcerative colitis", + "relevance_score": 0.22893069359058985, + "mesh_terms": [ + "Humans", + "Uveomeningoencephalitic Syndrome", + "Leukocytes, Mononuclear", + "Gastrointestinal Microbiome", + "Uveitis", + "Behcet Syndrome" + ], + "raw_abstract": "BACKGROUND: A number of public metagenomic studies reveal an association between the gut microbiome and various immune-mediated diseases including Behcet's uveitis (BU) and Vogt-Koyanagi-Harada disease (VKH). Integrated-analysis and subsequent validation of these results could be a potentially powerful way to understand the microbial signatures and their functions in these two uveitis entities. METHODS: We integrated the sequencing data of our previous metagenomic studies on two major uveitis entities, BU and VKH as well as four other publicly available immune-mediated diseases datasets, including Ankylosing Spondylitis (AS), Rheumatoid Arthritis (RA), Crohn's disease (CD) and Ulcerative Colitis (UC). Alpha-diversity and beta-diversity analysis were used to compare the gut microbiome signatures between both uveitis entities and other immune-mediated diseases and healthy controls. Amino acid homology between microbial proteins and a uveitogenic peptide of the interphotoreceptor retinoid-binding protein (IRBP) RESULTS: Depleted Dorea, Blautia, Coprococcus, Erysipelotrichaceae and Lachnospiraceae as well as enriched Bilophila and Stenotrophomonas were identified in BU patients. An enriched Alistipes along with a lower level of Dorea were observed in VKH patients. A peptide antigen (SteTDR) encoded by BU specifically enriched Stenotrophomonas was identified to share homology with IRBP CONCLUSIONS: Our study revealed specific gut microbial signatures and their potentially functional roles in BU and VKH pathogenesis that differ significantly from other immune-mediated diseases as well as healthy controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39574001", + "title": "Changes in amino acid concentrations and the gut microbiota composition are implicated in the mucosal healing of ulcerative colitis and can be used as noninvasive diagnostic biomarkers.", + "year": 2024, + "journal": "Clinical proteomics", + "authors": [ + "Wu J", + "Li M", + "Zhou C", + "Rong J", + "Zhang F", + "Wen Y", + "Qu J", + "Wu R", + "Miao Y", + "Niu J" + ], + "bacteria": "Adlercreutzia", + "condition": "ulcerative colitis", + "relevance_score": 0.6679002620268726, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Mucosal healing is the therapeutic target for ulcerative colitis (UC). While amino acids (AAs) and the gut microbiota are known to be involved in the pathogenesis of UC, their specific roles in mucosal healing have not been fully defined. OBJECTIVES: To longitudinally assess the changes in AA concentrations and the gut microbiota composition in the context of mucosal healing in UC patients, with the aim of identifying new biomarkers with predictive value for mucosal healing in UC patients and providing a new theoretical basis for dietary therapy. METHODS: A total of 15 UC patients with infliximab-induced mucosal healing were enrolled. Serum and fecal AA concentrations before and after mucosal healing were determined via targeted metabolomics. A receiver operating characteristic (ROC) curve was plotted to evaluate the value of different AAs in predicting mucosal healing in UC patients. The changes in the composition of the fecal gut microbiota were analyzed via metagenomics, and bioinformatics was used to analyze the functional genes and metabolic pathways associated with different bacterial species. Spearman correlation analyses of fecal AAs with significantly different concentrations and the differentially abundant bacterial species before and after mucosal healing were performed. RESULTS: 1. The fecal concentrations of alanine, aspartic acid, glutamic acid, glutamine, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine were significantly decreased after mucosal healing. The serum concentrations of alanine, cysteine and valine significantly increased, whereas that of aspartic acid significantly decreased. Glutamic acid, leucine, lysine, methionine and threonine could accurately predict mucosal healing in UC patients, and the area under the curve (AUC) was >\u20090.9. After combining the 5 amino acids, the AUC reached 0.96. 2. There were significant differences in the gut microbiota composition before and after mucosal healing in UC, characterized by an increase in the abundance of beneficial microbiota (Faecalibacterium prausnitzii and Bacteroides fragilis) and a decrease in the abundance of harmful microbiota (Enterococcus faecalis). LEfSe analysis identified 57 species that could predict mucosal healing, and the AUC was 0.7846. 3. Amino acid metabolic pathways were enriched in samples after mucosal healing, was associated with the abundance of multiple species, such as Faecalibacterium prausnitzi, Bacteroides fragilis, Bacteroides vulgatus and Alistipes putredinis. 4. The fecal concentrations of several AAs were negatively correlated with the abundance of a variety of beneficial strains, such as Bacteroides fragilis, uncultured Clostridium sp., Firmicutes bacterium CAG:103, Adlercreutzia equolifaciens, Coprococcus comes and positively correlated with the abundance of several harmful strains, such as Citrobacter freundii, Enterococcus faecalis, Klebsiella aerogenes, Salmonella enterica. CONCLUSION: Altered concentrations of amino acids and their associations with the gut microbiota are implicated in the mucosal healing of UC patients and can serve as noninvasive diagnostic biomarkers.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39162211", + "title": "Washed microbiota transplantation improved the level of serum vitamin D in ulcerative colitis.", + "year": 2024, + "journal": "Journal of gastroenterology and hepatology", + "authors": [ + "Zhang H", + "Xiao Y", + "Wen Q", + "Zhang S", + "Li P", + "Marcella C", + "Hu B", + "Liu H", + "Zhang F", + "Cui B" + ], + "bacteria": "Adlercreutzia", + "condition": "ulcerative colitis", + "relevance_score": 0.6665413533883564, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Male", + "Vitamin D", + "Female", + "Adult", + "Fecal Microbiota Transplantation", + "Middle Aged", + "Receptors, Calcitriol", + "Gastrointestinal Microbiome", + "Vitamin D Deficiency", + "Treatment Outcome", + "Mesalamine" + ], + "raw_abstract": "BACKGROUND AND AIM: Vitamin D (VD) deficiency was reported to correlate with ulcerative colitis (UC) activity, which might be closely related to gut microbiota dysbiosis. This study aims to investigate the effects of washed microbiota transplantation (WMT) on VD metabolism in UC. METHODS: The serum levels of 25-hdroxyvitamin D [25(OH)D] in 121 patients with UC and 53 healthy controls (HC) were detected. Subsequently, a non-randomized control trial (non-RCT) was conducted. Patients with UC were non-randomly assigned to undergo WMT (n\u00a0=\u00a028) vs. conventional treatment (5-aminosalicylic acid, 5-ASA, n\u00a0=\u00a010). Serum levels of 25(OH)D, fecal microbiota, and the expression of vitamin D receptor (VDR) in patients with UC were evaluated with a 3-month follow-up. RESULTS: Serum VD levels collected in the clinic practice indicated that patients with UC had significantly lower VD levels than HC (P\u00a0<\u00a00.001). In the non-RCT, serum 25(OH)D level and VDR expression significantly increased (P\u00a0=\u00a00.011, 0.026, respectively) in the WMT group, while no noticeable changes were observed in the non-WMT group. Microbiome profiling revealed that the increase in VD levels after WMT was positively associated with the abundances of Adlercreutzia_equolifaciens, Ruminococcus_obeum, and Dorea but negatively correlated with Escherichia. CONCLUSIONS: The study suggested that WMT increases the levels of VD with characteristic changes of specific microbiota, which indicated the association between the VD and the activity of UC might be regulated by gut microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27412252", + "title": "Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.", + "year": 2016, + "journal": "Genome medicine", + "authors": [ + "Shaw KA", + "Bertha M", + "Hofmekler T", + "Chopra P", + "Vatanen T", + "Srivatsa A", + "Prince J", + "Kumar A", + "Sauer C", + "Zwick ME", + "Satten GA", + "Kostic AD", + "Mulle JG", + "Xavier RJ", + "Kugathasan S" + ], + "bacteria": "Adlercreutzia", + "condition": "ulcerative colitis", + "relevance_score": 0.3912722894782307, + "mesh_terms": [ + "Adolescent", + "Bacteria", + "Biomarkers", + "Case-Control Studies", + "Child", + "Child, Preschool", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Immunologic Factors", + "Inflammation", + "Intestinal Mucosa", + "Leukocyte L1 Antigen Complex", + "Longitudinal Studies", + "Male", + "Severity of Illness Index", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Gut microbiome dysbiosis has been demonstrated in subjects with newly diagnosed and chronic inflammatory bowel disease (IBD). In this study we sought to explore longitudinal changes in dysbiosis and ascertain associations between dysbiosis and markers of disease activity and treatment outcome. METHODS: We performed a prospective cohort study of 19 treatment-na\u00efve pediatric IBD subjects and 10 healthy controls, measuring fecal calprotectin and assessing the gut microbiome via repeated stool samples. Associations between clinical characteristics and the microbiome were tested using generalized estimating equations. Random forest classification was used to predict ultimate treatment response (presence of mucosal healing at follow-up colonoscopy) or non-response using patients' pretreatment samples. RESULTS: Patients with Crohn's disease had increased markers of inflammation and dysbiosis compared to controls. Patients with ulcerative colitis had even higher inflammation and dysbiosis compared to those with Crohn's disease. For all cases, the gut microbial dysbiosis index associated significantly with clinical and biological measures of disease severity, but did not associate with treatment response. We found differences in specific gut microbiome genera between cases/controls and responders/non-responders including Akkermansia, Coprococcus, Fusobacterium, Veillonella, Faecalibacterium, and Adlercreutzia. Using pretreatment microbiome data in a weighted random forest classifier, we were able to obtain 76.5\u00a0% accuracy for prediction of responder status. CONCLUSIONS: Patient dysbiosis improved over time but persisted even among those who responded to treatment and achieved mucosal healing. Although dysbiosis index was not significantly different between responders and non-responders, we found specific genus-level differences. We found that pretreatment microbiome signatures are a promising avenue for prediction of remission and response to treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27484096", + "title": "Reduced Mucosa-associated Butyricicoccus Activity in Patients with Ulcerative Colitis Correlates with Aberrant Claudin-1 Expression.", + "year": 2017, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Devriese S", + "Eeckhaut V", + "Geirnaert A", + "Van den Bossche L", + "Hindryckx P", + "Van de Wiele T", + "Van Immerseel F", + "Ducatelle R", + "De Vos M", + "Laukens D" + ], + "bacteria": "Butyricicoccus", + "condition": "ulcerative colitis", + "relevance_score": 0.7521702802346611, + "mesh_terms": [ + "Adult", + "Biopsy", + "Butyrates", + "Caco-2 Cells", + "Claudin-1", + "Colitis, Ulcerative", + "Eubacterium", + "Feces", + "Female", + "Host-Pathogen Interactions", + "Humans", + "Intestinal Mucosa", + "Male", + "Occludin", + "Patient Acuity", + "RNA, Ribosomal, 16S", + "Statistics as Topic", + "Tight Junctions", + "Tumor Necrosis Factor-alpha", + "Zonula Occludens-1 Protein" + ], + "raw_abstract": "BACKGROUND AND AIMS: Butyricicoccus is a butyrate-producing clostridial cluster IV genus whose numbers are reduced in the stool of ulcerative colitis [UC] patients. Conditioned medium of Butyricicoccus [B.] pullicaecorum prevents tumour necrosis factor alpha [TNF\u03b1]-induced increase in epithelial permeability in vitro. Since butyrate influences intestinal barrier integrity, we further investigated the relationship between the abundance of mucosa-associated Butyricicoccus and the expression of butyrate-regulated tight junction [TJ] genes. METHODS: Tight junction protein 1 [TJP1], occludin [OCLN], claudin-1 [CLDN1], and Butyricicoccus 16S rRNA expression was analysed in a collection of colonic biopsies of healthy controls and UC patients with active disease. The effect of butyrate and B. pullicaecorum conditioned medium on TJ gene expression was investigated in TNF\u03b1-stimulated Caco-2 monolayers and inflamed mucosal biopsies of UC patients. RESULTS: TJP1 expression was significantly decreased in inflamed UC mucosa, whereas CLDN1 mRNA levels were increased. OCLN did not differ significantly between the groups. Mucosa-associated Butyricicoccus 16S rRNA transcripts were reduced in active UC patients compared with healthy controls. Interestingly, Butyricicoccus activity negatively correlated with CLDN1 expression. Butyrate reversed the inflammation-induced increase of CLDN1 protein levels, and stimulation of inflamed UC biopsies with B. pullicaecorum conditioned medium normalized CLDN1 mRNA levels. CONCLUSIONS: Butyricicoccus is a mucosa-associated bacterial genus under-represented in colonic mucosa of patients with active UC, whose activity inversely correlates with CLDN1 expression. Butyrate and B. pullicaecorum conditioned medium reduce CLDN1 expression, supporting its use as a pharmabiotic preserving epithelial TJ integrity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32476236", + "title": "Microbiota changes induced by microencapsulated sodium butyrate in patients with inflammatory bowel disease.", + "year": 2020, + "journal": "Neurogastroenterology and motility", + "authors": [ + "Facchin S", + "Vitulo N", + "Calgaro M", + "Buda A", + "Romualdi C", + "Pohl D", + "Perini B", + "Lorenzon G", + "Marinelli C", + "D'Inc\u00e0 R", + "Sturniolo GC", + "Savarino EV" + ], + "bacteria": "Butyricicoccus", + "condition": "ulcerative colitis", + "relevance_score": 0.46562343738325535, + "mesh_terms": [ + "Administration, Oral", + "Adult", + "Aged", + "Butyric Acid", + "Capsules", + "Double-Blind Method", + "Female", + "Gastrointestinal Microbiome", + "Histamine Antagonists", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "Pilot Projects", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Butyrate has shown anti-inflammatory and regenerative properties, providing symptomatic relief when orally supplemented in patients suffering from various colonic diseases. We investigated the effect of a colonic-delivery formulation of butyrate on the fecal microbiota of patients with inflammatory bowel diseases (IBDs). METHODS: In this double-blind, placebo-controlled, pilot study, 49 IBD patients (n\u00a0=\u00a019 Crohn's disease, CD and n\u00a0=\u00a030 ulcerative colitis, UC) were randomized to oral administration of microencapsulated-sodium-butyrate (BLM) or placebo for 2\u00a0months, in addition to conventional therapy. Eighteen healthy volunteers (HVs) were recruited to provide a healthy microbiota model of the local people. Fecal microbiota from stool samples was assessed by 16S sequencing. Clinical disease activity and quality of life (QoL) were evaluated before and after treatment. KEY RESULTS: At baseline, HVs showed a different microbiota composition compared with IBD patients. Sodium-butyrate altered the gut microbiota of IBD patients by increasing bacteria able to produce SCFA in UC patients (Lachnospiraceae spp.) and the butyrogenic colonic bacteria in CD patients (Butyricicoccus). In UC patients, QoL was positively affected by treatment. CONCLUSIONS AND INFERENCES: Sodium-butyrate supplementation increases the growth of bacteria able to produce SCFA with potentially anti-inflammatory action. The clinical impact of this finding requires further investigation.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33970546", + "title": "Gut dysbiosis and clinical phases of pancolitis in patients with ulcerative colitis.", + "year": 2021, + "journal": "MicrobiologyOpen", + "authors": [ + "Maldonado-Arriaga B", + "Sandoval-Jim\u00e9nez S", + "Rodr\u00edguez-Silverio J", + "Lizeth Alcar\u00e1z-Estrada S", + "Cort\u00e9s-Espinosa T", + "P\u00e9rez-Cabeza de Vaca R", + "Licona-Cassani C", + "G\u00e1mez-Valdez JS", + "Shaw J", + "Mondrag\u00f3n-Ter\u00e1n P", + "Hern\u00e1ndez-Cortez C", + "Su\u00e1rez-Cuenca JA", + "Castro-Escarpulli G" + ], + "bacteria": "Bilophila", + "condition": "ulcerative colitis", + "relevance_score": 0.7590635473007195, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biodiversity", + "Colitis", + "Colitis, Ulcerative", + "DNA, Bacterial", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "RNA, Ribosomal, 16S", + "Severity of Illness Index" + ], + "raw_abstract": "Ulcerative colitis (UC) is a frequent type of inflammatory bowel disease, characterized by periods of remission and exacerbation. Gut dysbiosis may influence pathophysiology and clinical response in UC. The purpose of this study was to evaluate whether gut microbiota is related to the active and remission phases of pancolitis in patients with UC as well as in healthy participants. Fecal samples were obtained from 18 patients with UC and clinical-endoscopic evidenced pancolitis (active phase n\u00a0=\u00a09 and remission phase n\u00a0=\u00a09), as well as 15 healthy participants. After fecal DNA extraction, the 16S rRNA gene was amplified and sequenced (Illumina MiSeq), operational taxonomic units were analyzed with the QIIME software. Gut microbiota composition revealed a higher abundance of the phyla Proteobacteria and Fusobacteria in active pancolitis, as compared with remission and healthy participants. Likewise, a marked abundance of the genus Bilophila and Fusobacteria were present in active pancolitis, whereas a higher abundance of Faecalibacterium characterized both remission and healthy participants. LEfSe analysis showed that the genus\u00a0Roseburia\u00a0and Faecalibacterium were enriched in remission pancolitis, and genera\u00a0Bilophila\u00a0and\u00a0Fusobacterium\u00a0were enriched in active pancolitis. The relative abundance of Fecalibacterium and Roseburia showed a higher correlation with fecal calprotectin, while Bilophila and Fusobacterium showed AUCs (area under the curve) of 0.917 and 0.988 for active vs. remission pancolitis. The results of our study highlight the relation of gut dysbiosis with clinically relevant phases of pancolitis in patients with UC. Particularly, Fecalibacterium, Roseburia, Bilophila, and Fusobacterium were identified as genera highly related to the different clinical phases of pancolitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33977948", + "title": "No Title", + "year": 2021, + "journal": "Food & function", + "authors": [ + "Pang B", + "Jin H", + "Liao N", + "Li J", + "Jiang C", + "Shao D", + "Shi J" + ], + "bacteria": "Bilophila", + "condition": "ulcerative colitis", + "relevance_score": 0.6306895291173065, + "mesh_terms": [ + "Animals", + "Mice", + "Anti-Inflammatory Agents", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "Disease Models, Animal", + "Fatty Acids, Volatile", + "Feces", + "Gastrointestinal Microbiome", + "Intestines", + "Lacticaseibacillus rhamnosus", + "Mice, Inbred C57BL", + "Milk, Human", + "RNA, Ribosomal, 16S", + "Tight Junction Proteins" + ], + "raw_abstract": "Gut microbiota imbalance is one of the major causes of ulcerative colitis (UC). L. rhamnosus SHA113 (LRS), a strain isolated from healthy human milk, influences the regulation of gut flora. This study aims to determine whether this strain can ameliorate UC by modulating gut microbiota. Mouse models of UC were established using C57BL/6Cnc mice with intragastric administration of 3.0% (w/v) dextran sodium sulfate (DSS). LRS was used to treat the mouse models of UC with 109 cfu mL-1 cell suspension via intragastric administration. To verify the effect of gut microbiota on UC, fecal microbiota collected from the mice after the treatment with LRS were also used to treat the UC mouse models (FMT). The severity of UC was evaluated based on body weight, colon length, disease activity index (DAI), and hematoxylin-eosin staining. The microbial composition was analyzed by 16S rRNA sequencing. The mRNA expression levels of cytokines, mucins, tight junction proteins, and antimicrobial peptides in the gastrointestinal tract were detected by quantitative real-time polymerase chain reaction. The short-chain fatty acid (SCFAs) in the cecal contents of all mice were quantitatively detected by gas chromatography and mass spectrometry. Both LRS and FMT exerted excellent therapeutic effects on UC, as evidenced by the reduction in body weight loss, colon length, and colon structural integrity, as well as the increase in the DAI (disease activity index). LRS and FMT treatments showed similar effects: (1) an increase of total SCFA production in the cecal contents and the abundance of gut microbial diversity and flora composition; (2) decreases in two genera (Parabacteroides and Escherichia/Shigella) related to the DAI and the enhancement of SCFAs and IL-10 positively related genera in the gut microbiota (Bilophila, Roseburia, Akkermansia, and Bifidobacterium); (3) downregulation of the expression of tumor necrosis factor-\u03b1, interleukin IL-6, and IL-1\u03b2, and upregulation of the expression of the anti-inflammatory cytokine IL-10; and (4) upregulation of the expression of mucins (Muc1-4) and tight junction protein ZO-1. Overall, L. rhamnosus SHA113 relieves UC via the regulation of gut microbiota: increases in SCFA-producing genera and decreases in UC-related genera. In addition, a single strain is sufficient to induce a significant change in the gut microbiota and exert therapeutic effects on UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36634565", + "title": "The gut microbiota and metabolome are associated with diminished COVID-19 vaccine-induced antibody responses in immunosuppressed inflammatory bowel disease patients.", + "year": 2023, + "journal": "EBioMedicine", + "authors": [ + "Alexander JL", + "Mullish BH", + "Danckert NP", + "Liu Z", + "Olbei ML", + "Saifuddin A", + "Torkizadeh M", + "Ibraheim H", + "Blanco JM", + "Roberts LA", + "Bewshea CM", + "Nice R", + "Lin S", + "Prabhudev H", + "Sands C", + "Horneffer-van der Sluis V", + "Lewis M", + "Sebastian S", + "Lees CW", + "Teare JP", + "Hart A", + "Goodhand JR", + "Kennedy NA", + "Korcsmaros T", + "Marchesi JR", + "Ahmad T", + "Powell N" + ], + "bacteria": "Bilophila", + "condition": "ulcerative colitis", + "relevance_score": 0.39013270817304896, + "mesh_terms": [ + "Humans", + "COVID-19 Vaccines", + "Antibody Formation", + "Gastrointestinal Microbiome", + "ChAdOx1 nCoV-19", + "BNT162 Vaccine", + "Infliximab", + "RNA, Ribosomal, 16S", + "Tumor Necrosis Factor Inhibitors", + "COVID-19", + "SARS-CoV-2", + "Inflammatory Bowel Diseases", + "Metabolome" + ], + "raw_abstract": "BACKGROUND: Patients with inflammatory bowel disease (IBD) treated with anti-TNF therapy exhibit attenuated humoral immune responses to vaccination against SARS-CoV-2. The gut microbiota and its functional metabolic output, which are perturbed in IBD, play an important role in shaping host immune responses. We explored whether the gut microbiota and metabolome could explain variation in anti-SARS-CoV-2 vaccination responses in immunosuppressed IBD patients. METHODS: Faecal and serum samples were prospectively collected from infliximab-treated patients with IBD in the CLARITY-IBD study undergoing vaccination against SARS-CoV-2. Antibody responses were measured following two doses of either ChAdOx1 nCoV-19 or BNT162b2 vaccine. Patients were classified as having responses above or below the geometric mean of the wider CLARITY-IBD cohort. 16S rRNA gene amplicon sequencing, nuclear magnetic resonance (NMR) spectroscopy and bile acid profiling with ultra-high-performance liquid chromatography mass spectrometry (UHPLC-MS) were performed on faecal samples. Univariate, multivariable and correlation analyses were performed to determine gut microbial and metabolomic predictors of response to vaccination. FINDINGS: Forty-three infliximab-treated patients with IBD were recruited (30 Crohn's disease, 12 ulcerative colitis, 1\u00a0IBD-unclassified; 26 with concomitant thiopurine therapy). Eight patients had evidence of prior SARS-CoV-2 infection. Seventeen patients (39.5%) had a serological response below the geometric mean. Gut microbiota diversity was lower in below average responders (p\u00a0=\u00a00.037). Bilophila abundance was associated with better serological response, while Streptococcus was associated with poorer response. The faecal metabolome was distinct between above and below average responders (OPLS-DA R INTERPRETATION: Our data suggest that there is an association between the gut microbiota and variable serological response to vaccination against SARS-CoV-2 in immunocompromised patients. Microbial metabolites including trimethylamine may be important in mitigating anti-TNF-induced attenuation of the immune response. FUNDING: JLA is the recipient of an NIHR Academic Clinical Lectureship (CL-2019-21-502), funded by Imperial College London and The Joyce and Norman Freed Charitable Trust. BHM is the recipient of an NIHR Academic Clinical Lectureship (CL-2019-21-002). The Division of Digestive Diseases at Imperial College London receives financial and infrastructure support from the NIHR Imperial Biomedical Research Centre (BRC) based at Imperial College Healthcare NHS Trust and Imperial College London. Metabolomics studies were performed at the MRC-NIHR National Phenome Centre at Imperial College London; this work was supported by the Medical Research Council (MRC), the National Institute of Health Research (NIHR) (grant number MC_PC_12025) and infrastructure support was provided by the NIHR Imperial Biomedical Research Centre (BRC). The NIHR Exeter Clinical Research Facility is a partnership between the University of Exeter Medical School College of Medicine and Health, and Royal Devon and Exeter NHS Foundation Trust. This project is supported by the National Institute for Health Research (NIHR) Exeter Clinical Research Facility. The views expressed are those of the authors and not necessarily those of the NIHR or the UK Department of Health and Social Care.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37208257", + "title": "Gut microbial signatures and their functions in Behcet's uveitis and Vogt-Koyanagi-Harada disease.", + "year": 2023, + "journal": "Journal of autoimmunity", + "authors": [ + "Wang Q", + "Wu S", + "Ye X", + "Tan S", + "Huang F", + "Su G", + "Kijlstra A", + "Yang P" + ], + "bacteria": "Bilophila", + "condition": "ulcerative colitis", + "relevance_score": 0.22893069359058985, + "mesh_terms": [ + "Humans", + "Uveomeningoencephalitic Syndrome", + "Leukocytes, Mononuclear", + "Gastrointestinal Microbiome", + "Uveitis", + "Behcet Syndrome" + ], + "raw_abstract": "BACKGROUND: A number of public metagenomic studies reveal an association between the gut microbiome and various immune-mediated diseases including Behcet's uveitis (BU) and Vogt-Koyanagi-Harada disease (VKH). Integrated-analysis and subsequent validation of these results could be a potentially powerful way to understand the microbial signatures and their functions in these two uveitis entities. METHODS: We integrated the sequencing data of our previous metagenomic studies on two major uveitis entities, BU and VKH as well as four other publicly available immune-mediated diseases datasets, including Ankylosing Spondylitis (AS), Rheumatoid Arthritis (RA), Crohn's disease (CD) and Ulcerative Colitis (UC). Alpha-diversity and beta-diversity analysis were used to compare the gut microbiome signatures between both uveitis entities and other immune-mediated diseases and healthy controls. Amino acid homology between microbial proteins and a uveitogenic peptide of the interphotoreceptor retinoid-binding protein (IRBP) RESULTS: Depleted Dorea, Blautia, Coprococcus, Erysipelotrichaceae and Lachnospiraceae as well as enriched Bilophila and Stenotrophomonas were identified in BU patients. An enriched Alistipes along with a lower level of Dorea were observed in VKH patients. A peptide antigen (SteTDR) encoded by BU specifically enriched Stenotrophomonas was identified to share homology with IRBP CONCLUSIONS: Our study revealed specific gut microbial signatures and their potentially functional roles in BU and VKH pathogenesis that differ significantly from other immune-mediated diseases as well as healthy controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37950921", + "title": "Exclusive Enteral Nutrition Mediates Beneficial Gut Microbiome Enrichment in Acute Severe Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Bajaj A", + "Markandey M", + "Singh M", + "Sahu P", + "Vuyyuru SK", + "Kante B", + "Kumar P", + "Verma M", + "Makharia G", + "Kedia S", + "Travis SPL", + "Ahuja V" + ], + "bacteria": "Granulicatella", + "condition": "ulcerative colitis", + "relevance_score": 0.49560460482326757, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Crohn Disease", + "Enteral Nutrition", + "Colitis, Ulcerative", + "Bacteria", + "Adrenal Cortex Hormones", + "Remission Induction" + ], + "raw_abstract": "BACKGROUND: Exclusive enteral nutrition (EEN) supplementation of the standard of care (SOC) augments steroid responsiveness in patients with acute severe ulcerative colitis (ASUC). EEN is known to alter gut microbial composition. The present study investigates EEN-driven gut microbial alterations in patients with ASUC and examines their correlations with clinical parameters. METHODS: Stool samples from patients with ASUC (n\u2005=\u200544) who received either EEN-supplemented SOC (EEN group; n\u2005=\u200520) or SOC alone (SOC group; n\u2005=\u200524) for 7 days were collected at baseline (day 0) and postintervention (day 7). Microbiome analysis was carried out using 16S ribosomal RNA gene sequencing followed by data processing using QIIME2 and R packages. RESULTS: Seven-day EEN-conjugated corticosteroid therapy in patients with ASUC enhanced the abundances of beneficial bacterial genera Faecalibacterium and Veillonella and reduced the abundance of Sphingomonas (generalized linear model fitted with Lasso regularization with robustness of 100%), while no such improvements in gut microbiota were observed in the SOC group. The EEN-associated taxa correlated with the patient's clinical parameters (serum albumin and C-reactive protein levels). Unlike the SOC group, which retained its preintervention core microbiota, EEN contributed Faecalibacterium prausnitzii, a beneficial gut bacterial taxon, to the gut microbial core. EEN responders showed enhancement of Ligilactobacillus and Veillonella and reduction in Prevotella and Granulicatella. Analysis of baseline gut microbiota showed relative enhancement of certain microbial genera being associated with corticosteroid response and baseline clinical parameters and that this signature could conceivably be used as a predictive tool. CONCLUSIONS: Augmentation of clinical response by EEN-conjugated corticosteroid therapy is accompanied by beneficial gut microbial changes in patients with ASUC. Exclusive enteral nutrition\u2013supplemented corticosteroid therapy in acute severe ulcerative colitis (ASUC) is accompanied by the enrichment of beneficial gut microbial genera, which correlate negatively with the disease activity scores and objective inflammatory markers in ASUC. The baseline gut microbiota in ASUC associates with and may predict corticosteroid response.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35796402", + "title": "Heterophyllin B an Active Cyclopeptide Alleviates Dextran Sulfate Sodium-Induced Colitis by Modulating Gut Microbiota and Repairing Intestinal Mucosal Barrier via AMPK Activation.", + "year": 2022, + "journal": "Molecular nutrition & food research", + "authors": [ + "Chen C", + "Liang H", + "Wang J", + "Ren G", + "Li R", + "Cui ZG", + "Zhang C" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.7853992955332008, + "mesh_terms": [ + "AMP-Activated Protein Kinases", + "Animals", + "Colitis", + "Colitis, Ulcerative", + "Colon", + "Dextran Sulfate", + "Disease Models, Animal", + "Dysbiosis", + "Gastrointestinal Microbiome", + "Humans", + "Mice", + "Mice, Inbred C57BL", + "Peptides, Cyclic" + ], + "raw_abstract": "SCOPE: Advances in pathology broaden the perception of the intimate interaction between gut microbiota dysbiosis and the pathogenesis of ulcerative colitis (UC), but the potential modulating roles remain to be elucidated. METHODS AND RESULTS: DSS-induced colitis is used to investigate the effect of Heterophyllin B (HB), a typical active cyclopeptide extracted from Pseudostellaria heterophylla, on colitis and gut microbiota. Administration of HB substantially mitigates the symptoms of UC as evidenced by increasing body weight and colon length, as well as decreased macrophages infiltration in the colon. Meanwhile, HB significantly alleviates intestinal mucosal barrier dysfunction by reducing the production of inflammatory cytokines, while all the mentioned beneficial effects are significantly eliminated by co-treatment with compound C, a selective AMPK inhibitor. In addition, 16S rDNA gene analyses and fecal microbiota transplantation also reveal that HB dramatically prevents against UC by reshaping intestinal dysbiosis, especially elevates the relative abundance of Akkermansia muciniphila. CONCLUSION: These findings illustrate that HB prominently improves intestinal epithelial homeostasis via activating AMPK and ameliorates the colonic inflammation in a gut microbiota-dependent manner, which provide evidence for microbial contribution to UC pathogenesis and suggesting a novel approach for colitis prevention.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26875998", + "title": "Akkermansia muciniphila and its role in regulating host functions.", + "year": 2017, + "journal": "Microbial pathogenesis", + "authors": [ + "Derrien M", + "Belzer C", + "de Vos WM" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.7700401399478668, + "mesh_terms": [ + "Animals", + "Anti-Bacterial Agents", + "Clinical Studies as Topic", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Intestines", + "Metabolic Diseases", + "Metagenome", + "Mice", + "Models, Animal", + "Obesity", + "Phylogeny", + "Verrucomicrobia" + ], + "raw_abstract": "Akkermansia muciniphila is an intestinal bacterium that was isolated a decade ago from a human fecal sample. Its specialization in mucin degradation makes it a key organism at the mucosal interface between the lumen and host cells. Although it was isolated quite recently, it has rapidly raised significant interest as A.\u00a0muciniphila is the only cultivated intestinal representative of the Verrucomicrobia, one of the few phyla in the human gut that can be easily detected in phylogenetic and metagenome analyses. There has also been a growing interest in A.\u00a0muciniphila, due to its association with health in animals and humans. Notably, reduced levels of A.\u00a0muciniphila have been observed in patients with inflammatory bowel diseases (mainly ulcerative colitis) and metabolic disorders, which suggests it may have potential anti-inflammatory properties. The aims of this review are to summarize the existing data on the intestinal distribution of A.\u00a0muciniphila in health and disease, to provide insight into its ecology and its role in founding microbial networks at the mucosal interface, as well as to discuss recent research on its role in regulating host functions that are disturbed in various diseases, with a specific focus on metabolic disorders in both animals and humans.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37696680", + "title": "Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Del Chierico F", + "Cardile S", + "Baldelli V", + "Alterio T", + "Reddel S", + "Bramuzzo M", + "Knafelz D", + "Lega S", + "Bracci F", + "Torre G", + "Maggiore G", + "Putignani L" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.68245755731191, + "mesh_terms": [ + "Humans", + "Child", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Cholangitis, Sclerosing", + "Dysbiosis", + "RNA, Ribosomal, 16S", + "Bacteria", + "Bacteroidetes", + "Italy" + ], + "raw_abstract": "BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis. METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs). RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients. CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC. In this study, we report the gut microbiota and mycobiota dysbiosis in pediatric patients affected by primary sclerosing cholangitis (PSC) associated with ulcerative colitis (UC), with an increase in pro-inflammatory pathobionts and a reduction in anti-inflammatory commensals.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34087350", + "title": "Main active components of Jiawei Gegen Qinlian decoction protects against ulcerative colitis under different dietary environments in a gut microbiota-dependent manner.", + "year": 2021, + "journal": "Pharmacological research", + "authors": [ + "Li Q", + "Cui Y", + "Xu B", + "Wang Y", + "Lv F", + "Li Z", + "Li H", + "Chen X", + "Peng X", + "Chen Y", + "Wu E", + "Qu D", + "Jian Y", + "Si H" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.6752096329185493, + "mesh_terms": [ + "Animals", + "Anti-Inflammatory Agents", + "Bacteria", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "Disease Models, Animal", + "Drugs, Chinese Herbal", + "Dysbiosis", + "Female", + "Gastrointestinal Agents", + "Gastrointestinal Microbiome", + "Inflammation Mediators", + "Male", + "Oxidative Stress", + "Rats, Sprague-Dawley", + "Rats" + ], + "raw_abstract": "As an effective drug against acute enteritis diarrhea, Gegen Qinlian decoction (GQD) has a history of 2000 years. However, the potential molecular mechanism through which GQD could protect intestinal barrier from ulcerative colitis (UC) still remains undefined. As an important part of the homeostasis of the colon, gut microbiota is closely related to the dynamic evolution of the surrounding environment and the adjustment of dietary structure. At present, the effectiveness and mechanism of Jiawei Gegen Qinlian decoction against UC in different dietary environments are not clear. Here, the main active components of Jiawei Gegen Qinlian Decoction (PBM), were selected to construct a reasonable and effective compound scheme. We adopted \"5% dextran sulfate sodium (DSS)\" and \"high temperature and humidity + high sugar and high fat + alcohol + 5%DSS\" to induce UC rat models in general environment and UC rat models in Lingnan area, respectively. Then, we examined the therapeutic effects of PBM (89.96\u00a0mg/kg and 179.92\u00a0mg/kg) on two kinds of UC rats. The role of gut microbiota in the anti-UC effect of PBM was identified by intestinal flora consumption and fecal microbiota transplantation (FMT) experiments. Subsequently, we monitored the alterations of gut microbiota and fecal metabolism in the rat colon by 16Sr DNA technique and targeted metabonomics, respectively. The colon inflammation of the PBM-treated and the FMT-treated rats both showed significant relief, as evidenced by a reduction in body weight loss, bloody stool, diarrhea, disease activity index (DAI) score, shortening of colon length as well as decreased colon histology damage. Interestingly enough, the depletion of intestinal flora took away the protective effect of PBM, confirming the importance of intestinal flora in the anti-UC effect of PBM. Then our findings suggested that PBM could not only regulate the gut microbiota by increasing Akkermansia and Romboutsia but also decrease Escherichia-Shigella. More importantly, PBM could increase the production of propionate and total short-chain fatty acids (SCFAs) in colitis rats, regulate medium and long chain fatty acids (M-LCFAs), maintain bile acids (BAs) homeostasis, and regulate amino acids (AAs) metabolism. The transformation of intestinal environment might be related to the upregulation of anti-inflammation, anti-oxidation and tight junction protein expression in colonic mucosa. In summary, PBM showed potential for anti-UC activity through gut microbiota dependence and was expected to be a complementary and alternative medicine herb therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37951857", + "title": "Diagnosis of Crohn's disease and ulcerative colitis using the microbiome.", + "year": 2023, + "journal": "BMC microbiology", + "authors": [ + "Kang DY", + "Park JL", + "Yeo MK", + "Kang SB", + "Kim JM", + "Kim JS", + "Kim SY" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.6658978930739262, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Crohn Disease", + "Inflammatory Bowel Diseases", + "Gastrointestinal Microbiome", + "Bacteria", + "Biomarkers" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is a multifactorial chronic inflammatory disease resulting from dysregulation of the mucosal immune response and gut microbiota. Crohn's disease (CD) and ulcerative colitis (UC) are difficult to distinguish, and differential diagnosis is essential for establishing a long-term treatment plan for patients. Furthermore, the abundance of mucosal bacteria is associated with the severity of the disease. This study aimed to differentiate and diagnose these two diseases using the microbiome and identify specific biomarkers associated with disease activity. RESULTS: Differences in the abundance and composition of the microbiome between IBD patients and healthy controls (HC) were observed. Compared to HC, the diversity of the gut microbiome in patients with IBD decreased; the diversity of the gut microbiome in patients with CD was significantly lower. Sixty-eight microbiota members (28 for CD and 40 for UC) associated with these diseases were identified. Additionally, as the disease progressed through different stages, the diversity of the bacteria decreased. The abundances of Alistipes shahii and Pseudodesulfovibrio aespoeensis were negatively correlated with the severity of CD, whereas the abundance of Polynucleobacter wianus was positively correlated. The severity of UC was negatively correlated with the abundance of A. shahii, Porphyromonas asaccharolytica and Akkermansia muciniphilla, while it was positively correlated with the abundance of Pantoea candidatus pantoea carbekii. A regularized logistic regression model was used for the differential diagnosis of the two diseases. The area under the curve (AUC) was used to examine the performance of the model. The model discriminated UC and CD at an AUC of 0.873 (train set), 0.778 (test set), and 0.633 (validation set) and an area under the precision-recall curve (PRAUC) of 0.888 (train set), 0.806 (test set), and 0.474 (validation set). CONCLUSIONS: Based on fecal whole-metagenome shotgun (WMS) sequencing, CD and UC were diagnosed using a machine-learning predictive model. Microbiome biomarkers associated with disease activity (UC and CD) are also proposed.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34259969", + "title": "Novel Gut Microbiota Modulator, Which Markedly Increases Akkermansia muciniphila Occupancy, Ameliorates Experimental Colitis in Rats.", + "year": 2022, + "journal": "Digestive diseases and sciences", + "authors": [ + "Nakashima T", + "Fujii K", + "Seki T", + "Aoyama M", + "Azuma A", + "Kawasome H" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.6581646853162768, + "mesh_terms": [ + "Akkermansia", + "Animals", + "Anti-Bacterial Agents", + "Colitis", + "Dextran Sulfate", + "Disease Models, Animal", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Mice", + "Mice, Inbred C57BL", + "Mucins", + "Rats", + "Verrucomicrobia" + ], + "raw_abstract": "BACKGROUND: Since gut microbiota is involved in the pathogenesis of inflammatory bowel disease (IBD), antibiotics or probiotics may be attractive options for the treatment of IBD. Akkermansia\u00a0muciniphila is expected as a next-generation probiotic for IBD, and OPS-2071 is a novel quinolone with potent antibacterial activity against Clostridioides\u00a0difficile. AIMS: The aim of this study is to assess the potential of OPS-2071 as a gut microbiota modulator for IBD. METHODS: Minimum inhibitory concentrations of several bacteria in the human intestinal microbiota were determined. Microbiota changes in the feces were typed using metagenomic analysis after oral administration of OPS-2071 (100\u00a0mg/kg) twice a day to normal rats. The amounts of mucin were determined using the Fecal Mucin Assay Kit. The effects of OPS-2071 (1, 3, 10\u00a0mg/kg) twice a day on fecal symptoms and fecal microbiota were evaluated in a colitis rat model induced by free access to drinking water containing 3% dextran sulfate sodium for 10\u00a0days. RESULTS: OPS-2071 showed notably low antibacterial activity against only A.\u00a0muciniphila in spite of higher antimicrobial activity against other strains of intestinal bacteria. OPS-2071 rapidly and dramatically increased the occupancy of A.\u00a0muciniphila as well as the amount of mucin in the feces of normal rats. OPS-2071 (10\u00a0mg/kg) significantly suppressed the exacerbation of stool scores, especially the bloody stool score, with the increase in A.\u00a0muciniphila occupancy. CONCLUSIONS: OPS-2071 is expected to be a new therapeutic option for IBD as a gut microbiota modulator by significantly increasing A.\u00a0muciniphila occupancy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29788382", + "title": "Colonic Inhibition of Phosphatase and Tensin Homolog Increases Colitogenic Bacteria, Causing Development of Colitis in Il10-/- Mice.", + "year": 2018, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Mitchell J", + "Kim SJ", + "Koukos G", + "Seelmann A", + "Veit B", + "Shepard B", + "Blumer-Schuette S", + "Winter HS", + "Iliopoulos D", + "Pothoulakis C", + "Im E", + "Rhee SH" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.6519030248558214, + "mesh_terms": [ + "Animals", + "Colitis", + "Colitis, Ulcerative", + "Colon", + "Disease Models, Animal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Interleukin-10", + "Intestinal Mucosa", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Mice, Knockout", + "Organometallic Compounds", + "PTEN Phosphohydrolase" + ], + "raw_abstract": "BACKGROUND: Phosphatase and tensin homolog (Pten) is capable of mediating microbe-induced immune responses in the gut. Thus, Pten deficiency in the intestine accelerates colitis development in Il10-/- mice. As some ambient pollutants inhibit Pten function and exposure to ambient pollutants may increase inflammatory bowel disease (IBD) incidence, it is of interest to examine how Pten inhibition could affect colitis development in genetically susceptible hosts. METHODS: With human colonic mucosa biopsies from pediatric ulcerative colitis and non-IBD control subjects, we assessed the mRNA levels of the PTEN gene and the gene involved in IL10 responses. The data from the human tissues were corroborated by treating Il10-/-, Il10rb-/-, and wild-type C57BL/6 mice with Pten-specific inhibitor VO-OHpic. We evaluated the severity of mouse colitis by investigating the tissue histology and cytokine production. The gut microbiome was investigated by analyzing the 16S ribosomal RNA gene sequence with mouse fecal samples. RESULTS: PTEN and IL10RB mRNA levels were reduced in the human colonic mucosa of pediatric ulcerative colitis compared with non-IBD subjects. Intracolonic treatment of the Pten inhibitor induced colitis in Il10-/- mice, characterized by reduced body weight, marked colonic damage, and increased production of inflammatory cytokines, whereas Il10rb-/- and wild-type C57BL/6 mice treated with the inhibitor did not develop colitis. Pten inhibitor treatment changed the fecal microbiome, with increased abundance of colitogenic bacteria Bacteroides and Akkermansia in Il10-/- mice. CONCLUSIONS: Loss of Pten function increases the levels of colitogenic bacteria in the gut, thereby inducing deleterious colitis in an Il10-deficient condition.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37507685", + "title": "Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population.", + "year": 2023, + "journal": "BMC gastroenterology", + "authors": [ + "Alsulaiman RM", + "Al-Quorain AA", + "Al-Muhanna FA", + "Piotrowski S", + "Kurdi EA", + "Vatte C", + "Alquorain AA", + "Alfaraj NH", + "Alrezuk AM", + "Robinson F", + "Dowdell AK", + "Alamri TA", + "Hamilton L", + "Lad H", + "Gao H", + "Gandla D", + "Keating BJ", + "Meng R", + "Piening B", + "Al-Ali AK" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.6427295074351848, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Saudi Arabia", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Crohn Disease" + ], + "raw_abstract": "BACKGROUND: Crohn's diseases and ulcerative colitis, both of which are chronic immune-mediated disorders of the gastrointestinal tract are major contributors to the overarching Inflammatory bowel diseases. It has become increasingly evident that the pathological processes of IBDs results from interactions between genetic and environmental factors, which can skew immune responses against normal intestinal flora. METHODS: The aim of this study is to assess and analyze the taxa diversity and relative abundances in CD and UC in the Saudi population. We utilized a sequencing strategy that targets all variable regions in the 16\u00a0S rRNA gene using the Swift Amplicon 16\u00a0S rRNA Panel on Illumina NovaSeq 6000. RESULTS: The composition of stool 16\u00a0S rRNA was analyzed from 219 patients with inflammatory bowel disease and from 124 healthy controls. We quantified the abundance of microbial communities to examine any significant differences between subpopulations of samples. At the genus level, two genera in particular, Veillonella and Lachnoclostridium showed significant association with CD versus controls. There were significant differences between subjects with CD versus UC, with the top differential genera spanning Akkermansia, Harryflintia, Maegamonas and Phascolarctobacterium. Furthermore, statistically significant taxa diversity in microbiome composition was observed within the UC and CD groups. CONCLUSIONS: In conclusion we have shown that there are significant differences in gut microbiota between UC, CD and controls in a Saudi Arabian inflammatory bowel disease cohort. This reinforces the need for further studies in large populations that are ethnically and geographically diverse. In addition, our results show the potential to develop classifiers that may have add additional richness of context to clinical diagnosis of UC and CD with larger inflammatory bowel disease cohorts.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33977948", + "title": "No Title", + "year": 2021, + "journal": "Food & function", + "authors": [ + "Pang B", + "Jin H", + "Liao N", + "Li J", + "Jiang C", + "Shao D", + "Shi J" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.6306895291173065, + "mesh_terms": [ + "Animals", + "Mice", + "Anti-Inflammatory Agents", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "Disease Models, Animal", + "Fatty Acids, Volatile", + "Feces", + "Gastrointestinal Microbiome", + "Intestines", + "Lacticaseibacillus rhamnosus", + "Mice, Inbred C57BL", + "Milk, Human", + "RNA, Ribosomal, 16S", + "Tight Junction Proteins" + ], + "raw_abstract": "Gut microbiota imbalance is one of the major causes of ulcerative colitis (UC). L. rhamnosus SHA113 (LRS), a strain isolated from healthy human milk, influences the regulation of gut flora. This study aims to determine whether this strain can ameliorate UC by modulating gut microbiota. Mouse models of UC were established using C57BL/6Cnc mice with intragastric administration of 3.0% (w/v) dextran sodium sulfate (DSS). LRS was used to treat the mouse models of UC with 109 cfu mL-1 cell suspension via intragastric administration. To verify the effect of gut microbiota on UC, fecal microbiota collected from the mice after the treatment with LRS were also used to treat the UC mouse models (FMT). The severity of UC was evaluated based on body weight, colon length, disease activity index (DAI), and hematoxylin-eosin staining. The microbial composition was analyzed by 16S rRNA sequencing. The mRNA expression levels of cytokines, mucins, tight junction proteins, and antimicrobial peptides in the gastrointestinal tract were detected by quantitative real-time polymerase chain reaction. The short-chain fatty acid (SCFAs) in the cecal contents of all mice were quantitatively detected by gas chromatography and mass spectrometry. Both LRS and FMT exerted excellent therapeutic effects on UC, as evidenced by the reduction in body weight loss, colon length, and colon structural integrity, as well as the increase in the DAI (disease activity index). LRS and FMT treatments showed similar effects: (1) an increase of total SCFA production in the cecal contents and the abundance of gut microbial diversity and flora composition; (2) decreases in two genera (Parabacteroides and Escherichia/Shigella) related to the DAI and the enhancement of SCFAs and IL-10 positively related genera in the gut microbiota (Bilophila, Roseburia, Akkermansia, and Bifidobacterium); (3) downregulation of the expression of tumor necrosis factor-\u03b1, interleukin IL-6, and IL-1\u03b2, and upregulation of the expression of the anti-inflammatory cytokine IL-10; and (4) upregulation of the expression of mucins (Muc1-4) and tight junction protein ZO-1. Overall, L. rhamnosus SHA113 relieves UC via the regulation of gut microbiota: increases in SCFA-producing genera and decreases in UC-related genera. In addition, a single strain is sufficient to induce a significant change in the gut microbiota and exert therapeutic effects on UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32070388", + "title": "A randomized controlled trial investigating the effect of a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols on the intestinal microbiome and inflammation in patients with ulcerative colitis: study protocol for a randomized controlled trial.", + "year": 2020, + "journal": "Trials", + "authors": [ + "Milajerdi A", + "Sadeghi O", + "Siadat SD", + "Keshavarz SA", + "Sima A", + "Vahedi H", + "Adibi P", + "Esmaillzadeh A" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.6263466957590321, + "mesh_terms": [ + "Adult", + "Biomarkers", + "Colitis, Ulcerative", + "Diet, Carbohydrate-Restricted", + "Dietary Sugars", + "Female", + "Fermentation", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Male", + "Middle Aged", + "Monosaccharides", + "Oligosaccharides", + "Polymers", + "Randomized Controlled Trials as Topic", + "Severity of Illness Index", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: No conclusive treatment is available for irritable bowel disease (IBD). Adherence to a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) might alleviate clinical symptoms of IBD. However, no study has investigated the effect of low FODMAPs diet on the intestinal microbiota and inflammatory biomarkers in patients with IBD. The aim of current study is to examine the effect a low FODMAP diet on IBD symptoms, inflammation, and the intestinal microbiota in patients with ulcerative colitis. METHODS AND ANALYSIS: This study is a randomized clinical trial. Thirty patients with mild to moderate ulcerative colitis will be randomly allocated to receive a low FODMAP diet (n\u2009=\u200915) or to continue their usual diet as control (n\u2009=\u200915), for 4\u2009weeks. The quantity of intestinal microbiota including Clostridium cluster IV, Faecalibacterium prausnitzii, Rosburia spp., Lactobacillus spp., Bifidobacteria spp., Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., and the Firmicutes to Bacteroidetes ratio and calprotectin and lactoferrin levels will be explored in fecal samples from patients. In addition, anthropometric measures and biochemical assessments including serum concentrations of highly sensitive-C reactive protein (hs-CRP), tumour necrosis factor-\u03b1 (TNF-\u03b1) and IL-1\u03b2 will be taken from patients at baseline and end of the study. The study has been registered in IRCT (IRCT20181126041763N1; registration date: 2019-01-18). DISCUSSION: Consumption of a low-FODMAP diet might decrease systemic and intestinal inflammation, change the bacterial population in the gut, and modulate clinical symptoms in patients with ulcerative colitis. Further studies investigating the effect of such a diet on other variables, including other bacterial species and inflammatory cytokines, are required to confirm future findings of this trial.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35662877", + "title": "Zingiber officinale and Panax ginseng ameliorate ulcerative colitis in mice via modulating gut microbiota and its metabolites.", + "year": 2022, + "journal": "Journal of chromatography. B, Analytical technologies in the biomedical and life sciences", + "authors": [ + "Wan Y", + "Yang L", + "Li H", + "Ren H", + "Zhu K", + "Dong Z", + "Jiang S", + "Shang E", + "Qian D", + "Duan J" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.5981279443355652, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Zingiber officinale", + "Mice", + "Panax", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Zingiber officinale and Panax ginseng, as well-known traditional Chinese medicines, have been used together to clinically treat ulcerative colitis with synergistic effects for thousands of years. However, their compatibility mechanism remains unclear. In this study, the shift of gut microbiome and fecal metabolic profiles were monitored by 16S rRNA sequencing technology and ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry analysis, respectively, which aimed to reveal the synergistic mechanism of Zingiber officinale and Panax ginseng on the amelioration of ulcerative colitis. The results showed that the relative abundance of beneficial bacteria (such as Muribaculaceae_norank, Lachnospiraceae NK4A136 group and Akkermansia) was significantly increased and the abundance of pathogenic bacteria (such as Bacteroides, Parabacteroides and Desulfovibrio) was markedly decreased after the intervention of Zingiber officinale-Panax ginseng herb pair. And a total of 16 differential metabolites related to ulcerative colitis were identified by the metabolomics analysis, which were majorly associated with the metabolic pathways, including arachidonic acid metabolism, tryptophan metabolism, and steroid biosynthesis. Based on these findings, it was suggested that the regulation of the gut microbiota-metabolite axis might be a potential target for the synergistic mechanism of Zingiber officinale-Panax ginseng herb pair in the treatment of ulcerative colitis. Furthermore, the integrated analysis of microbiome and metabolomics used in this study could also serve as a useful template for exploring the mechanism of other drugs.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35104755", + "title": "Integrated microbiome-metabolomics analysis reveals the potential therapeutic mechanism of Zuo-Jin-Wan in ulcerative colitis.", + "year": 2022, + "journal": "Phytomedicine : international journal of phytotherapy and phytopharmacology", + "authors": [ + "Cai Y", + "Li S", + "Zhang X", + "Cao X", + "Liu D", + "Zhu Y", + "Ye S", + "Xu Z", + "Liao Q", + "Hong Y", + "Xie Z" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.5814548368548027, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Dysregulation in gut microbiota and host cometabolome contributes to the complicated pathology of ulcerative colitis (UC), while Zuo-Jin-Wan (ZJW), a traditional Chinese medicine has shown therapeutic effects against UC with its underlying mechanism remains elusive. PURPOSE: This study utilized an integrated analysis combining gut microbiome and host cometabolism to disclose the potential therapeutic mechanism of ZJW on dextran sulfate sodium (DSS)-induced UC in rats. METHODS: We first evaluated the therapeutic effects of ZJW treatment in DSS-induced rat model. 16S rRNA sequencing, RESULTS: Our results showed that UC symptoms in ZJW rats were significantly attenuated. Marked decline in microbial diversity in ZJW group was accompanied by its correspondent function adjustment. Specific enrichment of genus Bacteroides, Sutterella, Akkermansia and Roseburia along with the major varying amino acid metabolism and lipid metabolism were observed meantime. Metabolic data further corroborated that ZJW-related metabolic changes were basically gathered in amino acid metabolism, carbohydrate/energy metabolism and lipid metabolism. Of note, some biochemical parameters were deeply implicated with the discriminative microbial genera and metabolites involved in tricarboxylic acid (TCA) cycle and amino acid metabolism, indicating the microbiome-metabolome association in gut microbiota-metabolite-phenotype axis during UC treatment of ZJW. CONCLUSION: For the first time, integrated microbiome-metabolome analysis depicted that ZJW could alleviate DSS-induced UC in rats via a crosstalk between gut microbiota and host cometabolites.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "25037189", + "title": "Abnormal fibre usage in UC in remission.", + "year": 2015, + "journal": "Gut", + "authors": [ + "James SL", + "Christophersen CT", + "Bird AR", + "Conlon MA", + "Rosella O", + "Gibson PR", + "Muir JG" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.5685299804252014, + "mesh_terms": [ + "Adult", + "Aged", + "Colitis, Ulcerative", + "Cross-Over Studies", + "Dietary Fiber", + "Female", + "Humans", + "Male", + "Middle Aged", + "Polysaccharides", + "Remission Induction", + "Single-Blind Method", + "Starch" + ], + "raw_abstract": "OBJECTIVE: Colonic fermentation in patients with UC in remission was compared with that in matched healthy subjects on habitual diets and when dietary fibre was increased. DESIGN: Fibre intake, faecal output of fibre (measured as non-starch polysaccharide (NSP)), starch, microbiota and fermentation products, and whole gut transit time (WGTT) were assessed in association with habitual diet and when dietary intake of wheat bran (WB)-associated fibre and high amylose-associated resistant starch (RS) was increased in an 8-week, randomised, single-blind, cross-over study. RESULTS: Despite a tendency to lower habitual fibre intake in UC patients, faecal NSP and starch concentrations were threefold higher than in controls, whereas concentrations of phenols and short-chain fatty acids, pH and WGTT were similar. Increasing RS/WB intake was well tolerated. In controls (n=10), it more than doubled faecal NSP and starch excretion (p=0.002 for both), had no effect on NSP usage and reduced WGTT (p=0.024). In UC patients (n=19), high intake of RS/WB tended to normalise gut transit, but did not increase the proportion of NSP fermented. Increasing intake of RS/WB had little effect on faecal fermentation patterns or the structure of the microbiota. However, faeces from the UC cohort had lower proportions of Akkermansia muciniphila and increased diversity within Clostridium cluster XIVa compared to controls. CONCLUSIONS: Gut fermentation of NSP and starch is diminished in patients with UC. This cannot be explained by abnormal gut transit and was not corrected by increasing RS/WB intake, and may be due to abnormal functioning of the gut microbiota. TRIAL REGISTRATION NUMBER: Australian New Zealand Clinical Trials Registry: ACTRN12614000271606.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37655859", + "title": "Gut Microbiota Composition in Long-Remission Ulcerative Colitis is Close to a Healthy Gut Microbiota.", + "year": 2023, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Herrera-deGuise C", + "Varela E", + "Sarrabayrouse G", + "Pozuelo Del R\u00edo M", + "Alonso VR", + "Sainz NB", + "Casellas F", + "Mayorga LF", + "Manichanh C", + "Vidaur FA", + "Guarner F" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.566220703399835, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Colitis, Ulcerative", + "Microbiota", + "Butyrates", + "Feces" + ], + "raw_abstract": "BACKGROUND: Microbiome studies report low gut microbial richness and diversity in ulcerative colitis (UC) patients. We explored whether UC patients who reach long-term clinical, endoscopic, and histological remission show a gut microbial ecosystem that is similar to healthy individuals. METHODS: We collected 184 stool samples from 111 individuals (UC patients in long remission, short remission, flare, and healthy control subjects). Microbiota was analyzed by amplicon sequencing (16S ribosomal RNA) and quantitative polymerase chain reaction for specific taxa. All UC remission patients were followed-up for 2 years. FINDINGS: A drop in species diversity and richness, underrepresentation of butyrate producers, and gain of potentially harmful bacteria were significantly detected in samples from disease-flare and short-remission patients. In contrast, Chao1 and Shannon indexes of diversity did not differ among patients in long remission and healthy control subjects. Long-remission patients also presented fecal bacterial composition closer to that in healthy control subjects. There was a positive correlation between Akkermansia muciniphila abundance and time in remission (rs\u2005=\u20050.53, P\u2005<\u2005.001). Logistic regression analysis showed that a high Shannon index (odds ratio, 4.83; 95% confidence interval, 1.5-20.6) or presence of A. muciniphila (odds ratio, 4.9; 95% confidence interval, 1.12-29.08) in fecal samples at entry was independently associated with clinical remission over a follow-up period of 24 months. INTERPRETATION: UC patients who achieve long-term remission show evidence of substantial recovery of the gut microbial ecosystem in terms of diversity and composition. Recovery may just reflect adequate control of inflammatory activity, but higher bacterial diversity or the presence of A. muciniphila in fecal samples predicts flare-free outcomes. Microbiome studies have shown low gut microbial richness and diversity in ulcerative colitis patients. Patients who achieve long-term remission show evidence of substantial recovery of the gut microbial ecosystem in terms of diversity and composition.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32576228", + "title": "Effects of soy milk consumption on gut microbiota, inflammatory markers, and disease severity in patients with ulcerative colitis: a study protocol for a randomized clinical trial.", + "year": 2020, + "journal": "Trials", + "authors": [ + "Sadeghi O", + "Milajerdi A", + "Siadat SD", + "Keshavarz SA", + "Sima AR", + "Vahedi H", + "Adibi P", + "Esmaillzadeh A" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.5496370877772266, + "mesh_terms": [ + "Adult", + "Anti-Inflammatory Agents", + "Biomarkers", + "Colitis, Ulcerative", + "Eating", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Iran", + "Male", + "Middle Aged", + "Phytoestrogens", + "Quality of Life", + "Randomized Controlled Trials as Topic", + "Severity of Illness Index", + "Soy Milk", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Several strategies are recommended to alleviate clinical symptoms of ulcerative colitis (UC). Soy milk may affect UC through its anti-inflammatory properties. However, no study has examined the effects of soy milk consumption on gut microbiota and inflammatory biomarkers in patients with UC. The current study will be done to examine the effects of soy milk consumption on UC symptoms, inflammation, and gut microbiota in patients with UC. METHODS: This study is a randomized clinical trial, in which thirty patients with mild to moderate severity of UC will be randomly allocated to receive either 250\u2009mL/day soy milk plus routine treatments (n\u2009=\u200915) or only routine treatments (n\u2009=\u200915) for 4\u2009weeks. Assessment of anthropometric measures and biochemical indicators including serum concentrations of high-sensitivity C-reactive protein (hs-CRP), tumor necrosis factor-\u03b1 (TNF-\u03b1), interleukin-1\u03b2 (IL-1\u03b2), and interferon gamma (IFN-\u03b3) will be done at the study baseline and end of trial. In addition, the quantity of butyrate-producing bacteria including Clostridium cluster IV, Faecalibacterium prausnitzii, and Roseburia spp.; prebiotic bacteria including Lactobacillus spp. and Bifidobacteria spp.; and mucus-degrading bacteria including Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., as well as calprotectin and lactoferrin levels, will be explored in fecal samples. Also, the Firmicutes to Bacteroidetes ratio which is of significant relevance in human gut microbiota composition will be assessed. DISCUSSION: Altered gut microbiota has been reported as an important contributing factor to inflammation in patients with inflammatory bowel disease (IBD). Soy milk contains several components such as phytoestrogens with potential anti-inflammatory properties. This product might affect gut microbiota through its protein and fiber content. Therefore, soy milk might beneficially affect systemic inflammation, gut microbiota, and then clinical symptoms in patients with UC. TRIAL REGISTRATION: Iranian Registry of Clinical Trials (www.irct.ir) IRCT20181205041859N1. Registered on 27 January 2019.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31094471", + "title": "Markers of dysbiosis in patients with ulcerative colitis and Crohn's disease.", + "year": 2019, + "journal": "Terapevticheskii arkhiv", + "authors": [ + "Danilova NA", + "Abdulkhakov SR", + "Grigoryeva TV", + "Markelova MI", + "Vasilyev IY", + "Boulygina EA", + "Ardatskaya MD", + "Pavlenko AV", + "Tyakht AV", + "Odintsova AK", + "Abdulkhakov RA" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.5211650934273171, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans" + ], + "raw_abstract": "AIM: The aim of the study was to study the taxonomic and functional composition of the gut microbiota in ulcerative colitis (UC) and Crohn's disease (CD) patients to identify key markers of dysbiosis in IBD. MATERIALS AND METHODS: Fecal samples obtained from 95 IBD patients (78 UC and 17 CD) as well as 96 healthy volunteers were used for whole-genome sequencing carried out on the SOLiD 5500 W platform. Taxonomic profiling was performed by aligning the reeds, not maped on hg19, on MetaPhlAn2 reference database. Reeds were mapped using the HUNAnN2 algorithm to the ChocoPhlAn database to assess the representation of microbial metabolic pathways. Short-chain fatty acids (SCFA) level were measured in fecal samples by gas-liquid chromatographic analysis. RESULTS: Changes in IBD patients gut microbiota were characterized by an increase in the representation of Proteobacteria and Bacteroidetes phyla bacteria and decrease in the number of Firmicutes phylum bacteria and Euryarchaeota phylum archaea; a decrease in the alpha-diversity index, relative representation of butyrate-producing, hydrogen-utilizing bacteria, and Methanobrevibacter smithii; increase in the relative representation of Ruminococcus gnavus in UC and CD patients and Akkermansia muciniphila in CD patients. Reduction of Butyryl-CoA: acetate CoA transferase gene relative representation in CD patients, decrease of absolute content of SCFA total number as well as particular SCFAs and main SCFAs ratio in IBD patients may indicate inhibition of functional activity and number of anaerobic microflora and/or an change in SCFA utilization by colonocytes. CONCLUSION: the revealed changes can be considered as typical signs of dysbiosis in IBD patients and can be used as potential targets for IBD patients personalized treatment development.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38428658", + "title": "Gegen Qinlian decoction ameliorates TNBS-induced ulcerative colitis by regulating Th2/Th1 and Tregs/Th17\u00a0cells balance, inhibiting NLRP3 inflammasome activation and reshaping gut microbiota.", + "year": 2024, + "journal": "Journal of ethnopharmacology", + "authors": [ + "Hu Y", + "Tang J", + "Xie Y", + "Xu W", + "Zhu W", + "Xia L", + "Fang J", + "Yu D", + "Liu J", + "Zheng Z", + "Zhou Q", + "Shou Q", + "Zhang W" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.5154108139017193, + "mesh_terms": [ + "Humans", + "Mice", + "Animals", + "Colitis, Ulcerative", + "Drugs, Chinese Herbal", + "Inflammasomes", + "Interleukin-18", + "Gastrointestinal Microbiome", + "NLR Family, Pyrin Domain-Containing 3 Protein", + "Th17 Cells", + "Occludin", + "RNA, Ribosomal, 16S", + "Mice, Inbred CBA", + "Colitis", + "Cytokines", + "Trinitrobenzenes", + "Anti-Inflammatory Agents", + "Body Weight", + "Caspases", + "Disease Models, Animal", + "Colon" + ], + "raw_abstract": "ETHNOPHARMACOLOGICAL RELEVANCE: Chinese herbal medicine Gegen Qinlian Decoction (GQD) has been clinically shown to be an effective treatment of ulcerative colitis (UC) in China. However, the underlying mechanism of GQD's anti-ulcerative colitis properties and its effect on gut microbiota still deserve further exploration. AIM OF THE STUDY: This study observed the regulatory effects of GQD on Th2/Th1 and Tregs/Th17\u00a0cells balance, the NOD-like receptor family pyrin domain containing 3 (NLRP3) infammasome and gut microbiota in TNBS-induced UC in BALB/c mice. MATERIALS AND METHODS: 61 main chemical compounds in the GQD were determined by UPLC-Q-TOF/MS. The UC BALB/c model was established by intrarectal administration of trinitrobenzene sulfonic acid (TNBS), and GQD was orally administered at low and high dosages of 2.96 and 11.83\u00a0g/kg/day, respectively. The anti-inflammatory effects of GQD for ulcerative colitis were evaluated by survival rate, body weight, disease activity index (DAI) score, colonic weight and index, spleen index, hematoxylin-eosin (HE) staining and histopathological scores. Flow cytometry was used to detect the percentage of CD4, Th1, Th2, Th17 and Tregs cells. The levels of Th1-/Th2-/Th17-/Tregs-related inflammatory cytokines and additional proinflammatory cytokines (IL-1\u03b2, IL-18) were detected by CBA, ELISA, and RT-PCR. The expressions of GATA3, T-bet, NLRP3, Caspase-1, IL-I\u03b2, Occludin and Zonula occludens-1 (ZO-1) on colon tissues were detected by Western blot and RT-PCR. Transcriptome sequencing was performed using colon tissue and 16S rRNA gene sequencing was performed on intestinal contents. Fecal microbiota transplantation (FMT) was employed to assess the contribution of intestinal microbiota and its correlation with CD4 T cells and the NLRP3 inflammasome. RESULTS: GQD increased the survival rate of TNBS-induced UC in BALB/c mice, and significantly improved their body weight, DAI score, colonic weight and index, spleen index, and histological characteristics. The intestinal barrier dysfunction was repaired after GQD administration through promoting the expression of tight junction proteins (Occludin and ZO-1). GQD restored the balance of Th2/Th1 and Tregs/Th17\u00a0cells immune response of colitis mice, primarily inhibiting the increase in Th2/Th1 ratio and their transcription factor production (GATA3 and T-bet). Morever, GQD changed the secretion of Th1-/Th2-/Th17-/Tregs-related cytokines (IL-2, IL-12, IL-5, IL-13, IL-6, IL-10, and IL-17A) and reduced the expressions of IL-1\u03b2, IL-18. Transcriptome results suggested that GQD could also remodel the immune inflammatory response of colitis by inhibiting NOD-like receptor signaling pathway, and Western blot, immunohistochemistry and RT-PCR further revealed that GQD exerted anti-inflammatory effects by inhibiting the NLRP3 inflammasome, such as down-regulating the expression of NLRP3, Caspase-1 and IL-1\u03b2. More interestingly, GQD regulated gut microbiota dysbiosis, suppressed the overgrowth of conditional pathogenic gut bacteria like Helicobacter, Proteobacteria, and Mucispirillum, while the probiotic gut microbiota, such as Lactobacillus, Muribaculaceae, Ruminiclostridium_6, Akkermansia, and Ruminococcaceae_unclassified were increased. We further confirmed that GQD-treated gut microbiota was sufficient to relieve TNBS-induced colitis by FMT, involving the modulation of Th2/Th1 and Tregs/Th17 balance, inhibition of NLRP3 inflammasome activation, and enhancement of colonic barrier function. CONCLUSIONS: GQD might alleviate TNBS-induced UC via regulating Th2/Th1 and Tregs/Th17 cells Balance, inhibiting NLRP3 inflammasome and reshaping gut microbiota, which may provide a novel strategy for patients with colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "24414342", + "title": "Immunological alteration and changes of gut microbiota after dextran sulfate sodium (DSS) administration in mice.", + "year": 2015, + "journal": "Clinical and experimental medicine", + "authors": [ + "H\u00e5kansson \u00c5", + "Tormo-Badia N", + "Baridi A", + "Xu J", + "Molin G", + "Hagsl\u00e4tt ML", + "Karlsson C", + "Jeppsson B", + "Cilio CM", + "Ahrn\u00e9 S" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.5150001383889982, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "Desulfovibrio", + "Dextran Sulfate", + "Enterobacteriaceae", + "Female", + "Humans", + "Immunity, Innate", + "Lactobacillus", + "Lymph Nodes", + "Mice", + "Mice, Inbred C57BL", + "Microbiota", + "Monocytes", + "Peroxidase", + "Peyer's Patches", + "Spleen", + "T-Lymphocytes" + ], + "raw_abstract": "Ulcerative colitis (UC) is characterized by chronic inflammation of the colonic mucosa. Administration of dextran sulfate sodium (DSS) to animals is a frequently used model to mimic human colitis. Deregulation of the immune response to the enteric microflora or pathogens as well as increased intestinal permeability have been proposed as disease-driving mechanisms. To enlarge the understanding of the pathogenesis, we have studied the effect of DSS on the immune system and gut microbiota in mice. Intestinal inflammation was verified through histological evaluation and myeloperoxidase activity. Immunological changes were assessed by flow cytometry in spleen, Peyer's patches and mesenteric lymph nodes and through multiplex cytokine profiling. In addition, quantification of the total amount of bacteria on colonic mucosa as well as the total amount of lactobacilli, Akkermansia, Desulfovibrio and Enterobacteriaceae was performed by the use of quantitative PCR. Diversity and community structure were analysed by terminal restriction fragment length polymorphism (T-RFLP) patterns, and principal component analysis was utilized on immunological and T-RFLP patterns. DSS-induced colitis show clinical and histological similarities to UC. The composition of the colonic microflora was profoundly changed and correlated with several alterations of the immune system. The results demonstrate a relationship between multiple immunological changes and alterations of the gut microbiota after DSS administration. These data highlight and improve the definition of the immunological basis of the disease and suggest a role for dysregulation of the gut microbiota in the pathogenesis of colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29052237", + "title": "The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis.", + "year": 2018, + "journal": "Alimentary pharmacology & therapeutics", + "authors": [ + "Kump P", + "Wurm P", + "Gr\u00f6chenig HP", + "Wenzl H", + "Petritsch W", + "Halwachs B", + "Wagner M", + "Stadlbauer V", + "Eherer A", + "Hoffmann KM", + "Deutschmann A", + "Reicht G", + "Reiter L", + "Slawitsch P", + "Gorkiewicz G", + "H\u00f6genauer C" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.4848185506562907, + "mesh_terms": [ + "Adult", + "Anti-Bacterial Agents", + "Colitis, Ulcerative", + "Fecal Microbiota Transplantation", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Prospective Studies", + "Remission Induction", + "Ruminococcus", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Faecal microbiota transplantation is an experimental approach for the treatment of patients with ulcerative colitis. Although there is growing evidence that faecal microbiota transplantation is effective in this disease, factors affecting its response are unknown. AIMS: To establish a faecal microbiota transplantation treatment protocol in ulcerative colitis patients, and to investigate which patient or donor factors are responsible for the treatment success. METHODS: This is an open controlled trial of repeated faecal microbiota transplantation after antibiotic pre-treatment (FMT-group, n\u00a0=\u00a017) vs antibiotic pre-treatment only (AB-group, n\u00a0=\u00a010) in 27 therapy refractory ulcerative colitis patients over 90\u00a0days. Faecal samples of donors and patients were analysed by 16SrRNA gene-based microbiota analysis. RESULTS: In the FMT-group, 10/17 (59%) of patients showed a response and 4/17 (24%) a remission to faecal microbiota transplantation. Response to faecal microbiota transplantation was mainly influenced by the taxonomic composition of the donor's microbiota. Stool of donors with a high bacterial richness (observed species remission 946\u00a0\u00b1\u00a093 vs no response 797\u00a0\u00b1\u00a0181 at 15367\u00a0rps) and a high relative abundance of Akkermansia muciniphila (3.3\u00a0\u00b1\u00a03.1% vs 0.1\u00a0\u00b1\u00a00.2%), unclassified Ruminococcaceae (13.8\u00a0\u00b1\u00a05.0% vs 7.5\u00a0\u00b1\u00a03.7%), and Ruminococcus spp. (4.9\u00a0\u00b1\u00a03.5% vs 1.0\u00a0\u00b1\u00a00.7%) were more likely to induce remission. In contrast antibiotic treatment alone (AB-group) was poorly tolerated, probably because of a sustained decrease of intestinal microbial richness. CONCLUSIONS: The taxonomic composition of the donor's intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in ulcerative colitis patients. The design of specific microbial preparation might lead to new treatments for ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39740381", + "title": "Gingerols: Preparation, encapsulation, and bioactivities focusing gut microbiome modulation and attenuation of disease symptoms.", + "year": 2025, + "journal": "Phytomedicine : international journal of phytotherapy and phytopharmacology", + "authors": [ + "Abdullah", + "Ahmad N", + "Xiao J", + "Tian W", + "Khan NU", + "Hussain M", + "Ahsan HM", + "Hamed YS", + "Zhong H", + "Guan R" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.46245133068003624, + "mesh_terms": [ + "Gastrointestinal Microbiome", + "Humans", + "Catechols", + "Fatty Alcohols", + "Animals", + "Zingiber officinale", + "Phytochemicals", + "Dysbiosis", + "Anti-Inflammatory Agents" + ], + "raw_abstract": "BACKGROUND: Gut dysbiosis, chronic diseases, and microbial recurrent infections concerns have driven the researchers to explore phytochemicals from medicinal and food homologous plants to modulate gut microbiota, mitigate diseases, and inhibit pathogens. Gingerols have attracted attention as therapeutic agents due to their diverse biological activities like gut microbiome regulation, gastro-protective, anti-inflammatory, anti-microbial, and anti-oxidative effects. PURPOSE: This review aimed to summarize the gingerols health-promoting potential, specifically focusing on the regulation of gut microbiome, attenuation of disease symptoms, mechanisms of action, and signaling pathways involved. METHOD: Research findings from experimental and clinical studies have been summarized regarding gingerols effects on the modulation of gut microbiome and its metabolites, and attenuation of disease symptoms. RESULTS: Gingerols are phenolic compounds characterized by a common 3-methoxy-4-hydroxyphenyl moiety in their chemical structures, and further divided into different gingerol types, including gingerols (major), shogaols, paradols, gingerdiols, gingerdiones, and zingerones (minor). Advanced extraction techniques (e.g., ionic liquid-based-, enzyme-assisted-, microwave-assisted-, pressurized liquid-, ultrasound-assisted-, and supercritical fluid extractions) were reported as optimal alternatives to conventional methods for gingerols extraction. Research studies reported that gingerols positively modulated the composition of gut microbiome that helped to combat disease symptoms (e.g., obesity by decreasing weight gain- (Lactobacillus reuteri and Lachnospiraceae) and increasing weight loss associated-bacteria (Akkermansia, Muribaculaceae, and Alloprevotella). Gingerols intervention also ameliorated ulcerative colitis by increasing relative abundance of the beneficial bacteria (Akkermansia, Lachnospiraceae NK4A136, and Muribaculaceae_norank), and decreasing pathogenic microorganisms (Bacteroides, Parabacteroides, and Desulfovibrio). Emerging delivery systems (e.g., microcapsules, nanoparticles, nanostructured lipid carriers, nanoemulsions, and nanoliposomes) can enhance the bioavailability and therapeutic efficacy of gingerols by preserving their inherent properties and addressing challenges of stability, solubility, and absorption. CONCLUSION: Gingerols are promising therapeutic agents to modulate gut microbiome (increase beneficial bacteria and inhibit pathogenic microbes), and attenuate chronic disease symptoms such as diabetes, colitis, obesity, oxidative stress, and cancer. Despite significant progress, challenges persist in transforming research findings into industrial applications, such as stability and solubility during processing and low bioavailability in the distal gut to impart desirable health benefits.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31812509", + "title": "Differences in Gut Microbiota in Patients With vs Without Inflammatory Bowel Diseases: A Systematic Review.", + "year": 2020, + "journal": "Gastroenterology", + "authors": [ + "Pittayanon R", + "Lau JT", + "Leontiadis GI", + "Tse F", + "Yuan Y", + "Surette M", + "Moayyedi P" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.4587921981899641, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestines" + ], + "raw_abstract": "BACKGROUND & AIMS: Altering the intestinal microbiota has been proposed as a treatment for inflammatory bowel diseases (IBDs), but there are no established associations between specific microbes and IBD. We performed a systematic review to identify frequent associations. METHODS: We searched the MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, and Cochrane Central Register of Controlled Trials databases, through April 2, 2018 for studies that compared intestinal microbiota (from fecal or colonic or ileal tissue samples) among patients (adult or pediatric) with IBD vs healthy individuals (controls). The primary outcome was difference in specific taxa in fecal or intestinal tissue samples from patients with IBD vs controls. We used the Newcastle-Ottawa scale to assess the quality of studies included in the review. RESULTS: We identified 2631 citations; 48 studies from 45 articles were included in the analysis. Most studies evaluated adults with Crohn's disease or ulcerative colitis. All 3 studies of Christensenellaceae and Coriobacteriaceae and 6 of 11 studies of Faecalibacterium prausnitzii reported a decreased amount of those organisms compared with controls, whereas 2 studies each of Actinomyces, Veillonella, and Escherichia coli revealed an increased amount in patients with Crohn's disease. For patients with ulcerative colitis, Eubacterium rectale and Akkermansia were decreased in all 3 studies, whereas E coli was increased in 4 of 9 studies. The microbiota diversity was either decreased or not different in patients with IBD vs controls. Fewer than 50% of the studies stated comparable sexes and ages of cases and controls. CONCLUSIONS: In a systematic review, we found evidence for differences in abundances of some bacteria in patients with IBD vs controls, but we cannot make conclusions due to inconsistent results and methods among studies. Further large-scale studies, with better methods of assessing microbe populations, are needed.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35138361", + "title": "Similar Gut Bacterial Composition Between Patients With Ulcerative Colitis and Healthy Controls in a High Incidence Population: A Cross-sectional Study of the Faroe Islands IBD Cohort.", + "year": 2022, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Berbis\u00e1 M\u00c1F", + "Nielsen KR", + "Ingham AC", + "Midjord J", + "Hammer T", + "Patursson P", + "Vest NMO", + "Gregersen NO", + "Burisch J", + "Vang A" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.44295875594401274, + "mesh_terms": [ + "Bacteria", + "Colitis, Ulcerative", + "Cross-Sectional Studies", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Incidence", + "Inflammatory Bowel Diseases", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: The Faroe Islands has the world's highest incidence of inflammatory bowel disease (IBD). Epidemiological studies have characterized this unique cohort and a decreased risk of developing IBD with emigration. Therefore, this well-characterized Faroese IBD cohort gives the opportunity to better understand this complex disease. This study represents the first investigation of the gut microbiota for the cohort. METHODS: This cross-sectional study consisted of 41 patients with established ulcerative colitis and 144 age- and sex-matched healthy controls recruited through the Faroe Genome project. Participants donated a 1-time fecal sample and completed questionnaires on food frequency, background health, and lifestyle. 16S rRNA amplicon sequencing of the V3-V4 region was performed followed by bioinformatic analysis of taxonomy and diversity metrics. RESULTS: The overall bacterial composition in both groups was dominated by Firmicutes and Bacteroidetes. No significant differences were found based on metrics of alpha or beta diversity. However, discriminatory analysis identified differential abundance of several indicator taxa in healthy controls and ulcerative colitis participants, whereas Akkermansia was completely absent from 27% of all study participants. Food frequency questionnaires revealed similar dietary patterns between the 2 groups. CONCLUSION: The similarity in bacterial community composition and absence of the beneficial Akkermansia genus in both groups raise further questions concerning the underlying susceptibility toward inflammatory disorders within this high-risk population. Results vary widely by study design and geographic location, which speaks to the need for regionally tuned reference groups and disease-based studies on the Faroe Islands. The Faroe Islands has the world\u2019s highest incidence of IBD. This is the first investigation characterizing gut microbiota for this unique cohort. No significant differences were found between ulcerative colitis and healthy controls based on alpha or beta diversity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35378331", + "title": "The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients.", + "year": 2022, + "journal": "Cellular and molecular gastroenterology and hepatology", + "authors": [ + "Gonzalez CG", + "Mills RH", + "Kordahi MC", + "Carrillo-Terrazas M", + "Secaira-Morocho H", + "Widjaja CE", + "Tsai MS", + "Mittal Y", + "Yee BA", + "Vargas F", + "Weldon K", + "Gauglitz JM", + "Delaroque C", + "Sauceda C", + "Rossitto LA", + "Ackermann G", + "Humphrey G", + "Swafford AD", + "Siegel CA", + "Buckey JC", + "Raffals LE", + "Sadler C", + "Lindholm P", + "Fisch KM", + "Valaseck M", + "Suriawinata A", + "Yeo GW", + "Ghosh P", + "Chang JT", + "Chu H", + "Dorrestein P", + "Zhu Q", + "Chassaing B", + "Knight R", + "Gonzalez DJ", + "Dulai PS" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.43056700276817994, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Humans", + "Hyperbaric Oxygenation", + "Interleukin-10", + "Mice", + "Microbiota", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND & AIMS: Hyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy. METHODS: Pre- and post-intervention mucosal biopsies, tissue, and fecal samples were collected from HBOT phase 2 clinical trials. Biopsies and fecal samples were subjected to shotgun metaproteomics, metabolomics, 16s rRNA sequencing, and metagenomics. Tissue was subjected to bulk RNA sequencing and digital spatial profiling (DSP) for single-cell RNA and protein analysis, and immunohistochemistry was performed. Fecal samples were also used for colonization experiments in IL10 RESULTS: Proteomics identified negative associations between HBOT response and neutrophil azurophilic granule abundance. DSP identified an HBOT-specific reduction of neutrophil STAT3, which was confirmed by immunohistochemistry. HBOT decreased microbial diversity with a proportional increase in Firmicutes and a secondary bile acid lithocholic acid. A major source of the reduction in diversity was the loss of mucus-adherent taxa, resulting in increased MUC2 levels post-HBOT. Targeted database searching revealed strain-level associations between Akkermansia muciniphila and HBOT response status. Colonization of IL10 CONCLUSIONS: HBOT reduces host neutrophil STAT3 and azurophilic granule activity in UC patients and changes in microbial composition and metabolism in ways that improve colitis activity. Intestinal microbiota, especially strain level variations in A muciniphila, may contribute to HBOT non-response.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27412252", + "title": "Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.", + "year": 2016, + "journal": "Genome medicine", + "authors": [ + "Shaw KA", + "Bertha M", + "Hofmekler T", + "Chopra P", + "Vatanen T", + "Srivatsa A", + "Prince J", + "Kumar A", + "Sauer C", + "Zwick ME", + "Satten GA", + "Kostic AD", + "Mulle JG", + "Xavier RJ", + "Kugathasan S" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.3912722894782307, + "mesh_terms": [ + "Adolescent", + "Bacteria", + "Biomarkers", + "Case-Control Studies", + "Child", + "Child, Preschool", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Immunologic Factors", + "Inflammation", + "Intestinal Mucosa", + "Leukocyte L1 Antigen Complex", + "Longitudinal Studies", + "Male", + "Severity of Illness Index", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Gut microbiome dysbiosis has been demonstrated in subjects with newly diagnosed and chronic inflammatory bowel disease (IBD). In this study we sought to explore longitudinal changes in dysbiosis and ascertain associations between dysbiosis and markers of disease activity and treatment outcome. METHODS: We performed a prospective cohort study of 19 treatment-na\u00efve pediatric IBD subjects and 10 healthy controls, measuring fecal calprotectin and assessing the gut microbiome via repeated stool samples. Associations between clinical characteristics and the microbiome were tested using generalized estimating equations. Random forest classification was used to predict ultimate treatment response (presence of mucosal healing at follow-up colonoscopy) or non-response using patients' pretreatment samples. RESULTS: Patients with Crohn's disease had increased markers of inflammation and dysbiosis compared to controls. Patients with ulcerative colitis had even higher inflammation and dysbiosis compared to those with Crohn's disease. For all cases, the gut microbial dysbiosis index associated significantly with clinical and biological measures of disease severity, but did not associate with treatment response. We found differences in specific gut microbiome genera between cases/controls and responders/non-responders including Akkermansia, Coprococcus, Fusobacterium, Veillonella, Faecalibacterium, and Adlercreutzia. Using pretreatment microbiome data in a weighted random forest classifier, we were able to obtain 76.5\u00a0% accuracy for prediction of responder status. CONCLUSIONS: Patient dysbiosis improved over time but persisted even among those who responded to treatment and achieved mucosal healing. Although dysbiosis index was not significantly different between responders and non-responders, we found specific genus-level differences. We found that pretreatment microbiome signatures are a promising avenue for prediction of remission and response to treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39891249", + "title": "Real-world of Limosilactobacillus reuteri in mitigation of acute experimental colitis.", + "year": 2025, + "journal": "Journal of nanobiotechnology", + "authors": [ + "Yue N", + "Zhao H", + "Hu P", + "Zhang Y", + "Tian C", + "Kong C", + "Mai Z", + "Huang L", + "Luo Q", + "Wei D", + "Shi R", + "Tang S", + "Nie Y", + "Liang Y", + "Yao J", + "Wang L", + "Li D" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.39009366876530555, + "mesh_terms": [ + "Animals", + "Limosilactobacillus reuteri", + "Mice", + "Probiotics", + "Dextran Sulfate", + "Colitis", + "Gastrointestinal Microbiome", + "Mice, Inbred C57BL", + "Akkermansia", + "Intestinal Mucosa", + "Zonula Occludens-1 Protein", + "Male", + "Cadherins", + "Disease Models, Animal", + "Humans", + "Heme Oxygenase-1", + "Occludin", + "Colitis, Ulcerative", + "Epithelial Cells", + "Membrane Proteins" + ], + "raw_abstract": "Probiotics have been proposed as a potential strategy for managing ulcerative colitis (UC). However, the underlying mechanisms mediating microbiota-host crosstalk remain largely elusive. Here, we report that Limosilactobacillus reuteri (L. reuteri), as a probiotic, secretes cytoplasmic membrane vesicles (CMVs) that communicate with host cells, alter host physiology, and alleviate dextran sulfate sodium (DSS)-induced colitis. First, L. reuteri-CMVs selectively promoted the proliferation of the beneficial bacterium Akkermansia muciniphila (AKK) by upregulating the expression of glycosidases (beta-N-acetylhexosaminidase and alpha-N-acetylglucosaminidase) involved in glycan degradation and metabolic pathways and restored the disrupted gut microbiota balance. Second, L. reuteri-CMVs were taken up by intestinal epithelial cells (IECs), elevated the expression of ZO-1, E-cadherin (Cdh1), and Occludin (Ocln), decreased intestinal permeability, and exerted protective effects on epithelial tight junction functionality. RNA sequencing analysis demonstrated that L. reuteri-CMVs repaired intestinal barrier by activating the HIF-1 signaling pathway and upregulating HMOX1 expression. Third, L. reuteri-CMVs increased the population of double positive (DP) CD4", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36195889", + "title": "Understanding the tonifying and the detoxifying properties of Chinese medicines from their impacts on gut microbiota and host metabolism: a case study with four medicinal herbs in experimental colitis rat model.", + "year": 2022, + "journal": "Chinese medicine", + "authors": [ + "Li T", + "Gao X", + "Yan Z", + "Wai TS", + "Yang W", + "Chen J", + "Yan R" + ], + "bacteria": "Akkermansia", + "condition": "ulcerative colitis", + "relevance_score": 0.339913374634281, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Chinese medicines (CMs) have emerged as an alternative therapy for ulcerative colitis through reinforcing the vital qi and/or eliminating the pathogenic factors according to the traditional Chinese medicinal theory. Presystemic interactions of CMs with gut microbiota and the associated metabolic network shift are believed to be essential to achieve their holistic health benefits in traditional oral application. METHODS: This study first employed 16S rDNA-based microbial profiling and mass spectrometry-based urinary metabolomics to simultaneously evaluate four\u00a0single CMs frequently prescribed as main constituent herbs for alleviating UC, the tonic ginseng and Astragali Radix (AR) and the detoxifying Scutellaria Radix (SR) and Rhubarb, on a dextran sodium sulfate (DSS)-induced colitis rat model, with aims to understanding the tonifying or detoxifying properties of CMs through clinical phenotypes, the common features and herb-specific signatures in gut microbial alterations and the associated host metabolic shifts. Colitis was induced in rats receiving 5% DSS for consecutive 7 days. Control group received water alone. Herbal groups received 5% DSS and respective herbal preparation by gavage once daily. Body weight, stool consistency, and rectal bleeding were recorded daily. Feces and urine were freshly collected at multiple time points. On day 7, blood and colon tissues were collected to determine anti-/pro-inflammatory cytokines levels, colonic myeloperoxidase activity, and histopathologic alterations. RESULTS: Gut microbiome was more prone to herb intervention than metabolome and displayed increasing associations with metabolic dynamics. Although both the tonic and the detoxifying herbs alleviated colitis and caused some similar changes in DSS-induced microbiome and metabolome disturbance, the tonic herbs were more effective and shared more common microbial and metabolic signatures. The detoxifying herbs elicited herb-specific changes. Rhubarb uniquely affected phenylalanine metabolism and established high correlations between Akkermansia muciniphila and Parasutterella and hydroxyphenylacetylglycine and phenylbutyrylglycine, while SR caused significant elevation of steroidal glucuronides dehydropregnenolone glucuronide and estriol glucuronide, both displaying exclusive correlations with genus Acetatifactor. CONCLUSION: Both tonic and detoxifying herbs tested ameliorated experimental colitis and elicited alternative microbial and host metabolic reprogramming. The findings highlight the importance of presystemic interactions with gut microbiota to host metabolic shifts and promote modern translation of tonic\u00a0and detoxifying properties of CMs.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29615776", + "title": "Dysbiosis of the salivary microbiota in pediatric-onset primary sclerosing cholangitis and its potential as a biomarker.", + "year": 2018, + "journal": "Scientific reports", + "authors": [ + "Iwasawa K", + "Suda W", + "Tsunoda T", + "Oikawa-Kawamoto M", + "Umetsu S", + "Takayasu L", + "Inui A", + "Fujisawa T", + "Morita H", + "Sogo T", + "Hattori M" + ], + "bacteria": "Rothia", + "condition": "ulcerative colitis", + "relevance_score": 0.7004462988893462, + "mesh_terms": [ + "Adolescent", + "Biomarkers", + "Case-Control Studies", + "Child", + "Cholangitis, Sclerosing", + "Dysbiosis", + "Female", + "Humans", + "Male", + "Phenotype", + "RNA, Ribosomal, 16S", + "Saliva" + ], + "raw_abstract": "Primary sclerosing cholangitis (PSC) is a liver disease known for its frequent concurrence with inflammatory bowel disease. Dysbiosis of the gut microbiota in PSC was reported in several studies, but the microbiological features of the salivary microbiota in PSC have not been established. Here we compared the salivary microbial communities of 24 pediatric-onset PSC patients, 16 age-matched ulcerative colitis (UC) patients, and 24 healthy controls (HCs) by analyzing the bacterial 16S rRNA gene sequence data. The species-richness (\u03b1-diversity) showed no significant between-group differences, whereas the overall salivary microbiota structure (\u03b2-diversity) showed significant differences among the three groups. Taxonomic assignment revealed that the PSC salivary microbiota were characterized by significant decreases in the abundance of Rothia and Haemophilus compared to the HC group, and significantly decreased Haemophilus and increased Oribacterium compared to the UC group. By combining the genera selected by the random forest algorithm in machine learning, followed by confirmation with 10-fold cross-validation, we were able to distinguish the PSC group from the HC group with the area under the curve (AUC) of 0.7423, and from the UC group with the AUC of 0.8756. Our results indicate the potential of salivary microbiota as biomarkers for a noninvasive diagnosis of PSC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39739648", + "title": "The Gut Microbiota Affects Anti-TNF Responsiveness by Activating the NAD", + "year": 2025, + "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", + "authors": [ + "Lei J", + "Lv L", + "Zhong L", + "Xu F", + "Su W", + "Chen Y", + "Wu Z", + "He S", + "Chen Y" + ], + "bacteria": "Romboutsia", + "condition": "ulcerative colitis", + "relevance_score": 0.7534439075030492, + "mesh_terms": [ + "Gastrointestinal Microbiome", + "Colitis, Ulcerative", + "Animals", + "Mice", + "NAD", + "Disease Models, Animal", + "Humans", + "Male", + "Infliximab", + "Fecal Microbiota Transplantation", + "Tumor Necrosis Factor-alpha", + "Fusobacterium nucleatum", + "Mice, Inbred C57BL" + ], + "raw_abstract": "Approximately 50% of the patients with ulcerative colitis (UC) are primarily nonresponsive to anti-tumor necrosis factor (TNF) therapy or lose their responsiveness over time. The gut microbiota plays an important role in the resistance of UC to anti-TNF therapy; however, the underlying mechanism remains unknown. Here, it is found that the transplantation of gut fecal microbiota from patients with UC alters the diversity of the gut microbiota in dextran sulfate sodium-induced colitis mice and may affect the therapeutic responsiveness of mice to infliximab. Furthermore, the abundances of Romboutsia and Fusobacterium increase in the tissues of patients with UC who do not respond to anti-TNF therapy. Differentially abundant metabolites are mainly enriched in nicotinate and nicotinamide metabolism in NCM460 cells after Fusobacterium nucleatum infection. Mechanistically, F. nucleatum promotes the nicotinamide adenine dinucleotide (NAD", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38029703", + "title": "Altered metabolome and microbiome features provide clues in predicting recurrence of ulcerative colitis.", + "year": 2024, + "journal": "Journal of pharmaceutical and biomedical analysis", + "authors": [ + "Liu H", + "Feng X", + "Wang D", + "Liu L", + "Liu Y", + "Liu B", + "Zhu L", + "Zhang C", + "Yang W" + ], + "bacteria": "Romboutsia", + "condition": "ulcerative colitis", + "relevance_score": 0.7330958613788674, + "mesh_terms": [ + "Humans", + "Animals", + "Colitis, Ulcerative", + "Chromatography, Liquid", + "RNA, Ribosomal, 16S", + "Tandem Mass Spectrometry", + "Microbiota", + "Metabolome", + "Biomarkers", + "Dextran Sulfate", + "Disease Models, Animal" + ], + "raw_abstract": "PURPOSE: Many studies have shown that the imbalance of the intestinal flora and metabolite can lead to the development of ulcerative colitis (UC), but their role in recurrent-UC is still unclear. We studied the intestinal flora and metabolites associated with recurrent-UC to elucidate the mechanism and biomarkers of recurrent-UC. METHODS: Ulcerative colitis (UC) models in active, remission, and recurrence stages were established, and the abundance of intestinal flora was determined by 16\u00a0S rRNA sequencing. The changes in the metabolites present in feces and serum were analyzed by UPLC-MS/MS. RESULTS: We identified 24 metabolites in feces and serum, which might be used as diagnostic and predictive biomarkers of recurrent-UC. The dominant flora of recurrent-UC included Romboutsia, UCG-005, etc. The results of a network analysis found that long-chain fatty acids and phenylalanine were strongly correlated with Firmicutes and Proteobacteria, which indicated that the recurrence of UC might be closely related to metabolites and microorganisms. CONCLUSION: The changes in intestinal microbiota and metabolites are closely related to the development of UC. Microbiota is an important inducer of UC, which can regulate metabolites through the 'microorganism-gut-metabolite' axis. It may provide a new method for the prediction and treatment of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34087350", + "title": "Main active components of Jiawei Gegen Qinlian decoction protects against ulcerative colitis under different dietary environments in a gut microbiota-dependent manner.", + "year": 2021, + "journal": "Pharmacological research", + "authors": [ + "Li Q", + "Cui Y", + "Xu B", + "Wang Y", + "Lv F", + "Li Z", + "Li H", + "Chen X", + "Peng X", + "Chen Y", + "Wu E", + "Qu D", + "Jian Y", + "Si H" + ], + "bacteria": "Romboutsia", + "condition": "ulcerative colitis", + "relevance_score": 0.6752096329185493, + "mesh_terms": [ + "Animals", + "Anti-Inflammatory Agents", + "Bacteria", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "Disease Models, Animal", + "Drugs, Chinese Herbal", + "Dysbiosis", + "Female", + "Gastrointestinal Agents", + "Gastrointestinal Microbiome", + "Inflammation Mediators", + "Male", + "Oxidative Stress", + "Rats, Sprague-Dawley", + "Rats" + ], + "raw_abstract": "As an effective drug against acute enteritis diarrhea, Gegen Qinlian decoction (GQD) has a history of 2000 years. However, the potential molecular mechanism through which GQD could protect intestinal barrier from ulcerative colitis (UC) still remains undefined. As an important part of the homeostasis of the colon, gut microbiota is closely related to the dynamic evolution of the surrounding environment and the adjustment of dietary structure. At present, the effectiveness and mechanism of Jiawei Gegen Qinlian decoction against UC in different dietary environments are not clear. Here, the main active components of Jiawei Gegen Qinlian Decoction (PBM), were selected to construct a reasonable and effective compound scheme. We adopted \"5% dextran sulfate sodium (DSS)\" and \"high temperature and humidity + high sugar and high fat + alcohol + 5%DSS\" to induce UC rat models in general environment and UC rat models in Lingnan area, respectively. Then, we examined the therapeutic effects of PBM (89.96\u00a0mg/kg and 179.92\u00a0mg/kg) on two kinds of UC rats. The role of gut microbiota in the anti-UC effect of PBM was identified by intestinal flora consumption and fecal microbiota transplantation (FMT) experiments. Subsequently, we monitored the alterations of gut microbiota and fecal metabolism in the rat colon by 16Sr DNA technique and targeted metabonomics, respectively. The colon inflammation of the PBM-treated and the FMT-treated rats both showed significant relief, as evidenced by a reduction in body weight loss, bloody stool, diarrhea, disease activity index (DAI) score, shortening of colon length as well as decreased colon histology damage. Interestingly enough, the depletion of intestinal flora took away the protective effect of PBM, confirming the importance of intestinal flora in the anti-UC effect of PBM. Then our findings suggested that PBM could not only regulate the gut microbiota by increasing Akkermansia and Romboutsia but also decrease Escherichia-Shigella. More importantly, PBM could increase the production of propionate and total short-chain fatty acids (SCFAs) in colitis rats, regulate medium and long chain fatty acids (M-LCFAs), maintain bile acids (BAs) homeostasis, and regulate amino acids (AAs) metabolism. The transformation of intestinal environment might be related to the upregulation of anti-inflammation, anti-oxidation and tight junction protein expression in colonic mucosa. In summary, PBM showed potential for anti-UC activity through gut microbiota dependence and was expected to be a complementary and alternative medicine herb therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37820918", + "title": "Scytosiphon lomentaria fucoidan ameliorates DSS-induced colitis in dietary fiber-deficient mice via modulating the gut microbiota and inhibiting the TLR4/NF-\u03baB/MLCK pathway.", + "year": 2023, + "journal": "International journal of biological macromolecules", + "authors": [ + "Jia J", + "Zheng W", + "Tang S", + "Song S", + "Ai C" + ], + "bacteria": "Romboutsia", + "condition": "ulcerative colitis", + "relevance_score": 0.6420246914011817, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "NF-kappa B", + "Toll-Like Receptor 4", + "Gastrointestinal Microbiome", + "Myosin-Light-Chain Kinase", + "Polysaccharides", + "Colitis", + "Colitis, Ulcerative", + "Dietary Fiber", + "Colon", + "Dextran Sulfate", + "Disease Models, Animal", + "Mice, Inbred C57BL" + ], + "raw_abstract": "The prevalence of ulcerative colitis (UC) poses a serious threat to human health. This study showed that fiber-deficient diet (FD) increased the susceptibility of mice to low dosage of DSS-induced UC, and a UC model was established by feeding mice with DSS and FD to evaluate the effect of Scytosiphon lomentaria fucoidan (SLF) on UC. SLF ameliorated the symptoms of UC, as evidenced by increases in colon length, goblet cells and glycoprotein and reduction in inflammatory cell infiltration and intestinal epithelial injury. SLF alleviated oxidative stress and inhibited colonic inflammation by reducing the levels of lipopolysaccharides and pro-inflammatory cytokines and suppressing the activation of nuclear factor kappa B pathway. SLF protected tight junction integrity by reducing the level of myosin light chain kinase and increasing the levels of claudin, zonula occludens-1 and occludin. SLF improved serum metabolites profile and affected multiple metabolic pathways that are crucial to human health, e.g. butanoate metabolism. The underlying mechanism can be associated with modulation of the gut microbiota and metabolites, including increases in short chain fatty acids and reduction in Proteobacteria, Bacteroides and Romboutsia. It suggests that SLF could be developed as a prebiotic polysaccharide to benefit human health by improving intestinal microecology.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39368133", + "title": "Investigating the mechanism of enhanced medicinal effects of Terminalia chebula fruit after processing based on intestinal flora and metabolomics.", + "year": 2024, + "journal": "International immunopharmacology", + "authors": [ + "An Y", + "Wang W", + "Gao H", + "Zhang Q", + "Yang W", + "Hao J", + "Li X", + "Ju C" + ], + "bacteria": "Romboutsia", + "condition": "ulcerative colitis", + "relevance_score": 0.4847520738307379, + "mesh_terms": [ + "Male", + "Rats", + "Biomarkers", + "Colitis, Ulcerative", + "Colon", + "Fatty Acids, Volatile", + "Feces", + "Gastrointestinal Microbiome", + "Phytotherapy", + "Plant Extracts", + "Rats, Sprague-Dawley", + "Terminalia", + "Animals" + ], + "raw_abstract": "BACKGROUND AND OBJECTIVE: Terminalia chebula is a classical medicine for the treatment of lingering dysentery, and both raw and processed T. chebula can alleviate ulcerative colitis (UC). The therapeutic efficacy of T. chebula is enhanced after processing, but the mechanism that processing improves this efficacy is still unknown. We investigated the medicinal effects of raw and processed T. chebula on dextran sulfate sodium (DSS)-induced UC model rats using intestinal flora and metabolomics analyses, in order to elucidate the mechanism by which processing enhances the therapeutic effect. METHODS: The major constituents of raw and processed T. chebula were detected by high-performance liquid chromatography (HPLC). UC model was replicated using the DSS method, and then UC rats were administered raw and processed T. chebula. The general physical signs, disease activity index (DAI) scores, colon histopathological morphology, and the expressions of inflammatory cytokines were used to evaluate the therapeutic effect of T. chebula. In addition, 16\u00a0s rRNA sequencing and gas chromatography-mass spectrometry (GC-MS) were used to characterize the intestinal flora and contents of short-chain fatty acids (SCFAs). Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) was utilized to identify the nontargeted fecal metabolites. RESULTS: Raw and processed T. chebula significantly improved the general physical signs and colon inflammatory symptoms and decreased DAI scores of UC rats. Both raw and processed T. chebula mitigated intestinal flora disorders in UC rats, increasing probiotic bacteria, including Lactobacillus and Romboutsia. However, the effect of processed\u00a0T. chebula was more pronounced. Moreover, the levels of SCFAs of DSS-induced UC rats were restored after drug administration, and the processed T. chebula had a better regulatory effect than raw T. chebula. In the fecal nontargeted metabolomics analysis, differential metabolites such as lipids and amino acids were identified. The processed\u00a0T. chebula can regulate purine metabolism and other pathways to improve UC, and the levels of the disordered metabolites gradually approached those of the control group. CONCLUSION: Raw and processed T. chebula had the capacity to mitigate DSS-induced UC by rebalancing the intestinal flora, restoring the contents of SCFAs, and regulating fecal metabolites, while processed T. chebula showed preferable effects.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Pseudoflavonifractor", + "condition": "ulcerative colitis", + "relevance_score": 0.47549133808592103, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "25931359", + "title": "Ileal pouch morphology and microbiology in ulcerative colitis patients.", + "year": 2015, + "journal": "Advances in clinical and experimental medicine : official organ Wroclaw Medical University", + "authors": [ + "Pawe\u0142ka D", + "Bednarz W", + "Krawczyk Z", + "Rzeszutko M", + "Olewi\u0144ski R", + "Czopnik P" + ], + "bacteria": "Staphylococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6831863078282585, + "mesh_terms": [ + "Biopsy", + "Colitis, Ulcerative", + "Colonic Pouches", + "Endoscopy, Gastrointestinal", + "Female", + "Humans", + "Intestinal Mucosa", + "Male", + "Pouchitis", + "Predictive Value of Tests", + "Proctocolectomy, Restorative", + "Severity of Illness Index", + "Time Factors", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Ideal pouch created during restorative proctocolectomy is a new gastrointestinal organ--\"neorectum\". Although it is made from the ileum, it takes over function of the removed rectum. This new function results in significant morphological changes in pouch's mucous membrane, which becomes similar to the large bowel mucosa. The most common pathology of the ileal pouch is its inflammation--pouchitis. One of the suspected causes of pouchitis is bacterial flora disturbance. OBJECTIVES: The aim of the study was to analyze the morphological and microbiological changes in ileal pouches in different time periods after ileostomy closure and to evaluate the influence of certain bacterial strains on the degree of inflammation. MATERIAL AND METHODS: The study involved 47 patients who had been treated surgically; they were investigated before and at different stages after ileostomy closure. They underwent repeated rectoscopies with biopsies of pouch mucosa and swabs for microbiological examination. In total 89 rectoscopies were performed, which provided 70 histopathological results according to the Heidelberg Pouchitis Activity Score and 87 microbiological test results. RESULTS: The assessment of the morphology of intestinal pouches showed increased signs of chronic inflammation as the length of time after the closure of a protective ileostomy increased. There was no correlation between the signs of acute inflammation and the length of time after surgery; there were more signs of acute inflammation in cases of pouchitis. The composition of the bacterial flora of intestinal pouches changed as the length of time after ileostomy closure increased, with significant increases in the number of enterobacteriaceae species. The presence of Staphylococcus aureus significantly correlates with a higher degree of chronic inflammation; this bacterium may be a potential infectious factor in pouchitis. CONCLUSIONS: Microbiological analysis of intestinal pouch lumen is a useful tool that can be used in routine follow-up assessment of intestinal pouches as well as in diagnosing pouchitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35184056", + "title": "Preliminary Comparison of Endoscopic Brush and Net Catheters as the Sampling Tool to Analyze the Intestinal Mucus in the Rectum with Ulcerative Colitis Patients.", + "year": 2022, + "journal": "Digestion", + "authors": [ + "Nakamura M", + "Maeda K", + "Yamamoto K", + "Yamamura T", + "Sawada T", + "Ishikawa E", + "Kakushima N", + "Furukawa K", + "Iida T", + "Mizutani Y", + "Ishikawa T", + "Ohno E", + "Honda T", + "Ishigami M", + "Kawashima H" + ], + "bacteria": "Staphylococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5484253849506656, + "mesh_terms": [ + "Catheters", + "Colitis, Ulcerative", + "Humans", + "Intestinal Mucosa", + "Mucus", + "RNA, Ribosomal, 16S", + "Rectum" + ], + "raw_abstract": "BACKGROUND: The pathophysiology of ulcerative colitis (UC) remains unclear, but early lesions on the colorectal mucosal surface may play an important role in its etiology. Intestinal mucus samples, including inner and outer layers, are collected by net or brush catheters, but the quality of the samples obtained by each method has not been fully investigated. OBJECTIVE: The purpose of this study was to compare the microbiome and protein content of intestinal mucus collected by net and brush catheters during colonoscopy. METHODS: Intestinal mucus samples from the lower rectum of 4 patients with UC were collected using a net catheter, a brush catheter, and intestinal fluid suction. Microbiome and protein content were analyzed using 16S rRNA gene sequencing and mass spectrometry. RESULTS: The patients demonstrated significant differences in microbiome alpha diversity (p < 0.05), but this difference was not observed between the sampling methods. Net catheter samples demonstrated higher total protein concentrations than brush catheter samples. The brush catheter group had more Lachnospira, a butyrate-producing bacterium, when compared to the net group. The brush catheter group also had more oral bacteria of Staphylococcus and Dialister in those with active phase when compared to the net group. CONCLUSIONS: Brush catheters are more likely to collect the intestinal mucus inner layer, whereas net catheters are more likely to collect larger samples that include the outer mucus layer, as well as the intestinal fluid. Two sampling methods with different types of collection of the mucosa may lead to different results among patients with mucosal vulnerabilities.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27239107", + "title": "Hydradenitis suppurativa and inflammatory bowel disease: An unusual, but existing association.", + "year": 2016, + "journal": "World journal of gastroenterology", + "authors": [ + "Principi M", + "Cassano N", + "Contaldo A", + "Iannone A", + "Losurdo G", + "Barone M", + "Mastrolonardo M", + "Vena GA", + "Ierardi E", + "Di Leo A" + ], + "bacteria": "Staphylococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5275023995204892, + "mesh_terms": [ + "Anti-Inflammatory Agents", + "Comorbidity", + "Genetic Predisposition to Disease", + "Hidradenitis", + "Humans", + "Immunosuppressive Agents", + "Inflammatory Bowel Diseases", + "Life Style", + "Prevalence", + "Prognosis", + "Risk Factors" + ], + "raw_abstract": "Inflammatory bowel disease (IBD) could be associated with several extra-intestinal manifestations (EIMs) involving musculoskeletal, hepatopancreatobiliary, ocular, renal, and pulmonary systems, as well as the skin. In the last years, hidradenitis suppurativa (HS) is acquiring an increasing interest. IBD, especially Crohn's disease (CD), is among the most reported associated diseases in HS patients. The aim of this paper is to give a brief overview of data showing a possible epidemiologic and pathogenetic association between IBD and HS. We performed a pooled-data analysis of four studies and pooled prevalence of HS in IBD patients was 12.8%, with a 95%CI of 11.7%-13.9%. HS was present in 17.3% of subjects with CD (95%CI: 15.5%-19.1%) and in 8.5% of UC patients (95%CI: 7.0%-9.9%). Some items, especially altered immune imbalance, are generally involved in IBD pathogenesis as well as invoked by HS. Smoking is one of the most relevant risk factors for both disorders, representing a predictor of their severity, despite, actually, there being a lack of studies analyzing a possible shared pathway. A role for inheritance in HS and CD pathogenesis has been supposed. Despite a genetic susceptibility having been demonstrated for both diseases, further studies are needed to investigate a genetic mutual route. Although the pathogenesis of IBD and HS is generally linked to alterations of the immune response, recent findings suggest a role for intestinal and skin microbiota, respectively. In detail, the frequent finding of Staphylococcus aureus and coagulase-negative staphylococci on HS cutaneous lesions suggests a bacterial involvement in disease pathogenesis. Moreover, microflora varies in the different cutaneous regions of the body and, consequently, two different profiles of HS patients have been identified on these bases. On the other hand, it is well-known that intestinal microbiota may be considered as \"the explosive mixture\" at the origin of IBD despite the exact relationship having not been completely clarified yet. A better comprehension of the role that some bacterial species play in the IBD pathogenesis may be essential to develop appropriate management strategies in the near future. A final point is represented by some similarities in the therapeutic management of HS and IBD, since they may be controlled by immunomodulatory drugs. In conclusion, an unregulated inflammation may cause the lesions typical of both HS and IBD, particularly when they coexist. However, this is still a largely unexplored field.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39187879", + "title": "Dynamic changes in the gut microbiota composition during adalimumab therapy in patients with ulcerative colitis: implications for treatment response prediction and therapeutic targets.", + "year": 2024, + "journal": "Gut pathogens", + "authors": [ + "Oh HN", + "Shin SY", + "Kim JH", + "Baek J", + "Kim HJ", + "Lee KM", + "Park SJ", + "Kim SY", + "Choi HK", + "Kim W", + "Sul WJ", + "Choi CH" + ], + "bacteria": "Staphylococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.48961183067760716, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: While significant research exists on gut microbiota changes after anti-tumor necrosis factor-alpha (anti TNF-\u03b1) therapy for ulcerative colitis, little is known about the longitudinal changes related to the effects of anti TNF-\u03b1. This study aimed to investigate the dynamics of gut microbiome changes during anti TNF-\u03b1 (adalimumab) therapy in patients with ulcerative colitis (UC). RESULTS: The microbiota composition was affected by the disease severity and extent in patients with UC. Regardless of clinical remission status at each time point, patients with UC exhibited microbial community distinctions from healthy controls. Distinct amplicon sequence variants (ASVs) differences were identified throughout the course of Adalimumab (ADA) treatment at each time point. A notable reduction in gut microbiome dissimilarity was observed only in remitters. Remitters demonstrated a decrease in the relative abundances of Burkholderia-Caballeronia-Paraburkholderia and Staphylococcus as the treatment progressed. Additionally, there was an observed increase in the relative abundances of Bifidobacterium and Dorea. Given the distribution of the 48 ASVs with high or low relative abundances in the pre-treatment samples according to clinical remission at week 8, a clinical remission at week 8 with a sensitivity and specificity of 72.4% and 84.3%, respectively, was predicted on the receiver operating characteristic curve (area under the curve, 0.851). CONCLUSIONS: The gut microbiota undergoes diverse changes according to the treatment response during ADA treatment. These changes provide insights into predicting treatment responses to ADA and offer new therapeutic targets for UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "25554637", + "title": "Red Ginseng and Semen Coicis can improve the structure of gut microbiota and relieve the symptoms of ulcerative colitis.", + "year": 2015, + "journal": "Journal of ethnopharmacology", + "authors": [ + "Guo M", + "Ding S", + "Zhao C", + "Gu X", + "He X", + "Huang K", + "Luo Y", + "Liang Z", + "Tian H", + "Xu W" + ], + "bacteria": "Staphylococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.42126340347186936, + "mesh_terms": [ + "Animals", + "Bacteria", + "Coix", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Panax", + "Plant Extracts", + "Probiotics", + "Rats, Wistar" + ], + "raw_abstract": "ETHNOPHARMACOLOGICAL RELEVANCE: Many Chinese herbs are traditionally used as medicine to improve the functions of gastrointestinal tract. Some of these herbs are also promising agents for the improvement of the gut microbiota and the treatment of ulcerative colitis. MATERIALS AND METHODS: By screening seven traditional Chinese herbs, we found that Red Ginseng and Semen Coicis were the most effective in promoting the growth of probiotics including Lactobacillus and Bifidobacterium in vitro. We then evaluated the effects of Red Ginseng and Semen Coicis on the growth of the bacterial pathogens (Escherichia coli, Staphylococcus aureus, and Salmonella spp.) in vitro. In in vivo experiment, we gavage administrated trinitro-benzene-sulfonic acid induced ulcerative colitis (UC) rats with Red Ginseng and Semen Coicis extracts. After two weeks treatment, we analyzed the structure of the gut microbiota and examined the UC symptoms by employing qPCR and animal pathology detection techniques. RESULTS: Both Red Ginseng and Semen Coicis promoted the growth of probiotics - Bifidobacterium and Lactobacillus in vitro. Red Ginseng also inhibited the growth of some pathogen strains. In vivo, Red Ginseng and Semen Coicis improved the structure of gut microbiota and relieved the symptoms of ulcerative colitis in vivo. Compared with Semen Coicis, Red Ginseng was more effective in relieving the symptoms of ulcerative colitis. CONCLUSIONS: Red Ginseng could promote the growth of probiotic bacteria in vitro. Red Ginseng and, to a lesser extent Semen Coicis, gave positive results in an experimental in vivo model for ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34627158", + "title": "Stool preparation under anaerobic conditions contributes to retention of obligate anaerobes: potential improvement for fecal microbiota transplantation.", + "year": 2021, + "journal": "BMC microbiology", + "authors": [ + "Shimizu H", + "Arai K", + "Asahara T", + "Takahashi T", + "Tsuji H", + "Matsumoto S", + "Takeuchi I", + "Kyodo R", + "Yamashiro Y" + ], + "bacteria": "Staphylococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.23346626192971684, + "mesh_terms": [ + "Anaerobiosis", + "Bacteria, Anaerobic", + "Fecal Microbiota Transplantation", + "Feces", + "Humans", + "RNA, Ribosomal, 16S", + "RNA, Ribosomal, 23S", + "Specimen Handling" + ], + "raw_abstract": "BACKGROUND: Fecal microbiota transplantation (FMT) in patients with ulcerative colitis has shown variable efficacy depending on the protocol used. A previous randomized controlled trial reported that anaerobic preparation of donor stool contributes to improved efficacy. Despite the suggestion that viable obligate anaerobes would be decreased through aerobic handling, there have been only a limited number of reports on how these aerobic or anaerobic procedures affect the composition of viable microbiota in the fecal slurries used for FMT. METHODS: We adopted 16S and 23S rRNA-targeted reverse transcription-quantitative polymerase chain reaction to quantify viable bacteria in fecal slurries. This study utilized specific primers designed to detect obligate anaerobes (including Clostridium coccoides group, C. leptum subgroup, Bacteroides fragilis group, Bifidobacterium, Atopobium cluster, and Prevotella) and facultative anaerobes (including total lactobacilli, Enterobacteriaceae, Enterococcus, Streptococcus, and Staphylococcus). We then calculated the ratio change (RC) between before and after mixing, and compared the resulting values between anaerobic-prep and aerobic-prep in samples fixed immediately after blending (RC RESULTS: For most obligate anaerobes, the median RC tended to be less than 1, indicating that the number of obligate anaerobes was decreased by the blending procedure. However, in samples maintained for 1\u2009h after blending, anaerobic-prep counteracted the decrease otherwise seen for the C. coccoides group and B. fragilis groups (P\u2009<\u20090.01 for both). The C. leptum subgroup also tended to show higher RC by anaerobic-prep than by aerobic-prep, although this effect was not statistically significant. Among facultative anaerobes, Enterobacteriaceae, Enterococcus, and Staphylococcus showed median RC values of more than 1, indicating that these organisms survived and even grew after mixing. Moreover, oxygen exposure had no significant influence on the survival of the facultative anaerobes. CONCLUSIONS: The conditions under which the blending procedure was performed affected the proportion of live anaerobes in fecal slurries. The obligate anaerobes tended to be decreased by blending processes, but anaerobic-prep significantly mitigated this effect. Anaerobic-prep may improve the efficacy of FMT by permitting the efficient transfer of obligate anaerobes to patients with ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39162211", + "title": "Washed microbiota transplantation improved the level of serum vitamin D in ulcerative colitis.", + "year": 2024, + "journal": "Journal of gastroenterology and hepatology", + "authors": [ + "Zhang H", + "Xiao Y", + "Wen Q", + "Zhang S", + "Li P", + "Marcella C", + "Hu B", + "Liu H", + "Zhang F", + "Cui B" + ], + "bacteria": "Dorea", + "condition": "ulcerative colitis", + "relevance_score": 0.6678350507553527, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Male", + "Vitamin D", + "Female", + "Adult", + "Fecal Microbiota Transplantation", + "Middle Aged", + "Receptors, Calcitriol", + "Gastrointestinal Microbiome", + "Vitamin D Deficiency", + "Treatment Outcome", + "Mesalamine" + ], + "raw_abstract": "BACKGROUND AND AIM: Vitamin D (VD) deficiency was reported to correlate with ulcerative colitis (UC) activity, which might be closely related to gut microbiota dysbiosis. This study aims to investigate the effects of washed microbiota transplantation (WMT) on VD metabolism in UC. METHODS: The serum levels of 25-hdroxyvitamin D [25(OH)D] in 121 patients with UC and 53 healthy controls (HC) were detected. Subsequently, a non-randomized control trial (non-RCT) was conducted. Patients with UC were non-randomly assigned to undergo WMT (n\u00a0=\u00a028) vs. conventional treatment (5-aminosalicylic acid, 5-ASA, n\u00a0=\u00a010). Serum levels of 25(OH)D, fecal microbiota, and the expression of vitamin D receptor (VDR) in patients with UC were evaluated with a 3-month follow-up. RESULTS: Serum VD levels collected in the clinic practice indicated that patients with UC had significantly lower VD levels than HC (P\u00a0<\u00a00.001). In the non-RCT, serum 25(OH)D level and VDR expression significantly increased (P\u00a0=\u00a00.011, 0.026, respectively) in the WMT group, while no noticeable changes were observed in the non-WMT group. Microbiome profiling revealed that the increase in VD levels after WMT was positively associated with the abundances of Adlercreutzia_equolifaciens, Ruminococcus_obeum, and Dorea but negatively correlated with Escherichia. CONCLUSIONS: The study suggested that WMT increases the levels of VD with characteristic changes of specific microbiota, which indicated the association between the VD and the activity of UC might be regulated by gut microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39126385", + "title": "Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis.", + "year": 2025, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Jangi S", + "Zhao N", + "Hsia K", + "Park YS", + "Michaud DS", + "Yoon H" + ], + "bacteria": "Dorea", + "condition": "ulcerative colitis", + "relevance_score": 0.5505885116520582, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Male", + "Adult", + "Female", + "Prospective Studies", + "Middle Aged", + "Clostridiales", + "Candida", + "Republic of Korea", + "Feces" + ], + "raw_abstract": "BACKGROUND AND AIMS: While there is increasing interest in microbiome-directed therapies for patients with ulcerative colitis (UC), the identification of microbial targets remains elusive, underlining the need for novel approaches. METHODS: Utilizing metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation, we used a tree-based dichotomous approach to assemble distinct clusters of species-level bacterial co-abundance groups (CAGs). We evaluated the abundance of bacterial CAGs and fungal taxa during remission (n\u2005=\u2005166) and activity (n\u2005=\u200546). We examined if the bacterial CAGs identified in our cohorts were conserved in 2 healthy cohorts and a Korean UC cohort. RESULTS: CAG3 and CAG8, dominated by bacteria from the family Lachnospiraceae, were associated with remission. Low abundance of CAG8 and elevated abundance of Candida genus were predictive of active UC. Constituents from CAG8 were influential hub species of the remission-associated microbial UC network, including Ruminococcus gnavus, Erysipelatoclostridium ramosum, Blautia, and Dorea species. These hub species interactions were preserved in 2 healthy cohorts and were partially recapitulated in a Korean UC cohort. CAG8 abundance correlated with the secondary bile acid production pathway. Bacterial CAGs did not correlate with Candida; however, Bifidobacterium adolescentis and Alistipes putredinis were negatively associated with Candida. CONCLUSIONS: Lachnospiraceae-dominated bacterial CAGs were associated with remission in UC, with key bacterial interactions within the CAG also observed in 2 healthy cohorts and a Korean UC cohort. Bacterial CAG-based analyses may aid in designing candidate consortia for microbiome-based therapeutics.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Dorea", + "condition": "ulcerative colitis", + "relevance_score": 0.505491338085921, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39187879", + "title": "Dynamic changes in the gut microbiota composition during adalimumab therapy in patients with ulcerative colitis: implications for treatment response prediction and therapeutic targets.", + "year": 2024, + "journal": "Gut pathogens", + "authors": [ + "Oh HN", + "Shin SY", + "Kim JH", + "Baek J", + "Kim HJ", + "Lee KM", + "Park SJ", + "Kim SY", + "Choi HK", + "Kim W", + "Sul WJ", + "Choi CH" + ], + "bacteria": "Dorea", + "condition": "ulcerative colitis", + "relevance_score": 0.48961183067760716, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: While significant research exists on gut microbiota changes after anti-tumor necrosis factor-alpha (anti TNF-\u03b1) therapy for ulcerative colitis, little is known about the longitudinal changes related to the effects of anti TNF-\u03b1. This study aimed to investigate the dynamics of gut microbiome changes during anti TNF-\u03b1 (adalimumab) therapy in patients with ulcerative colitis (UC). RESULTS: The microbiota composition was affected by the disease severity and extent in patients with UC. Regardless of clinical remission status at each time point, patients with UC exhibited microbial community distinctions from healthy controls. Distinct amplicon sequence variants (ASVs) differences were identified throughout the course of Adalimumab (ADA) treatment at each time point. A notable reduction in gut microbiome dissimilarity was observed only in remitters. Remitters demonstrated a decrease in the relative abundances of Burkholderia-Caballeronia-Paraburkholderia and Staphylococcus as the treatment progressed. Additionally, there was an observed increase in the relative abundances of Bifidobacterium and Dorea. Given the distribution of the 48 ASVs with high or low relative abundances in the pre-treatment samples according to clinical remission at week 8, a clinical remission at week 8 with a sensitivity and specificity of 72.4% and 84.3%, respectively, was predicted on the receiver operating characteristic curve (area under the curve, 0.851). CONCLUSIONS: The gut microbiota undergoes diverse changes according to the treatment response during ADA treatment. These changes provide insights into predicting treatment responses to ADA and offer new therapeutic targets for UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33154436", + "title": "Mucosal microbiota and gene expression are associated with long-term remission after discontinuation of adalimumab in ulcerative colitis.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Sakurai T", + "Nishiyama H", + "Sakai K", + "De Velasco MA", + "Nagai T", + "Komeda Y", + "Kashida H", + "Okada A", + "Kawai I", + "Nishio K", + "Ogata H", + "Kudo M" + ], + "bacteria": "Dorea", + "condition": "ulcerative colitis", + "relevance_score": 0.3808495908905304, + "mesh_terms": [ + "Adalimumab", + "Adolescent", + "Adult", + "Anti-Inflammatory Agents", + "Colitis, Ulcerative", + "Female", + "Gastrointestinal Microbiome", + "Gene Expression", + "Humans", + "Intestinal Mucosa", + "Male", + "Middle Aged", + "Remission Induction", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "Given that sustained remission is the ultimate treatment goal in the management of patients with ulcerative colitis (UC), the decision to stop anti-tumor necrosis factor (anti-TNF) treatment in UC patients is difficult. The aim of this study was to evaluate mucosal microbiota and gene expression profiles associated with long-term remission after discontinuation of anti-TNF therapy. In nine UC patients who received anti-TNF therapy for 6\u00a0months, microbiota isolated from uninflamed mucosae and gene expression in inflamed and uninflamed mucosae were investigated at week 0 and at week 24. At treatment initiation, Fusobacterium sp. and Veillonella dispar were over-represented in the relapse group compared with the non-relapse group. After treatment, Dorea sp. and Lachnospira sp. were over-represented in the non-relapse group. In the relapse group only, a significant shift in gut bacterial community composition was found between week 0 and week 24. Gene expression of ALIX (PDCD6IP) and SLC9A3 was significantly higher in the non-relapse group than in the relapse group. Lastly, we used machine learning methods to identify relevant gene signatures associated with sustained remission. Statistical analyses of microbiota and expression profiles revealed differences between UC patients who did or did not keep remission after the discontinuation of TNF inhibitors.Trial registration: UMIN000020785: Evaluation of adalimumab therapy in mesalazine-resistant or -intolerant ulcerative colitis; an observational study (EARLY study).", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39030520", + "title": "Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Joo M", + "Nam S" + ], + "bacteria": "Dorea", + "condition": "ulcerative colitis", + "relevance_score": 0.3668337016421349, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Adolescent", + "RNA, Ribosomal, 16S", + "Obesity", + "Female", + "Male", + "Bacteria", + "Phylogeny", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Colitis, Ulcerative", + "Dysbiosis", + "Prevotella", + "Faecalibacterium prausnitzii", + "Feces" + ], + "raw_abstract": "BACKGROUND: Recently, there has been an increase in the number of studies focusing on the association between the gut microbiome and obesity or inflammatory diseases, especially in adults. However, there is a lack of studies investigating the association between gut microbiome and gastrointestinal (GI) diseases in adolescents. METHOD: We obtained 16S rRNA-seq datasets for gut microbiome analysis from 202 adolescents, comprising ulcerative colitis (UC), Crohn's disease (CD), obesity (Ob), and healthy controls (HC). We utilized Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to acquire Operational Taxonomic Units (OTUs). Subsequently, we analyzed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) terms and pathway enrichment for the identified OTUs. RESULTS: In this study, we investigated the difference between the gut microbiomes in adolescents with GI diseases and those in healthy adolescents using 202 samples of 16S rRNA sequencing data. The distribution of the six main gut microbiota (i.e., unclassified Dorea, unclassified Lachnospiraceae, unclassified Ruminococcus, Faecalibacterium prausnitzii, Prevotella copri, unclassified Sutterella) was different based on the status of obesity and inflammatory diseases. Dysbiosis was observed within Lachnospiraceae in adolescents with inflammatory diseases (i.e., UC and CD), and in adolescents with obesity within Prevotella and Sutterella. More specifically, our results showed that the relative abundance of Faecalibacterium prausnitzii and unclassified Lachnospiraceae was more than 10% and 8% higher, respectively, in the UC group compared to the CD, Ob, and HC groups. Additionally, the Ob group had over 20% and over 3% higher levels of Prevotella copri and unclassified Sutterella, respectively, compared to the UC, CD, and HC groups. Also, inspecting associations between the six specific microbiota and KO terms, we found that the six microbiota -relating KO terms were associated with NOD-like receptor signaling. These six taxa differences may affect the immune system and inflammatory response by affecting NOD-like receptor signaling in the host during critical adolescence. CONCLUSION: In this study, we discovered that dysbiosis of the microbial community had varying degrees of influence on the inflammatory and immune response pathways in adolescents with inflammatory diseases and obesity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37208257", + "title": "Gut microbial signatures and their functions in Behcet's uveitis and Vogt-Koyanagi-Harada disease.", + "year": 2023, + "journal": "Journal of autoimmunity", + "authors": [ + "Wang Q", + "Wu S", + "Ye X", + "Tan S", + "Huang F", + "Su G", + "Kijlstra A", + "Yang P" + ], + "bacteria": "Dorea", + "condition": "ulcerative colitis", + "relevance_score": 0.3331995663173413, + "mesh_terms": [ + "Humans", + "Uveomeningoencephalitic Syndrome", + "Leukocytes, Mononuclear", + "Gastrointestinal Microbiome", + "Uveitis", + "Behcet Syndrome" + ], + "raw_abstract": "BACKGROUND: A number of public metagenomic studies reveal an association between the gut microbiome and various immune-mediated diseases including Behcet's uveitis (BU) and Vogt-Koyanagi-Harada disease (VKH). Integrated-analysis and subsequent validation of these results could be a potentially powerful way to understand the microbial signatures and their functions in these two uveitis entities. METHODS: We integrated the sequencing data of our previous metagenomic studies on two major uveitis entities, BU and VKH as well as four other publicly available immune-mediated diseases datasets, including Ankylosing Spondylitis (AS), Rheumatoid Arthritis (RA), Crohn's disease (CD) and Ulcerative Colitis (UC). Alpha-diversity and beta-diversity analysis were used to compare the gut microbiome signatures between both uveitis entities and other immune-mediated diseases and healthy controls. Amino acid homology between microbial proteins and a uveitogenic peptide of the interphotoreceptor retinoid-binding protein (IRBP) RESULTS: Depleted Dorea, Blautia, Coprococcus, Erysipelotrichaceae and Lachnospiraceae as well as enriched Bilophila and Stenotrophomonas were identified in BU patients. An enriched Alistipes along with a lower level of Dorea were observed in VKH patients. A peptide antigen (SteTDR) encoded by BU specifically enriched Stenotrophomonas was identified to share homology with IRBP CONCLUSIONS: Our study revealed specific gut microbial signatures and their potentially functional roles in BU and VKH pathogenesis that differ significantly from other immune-mediated diseases as well as healthy controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37951857", + "title": "Diagnosis of Crohn's disease and ulcerative colitis using the microbiome.", + "year": 2023, + "journal": "BMC microbiology", + "authors": [ + "Kang DY", + "Park JL", + "Yeo MK", + "Kang SB", + "Kim JM", + "Kim JS", + "Kim SY" + ], + "bacteria": "Pantoea", + "condition": "ulcerative colitis", + "relevance_score": 0.6672330191158602, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Crohn Disease", + "Inflammatory Bowel Diseases", + "Gastrointestinal Microbiome", + "Bacteria", + "Biomarkers" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is a multifactorial chronic inflammatory disease resulting from dysregulation of the mucosal immune response and gut microbiota. Crohn's disease (CD) and ulcerative colitis (UC) are difficult to distinguish, and differential diagnosis is essential for establishing a long-term treatment plan for patients. Furthermore, the abundance of mucosal bacteria is associated with the severity of the disease. This study aimed to differentiate and diagnose these two diseases using the microbiome and identify specific biomarkers associated with disease activity. RESULTS: Differences in the abundance and composition of the microbiome between IBD patients and healthy controls (HC) were observed. Compared to HC, the diversity of the gut microbiome in patients with IBD decreased; the diversity of the gut microbiome in patients with CD was significantly lower. Sixty-eight microbiota members (28 for CD and 40 for UC) associated with these diseases were identified. Additionally, as the disease progressed through different stages, the diversity of the bacteria decreased. The abundances of Alistipes shahii and Pseudodesulfovibrio aespoeensis were negatively correlated with the severity of CD, whereas the abundance of Polynucleobacter wianus was positively correlated. The severity of UC was negatively correlated with the abundance of A. shahii, Porphyromonas asaccharolytica and Akkermansia muciniphilla, while it was positively correlated with the abundance of Pantoea candidatus pantoea carbekii. A regularized logistic regression model was used for the differential diagnosis of the two diseases. The area under the curve (AUC) was used to examine the performance of the model. The model discriminated UC and CD at an AUC of 0.873 (train set), 0.778 (test set), and 0.633 (validation set) and an area under the precision-recall curve (PRAUC) of 0.888 (train set), 0.806 (test set), and 0.474 (validation set). CONCLUSIONS: Based on fecal whole-metagenome shotgun (WMS) sequencing, CD and UC were diagnosed using a machine-learning predictive model. Microbiome biomarkers associated with disease activity (UC and CD) are also proposed.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38608475", + "title": "Turtle peptide and its derivative peptide ameliorated DSS-induced ulcerative colitis by inhibiting inflammation and modulating the composition of the gut microbiota.", + "year": 2024, + "journal": "International immunopharmacology", + "authors": [ + "Guo HX", + "Wang BB", + "Wu HY", + "Feng HY", + "Zhang HY", + "Gao W", + "Yuan B" + ], + "bacteria": "Prevotellaceae_UCG-001", + "condition": "ulcerative colitis", + "relevance_score": 0.738520183736057, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Dextran Sulfate", + "Mice", + "Peptides", + "Anti-Inflammatory Agents", + "Turtles", + "Male", + "Mice, Inbred C57BL", + "Toll-Like Receptor 4", + "NF-kappa B", + "Disease Models, Animal", + "Intestinal Mucosa", + "Colon", + "Humans", + "Oxidative Stress", + "Signal Transduction" + ], + "raw_abstract": "Ulcerative colitis (UC) is a recurrent intestinal disease with an increasing incidence worldwide that seriously affects the life of patients. Turtle peptide (TP) is a bioactive peptide extracted from turtles that has anti-inflammatory, antioxidant and anti-aging properties. However, studies investigating the effect of TP on the progression of UC are lacking. The aim of this study was to investigate effects and underlying mechanisms of TP and its derivative peptide GPAGPIGPV (GP-9) in alleviating UC in mice. The results showed that 500\u00a0mg/kg TP treatment significantly ameliorated colitis symptoms and oxidative stress in UC mice. TP alleviated intestinal barrier damage in UC mice by promoting mucosal repair and increasing the expression of tight junction proteins (ZO1, occludin and claudin-1). TP also modulated the composition of the gut microbiota by increasing the abundance of the beneficial bacteria Anaerotignum, Prevotellaceae_UCG-001, Alistipes, and Lachno-spiraceae_NK4A136_group and decreasing the abundance of the harmful bacteria Prevotella_9 and Parasutterella. Furthermore, we characterized the peptide composition of TP and found that GP-9 ameliorated the symptoms of dextran sodium sulfate (DSS)-induced colitis in mice by inhibiting the TLR4/NF-\u03baB signaling pathway. In conclusion, TP and its derivative peptides ameliorated DSS-induced ulcerative colitis by inhibiting the expression of inflammatory factors and modulating the composition of the intestinal microbiota; this study provides a theoretical basis for the application of TP and its derivative peptides for their anti-inflammatory activity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37295481", + "title": "Quantitative analysis of the three gut microbiota in UC and non-UC patients using real-time PCR.", + "year": 2023, + "journal": "Microbial pathogenesis", + "authors": [ + "Al-Bayati L", + "Nayeri Fasaei B", + "Merat S", + "Bahonar A", + "Ghoddusi A" + ], + "bacteria": "Peptostreptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7578967536905448, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Real-Time Polymerase Chain Reaction", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Feces" + ], + "raw_abstract": "BACKGROUND: and study aims: Gastrointestinal microbiota are closely related to the pathogenesis of ulcerative colitis (UC). This study aimed at quantification of F. prausnitzii, Provetella, and Peptostreptococcus in UC and non-UC patients using Real-Time PCR and a new set of primers were also validated for this purpose. MATERIALS AND METHODS: In this study, the relative abundance of microbial populations between the UC and non-UC subjects were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR). DNA extraction from biopsies and polymerase chain reaction (PCR) amplification of bacterial 16S rRNA gene-targeted species-specific primers was performed to detect the anaerobic bacterial species. The qRT-PCR was used to show the relative change in the bacterial populations of F. prausnitzii, Provetella, and Peptostreptococcus in the UC and non-UC subjects. RESULTS: Our data for detection of the anaerobic intestinal flora showed Faecalibacterium prausnitzii, Provetella and Peptostreptococcus were the predominant microflora in the controls and showed significant differences (p\u00a0=\u00a00.002, 0.025 and 0.039, respectively). The qRT-PCR analyses of F. prausnitzii, Provetella and Peptostreptococcus were 8.69-, 9.38- and 5.77-higher, respectively, in the control group than in the UC group. CONCLUSION: The results of this study showed decreased abundance of F. prausnitzii, Provetella and Peptostreptococcus in the intestine of UC patients in comparison to non-UC patients. Quantitative RT-PCR, as a progressive and sensitive method, could be useful for evaluation of bacterial populations in patients with inflammatory bowel diseases to attain appropriate therapeutic strategies.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28852861", + "title": "Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.", + "year": 2018, + "journal": "Journal of gastroenterology", + "authors": [ + "Nishino K", + "Nishida A", + "Inoue R", + "Kawada Y", + "Ohno M", + "Sakai S", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Kawahara M", + "Naito Y", + "Andoh A" + ], + "bacteria": "Peptostreptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6838575411226454, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Endoscopy, Gastrointestinal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. METHODS: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. RESULTS: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. \u03b1-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. CONCLUSIONS: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26994772", + "title": "Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India.", + "year": 2016, + "journal": "Journal of gastroenterology", + "authors": [ + "Kedia S", + "Rampal R", + "Paul J", + "Ahuja V" + ], + "bacteria": "Peptostreptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6830925576201456, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Dysentery, Amebic", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "India", + "Intestinal Mucosa" + ], + "raw_abstract": "The disease profile in the Indian population provides a unique opportunity for studying the host microbiome interaction in both infectious (amebiasis) and autoimmune diseases\u00a0like inflammatory bowel disease (IBD) from a similar environment and genetic background. Analysis of fecal samples from untreated amebic liver abscess (ALA) patients, Entamoeba histolytica (Eh)-negative and -positive asymptomatic individuals, and pus samples from naive ALA patients revealed a significant reduction in Lactobacillus in asymptomatic individuals (Eh +ve) and ALA patients. Two anaerobic genera, namely Bacteroides and Peptostreptococcus, were detected in naive ALA pus samples. Analysis of fecal samples from amoebic colitis patients showed a significant decline in population of Bacteroides, Clostridium coccoides and leptum subgroup, Lactobacillus, Campylobacter, and Eubacterium, whereas a significant increase in Bifidobacterium was observed. Mucosa-associated bacterial flora analysis from IBD patients and healthy controls revealed a significant difference in concentration of bacteria among predominating and subdominating genera between ulcerative colitis (UC), Crohn's disease (CD) patients, and controls. In contrast to the mucosal studies, we found a significant increase in lactobacilli population in fecal samples of active UC patients. Another study revealed a significant decrease of Clostridium coccoides and leptum clusters in fecal samples of active UC patients along with decreased concentrations of fecal SCFAs, especially of n-butyrate, iso-butyrate, and acetate. We therefore found similar perturbations in gut microbiome in both infectious and autoimmune diseases, indicating inflammation to be the major driver for changes in gut microbiome.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30634855", + "title": "Longitudinal Analyses of Gut-Associated Bacterial Microbiota in Ulcerative Colitis Patients.", + "year": 2018, + "journal": "Archives of Iranian medicine", + "authors": [ + "Al-Bayati L", + "Nayeri Fasaei B", + "Merat S", + "Bahonar A" + ], + "bacteria": "Peptostreptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5756596598115389, + "mesh_terms": [ + "Adult", + "Bacteria, Aerobic", + "Bacteria, Anaerobic", + "Case-Control Studies", + "Colitis, Ulcerative", + "Colonoscopy", + "DNA, Bacterial", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Iran", + "Longitudinal Studies", + "Male", + "Middle Aged", + "Polymerase Chain Reaction", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "BACKGROUND: The normal colonic microbiota is associated with the etiology of ulcerative colitis (UC). Several bacterial species are associated with the initiation and amplification of disease process. However, the etiology and mechanism of UC are poorly understood. The present study aimed to investigate, characterize, and compare the main composition of the mucosa-associated intestinal microflora in colonoscopic biopsy specimens of UC and non-UC patients. METHODS: Aerobic and facultative-anaerobic mucosa-associated bacteria were isolated and diagnosed from colonoscopic biopsy specimens of 40 UC patients and 40 patients without UC. Patients were selected as control from the same centers and colonoscopy was carried out for other reasons (mainly colorectal screening). Isolation and characterization for aerobic and facultative-anaerobic intestinal bacteria were carried out by conventional culture techniques. DNA extraction from biopsies and polymerase chain reaction (PCR) amplification of bacterial 16S rRNA with gene-targeted and species-specific primers was performed for detection of anaerobic bacterial species. RESULTS: Several species of mucosa-associated aerobic and facultative anaerobic bacteria were found in biopsy specimens and there were no significant differences between UC patients and non-UC patients. Our investigation for detection of the anaerobic intestinal flora showed Faecalibacterium prausnitzii, Prevotella, and Peptostreptococcus productus were the predominant microflora in controls and have significant differences (P = 0.002, 0.025 and 0.039, respectively). CONCLUSION: This is the first investigation of the intestinal mucosa-associated microflora in patients with UC in Iran. These results, although limited by sample size, allow a better understanding of changes in mucosa-associated bacterial flora in these patients, showing that decrease of Faecalibacterium prausnitzii, Provetella, and Peptostreptococcus productus in the intestinal tract may translate into a reduction in the important role of this beneficial bacterial species, which can lead to reduced protection of the gut mucosa and UC development.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Peptostreptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.47549133808592103, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31501882", + "title": "IL-13 mRNA Tissue Content Identifies Two Subsets of Adult Ulcerative Colitis Patients With Different Clinical and Mucosa-Associated Microbiota Profiles.", + "year": 2020, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Butera A", + "Di Paola M", + "Vitali F", + "De Nitto D", + "Covotta F", + "Borrini F", + "Pica R", + "De Filippo C", + "Cavalieri D", + "Giuliani A", + "Pronio A", + "Boirivant M" + ], + "bacteria": "Acidaminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.44207373116043497, + "mesh_terms": [ + "Acidaminococcus", + "Colitis, Ulcerative", + "Colon", + "Correlation of Data", + "Female", + "Humans", + "Interleukin-13", + "Intestinal Mucosa", + "Male", + "Medication Therapy Management", + "Middle Aged", + "Patient Selection", + "Prevotella", + "RNA, Messenger", + "RNA, Ribosomal, 16S", + "Severity of Illness Index" + ], + "raw_abstract": "BACKGROUND AND AIMS: A personalized approach to therapy hold great promise to improve disease outcomes. To this end, the identification of different subsets of patients according to the prevalent pathogenic process might guide the choice of therapeutic strategy. We hypothesize that ulcerative colitis [UC] patients might be stratified according to distinctive cytokine profiles and/or to a specific mucosa-associated microbiota. METHODS: In a cohort of clinically and endoscopic active UC patients and controls, we used quantitative PCR to analyse the mucosal cytokine mRNA content and 16S rRNA gene sequencing to assess the mucosa-associated microbiota composition. RESULTS: We demonstrate, by means of data-driven approach, the existence of a specific UC patient subgroup characterized by elevated IL-13 mRNA tissue content separate from patients with low IL-13 mRNA tissue content. The two subsets differ in clinical-pathological characteristics. High IL-13 mRNA patients are younger at diagnosis and have a higher prevalence of extensive colitis than low IL-13 mRNA patients. They also show more frequent use of steroid/immunosuppressant/anti-tumour necrosis factor \u03b1 therapy during 1 year of follow-up. The two subgroups show differential enrichment of mucosa-associated microbiota genera with a prevalence of Prevotella in patients with high IL-13 mRNA tissue content and Sutterella and Acidaminococcus in patients with low IL-13 mRNA tissue content. CONCLUSION: Assessment of mucosal IL-13 mRNA might help in the identification of a patient subgroup that might benefit from a therapeutic approach modulating IL-13. PODCAST: This article has an associated podcast which can be accessed at https://academic.oup.com/ecco-jcc/pages/podcast.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37161967", + "title": "Current insight into enteropathogens in flare-up ulcerative colitis. An observational study.", + "year": 2023, + "journal": "European journal of gastroenterology & hepatology", + "authors": [ + "Hassan EA", + "Abdel Rehim ASE", + "Ahmed AO", + "Salim SMAE", + "Soliman AMA", + "Rashed HG", + "Abd El-Kareem DM" + ], + "bacteria": "Raoultella", + "condition": "ulcerative colitis", + "relevance_score": 0.5759321567921674, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Escherichia coli", + "Cryptosporidiosis", + "Feces", + "Cryptosporidium", + "Bacteria", + "Anti-Infective Agents" + ], + "raw_abstract": "OBJECTIVE: Incidence of ulcerative colitis is globally increased. Enteric infections and their role in ulcerative colitis flares present a common health problem and a unique clinical challenge. We aimed to identify enteropathogens in flared ulcerative colitis patients and their antimicrobial susceptibilities and relation with the disease activity. METHODS: Stool samples were collected from 95 patients with ulcerative colitis (17 inactive cases and 78 active cases) according to the Mayo score assessment of ulcerative colitis severity. Enteropathogens were examined using an automated VITEK2 system and FilmArray gastrointestinal pathogen panel. RESULTS: Enteric infections were found in 81 patients (85.3%) with a significantly higher percentage in active ulcerative colitis (96.2% vs. 35.3%, P \u2005<\u20050.001). In 78 symptomatic patients, (78.7%) of bacteria as enteroaggregative and enteropathogenic E. coli , (11.5%) parasitic as Cryptosporidium and (7.7%) viral as Norovirus were the most detected microbial pathogens. Mixed, multidrug-resistant organisms (MDROs) and opportunistic infections were reported in 70.7%, 52.9% and 46.7% respectively. Raoultella ornithinolytica was reported for the first time as an enteropathogen in ulcerative colitis flare. Multiple organisms, MDROs, extended-spectrum beta-lactamases-producing and AmpC-resistant bacteria were significantly associated with disease severity. CONCLUSION: Identifying enteropathogens especially opportunistic and MDR organisms as a cause of ulcerative colitis flare-ups is a matter of worry increasing their diagnostic and therapeutic burden. Periodic studies evaluating changes in microbial profiles and their antimicrobial susceptibilities are needed to achieve antibiotic stewardship and improve management.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30545401", + "title": "A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?", + "year": 2018, + "journal": "Microbiome", + "authors": [ + "Forbes JD", + "Chen CY", + "Knox NC", + "Marrie RA", + "El-Gabalawy H", + "de Kievit T", + "Alfa M", + "Bernstein CN", + "Van Domselaar G" + ], + "bacteria": "Faecalicoccus", + "condition": "ulcerative colitis", + "relevance_score": 0.25943121788946266, + "mesh_terms": [ + "Adult", + "Arthritis, Rheumatoid", + "Bacteria", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "DNA, Bacterial", + "DNA, Ribosomal", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Machine Learning", + "Male", + "Metagenomics", + "Middle Aged", + "Multiple Sclerosis", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "BACKGROUND: Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology is common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of the gut microbiome in IMIDs. This study used 16S rRNA gene amplicon sequencing to compare the gut microbiota of patients with Crohn's disease (CD; N\u2009=\u200920), ulcerative colitis (UC; N\u2009=\u200919), multiple sclerosis (MS; N\u2009=\u200919), and rheumatoid arthritis (RA; N\u2009=\u200921) versus healthy controls (HC; N\u2009=\u200923). Biological replicates were collected from participants within a 2-month interval. This study aimed to identify common (or unique) taxonomic biomarkers of IMIDs using both differential abundance testing and a machine learning approach. RESULTS: Significant microbial community differences between cohorts were observed (pseudo F\u2009=\u20094.56; p\u2009=\u20090.01). Richness and diversity were significantly different between cohorts (pFDR <\u20090.001) and were lowest in CD while highest in HC. Abundances of Actinomyces, Eggerthella, Clostridium III, Faecalicoccus, and Streptococcus (pFDR <\u20090.001) were significantly higher in all disease cohorts relative to HC, whereas significantly lower abundances were observed for Gemmiger, Lachnospira, and Sporobacter (pFDR <\u20090.001). Several taxa were found to be differentially abundant in IMIDs versus HC including significantly higher abundances of Intestinibacter in CD, Bifidobacterium in UC, and unclassified Erysipelotrichaceae in MS and significantly lower abundances of Coprococcus in CD, Dialister in MS, and Roseburia in RA. A machine learning approach to classify disease versus HC was highest for CD (AUC\u2009=\u20090.93 and AUC\u2009=\u20090.95 for OTU and genus features, respectively) followed by MS, RA, and UC. Gemmiger and Faecalicoccus were identified as important features for classification of subjects to CD and HC. In general, features identified by differential abundance testing were consistent with machine learning feature importance. CONCLUSIONS: This study identified several gut microbial taxa with differential abundance patterns common to IMIDs. We also found differentially abundant taxa between IMIDs. These taxa may serve as biomarkers for the detection and diagnosis of IMIDs and suggest there may be a common component to IMID etiology.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37652126", + "title": "Fermentation patterns of prebiotics fructooligosaccharides-SCFA esters inoculated with fecal microbiota from ulcerative colitis patients.", + "year": 2023, + "journal": "Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association", + "authors": [ + "Chen W", + "Tan D", + "Yang Z", + "Tang J", + "Bai W", + "Tian L" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.7718677685829112, + "mesh_terms": [ + "Inflammation", + "Fatty Acids, Volatile", + "Humans", + "Microbiota", + "Prebiotics", + "Colitis, Ulcerative", + "Fermentation", + "Feces", + "Clostridiales" + ], + "raw_abstract": "Ulcerative colitis (UC) is believed to arise from an imbalance between the intestinal microbiota and mucosal immunity, leading to excessive intestinal inflammation. Modulating the gut microbial community through dietary components presents a valuable strategy in aiding the treatment of UC. In this study, esters formed by binding of well-known prebiotics, fructooligosaccharides (FOS), with short chain fatty acids (SCFAs) via both enzymatic and chemical methods were evaluated for their impact on the gut microbiota of UC patients. An in vitro human colonic fermentation model was employed to monitor changes in total carbohydrates and SCFAs production during the fermentation of these esters by microbiota from patients with active and remission UC. The results showed that pronounced abundance of [Ruminococcus]_gnavus_group, Escherichia_Shigella, Lachnoclostridium, Klebsiella and other potential pathogens were detected in the fecal samples from UC patients, with a milder condition observed during the remission phase. Significant higher levels of corresponding SCFA were observed in the groups with addition of FOS-SCFAs esters during fermentation. Butyrylated fructooligosaccharides (B-FOS) and propionylated fructooligosaccharides (P-FOS) by enzymatic synthesis successfully promoted the proliferation of Bifidobacterium and inhibited Clostridium_sensu_stricto_1 and Klebsiella. Overall, B-FOS and P-FOS exhibit promising potential for restoring intestinal homeostasis and alleviating intestinal inflammation in individuals with UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39026313", + "title": "Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease.", + "year": 2024, + "journal": "Microbiome", + "authors": [ + "Tian X", + "Li S", + "Wang C", + "Zhang Y", + "Feng X", + "Yan Q", + "Guo R", + "Wu F", + "Wu C", + "Wang Y", + "Huo X", + "Ma X" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.7398748548914773, + "mesh_terms": [ + "Humans", + "Virome", + "Gastrointestinal Microbiome", + "Animals", + "Feces", + "Mice", + "Inflammatory Bowel Diseases", + "Female", + "Male", + "Adult", + "Middle Aged", + "Crohn Disease", + "Bacteriophages", + "Colitis, Ulcerative", + "Bacteria", + "China", + "Fecal Microbiota Transplantation", + "Case-Control Studies", + "Viruses" + ], + "raw_abstract": "BACKGROUND: The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS: In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella\u00a0species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS: Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39574001", + "title": "Changes in amino acid concentrations and the gut microbiota composition are implicated in the mucosal healing of ulcerative colitis and can be used as noninvasive diagnostic biomarkers.", + "year": 2024, + "journal": "Clinical proteomics", + "authors": [ + "Wu J", + "Li M", + "Zhou C", + "Rong J", + "Zhang F", + "Wen Y", + "Qu J", + "Wu R", + "Miao Y", + "Niu J" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.6679002620268726, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Mucosal healing is the therapeutic target for ulcerative colitis (UC). While amino acids (AAs) and the gut microbiota are known to be involved in the pathogenesis of UC, their specific roles in mucosal healing have not been fully defined. OBJECTIVES: To longitudinally assess the changes in AA concentrations and the gut microbiota composition in the context of mucosal healing in UC patients, with the aim of identifying new biomarkers with predictive value for mucosal healing in UC patients and providing a new theoretical basis for dietary therapy. METHODS: A total of 15 UC patients with infliximab-induced mucosal healing were enrolled. Serum and fecal AA concentrations before and after mucosal healing were determined via targeted metabolomics. A receiver operating characteristic (ROC) curve was plotted to evaluate the value of different AAs in predicting mucosal healing in UC patients. The changes in the composition of the fecal gut microbiota were analyzed via metagenomics, and bioinformatics was used to analyze the functional genes and metabolic pathways associated with different bacterial species. Spearman correlation analyses of fecal AAs with significantly different concentrations and the differentially abundant bacterial species before and after mucosal healing were performed. RESULTS: 1. The fecal concentrations of alanine, aspartic acid, glutamic acid, glutamine, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine were significantly decreased after mucosal healing. The serum concentrations of alanine, cysteine and valine significantly increased, whereas that of aspartic acid significantly decreased. Glutamic acid, leucine, lysine, methionine and threonine could accurately predict mucosal healing in UC patients, and the area under the curve (AUC) was >\u20090.9. After combining the 5 amino acids, the AUC reached 0.96. 2. There were significant differences in the gut microbiota composition before and after mucosal healing in UC, characterized by an increase in the abundance of beneficial microbiota (Faecalibacterium prausnitzii and Bacteroides fragilis) and a decrease in the abundance of harmful microbiota (Enterococcus faecalis). LEfSe analysis identified 57 species that could predict mucosal healing, and the AUC was 0.7846. 3. Amino acid metabolic pathways were enriched in samples after mucosal healing, was associated with the abundance of multiple species, such as Faecalibacterium prausnitzi, Bacteroides fragilis, Bacteroides vulgatus and Alistipes putredinis. 4. The fecal concentrations of several AAs were negatively correlated with the abundance of a variety of beneficial strains, such as Bacteroides fragilis, uncultured Clostridium sp., Firmicutes bacterium CAG:103, Adlercreutzia equolifaciens, Coprococcus comes and positively correlated with the abundance of several harmful strains, such as Citrobacter freundii, Enterococcus faecalis, Klebsiella aerogenes, Salmonella enterica. CONCLUSION: Altered concentrations of amino acids and their associations with the gut microbiota are implicated in the mucosal healing of UC patients and can serve as noninvasive diagnostic biomarkers.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38054580", + "title": "Gut microbial signatures in clinically stable ulcerative colitis according to the mucosal state and associated symptoms.", + "year": 2024, + "journal": "Journal of gastroenterology and hepatology", + "authors": [ + "Kim S", + "Jung Y", + "Lee SB", + "Oh HS", + "Hong SN" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.6589431904769673, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Cicatrix", + "Intestinal Mucosa", + "Feces" + ], + "raw_abstract": "BACKGROUND AND AIM: The gut microbiome of patients with clinically stable ulcerative colitis (UC) differs from that of healthy individuals depending on the state of the colonic mucosa, especially with or without advanced scarring; however, the underlying mechanism is unclear. Therefore, this study examined the gut microbiome compositional signatures in patients with significant mucosal scarring and UC-related symptoms. METHODS: Stool samples for gut microbiome analysis were prospectively collected from 57 patients with clinically stable UC between January 1 and December 31, 2022. Data from 57 individuals without inflammatory bowel disease (non-IBD) paired by age and sex were selected from our previous study as the control group. The fecal samples were subjected to 16S rRNA gene sequencing. Associations between gut microbiome profiles and clinical or colonoscopic assessments were examined using diversity and differential abundance analyses. RESULTS: Gut microbiome compositions between the patients with clinically stable UC and non-IBD controls differed significantly. Furthermore, gut microbiome compositions varied between the preserved and altered mucosa groups identified based on mucosal changes in the UC group. Differential abundance test of patients with UC for symptomatic remission based on stool frequency from the two-item patient-reported outcome identified several overlapping taxa specified as gut microbiome signatures, including the Enterobacteriaceae unknown genera (Enterobacteriaceae_g), Klebsiella,\u00a0and several Lachnospiraceae spp. both in mucosal and symptom change analyses. CONCLUSIONS: The gut microbiome can change with mucosal changes, even in clinically stable UC, and some gut microbial signatures may explain the symptom manifestations in patients with UC showing significant mucosal changes.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35972440", + "title": "Patient-Reported Outcomes Correlate With Microbial Community Composition Independent of Mucosal Inflammation in Pediatric Inflammatory Bowel Disease.", + "year": 2023, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Hellmann J", + "Ta A", + "Ollberding NJ", + "Bezold R", + "Lake K", + "Jackson K", + "Dirksing K", + "Bonkowski E", + "Haslam DB", + "Denson LA" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.6339439202327025, + "mesh_terms": [ + "Humans", + "Child", + "Prospective Studies", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Crohn Disease", + "Microbiota", + "Feces", + "Leukocyte L1 Antigen Complex", + "Inflammation", + "Abdominal Pain", + "Patient Reported Outcome Measures" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel diseases (IBDs) involve an aberrant host response to intestinal microbiota causing mucosal inflammation and gastrointestinal symptoms. Patient-reported outcomes (PROs) are increasingly important in clinical care and research. Our aim was to examine associations between PROs and fecal microbiota in patients 0 to 22 years of age with IBD. METHODS: A longitudinal, prospective, single-center study tested for associations between microbial community composition via shotgun metagenomics and PROs including stool frequency and rectal bleeding in ulcerative colitis (UC) and abdominal pain and stool frequency in Crohn's disease (CD). Mucosal inflammation was assessed with fecal calprotectin. A negative binomial mixed-effects model including clinical characteristics and fecal calprotectin tested for differentially abundant species and metabolic pathways by PROs. RESULTS: In 70 CD patients with 244 stool samples, abdominal pain correlated with increased relative abundance of Haemophilus and reduced Clostridium spp. There were no differences relative to calprotectin level. In 23 UC patients with 76 samples, both rectal bleeding and increased stool frequency correlated with increased Klebsiella and reduced Bacteroides spp. Conversely, UC patients with lower calprotectin had reduced Klebsiella. Both UC and CD patients with active symptoms exhibited less longitudinal microbial community stability. No differences in metabolic pathways were observed in CD. Increased sulfoglycolysis and ornithine biosynthesis correlated with symptomatic UC. CONCLUSIONS: Microbial community composition correlated with PROs in both CD and UC. Metabolic pathways differed relative to PROs in UC, but not CD. Data suggest that microbiota may contribute to patient symptoms in IBD, in addition to effects of mucosal inflammation.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26091802", + "title": "The Toxin-Producing Pathobiont Klebsiella oxytoca Is Not Associated with Flares of Inflammatory Bowel Diseases.", + "year": 2015, + "journal": "Digestive diseases and sciences", + "authors": [ + "Zollner-Schwetz I", + "Herzog KA", + "Feierl G", + "Leitner E", + "Schneditz G", + "Sprenger H", + "Prattes J", + "Petritsch W", + "Wenzl H", + "Kump P", + "Gorkiewicz G", + "Zechner E", + "H\u00f6genauer C" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.6255384434690295, + "mesh_terms": [ + "Adult", + "Bacterial Typing Techniques", + "Benzodiazepinones", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "DNA, Bacterial", + "Disease Progression", + "Feces", + "Female", + "Humans", + "Intestines", + "Klebsiella Infections", + "Klebsiella oxytoca", + "Male", + "Middle Aged", + "Multilocus Sequence Typing", + "Prospective Studies", + "Risk Factors", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Alterations in the intestinal microbiota are thought to be involved in the pathogenesis of inflammatory bowel diseases (IBD). Klebsiella oxytoca is an intestinal pathobiont that can produce a cytotoxin (tillivaline). AIM: We aimed to elucidate the pathogenetic relevance of toxin-producing K. oxytoca in patients with IBD flares and investigated the clonal relationship of K. oxytoca isolates from IBD patients using multilocus sequence typing (MLST). METHODS: Fecal samples of 235 adult IBD patients were collected from January 2008 to May 2009 and were tested for K. oxytoca, C. difficile toxin, and other pathogens by standard microbiological methods. Clinical data and disease activity scores were collected. K. oxytoca isolates were tested for toxin production using cell culture assays. A total of 45 K. oxytoca isolates from IBD patients, healthy, asymptomatic carriers and from patients with antibiotic-associated hemorrhagic colitis in part from our strain collection were tested for their clonal relationship using MLST. RESULTS: The prevalence of K. oxytoca in IBD overall was 4.7%. Eleven K. oxytoca isolates were detected. Two of 11 isolates were tested positive for toxin production. There was no significant difference in the distribution of K. oxytoca isolates between the groups (active vs. remission in UC and CD). MLST yielded 33 sequence types. K. oxytoca isolates from IBD did not cluster separately from isolates from asymptomatic carriers. CONCLUSIONS: Our data demonstrate that toxin (tilivalline)-producing K. oxytoca is not associated with IBD flares.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37696680", + "title": "Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Del Chierico F", + "Cardile S", + "Baldelli V", + "Alterio T", + "Reddel S", + "Bramuzzo M", + "Knafelz D", + "Lega S", + "Bracci F", + "Torre G", + "Maggiore G", + "Putignani L" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.6157648362160162, + "mesh_terms": [ + "Humans", + "Child", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Cholangitis, Sclerosing", + "Dysbiosis", + "RNA, Ribosomal, 16S", + "Bacteria", + "Bacteroidetes", + "Italy" + ], + "raw_abstract": "BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis. METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs). RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients. CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC. In this study, we report the gut microbiota and mycobiota dysbiosis in pediatric patients affected by primary sclerosing cholangitis (PSC) associated with ulcerative colitis (UC), with an increase in pro-inflammatory pathobionts and a reduction in anti-inflammatory commensals.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35931020", + "title": "Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation.", + "year": 2022, + "journal": "Cell", + "authors": [ + "Federici S", + "Kredo-Russo S", + "Vald\u00e9s-Mas R", + "Kviatcovsky D", + "Weinstock E", + "Matiuhin Y", + "Silberberg Y", + "Atarashi K", + "Furuichi M", + "Oka A", + "Liu B", + "Fibelman M", + "Weiner IN", + "Khabra E", + "Cullin N", + "Ben-Yishai N", + "Inbar D", + "Ben-David H", + "Nicenboim J", + "Kowalsman N", + "Lieb W", + "Kario E", + "Cohen T", + "Geffen YF", + "Zelcbuch L", + "Cohen A", + "Rappo U", + "Gahali-Sass I", + "Golembo M", + "Lev V", + "Dori-Bachash M", + "Shapiro H", + "Moresi C", + "Cuevas-Sierra A", + "Mohapatra G", + "Kern L", + "Zheng D", + "Nobs SP", + "Suez J", + "Stettner N", + "Harmelin A", + "Zak N", + "Puttagunta S", + "Bassan M", + "Honda K", + "Sokol H", + "Bang C", + "Franke A", + "Schramm C", + "Maharshak N", + "Sartor RB", + "Sorek R", + "Elinav E" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.6108217071539682, + "mesh_terms": [ + "Animals", + "Bacteriophages", + "Colitis", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Inflammatory Bowel Diseases", + "Klebsiella pneumoniae", + "Mice" + ], + "raw_abstract": "Human gut commensals are increasingly suggested to impact non-communicable diseases, such as inflammatory bowel diseases (IBD), yet their targeted suppression remains a daunting unmet challenge. In four geographically distinct IBD cohorts (n\u00a0= 537), we identify a clade of Klebsiella pneumoniae (Kp) strains, featuring a unique antibiotics resistance and mobilome signature, to be strongly associated with disease exacerbation and severity. Transfer of clinical IBD-associated Kp strains into colitis-prone, germ-free, and colonized mice enhances intestinal inflammation. Stepwise generation of a lytic five-phage combination, targeting sensitive and resistant IBD-associated Kp clade members through distinct mechanisms, enables effective Kp suppression in colitis-prone mice, driving an attenuated inflammation and disease severity. Proof-of-concept assessment of Kp-targeting phages in an artificial human gut and in healthy volunteers demonstrates gastric acid-dependent phage resilience, safety, and viability in the lower gut. Collectively, we demonstrate the feasibility of orally administered combination phage therapy in avoiding resistance, while effectively inhibiting non-communicable disease-contributing pathobionts.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31055592", + "title": "Combined Signature of the Fecal Microbiome and Plasma Metabolome in Patients with Ulcerative Colitis.", + "year": 2019, + "journal": "Medical science monitor : international medical journal of experimental and clinical research", + "authors": [ + "Sun M", + "Du B", + "Shi Y", + "Lu Y", + "Zhou Y", + "Liu B" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.6053761928385026, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metabolome", + "Methylamines", + "Microbiota", + "Middle Aged", + "Plasma", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND Ulcerative colitis is a chronic, idiopathic in\ufb02ammatory disease that destroys the colon structure. Nevertheless, the exact pathogenesis is not clear and needs to be fully elucidated. MATERIAL AND METHODS Stool and plasma samples were used for 16S ribosomal RNA sequencing and liquid chromatography mass spectrometry, respectively. In addition, we detected the level of trimethylamine N-oxide. Finally, we performed Pearson correlation analysis between the microbiome and the metabolome. RESULTS Twenty-three active ulcerative colitis, 25 inactive ulcerative colitis, and 30 control cases were included. Thirty-four significantly different metabolites were found between the active ulcerative colitis and control groups, 38 were found between the inactive ulcerative colitis and control groups, and only 1 was found between the active ulcerative colitis and inactive ulcerative colitis groups. The plasma trimethylamine N-oxide level of the inactive ulcerative colitis and active ulcerative colitis groups was significantly higher than that of the control group. Moreover, we identified significant changes in 24, 18, and 12 bacterial genera for active ulcerative colitis-control, inactive ulcerative colitis-control, and active ulcerative colitis-inactive ulcerative colitis, respectively. Cross-correlation indicated an association between sphingosine 1-phosphate and Roseburia, Klebsiella, and Escherichia-Shigella. Through the pathway analysis, we found sphingolipid metabolism was one of the most significantly increased pathways. CONCLUSIONS Although levels of trimethylamine N-oxide were higher in ulcerative colitis patients, they did not achieve statistical significance in active ulcerative colitis and inactive ulcerative colitis groups. Sphingosine 1-phosphate was increased in ulcerative colitis patients and there were several microbiota associated with it. Although further study is still needed, sphingosine 1-phosphate will probably become a new target for treatment of ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37280117", + "title": "Gut Microbiota Signatures Are Associated With Psychopathological Profiles in Patients With Ulcerative Colitis: Results From an Italian Tertiary IBD Center.", + "year": 2023, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Scaldaferri F", + "D'Onofrio AM", + "Calia R", + "Di Vincenzo F", + "Ferrajoli GF", + "Petito V", + "Maggio E", + "Pafundi PC", + "Napolitano D", + "Masi L", + "Schiavoni E", + "Fanali C", + "Puca P", + "Turchini L", + "Lopetuso LR", + "Del Chierico F", + "Putignani L", + "Gasbarrini A", + "Camardese AG" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.5447925242892918, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Longitudinal Studies", + "Depressive Disorder, Major", + "Prospective Studies", + "Quality of Life", + "Bacteria" + ], + "raw_abstract": "BACKGROUND: Several patients with ulcerative colitis (UC) suffer from psychiatric disorders, such as major depressive disorder, anxiety, or bipolar disorder, and show specific personality traits. Despite this, there are few data about personality profiles' characterization in UC patients and about correlation of their psychopathological profile with their intestinal microbiota.The aim of our study is to analyze the psychopathological and personality profile of UC patients and correlate it with specific signatures of their gut microbiota. METHODS: This is a prospective interventional longitudinal cohort study. We enrolled consecutive patients affected by UC attending to the IBD Unit of Center for Digestive Disease of \"A. Gemelli\" IRCCS Hospital in Rome and a group of healthy subjects, matched for specific characteristics. Each patient was evaluated by a gastroenterologist and a psychiatrist. Moreover, all participants underwent psychological tests and a collection of stool samples. RESULTS: We recruited 39 UC patients and 37 healthy subjects. Most patients showed high level of alexithymia, anxiety symptoms, depressive symptoms, as well as neuroticism and hypochondria, with obsessive-compulsive features at the behavioral level, which significantly impaired their quality of life and abilities at work. Gut microbiota analysis in UC patients demonstrated an increase in actinobacteria, Proteobacteria and Saccharibacteria (TM7), with a reduction in verrucomicrobia, euryarchaeota and tenericutes. CONCLUSIONS: Our study confirmed the presence of high levels of psycho-emotional distress in UC patients, alongside alterations of the intestinal microbiota, and highlighted some families and genera of bacteria (Enterobacteriaceae, Streptococcus, Veillonella, Klebsiella, and Clostridiaceae) as potential markers of an altered gut-brain axis in these patients. Psychiatric disorders are more prevalent in IBD patients than in general population. In this prospective cohort study, we found a correlation between active UC, peculiar psychiatric distress (anxiety and depression above all), and specific taxonomic gut microbiota signatures.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31605691", + "title": "Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy.", + "year": 2020, + "journal": "Gastroenterology", + "authors": [ + "Dubinsky V", + "Reshef L", + "Bar N", + "Keizer D", + "Golan N", + "Rabinowitz K", + "Godny L", + "Yadgar K", + "Zonensain K", + "Tulchinsky H", + "Gophna U", + "Dotan I" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.36200188478650597, + "mesh_terms": [ + "Adult", + "Anti-Bacterial Agents", + "Bacteria", + "Ciprofloxacin", + "Cytokines", + "Drug Resistance, Bacterial", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "HT29 Cells", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Metagenomics", + "Metronidazole", + "Middle Aged", + "Point Mutation", + "Pouchitis", + "Prospective Studies", + "Recurrence", + "Treatment Outcome", + "Virulence Factors", + "Young Adult" + ], + "raw_abstract": "BACKGROUND & AIMS: Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic-dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial factors associated with response to antibiotic treatment and development of antibiotic dependence in patients with pouchitis. METHODS: We performed a prospective study of 49 patients who had undergone pouch surgery at a tertiary center. Disease activity was determined based on clinical, endoscopic, and histologic criteria. Pouch phenotype was defined as recurrent-acute pouchitis (n\u00a0= 6), chronic pouchitis and Crohn's-like disease of the pouch (n\u00a0= 27), normal pouch from patient with ulcerative colitis (n\u00a0= 10), and normal pouch from patient with familial adenomatous polyposis (n\u00a0= 6). Fecal samples (n\u00a0= 234) were collected over time during or in the absence of antibiotic treatment (ciprofloxacin and/or metronidazole). Thirty-three patients were treated with antibiotics, for a median of 425 days of cumulative antibiotic therapy, during follow-up. Calprotectin was measured and fecal DNA was sequenced using shotgun metagenomics and analyzed with specifically designed bioinformatic pipelines. Bacterial strains were isolated from fecal samples. We assessed their ciprofloxacin resistance and ability to induce secretion of inflammatory cytokines by HT-29 intestinal epithelial cells. RESULTS: Most antibiotic-treated patients (79%) had a clinical response to each course of antibiotics; however, 89% of those who completed a 4-week course relapsed within 3 months. Median calprotectin levels decreased by 40% in response to antibiotics. Antibiotic treatment reduced disease-associated bacteria such as Clostridium perfringens, Ruminococcus gnavus, and Klebsiella pneumoniae, but also beneficial species, such as Faecalibacterium prausnitzii. The microbiomes of antibiotic-responsive patients were dominated by facultative anaerobic genera (Escherichia, Enterococcus, and Streptococcus), with multiple ciprofloxacin-resistance mutations in drug target genes and confirmed drug resistance. However, these strains had lower potential for virulence and did not induce secretion of inflammatory cytokines by epithelial cells. After antibiotic cessation, patients had an abrupt shift in microbiome composition, with blooms of oral and disease-associated bacteria. In addition, antibiotic treatment enriched for strains that acquired multidrug resistance loci, encoding enzymes that confer resistance to nonrelated antibiotics, including extended-spectrum beta-lactamases. CONCLUSIONS: The efficacy of antibiotic treatment of pouchitis might be attributed to the establishment of an antibiotic-resistant microbiome with low inflammatory potential. This microbiome might provide resistance against colonization by bacteria that promote inflammation. To avoid progression to antibiotic-dependent disease and its consequences, strategies such as short-term alternating antibiotics and nutrition- and microbiome-based interventions should be considered.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34761733", + "title": "Attributes of intestinal microbiota composition and their correlation with clinical primary non-response to anti-TNF-\u03b1 agents in inflammatory bowel disease patients.", + "year": 2022, + "journal": "Bosnian journal of basic medical sciences", + "authors": [ + "Alatawi H", + "Mosli M", + "Saadah OI", + "Annese V", + "Al-Hindi R", + "Alatawy M", + "Al-Amrah H", + "Alshehri D", + "Bahieldin A", + "Edris S" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.3521580709254824, + "mesh_terms": [ + "Bacteria", + "Biomarkers", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "RNA, Ribosomal, 16S", + "Tumor Necrosis Factor Inhibitors" + ], + "raw_abstract": "The largest microbial aggregation in the human body exists in the gastrointestinal tract. The microbiota in the host gastrointestinal tract comprises a diverse ecosystem, and the intestinal microbiota plays a vital role in maintaining gut homeostasis. This study aims to examine whether the gut microbiota influences unresponsiveness to anti-TNF-\u03b1 treatments in primary nonresponder patients, and consequently identify the responsible microbes as biomarkers of unresponsiveness. Stool samples were collected from a cohort of patients with an established diagnosis of IBD, either ulcerative colitis (UC) or Crohn's disease (CD), following completion of the induction phase of anti TNF therapy. 16S rRNA sequencing analysis was used to examine the pattern of microbiota communities in fecal samples. The quality and quantity of fecal microbiota were compared in responder and primary nonresponder IBD patients following anti-TNF-\u03b1 therapy. As per our hypothesis, a difference in gut microbiome composition between the two patient subgroups was observed. A decreased abundance of short-chain fatty acid (SCFA)-producing bacteria, including Anaerostipes, Coprococcus, Lachnospira, Roseburia, and Ruminococcus, was detected in non-responsive patients, which was the hallmark of dysbiosis. Biomarkers of dysbiosis that were identified as predictors of clinical nonresponse, included Klebsiella, Eubacteriaceae, RF32, Bifidobacterium_animalis, and Muribaculaceae-previously known as S24-7. Signature biomarkers showed dramatic alteration in the composition of gut microbiota in patients who demonstrated primary nonresponse to anti-TNF-\u03b1 agents. Dysbiosis, with features including a dropped biodiversity, augmentation in opportunistic pathogenic microbiota, and a lack of SCFA-producing bacteria, is a prominent feature of the microbiome of primary nonresponders to anti-TNF-\u03b1 therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30739249", + "title": "Hepatic portal venous gas associated with Klebsiella oxytoca infection in the absence of preceding antibiotic treatment.", + "year": 2019, + "journal": "Clinical journal of gastroenterology", + "authors": [ + "Tanaka H", + "Watanabe T", + "Nagai T", + "Minaga K", + "Kamata K", + "Komeda Y", + "Kudo M" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.28357001015050304, + "mesh_terms": [ + "Aged, 80 and over", + "Anti-Bacterial Agents", + "Embolism, Air", + "Female", + "Humans", + "Ileitis", + "Klebsiella Infections", + "Klebsiella oxytoca", + "Portal Vein", + "Tomography, X-Ray Computed" + ], + "raw_abstract": "Klebsiella oxytoca (K. oxytoca) is a causative organism for hemorrhagic antibiotic-associated colitis. K. oxytoca infection is a typical example of microbial substitution diseases caused by exposure to antibiotics prior to the onset of diarrhea. Here, we repot a case with ileitis associated with K. oxytoca infection in the absence of preceding antibiotic treatment. Interestingly, abdominal computed tomography revealed wall thickening of the ileum and hepatic portal venous gas (HPVG). K. oxytoca was isolated from the stool. This very elderly patient had been treated with azathioprine for long-standing history of ulcerative colitis. Immuno-compromised state of this patient was considered to allow overgrowth of K. oxytoca in the small bowel to cause not only ileitis but also HPVG.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37770177", + "title": "Phage therapy in gut microbiome.", + "year": 2023, + "journal": "Progress in molecular biology and translational science", + "authors": [ + "Chen X", + "Mendes BG", + "Alves BS", + "Duan Y" + ], + "bacteria": "Klebsiella", + "condition": "ulcerative colitis", + "relevance_score": 0.2803441522492126, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Phage Therapy", + "Gastrointestinal Tract", + "Bacteria", + "Microbiota", + "Anti-Bacterial Agents" + ], + "raw_abstract": "Phage therapy, the use of bacteriophage viruses for bacterial infection treatment, has been around for almost a century, but with the increase in antibiotic use, its importance has declined rapidly. There has been renewed interest in revisiting this practice due to the general decline in the effectiveness of antibiotics, combined with improved understanding of human microbiota and advances in sequencing technologies. Phage therapy has been proposed as a clinical alternative to restore the gut microbiota in the absence of an effective treatment. That is due to its immunomodulatory and bactericidal effects against its target bacteria. In the gastrointestinal diseases field, phage therapy has been studied mainly as a promising tool in infectious diseases treatment, such as cholera and diarrhea. However, many studies have been conducted in non-communicable diseases, such as the targeting of adherent invasive Escherichia coli in Crohn's disease, the treatment of Clostridioides difficile in ulcerative colitis, the eradication of Fusobacterium nucleatum in colorectal cancer, the targeting of alcohol-producing Klebsiella pneumoniae in non-alcoholic fatty liver disease, or Enterococcus faecalis in alcohol-associated hepatitis. This review will summarize the changes in the gut microbiota and the phageome in association with some gastrointestinal and liver diseases and highlight the recent scientific advances in phage therapy as a therapeutic tool for their treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28842640", + "title": "Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients.", + "year": 2017, + "journal": "Scientific reports", + "authors": [ + "Santoru ML", + "Piras C", + "Murgia A", + "Palmas V", + "Camboni T", + "Liggi S", + "Ibba I", + "Lai MA", + "Orr\u00f9 S", + "Blois S", + "Loizedda AL", + "Griffin JL", + "Usai P", + "Caboni P", + "Atzori L", + "Manzin A" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7986079588356289, + "mesh_terms": [], + "raw_abstract": "Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract of uncertain origin, which includes ulcerative colitis (UC) and Crohn's disease (CD). The composition of gut microbiota may change in IBD affected individuals, but whether dysbiosis is the cause or the consequence of inflammatory processes in the intestinal tissue is still unclear. Here, the composition of the microbiota and the metabolites in stool of 183 subjects (82 UC, 50 CD, and 51 healthy controls) were determined. The metabolites content and the microbiological profiles were significantly different between IBD and healthy subjects. In the IBD group, Firmicutes, Proteobacteria, Verrucomicrobia, and Fusobacteria were significantly increased, whereas Bacteroidetes and Cyanobacteria were decreased. At genus level Escherichia, Faecalibacterium, Streptococcus, Sutterella and Veillonella were increased, whereas Bacteroides, Flavobacterium, and Oscillospira decreased. Various metabolites including biogenic amines, amino acids, lipids, were significantly increased in IBD, while others, such as two B group vitamins, were decreased in IBD compared to healthy subjects. This study underlines the potential role of an inter-omics approach in understanding the metabolic pathways involved in IBD. The combined evaluation of metabolites and fecal microbiome can be useful to discriminate between healthy subjects and patients with IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33970546", + "title": "Gut dysbiosis and clinical phases of pancolitis in patients with ulcerative colitis.", + "year": 2021, + "journal": "MicrobiologyOpen", + "authors": [ + "Maldonado-Arriaga B", + "Sandoval-Jim\u00e9nez S", + "Rodr\u00edguez-Silverio J", + "Lizeth Alcar\u00e1z-Estrada S", + "Cort\u00e9s-Espinosa T", + "P\u00e9rez-Cabeza de Vaca R", + "Licona-Cassani C", + "G\u00e1mez-Valdez JS", + "Shaw J", + "Mondrag\u00f3n-Ter\u00e1n P", + "Hern\u00e1ndez-Cortez C", + "Su\u00e1rez-Cuenca JA", + "Castro-Escarpulli G" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7563368219874711, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biodiversity", + "Colitis", + "Colitis, Ulcerative", + "DNA, Bacterial", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "RNA, Ribosomal, 16S", + "Severity of Illness Index" + ], + "raw_abstract": "Ulcerative colitis (UC) is a frequent type of inflammatory bowel disease, characterized by periods of remission and exacerbation. Gut dysbiosis may influence pathophysiology and clinical response in UC. The purpose of this study was to evaluate whether gut microbiota is related to the active and remission phases of pancolitis in patients with UC as well as in healthy participants. Fecal samples were obtained from 18 patients with UC and clinical-endoscopic evidenced pancolitis (active phase n\u00a0=\u00a09 and remission phase n\u00a0=\u00a09), as well as 15 healthy participants. After fecal DNA extraction, the 16S rRNA gene was amplified and sequenced (Illumina MiSeq), operational taxonomic units were analyzed with the QIIME software. Gut microbiota composition revealed a higher abundance of the phyla Proteobacteria and Fusobacteria in active pancolitis, as compared with remission and healthy participants. Likewise, a marked abundance of the genus Bilophila and Fusobacteria were present in active pancolitis, whereas a higher abundance of Faecalibacterium characterized both remission and healthy participants. LEfSe analysis showed that the genus\u00a0Roseburia\u00a0and Faecalibacterium were enriched in remission pancolitis, and genera\u00a0Bilophila\u00a0and\u00a0Fusobacterium\u00a0were enriched in active pancolitis. The relative abundance of Fecalibacterium and Roseburia showed a higher correlation with fecal calprotectin, while Bilophila and Fusobacterium showed AUCs (area under the curve) of 0.917 and 0.988 for active vs. remission pancolitis. The results of our study highlight the relation of gut dysbiosis with clinically relevant phases of pancolitis in patients with UC. Particularly, Fecalibacterium, Roseburia, Bilophila, and Fusobacterium were identified as genera highly related to the different clinical phases of pancolitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34397940", + "title": "Intestinal flora differences between patients with ulcerative colitis of different ethnic groups in China.", + "year": 2021, + "journal": "Medicine", + "authors": [ + "Liu H", + "Liu W", + "Huang X", + "Feng Y", + "Lu J", + "Gao F" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7432520728984736, + "mesh_terms": [ + "Adult", + "Bacteria", + "China", + "Colitis, Ulcerative", + "Ethnicity", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Incidence", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Retrospective Studies", + "Young Adult" + ], + "raw_abstract": "To determine the differences in intestinal flora between Uygur and Han patients with ulcerative colitis (UC).Microbial diversity and structural composition of fecal bacteria from patients with UC and their matched healthy spouses or first-degree relatives were analyzed using high-throughput sequencing technology.The fecal microbial diversity and abundance index of Uygur patients with UC (UUC) were significantly lower compared with the Uygur normal control group, while there was no significant difference between the Han UC patients (HUC) and the Han normal control group (HN). Compared with their respective control groups, Uygur UC patients and Han UC patients had a different main composition of human intestinal flora (P\u200a<\u200a.05). The abundance of Burkholderia, Caballeronia, Paraburkholderia in the UUC group were higher compared with the HUC group, while Faecalibacterium, Bifidobacterium, and Blautia in the HUC group were higher than those in the UUC group (P\u200a<\u200a.05). Veillonella in the UUC group was higher than that in the Uygur normal control group group, while Subdoligranulum and Ruminococcaceae_UCG-002 were significantly lower (P\u200a<\u200a.05). Prevotella_9 in the HUC group was significantly higher than that in HN group, while Blautia, Anaerostipes, and [Eubacterium]_hallii_group were significantly lower. Moreover, the top 6 species in order of importance were Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella.The difference in intestinal microflora structure may be one of the reasons for the clinical heterogeneity between Uygur and Han patients with UC. Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella could be used as potential biomarkers for predicting UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28852861", + "title": "Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.", + "year": 2018, + "journal": "Journal of gastroenterology", + "authors": [ + "Nishino K", + "Nishida A", + "Inoue R", + "Kawada Y", + "Ohno M", + "Sakai S", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Kawahara M", + "Naito Y", + "Andoh A" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7404425867634223, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Endoscopy, Gastrointestinal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. METHODS: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. RESULTS: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. \u03b1-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. CONCLUSIONS: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33598970", + "title": "Adsorptive granulomonocytapheresis alters the gut bacterial microbiota in patients with active ulcerative colitis.", + "year": 2021, + "journal": "Journal of clinical apheresis", + "authors": [ + "Chen X", + "Lou L", + "Tang H", + "Tan X", + "Bi J", + "Wu H", + "Li N", + "Wang Y", + "Mao J" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7241981999644483, + "mesh_terms": [ + "Adult", + "Colitis, Ulcerative", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Granulocytes", + "Humans", + "Leukapheresis", + "Male", + "Middle Aged", + "Monocytes", + "Prospective Studies" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is a refractory disease with unclear etiology. Studies have shown that UC is closely associated with gut microbiota dysbiosis. Adsorptive granulomonocytapheresis (GMA) using an Adacolumn has been found to treat UC effectively, but its underlying mechanism of treatment has not been fully elucidated. In this study, we aimed to investigate the influence of GMA on the gut microbiota in patients with active UC. METHODS: We conducted a single-center prospective analysis of patients with active UC who received GMA therapy and ultimately achieved clinical remission. Stool samples of healthy controls and patients before and after 5 or 10 sessions of GMA therapy were collected. Subsequently, high-throughput sequencing of the 16S rRNA V3 and V4 gene region of the stool was conducted and clustering of operational taxonomic units and species annotation were performed. RESULTS: Gut microbial profiles in patients with UC were characterized by low bacterial diversity. After 5 or 10 sessions of GMA therapy, the gut microbiota diversity in patients with UC increased and was similar to that of healthy controls. UC was further characterized by increased abundances of Proteobacteria and Bacteroides, as well as decreased abundances of Faecalibacterium, Roseburia, Firmicutes, and Dialister; however, after GMA therapy, the abundance of Bacteroides decreased, whereas those of Faecalibacterium, Roseburia, and Firmicutes increased. CONCLUSIONS: Active UC is associated with gut microbiota dysbiosis. GMA therapy exerts a strong regulatory effect on the gut microbiota in patients with UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26971052", + "title": "Similar Depletion of Protective Faecalibacterium prausnitzii in Psoriasis and Inflammatory Bowel Disease, but not in Hidradenitis Suppurativa.", + "year": 2016, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Eppinga H", + "Sperna Weiland CJ", + "Thio HB", + "van der Woude CJ", + "Nijsten TE", + "Peppelenbosch MP", + "Konstantinov SR" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7236049735399162, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Escherichia coli", + "Faecalibacterium prausnitzii", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Hidradenitis Suppurativa", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "Polymerase Chain Reaction", + "Psoriasis", + "Young Adult" + ], + "raw_abstract": "BACKGROUND AND AIMS: Psoriasis and hidradenitis suppurativa [HS] co-occur more often with inflammatory bowel disease [IBD] than expected, due to shared pathogenic and genetic features. It is known that IBD patients harbour an altered intestinal microbiome characterised by a depletion of Faecalibacterium prausnitzii and increase of Escherichia coli. At present, it is unclear whether a similar intestinal microbiome trend can be identified in IBD-associated skin disorders. We therefore investigated the F. prausnitzii and E. coli abundance in psoriasis and HS, with and without concomitant IBD. METHODS: Using quantitative polymerase chain reaction , we compared the F. prausnitzii and E. coli abundances in faecal samples from healthy controls [n = 33] with samples from patients with psoriasis [n = 29], IBD [n = 31], and concomitant IBD and psoriasis [n = 13]. Likewise, we analysed samples from patients with HS [n = 17], and concomitant IBD and HS [n = 17]. RESULTS: Psoriasis patients harboured a significantly lower abundance of F. prausnitzii in their stool than healthy controls [p < 0.001], which was similar to IBD patients. Together with the reduced F. prausnitzii levels, the psoriasis patients had a significantly higher abundance of E. coli [p < 0.001]. No significant difference in F. prausnitzii or E. coli abundance was found in HS. It was apparent that patients with concomitant IBD and associated skin disorder had the greatest decrease of F. prausnitzii and increase of E. coli. CONCLUSIONS: The study demonstrates, for the first time, an IBD-like decrease of F. prausnitzii together with an increase of E.coli in psoriasis, supporting the presence of a gut-microbiome-skin axis in psoriasis and IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39747467", + "title": "Gut microbiota and blood biomarkers in IBD-Related arthritis: insights from mendelian randomization.", + "year": 2025, + "journal": "Scientific reports", + "authors": [ + "Yang W", + "Cui M", + "Yang P", + "Liu C", + "Han X", + "Yao W", + "Li Z" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7189553345342085, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Mendelian Randomization Analysis", + "Biomarkers", + "Inflammatory Bowel Diseases", + "Polymorphism, Single Nucleotide", + "Genome-Wide Association Study", + "Arthritis", + "Linkage Disequilibrium" + ], + "raw_abstract": "With the ongoing rise in the incidence of inflammatory bowel disease (IBD), its extraintestinal manifestations have garnered significant attention. IBD-related arthritis is notable for its insidious onset and unpredictability, presenting considerable challenges for clinical diagnosis and management. Factors such as gut microbiota, plasma proteins, inflammatory proteins, and biomarkers found in blood and urine may be closely associated with IBD-related arthritis. However, the mechanisms by which these factors influence this condition remain poorly understood and require urgent investigation. We employed the method of linkage disequilibrium and the two-sample Mendelian randomization (MR) approach, utilizing single nucleotide polymorphisms (SNPs) identified from large-scale genome-wide association studies as instrumental variables. In this scientifically rigorous manner, we explored the potential causal relationship between gut microbiota, plasma proteins, inflammatory proteins, and blood and urine biomarkers in relation to arthritis resulting from inflammatory bowel disease (IBD). This method aids in elucidating the potential roles of these biomarkers in the development of arthritis following IBD, while minimizing the confounding factors and reverse causality commonly encountered in observational studies. To further verify and strengthen our findings, we conducted subsequent sensitivity analyses. These analyses will evaluate the strength of the association between SNPs and the studied biomarkers, as well as post-IBD arthritis, while accounting for variations in SNP distribution among populations and other potential genetic influencing factors. Through these rigorous analytical steps, our objective is to enhance the robustness and credibility of the research findings and provide more reliable scientific evidence regarding the pathogenesis of post-IBD arthritis. MR analysis provides evidence for the association between genetically predicted gut microbiota, plasma proteins, inflammatory proteins, and blood and urine biomarkers with the risk of IBD-related arthritis. This analysis investigates the characteristics of the associations between specific gut microbiota, plasma proteins, inflammatory proteins, and blood and urine biomarkers in relation to IBD-related arthritis. Among the plasma proteins, pterin-4-alpha-carbinolamine dehydratase, aldo-keto reductase family 1 member C4, cathepsin L2, angiostatin, hepatocyte growth factor-like protein, hepatitis A virus cellular receptor 2, protein O-linked mannose beta-1,4-N-acetylglucosaminyltransferase 2, epididymal-specific alpha-mannosidase, and platelet-derived growth factor receptor-like protein are associated with Crohn's disease-related arthritis. In contrast, agrin, methylenetetrahydrofolate synthetase domain-containing protein, neurotrophin-3 (NT-3) growth factor receptor, and neuropilin-1 are associated with ulcerative colitis-related arthritis. Furthermore, regarding gut bacterial pathway abundance, adenosylcobalamin, N-acetylglucosamine, N-acetylmannosamine, and N-acetylneuraminic acid degradation, as well as glycolysis metabolism and degradation pathways, are associated with Crohn's disease-related arthritis. Meanwhile, gut bacterial pathway abundance (pentose phosphate pathway) and gut microbiota abundance (Bacteroidetes, Bacteroidia, Bacteroidales, Porphyromonadaceae, Faecalibacterium, Eubacterium eligens) are linked to ulcerative colitis-related arthritis. Notably, we did not identify any connections between inflammatory protein factors, blood and urine biomarkers, and IBD-related arthritis. Lastly, in the reverse MR study, the insufficient number of SNPs available for analysis precluded the detection of a reverse causal relationship. This study employs the MR method to elucidate the potential causal relationships among gut microbiota, plasma proteins, inflammatory proteins, and blood and urine biomarkers in relation to the occurrence and progression of IBD-related arthritis. This research offers a novel perspective for a deeper understanding of the pathogenesis of IBD-related arthritis and highlights future directions for the diagnosis and treatment strategies of this condition.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31521614", + "title": "Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis.", + "year": 2019, + "journal": "EBioMedicine", + "authors": [ + "Yamada T", + "Hino S", + "Iijima H", + "Genda T", + "Aoki R", + "Nagata R", + "Han KH", + "Hirota M", + "Kinashi Y", + "Oguchi H", + "Suda W", + "Furusawa Y", + "Fujimura Y", + "Kunisawa J", + "Hattori M", + "Fukushima M", + "Morita T", + "Hase K" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7113364773222377, + "mesh_terms": [ + "Adult", + "Animals", + "Biomarkers", + "Butyrates", + "Case-Control Studies", + "Female", + "Gastrointestinal Microbiome", + "Homeostasis", + "Humans", + "Immunity, Mucosal", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Male", + "Metagenome", + "Metagenomics", + "Mice", + "Middle Aged", + "Mucins", + "Polysaccharides", + "Symbiosis" + ], + "raw_abstract": "BACKGROUND: The dysbiosis of gut microbiota has been implicated in the pathogenesis of inflammatory bowel diseases; however, the underlying mechanisms have not yet been elucidated. Heavily glycosylated mucin establishes a first-line barrier against pathogens and serves as a niche for microbial growth. METHODS: To elucidate relationships among dysbiosis, abnormal mucin utilisation, and microbial metabolic dysfunction, we analysed short-chain fatty acids (SCFAs) and mucin components in stool samples of 40 healthy subjects, 49 ulcerative colitis (UC) patients, and 44 Crohn's disease (CD) patients from Japan. FINDINGS: Levels of n-butyrate were significantly lower in stools of both CD and UC patients than in stools of healthy subjects. Correlation analysis identified seven bacterial species positively correlated with n-butyrate levels; the major n-butyrate producer, Faecalibacterium prausnitzii, was particularly underrepresented in CD patients, but not in UC patients. In UC patients, there were inverse correlations between mucin O-glycan levels and the production of SCFAs, such as n-butyrate, suggesting that mucin O-glycans serve as an endogenous fermentation substrate for n-butyrate production. Indeed, mucin-fed rodents exhibited enhanced n-butyrate production, leading to the expansion of RORgt INTERPRETATION: Mucin O-glycans facilitate symbiosynthesis of n-butyrate by gut microbiota. Abnormal mucin utilisation may lead to reduced n-butyrate production in UC patients. FUND: Japan Society for the Promotion of Science, Health Labour Sciences Research Grant, AMED-Crest, AMED, Yakult Foundation, Keio Gijuku Academic Development Funds, The Aashi Grass Foundation, and The Canon Foundation.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30895635", + "title": "Mucosal 5-aminosalicylic acid concentration, drug formulation and mucosal microbiome in patients with quiescent ulcerative colitis.", + "year": 2019, + "journal": "Alimentary pharmacology & therapeutics", + "authors": [ + "Olaisen M", + "Spigset O", + "Flatberg A", + "Granlund AVB", + "Brede WR", + "Albrektsen G", + "R\u00f8yset ES", + "Gilde B", + "Sandvik AK", + "Martinsen TC", + "Fossmark R" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7075576388717596, + "mesh_terms": [ + "Adult", + "Anti-Inflammatory Agents, Non-Steroidal", + "Arylamine N-Acetyltransferase", + "Colitis, Ulcerative", + "Drug Compounding", + "Feces", + "Female", + "Humans", + "Intestinal Mucosa", + "Isoenzymes", + "Male", + "Mesalamine", + "Microbiota", + "Middle Aged", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: 5-aminosalicylic acid (5-ASA) is the first-line therapy for ulcerative colitis (UC). 5-ASA acts locally in the colonic mucosa by numerous proposed mechanisms, and is metabolised by N-acetyltransferase (NAT). Large variations in mucosal 5-ASA concentrations have been reported, but the underlying mechanisms are not understood. AIM: To study the relationship between 5-ASA concentration, 5-ASA formulation, NAT genotype and bacterial microbiome in patients with UC. METHODS: Patients with quiescent UC, using monotherapy of Mezavant (n\u00a0=\u00a018), Asacol (n\u00a0=\u00a014) or Pentasa (n\u00a0=\u00a010), 4.0-4.8\u00a0g/day were included. 5-ASA was measured in colonic mucosal biopsies and serum by ultra-high performance liquid chromatography. NAT genotypes were determined by Sanger sequencing. Bacterial microbiome was sequenced from faeces and mucosa by 16S rRNA sequencing using Illumina Miseq. RESULTS: Mezavant provided the highest mucosal 5-ASA levels (geometric mean 2.39\u00a0ng/mg), followed by Asacol (1.60\u00a0ng/mg, 33% lower, P\u00a0=\u00a00.50) and Pentasa (0.57\u00a0ng/mg, 76% lower, P\u00a0=\u00a00.033). Mucosal 5-ASA concentration was not associated with NAT genotype, but serum 5-ASA concentration and NAT1 genotype was associated (P\u00a0=\u00a00.044). Mucosal 5-ASA concentration was positively associated with mucosal bacterial diversity (P\u00a0=\u00a00.0005) and bacterial composition. High mucosal 5-ASA concentration was related to reduced abundance of pathogenic bacteria such as Proteobacteria, and increased abundance of several favourable bacteria such as Faecalibacterium. CONCLUSIONS: Mucosal 5-ASA concentration is positively associated with bacterial diversity and a mucosal bacterial composition that are perceived favourable in UC. Mezavant yielded higher mucosal 5-ASA concentrations than Pentasa. 5-ASA may have beneficial effects on the mucosal microbiome, and high concentrations possibly amend dysbiosis in UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38367851", + "title": "Microbiome and its relevance to indigenous inflammatory bowel diseases in China.", + "year": 2024, + "journal": "Gene", + "authors": [ + "Han A", + "Yang M", + "Chen B", + "Cao G", + "Xu J", + "Meng T", + "Liu Y", + "Wang Z", + "Zhou Y", + "Xu N", + "Han W", + "Sun H", + "Mei Q", + "Zhu L", + "Xiong M" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6950034090466982, + "mesh_terms": [ + "Humans", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Colitis, Ulcerative", + "Microbiota", + "Feces", + "Dysbiosis" + ], + "raw_abstract": "BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract with an unknown etiology. Although dysbiosis is implicated in its pathogenesis, deep sequencing and oral microbiota study in Chinese IBD patients is absent. AIM: To explore the role of oral / intestinal microbiota in patients with IBD and the potential associations therein. METHODS: Clinical data, fecal and saliva samples were harvested from 80 patients with IBD (Crohn's disease, CD, n\u00a0=\u00a069; Ulcerative colitis, UC, n\u00a0=\u00a011) and 24 normal controls. Microbiomics (16S rRNA sequencing and 16S rRNA full-length sequencing) were used to detect and analyze the difference between IBD patients and normal control. RESULTS: Compared with normal controls, a higher abundance of the intestinal Shigella spp. (Shigella flexneri and Shigella sonnei, which were positively relate to the severity of IBD), lower abundance of intestinal probiotics (Prevotella, Faecalibacterium and Roseburia), and higher abundance of oral Neisseria were present in IBD patients with microbiome. The higher inflammation-related markers, impaired hepatic and renal function, and dyslipidaemia were present in patients with IBD. A higher intake of red meat and increased abundance of Clostridium in the gut were found in CD patients, while the elevated abundance of Ruminococcus in the gut was showed in UC ones. The bacterial composition of saliva and fecal samples was completely different, yet there was some correlation in the distribution of dominant probiotics. CONCLUSION: Enteric dysbacteriosis and the infections of pathogenic bacteria (Shigella) may associate with the occurrence or development of IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33871395", + "title": "Fecal microbiota profile in patients with inflammatory bowel disease in Taiwan.", + "year": 2021, + "journal": "Journal of the Chinese Medical Association : JCMA", + "authors": [ + "Chang TE", + "Luo JC", + "Yang UC", + "Huang YH", + "Hou MC", + "Lee FY" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6921983167411163, + "mesh_terms": [ + "Adult", + "Cross-Sectional Studies", + "Feces", + "Female", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Microbiota", + "Middle Aged", + "Taiwan" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with complicated interaction between immune, gut microbiota, and environmental factors in a genetically vulnerable host. Dysbiosis is often seen in patients with IBD. We aimed to investigate the fecal microbiota in patients with IBD and compared them with a control group in Taiwan. METHODS: In this cross-sectional study, we investigated fecal microbiota in 20 patients with IBD and 48 healthy controls. Fecal samples from both IBD patients and controls were analyzed by the next-generation sequencing method and relevant software. RESULTS: The IBD group showed lower bacterial richness and diversity compared with the control group. The principal coordinate analysis also revealed the significant structural differences between the IBD group and the control group. These findings were consistent whether the analysis was based on an operational taxonomic unit or amplicon sequence variant. However, no significant difference was found when comparing the composition of fecal microbiota between ulcerative colitis (UC) and Crohn's disease (CD). Further analysis showed that Lactobacillus, Enterococcus, and Bifidobacterium were dominant in the IBD group, whereas Faecalibacterium and Subdoligranulum were dominant in the control group at the genus level. When comparing UC, CD, and control group, Lactobacillus, Bifidobacterium, and Enterococcus were identified as dominant genera in the UC group. Fusobacterium and Escherichia_Shigella were dominant in the CD group. CONCLUSION: Compared with the healthy control, the IBD group showed dysbiosis with a significant decrease in both richness and diversity of gut microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39574001", + "title": "Changes in amino acid concentrations and the gut microbiota composition are implicated in the mucosal healing of ulcerative colitis and can be used as noninvasive diagnostic biomarkers.", + "year": 2024, + "journal": "Clinical proteomics", + "authors": [ + "Wu J", + "Li M", + "Zhou C", + "Rong J", + "Zhang F", + "Wen Y", + "Qu J", + "Wu R", + "Miao Y", + "Niu J" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6911426965077664, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Mucosal healing is the therapeutic target for ulcerative colitis (UC). While amino acids (AAs) and the gut microbiota are known to be involved in the pathogenesis of UC, their specific roles in mucosal healing have not been fully defined. OBJECTIVES: To longitudinally assess the changes in AA concentrations and the gut microbiota composition in the context of mucosal healing in UC patients, with the aim of identifying new biomarkers with predictive value for mucosal healing in UC patients and providing a new theoretical basis for dietary therapy. METHODS: A total of 15 UC patients with infliximab-induced mucosal healing were enrolled. Serum and fecal AA concentrations before and after mucosal healing were determined via targeted metabolomics. A receiver operating characteristic (ROC) curve was plotted to evaluate the value of different AAs in predicting mucosal healing in UC patients. The changes in the composition of the fecal gut microbiota were analyzed via metagenomics, and bioinformatics was used to analyze the functional genes and metabolic pathways associated with different bacterial species. Spearman correlation analyses of fecal AAs with significantly different concentrations and the differentially abundant bacterial species before and after mucosal healing were performed. RESULTS: 1. The fecal concentrations of alanine, aspartic acid, glutamic acid, glutamine, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine were significantly decreased after mucosal healing. The serum concentrations of alanine, cysteine and valine significantly increased, whereas that of aspartic acid significantly decreased. Glutamic acid, leucine, lysine, methionine and threonine could accurately predict mucosal healing in UC patients, and the area under the curve (AUC) was >\u20090.9. After combining the 5 amino acids, the AUC reached 0.96. 2. There were significant differences in the gut microbiota composition before and after mucosal healing in UC, characterized by an increase in the abundance of beneficial microbiota (Faecalibacterium prausnitzii and Bacteroides fragilis) and a decrease in the abundance of harmful microbiota (Enterococcus faecalis). LEfSe analysis identified 57 species that could predict mucosal healing, and the AUC was 0.7846. 3. Amino acid metabolic pathways were enriched in samples after mucosal healing, was associated with the abundance of multiple species, such as Faecalibacterium prausnitzi, Bacteroides fragilis, Bacteroides vulgatus and Alistipes putredinis. 4. The fecal concentrations of several AAs were negatively correlated with the abundance of a variety of beneficial strains, such as Bacteroides fragilis, uncultured Clostridium sp., Firmicutes bacterium CAG:103, Adlercreutzia equolifaciens, Coprococcus comes and positively correlated with the abundance of several harmful strains, such as Citrobacter freundii, Enterococcus faecalis, Klebsiella aerogenes, Salmonella enterica. CONCLUSION: Altered concentrations of amino acids and their associations with the gut microbiota are implicated in the mucosal healing of UC patients and can serve as noninvasive diagnostic biomarkers.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37295481", + "title": "Quantitative analysis of the three gut microbiota in UC and non-UC patients using real-time PCR.", + "year": 2023, + "journal": "Microbial pathogenesis", + "authors": [ + "Al-Bayati L", + "Nayeri Fasaei B", + "Merat S", + "Bahonar A", + "Ghoddusi A" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6724538347353421, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Real-Time Polymerase Chain Reaction", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Feces" + ], + "raw_abstract": "BACKGROUND: and study aims: Gastrointestinal microbiota are closely related to the pathogenesis of ulcerative colitis (UC). This study aimed at quantification of F. prausnitzii, Provetella, and Peptostreptococcus in UC and non-UC patients using Real-Time PCR and a new set of primers were also validated for this purpose. MATERIALS AND METHODS: In this study, the relative abundance of microbial populations between the UC and non-UC subjects were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR). DNA extraction from biopsies and polymerase chain reaction (PCR) amplification of bacterial 16S rRNA gene-targeted species-specific primers was performed to detect the anaerobic bacterial species. The qRT-PCR was used to show the relative change in the bacterial populations of F. prausnitzii, Provetella, and Peptostreptococcus in the UC and non-UC subjects. RESULTS: Our data for detection of the anaerobic intestinal flora showed Faecalibacterium prausnitzii, Provetella and Peptostreptococcus were the predominant microflora in the controls and showed significant differences (p\u00a0=\u00a00.002, 0.025 and 0.039, respectively). The qRT-PCR analyses of F. prausnitzii, Provetella and Peptostreptococcus were 8.69-, 9.38- and 5.77-higher, respectively, in the control group than in the UC group. CONCLUSION: The results of this study showed decreased abundance of F. prausnitzii, Provetella and Peptostreptococcus in the intestine of UC patients in comparison to non-UC patients. Quantitative RT-PCR, as a progressive and sensitive method, could be useful for evaluation of bacterial populations in patients with inflammatory bowel diseases to attain appropriate therapeutic strategies.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26026389", + "title": "Pouch Inflammation Is Associated With a Decrease in Specific Bacterial Taxa.", + "year": 2015, + "journal": "Gastroenterology", + "authors": [ + "Reshef L", + "Kovacs A", + "Ofer A", + "Yahav L", + "Maharshak N", + "Keren N", + "Konikoff FM", + "Tulchinsky H", + "Gophna U", + "Dotan I" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6569048125120381, + "mesh_terms": [ + "Adult", + "Aged", + "Anti-Bacterial Agents", + "Bacteria", + "C-Reactive Protein", + "Case-Control Studies", + "Colitis, Ulcerative", + "Colonic Pouches", + "Dysbiosis", + "Feces", + "Female", + "Humans", + "Immunologic Factors", + "Inflammation Mediators", + "Israel", + "Male", + "Microbiota", + "Middle Aged", + "Pouchitis", + "Proctocolectomy, Restorative", + "Prospective Studies", + "RNA, Bacterial", + "RNA, Ribosomal, 16S", + "Ribotyping", + "Risk Factors", + "Severity of Illness Index", + "Young Adult" + ], + "raw_abstract": "BACKGROUND & AIMS: Pouchitis is a common long-term complication in patients with ulcerative colitis (UC) undergoing proctocolectomy with ileal pouch-anal anastomosis. Because the inflammation occurs in a previously normal small bowel, studies of this process might provide information about the development of Crohn's disease. Little is known about the intestinal microbiome of patients with pouchitis. We investigated whether specific bacterial populations correlate with the pouch disease phenotype and inflammatory activity. METHODS: We performed a prospective study of patients with UC who underwent pouch surgery (N = 131) from 1981 through 2012 and were followed at Tel Aviv Medical Center. Patients were assigned to groups based on their degree and type of pouch inflammation. Patients with familial adenomatous polyposis after pouch surgery (n = 9), individuals with intact colons undergoing surveillance colonoscopy (n = 10), and patients with UC who did not undergo surgery (n = 9) served as controls. We collected demographic and disease activity data (based on the Pouchitis Disease Activity Index) and measured levels of C-reactive protein. Fecal samples were collected, levels of calprotectin were measured, and microbiota were analyzed by 16S ribosomal RNA gene amplicon pyrosequencing. RESULTS: Increased proportions of the Fusobacteriaceae family correlated with increased disease activity and levels of C-reactive protein in patients with UC who underwent pouch surgery. In contrast, proportions of Faecalibacterium were reduced in patients with pouchitis vs controls; there was a negative correlation between proportion of Faecalibacterium and level of C-reactive protein. There was an association between antibiotic treatment, but not biologic or immunomodulatory therapy, with reduced proportions of 11 genera and with increased proportions of Enterococcus and Enterobacteriaceae. CONCLUSIONS: Reductions in protective bacteria and increases in inflammatory bacteria are associated with pouch inflammation in patients with UC who underwent pouch surgery. The finding that antibiotics exacerbate dysbiosis indicates that these drugs might not provide long-term benefit for patients with pouchitis. Additional studies of this form of dysbiosis could provide information about the pathogenesis of Crohn's disease.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32265456", + "title": "Seasonal changes of circulating 25-hydroxyvitamin D correlate with the lower gut microbiome composition in inflammatory bowel disease patients.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Soltys K", + "Stuchlikova M", + "Hlavaty T", + "Gaalova B", + "Budis J", + "Gazdarica J", + "Krajcovicova A", + "Zelinkova Z", + "Szemes T", + "Kuba D", + "Drahovska H", + "Turna J", + "Stuchlik S" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6560260020108714, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteria", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Seasons", + "Vitamin D", + "Young Adult" + ], + "raw_abstract": "Higher probability of the development of Crohn's disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/Shigella spp.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32070388", + "title": "A randomized controlled trial investigating the effect of a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols on the intestinal microbiome and inflammation in patients with ulcerative colitis: study protocol for a randomized controlled trial.", + "year": 2020, + "journal": "Trials", + "authors": [ + "Milajerdi A", + "Sadeghi O", + "Siadat SD", + "Keshavarz SA", + "Sima A", + "Vahedi H", + "Adibi P", + "Esmaillzadeh A" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6263466957590321, + "mesh_terms": [ + "Adult", + "Biomarkers", + "Colitis, Ulcerative", + "Diet, Carbohydrate-Restricted", + "Dietary Sugars", + "Female", + "Fermentation", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Male", + "Middle Aged", + "Monosaccharides", + "Oligosaccharides", + "Polymers", + "Randomized Controlled Trials as Topic", + "Severity of Illness Index", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: No conclusive treatment is available for irritable bowel disease (IBD). Adherence to a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) might alleviate clinical symptoms of IBD. However, no study has investigated the effect of low FODMAPs diet on the intestinal microbiota and inflammatory biomarkers in patients with IBD. The aim of current study is to examine the effect a low FODMAP diet on IBD symptoms, inflammation, and the intestinal microbiota in patients with ulcerative colitis. METHODS AND ANALYSIS: This study is a randomized clinical trial. Thirty patients with mild to moderate ulcerative colitis will be randomly allocated to receive a low FODMAP diet (n\u2009=\u200915) or to continue their usual diet as control (n\u2009=\u200915), for 4\u2009weeks. The quantity of intestinal microbiota including Clostridium cluster IV, Faecalibacterium prausnitzii, Rosburia spp., Lactobacillus spp., Bifidobacteria spp., Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., and the Firmicutes to Bacteroidetes ratio and calprotectin and lactoferrin levels will be explored in fecal samples from patients. In addition, anthropometric measures and biochemical assessments including serum concentrations of highly sensitive-C reactive protein (hs-CRP), tumour necrosis factor-\u03b1 (TNF-\u03b1) and IL-1\u03b2 will be taken from patients at baseline and end of the study. The study has been registered in IRCT (IRCT20181126041763N1; registration date: 2019-01-18). DISCUSSION: Consumption of a low-FODMAP diet might decrease systemic and intestinal inflammation, change the bacterial population in the gut, and modulate clinical symptoms in patients with ulcerative colitis. Further studies investigating the effect of such a diet on other variables, including other bacterial species and inflammatory cytokines, are required to confirm future findings of this trial.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31971239", + "title": "Temporal Gut Microbial Changes Predict Recurrent Clostridiodes Difficile Infection in Patients With and Without Ulcerative Colitis.", + "year": 2020, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Lee AA", + "Rao K", + "Limsrivilai J", + "Gillilland M", + "Malamet B", + "Briggs E", + "Young VB", + "Higgins PDR" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6021550654374555, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Aged, 80 and over", + "Anti-Bacterial Agents", + "Clostridioides difficile", + "Clostridium Infections", + "Colitis, Ulcerative", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Logistic Models", + "Male", + "Middle Aged", + "Prospective Studies", + "RNA, Ribosomal, 16S", + "Recurrence", + "Symptom Flare Up", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) carries an increased risk of primary and recurrent Clostridiodes difficile infection (rCDI), and CDI is associated with UC flares. We hypothesized that specific fecal microbial changes associate with UC flare and rCDI. METHODS: We conducted a prospective observational cohort study of 57 patients with UC and CDI, CDI only, and UC only. Stool samples were collected at baseline, at the end of antibiotic therapy, and after reconstitution for 16S rRNA sequencing. The primary outcomes were recurrent UC flare and rCDI. Logistic regression and Lasso models were constructed for analysis. RESULTS: There were 21 (45.7%) patients with rCDI, whereas 11 (34.4%) developed UC flare. Patients with rCDI demonstrated significant interindividual (P\u2005=\u20050.008) and intraindividual differences (P\u2005=\u20050.004) in community structure by Jensen-Shannon distance (JSD) compared with non-rCDI. Two cross-validated Lasso regression models predicted risk of rCDI: a baseline model with female gender, hospitalization for UC in the past year, increased Ruminococcaceae and Verrucomicrobia, and decreased Eubacteriaceae, Enterobacteriaceae, Lachnospiraceae, and Veillonellaceae (AuROC,\u20050.94); and a model 14 days after completion of antibiotics with female gender, increased Shannon diversity, Ruminococcaceae and Enterobacteriaceae, and decreased community richness and Faecalibacterium (AuROC,\u20050.9). Adding JSD between baseline and post-treatment samples to the latter model improved fit (AuROC,\u20050.94). A baseline model including UC hospitalization in the past year and increased Bacteroidetes was associated with increased risk for UC flare (AuROC,\u20050.88). CONCLUSION: Fecal microbial features at baseline and after therapy predict rCDI risk in patients with and without UC. These results may help risk stratify patients to guide management.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30828722", + "title": "Fruit Consumption is Associated with Alterations in Microbial Composition and Lower Rates of Pouchitis.", + "year": 2019, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Godny L", + "Maharshak N", + "Reshef L", + "Goren I", + "Yahav L", + "Fliss-Isakov N", + "Gophna U", + "Tulchinsky H", + "Dotan I" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6005158153363146, + "mesh_terms": [ + "Adult", + "Colitis, Ulcerative", + "Diet", + "Feces", + "Female", + "Fruit", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Pouchitis", + "Proctocolectomy, Restorative", + "RNA, Ribosomal, 16S", + "Surveys and Questionnaires" + ], + "raw_abstract": "BACKGROUND: Patients with ulcerative colitis [UC] who undergo proctocolectomy with an ileal pouch-anal anastomosis commonly develop pouch inflammation [pouchitis]. Pouchitis develops in a previously normal small intestine and may involve environmental factors. We explored whether diet and microbiota alterations contributed to the pathogenesis of pouchitis. METHODS: Patients were recruited and prospectively followed at a comprehensive pouch clinic. Pouch behaviour was clinically defined as a normal pouch [NP] or pouchitis. Patients completed Food Frequency Questionnaires [FFQs]. Faecal samples were analysed for microbial composition [16S rRNA gene pyrosequencing]. RESULTS: Nutritional evaluation was performed in 172 patients [59% females], and of these, faecal microbial analysis was performed in 75 patients (microbiota cohort: NP [n = 22], pouchitis [n = 53]). Of the entire cohort, a subgroup of 39 [22.6%] patients had NP at recruitment [NP cohort]. Of these, 5 [12.8%] developed pouchitis within a year. Patients at the lowest tertile of fruit consumption [<1.45 servings/day] had higher rates of pouchitis compared with those with higher consumption [30.8% vs 3.8%, log rank, p = 0.03]. Fruit consumption was correlated with microbial diversity [r = 0.35, p = 0.002] and with the abundance of several microbial genera, including Faecalibacterium [r = 0.29, p = 0.01], Lachnospira [r = 0.38, p = 0.001], and a previously uncharacterized genus from the Ruminococcaceae family [r = 0.25, p = 0.05]. Reduction in fruit consumption over time was associated with disease recurrence and with reduced microbial diversity [\u0394 = -0.8 \u00b1 0.3, p = 0.008]. CONCLUSIONS: Fruit consumption is associated with modification of microbial composition, and lower consumption was correlated with the development of pouchitis. Thus, fruit consumption may protect against intestinal inflammation via alteration of microbial composition.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38442454", + "title": "Gut microbiota and metabolites as predictors of biologics response in inflammatory bowel disease: A comprehensive systematic review.", + "year": 2024, + "journal": "Microbiological research", + "authors": [ + "Wang C", + "Gu Y", + "Chu Q", + "Wang X", + "Ding Y", + "Qin X", + "Liu T", + "Wang S", + "Liu X", + "Wang B", + "Cao H" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5745563121682309, + "mesh_terms": [ + "Humans", + "Bacteria", + "Biological Products", + "Butyrates", + "Feces", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Tumor Necrosis Factor Inhibitors" + ], + "raw_abstract": "Nonresponse to biologic agents in patients with inflammatory bowel disease (IBD) poses a significant public health burden, and the prediction of response to biologics offers valuable insights for IBD management. Given the pivotal role of gut microbiota and their endogenous metabolites in IBD, we conducted a systematic review to investigate the potential of fecal microbiota and mucosal microbiota and endogenous metabolomic markers as predictors for biotherapy response in IBD patients. A total of 38 studies were included in the review. Following anti-TNF-\u03b1 treatment, the bacterial community characteristics of IBD patients exhibited a tendency to resemble those observed in healthy controls, indicating an improved clinical response. The levels of endogenous metabolites butyrate and deoxycholic acid were significantly associated with clinical remission following anti-TNF-\u03b1 therapy. IBD patients who responded well to vedolizumab treatment had higher levels of specific bacteria that produce butyrate, along with increased levels of metabolites such as butyrate, branched-chain amino acids and acetamide following vedolizumab treatment. Crohn's disease patients who responded positively to ustekinumab treatment showed higher levels of Faecalibacterium and lower levels of Escherichia/Shigella. In conclusion, fecal microbiota and mucosal microbiota as well as their endogenous metabolites could provide a predictive tool for assessing the response of IBD patients to various biological agents and serve as a valuable reference for precise drug selection in clinical IBD patients.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26839545", + "title": "Quantitative Analysis of Intestinal Flora of Uygur and Han Ethnic Chinese Patients with Ulcerative Colitis.", + "year": 2016, + "journal": "Gastroenterology research and practice", + "authors": [ + "Yao P", + "Cui M", + "Wang H", + "Gao H", + "Wang L", + "Yang T", + "Cheng Y" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5567159290923367, + "mesh_terms": [], + "raw_abstract": "Aim. To study the correlation between intestinal flora and ulcerative colitis by analyzing the abundance of Bacteroides, Fusobacterium, Clostridium, Bifidobacterium spp., and Faecalibacterium prausnitzii in the intestinal of ulcerative colitis (UC) patients and healthy controls with Uygur and Han ethnic. Methods. Bacterial genomic DNA was extracted from fecal samples and analyzed with real-time fluorescence quantitative polymerase chain reaction (PCR) to identify the abundance of Bacteroides, Fusobacterium, Clostridium, Bifidobacterium spp., and Faecalibacterium prausnitzii. Results. The samples from UC patients, Uygur and Han ethnic combined, had higher abundance of Bacteroides (P = 0.026) but lower Clostridium (P = 0.004), Bifidobacterium spp. (P = 0.009), and Faecalibacterium prausnitzii (P = 0.008) than those from healthy controls. Among UC patients, Bacteroides population was raised in acute UC patients (P \u2264 0.05), while the abundance of Clostridium, Bifidobacterium spp., Fusobacterium, and Faecalibacterium prausnitzii decreased (P \u2264 0.05) compared with the remission. In both UC patients group and control group, no difference was observed in the abundance of these 5 bacteria between the Han and the Uygur group. Conclusions. Variations in the abundance of these five bacterial strains in intestines may be associated with the occurrence of UC in Uygur and Han populations; however, these variations were not associated with ethnic difference.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36344781", + "title": "Impact of gut Microbiome alteration in Ulcerative Colitis patients on disease severity and outcome.", + "year": 2023, + "journal": "Clinical and experimental medicine", + "authors": [ + "Basha OM", + "Hafez RA", + "Salem SM", + "Anis RH", + "Hanafy AS" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5560016249638015, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Patient Acuity", + "Recurrence" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis is a heterogeneous disease in terms of disease course, location, and therapeutic response. The current study was done to assess the alteration of the gut microbiome in UC patients and its relationship to severity, response to therapy, and outcome. PATIENTS AND METHODS: The study included 96 participants who were divided into a case group (n\u2009=\u200948, recent onset, treatment naive ulcerative colitis patients who were subdivided into mild, moderate, and severe subgroups based on Truelove-Witts and endoscopic severity) and a healthy control group (n\u2009=\u200948). All were subjected to a thorough history, clinical examination, colonoscopy, routine laboratory tests, and quantitative real-time PCR to quantify Bacteroides, Lactobacilli, Faecalibacterium prausnitzii, Veillonella, and Hemophilus in fecal samples at baseline and 6\u00a0months after treatment. RESULTS: Bacterial 16S rRNA gene sequencing revealed a significant reduction in the phylum Firmicutes in UC patients, with a significant predominance of the phylum Bacteriodetes. F. prausnitzii and lactobacilli were inversely proportional to disease severity, whereas Bacteroides, Hemophilus, and Veillonella were directly proportional to it. Six months after therapy, a statistically significant increase in F. prausnitzii and lactobacilli was observed, with a decrease in the levels of other bacteria. Lower baseline F. praustinizii (<\u20098.5) increased the risk of relapse; however, lower ESR (<\u200910), lower post-treatment CRP (<\u20096), lower Bacteroides (<\u200910.6) indefinitely protect against relapse. CONCLUSION: The gut microbiome of recently diagnosed UC showed lower levels of Lactobacilli, Faecalibacterium, and higher levels of Bacteroides and Veillonella, and the change in their levels can be used to predict response to therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37950921", + "title": "Exclusive Enteral Nutrition Mediates Beneficial Gut Microbiome Enrichment in Acute Severe Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Bajaj A", + "Markandey M", + "Singh M", + "Sahu P", + "Vuyyuru SK", + "Kante B", + "Kumar P", + "Verma M", + "Makharia G", + "Kedia S", + "Travis SPL", + "Ahuja V" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5520079542814857, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Crohn Disease", + "Enteral Nutrition", + "Colitis, Ulcerative", + "Bacteria", + "Adrenal Cortex Hormones", + "Remission Induction" + ], + "raw_abstract": "BACKGROUND: Exclusive enteral nutrition (EEN) supplementation of the standard of care (SOC) augments steroid responsiveness in patients with acute severe ulcerative colitis (ASUC). EEN is known to alter gut microbial composition. The present study investigates EEN-driven gut microbial alterations in patients with ASUC and examines their correlations with clinical parameters. METHODS: Stool samples from patients with ASUC (n\u2005=\u200544) who received either EEN-supplemented SOC (EEN group; n\u2005=\u200520) or SOC alone (SOC group; n\u2005=\u200524) for 7 days were collected at baseline (day 0) and postintervention (day 7). Microbiome analysis was carried out using 16S ribosomal RNA gene sequencing followed by data processing using QIIME2 and R packages. RESULTS: Seven-day EEN-conjugated corticosteroid therapy in patients with ASUC enhanced the abundances of beneficial bacterial genera Faecalibacterium and Veillonella and reduced the abundance of Sphingomonas (generalized linear model fitted with Lasso regularization with robustness of 100%), while no such improvements in gut microbiota were observed in the SOC group. The EEN-associated taxa correlated with the patient's clinical parameters (serum albumin and C-reactive protein levels). Unlike the SOC group, which retained its preintervention core microbiota, EEN contributed Faecalibacterium prausnitzii, a beneficial gut bacterial taxon, to the gut microbial core. EEN responders showed enhancement of Ligilactobacillus and Veillonella and reduction in Prevotella and Granulicatella. Analysis of baseline gut microbiota showed relative enhancement of certain microbial genera being associated with corticosteroid response and baseline clinical parameters and that this signature could conceivably be used as a predictive tool. CONCLUSIONS: Augmentation of clinical response by EEN-conjugated corticosteroid therapy is accompanied by beneficial gut microbial changes in patients with ASUC. Exclusive enteral nutrition\u2013supplemented corticosteroid therapy in acute severe ulcerative colitis (ASUC) is accompanied by the enrichment of beneficial gut microbial genera, which correlate negatively with the disease activity scores and objective inflammatory markers in ASUC. The baseline gut microbiota in ASUC associates with and may predict corticosteroid response.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32576228", + "title": "Effects of soy milk consumption on gut microbiota, inflammatory markers, and disease severity in patients with ulcerative colitis: a study protocol for a randomized clinical trial.", + "year": 2020, + "journal": "Trials", + "authors": [ + "Sadeghi O", + "Milajerdi A", + "Siadat SD", + "Keshavarz SA", + "Sima AR", + "Vahedi H", + "Adibi P", + "Esmaillzadeh A" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5496370877772266, + "mesh_terms": [ + "Adult", + "Anti-Inflammatory Agents", + "Biomarkers", + "Colitis, Ulcerative", + "Eating", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Iran", + "Male", + "Middle Aged", + "Phytoestrogens", + "Quality of Life", + "Randomized Controlled Trials as Topic", + "Severity of Illness Index", + "Soy Milk", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Several strategies are recommended to alleviate clinical symptoms of ulcerative colitis (UC). Soy milk may affect UC through its anti-inflammatory properties. However, no study has examined the effects of soy milk consumption on gut microbiota and inflammatory biomarkers in patients with UC. The current study will be done to examine the effects of soy milk consumption on UC symptoms, inflammation, and gut microbiota in patients with UC. METHODS: This study is a randomized clinical trial, in which thirty patients with mild to moderate severity of UC will be randomly allocated to receive either 250\u2009mL/day soy milk plus routine treatments (n\u2009=\u200915) or only routine treatments (n\u2009=\u200915) for 4\u2009weeks. Assessment of anthropometric measures and biochemical indicators including serum concentrations of high-sensitivity C-reactive protein (hs-CRP), tumor necrosis factor-\u03b1 (TNF-\u03b1), interleukin-1\u03b2 (IL-1\u03b2), and interferon gamma (IFN-\u03b3) will be done at the study baseline and end of trial. In addition, the quantity of butyrate-producing bacteria including Clostridium cluster IV, Faecalibacterium prausnitzii, and Roseburia spp.; prebiotic bacteria including Lactobacillus spp. and Bifidobacteria spp.; and mucus-degrading bacteria including Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., as well as calprotectin and lactoferrin levels, will be explored in fecal samples. Also, the Firmicutes to Bacteroidetes ratio which is of significant relevance in human gut microbiota composition will be assessed. DISCUSSION: Altered gut microbiota has been reported as an important contributing factor to inflammation in patients with inflammatory bowel disease (IBD). Soy milk contains several components such as phytoestrogens with potential anti-inflammatory properties. This product might affect gut microbiota through its protein and fiber content. Therefore, soy milk might beneficially affect systemic inflammation, gut microbiota, and then clinical symptoms in patients with UC. TRIAL REGISTRATION: Iranian Registry of Clinical Trials (www.irct.ir) IRCT20181205041859N1. Registered on 27 January 2019.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29385143", + "title": "Longitudinal microbiome analysis of single donor fecal microbiota transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis.", + "year": 2018, + "journal": "PloS one", + "authors": [ + "Mintz M", + "Khair S", + "Grewal S", + "LaComb JF", + "Park J", + "Channer B", + "Rajapakse R", + "Bucobo JC", + "Buscaglia JM", + "Monzur F", + "Chawla A", + "Yang J", + "Robertson CE", + "Frank DN", + "Li E" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.512049939318857, + "mesh_terms": [ + "Clostridioides difficile", + "Clostridium Infections", + "Colitis, Ulcerative", + "Fecal Microbiota Transplantation", + "Feces", + "Humans", + "Longitudinal Studies", + "Microbiota", + "Polymerase Chain Reaction", + "Prospective Studies", + "Recurrence", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Studies of colonoscopic fecal microbiota transplant (FMT) in patients with recurrent CDI, indicate that this is a very effective treatment for preventing further relapses. In order to provide this service at Stony Brook University Hospital, we initiated an open-label prospective study of single colonoscopic FMT among patients with \u2265 2 recurrences of CDI, with the intention of monitoring microbial composition in the recipient before and after FMT, as compared with their respective donor. We also initiated a concurrent open label prospective trial of single colonoscopic FMT of patients with ulcerative colitis (UC) not responsive to therapy, after obtaining an IND permit (IND 15642). To characterize how FMT alters the fecal microbiota in patients with recurrent Clostridia difficile infections (CDI) and/or UC, we report the results of a pilot microbiome analysis of 11 recipients with a history of 2 or more recurrences of C. difficile infections without inflammatory bowel disease (CDI-only), 3 UC recipients with recurrent C. difficile infections (CDI + UC), and 5 UC recipients without a history of C. difficile infections (UC-only). METHOD: V3V4 Illumina 16S ribosomal RNA (rRNA) gene sequencing was performed on the pre-FMT, 1-week post-FMT, and 3-months post-FMT recipient fecal samples along with those collected from the healthy donors. Fitted linear mixed models were used to examine the effects of Group (CDI-only, CDI + UC, UC-only), timing of FMT (Donor, pre-FMT, 1-week post-FMT, 3-months post-FMT) and first order Group*FMT interactions on the diversity and composition of fecal microbiota. Pairwise comparisons were then carried out on the recipient vs. donor and between the pre-FMT, 1-week post-FMT, and 3-months post-FMT recipient samples within each group. RESULTS: Significant effects of FMT on overall microbiota composition (e.g., beta diversity) were observed for the CDI-only and CDI + UC groups. Marked decreases in the relative abundances of the strictly anaerobic Bacteroidetes phylum, and two Firmicutes sub-phyla associated with butyrate production (Ruminococcaceae and Lachnospiraceae) were observed between the CDI-only and CDI + UC recipient groups. There were corresponding increases in the microaerophilic Proteobacteria phylum and the Firmicutes/Bacilli group in the CDI-only and CDI + UC recipient groups. At a more granular level, significant effects of FMT were observed for 81 genus-level operational taxonomic units (OTUs) in at least one of the three recipient groups (p<0.00016 with Bonferroni correction). Pairwise comparisons of the estimated pre-FMT recipient/donor relative abundance ratios identified 6 Gammaproteobacteria OTUs, including the Escherichia-Shigella genus, and 2 Fusobacteria OTUs with significantly increased relative abundance in the pre-FMT samples of all three recipient groups (FDR < 0.05), however the magnitude of the fold change was much larger in the CDI-only and CDI + UC recipients than in the UC-only recipients. Depletion of butyrate producing OTUs, such as Faecalibacterium, in the CDI-only and CDI + UC recipients, were restored after FMT. CONCLUSION: The results from this pilot study suggest that the microbial imbalances in the CDI + UC recipients more closely resemble those of the CDI-only recipients than the UC-only recipients.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38836628", + "title": "Gut Microbial Species and Endotypes Associate with Remission in Ulcerative Colitis Patients Treated with Anti-TNF or Anti-integrin Therapy.", + "year": 2024, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Tamburini FB", + "Tripathi A", + "Gold MP", + "Yang JC", + "Biancalani T", + "McBride JM", + "Keir ME", + "Gardenia Study Group" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5059967618256986, + "mesh_terms": [ + "Adult", + "Female", + "Humans", + "Male", + "Middle Aged", + "Antibodies, Monoclonal, Humanized", + "Colitis, Ulcerative", + "Feces", + "Gastrointestinal Agents", + "Gastrointestinal Microbiome", + "Infliximab", + "Remission Induction", + "Tumor Necrosis Factor Inhibitors" + ], + "raw_abstract": "BACKGROUND AND AIMS: The gut microbiota contributes to aberrant inflammation in inflammatory bowel disease, but the bacterial factors causing or exacerbating inflammation are not fully understood. Further, the predictive or prognostic value of gut microbial biomarkers for remission in response to biologic therapy is unclear. METHODS: We perform whole metagenomic sequencing of 550 stool samples from 287 ulcerative colitis patients from a large, phase 3, head-to-head study of infliximab and etrolizumab. RESULTS: We identify several bacterial species in baseline and/or post-treatment samples that associate with clinical remission. These include previously described associations [Faecalibacterium prausnitzii_F] as well as new associations with remission to biologic therapy [Flavonifractor plautii]. We build multivariate models and find that gut microbial species are better predictors for remission than clinical variables alone. Finally, we describe patient groups that differ in microbiome composition and remission rate after induction therapy, suggesting the potential utility of microbiome-based endotyping. CONCLUSIONS: In this large study of ulcerative colitis patients, we show that few individual species associate strongly with clinical remission, but multivariate models including microbiome can predict clinical remission and have better predictive power compared with clinical data alone.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33548121", + "title": "Gut microbiota changes in inflammatory bowel diseases and ankylosing spondilytis.", + "year": 2021, + "journal": "Journal of gastrointestinal and liver diseases : JGLD", + "authors": [ + "Cardoneanu A", + "Mihai C", + "Rezus E", + "Burlui A", + "Popa I", + "Cijevschi Prelipcean C" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.4916152688028099, + "mesh_terms": [ + "Bacteria", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Escherichia coli", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases" + ], + "raw_abstract": "BACKGROUND AND AIMS: Both inflammatory bowel diseases (IBD) and ankylosing spondylitis (AS) can be considered chronic immune disorders sharing common etiopathogenetic mechanisms. Changes in the composition of the intestinal microbiota, which can lead to an abnormal mucosal response, could be the missing link between these two diseases. Our study evaluate the composition of intestinal microbiota and to characterize gut dysbiosis in patients with IBD and AS. METHODS: We conducted a prospective case-control study that enrolled 124 patients [20 Crohn's disease (CD), 27 ulcerative colitis (UC), 28 AS, 17 IBD + AS and 32 controls). Intestinal microbiota analysis was performed by real-time polymerase chain reaction in stool samples. RESULTS: The total quantity of bacteria was decreased in all investigated groups compared to the control group. In studied groups, we noticed an increased percentage of Bacteroides and Escherichia coli (E.coli) and a decreased percentage of Clostridium coccoides, Clostridium leptum, and Faecalibacterium prausnitzii compared to the control group. The percentages of Bifidobacterium (p=0.010) as well as Lactobacillus group (p=0.023) were higher in the L3 form of CD patients. In the E2 form of UC, the quantity of Bacteroides was much higher compared to the E3 form (p=0.004). In AS patients, significant correlations were observed only for the Bifidobacterium species, significantly increased in the axial form compared to peripheral disease (p=0.035). Statistically significant correlations were demonstrated between the Crohn Disease Activity Index score and the total bacterial group (p=0.023, r=-0.507), respectively Bacteroides (p=0.021, r=-0.511) and between the Mayo score and Lactobacillus (p=0.001), respectively E. coli (p=0.001). In IBD + AS group, the Crohn Disease Activity Index score was inversely correlated with the total bacterial group (p=0.010) and directly correlated with Lactobacillus (p=0.047). CONCLUSIONS: Intestinal dysbiosis is associated with both IBD and AS. In the association of IBD with AS, dysbiosis is intermediate, but it is associated with the more severe articular disease. Bifidobacterium and Lactobacillus (commonly used as probiotics!) were found to be increased in the association between active IBD and active AS. Further studies are needed to understand how dysbiosis regulates the gut immune system and contributes to intestinal and articular inflammation.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31812509", + "title": "Differences in Gut Microbiota in Patients With vs Without Inflammatory Bowel Diseases: A Systematic Review.", + "year": 2020, + "journal": "Gastroenterology", + "authors": [ + "Pittayanon R", + "Lau JT", + "Leontiadis GI", + "Tse F", + "Yuan Y", + "Surette M", + "Moayyedi P" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.4864845058822719, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestines" + ], + "raw_abstract": "BACKGROUND & AIMS: Altering the intestinal microbiota has been proposed as a treatment for inflammatory bowel diseases (IBDs), but there are no established associations between specific microbes and IBD. We performed a systematic review to identify frequent associations. METHODS: We searched the MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, and Cochrane Central Register of Controlled Trials databases, through April 2, 2018 for studies that compared intestinal microbiota (from fecal or colonic or ileal tissue samples) among patients (adult or pediatric) with IBD vs healthy individuals (controls). The primary outcome was difference in specific taxa in fecal or intestinal tissue samples from patients with IBD vs controls. We used the Newcastle-Ottawa scale to assess the quality of studies included in the review. RESULTS: We identified 2631 citations; 48 studies from 45 articles were included in the analysis. Most studies evaluated adults with Crohn's disease or ulcerative colitis. All 3 studies of Christensenellaceae and Coriobacteriaceae and 6 of 11 studies of Faecalibacterium prausnitzii reported a decreased amount of those organisms compared with controls, whereas 2 studies each of Actinomyces, Veillonella, and Escherichia coli revealed an increased amount in patients with Crohn's disease. For patients with ulcerative colitis, Eubacterium rectale and Akkermansia were decreased in all 3 studies, whereas E coli was increased in 4 of 9 studies. The microbiota diversity was either decreased or not different in patients with IBD vs controls. Fewer than 50% of the studies stated comparable sexes and ages of cases and controls. CONCLUSIONS: In a systematic review, we found evidence for differences in abundances of some bacteria in patients with IBD vs controls, but we cannot make conclusions due to inconsistent results and methods among studies. Further large-scale studies, with better methods of assessing microbe populations, are needed.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29311644", + "title": "Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.", + "year": 2018, + "journal": "Nature microbiology", + "authors": [ + "Schirmer M", + "Franzosa EA", + "Lloyd-Price J", + "McIver LJ", + "Schwager R", + "Poon TW", + "Ananthakrishnan AN", + "Andrews E", + "Barron G", + "Lake K", + "Prasad M", + "Sauk J", + "Stevens B", + "Wilson RG", + "Braun J", + "Denson LA", + "Kugathasan S", + "McGovern DPB", + "Vlamakis H", + "Xavier RJ", + "Huttenhower C" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.4825950383560378, + "mesh_terms": [ + "Adolescent", + "Adult", + "Child", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gene Expression Profiling", + "Humans", + "Inflammatory Bowel Diseases", + "Longitudinal Studies", + "Male", + "Metagenomics", + "Phenotype", + "Transcription, Genetic", + "Young Adult" + ], + "raw_abstract": "Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period. Here, we present the first results based on 78 paired faecal metagenomes\u00a0and\u00a0metatranscriptomes, and 222 additional metagenomes from 59 patients with Crohn's disease, 34 with ulcerative colitis and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, although many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microorganisms per host (for example, by Faecalibacterium prausnitzii). Thus, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Furthermore, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (for example, Dialister invisus). Last, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways that were predominantly expressed by different organisms in patients with IBD (for example, Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypical changes that are complementary to those linked to metagenomic abundances. The study's results highlight the strength of analysing both the activity and the presence of gut microorganisms to provide insight into the role of the microbiome in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34798830", + "title": "Fecal microbiota profiling in irritable bowel syndrome and inflammatory bowel disease patients with irritable bowel syndrome-type symptoms.", + "year": 2021, + "journal": "BMC gastroenterology", + "authors": [ + "Cui X", + "Wang H", + "Ye Z", + "Li Y", + "Qiu X", + "Zhang H" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.47409464269823487, + "mesh_terms": [ + "Cross-Sectional Studies", + "Feces", + "Humans", + "Inflammatory Bowel Diseases", + "Irritable Bowel Syndrome", + "Microbiota" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota is thought to be involved in the occurrence of inflammatory bowel disease in remission with irritable bowel syndrome (IBS)-type symptoms, but the specific distinct profile of these bacteria remains unclear. This cross-sectional study aims to investigate the fecal microbiota profiling in patients with these diseases. METHODS: Fecal samples from 97 subjects, including Crohn's disease patients in remission with IBS-type symptoms (CDR-IBS RESULTS: The richness of the intestinal microbiota in the CDR-IBS group was markedly lower than those in the control and IBS groups based on the analysis of observed species and the Chao index (P\u2009<\u20090.05). The observed species index in the CDR-IBS CONCLUSIONS: The IBS-type symptoms in CD patients in remission may be related to an increase in Faecalibacterium and a decrease in Fusobacterium. The IBS-type symptoms in UC patients in remission cannot be explained by changes in the abundance and structure of the intestinal microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36569858", + "title": "Pyruvate: Ferredoxin oxidoreductase is involved in IgA-related microbiota dysbiosis and intestinal inflammation.", + "year": 2022, + "journal": "Frontiers in immunology", + "authors": [ + "Wang K", + "Guo Y", + "Liu Y", + "Cui X", + "Gu X", + "Li L", + "Li Y", + "Li M" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.4735099116553783, + "mesh_terms": [ + "Animals", + "Rabbits", + "Ferredoxins", + "Pyruvic Acid", + "Dysbiosis", + "Leukocytes, Mononuclear", + "Phylogeny", + "Colitis, Ulcerative", + "Microbiota", + "Inflammation", + "Oxidoreductases", + "Immunoglobulin A" + ], + "raw_abstract": "INTRODUCTION: Inflammatory bowel diseases (IBDs) are associated with both immune abnormalities and dysbiosis, characterized by a loss of Faecalibacterium prausnitzii (F. prausnitzii). However, the reason for F. prausnitzii deficiency remains unclear. METHODS: 16S rDNA seque-ncing and IgA enzyme-linked immunosorbent assay (ELISA) were applied to identify bacterial community and IgA changes in ulcerative colitis (UC) patients. Forced immunization with F. prausnitzii in rabbits was conducted. To screen for potential IgA-reactive proteins in F. prausnitzii lysates, we performed western blotting and mass spectrometry analyses. Pyruvate: ferredoxin oxidoreductase (PFOR) was cloned and purified, then the immunoreactivity of PFOR was verified in peripheral blood mononuclear cells (PBMCs) through PCR, ELISpot assay and single-cell sequencing (scRNA-seq). Finally, the UC fecal dysbiosis was re-analyzed in the context of the phylogenetic tree of PFOR. RESULTS: F. prausnitzii was underrepresented in UC patients with elevated F. prausnitzii-reactive IgA in the fecal supernatant. Forced immunization with F. prausnitzii in rabbits led to high interferon-\u03b3 (IFN-\u03b3) transcription in the colon, along with beta diversity disturbance and intestinal inflammation. PFOR was identified as an IgA-binding antigen of F. prausnitzii and the immunoreactivity was validated in PBMCs, which showed elevated expression of inflammatory cytokines. The scRNA-seq revealed enhanced signals in both T regulatory cells (Tregs) and monocytes after PFOR incubation. Furthermore, phylogenetic analysis revealed that PFOR was a common but conserved protein among the gut bacteria. DISCUSSION: Our results collectively suggest that PFOR is a bioactive protein in the immune system and may contribute to host-microbial crosstalk. Conserved but bioactive microbial proteins, such as PFOR, warrant more attention in future host-microbial interaction studies.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31771630", + "title": "A distinct gut microbiota composition in patients with ankylosing spondylitis is associated with increased levels of fecal calprotectin.", + "year": 2019, + "journal": "Arthritis research & therapy", + "authors": [ + "Klingberg E", + "Magnusson MK", + "Strid H", + "Deminger A", + "St\u00e5hl A", + "Sundin J", + "Simr\u00e9n M", + "Carlsten H", + "\u00d6hman L", + "Forsblad-d'Elia H" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.4568500689462167, + "mesh_terms": [ + "Adult", + "Bacteria", + "C-Reactive Protein", + "Colitis, Ulcerative", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Middle Aged", + "Population Dynamics", + "Spondylitis, Ankylosing", + "Surveys and Questionnaires", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Ankylosing spondylitis (AS) shares many characteristics with inflammatory bowel disease (IBD). Intestinal microbiota most likely plays an important role in the development of IBDs and may also be involved in the pathogenesis of AS. We aimed to define and compare the fecal microbiota composition in patients with AS, ulcerative colitis (UC), and healthy controls (HC) and to determine relationships between fecal microbiota, fecal calprotectin, and disease-related variables in AS. METHODS: Fecal microbiota composition was assessed with GA-map\u2122 Dysbiosis Test (Genetic Analysis, Oslo, Norway), which also reports the degree of deviation of the microbiota composition compared with a healthy control population, a Dysbiosis Index (DI) score 1-5. The AS patients were assessed with questionnaires, back mobility tests, fecal calprotectin, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP). RESULTS: Totally, 150 patients with AS (55% men, median age 55.5\u2009years, median BASDAI 3.2), 18 patients with UC (56% men, median age 30.5\u2009years), and 17 HC (65% men, median age 22\u2009years) were included. Principal component analysis showed highly separate clustering of fecal microbiota from the patients with AS, UC, and HC. Compared with HC, fecal microbiota in AS was characterized by a higher abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcus species, and Actinobacteria, but lower abundance of Bacteroides and Lachnospiraceae. Further, fecal microbiota composition differed between patients with normal (\u2264\u200950\u2009mg/kg, n\u2009=\u200957) and increased (\u2265\u2009200\u2009mg/kg, n\u2009=\u200936) fecal calprotectin. Patients with increased fecal calprotectin had lower abundance of bacteria with anti-inflammatory properties such as Faecalibacterium prausnitzii and Clostridium and higher abundance of the genus Streptococcus. No association was found between the fecal microbiota composition and HLAB27 status, disease activity, function, or medication. Dysbiosis (defined as DI\u2009\u2265\u20093) was found in 87% of AS patients. CONCLUSIONS: Patients with AS have a distinct fecal microbiota signature, which is linked to fecal calprotectin levels, a marker of intestinal inflammation, but not to other clinical parameters. These findings suggest a local interplay between intestinal microbiota and gut inflammation in AS. TRIAL REGISTRATION: ClinicalTrials.gov, NCT00858819. Registered March 9, 2009.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28683448", + "title": "Gut Microbiota in Health, Diverticular Disease, Irritable Bowel Syndrome, and Inflammatory Bowel Diseases: Time for Microbial Marker of Gastrointestinal Disorders.", + "year": 2018, + "journal": "Digestive diseases (Basel, Switzerland)", + "authors": [ + "Lopetuso LR", + "Petito V", + "Graziani C", + "Schiavoni E", + "Paroni Sterbini F", + "Poscia A", + "Gaetani E", + "Franceschi F", + "Cammarota G", + "Sanguinetti M", + "Masucci L", + "Scaldaferri F", + "Gasbarrini A" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.4534132317471234, + "mesh_terms": [ + "Adult", + "Biomarkers", + "Diverticular Diseases", + "Female", + "Gastrointestinal Microbiome", + "Health", + "Humans", + "Inflammatory Bowel Diseases", + "Irritable Bowel Syndrome", + "Male", + "Middle Aged", + "Phylogeny", + "Principal Component Analysis", + "Species Specificity" + ], + "raw_abstract": "Few data exist on differences in gut microbiota composition among principal gastrointestinal (GI) diseases. We evaluated the differences in gut microbiota composition among uncomplicated diverticular disease (DD), irritable bowel syndrome (IBS) and inflammatory bowel diseases (IBD) patients. DD, IBS, and IBD patients along with healthy controls (CT) were enrolled in our Italian GI outpatient clinic. Stool samples were collected. Microbiota composition was evaluated through a metagenomic gene-targeted approach. GI pathology represented a continuous spectrum of diseases where IBD displayed one extreme, while CT displayed the other. Among Phyla, Biplot PC2/PC3 and dendogram plot showed major differences in samples from IBS and IBD. DD resembled species CT composition, but not for Bacteroides fragilis. In IBS, Dialister spp. and then Faecalibacterium prausnitzii were the most representative species. Ulcerative colitis showed a reduced concentration of Clostridium difficile and an increase of Bacteroides fragilis. In Crohn's disease, Parabacteroides distasonis was the most represented, while Faecalibacterium prausnitzii and Bacteroides fragilis were significantly reduced. Each disorder has its definite overall microbial signature, which produces a clear differentiation from the others. On the other hand, shared alterations constitute the \"core dysbiosis\" of GI diseases. The assessment of these microbial markers represents a parameter that may complete the diagnostic assessment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27687331", + "title": "The association between the gut microbiota and the inflammatory bowel disease activity: a systematic review and meta-analysis.", + "year": 2016, + "journal": "Scandinavian journal of gastroenterology", + "authors": [ + "Prosberg M", + "Bendtsen F", + "Vind I", + "Petersen AM", + "Gluud LL" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.4530931865773072, + "mesh_terms": [ + "Bifidobacterium", + "Clostridium", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Faecalibacterium", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Remission Induction" + ], + "raw_abstract": "BACKGROUND: The pathogenesis of inflammatory bowel diseases (IBD) involves complex interactions between the microbiome and the immune system. We evaluated the association between the gut microbiota and disease activity in IBD patients. METHODS: Systematic review of clinical studies based on a published protocol. Included patients had ulcerative colitis (UC) or Crohn's disease (CD) classified as active or in remission. We selected bacteria assessed in at least three studies identified through electronic and manual searches (November 2015). Bias control was evaluated with the Newcastle Ottawa scale (NOS). Results of random-effects meta-analyses were presented as mean differences (MD). RESULTS: Three prospective and seven cross-sectional studies (NOS score 6-8) were included. Five studies included patients with CD (231 patients) and eight included patients with UC (392 patients). Compared to patients in remission, patients with active IBD had lower abundance of Clostridium coccoides (MD\u2009=\u2009-0.49, 95% CI: -0.79 to -0.19), Clostridium leptum (MD\u2009=\u2009-0.44, 95% CI: -0.74 to -0.14), Faecalibacterium prausnitzii (MD\u2009=\u2009-0.81, 95% CI: -1.23 to -0.39) and Bifidobacterium (MD\u2009=\u2009-0.37, 95% CI: -0.56 to -0.17). Subgroup analyses showed a difference in all four bacteria between patients with UC classified as active or in remission. Patients with active CD had fewer C. leptum, F. prausnitzii and Bifidobacterium, but not C. coccoides. CONCLUSION: This systematic review suggests that dysbiosis may be involved in the activity of IBD and that there may be differences between patients with CD and UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32184182", + "title": "Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases.", + "year": 2021, + "journal": "Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association", + "authors": [ + "Borren NZ", + "Plichta D", + "Joshi AD", + "Bonilla G", + "Peng V", + "Colizzo FP", + "Luther J", + "Khalili H", + "Garber JJ", + "Janneke van der Woude C", + "Sadreyev R", + "Vlamakis H", + "Xavier RJ", + "Ananthakrishnan AN" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.44987113945563206, + "mesh_terms": [ + "Adult", + "Clostridiales", + "Colitis, Ulcerative", + "Fatigue", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Metabolome", + "Proteomics" + ], + "raw_abstract": "BACKGROUND & AIMS: Fatigue is frequent and disabling in patients with inflammatory bowel diseases (IBD) but its mechanisms are poorly understood. We investigated alterations in fecal microbiomes and serum metabolomes and proteomes in patients with quiescent IBD, with vs without fatigue. METHODS: We performed a prospective observational study of patients (44% women; mean age, 39.8 y) with clinically and endoscopically quiescent Crohn's disease (n\u00a0= 106) or ulcerative colitis (n\u00a0=\u00a060) at a tertiary hospital, from March 2016 through December 2018. Fatigue was assessed using the functional assessment of chronic illness therapy-fatigue scoring system and defined as a score of 43 or less. We performed metabolomic analysis of serum samples using liquid chromatography-mass spectrometry methods and proteomic analysis using multiplex proximity extension assay (PEA) technology. Stool samples were obtained from 50 patients and analyzed by shotgun metagenomic sequencing on Illumina HiSeq platform. RESULTS: Of the 166 study participants, 91 (55%) were fatigued. Serum samples from patients with fatigue (n\u00a0= 59) did not have significant increases in levels of inflammatory cytokines compared with serum samples from nonfatigued patients (n\u00a0= 72). We found a statistically significant difference in a cluster of 18 serum metabolites between patients with fatigue (n\u00a0= 84) vs without fatigue (n\u00a0= 72) (P = .033); serum samples from patients with fatigue had significant reductions in levels of methionine (P = .020), tryptophan (P = .042), proline (P = .017), and sarcosine (P = .047). Fecal samples from patients with fatigue had a less diverse gut microbiome, with significant reductions in butyrate-producing bacteria, including Faecalibacterium prausnitzii (P = .0002, q =.007) and\u00a0Roseburia hominis (P = .0079, q = 0.105). This fatigue-like microbiome was associated with fatigue scales and correlated with progressive depletion of metabolites from serum samples. CONCLUSIONS: In an analysis of fecal and serum samples from 166 patients with IBD, we found alterations in serum metabolites and fecal microbes that were associated with fatigue.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37940667", + "title": "Inflammatory bowel disease biomarkers revealed by the human gut microbiome network.", + "year": 2023, + "journal": "Scientific reports", + "authors": [ + "Hu M", + "Caldarelli G", + "Gili T" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.43620764460829736, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Microbiota", + "Colitis, Ulcerative", + "Biomarkers", + "Escherichia coli" + ], + "raw_abstract": "Inflammatory bowel diseases (IBDs) are complex medical conditions in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when exposed to yet unclear environmental factors. The complexity of this class of diseases makes them suitable to be represented and studied with network science. In this paper, the metagenomic data of control, Crohn's disease, and ulcerative colitis subjects' gut microbiota were investigated by representing this data as correlation networks and co-expression networks. We obtained correlation networks by calculating Pearson's correlation between gene expression across subjects. A percolation-based procedure was used to threshold and binarize the adjacency matrices. In contrast, co-expression networks involved the construction of the bipartite subjects-genes networks and the monopartite genes-genes projection after binarization of the biadjacency matrix. Centrality measures and community detection were used on the so-built networks to mine data complexity and highlight possible biomarkers of the diseases. The main results were about the modules of Bacteroides, which were connected in the control subjects' correlation network, Faecalibacterium prausnitzii, where co-enzyme A became central in IBD correlation networks and Escherichia coli, whose module has different patterns of integration within the whole network in the different diagnoses.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26896085", + "title": "Anti-TNF Therapy Response in Patients with Ulcerative Colitis Is Associated with Colonic Antimicrobial Peptide Expression and Microbiota Composition.", + "year": 2016, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Magnusson MK", + "Strid H", + "Sapnara M", + "Lasson A", + "Bajor A", + "Ung KA", + "\u00d6hman L" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3998769019837784, + "mesh_terms": [ + "Adalimumab", + "Adolescent", + "Adult", + "Aged", + "Anti-Inflammatory Agents", + "Antimicrobial Cationic Peptides", + "Biomarkers", + "Biopsy", + "Colitis, Ulcerative", + "Cytokines", + "Faecalibacterium prausnitzii", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Infliximab", + "Intestinal Mucosa", + "Male", + "Middle Aged", + "Proteome", + "Real-Time Polymerase Chain Reaction", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "BACKGROUND AND AIMS: Anti-tumour necrosis factor [TNF] therapy is used in patients with ulcerative colitis [UC], but not all patients respond to treatment. Antimicrobial peptides [AMPs] and the gut microbiota are essential for gut homeostasis and may be important for treatment outcome. The aim of this study was to determine AMP and microbiota profiles in patients with UC before anti-TNF therapy start and correlate these data to treatment outcome. METHODS: Serum and biopsies were obtained from UC patients na\u00efve to biological therapy [n = 56] before anti-TNF therapy start [baseline]. Fecal samples were taken at baseline and Weeks 2 and 6. Quantitative proteomic analysis was performed in mucosal biopsies. Expression of AMPs and cytokines was determined in biopsies and serum. Microbiota analysis of fecal samples was performed using GA-map\u2122 Dysbiosis Test and real-time quantitative polymerase chain reaction [rtPCR]. Treatment response was evaluated 12-14 weeks after baseline. RESULTS: At baseline, proteomic analysis of biopsies showed that treatment responders and non-responders had differential expression of AMPs. Eleven AMP and AMP-related genes were analysed by rtPCR in mucosal biopsies and could together discriminate responders from non-responders at baseline. The most important nominators for response were increased expression of defensin 5 and eosinophilic cationic protein. Microbiota analysis revealed lower dysbiosis indexes and higher abundance of Faecalibacterium prausnitzii in responders compared with non-responders at baseline. Also, abundance of F. prausnitzii increased during induction therapy in responders. CONCLUSIONS: Anti-TNF therapy responders and non-responders display distinctly separate patterns of mucosal AMP expression and gut microbiota before treatment start. This indicates that intestinal antimicrobial/microbial composition can influence treatment outcome.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39030520", + "title": "Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Joo M", + "Nam S" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3956832387746775, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Adolescent", + "RNA, Ribosomal, 16S", + "Obesity", + "Female", + "Male", + "Bacteria", + "Phylogeny", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Colitis, Ulcerative", + "Dysbiosis", + "Prevotella", + "Faecalibacterium prausnitzii", + "Feces" + ], + "raw_abstract": "BACKGROUND: Recently, there has been an increase in the number of studies focusing on the association between the gut microbiome and obesity or inflammatory diseases, especially in adults. However, there is a lack of studies investigating the association between gut microbiome and gastrointestinal (GI) diseases in adolescents. METHOD: We obtained 16S rRNA-seq datasets for gut microbiome analysis from 202 adolescents, comprising ulcerative colitis (UC), Crohn's disease (CD), obesity (Ob), and healthy controls (HC). We utilized Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to acquire Operational Taxonomic Units (OTUs). Subsequently, we analyzed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) terms and pathway enrichment for the identified OTUs. RESULTS: In this study, we investigated the difference between the gut microbiomes in adolescents with GI diseases and those in healthy adolescents using 202 samples of 16S rRNA sequencing data. The distribution of the six main gut microbiota (i.e., unclassified Dorea, unclassified Lachnospiraceae, unclassified Ruminococcus, Faecalibacterium prausnitzii, Prevotella copri, unclassified Sutterella) was different based on the status of obesity and inflammatory diseases. Dysbiosis was observed within Lachnospiraceae in adolescents with inflammatory diseases (i.e., UC and CD), and in adolescents with obesity within Prevotella and Sutterella. More specifically, our results showed that the relative abundance of Faecalibacterium prausnitzii and unclassified Lachnospiraceae was more than 10% and 8% higher, respectively, in the UC group compared to the CD, Ob, and HC groups. Additionally, the Ob group had over 20% and over 3% higher levels of Prevotella copri and unclassified Sutterella, respectively, compared to the UC, CD, and HC groups. Also, inspecting associations between the six specific microbiota and KO terms, we found that the six microbiota -relating KO terms were associated with NOD-like receptor signaling. These six taxa differences may affect the immune system and inflammatory response by affecting NOD-like receptor signaling in the host during critical adolescence. CONCLUSION: In this study, we discovered that dysbiosis of the microbial community had varying degrees of influence on the inflammatory and immune response pathways in adolescents with inflammatory diseases and obesity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27412252", + "title": "Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.", + "year": 2016, + "journal": "Genome medicine", + "authors": [ + "Shaw KA", + "Bertha M", + "Hofmekler T", + "Chopra P", + "Vatanen T", + "Srivatsa A", + "Prince J", + "Kumar A", + "Sauer C", + "Zwick ME", + "Satten GA", + "Kostic AD", + "Mulle JG", + "Xavier RJ", + "Kugathasan S" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3912722894782307, + "mesh_terms": [ + "Adolescent", + "Bacteria", + "Biomarkers", + "Case-Control Studies", + "Child", + "Child, Preschool", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Immunologic Factors", + "Inflammation", + "Intestinal Mucosa", + "Leukocyte L1 Antigen Complex", + "Longitudinal Studies", + "Male", + "Severity of Illness Index", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Gut microbiome dysbiosis has been demonstrated in subjects with newly diagnosed and chronic inflammatory bowel disease (IBD). In this study we sought to explore longitudinal changes in dysbiosis and ascertain associations between dysbiosis and markers of disease activity and treatment outcome. METHODS: We performed a prospective cohort study of 19 treatment-na\u00efve pediatric IBD subjects and 10 healthy controls, measuring fecal calprotectin and assessing the gut microbiome via repeated stool samples. Associations between clinical characteristics and the microbiome were tested using generalized estimating equations. Random forest classification was used to predict ultimate treatment response (presence of mucosal healing at follow-up colonoscopy) or non-response using patients' pretreatment samples. RESULTS: Patients with Crohn's disease had increased markers of inflammation and dysbiosis compared to controls. Patients with ulcerative colitis had even higher inflammation and dysbiosis compared to those with Crohn's disease. For all cases, the gut microbial dysbiosis index associated significantly with clinical and biological measures of disease severity, but did not associate with treatment response. We found differences in specific gut microbiome genera between cases/controls and responders/non-responders including Akkermansia, Coprococcus, Fusobacterium, Veillonella, Faecalibacterium, and Adlercreutzia. Using pretreatment microbiome data in a weighted random forest classifier, we were able to obtain 76.5\u00a0% accuracy for prediction of responder status. CONCLUSIONS: Patient dysbiosis improved over time but persisted even among those who responded to treatment and achieved mucosal healing. Although dysbiosis index was not significantly different between responders and non-responders, we found specific genus-level differences. We found that pretreatment microbiome signatures are a promising avenue for prediction of remission and response to treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31586453", + "title": "Effects of Low FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial.", + "year": 2020, + "journal": "Gastroenterology", + "authors": [ + "Cox SR", + "Lindsay JO", + "Fromentin S", + "Stagg AJ", + "McCarthy NE", + "Galleron N", + "Ibraim SB", + "Roume H", + "Levenez F", + "Pons N", + "Maziers N", + "Lomer MC", + "Ehrlich SD", + "Irving PM", + "Whelan K" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3797854658089844, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biomarkers", + "Diet, Carbohydrate-Restricted", + "Disaccharides", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "Monosaccharides", + "Quality of Life", + "Severity of Illness Index", + "Single-Blind Method", + "Treatment Outcome", + "United Kingdom", + "Young Adult" + ], + "raw_abstract": "BACKGROUND & AIMS: There is limited evidence that a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) reduces gut symptoms in quiescent inflammatory bowel disease (IBD). We performed a randomized, controlled trial to investigate the effects of a low FODMAP diet on persistent gut symptoms, the intestinal microbiome, and circulating markers of inflammation in patients with quiescent IBD. METHODS: We performed a single-blind trial of 52 patients with quiescent Crohn's disease or ulcerative colitis and persistent gut symptoms at 2 large gastroenterology clinics in the United Kingdom. Patients were randomly assigned to groups that followed a diet low in FODMAPs (n\u00a0= 27) or a control diet (n\u00a0= 25), with dietary advice, for 4 weeks. Gut symptoms and health-related quality of life were measured using validated questionnaires. Stool and blood samples were collected at baseline and end of trial. We assessed fecal microbiome composition and function using shotgun metagenomic sequencing and phenotypes of T cells in blood using flow cytometry. RESULTS: A higher proportion of patients reported adequate relief of gut symptoms following the low FODMAP diet (14/27, 52%) than the control diet (4/25, 16%, P=.007). Patients had a greater reduction in irritable bowel syndrome severity scores following the low FODMAP diet (mean reduction of 67; standard error, 78) than the control diet (mean reduction of 34; standard error, 50), although this difference was not statistically significant (P\u00a0= .075). Following the low FODMAP diet, patients had higher health-related quality of life scores (81.9 \u00b1 1.2) than patients on the control diet (78.3 \u00b1 1.2, P\u00a0= .042). A targeted analysis revealed that in stool samples collected at the end of the study period, patients on the low FODMAP diet had significantly lower abundance of Bifidobacterium adolescentis, Bifidobacterium longum, and Faecalibacterium prausnitzii than patients on control diet. However, microbiome diversity and markers of inflammation did not differ significantly between groups. CONCLUSIONS: In a trial of the low FODMAP diet vs a control diet in patients with quiescent IBD, we found no significant difference after 4 weeks in change in irritable bowel syndrome severity scores, but significant improvements in specific symptom scores and numbers reporting adequate symptom relief. The low FODMAP diet reduced fecal abundance of microbes believed to regulate the immune response, compared with the control diet, but had no significant effect on markers of inflammation. We conclude that a 4-week diet low in FODMAPs is safe and effective for managing persistent gut symptoms in patients with quiescent IBD. www.isrctn.com no.: ISRCTN17061468.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38037086", + "title": "Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis-a case study using metatranscriptomics.", + "year": 2023, + "journal": "Microbiome", + "authors": [ + "Deng ZL", + "Pieper DH", + "Stallmach A", + "Steube A", + "Vital M", + "Reck M", + "Wagner-D\u00f6bler I" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3749858641496464, + "mesh_terms": [ + "Humans", + "Pouchitis", + "Fecal Microbiota Transplantation", + "Anti-Bacterial Agents", + "Feces", + "Microbiota", + "Colitis, Ulcerative", + "Butyrates" + ], + "raw_abstract": "BACKGROUND: Ileal pouch-anal anastomosis (IPAA) is the standard of care after total proctocolectomy for ulcerative colitis (UC). Around 50% of patients will experience pouchitis, an idiopathic inflammatory condition. Antibiotics are the backbone of treatment of pouchitis; however, antibiotic-resistant pouchitis develops in 5-10% of those patients. It has been shown that fecal microbiota transplantation (FMT) is an effective treatment for UC, but results for FMT antibiotic-resistant pouchitis are inconsistent. METHODS: To uncover which metabolic activities were transferred to the recipients during FMT and helped the remission, we performed a longitudinal case study of the gut metatranscriptomes from three patients and their donors. The patients were treated by two to three FMTs, and stool samples were analyzed for up to 140\u00a0days. RESULTS: Reduced expression in pouchitis patients compared to healthy donors was observed for genes involved in biosynthesis of amino acids, cofactors, and B vitamins. An independent metatranscriptome dataset of UC patients showed a similar result. Other functions including biosynthesis of butyrate, metabolism of bile acids, and tryptophan were also much lower expressed in pouchitis. After FMT, these activities transiently increased, and the overall metatranscriptome profiles closely mirrored those of the respective donors with notable fluctuations during the subsequent weeks. The levels of the clinical marker fecal calprotectin were concordant with the metatranscriptome data. Faecalibacterium prausnitzii represented the most active species contributing to butyrate synthesis via the acetyl-CoA pathway. Remission occurred after the last FMT in all patients and was characterized by a microbiota activity profile distinct from donors in two of the patients. CONCLUSIONS: Our study demonstrates the clear but short-lived activity engraftment of donor microbiota, particularly the butyrate biosynthesis after each FMT. The data suggest that FMT triggers shifts in the activity of patient microbiota towards health which need to be repeated to reach critical thresholds. As a case study, these insights warrant cautious interpretation, and validation in larger cohorts is necessary for generalized applications. In the long run, probiotics with high taxonomic diversity consisting of well characterized strains could replace FMT to avoid the costly screening of donors and the risk of transferring unwanted genetic material. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38297219", + "title": "Clinical features and fecal microbiota characteristics of patients with both ulcerative colitis and axial spondyloarthritis.", + "year": 2024, + "journal": "BMC gastroenterology", + "authors": [ + "Zhangni L", + "Mofan X", + "Yuling C", + "Yingchao L" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3646216276774149, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Inflammatory Bowel Diseases", + "Feces", + "Axial Spondyloarthritis", + "Gastrointestinal Microbiome" + ], + "raw_abstract": "BACKGROUND: The role of the intestinal microbiota in the pathogenesis of inflammatory bowel disease combined with axial spondyloarthritis (axSpA) is gaining widespread interest. AIMS: This study was conducted to investigate the clinical and fecal microbiota characteristics of patients with both ulcerative colitis (UC) and axSpA. METHODS: Clinical data were collected from patients with UC. Patients were divided into the axSpA and non-axSpA groups according to human leukocyte antigen-B27 serology and sacroiliac joint imaging results. We obtained fecal specimens from 14 axSpA and 26 non-axSpA patients. All samples underwent 16S ribosomal DNA sequencing. RESULTS: Seventy-three patients with UC were included in this study, and the axSpA incidence was 19.2%. This incidence was significantly higher in patients with C-reactive protein\u2009>\u200910\u00a0mg/L. Firmicutes and Faecalibacterium abundances were decreased, and Proteobacteria and Escherichia_Shigella abundances were increased in the axSpA group compared with those of the non-axSpA group. Indicator analysis showed that Escherichia_Shigella was more likely to be an indicator species of axSpA. Additionally, many biosynthetic and metabolic pathways, including glutathione metabolism, fatty acid degradation, geraniol degradation, and biosynthesis of siderophore group nonribosomal peptides, were upregulated in the axSpA group. CONCLUSION: Patients with UC have a high axSpA incidence, which may be related to the relative abundances of Escherichia_Shigella in these patients. The abundances of various biosynthetic and metabolic pathways of the fecal flora were upregulated in patients with axSpA.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31605691", + "title": "Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy.", + "year": 2020, + "journal": "Gastroenterology", + "authors": [ + "Dubinsky V", + "Reshef L", + "Bar N", + "Keizer D", + "Golan N", + "Rabinowitz K", + "Godny L", + "Yadgar K", + "Zonensain K", + "Tulchinsky H", + "Gophna U", + "Dotan I" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.36200188478650597, + "mesh_terms": [ + "Adult", + "Anti-Bacterial Agents", + "Bacteria", + "Ciprofloxacin", + "Cytokines", + "Drug Resistance, Bacterial", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "HT29 Cells", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Metagenomics", + "Metronidazole", + "Middle Aged", + "Point Mutation", + "Pouchitis", + "Prospective Studies", + "Recurrence", + "Treatment Outcome", + "Virulence Factors", + "Young Adult" + ], + "raw_abstract": "BACKGROUND & AIMS: Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic-dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial factors associated with response to antibiotic treatment and development of antibiotic dependence in patients with pouchitis. METHODS: We performed a prospective study of 49 patients who had undergone pouch surgery at a tertiary center. Disease activity was determined based on clinical, endoscopic, and histologic criteria. Pouch phenotype was defined as recurrent-acute pouchitis (n\u00a0= 6), chronic pouchitis and Crohn's-like disease of the pouch (n\u00a0= 27), normal pouch from patient with ulcerative colitis (n\u00a0= 10), and normal pouch from patient with familial adenomatous polyposis (n\u00a0= 6). Fecal samples (n\u00a0= 234) were collected over time during or in the absence of antibiotic treatment (ciprofloxacin and/or metronidazole). Thirty-three patients were treated with antibiotics, for a median of 425 days of cumulative antibiotic therapy, during follow-up. Calprotectin was measured and fecal DNA was sequenced using shotgun metagenomics and analyzed with specifically designed bioinformatic pipelines. Bacterial strains were isolated from fecal samples. We assessed their ciprofloxacin resistance and ability to induce secretion of inflammatory cytokines by HT-29 intestinal epithelial cells. RESULTS: Most antibiotic-treated patients (79%) had a clinical response to each course of antibiotics; however, 89% of those who completed a 4-week course relapsed within 3 months. Median calprotectin levels decreased by 40% in response to antibiotics. Antibiotic treatment reduced disease-associated bacteria such as Clostridium perfringens, Ruminococcus gnavus, and Klebsiella pneumoniae, but also beneficial species, such as Faecalibacterium prausnitzii. The microbiomes of antibiotic-responsive patients were dominated by facultative anaerobic genera (Escherichia, Enterococcus, and Streptococcus), with multiple ciprofloxacin-resistance mutations in drug target genes and confirmed drug resistance. However, these strains had lower potential for virulence and did not induce secretion of inflammatory cytokines by epithelial cells. After antibiotic cessation, patients had an abrupt shift in microbiome composition, with blooms of oral and disease-associated bacteria. In addition, antibiotic treatment enriched for strains that acquired multidrug resistance loci, encoding enzymes that confer resistance to nonrelated antibiotics, including extended-spectrum beta-lactamases. CONCLUSIONS: The efficacy of antibiotic treatment of pouchitis might be attributed to the establishment of an antibiotic-resistant microbiome with low inflammatory potential. This microbiome might provide resistance against colonization by bacteria that promote inflammation. To avoid progression to antibiotic-dependent disease and its consequences, strategies such as short-term alternating antibiotics and nutrition- and microbiome-based interventions should be considered.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35999575", + "title": "Location-specific signatures of Crohn's disease at a multi-omics scale.", + "year": 2022, + "journal": "Microbiome", + "authors": [ + "Gonzalez CG", + "Mills RH", + "Zhu Q", + "Sauceda C", + "Knight R", + "Dulai PS", + "Gonzalez DJ" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3530891007040926, + "mesh_terms": [ + "Bile Acids and Salts", + "Crohn Disease", + "Cross-Sectional Studies", + "Feces", + "Humans", + "Metagenomics", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Crohn's disease (CD), an inflammatory bowel disease (IBD) subtype, results from pathologic interactions between host cells and its resident gut microbes. CD manifests in both isolated disease locations (ileum or colon) or a combination of locations (ileocolonic). To date, a comprehensive understanding of how isolated CD subtypes influence molecular profiles remains outstanding. To address this, we sought to define CD location signatures by leveraging a large cross-sectional feature set captured from the stool of over 200 IBD patients and healthy controls using metaproteomics, shotgun metagenomics, 16S rRNA sequencing, metabolomic profiling, and host genetics paired with clinical endoscopic assessments. RESULTS: Neither metagenomic nor host genetics alone distinguished CD location subtypes. In contrast, ileal and colonic CD were distinguished using mass spectrometry-based methods (metabolomics or metaproteomics) or a combined multi-omic feature set. This multi-omic feature set revealed colonic CD was strongly associated with neutrophil-related proteins. Additionally, colonic CD displayed a disease-severity-related association with Bacteroides vulgatus. Colonic CD and ulcerative colitis profiles harbored strikingly similar feature enrichments compared to ileal CD, including neutrophil-related protein enrichments. Compared to colonic CD, ileal CD profiles displayed increased primary and secondary bile acid levels and concomitant shifts in taxa with noted sensitivities such as Faecalibacterium prausnitzii or affinities for bile acid-rich environments, including Gammaproteobacteria and Blautia sp. Having shown robust molecular and microbial distinctions tied to CD locations, we leveraged these profiles to generate location-specific disease severity biomarkers that surpass the performance of Calprotectin. CONCLUSIONS: When compared using multi-omics features, colonic- and ileal-isolated CD subtypes display striking differences that suggest separate location-specific pathologies. Colonic CD's strong similarity to ulcerative colitis, including neutrophil and Bacteroides vulgatus involvement, is also evidence of a shared pathology for colonic-isolated IBD subtypes, while ileal CD maintains a unique, bile acid-driven profile. More broadly, this study demonstrates the power of multi-omics approaches for IBD biomarker discovery and elucidating the underlying biology. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35681546", + "title": "Ulcerative Colitis in Response to Fecal Microbiota Transplantation via Modulation of Gut Microbiota and Th17/Treg Cell Balance.", + "year": 2022, + "journal": "Cells", + "authors": [ + "Huang C", + "Mei Q", + "Lou L", + "Huang Z", + "Fu Y", + "Fan J", + "Wang J", + "Yin N", + "Zheng Y", + "Lu Y", + "Zeng Y" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3490148582755445, + "mesh_terms": [ + "Colitis, Ulcerative", + "Fecal Microbiota Transplantation", + "Forkhead Transcription Factors", + "Gastrointestinal Microbiome", + "Humans", + "Leukocyte L1 Antigen Complex", + "Nuclear Receptor Subfamily 1, Group F, Member 3", + "RNA, Ribosomal, 16S", + "T-Lymphocytes, Regulatory", + "Transcription Factors" + ], + "raw_abstract": "Background: Fecal microbiota transplantation (FMT) may contribute to disease remission in ulcerative colitis (UC). We studied the microbiota change and its regulation on T cells after FMT. Methods: Patients with mild to moderately active UC were included to receive FMT. The intestinal histopathological changes and barrier function were evaluated. The fecal samples of donors and patients were analyzed by 16S rRNA gene-based microbiota analysis, and the colon Th17 and Treg cells were assessed. Results: Fifteen patients completed the 8-week-follow-up. A total of 10 patients (66.7%) were in the responders (RE) group and five in the non-responders (NR) group. The Nancy histological index and fecal calprotectin decreased (p < 0.001, p = 0.06, respectively) and Occludin and Claudin1 increased in the RE group. The abundance of Faecalibaterium increased significantly by 2.3-fold in the RE group at week 8 (p = 0.043), but it was suppressed in the NR group. Fecal calprotectin (r = \u22120.382, p = 0.003) and Nancy index (r = \u22120.497, p = 0.006) were correlated inversely with the abundance of Faecalibacterium, respectively. In the RE group the relative mRNA expression of ROR\u03b3t decreased and Foxp3 increased. Significantly decreased CD4+ ROR\u03b3t+ Th17 and increased CD4+ Foxp3+ Treg were also observed in the RE group. The relative abundance of Faecalibacterium correlated with CD4+ ROR\u03b3t+ Th17 (r = \u22120.430, p = 0.018) and CD4+ Foxp3+ Treg (r = 0.571, p = 0.001). Conclusions: The long-term Faecalibaterium colonization following FMT plays a crucial role in UC remission by alleviating intestinal inflammation. This anti-inflammatory effect of Faecalibacterium may be achieved by regulating the imbalance of Th17/Treg levels in UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32445952", + "title": "Low-Fat, High-Fiber Diet Reduces Markers of Inflammation and Dysbiosis and Improves Quality of Life in Patients With Ulcerative Colitis.", + "year": 2021, + "journal": "Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association", + "authors": [ + "Fritsch J", + "Garces L", + "Quintero MA", + "Pignac-Kobinger J", + "Santander AM", + "Fern\u00e1ndez I", + "Ban YJ", + "Kwon D", + "Phillips MC", + "Knight K", + "Mao Q", + "Santaolalla R", + "Chen XS", + "Maruthamuthu M", + "Solis N", + "Damas OM", + "Kerman DH", + "Deshpande AR", + "Lewis JE", + "Chen C", + "Abreu MT" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3266318384107212, + "mesh_terms": [ + "Colitis, Ulcerative", + "Cross-Over Studies", + "Diet", + "Dysbiosis", + "Feces", + "Female", + "Humans", + "Inflammation", + "Male", + "Quality of Life" + ], + "raw_abstract": "BACKGROUND & AIMS: A high-fat diet has been associated with an increased risk of ulcerative colitis (UC). We studied the effects of a low-fat, high-fiber diet (LFD) vs an improved standard American diet (iSAD, included higher quantities of fruits, vegetables, and fiber than a typical SAD). We collected data on quality of life, markers of inflammation, and fecal markers of intestinal dysbiosis in patients with UC. METHODS: We analyzed data from a parallel-group, cross-over study of 17 patients with UC in remission or with mild disease (with a flare within the past 18 mo), from February 25, 2015, through September 11, 2018. Participants were assigned randomly to 2 groups and received a LFD (10% of calories from fat) or an iSAD (35%-40% of calories from fat) for the first 4-week period, followed by a 2-week washout period, and then switched to the other diet for 4 weeks. All diets were catered and delivered to patients' homes, and each participant served as her or his own control. Serum and stool samples were collected at baseline and week 4 of each diet and analyzed for markers of inflammation. We performed 16s ribosomal RNA sequencing and untargeted and targeted metabolomic analyses on stool samples. The primary outcome was quality of life, which was measured by the short inflammatory bowel disease (IBD) questionnaire at baseline and week 4 of the diets. Secondary outcomes included changes in the Short-Form 36 health survey, partial Mayo score, markers of inflammation, microbiome and metabolome analysis, and adherence to the diet. RESULTS: Participants' baseline diets were unhealthier than either study diet. All patients remained in remission throughout the study period. Compared with baseline, the iSAD and LFD each increased quality of life, based on the short IBD questionnaire and Short-Form 36 health survey scores (baseline short IBD questionnaire score, 4.98; iSAD, 5.55; LFD, 5.77; baseline vs iSAD, P\u00a0= .02; baseline vs LFD, P\u00a0= .001). Serum amyloid A decreased significantly from 7.99 mg/L at baseline to 4.50 mg/L after LFD (P\u00a0= .02), but did not decrease significantly compared with iSAD (7.20 mg/L; iSAD vs LFD, P\u00a0= .07). The serum level of C-reactive protein decreased numerically from 3.23 mg/L at baseline to 2.51 mg/L after LFD (P\u00a0= .07). The relative abundance of Actinobacteria in fecal samples decreased from 13.69% at baseline to 7.82% after LFD (P\u00a0= .017), whereas the relative abundance of Bacteroidetes increased from 14.6% at baseline to 24.02% on LFD (P\u00a0= .015). The relative abundance of Faecalibacterium prausnitzii was higher after 4 weeks on the LFD (7.20%) compared with iSAD (5.37%; P\u00a0= .04). Fecal levels of acetate (an anti-inflammatory metabolite) increased from a relative abundance of 40.37 at baseline to 42.52 on the iSAD and 53.98 on the LFD (baseline vs LFD, P\u00a0= .05; iSAD vs LFD, P\u00a0= .09). The fecal level of tryptophan decreased from a relative abundance of 1.33 at baseline to 1.08 on the iSAD (P\u00a0= .43), but increased to a relative abundance of 2.27 on the LFD (baseline vs LFD, P\u00a0= .04; iSAD vs LFD, P\u00a0= .08); fecal levels of lauric acid decreased after LFD (baseline, 203.4; iSAD, 381.4; LFD, 29.91; baseline vs LFD, P\u00a0= .04; iSAD vs LFD, P\u00a0= .02). CONCLUSIONS: In a cross-over study of patients with UC in remission, we found that a catered LFD or iSAD were each well tolerated and increased quality of life. However, the LFD decreased markers of inflammation and reduced intestinal dysbiosis in fecal samples. Dietary interventions therefore might benefit patients with UC in remission. ClinicalTrials.gov no: NCT04147598.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38915068", + "title": "Siderophore-harboring gut bacteria and fecal siderophore genes for predicting the responsiveness of fecal microbiota transplantation for active ulcerative colitis.", + "year": 2024, + "journal": "Journal of translational medicine", + "authors": [ + "Yan J", + "Zhou G", + "Ren R", + "Zhang X", + "Zhang N", + "Wang Z", + "Peng L", + "Yang Y" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.2843196471100417, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Male", + "Female", + "Feces", + "Fecal Microbiota Transplantation", + "Adult", + "Middle Aged", + "Gastrointestinal Microbiome", + "Siderophores", + "Treatment Outcome", + "Bacteria", + "Genes, Bacterial", + "Gene Dosage", + "ROC Curve" + ], + "raw_abstract": "BACKGROUND: Predictive markers for fecal microbiota transplantation (FMT) outcomes in patients with active ulcerative colitis (UC) are poorly defined. We aimed to investigate changes in gut microbiota pre- and post-FMT and to assess the potential value in determining the total copy number of fecal bacterial siderophore genes in predicting FMT responsiveness. METHODS: Patients with active UC (Mayo score\u2009\u2265\u20093) who had undergone two FMT procedures were enrolled. Fecal samples were collected before and 8\u00a0weeks after each FMT session. Patients were classified into clinical response and non-response groups, based on their Mayo scores. The fecal microbiota profile was accessed using metagenomic sequencing, and the total siderophore genes copy number via quantitative real-time polymerase chain reaction. Additionally, we examined the association between the total siderophore genes copy number and FMT efficacy. RESULTS: Seventy patients with UC had undergone FMT. The clinical response and remission rates were 50% and 10% after the first FMT procedure, increasing to 72.41% and 27.59% after the second FMT. The cumulative clinical response and clinical remission rates were 72.86% and 25.71%. Compared with baseline, the response group showed a significant increase in Faecalibacterium, and decrease in Enterobacteriaceae, consisted with the changes of the total bacterial siderophore genes copy number after the second FMT (1889.14 vs. 98.73 copies/ng, P\u2009<\u20090.01). Virulence factor analysis showed an enriched iron uptake system, especially bacterial siderophores, in the pre-FMT response group, with a greater contribution from Escherichia coli. The total baseline copy number was significantly higher in the response group than non-response group (1889.14 vs. 94.86 copies/ng, P\u2009<\u20090.01). A total baseline copy number cutoff value of 755.88 copies/ng showed 94.7% specificity and 72.5% sensitivity in predicting FMT responsiveness. CONCLUSIONS: A significant increase in Faecalibacterium, and decrease in Enterobacteriaceae and the total fecal siderophore genes copy number were observed in responders after\u00a0FMT. The siderophore genes and its encoding bacteria may be of predictive value for the clinical responsiveness of FMT to active ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32383181", + "title": "A disease-specific decline of the relative abundance of Bifidobacterium in patients with autoimmune hepatitis.", + "year": 2020, + "journal": "Alimentary pharmacology & therapeutics", + "authors": [ + "Liwinski T", + "Casar C", + "Ruehlemann MC", + "Bang C", + "Sebode M", + "Hohenester S", + "Denk G", + "Lieb W", + "Lohse AW", + "Franke A", + "Schramm C" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.2794166419286227, + "mesh_terms": [ + "Adult", + "Aged", + "Bacterial Load", + "Bifidobacterium", + "Case-Control Studies", + "Cohort Studies", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Hepatitis, Autoimmune", + "Humans", + "Liver Cirrhosis, Biliary", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: The pathogenesis of autoimmune hepatitis (AIH) is poorly understood and little is known about enteric microbiota in AIH. AIM: To investigate disease-specific microbiome alterations in AIH. METHODS: The V1-V2 variable regions of the 16S rRNA gene were sequenced in faecal samples from 347 patients with AIH and controls (AIH n\u00a0=\u00a072, healthy controls (HC) n\u00a0=\u00a095, primary biliary cholangitis (PBC) n\u00a0=\u00a099 and ulcerative colitis (UC) n\u00a0=\u00a081). RESULTS: Biodiversity (Shannon entropy) was decreased in AIH patients compared to HC (P\u00a0=\u00a00.016), which was partially reversed by azathioprine (P\u00a0=\u00a00.011). Regarding between-sample diversity, AIH patients separated from HC, PBC and UC individuals (all P\u00a0=\u00a00.001). Compared to HC, decreased relative abundance of anaerobic genera such as Faecalibacterium and an increase of Veillonella and the facultative anaerobic genera Streptococcus and Lactobacillus were detected. Importantly, a disease-specific decline of relative abundance of Bifidobacterium was observed in AIH patients. Lack of Bifidobacterium was associated with failure to achieve remission of AIH (P\u00a0<\u00a00.001). Of potential therapeutic implication, Bifidobacterium abundance correlated with average protein intake (P\u00a0<\u00a00.001). Random forests classification between AIH and PBC on the microbiome signature yielded an area under receiver operating characteristic curve (AUC) of 0.787 in the training cohort, and an AUC of 0.849 in an external validation cohort. CONCLUSION: Disease-specific faecal microbial alterations were identified in patients with AIH. Intestinal dysbiosis in AIH was characterised by a decline of Bifidobacterium, which was associated with increased disease activity. These results point to the contribution of intestinal microbiota to AIH pathogenesis and to novel therapeutic targets.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26548336", + "title": "Probiotics: a proactive approach to health. A symposium report.", + "year": 2015, + "journal": "The British journal of nutrition", + "authors": [ + "Thomas LV", + "Suzuki K", + "Zhao J" + ], + "bacteria": "Faecalibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.2645465952450497, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Bacteria", + "Bacterial Infections", + "Child", + "Diarrhea", + "Gastrointestinal Diseases", + "HIV Infections", + "Humans", + "Integrative Medicine", + "Intestinal Mucosa", + "Metabolic Diseases", + "Microbiota", + "Neoplasms", + "Practice Guidelines as Topic", + "Probiotics" + ], + "raw_abstract": "This report summarises talks given at the 8th International Yakult Symposium, held on 23-24 April 2015 in Berlin. Two presentations explored different aspects of probiotic intervention: the small intestine as a probiotic target and inclusion of probiotics into integrative approaches to gastroenterology. Probiotic recommendations in gastroenterology guidelines and current data on probiotic efficacy in paediatric patients were reviewed. Updates were given on probiotic and gut microbiota research in obesity and obesity-related diseases, the gut-brain axis and development of psychobiotics, and the protective effects of equol-producing strains for prostate cancer. Recent studies were presented on probiotic benefit for antibiotic-associated diarrhoea and people with HIV, as well as protection against the adverse effects of a short-term high-fat diet. Aspects of probiotic mechanisms of activity were discussed, including immunomodulatory mechanisms and metabolite effects, the anti-inflammatory properties of Faecalibacterium prausnitzii, the relationship between periodontitis, microbial production of butyrate in the oral cavity and ageing, and the pathogenic mechanisms of Campylobacter. Finally, an insight was given on a recent expert meeting, which re-examined the probiotic definition, advised on the appropriate use and scope of the term and outlined different probiotic categories and the prevalence of different mechanisms of activity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29401402", + "title": "Potential of Lactobacillus plantarum ZDY2013 and Bifidobacterium bifidum WBIN03 in relieving colitis by gut microbiota, immune, and anti-oxidative stress.", + "year": 2018, + "journal": "Canadian journal of microbiology", + "authors": [ + "Wang Y", + "Guo Y", + "Chen H", + "Wei H", + "Wan C" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.8088189266855677, + "mesh_terms": [ + "Animals", + "Bifidobacterium bifidum", + "Colitis", + "Cytokines", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "HT29 Cells", + "Humans", + "Hydrogen Peroxide", + "Lactobacillus plantarum", + "Mice", + "Mice, Inbred BALB C", + "Oxidative Stress", + "Probiotics" + ], + "raw_abstract": "Ulcerative colitis (UC) is an inflammatory bowel disease that is difficult to cure, with rising incidence in recent decades. Probiotics have become a new strategy for UC treatment. In this study, we chose 2 new multisource probiotics, Lactobacillus plantarum ZDY2013 from acid beans and Bifidobacterium bifidum WBIN03 from infant feces, and a mixture of both, to investigate the anti-inflammatory and antioxidant effect on H", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35906158", + "title": "Study of the gut microbiome in Egyptian patients with active ulcerative colitis.", + "year": 2023, + "journal": "Revista de gastroenterologia de Mexico (English)", + "authors": [ + "Ahmed EA", + "Ahmed SM", + "Zakaria NH", + "Baddour NM", + "Header DA" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7744841040992952, + "mesh_terms": [], + "raw_abstract": "INTRODUCTION AND AIM: Ulcerative colitis (UC) is characterized by chronic, uncontrolled inflammation of the intestinal mucosa. Gut microbiota dysbiosis was reported to be a factor in intestinal inflammation. The aim of the present study was to study changes in the gut microbiome in Egyptian patients with active UC. MATERIALS AND METHODS: In this cross-sectional study, the gut bacterial microbiome of 21 UC patients and 20 control subjects was analyzed using the quantitative SYBR Green real-time PCR technique, targeting the 16S rRNA gene of selected bacterial phyla/genera and/or species. RESULTS: UC patients showed marked dysbiosis evidenced by a significant decrease in the Firmicutes and F. prausnitzii anti-inflammatory bacteria. The Firmicutes/Bacteroidetes ratio was also lower in the UC cases (1.65), compared with the healthy controls (2.93). In addition, the UC cases showed a statistically significant decrease in Ruminococcus, compared with the control group. However, there were no statistically significant differences between UC patients and the controls, regarding A. muciniphila, Bifidobacterium, Lactobacillus, Bacteroides, and Prevotella. One UC case was positive for the pathogenic bacterium, Clostridioides difficile, with low relative abundance. CONCLUSION: The current study showed differences in the gut microbiome of UC patients, compared with healthy controls. This may help in identifying the gut microbiome and specific bacterial changes that can be targeted for treatment of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27604252", + "title": "Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers.", + "year": 2016, + "journal": "FEMS microbiology ecology", + "authors": [ + "Duranti S", + "Gaiani F", + "Mancabelli L", + "Milani C", + "Grandi A", + "Bolchi A", + "Santoni A", + "Lugli GA", + "Ferrario C", + "Mangifesta M", + "Viappiani A", + "Bertoni S", + "Vivo V", + "Serafini F", + "Barbaro MR", + "Fugazza A", + "Barbara G", + "Gioiosa L", + "Palanza P", + "Cantoni AM", + "de'Angelis GL", + "Barocelli E", + "de'Angelis N", + "van Sinderen D", + "Ventura M", + "Turroni F" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7580222409556477, + "mesh_terms": [ + "Animals", + "Bifidobacterium", + "Biomarkers", + "Colitis, Ulcerative", + "Dysbiosis", + "Female", + "Fimbriae, Bacterial", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Mice", + "Mice, Inbred BALB C", + "Probiotics", + "RNA, Ribosomal, 16S", + "T-Lymphocytes" + ], + "raw_abstract": "Ulcerative colitis (UC) is associated with a substantial alteration of specific gut commensals, some of which may be involved in microbiota-mediated protection. In this study, microbiota cataloging of UC patients by 16S rRNA microbial profiling revealed a marked reduction of bifidobacteria, in particular the Bifidobacterium bifidum species, thus suggesting that this taxon plays a biological role in the aetiology of UC. We investigated this further through an in vivo trial by testing the effects of oral treatment with B. bifidum PRL2010 in a wild-type murine colitis model. TNBS-treated mice receiving 10(9) cells of B. bifidum PRL2010 showed a marked reduction of all colitis-associated histological indices as well as maintenance of mucosal integrity as it was shown by the increase in the expression of many tight junction-encoding genes. The protective role of B. bifidum PRL2010, as well as its sortase-dependent pili, appears to be established through the induction of an innate immune response of the host. These results highlight the importance of B. bifidum as a microbial biomarker for UC, revealing its role in protection against experimentally induced colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39482823", + "title": "Gut microbiome-targeted therapies as adjuvant treatments in inflammatory bowel diseases: a systematic review and network meta-analysis.", + "year": 2025, + "journal": "Journal of gastroenterology and hepatology", + "authors": [ + "Zhang T", + "Li X", + "Li J", + "Sun F", + "Duan L" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7545750450159593, + "mesh_terms": [ + "Humans", + "Probiotics", + "Gastrointestinal Microbiome", + "Fecal Microbiota Transplantation", + "Prebiotics", + "Network Meta-Analysis as Topic", + "Synbiotics", + "Crohn Disease", + "Randomized Controlled Trials as Topic", + "Treatment Outcome", + "Colitis, Ulcerative", + "Inflammatory Bowel Diseases", + "Combined Modality Therapy" + ], + "raw_abstract": "BACKGROUND AND AIM: Gut microbiome-targeted therapies (MTTs), including prebiotics, probiotics, synbiotics, and fecal microbiota transplantation (FMT), have been widely used in inflammatory bowel diseases (IBD), but the best MTTs has not yet been confirmed. We performed a network meta-analysis (NMA) to examine this in ulcerative colitis (UC) and Crohn's disease (CD). METHODS: We searched for randomized controlled trials (RCTs) on the efficacy and safety of MTTs as adjuvant therapies for IBD until December 10, 2023. Data were pooled using a random effects model, with efficacy reported as pooled relative risks with 95% CIs, and interventions ranked according to means of surfaces under cumulative ranking values. RESULTS: Thirty-eight RCTs met the inclusion criteria. Firstly, we compared the efficacy of MTTs in IBD patients. Only FMT and probiotics were superior to placebo in all outcomes, but FMT ranked best in improving clinical response rate and clinical and endoscopic remission rate, and probiotics ranked second in reducing clinical relapse rate showed significant efficacy, while prebiotics ranked first showed nonsignificant efficacy. Subsequently, we conducted NMA for specific MTT formulations in UC and CD separately, which revealed that FMT, especially combined FMT via colonoscopy and enema, showed significant efficacy and was superior in improving clinical response and remission rate of active UC patients. As for endoscopic remission and clinical relapse, multistrain probiotics based on specific genera of Lactobacillus and Bifidobacterium showed significant efficacy and ranked best in UC. In CD, we found that no MTTs were significantly better than placebo, but synbiotics comprising Bifidobacterium and fructo-oligosaccharide/inulin mix and Saccharomyces ranked best in improving clinical remission and reducing clinical relapse, respectively. Moreover, FMT was safe in both UC and CD. CONCLUSIONS: FMT and multistrain probiotics showed superior efficacy in UC. However, the efficacy of MTTs varies among different IBD subtypes and disease stages; thus, the personalized treatment strategies of MTTs are necessary.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34397940", + "title": "Intestinal flora differences between patients with ulcerative colitis of different ethnic groups in China.", + "year": 2021, + "journal": "Medicine", + "authors": [ + "Liu H", + "Liu W", + "Huang X", + "Feng Y", + "Lu J", + "Gao F" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7432520728984736, + "mesh_terms": [ + "Adult", + "Bacteria", + "China", + "Colitis, Ulcerative", + "Ethnicity", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Incidence", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Retrospective Studies", + "Young Adult" + ], + "raw_abstract": "To determine the differences in intestinal flora between Uygur and Han patients with ulcerative colitis (UC).Microbial diversity and structural composition of fecal bacteria from patients with UC and their matched healthy spouses or first-degree relatives were analyzed using high-throughput sequencing technology.The fecal microbial diversity and abundance index of Uygur patients with UC (UUC) were significantly lower compared with the Uygur normal control group, while there was no significant difference between the Han UC patients (HUC) and the Han normal control group (HN). Compared with their respective control groups, Uygur UC patients and Han UC patients had a different main composition of human intestinal flora (P\u200a<\u200a.05). The abundance of Burkholderia, Caballeronia, Paraburkholderia in the UUC group were higher compared with the HUC group, while Faecalibacterium, Bifidobacterium, and Blautia in the HUC group were higher than those in the UUC group (P\u200a<\u200a.05). Veillonella in the UUC group was higher than that in the Uygur normal control group group, while Subdoligranulum and Ruminococcaceae_UCG-002 were significantly lower (P\u200a<\u200a.05). Prevotella_9 in the HUC group was significantly higher than that in HN group, while Blautia, Anaerostipes, and [Eubacterium]_hallii_group were significantly lower. Moreover, the top 6 species in order of importance were Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella.The difference in intestinal microflora structure may be one of the reasons for the clinical heterogeneity between Uygur and Han patients with UC. Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella could be used as potential biomarkers for predicting UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39026313", + "title": "Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease.", + "year": 2024, + "journal": "Microbiome", + "authors": [ + "Tian X", + "Li S", + "Wang C", + "Zhang Y", + "Feng X", + "Yan Q", + "Guo R", + "Wu F", + "Wu C", + "Wang Y", + "Huo X", + "Ma X" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7398748548914773, + "mesh_terms": [ + "Humans", + "Virome", + "Gastrointestinal Microbiome", + "Animals", + "Feces", + "Mice", + "Inflammatory Bowel Diseases", + "Female", + "Male", + "Adult", + "Middle Aged", + "Crohn Disease", + "Bacteriophages", + "Colitis, Ulcerative", + "Bacteria", + "China", + "Fecal Microbiota Transplantation", + "Case-Control Studies", + "Viruses" + ], + "raw_abstract": "BACKGROUND: The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS: In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella\u00a0species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS: Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37652126", + "title": "Fermentation patterns of prebiotics fructooligosaccharides-SCFA esters inoculated with fecal microbiota from ulcerative colitis patients.", + "year": 2023, + "journal": "Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association", + "authors": [ + "Chen W", + "Tan D", + "Yang Z", + "Tang J", + "Bai W", + "Tian L" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7251184336916032, + "mesh_terms": [ + "Inflammation", + "Fatty Acids, Volatile", + "Humans", + "Microbiota", + "Prebiotics", + "Colitis, Ulcerative", + "Fermentation", + "Feces", + "Clostridiales" + ], + "raw_abstract": "Ulcerative colitis (UC) is believed to arise from an imbalance between the intestinal microbiota and mucosal immunity, leading to excessive intestinal inflammation. Modulating the gut microbial community through dietary components presents a valuable strategy in aiding the treatment of UC. In this study, esters formed by binding of well-known prebiotics, fructooligosaccharides (FOS), with short chain fatty acids (SCFAs) via both enzymatic and chemical methods were evaluated for their impact on the gut microbiota of UC patients. An in vitro human colonic fermentation model was employed to monitor changes in total carbohydrates and SCFAs production during the fermentation of these esters by microbiota from patients with active and remission UC. The results showed that pronounced abundance of [Ruminococcus]_gnavus_group, Escherichia_Shigella, Lachnoclostridium, Klebsiella and other potential pathogens were detected in the fecal samples from UC patients, with a milder condition observed during the remission phase. Significant higher levels of corresponding SCFA were observed in the groups with addition of FOS-SCFAs esters during fermentation. Butyrylated fructooligosaccharides (B-FOS) and propionylated fructooligosaccharides (P-FOS) by enzymatic synthesis successfully promoted the proliferation of Bifidobacterium and inhibited Clostridium_sensu_stricto_1 and Klebsiella. Overall, B-FOS and P-FOS exhibit promising potential for restoring intestinal homeostasis and alleviating intestinal inflammation in individuals with UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33871395", + "title": "Fecal microbiota profile in patients with inflammatory bowel disease in Taiwan.", + "year": 2021, + "journal": "Journal of the Chinese Medical Association : JCMA", + "authors": [ + "Chang TE", + "Luo JC", + "Yang UC", + "Huang YH", + "Hou MC", + "Lee FY" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7212587404993733, + "mesh_terms": [ + "Adult", + "Cross-Sectional Studies", + "Feces", + "Female", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Microbiota", + "Middle Aged", + "Taiwan" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with complicated interaction between immune, gut microbiota, and environmental factors in a genetically vulnerable host. Dysbiosis is often seen in patients with IBD. We aimed to investigate the fecal microbiota in patients with IBD and compared them with a control group in Taiwan. METHODS: In this cross-sectional study, we investigated fecal microbiota in 20 patients with IBD and 48 healthy controls. Fecal samples from both IBD patients and controls were analyzed by the next-generation sequencing method and relevant software. RESULTS: The IBD group showed lower bacterial richness and diversity compared with the control group. The principal coordinate analysis also revealed the significant structural differences between the IBD group and the control group. These findings were consistent whether the analysis was based on an operational taxonomic unit or amplicon sequence variant. However, no significant difference was found when comparing the composition of fecal microbiota between ulcerative colitis (UC) and Crohn's disease (CD). Further analysis showed that Lactobacillus, Enterococcus, and Bifidobacterium were dominant in the IBD group, whereas Faecalibacterium and Subdoligranulum were dominant in the control group at the genus level. When comparing UC, CD, and control group, Lactobacillus, Bifidobacterium, and Enterococcus were identified as dominant genera in the UC group. Fusobacterium and Escherichia_Shigella were dominant in the CD group. CONCLUSION: Compared with the healthy control, the IBD group showed dysbiosis with a significant decrease in both richness and diversity of gut microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28852861", + "title": "Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.", + "year": 2018, + "journal": "Journal of gastroenterology", + "authors": [ + "Nishino K", + "Nishida A", + "Inoue R", + "Kawada Y", + "Ohno M", + "Sakai S", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Kawahara M", + "Naito Y", + "Andoh A" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6838575411226454, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Endoscopy, Gastrointestinal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. METHODS: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. RESULTS: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. \u03b1-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. CONCLUSIONS: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33686049", + "title": "Effects of Pretreatment with Bifidobacterium bifidum Using 16S Ribosomal RNA Gene Sequencing in a Mouse Model of Acute Colitis Induced by Dextran Sulfate Sodium.", + "year": 2021, + "journal": "Medical science monitor : international medical journal of experimental and clinical research", + "authors": [ + "Weng YJ", + "Jiang DX", + "Liang J", + "Ye SC", + "Tan WK", + "Yu CY", + "Zhou Y" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.672218383280948, + "mesh_terms": [ + "Animals", + "Bacteria", + "Bifidobacterium bifidum", + "Colitis", + "Colitis, Ulcerative", + "Colon", + "Dextran Sulfate", + "Disease Models, Animal", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Mice", + "Mice, Inbred C57BL", + "Probiotics", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND Bifidobacterium is a potentially effective and safe treatment for patients with inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease. However, information on the influence of B. bifidum on gut microbial diversity of treated and pretreated IBD patients is limited. MATERIAL AND METHODS Our study investigated therapeutic and preventive effects of B. bifidum ATCC 29521 on C57BL/6 mice with dextran sulfate sodium (DSS)-induced acute colitis via 16S ribosomal ribonucleic acid (rRNA) gene sequencing. RESULTS Treatment and pretreatment of mice with B. bifidum ATCC 29521 significantly alleviated the severity of acute colitis on the basis of clinical and pathologic indicators. 16S rRNA gene sequencing showed that administration of B. bifidum shifted composition of the gut microbiome in mice with DSS-induced colitis in both treated and pretreated groups. Mice pretreated with B. bifidum ATCC 29521 for 21 days exhibited a significant increase in diversity of the gut microbiome. Principal coordinate analysis showed that gut microbiota structure was shaped by different treatments and time points. On the basis of linear discriminant analysis of effect size, the abundance of the genus Escherichia-Shigella, belonging to the family Enterobacteriaceae, was reduced in the B. bifidum-treated group, indicating that pathogens were inhibited by the B. bifidum treatment. Furthermore, the genera Intestinimonas and Bacteroides were significantly associated with the B. bifidum-pretreated group. CONCLUSIONS 16S rRNA gene sequencing showed that pretreatment with B. bifidum ATCC 29521 reduced intestinal inflammation and altered the gut microbiota to favor the genera Intestinimonas and Bacteroides.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33555375", + "title": "Clinical effects and gut microbiota changes of using probiotics, prebiotics or synbiotics in inflammatory bowel disease: a systematic review and meta-analysis.", + "year": 2021, + "journal": "European journal of nutrition", + "authors": [ + "Zhang XF", + "Guan XX", + "Tang YJ", + "Sun JF", + "Wang XK", + "Wang WD", + "Fan JM" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6494337705850267, + "mesh_terms": [ + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Prebiotics", + "Probiotics", + "Synbiotics" + ], + "raw_abstract": "PURPOSE: Probiotics have been reported to be beneficial for inflammatory bowel disease (IBD), but the types, number of strains, dosage, and intervention time of probiotics used remain controversial. Furthermore, the changes of gut microbiota in IBD's patients are also intriguing. Thus, this meta-analysis was to explore the clinical effects and gut microbiota changes of using probiotics, prebiotics and synbiotics in IBD. METHODS: The search was performed in PubMed, Web of Science and the Cochrane library from inception to April 2020. Qualified randomized controlled trials were included. IBD's remission rate, disease activity index and recurrence rate were extracted and analyzed. Changes in the gut microbiota of patients with IBD are comprehensively described. RESULTS: Thirty-eight articles were included. Probiotics, prebiotics and synbiotics can induce/maintain IBD's remission and reduce ulcerative colitis (UC) disease activity index (RR\u2009=\u20091.13, 95% CI 1.02, 1.26, P\u2009<\u20090.05; SMD\u2009=\u20091.00, 95% CI 0.27, 1.73, P\u2009<\u20090.05). In subgroup analyses of IBD remission rate and UC disease activity index, we obtained some statistically significant results in some subgroup (P\u2009<\u20090.05). To some extent, probiotic supplements can increase the number of beneficial bacteria (especially Bifidobacteria) in the intestinal tract of patients with IBD. CONCLUSIONS: Our results support the treatment of IBD (especially UC) with pro/pre/synbiotics, and synbiotics are more effective. Probiotic supplements that are based on Lactobacillus and Bifidobacterium or more than one strain are more likely to be beneficial for IBD remission. The dose of 10", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26994772", + "title": "Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India.", + "year": 2016, + "journal": "Journal of gastroenterology", + "authors": [ + "Kedia S", + "Rampal R", + "Paul J", + "Ahuja V" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6380925576201456, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Dysentery, Amebic", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "India", + "Intestinal Mucosa" + ], + "raw_abstract": "The disease profile in the Indian population provides a unique opportunity for studying the host microbiome interaction in both infectious (amebiasis) and autoimmune diseases\u00a0like inflammatory bowel disease (IBD) from a similar environment and genetic background. Analysis of fecal samples from untreated amebic liver abscess (ALA) patients, Entamoeba histolytica (Eh)-negative and -positive asymptomatic individuals, and pus samples from naive ALA patients revealed a significant reduction in Lactobacillus in asymptomatic individuals (Eh +ve) and ALA patients. Two anaerobic genera, namely Bacteroides and Peptostreptococcus, were detected in naive ALA pus samples. Analysis of fecal samples from amoebic colitis patients showed a significant decline in population of Bacteroides, Clostridium coccoides and leptum subgroup, Lactobacillus, Campylobacter, and Eubacterium, whereas a significant increase in Bifidobacterium was observed. Mucosa-associated bacterial flora analysis from IBD patients and healthy controls revealed a significant difference in concentration of bacteria among predominating and subdominating genera between ulcerative colitis (UC), Crohn's disease (CD) patients, and controls. In contrast to the mucosal studies, we found a significant increase in lactobacilli population in fecal samples of active UC patients. Another study revealed a significant decrease of Clostridium coccoides and leptum clusters in fecal samples of active UC patients along with decreased concentrations of fecal SCFAs, especially of n-butyrate, iso-butyrate, and acetate. We therefore found similar perturbations in gut microbiome in both infectious and autoimmune diseases, indicating inflammation to be the major driver for changes in gut microbiome.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35888992", + "title": "Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease.", + "year": 2022, + "journal": "Microorganisms", + "authors": [ + "Olbj\u00f8rn C", + "Sm\u00e5stuen MC", + "Moen AEF" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6325639278232621, + "mesh_terms": [], + "raw_abstract": "We explored the fecal microbiota in pediatric patients <18 years of age with treatment-na\u00efve IBD (80 Crohn\u2019s disease (CD), 27 ulcerative colitis (UC)), in 50 non-IBD patients with gastrointestinal symptoms without inflammation and in 75 healthy children. Using a targeted qPCR approach, the quantities of more than 100 different bacterial species were measured. Results: The bacterial abundance was statistically significantly reduced in the IBD and non-IBD patients compared to the healthy children for several beneficial species. The CD patients had a lower abundance of Bifidobacterium species compared to the UC patients, and the IBD patients in need of biologic therapy had a lower abundance of butyrate producing bacteria. Based on the abundance of bacterial species at diagnosis, we constructed Diagnostic, Phenotype and Prognostic Indexes. Patients with a high Diagnostic Index had 2.5 times higher odds for having IBD than those with a lower index. The CD patients had a higher Phenotype Index than the UC patients. Patients with a high Prognostic Index had 2.1 higher odds for needing biologic therapy compared to those with a lower index. Conclusions: The fecal abundance of bacterial species can aid in diagnosing IBD, in distinguishing CD from UC and in identifying children with IBD in need of biologic therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33977948", + "title": "No Title", + "year": 2021, + "journal": "Food & function", + "authors": [ + "Pang B", + "Jin H", + "Liao N", + "Li J", + "Jiang C", + "Shao D", + "Shi J" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6306895291173065, + "mesh_terms": [ + "Animals", + "Mice", + "Anti-Inflammatory Agents", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "Disease Models, Animal", + "Fatty Acids, Volatile", + "Feces", + "Gastrointestinal Microbiome", + "Intestines", + "Lacticaseibacillus rhamnosus", + "Mice, Inbred C57BL", + "Milk, Human", + "RNA, Ribosomal, 16S", + "Tight Junction Proteins" + ], + "raw_abstract": "Gut microbiota imbalance is one of the major causes of ulcerative colitis (UC). L. rhamnosus SHA113 (LRS), a strain isolated from healthy human milk, influences the regulation of gut flora. This study aims to determine whether this strain can ameliorate UC by modulating gut microbiota. Mouse models of UC were established using C57BL/6Cnc mice with intragastric administration of 3.0% (w/v) dextran sodium sulfate (DSS). LRS was used to treat the mouse models of UC with 109 cfu mL-1 cell suspension via intragastric administration. To verify the effect of gut microbiota on UC, fecal microbiota collected from the mice after the treatment with LRS were also used to treat the UC mouse models (FMT). The severity of UC was evaluated based on body weight, colon length, disease activity index (DAI), and hematoxylin-eosin staining. The microbial composition was analyzed by 16S rRNA sequencing. The mRNA expression levels of cytokines, mucins, tight junction proteins, and antimicrobial peptides in the gastrointestinal tract were detected by quantitative real-time polymerase chain reaction. The short-chain fatty acid (SCFAs) in the cecal contents of all mice were quantitatively detected by gas chromatography and mass spectrometry. Both LRS and FMT exerted excellent therapeutic effects on UC, as evidenced by the reduction in body weight loss, colon length, and colon structural integrity, as well as the increase in the DAI (disease activity index). LRS and FMT treatments showed similar effects: (1) an increase of total SCFA production in the cecal contents and the abundance of gut microbial diversity and flora composition; (2) decreases in two genera (Parabacteroides and Escherichia/Shigella) related to the DAI and the enhancement of SCFAs and IL-10 positively related genera in the gut microbiota (Bilophila, Roseburia, Akkermansia, and Bifidobacterium); (3) downregulation of the expression of tumor necrosis factor-\u03b1, interleukin IL-6, and IL-1\u03b2, and upregulation of the expression of the anti-inflammatory cytokine IL-10; and (4) upregulation of the expression of mucins (Muc1-4) and tight junction protein ZO-1. Overall, L. rhamnosus SHA113 relieves UC via the regulation of gut microbiota: increases in SCFA-producing genera and decreases in UC-related genera. In addition, a single strain is sufficient to induce a significant change in the gut microbiota and exert therapeutic effects on UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39212113", + "title": "Ulva lactuca polysaccharides combined with fecal microbiota transplantation ameliorated dextran sodium sulfate-induced colitis in C57BL/6J mice.", + "year": 2025, + "journal": "Journal of the science of food and agriculture", + "authors": [ + "Liu Z", + "Wang M", + "Hu Y", + "Li J", + "Gong W", + "Guo X", + "Song S", + "Zhu B" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6139398496485432, + "mesh_terms": [ + "Animals", + "Fecal Microbiota Transplantation", + "Mice, Inbred C57BL", + "Mice", + "Dextran Sulfate", + "Polysaccharides", + "Gastrointestinal Microbiome", + "Male", + "Humans", + "Feces", + "Ulva", + "Colitis, Ulcerative", + "Plant Extracts", + "Colitis", + "Bacteria", + "Disease Models, Animal", + "Edible Seaweeds" + ], + "raw_abstract": "BACKGROUND: Fecal microbiota transplantation (FMT) of healthy donors improves ulcerative colitis (UC) patients by restoring the balance of the gut microbiota. However, donors vary in microbial diversity and composition, often resulting in weak or even ineffective FMT. Improving the efficacy of FMT through combination treatment has become a promising strategy. Ulva lactuca polysaccharides (ULP) have been found to benefit host health by regulating gut microbiota. The effect of the combination of ULP and FMT in ameliorating UC has not yet been evaluated. RESULTS: The present study found that supplementation with ULP combined with FMT showed better effects in ameliorating UC than supplementation with FMT alone. Results suggested that FMT or ULP combined with FMT alleviated the symptoms of UC in mice, as evidenced by prevention of body weight loss, improvement of disease activity index and protection of the intestinal mucus. Notably, ULP in combination with FMT was more effective than FMT in reducing levels of cytokines and related inflammatory enzymes. In addition, ULP combined with FMT effectively restored the dysbiosis induced by dextran sulfate sodium (DSS) and further enriched probiotics (such as Bifidobacterium). The production of short-chain fatty acids, especially acetic acid, was also significantly enriched by ULP combined with FMT. CONCLUSION: Supplementation of ULP combined with FMT could significantly ameliorate DSS-induced colitis in mice by inhibiting inflammation and restoring dysbiosis of gut microbiota. These results suggested that ULP combined with FMT has potential application in ameliorating UC. \u00a9 2024 Society of Chemical Industry.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38553410", + "title": "Efficacy of probiotic supplementation and impact on fecal microbiota in patients with inflammatory bowel disease: a systematic review and meta-analysis of randomized controlled trials.", + "year": 2025, + "journal": "Nutrition reviews", + "authors": [ + "Xu M", + "Zhang W", + "Lin B", + "Lei Y", + "Zhang Y", + "Zhang Y", + "Chen B", + "Mao Q", + "Kim JJ", + "Cao Q" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.612303111349618, + "mesh_terms": [ + "Humans", + "Bifidobacterium", + "Dietary Supplements", + "Feces", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Probiotics", + "Randomized Controlled Trials as Topic", + "Treatment Outcome" + ], + "raw_abstract": "UNLABELLED: Context: Research regarding the treatment of inflammatory bowel disease (IBD) with probiotics has not yielded consistent results. OBJECTIVE: The aim of this meta-analysis was to evaluate the efficacy of probiotics supplementation in patients with IBD. DATA SOURCES: Randomized controlled trials (RCTs) evaluating the efficacy of probiotics in patients with IBD were searched in PubMed, the Google Scholar database, Web of Science, and CrossRef for the period July 2003 to June 2023. DATA EXTRACTION: The RCTs were extracted, independently by 2 authors, according to the PICOS criteria. DATA ANALYSIS: Seven studies, including a total of 795 patients, met the study criteria. Five end points were selected to evaluate the efficacy. Of these, 3 indicators showed a statistically significant difference in efficacy: C-reactive protein (odds ratio [OR]: -2.45, 95% confidence interval [CI]: -3.16, -1.73, P\u2009<\u2009.01), the number of fecal Bifidobacterium (OR: 3.37, 95% CI: 3.28, 3.47, P\u2009<\u2009.01), and Lactobacillus(OR: 2.00, 95% CI: 1.91, 2.09, P\u2009<\u2009.01). The other 2 indicators (disease activity for Crohn's disease and for ulcerative colitis) showed no statistically significant difference, while the OR reflected a positive correlation. CONCLUSION: Probiotics supplementation may have a positive effect on IBD by reducing clinical symptoms, reducing the serological inflammatory markers, and increasing favorable gut flora in patients with IBD. Additional RCTs are needed to evaluate the therapeutic effect of probiotics in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39520912", + "title": "Rubidium salt can effectively relieve the symptoms of DSS-induced ulcerative colitis.", + "year": 2024, + "journal": "Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie", + "authors": [ + "Zhao L", + "Weng W", + "Ni M", + "Shen H", + "Zhang S", + "Chen Y", + "Jia R", + "Fan L", + "Mao Y", + "Qin L", + "Liu S", + "Wang Y" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5918563346137883, + "mesh_terms": [ + "Colitis, Ulcerative", + "Animals", + "Gastrointestinal Microbiome", + "Dextran Sulfate", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Salts", + "Colon", + "Disease Models, Animal" + ], + "raw_abstract": "Inflammatory bowel disease (IBD) is a chronic condition that afflicts individuals repeatedly and cannot be cured at present, which has seriously affected the quality of life of patients. Minerals Containing Rubidium (MCR) from Guangxi Yuechengling, which Professor Zhao Lichun purified, were explored. Against this backdrop, the present study investigates the efficacy of rubidium salt in ulcerative colitis. Rubidium salt reduced levels of inflammatory markers and improved intestinal barrier function through the Elisa kit, immunohistochemistry, and qPCR. Next, we detected the level of short-chain fatty acid and found that the content of propanoic acid, butyric acid, and n-butyric acid increased after treatment with rubidium salt. We used fecal metagenomics to explore the underlying reasons further and found that rubidium salt significantly adjusted the structure of intestinal flora, increased the abundance of beneficial bacteria such as lactobacillus and bifidobacterium, and inhibited the abundance of harmful bacteria such as Enterobacteriaceae and Escherichia coli. We also learned that rubidium salt directly weakened pathogenic bacteria's infection and survival ability by reducing the expression of virulence factors such as fimH, invA, and hilA and virulence genes such as acrA and ompR. Overall, rubidium salt can reduce harmful bacteria and increase beneficial bacteria. The increased beneficial bacteria help enhance the gut barrier and regulate inflammatory factors by raising the levels of short-chain fatty acids. A strengthened gut barrier further stabilizes microbial homeostasis, ultimately alleviating ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39073916", + "title": "Core microbiome-associated proteins associated with ulcerative colitis interact with cytokines for synergistic or antagonistic effects on gut bacteria.", + "year": 2024, + "journal": "The ISME journal", + "authors": [ + "Zhang T", + "Zhong H", + "Lin L", + "Zhang Z", + "Xue K", + "He F", + "Luo Y", + "Wang P", + "Zhao Z", + "Cong L", + "Pang P", + "Li X", + "Shan H", + "Yan Z" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5828772262635463, + "mesh_terms": [ + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Humans", + "Cytokines", + "Calgranulin B", + "Calgranulin A", + "Proteomics", + "Feces", + "Ruminococcus", + "Host Microbial Interactions", + "Clostridiales" + ], + "raw_abstract": "Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is associated with a loss or an imbalance of host-microorganism interactions. However, such interactions at protein levels remain largely unknown. Here, we applied a depletion-assisted metaproteomics approach to obtain in-depth host-microbiome association networks of IBD, where the core host proteins shifted from those maintaining mucosal homeostasis in controls to those involved in inflammation, proteolysis, and intestinal barrier in IBD. Microbial nodes such as short-chain fatty-acid producer-related host-microbial crosstalk were lost or suppressed by inflammatory proteins in IBD. Guided by protein-protein association networks, we employed proteomics and lipidomics to investigate the effects of UC-related core proteins S100A8, S100A9, and cytokines (IL-1\u03b2, IL-6, and TNF-\u03b1) on gut bacteria. These proteins suppressed purine nucleotide biosynthesis in stool-derived in vitro communities, which was also reduced in IBD stool samples. Single species study revealed that S100A8, S100A9, and cytokines can synergistically or antagonistically alter gut bacteria intracellular and secreted proteome, with combined S100A8 and S100A9 potently inhibiting beneficial Bifidobacterium adolescentis. Furthermore, these inflammatory proteins only altered the extracellular but not intracellular proteins of Ruminococcus gnavus. Generally, S100A8 induced more significant bacterial proteome changes than S100A9, IL-1\u03b2, IL-6, and TNF-\u03b1 but gut bacteria degrade significantly more S100A8 than S100A9 in the presence of both proteins. Among the investigated species, distinct lipid alterations were only observed in Bacteroides vulgatus treated with combined S100A8, S100A9, and cytokines. These results provided a valuable resource of inflammatory protein-centric host-microbial molecular interactions.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39126385", + "title": "Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis.", + "year": 2025, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Jangi S", + "Zhao N", + "Hsia K", + "Park YS", + "Michaud DS", + "Yoon H" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5805885116520583, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Male", + "Adult", + "Female", + "Prospective Studies", + "Middle Aged", + "Clostridiales", + "Candida", + "Republic of Korea", + "Feces" + ], + "raw_abstract": "BACKGROUND AND AIMS: While there is increasing interest in microbiome-directed therapies for patients with ulcerative colitis (UC), the identification of microbial targets remains elusive, underlining the need for novel approaches. METHODS: Utilizing metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation, we used a tree-based dichotomous approach to assemble distinct clusters of species-level bacterial co-abundance groups (CAGs). We evaluated the abundance of bacterial CAGs and fungal taxa during remission (n\u2005=\u2005166) and activity (n\u2005=\u200546). We examined if the bacterial CAGs identified in our cohorts were conserved in 2 healthy cohorts and a Korean UC cohort. RESULTS: CAG3 and CAG8, dominated by bacteria from the family Lachnospiraceae, were associated with remission. Low abundance of CAG8 and elevated abundance of Candida genus were predictive of active UC. Constituents from CAG8 were influential hub species of the remission-associated microbial UC network, including Ruminococcus gnavus, Erysipelatoclostridium ramosum, Blautia, and Dorea species. These hub species interactions were preserved in 2 healthy cohorts and were partially recapitulated in a Korean UC cohort. CAG8 abundance correlated with the secondary bile acid production pathway. Bacterial CAGs did not correlate with Candida; however, Bifidobacterium adolescentis and Alistipes putredinis were negatively associated with Candida. CONCLUSIONS: Lachnospiraceae-dominated bacterial CAGs were associated with remission in UC, with key bacterial interactions within the CAG also observed in 2 healthy cohorts and a Korean UC cohort. Bacterial CAG-based analyses may aid in designing candidate consortia for microbiome-based therapeutics.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29895146", + "title": "Camellia Oil ( Camellia oleifera Abel.) Modifies the Composition of Gut Microbiota and Alleviates Acetic Acid-Induced Colitis in Rats.", + "year": 2018, + "journal": "Journal of agricultural and food chemistry", + "authors": [ + "Lee WT", + "Tung YT", + "Wu CC", + "Tu PS", + "Yen GC" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5803532142982203, + "mesh_terms": [ + "Acetic Acid", + "Animals", + "Bacteria", + "Camellia", + "Colitis", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Intestines", + "Male", + "Plant Oils", + "Rats" + ], + "raw_abstract": "Ulcerative colitis (UC), one type of chronic inflammatory bowel disease (IBD), is a chronic and recurrent disorder of the gastrointestinal (GI) tract. As camellia oil (CO) is traditionally used to treat GI disorders, this study investigated the role of CO on acetic acid-induced colitis in the rat. The composition of the gut microbial community is related to many diseases; thus, this study also investigated the effects of CO on the composition of the gut microbiota. The rats were fed a dose of 2 mL/kg body weight CO, olive oil (OO), or soybean oil (SO) once a day for 20 days, and the gut microbiota was analyzed using 16S rRNA gene sequencing. Results of the gut microbiota examination showed significant clustering of feces after treatment with CO and OO; however, individual differences with OO varied considerably. Compared to SO and OO, the intake of CO increased the ratio of Firmicutes/Bacteroidetes, the \u03b1-diversity, relative abundance of the Bifidobacterium, and reduced Prevotella of the gut microbiota. On day 21, colitis was induced by a single transrectal administration of 2 mL of 4% acetic acid. However, pretreatment of rats with CO or OO for 24 days slightly enhanced antioxidant and antioxidant enzyme activities and significantly reduced inflammatory damage and lipid peroxidation, thus ameliorating acetic acid-induced colitis. These results indicated that CO was better able to ameliorate impairment of the antioxidant system induced by acetic acid compared to OO and SO, which may have been due to CO modifying the composition of the gut microbiota or CO being a rich source of phytochemicals.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38951788", + "title": "Taxonomic and phenotypic analysis of bifidobacteria isolated from IBD patients as potential probiotic strains.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Bosselaar S", + "Dhelin L", + "Dautel E", + "Titecat M", + "Duthoy S", + "Stelmaszczyk M", + "Delory N", + "De Sousa Violante M", + "Machuron F", + "Ait-Abderrahim H", + "Desreumaux P", + "Folign\u00e9 B", + "Monnet C" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5802714497287536, + "mesh_terms": [ + "Humans", + "Probiotics", + "Bifidobacterium", + "Adult", + "Female", + "Male", + "Middle Aged", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Young Adult", + "Aged", + "Colitis, Ulcerative", + "Crohn Disease", + "Phylogeny", + "Feces", + "RNA, Ribosomal, 16S", + "Phenotype", + "Adolescent", + "Anti-Bacterial Agents" + ], + "raw_abstract": "BACKGROUND: Inflammatory Bowel Diseases (IBD) are a major public health issue with unclear aetiology. Changes in the composition and functionality of the intestinal microbiota are associated with these pathologies, including the depletion of strict anaerobes such as Feacalibacterium prausnitzii. Less evidence is observed for depletion in other anaerobes, among which bifidobacteria. This study characterized the taxonomic and functional diversity of bifidobacteria isolated from the human intestinal microbiota in active and non-active IBD patients by a culturomics approach and evaluated if these bifidobacteria might be used as probiotics for gut health. RESULTS: A total of 341 bifidobacteria were isolated from the intestinal microbiota of IBD patients (52 Crohn's disease and 26 ulcerative colitis patients), with a high proportion of Bifidobacterium dentium strains (28% of isolated bifidobacteria). In ulcerative colitis, the major species identified was B.\u00a0dentium (39% of isolated bifidobacteria), in active and non-active ulcerative colitis. In Crohn's disease, B.\u00a0adolescentis was the major species isolated from non-active patients (40%), while similar amounts of B.\u00a0dentium and B.\u00a0adolescentis were found in active Crohn's disease patients. The relative abundance of B.\u00a0dentium was increased with age, both in Crohn's disease and ulcerative colitis and active and non-active IBD patients. Antibacterial capacities of bifidobacteria isolated from non-active ulcerative colitis against Escherichia\u00a0coli LF82 and Salmonella enterica ATCC 14028 were observed more often compared to strains isolated from active ulcerative colitis. Finally, B.\u00a0longum were retained as strains with the highest probiotic potential as they were the major strains presenting exopolysaccharide synthesis, antibacterial activity, and anti-inflammatory capacities. Antimicrobial activity and EPS synthesis were further correlated to the presence of antimicrobial and EPS gene clusters by in silico analysis. CONCLUSIONS: Different bifidobacterial taxonomic profiles were identified in the microbiota of IBD patients. The most abundant species were B.\u00a0dentium, mainly associated to the microbiota of ulcerative colitis patients and B.\u00a0adolescentis, in the intestinal microbiota of Crohn's disease patients. Additionally, the relative abundance of B.\u00a0dentium significantly increased with age. Furthermore, this study evidenced that bifidobacteria with probiotic potential (antipathogenic activity, exopolysaccharide production and anti-inflammatory activity), especially B.\u00a0longum strains, can be isolated from the intestinal microbiota of both active and non-active Crohn's disease and ulcerative colitis patients.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33548121", + "title": "Gut microbiota changes in inflammatory bowel diseases and ankylosing spondilytis.", + "year": 2021, + "journal": "Journal of gastrointestinal and liver diseases : JGLD", + "authors": [ + "Cardoneanu A", + "Mihai C", + "Rezus E", + "Burlui A", + "Popa I", + "Cijevschi Prelipcean C" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5790963912321858, + "mesh_terms": [ + "Bacteria", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Escherichia coli", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases" + ], + "raw_abstract": "BACKGROUND AND AIMS: Both inflammatory bowel diseases (IBD) and ankylosing spondylitis (AS) can be considered chronic immune disorders sharing common etiopathogenetic mechanisms. Changes in the composition of the intestinal microbiota, which can lead to an abnormal mucosal response, could be the missing link between these two diseases. Our study evaluate the composition of intestinal microbiota and to characterize gut dysbiosis in patients with IBD and AS. METHODS: We conducted a prospective case-control study that enrolled 124 patients [20 Crohn's disease (CD), 27 ulcerative colitis (UC), 28 AS, 17 IBD + AS and 32 controls). Intestinal microbiota analysis was performed by real-time polymerase chain reaction in stool samples. RESULTS: The total quantity of bacteria was decreased in all investigated groups compared to the control group. In studied groups, we noticed an increased percentage of Bacteroides and Escherichia coli (E.coli) and a decreased percentage of Clostridium coccoides, Clostridium leptum, and Faecalibacterium prausnitzii compared to the control group. The percentages of Bifidobacterium (p=0.010) as well as Lactobacillus group (p=0.023) were higher in the L3 form of CD patients. In the E2 form of UC, the quantity of Bacteroides was much higher compared to the E3 form (p=0.004). In AS patients, significant correlations were observed only for the Bifidobacterium species, significantly increased in the axial form compared to peripheral disease (p=0.035). Statistically significant correlations were demonstrated between the Crohn Disease Activity Index score and the total bacterial group (p=0.023, r=-0.507), respectively Bacteroides (p=0.021, r=-0.511) and between the Mayo score and Lactobacillus (p=0.001), respectively E. coli (p=0.001). In IBD + AS group, the Crohn Disease Activity Index score was inversely correlated with the total bacterial group (p=0.010) and directly correlated with Lactobacillus (p=0.047). CONCLUSIONS: Intestinal dysbiosis is associated with both IBD and AS. In the association of IBD with AS, dysbiosis is intermediate, but it is associated with the more severe articular disease. Bifidobacterium and Lactobacillus (commonly used as probiotics!) were found to be increased in the association between active IBD and active AS. Further studies are needed to understand how dysbiosis regulates the gut immune system and contributes to intestinal and articular inflammation.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29450747", + "title": "Efficacy of Bifidobacterium breve Fermented Milk in Maintaining Remission of Ulcerative Colitis.", + "year": 2018, + "journal": "Digestive diseases and sciences", + "authors": [ + "Matsuoka K", + "Uemura Y", + "Kanai T", + "Kunisaki R", + "Suzuki Y", + "Yokoyama K", + "Yoshimura N", + "Hibi T" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5484218269579456, + "mesh_terms": [ + "Adult", + "Aged", + "Bifidobacterium breve", + "Colitis, Ulcerative", + "Cultured Milk Products", + "Disease-Free Survival", + "Double-Blind Method", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestines", + "Japan", + "Lactobacillus acidophilus", + "Male", + "Middle Aged", + "Recurrence", + "Remission Induction", + "Time Factors", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Fermented milk products containing Bifidobacterium breve strain Yakult (BFM) may improve clinical status in ulcerative colitis (UC) patients. AIMS: To assess efficacy of BFM in maintaining remission in Japanese patients with quiescent UC. METHODS: This double-blind study (B-FLORA) enrolled 195 patients with quiescent UC, randomized to receive one pack of BFM fermented milk per day [Bifidobacterium breve strain Yakult (10\u00a0billion bacteria) and Lactobacillus acidophilus (1\u00a0billion bacteria)] (n\u00a0=\u00a098) or matching placebo (n\u00a0=\u00a097) for 48\u00a0weeks. The primary efficacy endpoint was relapse-free survival (relapse: rectal bleeding score\u00a0\u2265\u00a02 on Sutherland disease activity index scale for 3 consecutive days and/or initiation of remission induction therapy for worsening of UC). RESULTS: An interim analysis was conducted after inclusion and follow-up of one-third of patients for the first phase of the study (n\u00a0=\u00a0195). Relapse-free survival was not significantly different between the BFM and placebo groups (P\u00a0=\u00a00.643; hazard ratio 1.16; 95% CI 0.63-2.14, log-rank test), nor was the incidence of relapse. Therefore, the study was discontinued for lack of efficacy. An exploratory analysis of fecal samples from a subgroup of patients revealed no effects of either study beverage on intestinal microbiota, but there was a significant decrease in Bifidobacterium species before relapse, regardless of treatment group. Three mild adverse events occurred for which a causal relationship with the study beverage could not be ruled out (placebo: abdominal bloating and stress in one patient; BFM: body odor in one patient). CONCLUSIONS: BFM had no effect on time to relapse in UC patients compared with placebo. STUDY REGISTRATION: UMIN000007593.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "25986361", + "title": "Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation.", + "year": 2015, + "journal": "The American journal of gastroenterology", + "authors": [ + "Kolho KL", + "Korpela K", + "Jaakkola T", + "Pichai MV", + "Zoetendal EG", + "Salonen A", + "de Vos WM" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5426897323370067, + "mesh_terms": [ + "Adolescent", + "Anti-Inflammatory Agents", + "Bacteroides fragilis", + "Bifidobacterium", + "Case-Control Studies", + "Child", + "Clostridium", + "Colitis, Ulcerative", + "Crohn Disease", + "Eubacterium", + "Feces", + "Female", + "Humans", + "Inflammation", + "Leukocyte L1 Antigen Complex", + "Male", + "Microbiota", + "Molecular Typing", + "Prospective Studies", + "Tumor Necrosis Factor-alpha" + ], + "raw_abstract": "OBJECTIVES: Inflammatory bowel disease (IBD) is considered to result from interplay between host and intestinal microbiota. While IBD in adults has shown to be associated with marked changes in the intestinal microbiota, there are only a few studies in children, and particularly studies focusing on therapeutic responses are lacking. Hence, this prospective study addressed the intestinal microbiota in pediatric IBD especially related to the level of inflammation. METHODS: In total, 68 pediatric patients with IBD and 26 controls provided stool and blood samples in a tertiary care hospital and 32 received anti-tumor necrosis factor-\u03b1 (anti-TNF-\u03b1). Blood inflammatory markers and fecal calprotectin levels were determined. The intestinal microbiota was characterized by phylogenetic microarray and qPCR analysis. RESULTS: The microbiota varied along a gradient of increasing intestinal inflammation (indicated by calprotectin levels), which was associated with reduced microbial richness, abundance of butyrate producers, and relative abundance of Gram-positive bacteria (especially Clostridium clusters IV and XIVa). A significant association between microbiota composition and inflammation was indicated by a set of bacterial groups predicting the calprotectin levels (area under curve (AUC) of 0.85). During the induction of anti-TNF-\u03b1, the microbial diversity and similarity to the microbiota of controls increased in the responder group by week 6, but not in the non-responders (P<0.01; response related to calprotectin levels). The abundance of six groups of bacteria including those related to Eubacterium rectale and Bifidobacterium spp. predicted the response to anti-TNF-\u03b1 medication. CONCLUSIONS: Intestinal microbiota represents a potential biomarker for correlating the level of inflammation and therapeutic responses to be further validated.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31546058", + "title": "Association of Alterations in Intestinal Microbiota With Impaired Psychological Function in Patients With Inflammatory Bowel Diseases in Remission.", + "year": 2020, + "journal": "Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association", + "authors": [ + "Humbel F", + "Rieder JH", + "Franc Y", + "Juillerat P", + "Scharl M", + "Misselwitz B", + "Schreiner P", + "Begr\u00e9 S", + "Rogler G", + "von K\u00e4nel R", + "Yilmaz B", + "Biedermann L" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.536965525003367, + "mesh_terms": [ + "Cohort Studies", + "Colitis, Ulcerative", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Prospective Studies", + "Quality of Life", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND & AIMS: Depression and anxiety are frequent comorbidities with inflammatory bowel diseases (IBD). Alterations to the intestinal microbiome promote not only intestinal inflammation but also psychologic function. We studied the interactions between the composition of\u00a0the intestinal microbiota and psychological outcomes in patients with IBD in Switzerland. METHODS: We performed a prospective study of psychological comorbidities and quality of life (QoL) in 171 participants in the Swiss IBD Cohort Study with IBD in remission. Participants complete the Hospital Anxiety and Depression Scale, Perceived Stress Questionnaire, the 36-Item Short Form Survey, and the IBD QoL Questionnaire. Microbes were collected from intestinal biopsies and analyzed by 16S rRNA high-throughput sequencing. RESULTS: Microbiomes of patients with higher perceived stress had significantly lower alpha diversity. Anxiety and depressive symptoms were significantly associated with beta diversity. We found a negative correlation between psychological distress and abundance of Clostridia, Bacilli, Bacteroidia, and Beta- and Gamma-proteobacteria. Psychological distress was also associated with decreases in operational taxonomic units from the lineages of Lachnospiraceae, Fusobacteriaceae, Ruminococcaceae, Veillonellaceae, Alcaligenaceae, Desulfovibrionaceae, and Bacteroidaceae families. The relative abundance of Bifidobacterium in patients with Crohn's disease and Desulfovibrio in patients with ulcerative colitis correlated with depression, whereas abundance of Sutterella, RF 32, and Lactococcus correlated with quality of life in patients with Crohn's disease. CONCLUSIONS: We identified correlations between the composition of the intestinal microbiota in patients with IBD and remission, psychological well-being, and QoL. Further studies should investigate how intestinal inflammation, the microbiome, and microbial metabolites affect psychological well-being and whether these components are mono- or bi-directionally linked.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26839545", + "title": "Quantitative Analysis of Intestinal Flora of Uygur and Han Ethnic Chinese Patients with Ulcerative Colitis.", + "year": 2016, + "journal": "Gastroenterology research and practice", + "authors": [ + "Yao P", + "Cui M", + "Wang H", + "Gao H", + "Wang L", + "Yang T", + "Cheng Y" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5239886563650639, + "mesh_terms": [], + "raw_abstract": "Aim. To study the correlation between intestinal flora and ulcerative colitis by analyzing the abundance of Bacteroides, Fusobacterium, Clostridium, Bifidobacterium spp., and Faecalibacterium prausnitzii in the intestinal of ulcerative colitis (UC) patients and healthy controls with Uygur and Han ethnic. Methods. Bacterial genomic DNA was extracted from fecal samples and analyzed with real-time fluorescence quantitative polymerase chain reaction (PCR) to identify the abundance of Bacteroides, Fusobacterium, Clostridium, Bifidobacterium spp., and Faecalibacterium prausnitzii. Results. The samples from UC patients, Uygur and Han ethnic combined, had higher abundance of Bacteroides (P = 0.026) but lower Clostridium (P = 0.004), Bifidobacterium spp. (P = 0.009), and Faecalibacterium prausnitzii (P = 0.008) than those from healthy controls. Among UC patients, Bacteroides population was raised in acute UC patients (P \u2264 0.05), while the abundance of Clostridium, Bifidobacterium spp., Fusobacterium, and Faecalibacterium prausnitzii decreased (P \u2264 0.05) compared with the remission. In both UC patients group and control group, no difference was observed in the abundance of these 5 bacteria between the Han and the Uygur group. Conclusions. Variations in the abundance of these five bacterial strains in intestines may be associated with the occurrence of UC in Uygur and Han populations; however, these variations were not associated with ethnic difference.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38012477", + "title": "Integrated Metabolomics and Gut Microbiome Analysis Reveals the Efficacy of a Phytochemical Constituent in the Management of Ulcerative Colitis.", + "year": 2024, + "journal": "Molecular nutrition & food research", + "authors": [ + "Zhang K", + "Ji J", + "Li N", + "Yin Z", + "Fan G" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5184782244216902, + "mesh_terms": [ + "Rats", + "Animals", + "Mice", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Bacteria", + "Inflammation", + "Phytochemicals", + "Dextran Sulfate", + "Disease Models, Animal", + "Colitis", + "Colon", + "Mice, Inbred C57BL" + ], + "raw_abstract": "SCOPE: Cinnamaldehyde (CAH), a phytochemical constituent isolated from cinnamon, is gaining attention due to its nutritional and medicinal benefits. This study aimed to investigate the potential role of CAH in the treatment of ulcerative colitis (UC). METHODS AND RESULTS: Integrated metabolomics and gut microbiome analysis are performed for 2,4,6-trinitrobenzenesulfonic acid (TNBS) induced UC rats. The effect of CAH on colonic inflammation, lipid peroxidation, metabolic profiles, and gut microbiota is systematically explored. It finds that CAH improves the colitis-related symptoms, decreases disease activity index, increases the colon length and body weight, and alleviates histologic inflammation of UC rats. These therapeutic effects of CAH are due to suppression of inflammation and lipid peroxidation. Moreover, multi-omics analysis reveals that CAH treatment cause changes in plasma metabolome and gut microbiome in UC rats. CAH regulates lipid metabolic processes, especially phosphatidylcholines, lysophosphatidylcholines, and polyunsaturated fatty acids. Meanwhile, CAH modulates the gut microbial structure by restraining pathogenic bacteria (such as Helicobacter) and increasing probiotic bacteria (such as Bifidobacterium and Lactobacillus). CONCLUSIONS: These results indicate that CAH exerts a beneficial role in UC by synergistic modulating the balance in gut microbiota and the associated metabolites, and highlights the nutritional and medicinal value of CAH in UC management.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27687331", + "title": "The association between the gut microbiota and the inflammatory bowel disease activity: a systematic review and meta-analysis.", + "year": 2016, + "journal": "Scandinavian journal of gastroenterology", + "authors": [ + "Prosberg M", + "Bendtsen F", + "Vind I", + "Petersen AM", + "Gluud LL" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.509838400804006, + "mesh_terms": [ + "Bifidobacterium", + "Clostridium", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Faecalibacterium", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Remission Induction" + ], + "raw_abstract": "BACKGROUND: The pathogenesis of inflammatory bowel diseases (IBD) involves complex interactions between the microbiome and the immune system. We evaluated the association between the gut microbiota and disease activity in IBD patients. METHODS: Systematic review of clinical studies based on a published protocol. Included patients had ulcerative colitis (UC) or Crohn's disease (CD) classified as active or in remission. We selected bacteria assessed in at least three studies identified through electronic and manual searches (November 2015). Bias control was evaluated with the Newcastle Ottawa scale (NOS). Results of random-effects meta-analyses were presented as mean differences (MD). RESULTS: Three prospective and seven cross-sectional studies (NOS score 6-8) were included. Five studies included patients with CD (231 patients) and eight included patients with UC (392 patients). Compared to patients in remission, patients with active IBD had lower abundance of Clostridium coccoides (MD\u2009=\u2009-0.49, 95% CI: -0.79 to -0.19), Clostridium leptum (MD\u2009=\u2009-0.44, 95% CI: -0.74 to -0.14), Faecalibacterium prausnitzii (MD\u2009=\u2009-0.81, 95% CI: -1.23 to -0.39) and Bifidobacterium (MD\u2009=\u2009-0.37, 95% CI: -0.56 to -0.17). Subgroup analyses showed a difference in all four bacteria between patients with UC classified as active or in remission. Patients with active CD had fewer C. leptum, F. prausnitzii and Bifidobacterium, but not C. coccoides. CONCLUSION: This systematic review suggests that dysbiosis may be involved in the activity of IBD and that there may be differences between patients with CD and UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39187879", + "title": "Dynamic changes in the gut microbiota composition during adalimumab therapy in patients with ulcerative colitis: implications for treatment response prediction and therapeutic targets.", + "year": 2024, + "journal": "Gut pathogens", + "authors": [ + "Oh HN", + "Shin SY", + "Kim JH", + "Baek J", + "Kim HJ", + "Lee KM", + "Park SJ", + "Kim SY", + "Choi HK", + "Kim W", + "Sul WJ", + "Choi CH" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.48961183067760716, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: While significant research exists on gut microbiota changes after anti-tumor necrosis factor-alpha (anti TNF-\u03b1) therapy for ulcerative colitis, little is known about the longitudinal changes related to the effects of anti TNF-\u03b1. This study aimed to investigate the dynamics of gut microbiome changes during anti TNF-\u03b1 (adalimumab) therapy in patients with ulcerative colitis (UC). RESULTS: The microbiota composition was affected by the disease severity and extent in patients with UC. Regardless of clinical remission status at each time point, patients with UC exhibited microbial community distinctions from healthy controls. Distinct amplicon sequence variants (ASVs) differences were identified throughout the course of Adalimumab (ADA) treatment at each time point. A notable reduction in gut microbiome dissimilarity was observed only in remitters. Remitters demonstrated a decrease in the relative abundances of Burkholderia-Caballeronia-Paraburkholderia and Staphylococcus as the treatment progressed. Additionally, there was an observed increase in the relative abundances of Bifidobacterium and Dorea. Given the distribution of the 48 ASVs with high or low relative abundances in the pre-treatment samples according to clinical remission at week 8, a clinical remission at week 8 with a sensitivity and specificity of 72.4% and 84.3%, respectively, was predicted on the receiver operating characteristic curve (area under the curve, 0.851). CONCLUSIONS: The gut microbiota undergoes diverse changes according to the treatment response during ADA treatment. These changes provide insights into predicting treatment responses to ADA and offer new therapeutic targets for UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39604394", + "title": "Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease.", + "year": 2024, + "journal": "Nature communications", + "authors": [ + "Akiyama S", + "Nishijima S", + "Kojima Y", + "Kimura M", + "Ohsugi M", + "Ueki K", + "Mizokami M", + "Hattori M", + "Tsuchiya K", + "Uemura N", + "Kawai T", + "Bork P", + "Nagata N" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.482130594685921, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Crohn Disease", + "Gastrointestinal Microbiome", + "Feces", + "Male", + "Metagenomics", + "Female", + "Bacteriophages", + "Adult", + "Escherichia coli", + "Middle Aged", + "Japan", + "Fungi", + "Bacteria", + "Metagenome", + "Saccharomyces cerevisiae", + "Bifidobacterium", + "Virome", + "Enterococcus faecium", + "Fatty Acids, Volatile", + "Young Adult", + "China", + "Case-Control Studies" + ], + "raw_abstract": "The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "25554637", + "title": "Red Ginseng and Semen Coicis can improve the structure of gut microbiota and relieve the symptoms of ulcerative colitis.", + "year": 2015, + "journal": "Journal of ethnopharmacology", + "authors": [ + "Guo M", + "Ding S", + "Zhao C", + "Gu X", + "He X", + "Huang K", + "Luo Y", + "Liang Z", + "Tian H", + "Xu W" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.4777370636967581, + "mesh_terms": [ + "Animals", + "Bacteria", + "Coix", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Panax", + "Plant Extracts", + "Probiotics", + "Rats, Wistar" + ], + "raw_abstract": "ETHNOPHARMACOLOGICAL RELEVANCE: Many Chinese herbs are traditionally used as medicine to improve the functions of gastrointestinal tract. Some of these herbs are also promising agents for the improvement of the gut microbiota and the treatment of ulcerative colitis. MATERIALS AND METHODS: By screening seven traditional Chinese herbs, we found that Red Ginseng and Semen Coicis were the most effective in promoting the growth of probiotics including Lactobacillus and Bifidobacterium in vitro. We then evaluated the effects of Red Ginseng and Semen Coicis on the growth of the bacterial pathogens (Escherichia coli, Staphylococcus aureus, and Salmonella spp.) in vitro. In in vivo experiment, we gavage administrated trinitro-benzene-sulfonic acid induced ulcerative colitis (UC) rats with Red Ginseng and Semen Coicis extracts. After two weeks treatment, we analyzed the structure of the gut microbiota and examined the UC symptoms by employing qPCR and animal pathology detection techniques. RESULTS: Both Red Ginseng and Semen Coicis promoted the growth of probiotics - Bifidobacterium and Lactobacillus in vitro. Red Ginseng also inhibited the growth of some pathogen strains. In vivo, Red Ginseng and Semen Coicis improved the structure of gut microbiota and relieved the symptoms of ulcerative colitis in vivo. Compared with Semen Coicis, Red Ginseng was more effective in relieving the symptoms of ulcerative colitis. CONCLUSIONS: Red Ginseng could promote the growth of probiotic bacteria in vitro. Red Ginseng and, to a lesser extent Semen Coicis, gave positive results in an experimental in vivo model for ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32383181", + "title": "A disease-specific decline of the relative abundance of Bifidobacterium in patients with autoimmune hepatitis.", + "year": 2020, + "journal": "Alimentary pharmacology & therapeutics", + "authors": [ + "Liwinski T", + "Casar C", + "Ruehlemann MC", + "Bang C", + "Sebode M", + "Hohenester S", + "Denk G", + "Lieb W", + "Lohse AW", + "Franke A", + "Schramm C" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.47713096522059373, + "mesh_terms": [ + "Adult", + "Aged", + "Bacterial Load", + "Bifidobacterium", + "Case-Control Studies", + "Cohort Studies", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Hepatitis, Autoimmune", + "Humans", + "Liver Cirrhosis, Biliary", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: The pathogenesis of autoimmune hepatitis (AIH) is poorly understood and little is known about enteric microbiota in AIH. AIM: To investigate disease-specific microbiome alterations in AIH. METHODS: The V1-V2 variable regions of the 16S rRNA gene were sequenced in faecal samples from 347 patients with AIH and controls (AIH n\u00a0=\u00a072, healthy controls (HC) n\u00a0=\u00a095, primary biliary cholangitis (PBC) n\u00a0=\u00a099 and ulcerative colitis (UC) n\u00a0=\u00a081). RESULTS: Biodiversity (Shannon entropy) was decreased in AIH patients compared to HC (P\u00a0=\u00a00.016), which was partially reversed by azathioprine (P\u00a0=\u00a00.011). Regarding between-sample diversity, AIH patients separated from HC, PBC and UC individuals (all P\u00a0=\u00a00.001). Compared to HC, decreased relative abundance of anaerobic genera such as Faecalibacterium and an increase of Veillonella and the facultative anaerobic genera Streptococcus and Lactobacillus were detected. Importantly, a disease-specific decline of relative abundance of Bifidobacterium was observed in AIH patients. Lack of Bifidobacterium was associated with failure to achieve remission of AIH (P\u00a0<\u00a00.001). Of potential therapeutic implication, Bifidobacterium abundance correlated with average protein intake (P\u00a0<\u00a00.001). Random forests classification between AIH and PBC on the microbiome signature yielded an area under receiver operating characteristic curve (AUC) of 0.787 in the training cohort, and an AUC of 0.849 in an external validation cohort. CONCLUSION: Disease-specific faecal microbial alterations were identified in patients with AIH. Intestinal dysbiosis in AIH was characterised by a decline of Bifidobacterium, which was associated with increased disease activity. These results point to the contribution of intestinal microbiota to AIH pathogenesis and to novel therapeutic targets.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34103031", + "title": "Effect of the standard herbal preparation, STW5, treatment on dysbiosis induced by dextran sodium sulfate in experimental colitis.", + "year": 2021, + "journal": "BMC complementary medicine and therapies", + "authors": [ + "Mohamed SS", + "Abdeltawab NF", + "Wadie W", + "Ahmed LA", + "Ammar RM", + "Rabini S", + "Abdel-Aziz H", + "Khayyal MT" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.4257270399023091, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Dextran Sulfate", + "Disease Models, Animal", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Plant Extracts", + "Rats, Wistar", + "Rats" + ], + "raw_abstract": "BACKGROUND: The standardized herbal preparation, STW 5, is effective clinically in functional gastrointestinal disorders and experimentally in ulcerative colitis (UC). The present study explores whether the beneficial effect of STW 5 involves influencing the intestinal microbiota. METHODS: UC was induced in Wistar rats by feeding them 5% dextran sodium sulfate (DSS) in drinking water for 7\u2009days. Rats were treated concurrently with STW 5 and sacrificed 24\u2009h after last drug administration. Fecal samples were used to determine changes in the abundance of selected microbial phyla and genera using real-time PCR. RESULTS: Induction of UC led to dysbiosis and changes in the gut microbiota. The changes included an increase in some genera of the Firmicutes, namely Enterococcus, and a decrease in others, namely Blautia, Clostridium, and Lactobacillus. DSS further induced a marked increase in the abundance of Bacteroidetes and Proteobacteria as well as in the relative abundance of Actinobacteria and its genus Bifidobacterium. Methanobrevibacter levels (phylum Euryarchaeota) were also increased. Microbial dysbiosis was associated with changes in various parameters of colonic inflammation. STW 5 effectively guarded against those changes and significantly affected the indices of edema and inflammation in the UC model. Changes in colon length, colon mass index, inflammatory and apoptotic markers, and histological changes induced by DSS were also prevented. CONCLUSIONS: Dysbiosis plays a contributing role in the development of DSS-induced UC. Derangements in the microbial flora and associated inflammatory processes were largely prevented by STW 5, suggesting that this effect might contribute towards its beneficial usefulness in this condition.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29135456", + "title": "Probiotics and Their Use in Inflammatory Bowel Disease.", + "year": 2018, + "journal": "Alternative therapies in health and medicine", + "authors": [ + "Amer M", + "Nadeem M", + "Nazir SUR", + "Fakhar M", + "Abid F", + "Ain QU", + "Asif E" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.42407637200730647, + "mesh_terms": [ + "Humans", + "Inflammatory Bowel Diseases", + "Lactobacillus", + "Pakistan", + "Probiotics" + ], + "raw_abstract": "Context \u2022 Crohn's disease and ulcerative colitis result in similar gastrointestinal (GI) symptoms, including pain, diarrhea, stools with mucus or blood, and ulceration or tissue damage within the alimentary canal. Gut microbiota play a crucial role in triggering, maintaining, and exacerbating inflammatory bowel disease (IBD). Probiotics might help to rebalance the gut flora in a positive way, shifting from pro- to anti-inflammatory. Objectives \u2022 The study intended to investigate the safety and use of probiotics and the biological effects of probiotic bacteria on IBD. Design \u2022 The research team performed a literature review. The team conducted a database search in April 2015 using Google Scholar and PubMed to find studies relevant to probiotics and their use in IBD. Only papers that were published in English were considered, and all available years in each database were searched. The initial search identified 38 published articles, for which the research team obtained full texts and independently read them in full to identify those papers suitable for inclusion in the review. Setting \u2022 The study took place in the main library of the University of Lahore (Islamabad, Pakistan). Results \u2022 Many strains of probiotics exist, but the most common strains available today are (1) the Bifidobacterium species, (2) Enterococcus faecium, (4) the Lactobacillus strains, (4) Saccharomyces boulardii, (5) the Bacillus species, and (6) Pediococcus, all used to produce beneficial health effects. These species showed their beneficial effects on the host using different mechanisms involving (1) production of proteins, quorum sensing signaling inhibitors, butyrate, immunoglobulin A, and short-chain fatty acids; (2) decreased production of tumor necrosis factor alpha and interleukin 8; (3) increased expression of mucin 2; and (4) increased upregulation of defensin. Conclusions \u2022 Studies on probiotics in animal models of IBD are promising, and clinical results in IBD patients are encouraging; however, the data are limited, and few studies are placebo controlled. Additional placebo-controlled, double-blind studies in IBD are required before recommendations can be offered for routine use of probiotics in IBD. Additional organisms may eventually be developed through genetic engineering. The current evidence also indicates that probiotic effects are strain specific; they do not act through the same mechanisms nor are all probiotics indicated for the same health conditions. More research is needed to determine what strains and at what dose probiotics become more useful as part of a clinical intervention.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33440046", + "title": "Randomised clinical trial: exclusive enteral nutrition versus standard of care for acute severe ulcerative colitis.", + "year": 2021, + "journal": "Alimentary pharmacology & therapeutics", + "authors": [ + "Sahu P", + "Kedia S", + "Vuyyuru SK", + "Bajaj A", + "Markandey M", + "Singh N", + "Singh M", + "Kante B", + "Kumar P", + "Ranjan M", + "Sahni P", + "Panwar R", + "Sharma R", + "Das P", + "Makharia G", + "Travis SPL", + "Ahuja V" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.396674664912267, + "mesh_terms": [ + "Adult", + "Colitis, Ulcerative", + "Enteral Nutrition", + "Feces", + "Female", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Middle Aged", + "Standard of Care", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Intravenous corticosteroids are the mainstay of therapy for acute severe ulcerative colitis (ASUC), but 30%-40% of patients fail to respond. AIM: To investigate the effectiveness of exclusive enteral nutrition (EEN) as adjunctive therapy to intravenous corticosteroids in patients with ASUC. METHODS: This was an open-label randomised controlled trial, in which patients who were admitted with ASUC between August 2018 and May 2020 were randomised 1:1 to EEN or standard of care (SOC). Patients on EEN received a semi-elemental formula for 7\u00a0days along with SOC. The primary outcome was corticosteroid failure, defined by the need for salvage medical therapy or colectomy. Faecal microbial analysis was performed on day 1 and day 7 by 16s ribosomal RNA sequencing in some patients. RESULTS: Of 62 patients (mean age 35.3\u00a0\u00b1\u00a012.1\u00a0years, 40% male), 32 were randomised to EEN and 30 to SOC. Corticosteroid failure was lower on EEN compared to SOC (intention-to-treat analysis 25% vs 43%, P\u00a0=\u00a00.051; per protocol analysis 19% vs 43%, P\u00a0=\u00a00.04), without any difference in colectomy rate (9% vs 13%; P\u00a0=\u00a00.41). Patients on EEN had a shorter hospital stay [median (range) 10 (8-17) vs 13 (8-24) days; P\u00a0=\u00a00.04], higher day 7 albumin level (34\u00a0\u00b1\u00a04 vs 29\u00a0\u00b1\u00a03\u00a0g/L, P\u00a0<\u00a00.01), greater reduction in serum C-reactive protein and faecal calprotectin levels (both P\u00a0=\u00a00.04) and a lower composite outcome of colectomy/hospitalisation at 6\u00a0months (16% vs 39%; P\u00a0=\u00a00.045) compared to SOC. Patients on EEN showed increased abundance of Erysipelotrichaceae on day 7, with reduced Bifidobacterium and Veillonellaceae compared to SOC. CONCLUSIONS: EEN for 7\u00a0days may augment corticosteroid responsiveness in patients with ASUC. (REF/2018/05/019844; CTRI/2020/06/025989).", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31586453", + "title": "Effects of Low FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial.", + "year": 2020, + "journal": "Gastroenterology", + "authors": [ + "Cox SR", + "Lindsay JO", + "Fromentin S", + "Stagg AJ", + "McCarthy NE", + "Galleron N", + "Ibraim SB", + "Roume H", + "Levenez F", + "Pons N", + "Maziers N", + "Lomer MC", + "Ehrlich SD", + "Irving PM", + "Whelan K" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.38064576299818137, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biomarkers", + "Diet, Carbohydrate-Restricted", + "Disaccharides", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "Monosaccharides", + "Quality of Life", + "Severity of Illness Index", + "Single-Blind Method", + "Treatment Outcome", + "United Kingdom", + "Young Adult" + ], + "raw_abstract": "BACKGROUND & AIMS: There is limited evidence that a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) reduces gut symptoms in quiescent inflammatory bowel disease (IBD). We performed a randomized, controlled trial to investigate the effects of a low FODMAP diet on persistent gut symptoms, the intestinal microbiome, and circulating markers of inflammation in patients with quiescent IBD. METHODS: We performed a single-blind trial of 52 patients with quiescent Crohn's disease or ulcerative colitis and persistent gut symptoms at 2 large gastroenterology clinics in the United Kingdom. Patients were randomly assigned to groups that followed a diet low in FODMAPs (n\u00a0= 27) or a control diet (n\u00a0= 25), with dietary advice, for 4 weeks. Gut symptoms and health-related quality of life were measured using validated questionnaires. Stool and blood samples were collected at baseline and end of trial. We assessed fecal microbiome composition and function using shotgun metagenomic sequencing and phenotypes of T cells in blood using flow cytometry. RESULTS: A higher proportion of patients reported adequate relief of gut symptoms following the low FODMAP diet (14/27, 52%) than the control diet (4/25, 16%, P=.007). Patients had a greater reduction in irritable bowel syndrome severity scores following the low FODMAP diet (mean reduction of 67; standard error, 78) than the control diet (mean reduction of 34; standard error, 50), although this difference was not statistically significant (P\u00a0= .075). Following the low FODMAP diet, patients had higher health-related quality of life scores (81.9 \u00b1 1.2) than patients on the control diet (78.3 \u00b1 1.2, P\u00a0= .042). A targeted analysis revealed that in stool samples collected at the end of the study period, patients on the low FODMAP diet had significantly lower abundance of Bifidobacterium adolescentis, Bifidobacterium longum, and Faecalibacterium prausnitzii than patients on control diet. However, microbiome diversity and markers of inflammation did not differ significantly between groups. CONCLUSIONS: In a trial of the low FODMAP diet vs a control diet in patients with quiescent IBD, we found no significant difference after 4 weeks in change in irritable bowel syndrome severity scores, but significant improvements in specific symptom scores and numbers reporting adequate symptom relief. The low FODMAP diet reduced fecal abundance of microbes believed to regulate the immune response, compared with the control diet, but had no significant effect on markers of inflammation. We conclude that a 4-week diet low in FODMAPs is safe and effective for managing persistent gut symptoms in patients with quiescent IBD. www.isrctn.com no.: ISRCTN17061468.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29915396", + "title": "Probiotics in Gastroenterology: How Pro Is the Evidence in Adults?", + "year": 2018, + "journal": "The American journal of gastroenterology", + "authors": [ + "Koretz RL" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3783592649061879, + "mesh_terms": [ + "Adult", + "Gastroenterology", + "Gastrointestinal Diseases", + "Humans", + "Practice Guidelines as Topic", + "Probiotics", + "Randomized Controlled Trials as Topic" + ], + "raw_abstract": "Probiotic usage has become popular with both medical practitioners and the community in general; patients commonly seek advice regarding what, if any, such preparation would be useful for their own diseases. Since such advice should be evidence-based, identified randomized clinical trials (RCTs) for a number of gastrointestinal conditions were reviewed; the data were organized by individual probiotic genera/species. Only trials in adults were considered. Most of the identified RCTs were small and low-quality, so any conclusions to be drawn will be limited at least by methodologic problems. Using the GRADE system to consider the reliability of the evidence generated from these RCTs, it did appear that the use of fecal microbial transplantation to treat recurrent Clostridium difficile infection is well justified. Given the methodologic issues, there was moderately good evidence for preventing antibiotic-associated diarrhea with Lactobacillus, Bifidobacterium, Streptococcus, or Saccharomyces boulardii and for using Lactobacillus, Bifidobacterium, or Saccharomyces as adjunct therapy in the treatment of Helicobacter pylori. There were other conditions for which some supportive evidence was available. These conditions include VSL#3 for maintaining remissions in patients with pouchitis or treating active ulcerative colitis (UC), fecal microbial transplantation for treating active UC, Bifidobacterium for treating patients with UC in remission, Lactobacillus in patients with painful diverticulosis, a variety of probiotics (Lactobacillus, Bifidobacterium, Streptococcus, or VSL#3) in patients with minimal hepatic encephalopathy, and providing synbiotics to patients postoperatively after liver transplantation. Unfortunately, other limitations in the evidence made it very likely that future research will have an effect on the estimated benefit; these interventions cannot yet be recommended for routine use.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27150635", + "title": "Effect of probiotics (Lactobacillus plantarum 299 plus Bifidobacterium Cure21) in patients with poor ileal pouch function: a randomised controlled trial.", + "year": 2016, + "journal": "Scandinavian journal of gastroenterology", + "authors": [ + "Bengtsson J", + "Adlerberth I", + "\u00d6stblom A", + "Saksena P", + "\u00d6resland T", + "B\u00f6rjesson L" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3756537617728133, + "mesh_terms": [ + "Adult", + "Aged", + "Bifidobacterium longum subspecies infantis", + "Biomarkers", + "Colitis, Ulcerative", + "Colonic Pouches", + "Double-Blind Method", + "Endoscopy", + "Feces", + "Female", + "Humans", + "Lactobacillus plantarum", + "Male", + "Middle Aged", + "Norway", + "Postoperative Complications", + "Pouchitis", + "Probiotics", + "Proctocolectomy, Restorative", + "Severity of Illness Index" + ], + "raw_abstract": "OBJECTIVE: Poor pouch function after restorative proctocolectomy for ulcerative colitis is a considerable problem. Pouchitis and functional disorders are the most common reasons. Probiotics seem to have a beneficial effect in pouchitis but have not been assessed in functional pouch disorders. The aim was to analyse the effects of probiotics in patients with poor pouch function. METHODS: Thirty-three patients were randomized to probiotics (Lactobacillus plantarum 299 and Bifidobacterium infantis Cure 21) or placebo in a double blinded, 1:1 fashion. The treatment effect was assessed by the pouch functional score (PFS; 0-15, 15 worst), pouchitis disease activity index (PDAI; 0-18, 18 worst), and levels of four faecal biomarkers of inflammation (calprotectin, lactoferrin, myeloperoxidase [MPO] and eosinophilic cationic protein [ECP]). RESULTS: Thirty-two patients were included (probiotics\u2009=\u200917, placebo\u2009=\u200916). There was no difference in change in the PFS from before to after treatment between the groups (median difference: -1.00, 95% C.I. -3.00 to 0.00, p\u2009=\u20090.119). Furthermore, probiotics had no effect on PDAI (median difference: 0.00, 95% C.I. 0.00-1.00, p\u2009=\u20090.786), or on faecal biomarkers. Significant correlations were observed between PDAI and each of the faecal biomarkers at study start. There were no correlations between PFS or PDAI symptom subscore and the biomarkers. PDAI endoscopic and histologic subscores correlated significantly to each of the biomarkers. CONCLUSION: The hypothesis that probiotics improves pouch-related dysfunction was not confirmed. Faecal biomarkers could play a future role in the management of pouch patients.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34761733", + "title": "Attributes of intestinal microbiota composition and their correlation with clinical primary non-response to anti-TNF-\u03b1 agents in inflammatory bowel disease patients.", + "year": 2022, + "journal": "Bosnian journal of basic medical sciences", + "authors": [ + "Alatawi H", + "Mosli M", + "Saadah OI", + "Annese V", + "Al-Hindi R", + "Alatawy M", + "Al-Amrah H", + "Alshehri D", + "Bahieldin A", + "Edris S" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3507753490750978, + "mesh_terms": [ + "Bacteria", + "Biomarkers", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "RNA, Ribosomal, 16S", + "Tumor Necrosis Factor Inhibitors" + ], + "raw_abstract": "The largest microbial aggregation in the human body exists in the gastrointestinal tract. The microbiota in the host gastrointestinal tract comprises a diverse ecosystem, and the intestinal microbiota plays a vital role in maintaining gut homeostasis. This study aims to examine whether the gut microbiota influences unresponsiveness to anti-TNF-\u03b1 treatments in primary nonresponder patients, and consequently identify the responsible microbes as biomarkers of unresponsiveness. Stool samples were collected from a cohort of patients with an established diagnosis of IBD, either ulcerative colitis (UC) or Crohn's disease (CD), following completion of the induction phase of anti TNF therapy. 16S rRNA sequencing analysis was used to examine the pattern of microbiota communities in fecal samples. The quality and quantity of fecal microbiota were compared in responder and primary nonresponder IBD patients following anti-TNF-\u03b1 therapy. As per our hypothesis, a difference in gut microbiome composition between the two patient subgroups was observed. A decreased abundance of short-chain fatty acid (SCFA)-producing bacteria, including Anaerostipes, Coprococcus, Lachnospira, Roseburia, and Ruminococcus, was detected in non-responsive patients, which was the hallmark of dysbiosis. Biomarkers of dysbiosis that were identified as predictors of clinical nonresponse, included Klebsiella, Eubacteriaceae, RF32, Bifidobacterium_animalis, and Muribaculaceae-previously known as S24-7. Signature biomarkers showed dramatic alteration in the composition of gut microbiota in patients who demonstrated primary nonresponse to anti-TNF-\u03b1 agents. Dysbiosis, with features including a dropped biodiversity, augmentation in opportunistic pathogenic microbiota, and a lack of SCFA-producing bacteria, is a prominent feature of the microbiome of primary nonresponders to anti-TNF-\u03b1 therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27730312", + "title": "Efficacy and safety of single fecal microbiota transplantation for Japanese patients with mild to moderately active ulcerative colitis.", + "year": 2017, + "journal": "Journal of gastroenterology", + "authors": [ + "Nishida A", + "Imaeda H", + "Ohno M", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Andoh A" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.34087792107711073, + "mesh_terms": [ + "Adult", + "Colitis, Ulcerative", + "Colonoscopy", + "Fecal Microbiota Transplantation", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Japan", + "Male", + "Middle Aged", + "Remission Induction", + "Severity of Illness Index", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The clinical utility of fecal microbiota transplantation (FMT) in patients with ulcerative colitis (UC) is still controversial. We investigated the efficacy and safety of single FMT for patients with mild to moderately active UC in a Japanese population. METHODS: Fifty-seven patients were evaluated for eligibility, and 16 patients were excluded. Forty-one patients with UC refractory to standard medical therapy were treated with single FMT by colonoscopic administration. Changes in the fecal microbiota were assessed by 16S ribosomal DNA based terminal restriction fragment length polymorphism analysis. RESULTS: At 8\u00a0weeks after FMT, no patient achieved clinical remission, and 11 of 41 patients (26.8\u00a0%) showed clinical response. The full Mayo score and the Mayo clinical score significantly decreased at week 8 [full Mayo score 5.5\u00a0\u00b1\u00a02.4 (mean\u00a0\u00b1\u00a0standard deviation) at initiation and 4.6\u00a0\u00b1\u00a02.2 at week 8, P\u00a0<\u00a00.004; Mayo clinical score 4.0\u00a0\u00b1\u00a02.0 at initiation and 3.0\u00a0\u00b1\u00a01.9 at week 8, P\u00a0<\u00a00.001], but there were no statistically significant effects on the Mayo endoscopic score. No adverse events occurred after FMT or during the follow-up period of 8\u00a0weeks. The proportion of Bifidobacterium was significantly higher in the donor feces used for responders than in the donor feces used for nonresponders. The proportion of Lactobacillales and Clostridium cluster IV were significantly higher in the donor feces used for nonresponders. CONCLUSIONS: Single FMT by colonoscopy was performed safely in all patients, but sufficient clinical efficacy and microbial restoration were not confirmed in patients with mild to moderately active UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38215655", + "title": "A metabolomics-driven model for early remission prediction following vedolizumab treatment in patients with moderate-to-severe active ulcerative colitis.", + "year": 2024, + "journal": "International immunopharmacology", + "authors": [ + "Jiang L", + "Liu X", + "Su Y", + "Chen Y", + "Yang S", + "Ke X", + "Yao K", + "Guo Z" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3396844219774742, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Putrescine", + "Gastrointestinal Agents", + "Treatment Outcome", + "Remission Induction", + "Acetamides", + "Taurine", + "Retrospective Studies", + "Antibodies, Monoclonal, Humanized" + ], + "raw_abstract": "To predict early remission following anti-integrin therapy (vedolizumab [VDZ]) in patients with moderate-to-severe active ulcerative colitis (UC) using non-invasive biomarkers. The clinical data of a cohort of 33 patients with moderate-to-severe active UC admitted to the Department of Gastroenterology at Suzhou Municipal Hospital between January 2021 and December 2022 were collected. Of these, 9 patients declined VDZ treatment, and 21 received VDZ at doses of 300\u00a0mg\u00a0weeks 0, 2, and 6, each administered within a 30-minute infusion period. The treatment regimen aimed to induce remission of clinical symptoms; hence, the same dose was administered every 8\u00a0weeks. At weeks 0 and 14, serum C-reactive protein (CRP) and erythrocyte sedimentation rate were measured using a modified Mayo score. In addition to clinical assessment, stool samples at baseline and weeks 14 were collected and evaluated using 16SrRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS). Clinical remission was determined based on the clinical symptoms and partial Mayo scores. In patients who received VDZ, the strains of bifidobacterium longum (P\u00a0=\u00a00.022) and bacteroides sartorii (P\u00a0=\u00a00.039) significantly increased after treatment than before treatment. GC-MS analysis showed that taurine (P\u00a0=\u00a00.047) and putrescine (P\u00a0=\u00a00.035) significantly decreased after treatment. Furthermore, while acetamide exhibited a notable increase (P\u00a0=\u00a00.001), arachidic acid (P\u00a0<\u00a00.001) and behenic acid (P\u00a0=\u00a00.005) demonstrated statistically significant elevations. The combined prediction model of acetamide, taurine, and putrescine demonstrated a high predictive value of early remission in patients with moderate-to-severe active UC following VDZ treatment (area under the curve\u00a0=\u00a00.911, P\u00a0=\u00a00.014).", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32017001", + "title": "Effects of mesalazine combined with bifid triple viable on intestinal flora, immunoglobulin and levels of cal, MMP-9, and MPO in feces of patients with ulcerative colitis.", + "year": 2020, + "journal": "European review for medical and pharmacological sciences", + "authors": [ + "Jiang XE", + "Yang SM", + "Zhou XJ", + "Zhang Y" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.31490811965989757, + "mesh_terms": [ + "Adult", + "Anti-Inflammatory Agents, Non-Steroidal", + "Colitis, Ulcerative", + "Combined Modality Therapy", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Immunity, Cellular", + "Immunoglobulins", + "Intestinal Mucosa", + "Leukocyte L1 Antigen Complex", + "Male", + "Matrix Metalloproteinase 9", + "Mesalamine", + "Middle Aged", + "Peroxidase", + "Probiotics", + "Treatment Outcome" + ], + "raw_abstract": "OBJECTIVE: Ulcerative colitis (UC) commonly occurs in young and middle-aged people and is characterized by frequent attacks and difficult cure. Mesalazine is often applied in the initial treatment of UC, but it can lead to serious adverse effects. Its combination with bifid triple viable could mitigate adverse effects. This study aims to explore the effects of mesalazine combined with bifid triple viable on the intestinal flora, immunoglobulin (Ig), and levels of calprotectin (Cal), matrix metalloproteinase-9 (MMP-9), myeloperoxidase (MPO) in feces of UC patients. PATIENTS AND METHODS: A total of 180 UC patients in our hospital were divided into two groups with 90 cases in each one. Patients in control group were treated with oral mesalazine (1.5 g/d), and those in the treatment group were treated with oral mesalazine (1.5 g/d) combined with bifid triple viable (1.26 g/d) for 2 months. Treatment effects in both groups following the therapeutic period were observed accordingly. Feces of patients in the two groups were collected for detecting intestinal microorganism and the levels of Cal, MMP-9, and MPO. Serum levels of IgG, IgA, and IgM in each patient were detected by enzyme-linked immunosorbent assay (ELISA). RESULTS: The overall response rate of the treatment group (91.11%) was significantly higher than that of control group (68.89%; p=0.000). The abundances of intestinal microflora, including Bifidobacterium, Actinomycetes, Rikenellaceae, Genus VI of Acidaminococcaceae, and Metascardovia in treatment group were remarkably higher than those in control group. The abundances of intestinal microorganisms such as Phocaeicola, Lawsonia intracelluaris, Streptococcus, Ruminococcaceae, and Clostridium in control group were significantly higher than those in treatment group. After treatment, serum levels of IgG and IgM of patients in treatment group were lower than those in control group, with IgG of (15.14\u00b10.98) (p=0.031) and IgM of (1.50\u00b10.18) (p=0.000). No statistical difference in IgG level was observed between treatment group and control group after treatment (p=0.871). After treatment, the levels of Cal and MMP-9 in feces of patients in treatment group were significantly lower than those in control group with Cal of (79.81\u00b15.42) (p=0.000) and MMP-9 of (4.89\u00b10.98) (p=0.000). There was no statistical difference in the MPO level between treatment group and control group after treatment (p=0.871). CONCLUSIONS: Mesalazine combined with bifid triple viable is able to enhance the curative effect for UC, improve the composition of intestinal flora, weaken the immune response, and reduce levels of Cal and MMP-9 in the intestinal tract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37463118", + "title": "Prediction of Response to Systemic Corticosteroids in Active UC by Microbial Composition-A Prospective Multicenter Study.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Blesl A", + "Wurm P", + "Waschina S", + "Gr\u00f6chenig HP", + "Novacek G", + "Primas C", + "Reinisch W", + "Kutschera M", + "Illiasch C", + "Hennlich B", + "Steiner P", + "Koch R", + "Tillinger W", + "Haas T", + "Reicht G", + "Mayer A", + "Ludwiczek O", + "Miehsler W", + "Steidl K", + "Binder L", + "Reider S", + "Watschinger C", + "F\u00fcrst S", + "Kump P", + "Moschen A", + "Aden K", + "Gorkiewicz G", + "H\u00f6genauer C" + ], + "bacteria": "Bifidobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.24187317587685042, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "RNA, Ribosomal, 16S", + "Prospective Studies", + "Feces", + "Adrenal Cortex Hormones", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Corticosteroids are used for induction of remission in patients with moderately to severely active ulcerative colitis. However, up to one-third of patients fail to this therapy. We investigated if fecal microbial composition or its metabolic capacity are associated with response to systemic corticosteroids. METHODS: In this prospective, multicenter study, patients with active ulcerative colitis (Lichtiger score \u22654) receiving systemic corticosteroids were eligible. Data were assessed and fecal samples collected before and after 4 weeks of treatment. Patients were divided into responders (decrease of Lichtiger Score \u226550%) and nonresponders. The fecal microbiome was assessed by the 16S rRNA gene marker and analyzed with QIIME 2. Microbial metabolic pathways were predicted using parsimonious flux balance analysis. RESULTS: Among 93 included patients, 69 (74%) patients responded to corticosteroids after 4 weeks. At baseline, responders could not be distinguished from nonresponders by microbial diversity and composition, except for a subgroup of biologic-na\u00efve patients. Within 4 weeks of treatment, responders experienced changes in beta diversity with enrichment of ascribed beneficial taxa, including Blautia, Anaerostipes, and Bifidobacterium, as well as an increase in predicted butyrate synthesis. Nonresponders had only minor longitudinal taxonomic changes with a significant increase of Streptococcus salivarius and a microbial composition shifting away from responders. CONCLUSION: Baseline microbial diversity and composition seem to be of limited use to predict response to systemic corticosteroids in active ulcerative colitis. Response is longitudinally associated with restoration of microbial composition and its metabolic capacity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36300959", + "title": "FMT: What's Next? A Narrative Review of Fecal Microbiota Transplantation in Clostridioides difficile Infection and Inflammatory Bowel Disease.", + "year": 2022, + "journal": "Rhode Island medical journal (2013)", + "authors": [ + "Patwa SA", + "Ward C", + "Kelly CR" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.7998797552391995, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Clostridioides difficile", + "Treatment Outcome", + "Clostridium Infections", + "Inflammatory Bowel Diseases", + "Chronic Disease" + ], + "raw_abstract": "Fecal microbiota transplantation (FMT) is an increasingly employed treatment option for Clostridioides difficile infection (CDI), with growing data supporting its safety and effectiveness in patients with concurrent inflammatory bowel disease (IBD). Given that alterations in the gut microbiome are associated with both ulcerative colitis (UC) and Crohn's disease (CD), the use of FMT for the treatment of IBD itself is another area of active investigation. In this narrative review, we highlight the evidence for use of FMT in the treatment of CDI in patients with IBD, as well as for IBD alone, and provide insight into the future of microbiome therapeutics.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35906158", + "title": "Study of the gut microbiome in Egyptian patients with active ulcerative colitis.", + "year": 2023, + "journal": "Revista de gastroenterologia de Mexico (English)", + "authors": [ + "Ahmed EA", + "Ahmed SM", + "Zakaria NH", + "Baddour NM", + "Header DA" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.7744841040992952, + "mesh_terms": [], + "raw_abstract": "INTRODUCTION AND AIM: Ulcerative colitis (UC) is characterized by chronic, uncontrolled inflammation of the intestinal mucosa. Gut microbiota dysbiosis was reported to be a factor in intestinal inflammation. The aim of the present study was to study changes in the gut microbiome in Egyptian patients with active UC. MATERIALS AND METHODS: In this cross-sectional study, the gut bacterial microbiome of 21 UC patients and 20 control subjects was analyzed using the quantitative SYBR Green real-time PCR technique, targeting the 16S rRNA gene of selected bacterial phyla/genera and/or species. RESULTS: UC patients showed marked dysbiosis evidenced by a significant decrease in the Firmicutes and F. prausnitzii anti-inflammatory bacteria. The Firmicutes/Bacteroidetes ratio was also lower in the UC cases (1.65), compared with the healthy controls (2.93). In addition, the UC cases showed a statistically significant decrease in Ruminococcus, compared with the control group. However, there were no statistically significant differences between UC patients and the controls, regarding A. muciniphila, Bifidobacterium, Lactobacillus, Bacteroides, and Prevotella. One UC case was positive for the pathogenic bacterium, Clostridioides difficile, with low relative abundance. CONCLUSION: The current study showed differences in the gut microbiome of UC patients, compared with healthy controls. This may help in identifying the gut microbiome and specific bacterial changes that can be targeted for treatment of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34788420", + "title": "Efficacy and Outcomes of Faecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection in Children with Inflammatory Bowel Disease.", + "year": 2022, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Nicholson MR", + "Alexander E", + "Ballal S", + "Davidovics Z", + "Docktor M", + "Dole M", + "Gisser JM", + "Goyal A", + "Hourigan SK", + "Jensen MK", + "Kaplan JL", + "Kellermayer R", + "Kelsen JR", + "Kennedy MA", + "Khanna S", + "Knackstedt ED", + "Lentine J", + "Lewis JD", + "Michail S", + "Mitchell PD", + "Oliva-Hemker M", + "Patton T", + "Queliza K", + "Sidhu S", + "Solomon AB", + "Suskind DL", + "Weatherly M", + "Werlin S", + "de Zoeten EF", + "Kahn SA" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.7536095562717814, + "mesh_terms": [ + "Adult", + "Child", + "Chronic Disease", + "Clostridioides difficile", + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Feces", + "Humans", + "Inflammatory Bowel Diseases", + "Recurrence", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Children with inflammatory bowel disease [IBD] are disproportionally affected by recurrent Clostridioides difficile infection [rCDI]. Although faecal microbiota transplantation [FMT] has been used with good efficacy in adults with IBD, little is known about outcomes associated with FMT in paediatric IBD. METHODS: We performed a retrospective review of FMT at 20 paediatric centres in the USA from March 2012 to March 2020. Children with and without IBD were compared with determined differences in the efficacy of FMT for rCDI. In addition, children with IBD with and without a successful outcome were compared with determined predictors of success. Safety data and IBD-specific outcomes were obtained. RESULTS: A total of 396 paediatric patients, including 148 with IBD, were included. Children with IBD were no less likely to have a successful first FMT then the non-IBD affected cohort [76% vs 81%, p = 0.17]. Among children with IBD, patients were more likely to have a successful FMT if they received FMT with fresh stool [p = 0.03], were without diarrhoea prior to FMT [p = 0.03], or had a shorter time from rCDI diagnosis until FMT [p = 0.04]. Children with a failed FMT were more likely to have clinically active IBD post-FMT [p = 0.002] and 19 [13%] patients had an IBD-related hospitalisation in the 3-month follow-up. CONCLUSIONS: Based on the findings from this large US multicentre cohort, the efficacy of FMT for the treatment of rCDI did not differ in children with IBD. Failed FMT among children with IBD was possibly related to the presence of clinically active IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39862395", + "title": "Safety and Efficacy of Fecal Microbiota, Live-jslm (REBYOTA\u00ae), for the Prevention of Recurrent Clostridioides difficile Infection in Participants With Inflammatory Bowel Disease in PUNCH CD3-OLS.", + "year": 2025, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Allegretti JR", + "Feuerstadt P", + "Knapple WL", + "Orenstein R", + "Pinton P", + "Sheh A", + "Khanna S" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.747928289458475, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Fecal microbiota, live-jslm (RBL; REBYOTA\u00ae), is the first single-dose, broad consortia, microbiota-based live biotherapeutic approved by the US Food and Drug Administration to prevent recurrent Clostridioides difficile infection (rCDI) in adults following standard-of-care antimicrobials. Inflammatory bowel disease (IBD) is a common risk factor for rCDI, yet patients with IBD are often excluded from prospective trials. This subgroup analysis of PUNCH CD3-OLS (NCT03931941) evaluated the safety and efficacy of RBL in participants with rCDI and IBD. METHODS: Participants with IBD (ulcerative colitis [UC], Crohn's disease [CD], or unspecified) who had rCDI were included. Treatment-emergent adverse event (TEAE) data were collected for up to 6 months following RBL administration. Efficacy outcomes included treatment success at 8 weeks and sustained clinical response at 6 months. RESULTS: Overall, 793 participants were enrolled, and 697 received RBL; 74 had IBD (UC: n\u2005=\u200545; CD: n\u2005=\u200525; unspecified IBD: n\u2005=\u20054). TEAEs within 8 weeks of administration were reported by 45.9% and 47.5% of participants with and without IBD, respectively; most were mild or moderate gastrointestinal symptoms. Serious TEAEs within 8 weeks of administration were reported by 1.4% and 4.2% of participants with and without IBD, respectively. The treatment success rate at 8 weeks was 78.9%, and the sustained clinical response rate at 6 months was 91.1% in participants with IBD, similar to rates in participants without IBD (73.2% and 91.0%, respectively). CONCLUSIONS: The results of this subgroup analysis of PUNCH CD3-OLS suggest RBL is safe and efficacious in patients with IBD. This post hoc subgroup analysis of PUNCH CD3-OLS reports that fecal microbiota, live-jslm (RBL), was well-tolerated and efficacious for preventing recurrent Clostridioides difficile infection in individuals with inflammatory bowel disease, supporting the use of RBL in this high-risk patient population.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37874904", + "title": "Dysregulated Immunity to Clostridioides difficile in IBD Patients Without a History of Recognized Infection.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Cook L", + "Wong MQ", + "Rees WD", + "Schick A", + "Lisko DJ", + "Lunken GR", + "Wang X", + "Peters H", + "Oliveira L", + "Lau T", + "Mah R", + "Bressler B", + "Levings MK", + "Steiner TS" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.7392857901391011, + "mesh_terms": [ + "Humans", + "Male", + "Female", + "Clostridioides difficile", + "Adult", + "Clostridium Infections", + "Case-Control Studies", + "Middle Aged", + "Feces", + "Gastrointestinal Microbiome", + "CD4-Positive T-Lymphocytes", + "Bacterial Toxins", + "Colitis, Ulcerative", + "Th17 Cells", + "Inflammatory Bowel Diseases", + "RNA, Ribosomal, 16S", + "Crohn Disease", + "Integrin beta Chains", + "Young Adult", + "Bacterial Proteins" + ], + "raw_abstract": "BACKGROUND & AIMS: Clostridioides difficile is a toxin-secreting bacteria that is an urgent antimicrobial resistance threat, with approximately 25% of patients developing recurrent infections. Inflammatory bowel disease (IBD) patients are at increased risk of severe, recurrent C. difficile infection. METHODS: To investigate a role for C. difficile infection in IBD pathogenesis, we collected peripheral blood and stool from 20 each of ulcerative colitis patients, Crohn's disease patients, and healthy control subjects. We used a flow cytometric activation induced marker assay to quantify C. difficile toxin-specific CD4+ T cells and 16S ribosomal RNA sequencing to study microbiome diversity. RESULTS: We found IBD patients had significantly increased levels of C. difficile toxin B-specific CD4+ T cells, but not immunoglobulin G or immunoglobulin A, compared with healthy control subjects. Within antigen-specific CD4+ T cells, T helper type 17 cells and cells expressing the gut homing receptor integrin \u03b27 were reduced compared with healthy control subjects, similar to our previous study of non-IBD patients with recurrent C. difficile infection. Stool microbiome analysis revealed that gut homing, toxin-specific CD4+ T cells negatively associated with microbial diversity and, along with T helper type 17 cells, positively associated with bacteria enriched in healthy control subjects. CONCLUSIONS: These data suggest that IBD patients, potentially due to underlying intestinal dysbiosis, experience undiagnosed C. difficile infections that result in impaired toxin-specific immunity. This may contribute to the development of inflammatory T cell responses toward commensal bacteria and provide a rationale for C. difficile testing in IBD patients. Crohn\u2019s disease and ulcerative colitis patients with no history of Clostridioides difficile infection had dysregulated T cell immunity to C. difficile toxin B. This was significantly different from healthy control subjects but similar to non\u2013inflammatory bowel disease patients with recurrent C. difficile infection.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38334893", + "title": "Current perspectives on fecal microbiota transplantation in inflammatory bowel disease.", + "year": 2024, + "journal": "Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology", + "authors": [ + "Singh A", + "Midha V", + "Chauhan NS", + "Sood A" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.7280669173963281, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Inflammatory Bowel Diseases", + "Clostridium Infections", + "Longitudinal Studies", + "Inflammation", + "Dysbiosis", + "Treatment Outcome" + ], + "raw_abstract": "Fecal microbiota transplantation (FMT) has emerged as a promising therapeutic modality within the domain of inflammatory bowel disease (IBD). While FMT has secured approval and demonstrated efficacy in addressing recurrent and refractory Clostridioides difficile infection, its application in IBD remains an area of active exploration and research. The current status of FMT in IBD reflects a nuanced landscape, with ongoing investigations delving into its effectiveness, safety and optimal implementation. Early-stage clinical trials and observational studies have provided insights into the potential of FMT to modulate the dysbiotic gut microbiota associated with IBD, aiming to mitigate inflammation and promote mucosal healing. However, considerable complexities persist, including variations in donor selection, treatment protocols and outcome assessments. Challenges in standardizing FMT protocols for IBD treatment are compounded by the dynamic nature of the gut microbiome and the heterogeneity of IBD itself. Despite these challenges, enthusiasm for FMT in IBD emanates from its capacity to address gut microbial dysbiosis, signifying a paradigm shift towards more comprehensive approaches in IBD management. As ongoing research progresses, an enhanced understanding of FMT's role in IBD therapy is anticipated. This article synthesizes the current status of FMT in IBD, elucidating the attendant challenges and aspiring towards the refinement of its application for improved patient outcomes.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33121693", + "title": "Fecal Microbiota Transplantation for Ulcerative Colitis. Are We Ready for Primetime?", + "year": 2020, + "journal": "Gastroenterology clinics of North America", + "authors": [ + "Cheng YW", + "Fischer M" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.7234113584081548, + "mesh_terms": [ + "Colitis, Ulcerative", + "Dysbiosis", + "Fecal Microbiota Transplantation", + "Humans", + "Randomized Controlled Trials as Topic", + "Severity of Illness Index", + "Treatment Outcome" + ], + "raw_abstract": "\"Patients with inflammatory bowel disease, including ulcerative colitis (UC) and Crohn disease, have altered gut microbiomes. The success of fecal microbiota transplantation (FMT) in the treatment of Clostridioides difficile infection, a disease that is also marked by dysbiosis, has spurred research in applying FMT to UC. So far, 3 randomized controlled trials have demonstrated benefit in mild to moderate UC disease course after FMT. However, important questions regarding optimal stool preparation, route, and frequency of administration, as well as characteristics of the stool donor and recipient still remain.\"", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38335423", + "title": "Primary clostridium difficile infection in patients with ulcerative colitis: Case report and literature review.", + "year": 2024, + "journal": "Medicine", + "authors": [ + "Gao X", + "Zhou H", + "Hu Z", + "Wang Q", + "Chen Y", + "Zh F", + "Zhou G" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.7069280701914488, + "mesh_terms": [ + "Male", + "Humans", + "Adult", + "Colitis, Ulcerative", + "Vancomycin", + "Infliximab", + "Anti-Bacterial Agents", + "Clostridioides difficile", + "Inflammatory Bowel Diseases", + "Clostridium Infections", + "Inflammation" + ], + "raw_abstract": "RATIONALE: Inflammatory bowel disease (IBD), including Crohn disease (CD) and ulcerative colitis (UC), is a chronic immune-mediated disorder characterized by inflammation of the gastrointestinal tract. Patients with IBD are susceptible to various complications, including the coexistence of Clostridioides difficile infection (CDI). The incidence of IBD combined with difficile infection is higher in patients with compromised immune function, which can lead to increased mortality. PATIENT CONCERNS: A 43-year-old male presented with recurrent episodes of mucus and bloody stools persisting for more than a month without any identifiable triggering factors. Initially, the stool consistency was normal, but it progressively shifted to a loose and watery texture, with up to 8 occurrences daily. DIAGNOSES: This case underscores the diagnosis of severe UC through colonoscopy and colonic biopsy, along with the supplementary identification of a positive result for Clostridioides difficile in the fecal sample. INTERVENTIONS: The patient initiated infliximab therapy alongside a full vancomycin course, demonstrating the potential effectiveness of this intervention in managing early-stage ulcerative colitis with concurrent Clostridioides difficile infection. OUTCOMES: Following the completion of a full vancomycin course, the patient initiated infliximab therapy. The patient was free from significant discomfort, exhibited no fever, and had no mucopurulent bloody stools. A follow-up blood test indicated reduced inflammatory markers compared to the preoperative period, and the stools were normal. LESSONS: We illustrate the potential effectiveness of this medication by presenting an in-depth case report of a patient with early-stage UC. The report outlines the patient inclusion of infliximab to better manage UC inflammation alongside an adjunct vancomycin regimen, given the ineffectiveness of mesalazine therapy and the concurrent presence of Clostridium difficile infection. This case prompts consideration of therapeutic approaches for complex UC and contributes to advancing both research and clinical practice. Nonetheless, we should remain attentive to the variations and potential risks unique to each patient in order to formulate personalized treatment strategies.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31756948", + "title": "Fecal Eosinophil Cationic Protein Is a Diagnostic and Predictive Biomarker in Young Adults with Inflammatory Bowel Disease.", + "year": 2019, + "journal": "Journal of clinical medicine", + "authors": [ + "Abedin N", + "Seemann T", + "Kleinfeld S", + "Ruehrup J", + "R\u00f6seler S", + "Trautwein C", + "Streetz K", + "Sellge G" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.6627486675698188, + "mesh_terms": [], + "raw_abstract": "BACKGROUND AND AIMS: Fecal biomarkers are important non-invasive markers monitoring disease activity in inflammatory bowel disease (IBD). We compared the significance of fecal eosinophil cationic protein (fECP) and fecal calprotectin (fCal). METHODS: fECP and fCal were measured in patients with Crohn's disease (CD, n = 97), ulcerative colitis (UC, n = 53), Clostridioides difficile infection (CDI, n = 9), primary food allergy (PFA, n = 11), pollen-associated food allergy (n = 25) and non-inflammatory controls (n = 78). Results were correlated with clinical and endoscopic IBD activity scores. RESULTS: fECP was significantly elevated in CD, UC, CDI and PFA compared to controls. fCal was significantly increased in CD, UC and CDI. fECP had lower diagnostic accuracy than fCal (area under the curve (AUC) = 0.88) in differentiating between endoscopically active and inactive patients with IBD (AUC = 0.77, ROC analysis). In contrast to fCal, fECP correlated negatively with age and levels were also elevated in clinically and endoscopically inactive patients with IBD <45 years (endoscopically inactive IBD vs controls; AUC for fECP = 0.86; AUC for fCal = 0.62). However, in those patients with low inflammatory activity (fCal <250 mg/kg), high fECP indicated the need for treatment modification or surgery (fECP <200 \u00b5g/kg = 22%; 200-600 \u00b5g/kg = 44%; >600 \u00b5g/kg = 82%) at month 48 of follow-up. CONCLUSIONS: fECP is a diagnostic and prognostic marker in young patients with IBD in remission.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35758181", + "title": "Histological features of Clostridioides difficile colitis in patients with inflammatory bowel disease.", + "year": 2022, + "journal": "Histopathology", + "authors": [ + "Sweeney JR", + "Crawford CV", + "Yantiss RK" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.6619057379428894, + "mesh_terms": [ + "Clostridioides", + "Clostridioides difficile", + "Clostridium Infections", + "Colitis", + "Humans", + "Inflammatory Bowel Diseases" + ], + "raw_abstract": "AIMS: Patients with inflammatory bowel disease (IBD) are at increased risk for Clostridioides difficile infection, although clinically important infections can be difficult to recognise. C. difficile infection does not produce pseudomembranes when it occurs in IBD patients. These individuals may also be colonised by the organism, in which case diarrhoeal symptoms are not necessarily attributed to C. difficile. We performed this study to determine whether any features distinguished C. difficile-associated colitis from an IBD flare. METHODS AND RESULTS: We reviewed the clinical, endoscopic and biopsy findings from 50 patients with established IBD and worsening diarrhoea, including 22 with concurrent positive C. difficile stool toxin polymerase chain reaction (PCR) assays and 28 with negative C. difficile assay results. We found that C. difficile-infected patients had symptoms and endoscopic findings that were indistinguishable from active IBD. Although most biopsy samples from patients with C. difficile infection showed chronic active colitis indistinguishable from IBD, some displayed neutrophilic infiltrates unaccompanied by plasma cell-rich inflammation involving superficial (41%) and crypt (18%) epithelium as well as neutrophilic infiltrates within lamina propria distant from foci of cryptitis (32%). All three of these features were significantly more common among infected than uninfected patients (4, 0 and 4%; P\u2009=\u20090.002, P\u2009=\u20090.03 and P\u2009=\u20090.02, respectively). CONCLUSIONS: Although colonic biopsies from IBD patients with C. difficile infection usually lack features that aid distinction from colitic flares, some cases show an acute colitis pattern not seen in IBD alone. When identified in biopsies from symptomatic IBD patients, these changes should alert pathologists to the possibility of this clinically important infection.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34259969", + "title": "Novel Gut Microbiota Modulator, Which Markedly Increases Akkermansia muciniphila Occupancy, Ameliorates Experimental Colitis in Rats.", + "year": 2022, + "journal": "Digestive diseases and sciences", + "authors": [ + "Nakashima T", + "Fujii K", + "Seki T", + "Aoyama M", + "Azuma A", + "Kawasome H" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.6581646853162768, + "mesh_terms": [ + "Akkermansia", + "Animals", + "Anti-Bacterial Agents", + "Colitis", + "Dextran Sulfate", + "Disease Models, Animal", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Mice", + "Mice, Inbred C57BL", + "Mucins", + "Rats", + "Verrucomicrobia" + ], + "raw_abstract": "BACKGROUND: Since gut microbiota is involved in the pathogenesis of inflammatory bowel disease (IBD), antibiotics or probiotics may be attractive options for the treatment of IBD. Akkermansia\u00a0muciniphila is expected as a next-generation probiotic for IBD, and OPS-2071 is a novel quinolone with potent antibacterial activity against Clostridioides\u00a0difficile. AIMS: The aim of this study is to assess the potential of OPS-2071 as a gut microbiota modulator for IBD. METHODS: Minimum inhibitory concentrations of several bacteria in the human intestinal microbiota were determined. Microbiota changes in the feces were typed using metagenomic analysis after oral administration of OPS-2071 (100\u00a0mg/kg) twice a day to normal rats. The amounts of mucin were determined using the Fecal Mucin Assay Kit. The effects of OPS-2071 (1, 3, 10\u00a0mg/kg) twice a day on fecal symptoms and fecal microbiota were evaluated in a colitis rat model induced by free access to drinking water containing 3% dextran sulfate sodium for 10\u00a0days. RESULTS: OPS-2071 showed notably low antibacterial activity against only A.\u00a0muciniphila in spite of higher antimicrobial activity against other strains of intestinal bacteria. OPS-2071 rapidly and dramatically increased the occupancy of A.\u00a0muciniphila as well as the amount of mucin in the feces of normal rats. OPS-2071 (10\u00a0mg/kg) significantly suppressed the exacerbation of stool scores, especially the bloody stool score, with the increase in A.\u00a0muciniphila occupancy. CONCLUSIONS: OPS-2071 is expected to be a new therapeutic option for IBD as a gut microbiota modulator by significantly increasing A.\u00a0muciniphila occupancy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39079826", + "title": "Washed microbiota transplantation combined with biological agents promotes histological remission in refractory severe ulcerative colitis with recurrent intestinal infection: A case report.", + "year": 2024, + "journal": "Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology", + "authors": [ + "Wu Q", + "Yang LS", + "Huang HL", + "Li YF", + "Zhou YJ", + "Xu HM" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.5991785211104504, + "mesh_terms": [ + "Humans", + "Female", + "Adult", + "Colitis, Ulcerative", + "Fecal Microbiota Transplantation", + "Recurrence", + "Antibodies, Monoclonal, Humanized", + "Cytomegalovirus Infections", + "Clostridium Infections", + "Combined Modality Therapy", + "Remission Induction", + "Gastrointestinal Agents" + ], + "raw_abstract": "Ulcerative colitis (UC) is a chronic non-specific colitis disease. In recent years, fecal microbiota transplantation (FMT), including improved washed microbiota transplantation (WMT), and biological agents have helped improve the prognosis of patients with UC. However, a significant number of patients with moderate to severe UC do not get relief from glucocorticoids, immunosuppressants, and TNF-\u03b1 antagonists. Patients with severe UC are frequently burdened with opportunistic infections and subsequent surgical interventions. Combined treatment modalities are crucial for patients with severe UC and opportunistic infections. Herein, we reported a case of a 25-year-old female with refractory severe UC complicated with recurrent Clostridioides difficile infection and recurrent cytomegalovirus infection for six years. Surgical removal of the affected bowel segment was almost unavoidable. She showed endoscopic and histological recovery after comprehensive WMT and Vedolizumab treatment. The following are our learnings from the case: 1. A combination of WMT and biological agents can potentially obviate the necessity for surgical treatment in patients with refractory severe UC and promote histological remission. 2. Personalized comprehensive treatment and chronic disease management models for patients with UC should be emphasized. 3. WMT can help treat opportunistic infections, which may also strengthen the treatment with gut-targeted biological agents when traditional TNF-\u03b1 antagonists show poor efficacy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33155639", + "title": "Inflammatory Bowel Disease Outcomes Following Fecal Microbiota Transplantation for Recurrent C. difficile Infection.", + "year": 2021, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Allegretti JR", + "Kelly CR", + "Grinspan A", + "Mullish BH", + "Hurtado J", + "Carrellas M", + "Marcus J", + "Marchesi JR", + "McDonald JAK", + "Gerardin Y", + "Silverstein M", + "Pechlivanis A", + "Barker GF", + "Miguens Blanco J", + "Alexander JL", + "Gallagher KI", + "Pettee W", + "Phelps E", + "Nemes S", + "Sagi SV", + "Bohm M", + "Kassam Z", + "Fischer M" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.5983259606843162, + "mesh_terms": [ + "Clostridioides difficile", + "Clostridium Infections", + "Colitis, Ulcerative", + "Crohn Disease", + "Fecal Microbiota Transplantation", + "Humans", + "Prospective Studies", + "Recurrence", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Recurrent Clostridioides difficile infection (CDI) in patients with inflammatory bowel disease (IBD) is a clinical challenge. Fecal microbiota transplantation (FMT) has emerged as a recurrent CDI therapy. Anecdotal concerns exist regarding worsening of IBD activity; however, prospective data among IBD patients are limited. METHODS: Secondary analysis from an open-label, prospective, multicenter cohort study among IBD patients with 2 or more CDI episodes was performed. Participants underwent a single FMT by colonoscopy (250 mL, healthy universal donor). Secondary IBD-related outcomes included rate of de novo IBD flares, worsening IBD, and IBD improvement-all based on Mayo or Harvey-Bradshaw index (HBI) scores. Stool samples were collected for microbiome and targeted metabolomic profiling. RESULTS: Fifty patients enrolled in the study, among which 15 had Crohn's disease (mean HBI, 5.8 \u00b1 3.4) and 35 had ulcerative colitis (mean partial Mayo score, 4.2 \u00b1 2.1). Overall, 49 patients received treatment. Among the Crohn's disease cohort, 73.3% (11 of 15) had IBD improvement, and 4 (26.6%) had no disease activity change. Among the ulcerative colitis cohort, 62% (22 of 34) had IBD improvement, 29.4% (11 of 34) had no change, and 4% (1 of 34) experienced a de novo flare. Alpha diversity significantly increased post-FMT, and ulcerative colitis patients became more similar to the donor than Crohn's disease patients (P = 0.04). CONCLUSION: This prospective trial assessing FMT in IBD-CDI patients suggests IBD outcomes are better than reported in retrospective studies.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32066975", + "title": "Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota.", + "year": 2020, + "journal": "Nature medicine", + "authors": [ + "Nagao-Kitamoto H", + "Leslie JL", + "Kitamoto S", + "Jin C", + "Thomsson KA", + "Gillilland MG", + "Kuffa P", + "Goto Y", + "Jenq RR", + "Ishii C", + "Hirayama A", + "Seekatz AM", + "Martens EC", + "Eaton KA", + "Kao JY", + "Fukuda S", + "Higgins PDR", + "Karlsson NG", + "Young VB", + "Kamada N" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.5590053581614581, + "mesh_terms": [ + "Animals", + "Bacteria", + "Clostridioides difficile", + "Clostridium Infections", + "Enterocolitis, Pseudomembranous", + "Female", + "Gastrointestinal Microbiome", + "Glycosylation", + "Host Microbial Interactions", + "Humans", + "Interleukins", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Mice, Knockout", + "Veillonellaceae", + "Interleukin-22" + ], + "raw_abstract": "The involvement of host immunity in the gut microbiota-mediated colonization resistance to Clostridioides difficile infection (CDI) is incompletely understood. Here, we show that interleukin (IL)-22, induced by colonization of the gut microbiota, is crucial for the prevention of CDI in human microbiota-associated (HMA) mice. IL-22 signaling in HMA mice regulated host glycosylation, which enabled the growth of succinate-consuming bacteria Phascolarctobacterium spp. within the gut microbiome. Phascolarctobacterium reduced the availability of luminal succinate, a crucial metabolite for the growth of C. difficile, and therefore prevented the growth of C. difficile. IL-22-mediated host N-glycosylation is likely impaired in patients with ulcerative colitis (UC) and renders UC-HMA mice more susceptible to CDI. Transplantation of healthy human-derived microbiota or Phascolarctobacterium reduced luminal succinate levels and restored colonization resistance in UC-HMA mice. IL-22-mediated host glycosylation thus fosters the growth of commensal bacteria that compete with C. difficile for the nutritional niche.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38841848", + "title": "Current and future microbiome-based therapies in inflammatory bowel disease.", + "year": 2024, + "journal": "Current opinion in gastroenterology", + "authors": [ + "Montrose JA", + "Kurada S", + "Fischer M" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.5390579777070572, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Gastrointestinal Microbiome", + "Dysbiosis", + "Inflammatory Bowel Diseases", + "Randomized Controlled Trials as Topic" + ], + "raw_abstract": "PURPOSE OF REVIEW: The role of the microbiome and dysbiosis is increasingly recognized in the pathogenesis of inflammatory bowel disease (IBD). Intestinal microbiota transplant (IMT), previously termed fecal microbiota transplant has demonstrated efficacy in restoring a healthy microbiome and promoting gut health in recurrent Clostridioides difficile infection. Several randomized trials (RCTs) highlighted IMT's potential in treating ulcerative colitis, while smaller studies reported on its application in managing Crohn's disease and pouchitis. RECENT FINDINGS: This review delves into the current understanding of dysbiosis in IBD, highlighting the distinctions in the microbiota of patients with IBD compared to healthy controls. It explores the mechanisms by which IMT can restore a healthy microbiome and provides a focused analysis of recent RCTs using IMT for inducing and maintaining remission in IBD. Lastly, we discuss the current knowledge gaps that limit its widespread use. SUMMARY: The body of evidence supporting the use of IMT in IBD is growing. The lack of a standardized protocol impedes its application beyond clinical trials. Further research is needed to identify patient profile and disease phenotypes that benefit from IMT, to delineate key donor characteristics, optimize the delivery route, dosage, and frequency.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33654015", + "title": "Diagnosis and management of Clostridioides difficile infection in patients with inflammatory bowel disease.", + "year": 2021, + "journal": "Current opinion in gastroenterology", + "authors": [ + "Dalal RS", + "Allegretti JR" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.5390220593850191, + "mesh_terms": [ + "Clostridioides", + "Clostridioides difficile", + "Clostridium Infections", + "Humans", + "Inflammatory Bowel Diseases", + "Neoplasm Recurrence, Local", + "Prospective Studies", + "Retrospective Studies" + ], + "raw_abstract": "PURPOSE OF REVIEW: Clostridioides difficile infection (CDI) may complicate the course of ulcerative colitis and Crohn's disease. The clinical presentation of CDI in this population is often atypical, and patients may experience exacerbations of their underlying inflammatory bowel disease (IBD) secondary to C. difficile. In this review, we aim to review the risk factors, diagnosis, and management of CDI in the context of IBD. RECENT FINDINGS: Patients with colonic involvement of their IBD are at higher risk for CDI and colonization may be more common than in the general population. Therefore, CDI is confirmed using a two-step approach to stool testing. Oral vancomycin or fidaxomicin are the preferred agents for nonfulminant disease, and oral metronidazole is no longer recommended as first-line therapy. For all patients with CDI recurrence, fecal microbiota transplant (FMT) should be considered, as this has been shown to be safe and effective. Among those who have worsening of their underlying IBD, retrospective research suggest that outcomes are improved for those who undergo escalation of immunosuppression with appropriate antimicrobial treatment of C. difficile, however prospective data are needed. SUMMARY: CDI may complicate the course of IBD, however the presentation may not be typical. Therefore, all patients with worsening gastrointestinal symptoms should be evaluated for both CDI and IBD exacerbation. Providers should consider FMT for all patients with recurrent CDI as well as escalation of immunosuppression for patients who fail to improve with appropriate antimicrobial therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35193638", + "title": "Transfer of FRozen Encapsulated multi-donor Stool filtrate for active ulcerative Colitis (FRESCO): study protocol for a prospective, multicenter, double-blind, randomized, controlled trial.", + "year": 2022, + "journal": "Trials", + "authors": [ + "Stallmach A", + "Grunert P", + "Stallhofer J", + "L\u00f6ffler B", + "Baier M", + "R\u00f6del J", + "Kiehntopf M", + "Neugebauer S", + "Pieper DH", + "Junca H", + "Tannapfel A", + "Merkel U", + "Schumacher U", + "Breternitz-Gruhne M", + "Heller T", + "Schauer A", + "Hartmann M", + "Steube A" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.5261207415869956, + "mesh_terms": [ + "Colitis, Ulcerative", + "Double-Blind Method", + "Fecal Microbiota Transplantation", + "Feces", + "Humans", + "Multicenter Studies as Topic", + "Prospective Studies", + "Randomized Controlled Trials as Topic", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory bowel disease with significant morbidity and mortality. Although the precise cause remains unknown, disturbances in the intestinal microbial community have been linked to its pathogenesis. Randomized controlled trials in UC and relapsing Clostridioides difficile infection (CDI) have established fecal microbiota (FM) transfer (FMT) as an effective therapy. In this context, preliminary results indicated that the transfer of sterile fecal microbiota filtrates (<0.2 \u03bcm; FMF, FMFT) of donor stool also drives gastrointestinal microbiota changes and eliminates symptoms in CDI patients. However, along with the success of FMT, regulatory agencies issued safety alerts following reports of serious adverse events due to transmission of enteric pathogens through FMT. To reduce this risk, we established an extensive test protocol for our donors and quarantine regulations for the produced capsules, but alternative concepts are desirable. METHODS: Our project is a randomized, controlled, longitudinal, prospective, three-arm, multicenter, double-blind study to determine the safety and efficacy of repeated long-term, multi-donor FM or FMF transfers compared to placebo using oral, frozen capsules in 174 randomized patients with mild to moderate active UC. The primary outcome will be clinical remission at week 12. DISCUSSION: This proposal aims to examine (a) the efficacy of encapsulated transfer of FM and FMF as a therapy for mild to moderate UC, (b) the short- and long-term safety of FMT and FMFT in patients with UC, and (c) the microbial and immunologic changes that occur after FMT and FMFT to help understand how and why it affects inflammatory bowel disease. TRIAL REGISTRATION: ClinicalTrials.gov NCT03843385 . DRKS (Deutsches Register f\u00fcr Klinische Studien) DRKS00020471.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37085337", + "title": "Fecal microbiota transplantation for recurrent Clostridioides difficile infection in patients with concurrent ulcerative colitis.", + "year": 2023, + "journal": "Journal of autoimmunity", + "authors": [ + "Porcari S", + "Severino A", + "Rondinella D", + "Bibb\u00f2 S", + "Quaranta G", + "Masucci L", + "Maida M", + "Scaldaferri F", + "Sanguinetti M", + "Gasbarrini A", + "Cammarota G", + "Ianiro G" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.5177731938049913, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Colitis, Ulcerative", + "Clostridioides difficile", + "Retrospective Studies", + "Cohort Studies", + "Recurrence", + "Clostridium Infections", + "Inflammatory Bowel Diseases", + "Treatment Outcome" + ], + "raw_abstract": "AIMS: Clostridioides difficile infection (CDI) is a major challenge for healthcare systems. Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease, is a risk factor for primary and recurrent CDI (rCDI). Moreover, CDI itself often worsens the clinical picture of IBD, increasing the risk of complications. Fecal microbiota transplantation (FMT) is a highly effective treatment for rCDI, but data from patients with IBD and CDI are limited and often referred to mixed cohorts. We aimed to report outcomes from a cohort of patients with UC treated with FMT for rCDI superinfection. METHODS AND RESULTS: In a retrospective, single-centre cohort study we evaluated characteristics and outcomes of patients with UC who received FMT for rCDI. The primary outcome was negative C. difficile toxin 8 weeks after FMT. Thirty-five patients were included in the analysis. Sixteen patients were cured after single FMT, while 19 patients received repeat FMT. Overall, FMT cured rCDI in 32 patients (91%), and repeat FMT was significantly associated with sustained cure of CDI compared with single FMT (84% vs 50%, p\u00a0=\u00a00.018). Twenty-four patients (69%) experienced remission or an amelioration of UC activity. Serious adverse events were not observed. CONCLUSIONS: In our cohort of patients with UC, FMT was highly effective in curing rCDI without severe adverse events and repeat FMT was significantly associated with CDI cure. Most patients also experienced remission or amelioration of UC activity after FMT. Our findings suggest that a sequential FMT protocol may be used routinely in patients with UC and rCDI.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31821444", + "title": "Efficacy of Fecal Microbiota Transplantation for Recurrent C. Difficile Infection in Inflammatory Bowel Disease.", + "year": 2020, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Tariq R", + "Disbrow MB", + "Dibaise JK", + "Orenstein R", + "Saha S", + "Solanky D", + "Loftus EV", + "Pardi DS", + "Khanna S" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.4684021736357129, + "mesh_terms": [ + "Adult", + "Clostridioides difficile", + "Colitis", + "Colitis, Ulcerative", + "Crohn Disease", + "Diarrhea", + "Enterocolitis, Pseudomembranous", + "Fecal Microbiota Transplantation", + "Female", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "Recurrence", + "Retrospective Studies", + "Symptom Flare Up", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Clostridioides difficile infection (CDI) is associated with poor outcomes in inflammatory bowel disease (IBD) patients. Data are scarce on efficacy of fecal microbiota transplant (FMT) for recurrent CDI in IBD patients. METHODS: We reviewed health records of IBD patients (18 years of age or older) with recurrent CDI who underwent FMT. Outcomes of FMT for CDI were assessed on the basis of symptoms and stool test results. RESULTS: We included 145 patients (75 women [51.7%]; median age, 46 years). Median IBD duration was 8 (range, 0-47) years, 36.6% had Crohn disease, 61.4% had ulcerative colitis, and 2.1% had indeterminate colitis. Median number of prior CDI episodes was 3 (range, 3-20), and 61.4% had received vancomycin taper. Diarrhea resolved after FMT in 48 patients (33.1%) without further testing. Ninety-five patients (65.5%) underwent CDI testing owing to post-FMT recurrent diarrhea; 29 (20.0%) had positive results. After FMT, 2 patients received empiric treatment of recurrent CDI without symptom resolution, suggesting IBD was the cause of symptoms. The overall cure rate of CDI after FMT was 80.0%, without CDI recurrence at median follow-up of 9.3 (range, 0.1-51) months. Forty-three patients (29.7%) had planned IBD therapy escalation after CDI resolution; none de-escalated or discontinued IBD therapy. Overall, 7.6% had worsening IBD symptoms after FMT that were treated as new IBD flares. No clinical predictors of FMT failure were identified. CONCLUSIONS: Few patients had new IBD flare after FMT. Fecal microbiota transplantation effectively treats recurrent CDI in IBD patients but has no apparent beneficial effect on the IBD course.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34383708", + "title": "Fecal microbiota transplantation for recurrent Clostridioides difficile infection in patients with concurrent ulcerative colitis.", + "year": 2021, + "journal": "Acta microbiologica et immunologica Hungarica", + "authors": [ + "Gholam-Mostafaei FS", + "Yadegar A", + "Asadzadeh Aghdaei H", + "Shahrokh S", + "Ebrahimi Daryani N", + "Zali MR" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.46448181561994006, + "mesh_terms": [], + "raw_abstract": "Treatment of recurrent Clostridioides difficile infection (rCDI) has emerged as an important management dilemma particularly in patients with underlying inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) has been used as a safe and highly effective treatment option for rCDI refractory to standard antibiotic therapies. The aim of this study was to report the efficacy of FMT in Iranian rCDI patients with concurrent IBD. A total of seven consecutive patients with ulcerative colitis (UC) who had experienced 3 episodes of rCDI were enrolled in this study. All patients received at least a single FMT administered during colonoscopy by direct infusion of minimally processed donor stool. Patients were followed for a minimum of 6 months for assessment of treatment efficacy and adverse events (AEs) attributable to FMT. All 7 UC patients (100%) experienced a durable clinical response to a single FMT following 2 months after the procedure. One patient received a second FMT in which a successful resolution of rCDI was ultimately achieved. No serious AEs from FMT were noted. FMT through colonoscopy was a safe, simple and effective alternative treatment approach for rCDI in patients with underlying IBD. However, its use and efficacy should be pursued in long-term prospective controlled trials.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37337469", + "title": "Fidaxomicin treatment for Clostridioides difficile infection in patients with inflammatory bowel disease.", + "year": 2023, + "journal": "Journal of gastroenterology and hepatology", + "authors": [ + "Koop AH", + "Travers PM", + "Khanna S", + "Pardi DS", + "Farraye FA", + "Hashash JG" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.46175314900302367, + "mesh_terms": [ + "Adult", + "Humans", + "Female", + "Male", + "Fidaxomicin", + "Anti-Bacterial Agents", + "Vancomycin", + "Clostridioides difficile", + "Retrospective Studies", + "Clostridium Infections", + "Inflammatory Bowel Diseases", + "Recurrence", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND AND AIM: Although fidaxomicin is an effective first-line treatment for Clostridioides difficile infection, it has not been well studied in patients with inflammatory bowel disease. We aimed to assess the effectiveness of fidaxomicin for the treatment of C.\u00a0difficile infection in patients with inflammatory bowel disease. METHODS: This was a multicenter retrospective study of adults with inflammatory bowel disease and C.\u00a0difficile infection treated with fidaxomicin with at least 3\u00a0months of follow up. The primary outcomes were treatment response, defined as resolution of C.\u00a0difficile infection-attributed diarrhea and/or negative C.\u00a0difficile infection stool test, and time to C.\u00a0difficile infection recurrence after fidaxomicin. RESULTS: Thirty-three patients (median age 42\u00a0years; 60.6% female) were included. Most patients had ulcerative colitis (26, 78.8%), were receiving treatment with a biologic or small molecule medication (19, 57.6%), and had a prior episode of C.\u00a0difficile infection (26, 78.8%, median 2 episodes, range 0-15). Fidaxomicin led to resolution of C.\u00a0difficile infection in 20 (60.6%) patients, with 6/20 (30.0%) developing a recurrence at a median of 55\u00a0days. Most patients who failed to respond to fidaxomicin underwent fecal microbiota transplantation (10/13, 76.9%) with resolution. CONCLUSIONS: In this cohort of patients with inflammatory bowel disease and C.\u00a0difficile infection, 60.6% responded to treatment with fidaxomicin. Of those who did not respond, fecal microbiota transplantation was an effective therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32516177", + "title": "Low glutamate dehydrogenase levels are associated with colonization in Clostridium difficile PCR-only positive patients with inflammatory bowel disease.", + "year": 2020, + "journal": "European journal of gastroenterology & hepatology", + "authors": [ + "Desai M", + "Knight K", + "Gray JM", + "Nguyen V", + "Boone J", + "Sorrentino D" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.4516421716027892, + "mesh_terms": [ + "Clostridioides difficile", + "Clostridium Infections", + "Feces", + "Glutamate Dehydrogenase", + "Humans", + "Inflammatory Bowel Diseases", + "Polymerase Chain Reaction" + ], + "raw_abstract": "BACKGROUND/AIMS: Clostridioides difficile infection (CDI) remains a diagnostic challenge in patients with inflammatory bowel disease (IBD). We tested novel biomarkers to differentiate CDI from colonization in patients without (CDI-only) and with IBD (IBD-CDI). METHODS: Samples were enzyme immunoassay (EIA)-tested for glutamate dehydrogenase (GDH) and toxin, followed by reflex PCR. Quantitative GDH [(qGDH) - a novel indicator of Clostridium difficile load] and stool lactoferrin were tested at days 0, 3 and 10 during antibiotic treatment. Samples were also analyzed for toxin B cytotoxicity neutralization assay (CNA) and toxigenic culture, gold standards to detect free toxin and virulent bacteria, respectively. RESULTS: Forty-five symptomatic patients (28 CDI-only, 13 with Crohn's disease, 4 with ulcerative colitis) were recruited with 3 sequential samples available for 36 (21 CDI-only, 15 IBD-CDI). Thirty-nine of 45 (87%) cases were toxigenic culture-positive. In the CDI-only group, 78.6% were positive for EIA-toxin, 21.4% were PCR-positive while 82.1% were CNA-positive. In the IBD-CDI group, only one patient (6%) was EIA-toxin positive and 17.6% CNA-positive. The median qGDH level at day 0 was higher in CNA-positive patients compared to CNA-negative patients (1111 vs. 146\u2009ng/g, P\u2009=\u20090.004) and dropped together with lactoferrin from day 0 to 10. CDI eradication improved symptoms in 72.2% of patients with CDI-only. In 60% of patients with IBD-CDI, eradication was ineffective, with symptoms improving in 89% of them after IBD therapy intensification. CONCLUSION: In patients with IBD-CDI, PCR-only positivity might mainly reflect colonization rather than disease. C. difficile load by qGDH correlates with CNA-detected toxin and together with stool lactoferrin might differentiate CDI from colonization in patients with IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34735024", + "title": "An update on fecal microbiota transplantation for the treatment of gastrointestinal diseases.", + "year": 2022, + "journal": "Journal of gastroenterology and hepatology", + "authors": [ + "Waller KMJ", + "Leong RW", + "Paramsothy S" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.44048986974631155, + "mesh_terms": [ + "Fecal Microbiota Transplantation", + "Gastrointestinal Diseases", + "Humans", + "Treatment Outcome" + ], + "raw_abstract": "Our understanding of the microbiome and its implications for human health and disease continues to develop. Fecal microbiota transplantation (FMT) is now an established treatment for recurrent Clostridioides difficile infection. There is also increasing evidence for the efficacy of FMT in inducing remission for mild-moderate ulcerative colitis. However, for other indications, data for FMT are limited, with randomized controlled trials rare, typically small and often conflicting. Studies are continuing to explore the role of FMT for many other conditions, including Crohn's disease, functional gut disorders, metabolic syndrome, modulating responses to chemotherapy, eradication of multidrug resistant organisms, and the gut-brain axis. In light of safety, logistical, and regulatory challenges, there is a move to standardized products including narrow spectrum consortia. However, the mechanisms underpinning FMT remain incompletely understood, including the role of non-bacterial components, which may limit success of novel microbial approaches.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30986885", + "title": "[Ulcerative colitis: Does the modulation of gut microbiota induce long-lasting remission?].", + "year": 2019, + "journal": "Zeitschrift fur Gastroenterologie", + "authors": [ + "Stallmach A", + "Grunert P", + "Pieper D", + "Steube A" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.4276805987200631, + "mesh_terms": [ + "Colitis, Ulcerative", + "Fecal Microbiota Transplantation", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Microbiota", + "Remission Induction", + "Treatment Outcome" + ], + "raw_abstract": "Although the pathogenesis of ulcerative colitis (UC) remains elusive, substantial progress in understanding its development and progression has been achieved in the past decades, and novel effective treatment strategies have been developed. Changes in gut microbiota, environmental triggers, deregulation of immunological responses, and genetic predisposition have been identified as pathogenic key factors. There are several lines of clinical observations, which support a close connection of altered gut microbiota with the development and course of UC. Despite a plethora of microbiota alterations in UC, it is currently unclear whether the observed changes in inflammation are cause or effect of the altered microbiota state.Fecal microbiota transplantation (FMT) provides a novel, perhaps complementary, strategy to restore gut microbial diversity, bacterial richness, and microbial homeostasis in UC. FMT is an already established treatment option for recurrent Clostridioides difficile infection, and several case series and randomized controlled trials have described its use in UC. In this review, we evaluate recent efficacy and safety data on FMT for UC, discuss possible pitfalls and show possible areas of future development. Although FMT could become a promising treatment modality for UC, based on currently available data, FMT should be only performed in clinical trials as controlled studies focusing on long-term outcomes and safety are warranted. Das Verst\u00e4ndnis der Colitis ulcerosa (CU) ist in den letzten Dekaden stetig gewachsen; unterschiedliche Therapiekonzepte sind f\u00fcr verschiedene Krankheitssituationen standardisiert. In der Pathogenese wird der gastrointestinalen Mikrobiota, Umweltfaktoren, \u00fcberschie\u00dfenden immunologischen Reaktionen und genetischen Faktoren eine immer gr\u00f6\u00dfere Bedeutung zugeordnet. So zeigen zahlreiche klinische Beobachtungen eine enge Verbindung zwischen einer dysbiotischen Mikrobiota und der Erstmanifestation und dem Verlauf der CU an. Vor dem Hintergrund, dass genetische Faktoren und inflammatorische Reaktionen die Mikrobiota selber ver\u00e4ndern k\u00f6nnen ist aber nicht klar, was Ursache und Folge ist. Der F\u00e4kale Mikrobiom Transfer (FMT) ist der drastischste Eingriff um eine dysbiotische Mikrobiota zu normalisieren. Mittlerweile ist ein FMT eine akzeptierte Behandlung der rezidivierenden Clostridioides difficile-Infektion; zahlreiche Fallserien und kontrollierte Studien untersuchen dieses Konzept auch bei Patienten mit CU. Vor diesem Hintergrund erfolgt eine Zusammenfassung der aktuellen Literatur bez\u00fcglich Effektivit\u00e4t und Sicherheit. M\u00f6gliche Limitationen und offene Fragen werden diskutiert, um das Konzept des FMT zur Therapie der CU zu verbessern. Ohne Zweifel sind dringend weitere kontrollierte Studien notwendig; ein FMT sollte bei CU nicht au\u00dferhalb dieser erfolgen.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30403550", + "title": "Clinical Application and Potential of Fecal Microbiota Transplantation.", + "year": 2019, + "journal": "Annual review of medicine", + "authors": [ + "Ooijevaar RE", + "Terveer EM", + "Verspaget HW", + "Kuijper EJ", + "Keller JJ" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.389638614164043, + "mesh_terms": [ + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Female", + "Forecasting", + "Humans", + "Irritable Bowel Syndrome", + "Male", + "Patient Safety", + "Randomized Controlled Trials as Topic", + "Risk Assessment", + "Treatment Outcome" + ], + "raw_abstract": "Fecal microbiota transplantation (FMT) is a well-established treatment for recurrent Clostridioides difficile infection. FMT has become a more readily available and useful new treatment option as a result of stool banks. The current state of knowledge indicates that dysbiosis of the gut microbiota is implicated in several disorders in addition to C. difficile infection. Randomized controlled studies have shown FMT to be somewhat effective in treating ulcerative colitis, irritable bowel syndrome, and hepatic encephalopathy. In addition, FMT has been beneficial in treating several other conditions, such as the eradication of multidrug-resistant organisms and graft-versus-host disease. We expect that FMT will soon be implemented as a treatment strategy for several new indications, although further studies are needed.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36777748", + "title": "Fecal Microbiota Transplantation for Ulcerative Colitis: An Evolving Therapy.", + "year": 2020, + "journal": "Crohn's & colitis 360", + "authors": [ + "Sood A", + "Singh A", + "Midha V", + "Mahajan R", + "Kao D", + "Rubin DT", + "Bernstein CN" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.3834288445681601, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Fecal microbiota transplantation (FMT) is currently an approved treatment for recurrent and refractory Clostridioides difficile infection. However, its use in ulcerative colitis is at an early stage and significant gaps remain in our understanding of the mechanisms and logistics of its practical application. METHODS AND RESULTS: This article aims to look into specific issues which remain unsettled for use of FMT in ulcerative colitis including donor and recipient selection, route of administration, and duration of therapy. We also discuss optimal ways to assess response to FMT and the current state of FMT regulations. In addition, we postulate the impact of diet on the microbiome profile of the donor and recipient. We also suggest a change in the nomenclature from FMT to fecal microbiome transfer. CONCLUSION: FMT is an evolving therapy. There are several considerations for its use in UC but its use and role should be directed by further clinical trials.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37725044", + "title": "Factors Associated With Response to Rescue Therapy in Acute Severe Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Li Wai Suen CFD", + "Seah D", + "Choy MC", + "De Cruz P" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.37699231448828247, + "mesh_terms": [ + "Humans", + "Acute Disease", + "C-Reactive Protein", + "Colectomy", + "Colitis, Ulcerative", + "Gastrointestinal Agents", + "Infliximab", + "Leukocyte L1 Antigen Complex", + "Prognosis", + "Severity of Illness Index", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Acute severe ulcerative colitis (ASUC) is a medical emergency for which colectomy is required in patients who do not respond to rescue therapy. While previous studies have predominantly focused on predicting outcome to first-line corticosteroid therapy, there is a need to understand the factors associated with response to rescue therapies in order to improve clinical outcomes. We reviewed the evidence regarding factors associated with response to rescue therapy in adults with ASUC and identified future directions for research. METHODS: A systematic search of the literature was conducted, and 2 reviewers independently assessed studies for inclusion. RESULTS: Of 3509 records screened, 101 completed studies were eligible for inclusion. We identified 42 clinical, hematological, biochemical, endoscopic, or pharmacological factors associated with response to rescue therapy. Older age (\u226550 years), thiopurine experience, and cytomegalovirus or Clostridioides difficile infection were associated with a higher risk of nonresponse to rescue therapy. Biochemical factors associated with poorer response included an elevated C-reactive protein (CRP) \u226530mg/L on admission, hypoalbuminemia and an elevated ratio of CRP to albumin. Severe endoscopic findings, including a Mayo endoscopic score of 3 or Ulcerative Colitis Endoscopic Index of Severity \u22655, portended poorer outcomes. The role of fecal calprotectin and therapeutic value of measuring infliximab drug levels in ASUC remain to be defined. CONCLUSIONS: Response to rescue therapy can be predicted by several specific factors, which would aid clinical decision-making. Existing and emerging factors should be integrated within predictive and prognostic models to help improve clinical outcomes. In this review, we summarize the clinical, hematological, biochemical, radiological, endoscopic, and drug-related factors that predict or are associated with response to rescue therapy in patients with acute severe ulcerative colitis. We also provide a clinical algorithm for clinicians.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35697847", + "title": "Mapping of etiologies of computed tomography-proven acute colitis: a prospective cohort study.", + "year": 2022, + "journal": "Scientific reports", + "authors": [ + "Meyer J", + "Schrenzel J", + "Balaphas A", + "Delaune V", + "Abbas M", + "Morel P", + "Puppa G", + "Rubbia-Brandt L", + "Bichard P", + "Frossard JL", + "Toso C", + "Buchs NC", + "Ris F" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.37409957471935085, + "mesh_terms": [ + "Biomarkers", + "Colitis", + "Colitis, Ischemic", + "Colitis, Ulcerative", + "Colonoscopy", + "Feces", + "Humans", + "Inflammatory Bowel Diseases", + "Leukocyte L1 Antigen Complex", + "Prospective Studies", + "Salmonella", + "Tomography", + "Tomography, X-Ray Computed" + ], + "raw_abstract": "Our objective was to describe the etiologies of acute colitis and to identify patients who require diagnostic endoscopy. Patients with symptoms of gastrointestinal infection and colonic inflammation on CT were prospectively included. Those immunosuppressed, with history of colorectal cancer or inflammatory bowel disease (IBD), were excluded. Microbiological analysis of the feces was performed using PCR assays BD-Max and FilmArray (GI panel,) and fecal cultures. Fecal calprotectin was determined. Patients with negative BD-Max underwent colonoscopy. One hundred and seventy-nine patients were included. BD-Max was positive in 93 patients (52%) and FilmArray in 108 patients (60.3%). Patients with infectious colitis (n\u2009=\u2009103, 57.5%) were positive for Campylobacter spp. (n\u2009=\u200957, 55.3%), Escherichia coli spp. (n\u2009=\u20098, 7.8%), Clostridioides difficile (n\u2009=\u200923, 22.3%), Salmonella spp. (n\u2009=\u20099, 8.7%), viruses (n\u2009=\u20097, 6.8%), Shigella spp. (n\u2009=\u20096, 5.8%), Entamoeba histolytica (n\u2009=\u20092, 1.9%) and others (n\u2009=\u20094, 3.9%). Eighty-six patients underwent colonoscopy, which was compatible with ischemic colitis in 18 patients (10.1%) and IBD in 4 patients (2.2%). Fecal calprotectin was elevated in all patients, with a mean concentration of 1922.1\u2009\u00b1\u20092895.6\u00a0\u03bcg/g, and was the highest in patients with IBD (8511\u2009\u00b1\u20099438\u00a0\u03bcg/g, p\u2009<\u20090.001). After exclusion of patients with infectious etiology, a fecal calprotectin\u2009>\u2009625\u00a0\u03bcg/g allowed identifying patients with IBD with an area under ROC curve of 85.1%. To conclude, computed tomography-proven colitis was of infectious etiology in 57.5% of patients. The main pathogens identified were Campylobacter spp. (55.3%), Clostridioides difficile (22.3%) and Salmonella spp. (8.7%). Ischemic colitis (10.1%) and IBD (2.2%) were seldom represented. No colorectal cancer was found.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36053300", + "title": "[Fecal microbiota transplantation: indications, risks and opportunities].", + "year": 2022, + "journal": "Innere Medizin (Heidelberg, Germany)", + "authors": [ + "Stallmach A", + "Steube A", + "Stallhofer J", + "Grunert PC", + "Merkel U", + "Hartmann M" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.36919133349307015, + "mesh_terms": [ + "COVID-19", + "Clostridioides difficile", + "Clostridium Infections", + "Fecal Microbiota Transplantation", + "Humans", + "SARS-CoV-2" + ], + "raw_abstract": "Fecal microbiome transfer (FMT) involving the transfer of the microbiome of healthy stool donors to patients with various diseases has been performed in Germany in clinical studies and individual treatment attempts. There is no doubt that FMT is an effective therapeutic principle for recurrent Clostridium difficile infection and ulcerative colitis. From a\u00a0medico-legal point of view, it should be stressed that, in Germany, the microbiome to be transferred is regarded as a\u00a0drug, the manufacture of which is subject to the Medicines Act and the risk information from the Federal Institute for Drugs and Medical Devices. The background of the severe acute respiratory syndrome coronavirus\u00a02 (SARS-CoV-2) pandemic and the potential risk of transmitting pathogens must also be considered. There is an obligation to notify the competent state authorities to perform FMTs in the context of individual treatment attempts. In the context of the limited availability and the fundamental problem of infection, future studies aim to identify the therapeutically active components in the microbiome. Recombinant production is the aim. Initial results represent preliminary steps, as these concepts are not yet established in clinical practice. Der f\u00e4kale Mikrobiomtransfer (FMT) mit der \u00dcbertragung des Mikrobioms gesunder Stuhlspender:innen auf Patient:innen mit ganz unterschiedlichen Erkrankungen wird in Deutschland in klinischen Studien, aber auch in individuellen Heilversuchen durchgef\u00fchrt. Ohne Zweifel ist ein FMT bei der rekurrenten Clostridioides-difficile-Infektion (rCDI) und der Colitis ulcerosa ein wirksames Therapieprinzip. Unter medikolegalen Aspekten ist darauf hinzuweisen, dass das zu transferierende Mikrobiom in Deutschland als ein Medikament angesehen wird, dessen Herstellung dem Arzneimittelgesetz unterliegt; zu beachten sind die Risikoinformationen des Bundesinstituts f\u00fcr Arzneimittel und Medizinprodukte (BfArM) vor dem Hintergrund der Severe-acute-respiratory-syndrome-coronavirus-2(SARS-CoV-2)-Pandemie und des potenziellen Risikos, Pathogene zu \u00fcbertragen. F\u00fcr die Durchf\u00fchrung von FMT im Rahmen individueller Heilversuche besteht eine Anzeigepflicht bei den zust\u00e4ndigen Landesbeh\u00f6rden (\u00a7\u00a067 Arzneimittelgesetz [AMG]), im Rahmen einer klinischen Studie muss eine Herstellungserlaubnis gem\u00e4\u00df \u00a7\u00a013 AMG durch die Landesbeh\u00f6rde erteilt sein. Aufgrund der limitierten Verf\u00fcgbarkeit und der grunds\u00e4tzlichen Infektionsproblematik wird in aktuellen Forschungsarbeiten versucht, die therapeutisch aktiven Bestandteile des Mikrobioms zu identifizieren; eine rekombinante Herstellung wird angestrebt, hier sind erste Fortschritte erkennbar, aber noch nicht in der klinischen Praxis etabliert.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34963635", + "title": "Clostridium innocuum infection in hospitalised patients with inflammatory bowel disease.", + "year": 2022, + "journal": "The Journal of infection", + "authors": [ + "Le PH", + "Chiu CT", + "Yeh PJ", + "Pan YB", + "Chiu CH" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.3369607358622184, + "mesh_terms": [ + "Clostridioides difficile", + "Clostridium Infections", + "Firmicutes", + "Humans", + "Inflammatory Bowel Diseases", + "Retrospective Studies" + ], + "raw_abstract": "BACKGROUND: Clostridium innocuum (CI) infection can lead to creeping fat in Crohn's disease and is associated with intestinal strictures. At present, no clinical study ever has evaluated the role of CI infection in inflammatory bowel disease (IBD). MATERIALS AND METHODS: In this retrospective cohort study, we enrolled hospitalized IBD patients with culture results for both CI and Clostridioides difficile (CD) in a medical center between October 2019 and April 2021. They were divided into the CI (CI+/CD-), control (CI-/CD-), coinfection (CI+/CD+), and CD (CI-/CD+) groups. We analyzed the risk factors, clinical presentations, and outcomes by comparing the CI and control groups. RESULTS: We enrolled a total of 90 patients, including 22, 39, 13, and 16 patients in the CI, control, coinfection, and CD groups. The incidence rates of CI (CI+) and CD (CD+) were 39% (35/90) and 32% (29/90), respectively. We analyzed the differences between CI and control groups. We identified the use of steroid (77.3%\u00a0vs. 46.2%, P\u00a0=\u00a00.018) and 5-aminosalicylic acid (90.9%\u00a0vs. 64.1%, P\u00a0=\u00a00.022) as risk factors of CI infection. Clinical analysis showed that more patients in CI group presented with bloody stool (77.3%\u00a0vs. 51.3%, P\u00a0=\u00a00.046). Although CI group had significantly lower overall occurrence of intraabdominal abscess (0%\u00a0vs. 17.9%, P\u00a0=\u00a00.042), it showed a lower clinical remission rate (50%\u00a0vs. 87.5%, P\u00a0=\u00a00.044) and higher Mayo score at the end of follow-up (10 points vs. 3 points, P\u00a0=\u00a00.008) in ulcerative colitis. CONCLUSIONS: CI infection may lead to a poorer clinical remission in ulcerative colitis. We should take it into consideration in IBD patents with active inflamamtion or refractory diarrhea with or without CD infection. Precise identification of CI is imperative to guide approproate antimicrobial therapy because of its intrinsic vancomycin resistance nature.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37461990", + "title": "P074\u2003Comparative Risk of Clostridioides Difficile Infection in Vedolizumab vs anti-TNFa Agents in Biologic-Na\u00efve Patients With Ulcerative Colitis.", + "year": 2021, + "journal": "The American journal of gastroenterology", + "authors": [ + "Dalal R", + "Mitri J", + "Goodrick H", + "Allegretti J" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.3243905851497679, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Clostridioides difficile infection (CDI) is associated with adverse outcomes in ulcerative colitis (UC). There is concern that vedolizumab, which inhibits lymphocyte trafficking to the intestines, may increase the risk of gastrointestinal infections such as CDI when compared to other biologics. We conducted a retrospective cohort study to determine if vedolizumab is associated with an increased risk of CDI compared to anti-TNFa agents in UC. METHODS: Retrospective cohort study of adult patients with UC initiating infliximab, adalimumab, or vedolizumab 6/1/14-12/31/20 at a large academic health system. Electronic records were manually reviewed. Patients with Crohn's disease, indeterminate colitis, prior biologic exposures, prior colectomy, and non-UC indications for biologics were excluded. Patients were followed until CDI, colectomy, biologic discontinuation/switch, or last gastroenterology encounter through 8/1/21. The primary outcome was time from biologic initiation to first CDI, defined as positive stool C. difficile toxin or toxigenic C. difficile polymerase chain reaction (PCR) with associated CDI antibiotic prescriptions. Secondary outcomes included CDI-related hospitalization, colectomy, or death within 30 days of CDI. The primary exposure was vedolizumab vs anti-TNFa therapy. Other independent variables included demographics and UC history/severity factors. Propensity scores (PSs) were calculated using logistic regression of vedolizumab vs anti-TNFa on the following covariates: age, sex, Caucasian, body mass index (BMI), disease duration, current systemic corticosteroid use, UC-related hospitalization within prior 12 months, last Mayo endoscopic subscore, Montreal disease extent, albumin, and malignancy history. Inverse probability of treatment weighting (IPTW) was performed using PSs. An univariable Cox proportional hazards model was fit to calculate the unadjusted hazard ratio (HR) of CDI for vedolizumab vs anti-TNFa. A multivariable, IPT-weighted Cox model was then fit with two additional covariates extrinsic to the PS: pre-biologic CDI and immunomodulator exposure (time-varying covariate). Patients were censored at loss of follow-up, biologic discontinuation, or colectomy. RESULTS: 805 UC patients initiated vedolizumab (n = 195) or anti-TNFa agents (n = 610). Vedolizumab patients were older and less commonly received systemic corticosteroids or had UC-related hospitalization within 12 months pre-biologic initiation. There were 43 CDIs over 1,436 patient-years follow-up. CDI and CDI hospitalization occurred less commonly with vedolizumab vs anti-TNFa (CDI: 1.0% vs 6.7%, p = 0.001; CDI hospitalization: 1.0% vs 3.8%, p = 0.042 by log-rank test). There were no differences in colectomies or deaths or exposure to antibiotics/corticosteroids during follow-up or within 30 days preceding CDI. The unadjusted Cox model demonstrated a lower hazard of CDI for vedolizumab vs anti-TNFa (HR 0.17, 95% CI 0.04-0.71). The multivariable IPT-weighted Cox model demonstrated no difference in hazard of CDI for vedolizumab vs anti-TNFa (HR 0.33, 95% CI 0.05-2.03) or immunomodulator exposure (HR 1.01, 95% CI 0.41-2.40). Pre-biologic CDI was associated with an increased hazard of CDI (HR 5.95, 95% CI 2.93-12.09). Among patients who developed CDI, 17/43 (39.5%) had pre-biologic CDI a median of 227 days (IQR 160-550 days) preceding CDI. CONCLUSION: Our study did not identify an increased risk of CDI associated with vedolizumab vs anti-TNFa agents after controlling for UC severity. We hope that these findings will reassure UC providers considering vedolizumab as a first-line biologic agent in the context of gastrointestinal infectious risks.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37770177", + "title": "Phage therapy in gut microbiome.", + "year": 2023, + "journal": "Progress in molecular biology and translational science", + "authors": [ + "Chen X", + "Mendes BG", + "Alves BS", + "Duan Y" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.2803441522492126, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Phage Therapy", + "Gastrointestinal Tract", + "Bacteria", + "Microbiota", + "Anti-Bacterial Agents" + ], + "raw_abstract": "Phage therapy, the use of bacteriophage viruses for bacterial infection treatment, has been around for almost a century, but with the increase in antibiotic use, its importance has declined rapidly. There has been renewed interest in revisiting this practice due to the general decline in the effectiveness of antibiotics, combined with improved understanding of human microbiota and advances in sequencing technologies. Phage therapy has been proposed as a clinical alternative to restore the gut microbiota in the absence of an effective treatment. That is due to its immunomodulatory and bactericidal effects against its target bacteria. In the gastrointestinal diseases field, phage therapy has been studied mainly as a promising tool in infectious diseases treatment, such as cholera and diarrhea. However, many studies have been conducted in non-communicable diseases, such as the targeting of adherent invasive Escherichia coli in Crohn's disease, the treatment of Clostridioides difficile in ulcerative colitis, the eradication of Fusobacterium nucleatum in colorectal cancer, the targeting of alcohol-producing Klebsiella pneumoniae in non-alcoholic fatty liver disease, or Enterococcus faecalis in alcohol-associated hepatitis. This review will summarize the changes in the gut microbiota and the phageome in association with some gastrointestinal and liver diseases and highlight the recent scientific advances in phage therapy as a therapeutic tool for their treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31165961", + "title": "Long-term durability and safety of fecal microbiota transplantation for recurrent or refractory Clostridioides difficile infection with or without antibiotic exposure.", + "year": 2019, + "journal": "European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology", + "authors": [ + "Lee CH", + "Chai J", + "Hammond K", + "Jeon SR", + "Patel Y", + "Goldeh C", + "Kim P" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.26968534930593263, + "mesh_terms": [ + "Adult", + "Aged", + "Aged, 80 and over", + "Anti-Bacterial Agents", + "Clostridioides difficile", + "Clostridium Infections", + "Enema", + "Fecal Microbiota Transplantation", + "Feces", + "Female", + "Follow-Up Studies", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Probiotics", + "Recurrence", + "Surveys and Questionnaires", + "Tertiary Care Centers", + "Treatment Outcome" + ], + "raw_abstract": "Fecal microbiota transplant (FMT) is a safe and effective treatment for recurrent or refractory Clostridioides (Clostridium) difficile infection (RCDI) in the short term. However, there are a paucity of data on long-term durability and safety of FMT. The aim of this study is to determine the long-term efficacy and safety of FMT for RCDI. Ninety-four patients underwent FMT via retention enema for RCDI between 2008 and 2012 and completed a follow-up questionnaire 4 to 8\u00a0years following the last FMT. Of these, 32 were unreachable and 37 were deceased; 23 of the remaining 25 participants completed the survey. No CDI recurrences were reported in patients treated with FMT; 12 of the 23 participants (52.2%) received at least one course of non-CDI antibiotic(s). Nine participants (40.9%) received probiotics and 4 (17.4%) received both non-CDI antibiotics and probiotics. All 23 participants rated their overall health compared with pre-FMT. Current health was considered \"much better\" in 17 patients (73.9%); \"somewhat better\" in 3 patients (13.0%); and \"about the same\" in 3 patients (13.0%). A total of 11 participants (47.8%) reported an increase in weight of more than 5\u00a0kg (kg) post-FMT and 9 participants (39.1%) reported no change in weight (\u00b1\u20095\u00a0kg). Four of the 23 participants (17.4%) reported improvement or resolution (undifferentiated colitis, n\u2009=\u20091; Crohn's disease, n\u2009=\u20092; ulcerative colitis, n\u2009=\u20091) of pre-existing gastrointestinal condition following FMT. Eight of 23 participants (34.8%) experienced new medical condition(s) post-FMT. The long-term efficacy (48-96\u00a0months) of FMT for RCDI appears to be durable even after non-CDI antibiotic use. Thirty percent had improvement of their pre-existing medical conditions following FMT; 73.9% reported \"much better\" overall health following FMT.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34405816", + "title": "Blastocystis and Clostridioides difficile: Evidence for a Synergistic Role in Colonization Among IBD Patients with Emphasis on Ulcerative Colitis.", + "year": 2021, + "journal": "The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology", + "authors": [ + "Azimirad M", + "Gol SMA", + "Javanmard E", + "Mirjalali H", + "Yadegar A", + "Aghdaei HA", + "Shahrokh S", + "Balaii H", + "Sadeghi A", + "Zali MR" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.26390273229031624, + "mesh_terms": [ + "Adolescent", + "Adult", + "Blastocystis", + "Blastocystis Infections", + "Child", + "Clostridioides difficile", + "Colitis, Ulcerative", + "Feces", + "Female", + "Humans", + "Inflammatory Bowel Diseases", + "Iran", + "Male", + "Middle Aged", + "Polymerase Chain Reaction", + "Prevalence", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Regarding the controversial role of Blastocystis in inflammatory bowel diseases (IBD) patients, it seems that this protozoan may lead to an overgrowth of some non-beneficial bacteria. The current study aimed to investigate the co-existence of Blastocystis and Clostridioides difficile in IBD patients. METHODS: Stool samples of 102 IBD patients were collected and cultivated for C. difficile and Blastocystis. DNA extraction was performed on positive samples and C. difficile and Blastocystis were toxinotyped and subtyped, respectively. Fisher's exact test and logistic regression were employed to calculate the correlation between the existence of Blastocystis and its subtypes (ST) with C. difficile and its type of toxins. Also, the co-existence of Blastocystis and C. difficile with the frequency of defecations was evaluated. RESULTS: Blastocystis and C. difficile were observed in 17 (16.7%) and 26 (25.5%) of stool samples, respectively. From 26 C. difficilepositive isolates, 24 (92.3%) and 2 (7.7%) were tcdA+/B+ and tcdA+/B-, respectively. Also, 10 (58.8%) and 7 (41.2%) were Blastocystis ST1 and ST3, respectively. Statistically significant correlations between co-existence of Blastocystis and C. difficile and co-existence of these microorganisms and frequency of defecation (P < .035) were seen. There was no statistically significant correlation between subtypes of Blastocystis and colonization of C. difficile or its toxinotypes. CONCLUSION: The co-existence of Blastocystis and C. difficile in IBD patients was observed in the current study. Moreover, it can be proposed that these microorganisms may have synergistic effects on their colonization in the gastrointestinal tract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31361830", + "title": "Predictors of Clostridioides difficile recurrence across a national cohort of veterans in outpatient, acute, and long-term care settings.", + "year": 2019, + "journal": "American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists", + "authors": [ + "Appaneal HJ", + "Caffrey AR", + "Beganovic M", + "Avramovic S", + "LaPlante KL" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.2594626325364104, + "mesh_terms": [ + "Aged", + "Aged, 80 and over", + "Ambulatory Care", + "Anti-Bacterial Agents", + "Case-Control Studies", + "Clostridioides difficile", + "Clostridium Infections", + "Cohort Studies", + "Female", + "Humans", + "Immunosuppressive Agents", + "Long-Term Care", + "Male", + "Middle Aged", + "Proton Pump Inhibitors", + "Recurrence", + "Risk Factors", + "Veterans" + ], + "raw_abstract": "PURPOSE: The greatest challenge in treating Clostridioides difficile infection (CDI) is disease recurrence, which occurs in about 20% of patients, usually within 30 days of treatment cessation. We sought to identify independent predictors of first recurrence among a national cohort of veterans with CDI. METHODS: We conducted a case-control study among acute and long-term care Veterans Affairs (VA) inpatients and outpatients with a first CDI episode (positive stool sample for C. difficile toxin[s] and receipt of at least 2 days of CDI treatment) between 2010 and 2014. Cases experienced first recurrence within 30 days from the end of treatment. Controls were those without first recurrence matched 4:1 to cases on year, facility, and severity. Multivariable conditional logistic regression was used to identify predictors of first recurrence. RESULTS: We identified 32 predictors of first recurrence among 974 cases and 3,896 matched controls. Significant predictors included medication use prior to (probiotics, fluoroquinolones, laxatives, third- or fourth-generation cephalosporins), during (first- or second-generation cephalosporins, penicillin/amoxicillin/ampicillin, third- and fourth-generation cephalosporins), and after CDI treatment (probiotics, any antibiotic, proton pump inhibitors [PPIs], and immunosuppressants). Other predictors included current biliary tract disease, malaise/fatigue, cellulitis/abscess, solid organ cancer, medical history of HIV, multiple myeloma, abdominal pain, and ulcerative colitis. CONCLUSION: In a large national cohort of outpatient and acute and long-term care inpatients, treatment with certain antibiotics, PPIs, immunosuppressants, and underlying disease were among the most important risk factors for first CDI recurrence.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38395525", + "title": "AGA Clinical Practice Guideline on Fecal Microbiota-Based Therapies for Select Gastrointestinal Diseases.", + "year": 2024, + "journal": "Gastroenterology", + "authors": [ + "Peery AF", + "Kelly CR", + "Kao D", + "Vaughn BP", + "Lebwohl B", + "Singh S", + "Imdad A", + "Altayar O" + ], + "bacteria": "Clostridioides", + "condition": "ulcerative colitis", + "relevance_score": 0.20887528400424274, + "mesh_terms": [ + "Adult", + "Humans", + "Irritable Bowel Syndrome", + "Clostridioides difficile", + "Treatment Outcome", + "Gastrointestinal Diseases", + "Fecal Microbiota Transplantation", + "Inflammatory Bowel Diseases", + "Clostridium Infections", + "Anti-Bacterial Agents", + "Microbiota", + "Recurrence" + ], + "raw_abstract": "BACKGROUND & AIMS: Fecal microbiota-based therapies include\u00a0conventional fecal microbiota transplant and US Food and Drug Administration-approved therapies, fecal microbiota live-jslm and fecal microbiota spores live-brpk. The American Gastroenterological Association (AGA) developed this guideline to provide recommendations on the use of fecal microbiota-based therapies in adults with recurrent Clostridioides difficile infection; severe to fulminant C difficile infection; inflammatory bowel diseases, including pouchitis; and irritable bowel syndrome. METHODS: The\u00a0guideline was developed using the GRADE (Grading of Recommendations, Assessment, Development, and Evaluation) framework to prioritize clinical questions, identify patient-centered outcomes, and conduct an evidence synthesis. The guideline panel used the Evidence-to-Decision framework to develop recommendations for the use of fecal microbiota-based therapies in the specified gastrointestinal conditions and provided implementation considerations for clinical practice. RESULTS: The guideline panel made 7 recommendations. In immunocompetent adults with recurrent C difficile infection, the AGA suggests select use of fecal microbiota-based therapies on completion of standard of care antibiotics to prevent recurrence. In mildly or moderately immunocompromised adults with recurrent C difficile infection, the AGA suggests select use of conventional fecal microbiota transplant. In severely immunocompromised adults, the AGA suggests against the use of any fecal microbiota-based therapies to prevent recurrent C difficile. In adults hospitalized with severe or fulminant C difficile not responding to standard of care antibiotics, the AGA suggests select use of conventional fecal microbiota transplant. The AGA suggests against the use of conventional fecal microbiota transplant as treatment for inflammatory bowel diseases or irritable bowel syndrome, except in the context of clinical trials. CONCLUSIONS: Fecal microbiota-based therapies are effective therapy to prevent recurrent C difficile in select patients. Conventional fecal microbiota transplant is an adjuvant treatment for select adults hospitalized with severe or fulminant C difficile infection not responding to standard of care antibiotics. Fecal microbiota transplant cannot yet be recommended in other gastrointestinal conditions.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38428658", + "title": "Gegen Qinlian decoction ameliorates TNBS-induced ulcerative colitis by regulating Th2/Th1 and Tregs/Th17\u00a0cells balance, inhibiting NLRP3 inflammasome activation and reshaping gut microbiota.", + "year": 2024, + "journal": "Journal of ethnopharmacology", + "authors": [ + "Hu Y", + "Tang J", + "Xie Y", + "Xu W", + "Zhu W", + "Xia L", + "Fang J", + "Yu D", + "Liu J", + "Zheng Z", + "Zhou Q", + "Shou Q", + "Zhang W" + ], + "bacteria": "Ruminiclostridium", + "condition": "ulcerative colitis", + "relevance_score": 0.5146027504422859, + "mesh_terms": [ + "Humans", + "Mice", + "Animals", + "Colitis, Ulcerative", + "Drugs, Chinese Herbal", + "Inflammasomes", + "Interleukin-18", + "Gastrointestinal Microbiome", + "NLR Family, Pyrin Domain-Containing 3 Protein", + "Th17 Cells", + "Occludin", + "RNA, Ribosomal, 16S", + "Mice, Inbred CBA", + "Colitis", + "Cytokines", + "Trinitrobenzenes", + "Anti-Inflammatory Agents", + "Body Weight", + "Caspases", + "Disease Models, Animal", + "Colon" + ], + "raw_abstract": "ETHNOPHARMACOLOGICAL RELEVANCE: Chinese herbal medicine Gegen Qinlian Decoction (GQD) has been clinically shown to be an effective treatment of ulcerative colitis (UC) in China. However, the underlying mechanism of GQD's anti-ulcerative colitis properties and its effect on gut microbiota still deserve further exploration. AIM OF THE STUDY: This study observed the regulatory effects of GQD on Th2/Th1 and Tregs/Th17\u00a0cells balance, the NOD-like receptor family pyrin domain containing 3 (NLRP3) infammasome and gut microbiota in TNBS-induced UC in BALB/c mice. MATERIALS AND METHODS: 61 main chemical compounds in the GQD were determined by UPLC-Q-TOF/MS. The UC BALB/c model was established by intrarectal administration of trinitrobenzene sulfonic acid (TNBS), and GQD was orally administered at low and high dosages of 2.96 and 11.83\u00a0g/kg/day, respectively. The anti-inflammatory effects of GQD for ulcerative colitis were evaluated by survival rate, body weight, disease activity index (DAI) score, colonic weight and index, spleen index, hematoxylin-eosin (HE) staining and histopathological scores. Flow cytometry was used to detect the percentage of CD4, Th1, Th2, Th17 and Tregs cells. The levels of Th1-/Th2-/Th17-/Tregs-related inflammatory cytokines and additional proinflammatory cytokines (IL-1\u03b2, IL-18) were detected by CBA, ELISA, and RT-PCR. The expressions of GATA3, T-bet, NLRP3, Caspase-1, IL-I\u03b2, Occludin and Zonula occludens-1 (ZO-1) on colon tissues were detected by Western blot and RT-PCR. Transcriptome sequencing was performed using colon tissue and 16S rRNA gene sequencing was performed on intestinal contents. Fecal microbiota transplantation (FMT) was employed to assess the contribution of intestinal microbiota and its correlation with CD4 T cells and the NLRP3 inflammasome. RESULTS: GQD increased the survival rate of TNBS-induced UC in BALB/c mice, and significantly improved their body weight, DAI score, colonic weight and index, spleen index, and histological characteristics. The intestinal barrier dysfunction was repaired after GQD administration through promoting the expression of tight junction proteins (Occludin and ZO-1). GQD restored the balance of Th2/Th1 and Tregs/Th17\u00a0cells immune response of colitis mice, primarily inhibiting the increase in Th2/Th1 ratio and their transcription factor production (GATA3 and T-bet). Morever, GQD changed the secretion of Th1-/Th2-/Th17-/Tregs-related cytokines (IL-2, IL-12, IL-5, IL-13, IL-6, IL-10, and IL-17A) and reduced the expressions of IL-1\u03b2, IL-18. Transcriptome results suggested that GQD could also remodel the immune inflammatory response of colitis by inhibiting NOD-like receptor signaling pathway, and Western blot, immunohistochemistry and RT-PCR further revealed that GQD exerted anti-inflammatory effects by inhibiting the NLRP3 inflammasome, such as down-regulating the expression of NLRP3, Caspase-1 and IL-1\u03b2. More interestingly, GQD regulated gut microbiota dysbiosis, suppressed the overgrowth of conditional pathogenic gut bacteria like Helicobacter, Proteobacteria, and Mucispirillum, while the probiotic gut microbiota, such as Lactobacillus, Muribaculaceae, Ruminiclostridium_6, Akkermansia, and Ruminococcaceae_unclassified were increased. We further confirmed that GQD-treated gut microbiota was sufficient to relieve TNBS-induced colitis by FMT, involving the modulation of Th2/Th1 and Tregs/Th17 balance, inhibition of NLRP3 inflammasome activation, and enhancement of colonic barrier function. CONCLUSIONS: GQD might alleviate TNBS-induced UC via regulating Th2/Th1 and Tregs/Th17 cells Balance, inhibiting NLRP3 inflammasome and reshaping gut microbiota, which may provide a novel strategy for patients with colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38064857", + "title": "Fucoidan alleviated dextran sulfate sodium-induced ulcerative colitis with improved intestinal barrier, reshaped gut microbiota composition, and promoted autophagy in male C57BL/6 mice.", + "year": 2024, + "journal": "Nutrition research (New York, N.Y.)", + "authors": [ + "Li S", + "Qian Q", + "Yang H", + "Wu Z", + "Xie Y", + "Yin Y", + "Cui Y", + "Li X" + ], + "bacteria": "Lachnospiraceae_NK4A136_group", + "condition": "ulcerative colitis", + "relevance_score": 0.7491337580602102, + "mesh_terms": [ + "Humans", + "Male", + "Animals", + "Mice", + "Mice, Inbred C57BL", + "Colitis, Ulcerative", + "Dextran Sulfate", + "Gastrointestinal Microbiome", + "Colon", + "Autophagy", + "Bacteroidetes", + "Clostridiales", + "Disease Models, Animal", + "Colitis", + "Polysaccharides" + ], + "raw_abstract": "Although previous research has unveiled the remedial effects of fucoidan, an extract from marine algae, on ulcerative colitis (UC), the precise mechanisms remain elusive. Animal studies have suggested a connection between autophagy and the beneficial influences of fucoidan intervention. We hypothesized that fucoidan's alleviative effects on dextran sulfate sodium (DSS)-induced UC could be ascribed to autophagy. For our study, we chose 36 male C57BL/6 mice and administered 100 or 400 mg/(kg/body weight/day) of fucoidan via gavage for 5 consecutive weeks. During the last week, the mice were given 3% DSS in drinking water to induce UC. In contrast to the DSS-induced UC model, fucoidan intervention prevented DSS-induced body weight loss, mitigated colon shortening, improved colon mucosa damage, enhanced the intestinal barrier, and reduced serum inflammatory factor concentrations. Furthermore, fucoidan intervention reshaped the gut microbiota compositions, increased the relative abundance of Bacteroidota, Muribaculaceae_unclassified, Clostridiales_unclassified, and Lachnospiraceae_NK4A136_group, and decreased the relative abundance of Firmicutes, Proteobacteria, and Escherichia-Shigella, which led to a lower Firmicutes/Bacteroidota ratio. Additionally, fucoidan treatment enhanced autophagy, as evidenced by upregulated protein expressions of BECLIN1, ATG5, ATG7, and an increased microtubule-associated-proteinlight-chain-3-II/microtubule-associated-proteinlight-chain-3-I ratio. Our findings corroborated the ameliorating effects of fucoidan intervention on DSS-induced UC through autophagy activation, reorganization of gut microbiota, and fortification of the intestinal barrier. This lends support to the therapeutic potential of fucoidan as a natural bioactive ingredient for future UC treatments in humans.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34397940", + "title": "Intestinal flora differences between patients with ulcerative colitis of different ethnic groups in China.", + "year": 2021, + "journal": "Medicine", + "authors": [ + "Liu H", + "Liu W", + "Huang X", + "Feng Y", + "Lu J", + "Gao F" + ], + "bacteria": "Subdoligranulum", + "condition": "ulcerative colitis", + "relevance_score": 0.7432520728984736, + "mesh_terms": [ + "Adult", + "Bacteria", + "China", + "Colitis, Ulcerative", + "Ethnicity", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Incidence", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Retrospective Studies", + "Young Adult" + ], + "raw_abstract": "To determine the differences in intestinal flora between Uygur and Han patients with ulcerative colitis (UC).Microbial diversity and structural composition of fecal bacteria from patients with UC and their matched healthy spouses or first-degree relatives were analyzed using high-throughput sequencing technology.The fecal microbial diversity and abundance index of Uygur patients with UC (UUC) were significantly lower compared with the Uygur normal control group, while there was no significant difference between the Han UC patients (HUC) and the Han normal control group (HN). Compared with their respective control groups, Uygur UC patients and Han UC patients had a different main composition of human intestinal flora (P\u200a<\u200a.05). The abundance of Burkholderia, Caballeronia, Paraburkholderia in the UUC group were higher compared with the HUC group, while Faecalibacterium, Bifidobacterium, and Blautia in the HUC group were higher than those in the UUC group (P\u200a<\u200a.05). Veillonella in the UUC group was higher than that in the Uygur normal control group group, while Subdoligranulum and Ruminococcaceae_UCG-002 were significantly lower (P\u200a<\u200a.05). Prevotella_9 in the HUC group was significantly higher than that in HN group, while Blautia, Anaerostipes, and [Eubacterium]_hallii_group were significantly lower. Moreover, the top 6 species in order of importance were Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella.The difference in intestinal microflora structure may be one of the reasons for the clinical heterogeneity between Uygur and Han patients with UC. Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella could be used as potential biomarkers for predicting UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33871395", + "title": "Fecal microbiota profile in patients with inflammatory bowel disease in Taiwan.", + "year": 2021, + "journal": "Journal of the Chinese Medical Association : JCMA", + "authors": [ + "Chang TE", + "Luo JC", + "Yang UC", + "Huang YH", + "Hou MC", + "Lee FY" + ], + "bacteria": "Subdoligranulum", + "condition": "ulcerative colitis", + "relevance_score": 0.6921983167411163, + "mesh_terms": [ + "Adult", + "Cross-Sectional Studies", + "Feces", + "Female", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Microbiota", + "Middle Aged", + "Taiwan" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with complicated interaction between immune, gut microbiota, and environmental factors in a genetically vulnerable host. Dysbiosis is often seen in patients with IBD. We aimed to investigate the fecal microbiota in patients with IBD and compared them with a control group in Taiwan. METHODS: In this cross-sectional study, we investigated fecal microbiota in 20 patients with IBD and 48 healthy controls. Fecal samples from both IBD patients and controls were analyzed by the next-generation sequencing method and relevant software. RESULTS: The IBD group showed lower bacterial richness and diversity compared with the control group. The principal coordinate analysis also revealed the significant structural differences between the IBD group and the control group. These findings were consistent whether the analysis was based on an operational taxonomic unit or amplicon sequence variant. However, no significant difference was found when comparing the composition of fecal microbiota between ulcerative colitis (UC) and Crohn's disease (CD). Further analysis showed that Lactobacillus, Enterococcus, and Bifidobacterium were dominant in the IBD group, whereas Faecalibacterium and Subdoligranulum were dominant in the control group at the genus level. When comparing UC, CD, and control group, Lactobacillus, Bifidobacterium, and Enterococcus were identified as dominant genera in the UC group. Fusobacterium and Escherichia_Shigella were dominant in the CD group. CONCLUSION: Compared with the healthy control, the IBD group showed dysbiosis with a significant decrease in both richness and diversity of gut microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38347087", + "title": "Microbial butyrate capacity is reduced in inflamed mucosa in patients with ulcerative colitis.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Jangi S", + "Moyer J", + "Sandlow S", + "Fu M", + "Chen H", + "Shum A", + "Hsia K", + "Cersosimo L", + "Yeliseyev V", + "Zhao N", + "Bry L", + "Michaud DS" + ], + "bacteria": "Subdoligranulum", + "condition": "ulcerative colitis", + "relevance_score": 0.6416246832663991, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Butyrates", + "Colon", + "Biopsy", + "Intestinal Mucosa", + "Bacteria" + ], + "raw_abstract": "Reduced butyrate-production capacity has been reported in fecal microbial communities in patients with active ulcerative colitis. However, the butyrate-production capacity of the mucosal microbiome from active vs quiescent mucosa in ulcerative colitis has been unexplored. We sought to determine the diversity and relative abundance of mucosal bacterial and fungal communities from endoscopically active vs quiescent mucosa in patients with UC, and aimed to predict contributions of mucosal microbial communities to butyrate synthesis. Systematic, segmental right- and left-sided biopsies were obtained from endoscopically active (n\u2009=\u200913) or quiescent (n\u2009=\u200917) colonic mucosa, among 15 patients with pan-colonic ulcerative colitis. Dietary fiber intake of patients was performed using the validated five-item FiberScreen questionnaire. Amplicon sequencing of mucosal bacteria and fungi was performed. The diversity and relative abundance of mucosal bacterial and fungal taxa were quantified, and predicted contributions to butyrate synthesis were ascertained. Bacterial alpha and beta diversity were similar between active vs quiescent mucosa. Butyrogenic taxa were significantly increased in quiescence, including Butyricimonas, Subdoligranulum, and Alistipes. Predicted butyrate kinase activity was significantly and concomitantly increased in quiescent mucosa. Fiber intake was positively correlated with butyrogenic microbes. Compared to mucosal bacterial prevalence, mucosal fungi were detected in low prevalence. Butyrogenic microbes are relatively increased in quiescent mucosa in ulcerative colitis, and may be related to increased fiber intake during quiescence. Manipulation of the mucosal microbiome towards butyrate-producing bacteria may be associated with endoscopic quiescence.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32322944", + "title": "Protective effect of baicalin on the regulation of Treg/Th17 balance, gut microbiota and short-chain fatty acids in rats with ulcerative colitis.", + "year": 2020, + "journal": "Applied microbiology and biotechnology", + "authors": [ + "Zhu L", + "Xu LZ", + "Zhao S", + "Shen ZF", + "Shen H", + "Zhan LB" + ], + "bacteria": "Subdoligranulum", + "condition": "ulcerative colitis", + "relevance_score": 0.5073693749337005, + "mesh_terms": [ + "Animals", + "Butyrates", + "Colitis, Ulcerative", + "Disease Models, Animal", + "Dysbiosis", + "Fatty Acids, Volatile", + "Flavonoids", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Prebiotics", + "Rats", + "T-Lymphocytes, Regulatory", + "Th17 Cells", + "Trinitrobenzenesulfonic Acid" + ], + "raw_abstract": "Baicalin is reported as an effective drug for ulcerative colitis (UC). However, its effect on gut microbiota and short-chain fatty acids (SCFAs) remains unknown. In this study, we investigated the role of baicalin on Th17/Treg balance, gut microbiota community, and SCFAs levels in trinitrobenzene sulphonic acid (TNBS)-induced UC rat model. We found the DAI scores were significantly increased in the TNBS-treated rats, while reduced in the baicalin-treated group in a dose-dependent manner, accompanied with the alleviation of mucosal injury, the reduction of ZO-1, Occludin, and MUC2 expression. At the meanwhile, baicalin repressed the increased levels of reactive oxygen species (ROS) and MDA, while deceased the GSH and SOD levels in colon tissue of rats treated with TNBS. On the other hand, administration of baicalin attenuated the TNBS-induced upregulations of Th17/Treg ratio, indicating a strong amelioration in the colorectal inflammation. More importantly, pyrosequencing of the V4 regions of 16S rRNA genes in rat feces revealed a deviation of the gut microbiota in response to baicalin treatment. In particular, the decreased Firmicutes-to-Bacteroidetes ratios and endotoxin-bearing Proteobacteria levels indicated that baicalin reversed TNBS-induced gut dysbiosis OTUs. In addition, we further investigated the fecal levels of major SCFAs in rats and found that baicalin significantly resorted the fecal butyrate levels in rats treated with TNBS. The increased butyrate levels were in consistent with the higher abundance of butyrate-producing species such as Butyricimonas spp., Roseburia spp., Subdoligranulum spp., and Eubacteriu spp. in baicalin-treated group. In conclusion, our findings suggest that baicalin possibly protected rats against ulcerative colitis by regulation of Th17/Treg balance, and modulation of both gut microbiota and SCFAs. Baicalin may be used as a prebiotic agent to treat ulcerative colitis-associated inflammation and gut dysbiosis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28852861", + "title": "Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.", + "year": 2018, + "journal": "Journal of gastroenterology", + "authors": [ + "Nishino K", + "Nishida A", + "Inoue R", + "Kawada Y", + "Ohno M", + "Sakai S", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Kawahara M", + "Naito Y", + "Andoh A" + ], + "bacteria": "Coprococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7115498488149531, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Endoscopy, Gastrointestinal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. METHODS: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. RESULTS: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. \u03b1-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. CONCLUSIONS: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39574001", + "title": "Changes in amino acid concentrations and the gut microbiota composition are implicated in the mucosal healing of ulcerative colitis and can be used as noninvasive diagnostic biomarkers.", + "year": 2024, + "journal": "Clinical proteomics", + "authors": [ + "Wu J", + "Li M", + "Zhou C", + "Rong J", + "Zhang F", + "Wen Y", + "Qu J", + "Wu R", + "Miao Y", + "Niu J" + ], + "bacteria": "Coprococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6679002620268726, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Mucosal healing is the therapeutic target for ulcerative colitis (UC). While amino acids (AAs) and the gut microbiota are known to be involved in the pathogenesis of UC, their specific roles in mucosal healing have not been fully defined. OBJECTIVES: To longitudinally assess the changes in AA concentrations and the gut microbiota composition in the context of mucosal healing in UC patients, with the aim of identifying new biomarkers with predictive value for mucosal healing in UC patients and providing a new theoretical basis for dietary therapy. METHODS: A total of 15 UC patients with infliximab-induced mucosal healing were enrolled. Serum and fecal AA concentrations before and after mucosal healing were determined via targeted metabolomics. A receiver operating characteristic (ROC) curve was plotted to evaluate the value of different AAs in predicting mucosal healing in UC patients. The changes in the composition of the fecal gut microbiota were analyzed via metagenomics, and bioinformatics was used to analyze the functional genes and metabolic pathways associated with different bacterial species. Spearman correlation analyses of fecal AAs with significantly different concentrations and the differentially abundant bacterial species before and after mucosal healing were performed. RESULTS: 1. The fecal concentrations of alanine, aspartic acid, glutamic acid, glutamine, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine were significantly decreased after mucosal healing. The serum concentrations of alanine, cysteine and valine significantly increased, whereas that of aspartic acid significantly decreased. Glutamic acid, leucine, lysine, methionine and threonine could accurately predict mucosal healing in UC patients, and the area under the curve (AUC) was >\u20090.9. After combining the 5 amino acids, the AUC reached 0.96. 2. There were significant differences in the gut microbiota composition before and after mucosal healing in UC, characterized by an increase in the abundance of beneficial microbiota (Faecalibacterium prausnitzii and Bacteroides fragilis) and a decrease in the abundance of harmful microbiota (Enterococcus faecalis). LEfSe analysis identified 57 species that could predict mucosal healing, and the AUC was 0.7846. 3. Amino acid metabolic pathways were enriched in samples after mucosal healing, was associated with the abundance of multiple species, such as Faecalibacterium prausnitzi, Bacteroides fragilis, Bacteroides vulgatus and Alistipes putredinis. 4. The fecal concentrations of several AAs were negatively correlated with the abundance of a variety of beneficial strains, such as Bacteroides fragilis, uncultured Clostridium sp., Firmicutes bacterium CAG:103, Adlercreutzia equolifaciens, Coprococcus comes and positively correlated with the abundance of several harmful strains, such as Citrobacter freundii, Enterococcus faecalis, Klebsiella aerogenes, Salmonella enterica. CONCLUSION: Altered concentrations of amino acids and their associations with the gut microbiota are implicated in the mucosal healing of UC patients and can serve as noninvasive diagnostic biomarkers.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33352216", + "title": "Changes in intestinal microbiota and correlation with TLRs in ulcerative colitis in the coastal area of northern China.", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Xu N", + "Bai X", + "Cao X", + "Yue W", + "Jiang W", + "Yu Z" + ], + "bacteria": "Coprococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6415885520933103, + "mesh_terms": [ + "China", + "Colitis, Ulcerative", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: To investigate the communities of fecal microbiota and the role of Toll-like receptors in patients with ulcerative colitis in the coastal area of northern China. METHODS: Stool samples from 31 patients with ulcerative colitis and 12 healthy individuals were collected. The total bacterial genomic DNA was extracted, and the V3+V4 hypervariable region in the bacterial 16S rRNA gene sequence was amplified by polymerase chain reaction (PCR). High-throughput sequencing analysis was performed on the Illumina Hiseq platform. The expression of TLR2, TLR4, Tollip, PPAR-\u03b3, IL-6, and TNF-\u03b1 in the colonic mucosa was measured by Western blots. RESULTS: The diversity of the fecal microbiota in patients with ulcerative colitis was significantly less than that in healthy control individuals (p\u00a0<\u00a00.05). The proportion of Bacteroidetes was significantly reduced (p\u00a0<\u00a00.01), whereas Proteobacteria was prevalent (p\u00a0<\u00a00.01) in patients with ulcerative colitis. At the genus level, the relative abundance of Streptococcus and Anaerostipes was significantly increased (p\u00a0<\u00a00.05), whereas the proportion of Bacteroides, Lachnospira, Ruminococcus, Phascolarctobacterium, and Coprococcus was significantly decreased in patients with ulcerative colitis (p\u00a0<\u00a00.05). The diversity indexes of fecal microbiota in patients with ulcerative colitis were negatively correlated with disease severity (p\u00a0<\u00a00.05). The relative abundance of Enterobacteriaceae was positively correlated with disease severity, and the relative abundance of Phascolarctobacterium, Anaerostipes, Fusobacterium, Parabacteroides, Oscillospira, and Ochrobactrum were negatively correlated with disease severity. The expression levels of TLR2 and TLR4 in the intestinal mucosa were positively correlated with the relative abundance of Streptococcus and Enterobacteriaceae, respectively (r\u00a0=\u00a00.481, p\u00a0=\u00a00.007; r\u00a0=\u00a00.455, p\u00a0=\u00a00.017). CONCLUSION: There were significant changes in the diversity and composition of the fecal microbiota in patients with ulcerative colitis compared to healthy individuals. The dysbiosis of gut microbiota and correlation with TLRs might play important roles in the pathogenesis and progression of ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34264407", + "title": "A case-control study on the association of intestinal flora with ulcerative colitis.", + "year": 2021, + "journal": "AMB Express", + "authors": [ + "Tang YH", + "Liu HC", + "Song G", + "Wu TT", + "Zhao Y", + "Shi LJ" + ], + "bacteria": "Coprococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5625006601305937, + "mesh_terms": [], + "raw_abstract": "The association between intestinal flora and ulcerative colitis (UC) was studied in order to provide a basis and method for clinical treatment. Fresh fecal samples were collected from 30 active UC patients and 10 healthy controls. The intestinal flora DNA from each sample was extracted and 16S rRNA gene sequencing was carried out using HiSeq platform to identify the intestinal flora in fecal samples. The richness and diversity of intestinal flora in UC patients were significantly lower than those in healthy control group (P\u2009<\u20090.05). Significant differences were observed between the intestinal flora-species of UC patients and healthy controls. Synergistetes (P\u2009<\u20090.01) and Firmicutes (P\u2009<\u20090.05), along with probiotics Veillonella (P\u2009<\u20090.01), Ruminococcus and Coprococcus (P\u2009<\u20090.05) in the UC patients were lower than that in the healthy controls significantly. Furthermore, compared with the control group, Tenericutes (P\u2009<\u20090.01) and intestinal pathogenic bacteria, including Bacteroides (P\u2009<\u20090.01), Escherichia and Sutterella (P\u2009<\u20090.05) were significantly increased. The incidence of UC is significantly associated with the changes in intestinal flora. Changes in intestinal flora may lead to a decrease in the diversity of intestinal flora or to the enrichment of a particular intestinal flora.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Coprococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.505491338085921, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27412252", + "title": "Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.", + "year": 2016, + "journal": "Genome medicine", + "authors": [ + "Shaw KA", + "Bertha M", + "Hofmekler T", + "Chopra P", + "Vatanen T", + "Srivatsa A", + "Prince J", + "Kumar A", + "Sauer C", + "Zwick ME", + "Satten GA", + "Kostic AD", + "Mulle JG", + "Xavier RJ", + "Kugathasan S" + ], + "bacteria": "Coprococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.3912722894782307, + "mesh_terms": [ + "Adolescent", + "Bacteria", + "Biomarkers", + "Case-Control Studies", + "Child", + "Child, Preschool", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Immunologic Factors", + "Inflammation", + "Intestinal Mucosa", + "Leukocyte L1 Antigen Complex", + "Longitudinal Studies", + "Male", + "Severity of Illness Index", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Gut microbiome dysbiosis has been demonstrated in subjects with newly diagnosed and chronic inflammatory bowel disease (IBD). In this study we sought to explore longitudinal changes in dysbiosis and ascertain associations between dysbiosis and markers of disease activity and treatment outcome. METHODS: We performed a prospective cohort study of 19 treatment-na\u00efve pediatric IBD subjects and 10 healthy controls, measuring fecal calprotectin and assessing the gut microbiome via repeated stool samples. Associations between clinical characteristics and the microbiome were tested using generalized estimating equations. Random forest classification was used to predict ultimate treatment response (presence of mucosal healing at follow-up colonoscopy) or non-response using patients' pretreatment samples. RESULTS: Patients with Crohn's disease had increased markers of inflammation and dysbiosis compared to controls. Patients with ulcerative colitis had even higher inflammation and dysbiosis compared to those with Crohn's disease. For all cases, the gut microbial dysbiosis index associated significantly with clinical and biological measures of disease severity, but did not associate with treatment response. We found differences in specific gut microbiome genera between cases/controls and responders/non-responders including Akkermansia, Coprococcus, Fusobacterium, Veillonella, Faecalibacterium, and Adlercreutzia. Using pretreatment microbiome data in a weighted random forest classifier, we were able to obtain 76.5\u00a0% accuracy for prediction of responder status. CONCLUSIONS: Patient dysbiosis improved over time but persisted even among those who responded to treatment and achieved mucosal healing. Although dysbiosis index was not significantly different between responders and non-responders, we found specific genus-level differences. We found that pretreatment microbiome signatures are a promising avenue for prediction of remission and response to treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34761733", + "title": "Attributes of intestinal microbiota composition and their correlation with clinical primary non-response to anti-TNF-\u03b1 agents in inflammatory bowel disease patients.", + "year": 2022, + "journal": "Bosnian journal of basic medical sciences", + "authors": [ + "Alatawi H", + "Mosli M", + "Saadah OI", + "Annese V", + "Al-Hindi R", + "Alatawy M", + "Al-Amrah H", + "Alshehri D", + "Bahieldin A", + "Edris S" + ], + "bacteria": "Coprococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.31943079819820963, + "mesh_terms": [ + "Bacteria", + "Biomarkers", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "RNA, Ribosomal, 16S", + "Tumor Necrosis Factor Inhibitors" + ], + "raw_abstract": "The largest microbial aggregation in the human body exists in the gastrointestinal tract. The microbiota in the host gastrointestinal tract comprises a diverse ecosystem, and the intestinal microbiota plays a vital role in maintaining gut homeostasis. This study aims to examine whether the gut microbiota influences unresponsiveness to anti-TNF-\u03b1 treatments in primary nonresponder patients, and consequently identify the responsible microbes as biomarkers of unresponsiveness. Stool samples were collected from a cohort of patients with an established diagnosis of IBD, either ulcerative colitis (UC) or Crohn's disease (CD), following completion of the induction phase of anti TNF therapy. 16S rRNA sequencing analysis was used to examine the pattern of microbiota communities in fecal samples. The quality and quantity of fecal microbiota were compared in responder and primary nonresponder IBD patients following anti-TNF-\u03b1 therapy. As per our hypothesis, a difference in gut microbiome composition between the two patient subgroups was observed. A decreased abundance of short-chain fatty acid (SCFA)-producing bacteria, including Anaerostipes, Coprococcus, Lachnospira, Roseburia, and Ruminococcus, was detected in non-responsive patients, which was the hallmark of dysbiosis. Biomarkers of dysbiosis that were identified as predictors of clinical nonresponse, included Klebsiella, Eubacteriaceae, RF32, Bifidobacterium_animalis, and Muribaculaceae-previously known as S24-7. Signature biomarkers showed dramatic alteration in the composition of gut microbiota in patients who demonstrated primary nonresponse to anti-TNF-\u03b1 agents. Dysbiosis, with features including a dropped biodiversity, augmentation in opportunistic pathogenic microbiota, and a lack of SCFA-producing bacteria, is a prominent feature of the microbiome of primary nonresponders to anti-TNF-\u03b1 therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37208257", + "title": "Gut microbial signatures and their functions in Behcet's uveitis and Vogt-Koyanagi-Harada disease.", + "year": 2023, + "journal": "Journal of autoimmunity", + "authors": [ + "Wang Q", + "Wu S", + "Ye X", + "Tan S", + "Huang F", + "Su G", + "Kijlstra A", + "Yang P" + ], + "bacteria": "Coprococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.22893069359058985, + "mesh_terms": [ + "Humans", + "Uveomeningoencephalitic Syndrome", + "Leukocytes, Mononuclear", + "Gastrointestinal Microbiome", + "Uveitis", + "Behcet Syndrome" + ], + "raw_abstract": "BACKGROUND: A number of public metagenomic studies reveal an association between the gut microbiome and various immune-mediated diseases including Behcet's uveitis (BU) and Vogt-Koyanagi-Harada disease (VKH). Integrated-analysis and subsequent validation of these results could be a potentially powerful way to understand the microbial signatures and their functions in these two uveitis entities. METHODS: We integrated the sequencing data of our previous metagenomic studies on two major uveitis entities, BU and VKH as well as four other publicly available immune-mediated diseases datasets, including Ankylosing Spondylitis (AS), Rheumatoid Arthritis (RA), Crohn's disease (CD) and Ulcerative Colitis (UC). Alpha-diversity and beta-diversity analysis were used to compare the gut microbiome signatures between both uveitis entities and other immune-mediated diseases and healthy controls. Amino acid homology between microbial proteins and a uveitogenic peptide of the interphotoreceptor retinoid-binding protein (IRBP) RESULTS: Depleted Dorea, Blautia, Coprococcus, Erysipelotrichaceae and Lachnospiraceae as well as enriched Bilophila and Stenotrophomonas were identified in BU patients. An enriched Alistipes along with a lower level of Dorea were observed in VKH patients. A peptide antigen (SteTDR) encoded by BU specifically enriched Stenotrophomonas was identified to share homology with IRBP CONCLUSIONS: Our study revealed specific gut microbial signatures and their potentially functional roles in BU and VKH pathogenesis that differ significantly from other immune-mediated diseases as well as healthy controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32265456", + "title": "Seasonal changes of circulating 25-hydroxyvitamin D correlate with the lower gut microbiome composition in inflammatory bowel disease patients.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Soltys K", + "Stuchlikova M", + "Hlavaty T", + "Gaalova B", + "Budis J", + "Gazdarica J", + "Krajcovicova A", + "Zelinkova Z", + "Szemes T", + "Kuba D", + "Drahovska H", + "Turna J", + "Stuchlik S" + ], + "bacteria": "Pediococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6560260020108714, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteria", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Seasons", + "Vitamin D", + "Young Adult" + ], + "raw_abstract": "Higher probability of the development of Crohn's disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/Shigella spp.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38521930", + "title": "Human-derived bacterial strains mitigate colitis via modulating gut microbiota and repairing intestinal barrier function in mice.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Dai J", + "Jiang M", + "Wang X", + "Lang T", + "Wan L", + "Wang J" + ], + "bacteria": "Pediococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5951787363092838, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "Gastrointestinal Microbiome", + "Intestinal Barrier Function", + "RNA, Ribosomal, 16S", + "Colitis", + "Colitis, Ulcerative", + "Bacteroidetes", + "Enterococcus faecium", + "Escherichia coli", + "Mice, Inbred C57BL", + "Disease Models, Animal", + "Colon" + ], + "raw_abstract": "BACKGROUND: Unbalanced gut microbiota is considered as a pivotal etiological factor in colitis. Nevertheless, the precise influence of the endogenous gut microbiota composition on the therapeutic efficacy of probiotics in colitis remains largely unexplored. RESULTS: In this study, we isolated bacteria from fecal samples of a healthy donor and a patient with ulcerative colitis in remission. Subsequently, we identified three bacterial strains that exhibited a notable ability to ameliorate dextran sulfate sodium (DSS)-induced colitis, as evidenced by increased colon length, reduced disease activity index, and improved histological score. Further analysis revealed that each of Pediococcus acidilactici CGMCC NO.17,943, Enterococcus faecium CGMCC NO.17,944 and Escherichia coli CGMCC NO.17,945 significantly attenuated inflammatory responses and restored gut barrier dysfunction in mice. Mechanistically, bacterial 16S rRNA gene sequencing indicated that these three strains partially restored the overall structure of the gut microbiota disrupted by DSS. Specially, they promoted the growth of Faecalibaculum and Lactobacillus murinus, which were positively correlated with gut barrier function, while suppressing Odoribacter, Rikenella, Oscillibacter and Parasutterella, which were related to inflammation. Additionally, these strains modulated the composition of short chain fatty acids (SCFAs) in the cecal content, leading to an increase in acetate and a decrease in butyrate. Furthermore, the expression of metabolites related receptors, such as receptor G Protein-coupled receptor (GPR) 43, were also affected. Notably, the depletion of endogenous gut microbiota using broad-spectrum antibiotics completely abrogated these protective effects. CONCLUSIONS: Our findings suggest that selected human-derived bacterial strains alleviate experimental colitis and intestinal barrier dysfunction through mediating resident gut microbiota and their metabolites in mice. This study provides valuable insights into the potential therapeutic application of probiotics in the treatment of colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29135456", + "title": "Probiotics and Their Use in Inflammatory Bowel Disease.", + "year": 2018, + "journal": "Alternative therapies in health and medicine", + "authors": [ + "Amer M", + "Nadeem M", + "Nazir SUR", + "Fakhar M", + "Abid F", + "Ain QU", + "Asif E" + ], + "bacteria": "Pediococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.42407637200730647, + "mesh_terms": [ + "Humans", + "Inflammatory Bowel Diseases", + "Lactobacillus", + "Pakistan", + "Probiotics" + ], + "raw_abstract": "Context \u2022 Crohn's disease and ulcerative colitis result in similar gastrointestinal (GI) symptoms, including pain, diarrhea, stools with mucus or blood, and ulceration or tissue damage within the alimentary canal. Gut microbiota play a crucial role in triggering, maintaining, and exacerbating inflammatory bowel disease (IBD). Probiotics might help to rebalance the gut flora in a positive way, shifting from pro- to anti-inflammatory. Objectives \u2022 The study intended to investigate the safety and use of probiotics and the biological effects of probiotic bacteria on IBD. Design \u2022 The research team performed a literature review. The team conducted a database search in April 2015 using Google Scholar and PubMed to find studies relevant to probiotics and their use in IBD. Only papers that were published in English were considered, and all available years in each database were searched. The initial search identified 38 published articles, for which the research team obtained full texts and independently read them in full to identify those papers suitable for inclusion in the review. Setting \u2022 The study took place in the main library of the University of Lahore (Islamabad, Pakistan). Results \u2022 Many strains of probiotics exist, but the most common strains available today are (1) the Bifidobacterium species, (2) Enterococcus faecium, (4) the Lactobacillus strains, (4) Saccharomyces boulardii, (5) the Bacillus species, and (6) Pediococcus, all used to produce beneficial health effects. These species showed their beneficial effects on the host using different mechanisms involving (1) production of proteins, quorum sensing signaling inhibitors, butyrate, immunoglobulin A, and short-chain fatty acids; (2) decreased production of tumor necrosis factor alpha and interleukin 8; (3) increased expression of mucin 2; and (4) increased upregulation of defensin. Conclusions \u2022 Studies on probiotics in animal models of IBD are promising, and clinical results in IBD patients are encouraging; however, the data are limited, and few studies are placebo controlled. Additional placebo-controlled, double-blind studies in IBD are required before recommendations can be offered for routine use of probiotics in IBD. Additional organisms may eventually be developed through genetic engineering. The current evidence also indicates that probiotic effects are strain specific; they do not act through the same mechanisms nor are all probiotics indicated for the same health conditions. More research is needed to determine what strains and at what dose probiotics become more useful as part of a clinical intervention.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34600098", + "title": "Probiotic potential of Lactobacillus isolated from horses and its therapeutic effect on DSS-induced colitis in mice.", + "year": 2022, + "journal": "Microbial pathogenesis", + "authors": [ + "Qin S", + "Huang Z", + "Wang Y", + "Pei L", + "Shen Y" + ], + "bacteria": "Pediococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.403603708266476, + "mesh_terms": [ + "Animals", + "Anti-Bacterial Agents", + "Caco-2 Cells", + "Colitis", + "Dextran Sulfate", + "Disease Models, Animal", + "Horses", + "Humans", + "Inflammatory Bowel Diseases", + "Lactobacillus", + "Lactobacillus plantarum", + "Lipopolysaccharides", + "Male", + "Mice", + "Phylogeny", + "Probiotics" + ], + "raw_abstract": "Inflammatory bowel disease (IBD) is a refractory disease that endangers both humans and animals. In recent times, Lactobacillus have been used to treat animal diseases. It may be a good choice to try to isolate Lactobacillus with probiotic potential to treat IBD. Equine, as a kind of hindgut fermentation animal has rich intestinal microflora, but data regarding this is scarce. The isolation of Lactobacillus with probiotic potential from equine may become a new method for the treatment of IBD. Four isolates of Lactobacillus were isolated from fresh feces of healthy male adult horses and analyzed their biological characteristics. According to the phylogenetic analysis, A2.5 and A7.1 were identified as Pediococcus pentosaceus, A3 as Lactobacillus plantarum, and B8.2 as Weissella cibaria. All four isolates showed tolerance to the environment of acid, bile salt concentration and simulated artificial gastrointestinal fluid. The hydrophobic rate and self-aggregation rate of A3 were close to 100%, and the adhesion rate was 28.85\u00a0\u00b1\u00a00.74%. Four isolates were negative in hemolysis test and sensitive to common antibiotics and different isolates had different sensitivity to antibiotics. The four isolates had antibacterial and antioxidant activities which can reflect their probiotic potential. Furthermore, they could regulate the LPS (Lipopolysaccharides) stimulated Caco-2\u00a0cells. We chose A3 as the treatment strain to intervene Dextran sulfate sodium salt (DSS)-induced mice. The results showed that compared with DSS group, DSS\u00a0+\u00a0A3 group exhibited reduced Disease activity index (DAI), increased colon length, reduced pathological score and regulated cytokine secretion at the level of gene expression. In this study, four isolates of Lactobacillus with probiotic potential were isolated, and Lactobacillus plantarum A3 with reduced ulcerative colitis in mice was screened. It might provide a potential treatment for IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37652126", + "title": "Fermentation patterns of prebiotics fructooligosaccharides-SCFA esters inoculated with fecal microbiota from ulcerative colitis patients.", + "year": 2023, + "journal": "Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association", + "authors": [ + "Chen W", + "Tan D", + "Yang Z", + "Tang J", + "Bai W", + "Tian L" + ], + "bacteria": "Lachnoclostridium", + "condition": "ulcerative colitis", + "relevance_score": 0.7251184336916032, + "mesh_terms": [ + "Inflammation", + "Fatty Acids, Volatile", + "Humans", + "Microbiota", + "Prebiotics", + "Colitis, Ulcerative", + "Fermentation", + "Feces", + "Clostridiales" + ], + "raw_abstract": "Ulcerative colitis (UC) is believed to arise from an imbalance between the intestinal microbiota and mucosal immunity, leading to excessive intestinal inflammation. Modulating the gut microbial community through dietary components presents a valuable strategy in aiding the treatment of UC. In this study, esters formed by binding of well-known prebiotics, fructooligosaccharides (FOS), with short chain fatty acids (SCFAs) via both enzymatic and chemical methods were evaluated for their impact on the gut microbiota of UC patients. An in vitro human colonic fermentation model was employed to monitor changes in total carbohydrates and SCFAs production during the fermentation of these esters by microbiota from patients with active and remission UC. The results showed that pronounced abundance of [Ruminococcus]_gnavus_group, Escherichia_Shigella, Lachnoclostridium, Klebsiella and other potential pathogens were detected in the fecal samples from UC patients, with a milder condition observed during the remission phase. Significant higher levels of corresponding SCFA were observed in the groups with addition of FOS-SCFAs esters during fermentation. Butyrylated fructooligosaccharides (B-FOS) and propionylated fructooligosaccharides (P-FOS) by enzymatic synthesis successfully promoted the proliferation of Bifidobacterium and inhibited Clostridium_sensu_stricto_1 and Klebsiella. Overall, B-FOS and P-FOS exhibit promising potential for restoring intestinal homeostasis and alleviating intestinal inflammation in individuals with UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37507685", + "title": "Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population.", + "year": 2023, + "journal": "BMC gastroenterology", + "authors": [ + "Alsulaiman RM", + "Al-Quorain AA", + "Al-Muhanna FA", + "Piotrowski S", + "Kurdi EA", + "Vatte C", + "Alquorain AA", + "Alfaraj NH", + "Alrezuk AM", + "Robinson F", + "Dowdell AK", + "Alamri TA", + "Hamilton L", + "Lad H", + "Gao H", + "Gandla D", + "Keating BJ", + "Meng R", + "Piening B", + "Al-Ali AK" + ], + "bacteria": "Lachnoclostridium", + "condition": "ulcerative colitis", + "relevance_score": 0.6754567801624576, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Saudi Arabia", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Crohn Disease" + ], + "raw_abstract": "BACKGROUND: Crohn's diseases and ulcerative colitis, both of which are chronic immune-mediated disorders of the gastrointestinal tract are major contributors to the overarching Inflammatory bowel diseases. It has become increasingly evident that the pathological processes of IBDs results from interactions between genetic and environmental factors, which can skew immune responses against normal intestinal flora. METHODS: The aim of this study is to assess and analyze the taxa diversity and relative abundances in CD and UC in the Saudi population. We utilized a sequencing strategy that targets all variable regions in the 16\u00a0S rRNA gene using the Swift Amplicon 16\u00a0S rRNA Panel on Illumina NovaSeq 6000. RESULTS: The composition of stool 16\u00a0S rRNA was analyzed from 219 patients with inflammatory bowel disease and from 124 healthy controls. We quantified the abundance of microbial communities to examine any significant differences between subpopulations of samples. At the genus level, two genera in particular, Veillonella and Lachnoclostridium showed significant association with CD versus controls. There were significant differences between subjects with CD versus UC, with the top differential genera spanning Akkermansia, Harryflintia, Maegamonas and Phascolarctobacterium. Furthermore, statistically significant taxa diversity in microbiome composition was observed within the UC and CD groups. CONCLUSIONS: In conclusion we have shown that there are significant differences in gut microbiota between UC, CD and controls in a Saudi Arabian inflammatory bowel disease cohort. This reinforces the need for further studies in large populations that are ethnically and geographically diverse. In addition, our results show the potential to develop classifiers that may have add additional richness of context to clinical diagnosis of UC and CD with larger inflammatory bowel disease cohorts.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Catenibacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.505491338085921, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32048723", + "title": "Aging Increases the Severity of Colitis and the Related Changes to the Gut Barrier and Gut Microbiota in Humans and Mice.", + "year": 2020, + "journal": "The journals of gerontology. Series A, Biological sciences and medical sciences", + "authors": [ + "Liu A", + "Lv H", + "Wang H", + "Yang H", + "Li Y", + "Qian J" + ], + "bacteria": "Turicibacter", + "condition": "ulcerative colitis", + "relevance_score": 0.47713650794681983, + "mesh_terms": [ + "Adult", + "Age Factors", + "Aged", + "Aging", + "Animals", + "Cadherins", + "Case-Control Studies", + "Colitis, Ulcerative", + "Disease Models, Animal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Middle Aged", + "Occludin", + "Severity of Illness Index" + ], + "raw_abstract": "This study aims to compare intestinal mucosal barrier function in older and young ulcerative colitis (UC) patients and the healthy population, and to explore the possible mechanisms through which aging increases the severity of colitis in mice. The old healthy group showed discontinued tight junction (TJ) strand. The E-cadherin and occludin protein expressions in the colonic tissue of the old healthy subjects were lower than those in the younger healthy people. The protein expressions of E-cadherin and occludin were lower in the old UC patients than in the younger UC patients. In mice, disease activity indexes induced by inflammatory stimulus differed as a function of age. Weight loss level, histological scores, and expression of proinflammatory factors were higher in the dextran sulfate sodium (DSS)-induced group of aged mice than in the young DSS-induced mice. Compared with the results observed in the young DSS-induced mice, the protein expressions of E-cadherin and occludin in the aged DSS-induced mice were lower. Furthermore, significant differences were observed in the composition of the gut microbiota between the young and aged mice. In the aged mice, the fraction of beneficial bacteria (Lactobacillus) was lower before the DSS treatment, while the fraction of the harmful bacteria (Turicibacter, Parasutterella) was higher than that observed in the young mice. After the DSS treatment in the aged mice, the fraction of beneficial bacteria (Odoribacter and Alistipes) was lower, while the fraction of harmful bacteria (Turicibacter) was higher than in the young mice. We demonstrate that the aging of the human colon is characterized by an impairment of the intestinal barrier. Aging leads to more severe disease following DSS challenge. Age-related deterioration of gastrointestinal barrier function and gut microbial dysbiosis may be involved in the pathogenesis of colitis in the aged mice.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35489324", + "title": "Xuanfei Baidu decoction attenuates intestinal disorders by modulating NF-\u03baB pathway, regulating T cell immunity and improving intestinal flora.", + "year": 2022, + "journal": "Phytomedicine : international journal of phytotherapy and phytopharmacology", + "authors": [ + "Ma L", + "Zhao X", + "Liu T", + "Wang Y", + "Wang J", + "Kong L", + "Zhao Q", + "Chen Y", + "Chen L", + "Zhang H" + ], + "bacteria": "Turicibacter", + "condition": "ulcerative colitis", + "relevance_score": 0.3132821208162478, + "mesh_terms": [ + "Animals", + "Colitis", + "Colitis, Ulcerative", + "Colon", + "Dextran Sulfate", + "Disease Models, Animal", + "Drugs, Chinese Herbal", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Mice", + "Mice, Inbred C57BL", + "NF-kappa B", + "RNA, Ribosomal, 16S", + "T-Lymphocytes, Regulatory", + "Tumor Necrosis Factor-alpha", + "COVID-19 Drug Treatment" + ], + "raw_abstract": "BACKGROUND: A number of studies have shown that gastrointestinal manifestations co-exist with respiratory symptoms in coronavirus disease 2019 (COVID-19) patients. Xuanfei Baidu decoction (XFBD) was recommended by the National Health Commission to treat mild and moderate COVID-19 patients and proved to effectively alleviate intestinal symptoms. However, the exact mechanisms remain elusive. PURPOSE: This study aimed at exploring potential mechanisms of XFBD by utilizing a mouse model of dextran sulfate sodium (DSS)-induced acute experimental colitis, mimicking the disease conditions of intestinal microecological disorders. METHODS: The network pharmacology approach was employed to identify the potential targets and pathways of XFBD on the intestinal disorders. Mice with DSS-induced intestinal disorders were utilized to evaluate the protective effect of XFBD in vivo, including body weight, disease activity index (DAI) score, colon length, spleen weight, and serum tumor necrosis factor-\u03b1 (TNF-\u03b1) level. Colon tissues were used to perform hematoxylin-eosin (H&E) staining, western blot analysis, and transcriptome sequencing. Macrophages, neutrophils and the proportions of T helper cell (Th) 1 and Th2 cells were measured by flow cytometry. Intestinal contents were collected for 16S rRNA gene sequencing. RESULTS: Network pharmacology analysis indicated that XFBD inhibited the progression of COVID-19-related intestinal diseases by repressing inflammation. In mice with DSS-induced intestinal inflammation, XFBD treatment significantly reduced weight loss, the spleen index, the disease activity index, TNF-\u03b1 levels, and colonic tissue damage, and prevented colon shortening. Transcriptomics and flow cytometry results suggested that XFBD remodeled intestinal immunity by downregulating the Th1/Th2 ratio. Western blot analysis showed that XFBD exerted its anti-inflammatory effects by blocking the nuclear factor-\u03baB (NF-\u03baB) signaling pathway. Indicator analysis of microbiota showed that 75 operational taxonomic units (OTUs) were affected after XFBD administration. Among them, Akkermansia, Muribaculaceae, Lachnospiraceae,\u00a0and\u00a0Enterorhabdus were simultaneously negatively correlated with intestinal disorders' parameters, and Bacteroides, Escherichia-Shigella, Eubacterium nodatum,Turicibacter, and\u00a0Clostridium\u00a0sensu stricto 1, showed positive correlations with intestinal disorders' parameters. CONCLUSIONS: Our data indicate that XFBD treatment attenuated intestinal disorders associated with inhibiting inflammation, remodeling of intestinal immunity, and improving intestinal flora. These findings provide a scientific basis for the clinical use of XFBD and offer a potential therapeutic approach for the treatment of COVID-19 patients with intestinal symptoms.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34397940", + "title": "Intestinal flora differences between patients with ulcerative colitis of different ethnic groups in China.", + "year": 2021, + "journal": "Medicine", + "authors": [ + "Liu H", + "Liu W", + "Huang X", + "Feng Y", + "Lu J", + "Gao F" + ], + "bacteria": "Ezakiella", + "condition": "ulcerative colitis", + "relevance_score": 0.7443901830789369, + "mesh_terms": [ + "Adult", + "Bacteria", + "China", + "Colitis, Ulcerative", + "Ethnicity", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Incidence", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Retrospective Studies", + "Young Adult" + ], + "raw_abstract": "To determine the differences in intestinal flora between Uygur and Han patients with ulcerative colitis (UC).Microbial diversity and structural composition of fecal bacteria from patients with UC and their matched healthy spouses or first-degree relatives were analyzed using high-throughput sequencing technology.The fecal microbial diversity and abundance index of Uygur patients with UC (UUC) were significantly lower compared with the Uygur normal control group, while there was no significant difference between the Han UC patients (HUC) and the Han normal control group (HN). Compared with their respective control groups, Uygur UC patients and Han UC patients had a different main composition of human intestinal flora (P\u200a<\u200a.05). The abundance of Burkholderia, Caballeronia, Paraburkholderia in the UUC group were higher compared with the HUC group, while Faecalibacterium, Bifidobacterium, and Blautia in the HUC group were higher than those in the UUC group (P\u200a<\u200a.05). Veillonella in the UUC group was higher than that in the Uygur normal control group group, while Subdoligranulum and Ruminococcaceae_UCG-002 were significantly lower (P\u200a<\u200a.05). Prevotella_9 in the HUC group was significantly higher than that in HN group, while Blautia, Anaerostipes, and [Eubacterium]_hallii_group were significantly lower. Moreover, the top 6 species in order of importance were Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella.The difference in intestinal microflora structure may be one of the reasons for the clinical heterogeneity between Uygur and Han patients with UC. Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella could be used as potential biomarkers for predicting UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34397940", + "title": "Intestinal flora differences between patients with ulcerative colitis of different ethnic groups in China.", + "year": 2021, + "journal": "Medicine", + "authors": [ + "Liu H", + "Liu W", + "Huang X", + "Feng Y", + "Lu J", + "Gao F" + ], + "bacteria": "UCG-002", + "condition": "ulcerative colitis", + "relevance_score": 0.7429331277835806, + "mesh_terms": [ + "Adult", + "Bacteria", + "China", + "Colitis, Ulcerative", + "Ethnicity", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Incidence", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Retrospective Studies", + "Young Adult" + ], + "raw_abstract": "To determine the differences in intestinal flora between Uygur and Han patients with ulcerative colitis (UC).Microbial diversity and structural composition of fecal bacteria from patients with UC and their matched healthy spouses or first-degree relatives were analyzed using high-throughput sequencing technology.The fecal microbial diversity and abundance index of Uygur patients with UC (UUC) were significantly lower compared with the Uygur normal control group, while there was no significant difference between the Han UC patients (HUC) and the Han normal control group (HN). Compared with their respective control groups, Uygur UC patients and Han UC patients had a different main composition of human intestinal flora (P\u200a<\u200a.05). The abundance of Burkholderia, Caballeronia, Paraburkholderia in the UUC group were higher compared with the HUC group, while Faecalibacterium, Bifidobacterium, and Blautia in the HUC group were higher than those in the UUC group (P\u200a<\u200a.05). Veillonella in the UUC group was higher than that in the Uygur normal control group group, while Subdoligranulum and Ruminococcaceae_UCG-002 were significantly lower (P\u200a<\u200a.05). Prevotella_9 in the HUC group was significantly higher than that in HN group, while Blautia, Anaerostipes, and [Eubacterium]_hallii_group were significantly lower. Moreover, the top 6 species in order of importance were Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella.The difference in intestinal microflora structure may be one of the reasons for the clinical heterogeneity between Uygur and Han patients with UC. Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella could be used as potential biomarkers for predicting UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Parascardovia", + "condition": "ulcerative colitis", + "relevance_score": 0.47549133808592103, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39922394", + "title": "L-theanine prevents ulcerative colitis by regulating the CD4+ T cell immune response through the gut microbiota and its metabolites.", + "year": 2025, + "journal": "The Journal of nutritional biochemistry", + "authors": [ + "Xu W", + "Liu A", + "Gong Z", + "Xiao W" + ], + "bacteria": "Alloprevotella", + "condition": "ulcerative colitis", + "relevance_score": 0.6410280682128435, + "mesh_terms": [], + "raw_abstract": "The disturbance of gut microbiota and its metabolites are considered to be the causes of ulcerative colitis (UC), which leads to immune abnormalities. Diet is the most important regulator of gut microbiota; therefore, it has a beneficial impact on UC. A novel food ingredient, l-theanine, alters the gut microbiota, thereby regulating gut immunity. However, whether l-theanine prevents UC by altering the gut microbiota, as well as the underlying mechanisms, remains unknown. Here, l-theanine was used to optimize the gut microbiota and its metabolites. Furthermore, to explore the mechanism by which l-theanine prevents UC, an l-theanine fecal microbiota solution was used to prevent dextran sulfate sodium-induced UC via fecal microbiota transplantation. Improvements in the colonic structure, colon histology scores, immune factors (IL-10), and inflammatory factors (IL-1\u03b2) demonstrated the preventive effect of l-theanine on UC. The 16S rDNA and metabolomic results showed that tryptophan-, short chain fatty acid-, and bile acid-related microbiota, such as Muribaculaceae, Lachnospiraceae, Alloprevotella, and Prevotellaceae were the dominant. Flow cytometry results showed that l-theanine decreased helper T (Th)1 and Th17 immune responses, and increased Th2 and T-regulatory immune responses via regulation of antigen-presenting cell responses, such as dendritic cells and macrophages. Therefore, l-theanine regulated the immune response of colon CD4 + T cells to dendritic cell and macrophage antigen presentation via tryptophan-, short chain fatty acid-, and bile acid-related microbiota, thereby preventing dextran sulfate sodium-induced UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39740381", + "title": "Gingerols: Preparation, encapsulation, and bioactivities focusing gut microbiome modulation and attenuation of disease symptoms.", + "year": 2025, + "journal": "Phytomedicine : international journal of phytotherapy and phytopharmacology", + "authors": [ + "Abdullah", + "Ahmad N", + "Xiao J", + "Tian W", + "Khan NU", + "Hussain M", + "Ahsan HM", + "Hamed YS", + "Zhong H", + "Guan R" + ], + "bacteria": "Alloprevotella", + "condition": "ulcerative colitis", + "relevance_score": 0.4285940312731841, + "mesh_terms": [ + "Gastrointestinal Microbiome", + "Humans", + "Catechols", + "Fatty Alcohols", + "Animals", + "Zingiber officinale", + "Phytochemicals", + "Dysbiosis", + "Anti-Inflammatory Agents" + ], + "raw_abstract": "BACKGROUND: Gut dysbiosis, chronic diseases, and microbial recurrent infections concerns have driven the researchers to explore phytochemicals from medicinal and food homologous plants to modulate gut microbiota, mitigate diseases, and inhibit pathogens. Gingerols have attracted attention as therapeutic agents due to their diverse biological activities like gut microbiome regulation, gastro-protective, anti-inflammatory, anti-microbial, and anti-oxidative effects. PURPOSE: This review aimed to summarize the gingerols health-promoting potential, specifically focusing on the regulation of gut microbiome, attenuation of disease symptoms, mechanisms of action, and signaling pathways involved. METHOD: Research findings from experimental and clinical studies have been summarized regarding gingerols effects on the modulation of gut microbiome and its metabolites, and attenuation of disease symptoms. RESULTS: Gingerols are phenolic compounds characterized by a common 3-methoxy-4-hydroxyphenyl moiety in their chemical structures, and further divided into different gingerol types, including gingerols (major), shogaols, paradols, gingerdiols, gingerdiones, and zingerones (minor). Advanced extraction techniques (e.g., ionic liquid-based-, enzyme-assisted-, microwave-assisted-, pressurized liquid-, ultrasound-assisted-, and supercritical fluid extractions) were reported as optimal alternatives to conventional methods for gingerols extraction. Research studies reported that gingerols positively modulated the composition of gut microbiome that helped to combat disease symptoms (e.g., obesity by decreasing weight gain- (Lactobacillus reuteri and Lachnospiraceae) and increasing weight loss associated-bacteria (Akkermansia, Muribaculaceae, and Alloprevotella). Gingerols intervention also ameliorated ulcerative colitis by increasing relative abundance of the beneficial bacteria (Akkermansia, Lachnospiraceae NK4A136, and Muribaculaceae_norank), and decreasing pathogenic microorganisms (Bacteroides, Parabacteroides, and Desulfovibrio). Emerging delivery systems (e.g., microcapsules, nanoparticles, nanostructured lipid carriers, nanoemulsions, and nanoliposomes) can enhance the bioavailability and therapeutic efficacy of gingerols by preserving their inherent properties and addressing challenges of stability, solubility, and absorption. CONCLUSION: Gingerols are promising therapeutic agents to modulate gut microbiome (increase beneficial bacteria and inhibit pathogenic microbes), and attenuate chronic disease symptoms such as diabetes, colitis, obesity, oxidative stress, and cancer. Despite significant progress, challenges persist in transforming research findings into industrial applications, such as stability and solubility during processing and low bioavailability in the distal gut to impart desirable health benefits.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27684872", + "title": "Increased Enterococcus faecalis infection is associated with clinically active Crohn disease.", + "year": 2016, + "journal": "Medicine", + "authors": [ + "Zhou Y", + "Chen H", + "He H", + "Du Y", + "Hu J", + "Li Y", + "Li Y", + "Zhou Y", + "Wang H", + "Chen Y", + "Nie Y" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7827380382483081, + "mesh_terms": [ + "Adult", + "China", + "Crohn Disease", + "DNA, Bacterial", + "Enterococcus faecalis", + "Feces", + "Female", + "Gram-Positive Bacterial Infections", + "Humans", + "Incidence", + "Male", + "Real-Time Polymerase Chain Reaction", + "Young Adult" + ], + "raw_abstract": "This study was performed to investigate the relationship between the abundance of pathogenic gut microbes in Chinese patients with inflammatory bowel disease (IBD) and disease severity.We collected clinical data and fecal samples from 47 therapy-naive Chinese patients with ulcerative colitis (UC), 67 patients with Crohn disease (CD), and 48 healthy volunteers. Bacteria levels of Fusobacterium species (spp), enterotoxigenic Bacteroides fragilis (B fragilis), enteropathogenic Escherichia coli (E coli), and Enterococcus faecalis (E faecalis) were assessed by quantitative real-time PCR (qRT-PCR). Spearman correlation coefficients were calculated to test associations between bacterial content and clinical parameters.Compared to healthy controls, the levels of both Fusobacterium spp and E faecalis were significantly increased in the feces of patients with IBD (P\u200a<\u200a0.01). B fragilis levels were higher (P\u200a<\u200a0.05) and E faecalis levels lower (P\u200a<\u200a0.05) in patients with CD compared to those with UC. Increased E faecalis colonization in CD associated positively with disease activity (P = 0.015), Crohn disease activity index (CDAI; R = 0.3118, P = 0.0108), and fecal calprotectin (P = 0.016).E faecalis and Fusobacterium spp are significantly enriched in patients with IBD, and increased E faecalis infection is associated with clinically active CD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33470709", + "title": "Fecal and mucosal microbiota profiling in pediatric inflammatory bowel diseases.", + "year": 2021, + "journal": "European journal of gastroenterology & hepatology", + "authors": [ + "Putignani L", + "Oliva S", + "Isoldi S", + "Del Chierico F", + "Carissimi C", + "Laudadio I", + "Cucchiara S", + "Stronati L" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7780324462517223, + "mesh_terms": [ + "Adult", + "Child", + "Colitis, Ulcerative", + "Feces", + "Humans", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Microbiota", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: An altered gut microbiota profile has been widely documented in inflammatory bowel diseases (IBD). The intestinal microbial community has been more frequently investigated in the stools than at the level of the mucosa, while most of the studies have been performed in adults. We aimed to define the gut microbiota profile either by assessing fecal and colonic mucosa samples (inflamed or not) from pediatric IBD patients. PATIENTS AND METHODS: Fecal and colonic samples from pediatric IBD (Crohn's disease or ulcerative colitis) and controls were analyzed. The relative abundance of bacteria at phylum and genus/species levels and bacterial diversity were determined through 16S rRNA sequence-based of fecal and mucosal microbiota analysis. RESULTS: A total of 59 children with IBD (26 Crohn's disease, 33 ulcerative colitis) and 39 controls were analyzed. A clear separation between IBD and controls in the overall composition of fecal and mucosal microbiota was found, as well as a reduced bacterial richness in the fecal microbiota of IBD. At the phylum level, abundance of Proteobacteria and Actinobacteria occurred in fecal microbiota of IBD, while species with anti-inflammatory properties (i.e., Ruminococcus) were reduced. Fusobacterium prevailed in inflamed IBD areas in comparison to noninflamed and controls samples. CONCLUSION: Significant alterations in gut microbiota profile were shown in our IBD pediatric patients, in whom an abundance of species with a proinflammatory mucosal activity was clearly detected. An analysis of gut microbiota could be incorporated in designing personalized IBD treatment scenarios in future.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33970546", + "title": "Gut dysbiosis and clinical phases of pancolitis in patients with ulcerative colitis.", + "year": 2021, + "journal": "MicrobiologyOpen", + "authors": [ + "Maldonado-Arriaga B", + "Sandoval-Jim\u00e9nez S", + "Rodr\u00edguez-Silverio J", + "Lizeth Alcar\u00e1z-Estrada S", + "Cort\u00e9s-Espinosa T", + "P\u00e9rez-Cabeza de Vaca R", + "Licona-Cassani C", + "G\u00e1mez-Valdez JS", + "Shaw J", + "Mondrag\u00f3n-Ter\u00e1n P", + "Hern\u00e1ndez-Cortez C", + "Su\u00e1rez-Cuenca JA", + "Castro-Escarpulli G" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7576783819583092, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biodiversity", + "Colitis", + "Colitis, Ulcerative", + "DNA, Bacterial", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "RNA, Ribosomal, 16S", + "Severity of Illness Index" + ], + "raw_abstract": "Ulcerative colitis (UC) is a frequent type of inflammatory bowel disease, characterized by periods of remission and exacerbation. Gut dysbiosis may influence pathophysiology and clinical response in UC. The purpose of this study was to evaluate whether gut microbiota is related to the active and remission phases of pancolitis in patients with UC as well as in healthy participants. Fecal samples were obtained from 18 patients with UC and clinical-endoscopic evidenced pancolitis (active phase n\u00a0=\u00a09 and remission phase n\u00a0=\u00a09), as well as 15 healthy participants. After fecal DNA extraction, the 16S rRNA gene was amplified and sequenced (Illumina MiSeq), operational taxonomic units were analyzed with the QIIME software. Gut microbiota composition revealed a higher abundance of the phyla Proteobacteria and Fusobacteria in active pancolitis, as compared with remission and healthy participants. Likewise, a marked abundance of the genus Bilophila and Fusobacteria were present in active pancolitis, whereas a higher abundance of Faecalibacterium characterized both remission and healthy participants. LEfSe analysis showed that the genus\u00a0Roseburia\u00a0and Faecalibacterium were enriched in remission pancolitis, and genera\u00a0Bilophila\u00a0and\u00a0Fusobacterium\u00a0were enriched in active pancolitis. The relative abundance of Fecalibacterium and Roseburia showed a higher correlation with fecal calprotectin, while Bilophila and Fusobacterium showed AUCs (area under the curve) of 0.917 and 0.988 for active vs. remission pancolitis. The results of our study highlight the relation of gut dysbiosis with clinically relevant phases of pancolitis in patients with UC. Particularly, Fecalibacterium, Roseburia, Bilophila, and Fusobacterium were identified as genera highly related to the different clinical phases of pancolitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39739648", + "title": "The Gut Microbiota Affects Anti-TNF Responsiveness by Activating the NAD", + "year": 2025, + "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", + "authors": [ + "Lei J", + "Lv L", + "Zhong L", + "Xu F", + "Su W", + "Chen Y", + "Wu Z", + "He S", + "Chen Y" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7555555105964018, + "mesh_terms": [ + "Gastrointestinal Microbiome", + "Colitis, Ulcerative", + "Animals", + "Mice", + "NAD", + "Disease Models, Animal", + "Humans", + "Male", + "Infliximab", + "Fecal Microbiota Transplantation", + "Tumor Necrosis Factor-alpha", + "Fusobacterium nucleatum", + "Mice, Inbred C57BL" + ], + "raw_abstract": "Approximately 50% of the patients with ulcerative colitis (UC) are primarily nonresponsive to anti-tumor necrosis factor (TNF) therapy or lose their responsiveness over time. The gut microbiota plays an important role in the resistance of UC to anti-TNF therapy; however, the underlying mechanism remains unknown. Here, it is found that the transplantation of gut fecal microbiota from patients with UC alters the diversity of the gut microbiota in dextran sulfate sodium-induced colitis mice and may affect the therapeutic responsiveness of mice to infliximab. Furthermore, the abundances of Romboutsia and Fusobacterium increase in the tissues of patients with UC who do not respond to anti-TNF therapy. Differentially abundant metabolites are mainly enriched in nicotinate and nicotinamide metabolism in NCM460 cells after Fusobacterium nucleatum infection. Mechanistically, F. nucleatum promotes the nicotinamide adenine dinucleotide (NAD", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37946238", + "title": "The oral bacterial microbiota facilitates the stratification for ulcerative colitis patients with oral ulcers.", + "year": 2023, + "journal": "Annals of clinical microbiology and antimicrobials", + "authors": [ + "Xu J", + "Zhang Y", + "Fang XH", + "Liu Y", + "Huang YB", + "Ke ZL", + "Wang Y", + "Zhang YF", + "Zhang Y", + "Zhou JH", + "Su HT", + "Chen N", + "Liu YL" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7553721693404465, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Oral Ulcer", + "RNA, Ribosomal, 16S", + "Gastrointestinal Microbiome", + "Microbiota", + "Inflammatory Bowel Diseases", + "Bacteria", + "Feces", + "Mesalamine" + ], + "raw_abstract": "BACKGROUND: Clinically, a large part of inflammatory bowel disease (IBD) patients is complicated by oral lesions. Although previous studies proved oral microbial dysbiosis in IBD patients, the bacterial community in the gastrointestinal (GI) tract of those IBD patients combined with oral ulcers has not been profiled yet. METHODS: In this study, we enrolled four groups of subjects, including healthy controls (CON), oral ulcer patients (OU), and ulcerative colitis patients with (UC_OU) and without (UC) oral ulcers. Bio-samples from three GI niches containing salivary, buccal, and fecal samples, were collected for 16S rRNA V3-V4 region sequencing. Bacterial abundance and related bio-functions were compared, and data showed that the fecal microbiota was more potent than salivary and buccal microbes in shaping the host immune system.\u2009~\u200922 UC and 10 UC_OU 5-aminosalicylate (5-ASA) routine treated patients were followed-up for six months; according to their treatment response (a decrease in the endoscopic Mayo score), they were further sub-grouped as responding and non-responding patients. RESULTS: We found those UC patients complicated with oral ulcers presented weaker treatment response, and three oral bacterial genera, i.e., Fusobacterium, Oribacterium, and Campylobacter, might be connected with treatment responding. Additionally, the salivary microbiome could be an indicator of treatment responding in 5-ASA routine treatment rather than buccal or fecal ones. CONCLUSIONS: The fecal microbiota had a strong effect on the host's immune indices, while the oral bacterial microbiota could help stratification for ulcerative colitis patients with oral ulcers. Additionally, the oral microbiota had the potential role in reflecting the treatment response of UC patients. Three oral bacteria genera (Fusobacterium, Oribacterium, and Campylobacter) might be involved in UC patients with oral ulcers lacking treatment responses, and monitoring oral microbiota may be meaningful in assessing the therapeutic response in UC patients.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34022363", + "title": "Fecal Fusobacterium nucleatum harbored virulence gene fadA are associated with ulcerative colitis and clinical outcomes.", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Li DH", + "Li ZP", + "Yan Zhang", + "Zhou GZ", + "Ren RR", + "Zhao HJ", + "Zhang NN", + "Li JF", + "Peng LH", + "Yang YS" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7454460787849465, + "mesh_terms": [ + "Adhesins, Bacterial", + "Colitis, Ulcerative", + "Fusobacterium nucleatum", + "Humans", + "RNA, Ribosomal, 16S", + "Virulence" + ], + "raw_abstract": "OBJECT: Fusobacterium nucleatum (F.nucleatum), a gram-negative, obligately anaerobe of oral commensal\uff0chas been regarded as culprit of periodontal diseases previously and is being unveiled as possible pathogen of gastrointestinal disorders. The key virulence factor of F.nucleatum is FadA adhesin for binding and invading of the host's epithelial cells. Here, we detected fecal F.nucleatum and virulence gene fadA in patients with ulcerative colitis(UC) and evaluated the clinical relevance with UC. METHODS AND SUBJECTS: A total of 310 subjects were enrolled including 100 patients with UC, 70 healthy controls (HC), 70 patients with irritable bowel syndrome subtype diarrhea(IBS-D), and 70 colorectal cancer patients(CRC). Stool samples of UC patients compared with healthy controls as well as IBS-D and CRC patients were collected for Polymerase Chain Reaction(PCR) detection of F.nucleatum (based on 16s rRNA) and virulence gene fadA. RESULTS: The detection rate of 16s rRNA based PCR for F.nucleatum of UC patients(39/100, 39.00%) and CRC(26/70, 37.14%) patients are significantly higher than HC (12/70, 17.14%, P\u00a0<\u00a00.01) and IBS-D patients (14/70, 20.00%, P\u00a0<\u00a00.01). Moreover, 19 samples were detected fadA positive from 39\u00a0F.nucleatum positive samples of UC patients (19/39, 48.72%), which is significantly higher than HC(2/12, 16.66%, P\u00a0<\u00a00.05). There were 3 samples detected fadA positive from 14\u00a0F.nucleatum positive samples of IBS-D patients(3/14, 21.43%) and 13 out of 26(50.00%) of CRC patients, which were both no significant differences compared with UC patients(21.4% vs 48.72%, P\u00a0>\u00a00.05; 50.00% vs 48.72%, P\u00a0>\u00a00.05). For both F.nucleatum and fadA gene positive patients, there were no statistical significances between erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), white blood cells(WBC), and hemoglobin compared with negative patients(defined by either F.nucleatum or fadA negative, or both negative). However, it is worth noting that detection rate of F.nucleatum with virulence gene fadA in patients of severe ulcerative colitis was significantly higher than patients with mild and moderate colitis(28.89% vs 10.91%, P\u00a0<\u00a00.05). In addition, the fecal F.nucleatum and fadA gene positive patients were more likely to have pancolitis other than left-sided colitis(pancolitis/left-sided colitis: 26.92% vs 10.42%, P\u00a0<\u00a00.05). CONCLUSIONS: The presence of F.nucleatum and fadA gene increased in UC patients, especially in patients with severe colitis and pancolitis. Strains of F.nucleatum harbored virulence gene fadA are suggested to play a role in the pathogenesis of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31240835", + "title": "Correlation of diet, microbiota and metabolite networks in inflammatory bowel disease.", + "year": 2019, + "journal": "Journal of digestive diseases", + "authors": [ + "Weng YJ", + "Gan HY", + "Li X", + "Huang Y", + "Li ZC", + "Deng HM", + "Chen SZ", + "Zhou Y", + "Wang LS", + "Han YP", + "Tan YF", + "Song YJ", + "Du ZM", + "Liu YY", + "Wang Y", + "Qin N", + "Bai Y", + "Yang RF", + "Bi YJ", + "Zhi FC" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7317350790133887, + "mesh_terms": [ + "Adult", + "Biopsy", + "Body Mass Index", + "Case-Control Studies", + "Diet", + "Dysbiosis", + "Feces", + "Female", + "Food Preferences", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Male", + "Metabolic Networks and Pathways", + "Metagenomics", + "Middle Aged", + "Nutrition Assessment", + "Young Adult" + ], + "raw_abstract": "OBJECTIVES: Microbiota dysbiosis in inflammatory bowel disease (IBD) has been widely reported. The gut microbiota connect diet to the metabolism by producing small molecules via diverse metabolic pathways. In this study we aimed to investigate the dietary preferences of IBD patients, and to explore the interactions among gut microbiota composition, dietary components, and metabolites in relation to IBD. METHODS: Dietary preferences of IBD patients (including those with ulcerative colitis [UC] and Crohn's disease [CD]) and health controls were investigated, and their gut microbiota were analyzed using 16S rRNA gene sequencing and metagenomic analyses of fecal and biopsy samples. The metabolite profiles of the samples were then analyzed using gas and liquid chromatography-mass spectrometry analyses. RESULTS: The daily intake of folic acid, niacin, vitamins C and D, calcium, and selenium differed significantly between patients with IBD and healthy controls. A decrease in long-chain (such as arachidic, and oleic acid) and medium-chain fatty acids (sebacic acid and isocaproic acid) as well as bile acid was observed in patients with IBD. Compared with healthy controls, 22 microbial species (including Sulfolobus acidocaldarius, and Clostridium clostridioforme CAG132) in the UC group and 37 microbial species (such as Bacteroides fragilis and Fusobacterium nucleatum) in the CD group were found to be correlated to diet and metabolites. Bacteroides fragilis was enriched in patients with IBD and associated with multi-nutrients, and 21 metabolites including 25-hydroxyvitamin D CONCLUSIONS: This study provides an interaction network to identify key micronutrients, microbiota components and metabolites that contribute to IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33871395", + "title": "Fecal microbiota profile in patients with inflammatory bowel disease in Taiwan.", + "year": 2021, + "journal": "Journal of the Chinese Medical Association : JCMA", + "authors": [ + "Chang TE", + "Luo JC", + "Yang UC", + "Huang YH", + "Hou MC", + "Lee FY" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7198906244334241, + "mesh_terms": [ + "Adult", + "Cross-Sectional Studies", + "Feces", + "Female", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Microbiota", + "Middle Aged", + "Taiwan" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with complicated interaction between immune, gut microbiota, and environmental factors in a genetically vulnerable host. Dysbiosis is often seen in patients with IBD. We aimed to investigate the fecal microbiota in patients with IBD and compared them with a control group in Taiwan. METHODS: In this cross-sectional study, we investigated fecal microbiota in 20 patients with IBD and 48 healthy controls. Fecal samples from both IBD patients and controls were analyzed by the next-generation sequencing method and relevant software. RESULTS: The IBD group showed lower bacterial richness and diversity compared with the control group. The principal coordinate analysis also revealed the significant structural differences between the IBD group and the control group. These findings were consistent whether the analysis was based on an operational taxonomic unit or amplicon sequence variant. However, no significant difference was found when comparing the composition of fecal microbiota between ulcerative colitis (UC) and Crohn's disease (CD). Further analysis showed that Lactobacillus, Enterococcus, and Bifidobacterium were dominant in the IBD group, whereas Faecalibacterium and Subdoligranulum were dominant in the control group at the genus level. When comparing UC, CD, and control group, Lactobacillus, Bifidobacterium, and Enterococcus were identified as dominant genera in the UC group. Fusobacterium and Escherichia_Shigella were dominant in the CD group. CONCLUSION: Compared with the healthy control, the IBD group showed dysbiosis with a significant decrease in both richness and diversity of gut microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33352216", + "title": "Changes in intestinal microbiota and correlation with TLRs in ulcerative colitis in the coastal area of northern China.", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Xu N", + "Bai X", + "Cao X", + "Yue W", + "Jiang W", + "Yu Z" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6692808597856181, + "mesh_terms": [ + "China", + "Colitis, Ulcerative", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: To investigate the communities of fecal microbiota and the role of Toll-like receptors in patients with ulcerative colitis in the coastal area of northern China. METHODS: Stool samples from 31 patients with ulcerative colitis and 12 healthy individuals were collected. The total bacterial genomic DNA was extracted, and the V3+V4 hypervariable region in the bacterial 16S rRNA gene sequence was amplified by polymerase chain reaction (PCR). High-throughput sequencing analysis was performed on the Illumina Hiseq platform. The expression of TLR2, TLR4, Tollip, PPAR-\u03b3, IL-6, and TNF-\u03b1 in the colonic mucosa was measured by Western blots. RESULTS: The diversity of the fecal microbiota in patients with ulcerative colitis was significantly less than that in healthy control individuals (p\u00a0<\u00a00.05). The proportion of Bacteroidetes was significantly reduced (p\u00a0<\u00a00.01), whereas Proteobacteria was prevalent (p\u00a0<\u00a00.01) in patients with ulcerative colitis. At the genus level, the relative abundance of Streptococcus and Anaerostipes was significantly increased (p\u00a0<\u00a00.05), whereas the proportion of Bacteroides, Lachnospira, Ruminococcus, Phascolarctobacterium, and Coprococcus was significantly decreased in patients with ulcerative colitis (p\u00a0<\u00a00.05). The diversity indexes of fecal microbiota in patients with ulcerative colitis were negatively correlated with disease severity (p\u00a0<\u00a00.05). The relative abundance of Enterobacteriaceae was positively correlated with disease severity, and the relative abundance of Phascolarctobacterium, Anaerostipes, Fusobacterium, Parabacteroides, Oscillospira, and Ochrobactrum were negatively correlated with disease severity. The expression levels of TLR2 and TLR4 in the intestinal mucosa were positively correlated with the relative abundance of Streptococcus and Enterobacteriaceae, respectively (r\u00a0=\u00a00.481, p\u00a0=\u00a00.007; r\u00a0=\u00a00.455, p\u00a0=\u00a00.017). CONCLUSION: There were significant changes in the diversity and composition of the fecal microbiota in patients with ulcerative colitis compared to healthy individuals. The dysbiosis of gut microbiota and correlation with TLRs might play important roles in the pathogenesis and progression of ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32265456", + "title": "Seasonal changes of circulating 25-hydroxyvitamin D correlate with the lower gut microbiome composition in inflammatory bowel disease patients.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Soltys K", + "Stuchlikova M", + "Hlavaty T", + "Gaalova B", + "Budis J", + "Gazdarica J", + "Krajcovicova A", + "Zelinkova Z", + "Szemes T", + "Kuba D", + "Drahovska H", + "Turna J", + "Stuchlik S" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6560260020108714, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteria", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Seasons", + "Vitamin D", + "Young Adult" + ], + "raw_abstract": "Higher probability of the development of Crohn's disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/Shigella spp.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36112501", + "title": "Searching for a Consensus Among Inflammatory Bowel Disease Studies: A Systematic Meta-Analysis.", + "year": 2023, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Abdel-Rahman LIH", + "Morgan XC" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.582126438860365, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Consensus", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Feces" + ], + "raw_abstract": "BACKGROUND: Numerous studies have examined the gut microbial ecology of patients with Crohn's disease (CD) and ulcerative colitis, but inflammatory bowel disease-associated taxa and ecological effect sizes are not consistent between studies. METHODS: We systematically searched PubMed and Google Scholar and performed a meta-analysis of 13 studies to analyze how variables such as sample type (stool, biopsy, and lavage) affect results in inflammatory bowel disease gut microbiome studies, using uniform bioinformatic methods for all primary data. RESULTS: Reduced alpha diversity was a consistent feature of both CD and ulcerative colitis but was more pronounced in CD. Disease contributed significantly variation in beta diversity in most studies, but effect size varied, and the effect of sample type was greater than the effect of disease. Fusobacterium was the genus most consistently associated with CD, but disease-associated genera were mostly inconsistent between studies. Stool studies had lower heterogeneity than biopsy studies, especially for CD. CONCLUSIONS: Our results indicate that sample type variation is an important contributor to study variability that should be carefully considered during study design, and stool is likely superior to biopsy for CD studies due to its lower heterogeneity. To assess reproducibility in inflammatory bowel disease microbiome research, we performed a meta-analysis of 13 inflammatory bowel disease studies, measuring effects of disease and sample type. Crohn\u2019s disease studies were more heterogeneous than ulcerative colitis studies, and sample type variation was a major contributor to inconsistency.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36484910", + "title": "Dark-purple rice extract modulates gut microbiota composition in acetic acid- and indomethacin-induced inflammatory bowel disease in rats.", + "year": 2023, + "journal": "International microbiology : the official journal of the Spanish Society for Microbiology", + "authors": [ + "Thipart K", + "Gruneck L", + "Phunikhom K", + "Sharpton TJ", + "Sattayasai J", + "Popluechai S" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.5448053773469497, + "mesh_terms": [ + "Animals", + "Rats", + "Oryza", + "Gastrointestinal Microbiome", + "Acetic Acid", + "Indomethacin", + "RNA, Ribosomal, 16S", + "Anthocyanins", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Colitis, Ulcerative", + "Bacteria" + ], + "raw_abstract": "Ulcerative colitis (UC) and Crohn's disease (CD) are two major forms of inflammatory bowel disease (IBD). The disease has been linked with gut microbiota dysbiosis in which the balance of commensal communities is disrupted. Accumulating evidence demonstrates that treatment with biologically active compounds can modulate gut microbiota composition in animal models. Our previous work has also shown the beneficial effect of Luem Pua (LP) rice extract, which is rich in anthocyanins, on inflammation. However, its effect on gut microbiota is yet to be explored. In this study, we profiled fecal microbiota of acetic acid (AA)-induced UC and indomethacin (ID)-induced CD rat models with and without pretreatment with LP rice extract by 16S rRNA gene sequencing. The results showed that gut microbiota communities of rats were altered by both AA-induced UC and ID-induced CD. The relative abundances of beneficial bacteria, especially the Lachnospiraceae NK4A136 group and Lactobacillus, were decreased in the AA-induced UC model, while some opportunistic pathogens (Bacteroides, Escherichia/Shigella, Fusobacterium, and Veillonella) were raised by ID-induced CD. Interestingly, pretreatment with LP rice extract before AA-inducing UC in rats increased the proportion of the butyrate-producing bacteria (Lachnospiraceae NK4A136 group). The abundances of these beneficial bacteria and other SCFA-producing bacteria were unaffected by the indomethacin treatment with LP. Overall, our study revealed different impacts of AA-induced UC and ID-induced CD on changes in community composition and hinted at how LP may protect against UC by modifying the gut microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26839545", + "title": "Quantitative Analysis of Intestinal Flora of Uygur and Han Ethnic Chinese Patients with Ulcerative Colitis.", + "year": 2016, + "journal": "Gastroenterology research and practice", + "authors": [ + "Yao P", + "Cui M", + "Wang H", + "Gao H", + "Wang L", + "Yang T", + "Cheng Y" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.48980520006691786, + "mesh_terms": [], + "raw_abstract": "Aim. To study the correlation between intestinal flora and ulcerative colitis by analyzing the abundance of Bacteroides, Fusobacterium, Clostridium, Bifidobacterium spp., and Faecalibacterium prausnitzii in the intestinal of ulcerative colitis (UC) patients and healthy controls with Uygur and Han ethnic. Methods. Bacterial genomic DNA was extracted from fecal samples and analyzed with real-time fluorescence quantitative polymerase chain reaction (PCR) to identify the abundance of Bacteroides, Fusobacterium, Clostridium, Bifidobacterium spp., and Faecalibacterium prausnitzii. Results. The samples from UC patients, Uygur and Han ethnic combined, had higher abundance of Bacteroides (P = 0.026) but lower Clostridium (P = 0.004), Bifidobacterium spp. (P = 0.009), and Faecalibacterium prausnitzii (P = 0.008) than those from healthy controls. Among UC patients, Bacteroides population was raised in acute UC patients (P \u2264 0.05), while the abundance of Clostridium, Bifidobacterium spp., Fusobacterium, and Faecalibacterium prausnitzii decreased (P \u2264 0.05) compared with the remission. In both UC patients group and control group, no difference was observed in the abundance of these 5 bacteria between the Han and the Uygur group. Conclusions. Variations in the abundance of these five bacterial strains in intestines may be associated with the occurrence of UC in Uygur and Han populations; however, these variations were not associated with ethnic difference.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34798830", + "title": "Fecal microbiota profiling in irritable bowel syndrome and inflammatory bowel disease patients with irritable bowel syndrome-type symptoms.", + "year": 2021, + "journal": "BMC gastroenterology", + "authors": [ + "Cui X", + "Wang H", + "Ye Z", + "Li Y", + "Qiu X", + "Zhang H" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.47409464269823487, + "mesh_terms": [ + "Cross-Sectional Studies", + "Feces", + "Humans", + "Inflammatory Bowel Diseases", + "Irritable Bowel Syndrome", + "Microbiota" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota is thought to be involved in the occurrence of inflammatory bowel disease in remission with irritable bowel syndrome (IBS)-type symptoms, but the specific distinct profile of these bacteria remains unclear. This cross-sectional study aims to investigate the fecal microbiota profiling in patients with these diseases. METHODS: Fecal samples from 97 subjects, including Crohn's disease patients in remission with IBS-type symptoms (CDR-IBS RESULTS: The richness of the intestinal microbiota in the CDR-IBS group was markedly lower than those in the control and IBS groups based on the analysis of observed species and the Chao index (P\u2009<\u20090.05). The observed species index in the CDR-IBS CONCLUSIONS: The IBS-type symptoms in CD patients in remission may be related to an increase in Faecalibacterium and a decrease in Fusobacterium. The IBS-type symptoms in UC patients in remission cannot be explained by changes in the abundance and structure of the intestinal microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32526285", + "title": "The protective effect of Lactobacillus versus 5-aminosalicylic acid in ulcerative colitis model by modulation of gut microbiota and Nrf2/Ho-1 pathway.", + "year": 2020, + "journal": "Life sciences", + "authors": [ + "El-Baz AM", + "Khodir AE", + "Adel El-Sokkary MM", + "Shata A" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.467006914433576, + "mesh_terms": [ + "Animals", + "Antioxidants", + "Colitis, Ulcerative", + "Escherichia coli", + "Fusobacterium", + "Gastrointestinal Microbiome", + "Heme Oxygenase-1", + "Humans", + "Inflammation", + "Lactobacillus", + "Male", + "Mesalamine", + "NF-E2-Related Factor 2", + "Oxidative Stress", + "Protective Agents", + "Rats", + "Rats, Sprague-Dawley", + "Tumor Necrosis Factor-alpha" + ], + "raw_abstract": "AIMS: Ulcerative colitis (UC) has many complications, from colonic damage to colorectal cancer. The mystery of both etiology and effective treatment of UC still challenging process. The role of gut microbiota in UC is still unclear. In the current study we compare the difference in gut microbiota abundance in both UC and normal colon besides the therapeutic effect of Lactobacillus spp. in treating UC versus the standard drug. MATERIALS AND METHODS: The experimental panel included five group of rats; normal control, UC diseased rats, sterilizing rats, ASA treated and Lactobacillus treated. The change in the microbiota abundance was investigated using conventional and real time PCR. In parallel, clinical evaluation of UC and macroscopic examination scoring was also done. Colonic oxidants/antioxidant stress biomarkers; MDA, GSH, catalase, myeloperoxidase activity, and SOD activity were assessed. Colon Nrf2, HO-1 contents and TNF-\u03b1 was evaluated. KEY FINDINGS: The current study revealed a significant difference in the relative abundance of microbiota where, UC is associated with massive increase of E. coli and Fusobacterium spp., while enormous decrease in Bifidobacteria spp. in contrast with negative control. Both 5-ASA and Lactobacillus show a significant amelioration of all antioxidant enzymes and marked decline of inflammatory and oxidative stress markers. Both Lactobacillus and 5-ASA show significant increase of NrF2 and HO-1 and marked decrease of TNF-\u03b1. SIGNIFICANCE: Lactobacillus spp. exerted a beneficial effect on the inflammation, oxidative stress and the symbiosis of gut microbiota that improve structural intestinal defect and promote healing in UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29361092", + "title": "Safety, Clinical Response, and Microbiome Findings Following Fecal Microbiota Transplant in Children With Inflammatory Bowel Disease.", + "year": 2018, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Goyal A", + "Yeh A", + "Bush BR", + "Firek BA", + "Siebold LM", + "Rogers MB", + "Kufen AD", + "Morowitz MJ" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.43112540066326294, + "mesh_terms": [ + "Adolescent", + "Bacteria", + "Biomarkers", + "Child", + "Fecal Microbiota Transplantation", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Prospective Studies", + "Remission Induction", + "Severity of Illness Index" + ], + "raw_abstract": "BACKGROUND: The role of fecal microbiota transplant (FMT) in the treatment of pediatric inflammatory bowel disease (IBD) is unknown. The aims of this study were to assess safety, clinical response, and gut microbiome alterations in children with Crohn's disease (CD), ulcerative colitis (UC), or indeterminate colitis (IC). METHODS: In this open-label, single-center prospective trial, patients with IBD refractory to medical therapy underwent a single FMT by upper and lower endoscopy. Adverse events, clinical response, gut microbiome, and biomarkers were assessed at baseline, 1 week, 1 month, and 6 months following FMT. RESULTS: Twenty-one subjects were analyzed, with a median age of 12 years, of whom 57% and 28% demonstrated clinical response at 1 and 6 months post-FMT, respectively. Two CD patients were in remission at 6 months. Adverse events attributable to FMT were mild to moderate and self-limited. Patients prior to FMT showed decreased species diversity and significant microbiome compositional differences characterized by increased Enterobacteriaceae, Enterococcus, Haemophilus, and Fusobacterium compared with donors and demonstrated increased species diversity at 30 days post-FMT. At 6 months, these changes shifted toward baseline. Clinical responders had a higher relative abundance of Fusobacterium and a lower diversity at baseline, as well as a greater shift toward donor-like microbiome after FMT compared with nonresponders. CONCLUSIONS: A single FMT is relatively safe and can result in a short-term response in young patients with active IBD. Responders possessed increased Fusobacterium prior to FMT and demonstrated more significant microbiome changes compared with nonresponders after FMT. Microbiome characteristics may help in predicting response.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27412252", + "title": "Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.", + "year": 2016, + "journal": "Genome medicine", + "authors": [ + "Shaw KA", + "Bertha M", + "Hofmekler T", + "Chopra P", + "Vatanen T", + "Srivatsa A", + "Prince J", + "Kumar A", + "Sauer C", + "Zwick ME", + "Satten GA", + "Kostic AD", + "Mulle JG", + "Xavier RJ", + "Kugathasan S" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3912722894782307, + "mesh_terms": [ + "Adolescent", + "Bacteria", + "Biomarkers", + "Case-Control Studies", + "Child", + "Child, Preschool", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Immunologic Factors", + "Inflammation", + "Intestinal Mucosa", + "Leukocyte L1 Antigen Complex", + "Longitudinal Studies", + "Male", + "Severity of Illness Index", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Gut microbiome dysbiosis has been demonstrated in subjects with newly diagnosed and chronic inflammatory bowel disease (IBD). In this study we sought to explore longitudinal changes in dysbiosis and ascertain associations between dysbiosis and markers of disease activity and treatment outcome. METHODS: We performed a prospective cohort study of 19 treatment-na\u00efve pediatric IBD subjects and 10 healthy controls, measuring fecal calprotectin and assessing the gut microbiome via repeated stool samples. Associations between clinical characteristics and the microbiome were tested using generalized estimating equations. Random forest classification was used to predict ultimate treatment response (presence of mucosal healing at follow-up colonoscopy) or non-response using patients' pretreatment samples. RESULTS: Patients with Crohn's disease had increased markers of inflammation and dysbiosis compared to controls. Patients with ulcerative colitis had even higher inflammation and dysbiosis compared to those with Crohn's disease. For all cases, the gut microbial dysbiosis index associated significantly with clinical and biological measures of disease severity, but did not associate with treatment response. We found differences in specific gut microbiome genera between cases/controls and responders/non-responders including Akkermansia, Coprococcus, Fusobacterium, Veillonella, Faecalibacterium, and Adlercreutzia. Using pretreatment microbiome data in a weighted random forest classifier, we were able to obtain 76.5\u00a0% accuracy for prediction of responder status. CONCLUSIONS: Patient dysbiosis improved over time but persisted even among those who responded to treatment and achieved mucosal healing. Although dysbiosis index was not significantly different between responders and non-responders, we found specific genus-level differences. We found that pretreatment microbiome signatures are a promising avenue for prediction of remission and response to treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29651370", + "title": "Effect of the Specific Carbohydrate Diet on the Microbiome of a Primary Sclerosing Cholangitis and Ulcerative Colitis Patient.", + "year": 2018, + "journal": "Cureus", + "authors": [ + "Dubrovsky A", + "Kitts CL" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.3761752508949818, + "mesh_terms": [], + "raw_abstract": "A 20-year-old female was diagnosed with ulcerative colitis (UC) at age 14 and primary sclerosing cholangitis (PSC) at age 16. The PSC was successfully treated with high doses of oral vancomycin; however, the UC was more difficult to manage. After many drug treatments failed to treat the UC, the patient began following the specific carbohydrate diet (SCD). This report documents fecal microbiome changes\u00a0resulting from following the SCD for two weeks. The DNA extracted from fecal samples was subjected to 16S rRNA\u00a0gene sequencing to quantify bacterial species abundance. Not only were substantial changes in the fecal bacterial composition detectable within two weeks, but all UC symptoms were also controlled as early as one week following the start of the diet. The patient's fecal microbiota was dramatically different from those of three healthy control subjects and showed remarkable loss of bacterial diversity in terms of species richness, evenness,\u00a0and overall diversity measures. Other specific\u00a0changes in bacterial composition included an increase\u00a0in Enterobacteriaceae, including Escherichia and Enterobacter species. A two- to three-fold decrease was observed in the prevalence of the most dominant fecal bacterial species, Fusobacterium ulcerans, after two weeks on the SCD. Overall species diversity and evenness increased to levels near the controls, although species richness remained low. These findings provide information on the fecal bacteria\u00a0from a patient with PSC and UC, following prolonged oral vancomycin treatment, and identifies a potentially specific microbial effect for the SCD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28214091", + "title": "Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial.", + "year": 2017, + "journal": "Lancet (London, England)", + "authors": [ + "Paramsothy S", + "Kamm MA", + "Kaakoush NO", + "Walsh AJ", + "van den Bogaerde J", + "Samuel D", + "Leong RWL", + "Connor S", + "Ng W", + "Paramsothy R", + "Xuan W", + "Lin E", + "Mitchell HM", + "Borody TJ" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.35083548012191096, + "mesh_terms": [ + "Adult", + "Colitis, Ulcerative", + "Colonoscopy", + "Double-Blind Method", + "Fecal Microbiota Transplantation", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "Remission Induction", + "Severity of Illness Index", + "Tissue Donors" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota is implicated in the pathogenesis of ulcerative colitis. Faecal microbiota transplantation is a novel form of therapeutic microbial manipulation, but its efficacy in ulcerative colitis is uncertain. We aimed to establish the efficacy of intensive-dosing, multidonor, faecal microbiota transplantation in active ulcerative colitis. METHODS: We conducted a multicentre, double-blind, randomised, placebo-controlled trial at three hospitals in Australia. We randomly allocated patients with active ulcerative colitis (Mayo score 4-10) in a 1:1 ratio, using a pre-established randomisation list, to either faecal microbiota transplantation or placebo colonoscopic infusion, followed by enemas 5 days per week for 8 weeks. Patients, treating clinicians, and other study staff were unaware of the assigned treatment. Faecal microbiota transplantation enemas were each derived from between three and seven unrelated donors. The primary outcome was steroid-free clinical remission with endoscopic remission or response (Mayo score \u22642, all subscores \u22641, and \u22651 point reduction in endoscopy subscore) at week 8. Analysis was by modified intention-to-treat and included all patients receiving one study dose. We performed 16S rRNA stool analysis to assess associated microbial changes. This trial is registered with ClinicalTrials.gov, number NCT01896635. The trial has ended; this report presents the final analysis. FINDINGS: From November, 2013, to May, 2015, 85 patients were enrolled to our trial, of whom 42 were randomly assigned faecal microbiota transplantation and 43 were allocated placebo. One patient assigned faecal microbiota transplantation and three allocated placebo did not receive study treatment and were excluded from the analysis. The primary outcome was achieved in 11 (27%) of 41 patients allocated faecal microbiota transplantation versus three (8%) of 40 who were assigned placebo (risk ratio 3\u00b76, 95% CI 1\u00b71-11\u00b79; p=0\u00b7021). Adverse events were reported by 32 (78%) of 41 patients allocated faecal microbiota transplantation and 33 (83%) of 40 who were assigned placebo; most were self-limiting gastrointestinal complaints, with no significant difference in number or type of adverse events between treatment groups. Serious adverse events occurred in two patients assigned faecal microbiota transplantation and in one allocated placebo. Microbial diversity increased with and persisted after faecal microbiota transplantation. Several bacterial taxa were associated with clinical outcome; in particular, the presence of Fusobacterium spp was associated with lack of remission. INTERPRETATION: Intensive-dosing, multidonor, faecal microbiota transplantation induces clinical remission and endoscopic improvement in active ulcerative colitis and is associated with distinct microbial changes that relate to outcome. Faecal microbiota transplantation is, thus, a promising new therapeutic option for ulcerative colitis. Future work should focus on precisely defining the optimum treatment intensity and the role of donor-recipient matching based on microbial profiles. FUNDING: Broad Medical Research Program, Gastroenterological Society of Australia, Mount Sinai (New York) SUCCESS fund, University of New South Wales.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37770177", + "title": "Phage therapy in gut microbiome.", + "year": 2023, + "journal": "Progress in molecular biology and translational science", + "authors": [ + "Chen X", + "Mendes BG", + "Alves BS", + "Duan Y" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.2803441522492126, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Phage Therapy", + "Gastrointestinal Tract", + "Bacteria", + "Microbiota", + "Anti-Bacterial Agents" + ], + "raw_abstract": "Phage therapy, the use of bacteriophage viruses for bacterial infection treatment, has been around for almost a century, but with the increase in antibiotic use, its importance has declined rapidly. There has been renewed interest in revisiting this practice due to the general decline in the effectiveness of antibiotics, combined with improved understanding of human microbiota and advances in sequencing technologies. Phage therapy has been proposed as a clinical alternative to restore the gut microbiota in the absence of an effective treatment. That is due to its immunomodulatory and bactericidal effects against its target bacteria. In the gastrointestinal diseases field, phage therapy has been studied mainly as a promising tool in infectious diseases treatment, such as cholera and diarrhea. However, many studies have been conducted in non-communicable diseases, such as the targeting of adherent invasive Escherichia coli in Crohn's disease, the treatment of Clostridioides difficile in ulcerative colitis, the eradication of Fusobacterium nucleatum in colorectal cancer, the targeting of alcohol-producing Klebsiella pneumoniae in non-alcoholic fatty liver disease, or Enterococcus faecalis in alcohol-associated hepatitis. This review will summarize the changes in the gut microbiota and the phageome in association with some gastrointestinal and liver diseases and highlight the recent scientific advances in phage therapy as a therapeutic tool for their treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30529583", + "title": "Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis.", + "year": 2019, + "journal": "Gastroenterology", + "authors": [ + "Paramsothy S", + "Nielsen S", + "Kamm MA", + "Deshpande NP", + "Faith JJ", + "Clemente JC", + "Paramsothy R", + "Walsh AJ", + "van den Bogaerde J", + "Samuel D", + "Leong RWL", + "Connor S", + "Ng W", + "Lin E", + "Borody TJ", + "Wilkins MR", + "Colombel JF", + "Mitchell HM", + "Kaakoush NO" + ], + "bacteria": "Fusobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.2678577146510703, + "mesh_terms": [ + "Bacteria", + "Biomarkers", + "Colitis, Ulcerative", + "Double-Blind Method", + "Fecal Microbiota Transplantation", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Metabolomics", + "New South Wales", + "Remission Induction", + "Ribotyping", + "Time Factors", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy. METHODS: We performed a double-blind trial of 81 patients with active UC randomly assigned to groups that received an initial colonoscopic infusion and then intensive multidonor FMT or placebo enemas, 5 d/wk for 8 weeks. Patients in the FMT group received blended homogenized stool from 3-7 unrelated donors. Patients in the placebo group were eligible to receive open-label FMT after the double-blind study period. We collected 314 fecal samples from the patients at screening, every 4 weeks during treatment, and 8 weeks after the blinded or open-label FMT therapy. We also collected 160 large-bowel biopsy samples from the patients at study entry, at completion of 8 weeks of blinded therapy, and at the end of open-label FMT, if applicable. We analyzed 105 fecal samples from the 14 individual donors (n\u00a0= 55), who in turn contributed to 21 multidonor batches (n\u00a0= 50). Bacteria in colonic and fecal samples were analyzed by both 16S ribosomal RNA gene and transcript amplicon sequencing; 285 fecal samples were analyzed by shotgun metagenomics, and 60 fecal samples were analyzed for metabolome features. RESULTS: FMT increased microbial diversity and altered composition, based on analyses of colon and fecal samples collected before vs after FMT. Diversity was greater in fecal and colon samples collected before and after FMT treatment from patients who achieved remission compared with patients who did not. Patients in remission after FMT had enrichment of Eubacterium hallii and Roseburia inulivorans compared with patients who did not achieve remission after FMT and had increased levels of short-chain fatty acid biosynthesis and secondary bile acids. Patients who did not achieve remission had enrichment of Fusobacterium gonidiaformans, Sutterella wadsworthensis, and Escherichia species and increased levels of heme and lipopolysaccharide biosynthesis. Bacteroides in donor stool were associated with remission in patients receiving FMT, and Streptococcus species in donor stool was associated with no response to FMT. CONCLUSIONS: In an analysis of fecal and colonic mucosa samples from patients receiving FMT for active UC and stool samples from donors, we associated specific bacteria and metabolic pathways with induction of remission. These findings may be of value in the design of microbe-based therapies for UC. ClinicalTrials.gov, Number NCT01896635.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28852861", + "title": "Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.", + "year": 2018, + "journal": "Journal of gastroenterology", + "authors": [ + "Nishino K", + "Nishida A", + "Inoue R", + "Kawada Y", + "Ohno M", + "Sakai S", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Kawahara M", + "Naito Y", + "Andoh A" + ], + "bacteria": "Cetobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7404425867634223, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Endoscopy, Gastrointestinal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. METHODS: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. RESULTS: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. \u03b1-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. CONCLUSIONS: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36169397", + "title": "Inflammatory Bowel Disease and Helicobacter pylori: Protective or Present?", + "year": 2023, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Tanner S", + "Katz J", + "Cominelli F", + "Regueiro M", + "Cooper G", + "Mansoor E" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.7950032196145708, + "mesh_terms": [ + "Humans", + "Helicobacter pylori", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Helicobacter Infections" + ], + "raw_abstract": "This article describes the prevalence of inflammatory bowel disease in patients with gastritis, duodenitis, and peptic ulcer disease, stratified by Helicobacter pylori infection. Inflammatory boweld is less prevalent in patients with H. pylori, and no increased risk of IBD is seen after H. pylori eradication therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26559250", + "title": "Enterohepatic Helicobacter Species as a Potential Causative Factor in Inflammatory Bowel Disease: A Meta-Analysis.", + "year": 2015, + "journal": "Medicine", + "authors": [ + "Yu Q", + "Zhang S", + "Li L", + "Xiong L", + "Chao K", + "Zhong B", + "Li Y", + "Wang H", + "Chen M" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.7787874985792044, + "mesh_terms": [ + "Helicobacter", + "Humans", + "Inflammatory Bowel Diseases" + ], + "raw_abstract": "The Helicobacter species in the gut microbiota comprise Helicobacter pylori (H pylori) and enterohepatic Helicobacter species (EHS), which can colonize the intestinal mucosa. However, it is unclear whether EHS are associated with inflammatory bowel disease (IBD). Therefore, we conducted this meta-analysis to examine the association between EHS and IBD.PubMed, Scopus, Cochrane Library, and Web of Science databases, as well as abstracts from conference proceedings were searched to identify studies that used polymerase chain reaction to detect Helicobacter species in intestinal samples from patients with IBD.After screening, we carefully reviewed 20 of the 2955 identified studies, and performed a meta-analysis of the findings from 14 studies (11 adult studies and 3 pediatric studies) using STATA v12.0. These studies evaluated 1407 individuals, including 433 patients with Crohn's disease, 306 patients with ulcerative colitis, and 668 controls. The prevalence of Helicobacter species was higher among the patients with IBD, compared to that among the controls, which corresponded to a pooled risk ratio (RR) of 1.59 (95% confidence interval [CI]: 1.12-2.27). The RRs for adult and pediatric patients with IBD were 1.61 (95% CI: 1.03-2.52) and 1.76 (95% CI: 1.17-2.64), respectively. Compared to the controls, the patients with IBD tended to have a higher prevalence of EHS in the intestinal mucosa (RR: 2.01, 95% CI: 1.36-2.98), although the prevalence of H pylori was not significantly higher (RR: 1.22, 95% CI: 0.77-1.95). Compared to the controls, the RRs for EHS in patients with Crohn's disease and ulcerative colitis were 1.72 (95% CI: 1.20-2.47) and 3.27 (95% CI: 0.93-11.44), respectively.It appears that EHS was associated with IBD, while intestinal H pylori infection was not significantly associated with IBD. Further studies are needed to determine the involvement of EHS in the microbiological etiology of IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36515237", + "title": "Helicobacter pylori and Inflammatory Bowel Disease: An Unresolved Enigma.", + "year": 2023, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Pokrotnieks J", + "Sitkin S" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.777383569474217, + "mesh_terms": [ + "Humans", + "Helicobacter pylori", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Helicobacter Infections" + ], + "raw_abstract": "The article describes the hypothesis that there may be a noncausal relationship between Helicobacter pylori infection and inflammatory bowel disease (IBD) that is related to the host mucin glycan fucosylation status in the gastrointestinal tract. The proposed hypothesis may explain why IBD is less prevalent in patients with H. pylori, and no increased risk of IBD is seen after H. pylori eradication therapy, as was shown in the study by Tanner et al.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30561399", + "title": "Inverse association between Helicobacter pylori and inflammatory bowel disease: myth or fact?", + "year": 2018, + "journal": "Acta bio-medica : Atenei Parmensis", + "authors": [ + "Kayali S", + "Gaiani F", + "Manfredi M", + "Minelli R", + "Nervi G", + "Nouvenne A", + "Leandro G", + "Di Mario F", + "De' Angelis GL" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.7589074038213857, + "mesh_terms": [ + "Comorbidity", + "Dysbiosis", + "Gastritis", + "Global Health", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Inflammatory Bowel Diseases", + "Prevalence" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel diseases (IBD), are chronic, relapsing-remitting diseases of the gastrointestinal tract, including Crohn's disease (CD), Ulcerative colitis (UC) and Unclassified IBD (IBDU). Their pathogenesis involves genes and environment as cofactors in inducing autoimmunity; particularly the interactions between enteric pathogens and immunity is being studied. Helicobacter pylori (HP) is common pathogen causing gastric inflammation. Studies found an inverse prevalence association between HP and IBD, suggesting a potential protecting role of HP from IBD. METHODS: A literature search of the PubMed database was performed using the key words ''helicobacter pylori'', ''inflammatory bowel disease'', ''crohn disease'', \"ulcerative colitis\". Embase, Medline (OvidSP), Web of Science, Scopus, PubMed publisher, Cochrane and Google Scholar were also searched. Prevalence rate-ratios among HP in IBD patients, HP in CD patients, HP in UC patients, HP in IBDU patients were extracted, each group was compared with controls, to verify the inverse association between HP and IBD prevalence. RESULTS: In all groups the dispersion of data suggested an inverse association between IBD group and controls, even when the comparison was carried out separately between each group of newly diagnosed patients and controls, to rule out the possible bias of ongoing pharmacologic therapy. CONCLUSIONS: The results of this review show a striking inverse association between HP infection and the prevalence of IBD, independently from the type of IBD considered across distinct geographic regions. Anyway, data should be interpreted cautiously, as wider, prospective and more homogeneous research on this topic are awaited, which could open new scenarios about environmental etiology of IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38951792", + "title": "Helicobacter Pylori infection in children with inflammatory bowel disease: a prospective multicenter study.", + "year": 2024, + "journal": "BMC pediatrics", + "authors": [ + "Dilaghi E", + "Felici E", + "Lahner E", + "Pilozzi E", + "Furio S", + "Lucchini L", + "Quatrale G", + "Piccirillo M", + "Parisi P", + "Curto S", + "Annibale B", + "Ferretti A", + "Mennini M", + "Persechino S", + "Di Nardo G" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.75863839423463, + "mesh_terms": [ + "Humans", + "Helicobacter Infections", + "Child", + "Male", + "Female", + "Adolescent", + "Prospective Studies", + "Helicobacter pylori", + "Child, Preschool", + "Colitis, Ulcerative", + "Crohn Disease", + "Severity of Illness Index", + "Inflammatory Bowel Diseases", + "Gastroscopy", + "Follow-Up Studies", + "Anti-Bacterial Agents" + ], + "raw_abstract": "BACKGROUND: The relationship between Helicobacter-pylori(Hp)infection and inflammatory-bowel-disease(IBD) in pediatric-patients remains controversial. We aimed to assess the Hp-infection occurrence in newly-diagnosed pediatric-patients with IBD compared to no-IBD patients. Additionally, we aimed to examine differences in clinical-activity-index(CAI) and endoscopic-severity-score(ESS)between IBD-patients with and without Hp-infection, at baseline and at 1-year-follow-up(FU), after eradication-therapy(ET). METHODS: IBD diagnosis was based on Porto-criteria, and all patients underwent gastroscopy at baseline and 1-year FU. For Crohn's-disease(CD) and ulcerative colitis(UC), IBD-CAI and -ESS were classified using PCDAI/SES-CD and PUCAI/UCEIS, respectively. RESULTS: 76 IBD-patients were included in the study[35 F(46.1%),median-age 12(range 2-17)]. CD and UC were diagnosed in 29(38.2%) and 45(59.2%)patients, respectively, and unclassified-IBD in two(2.6%)patients. Non-IBD patients were 148[71 F(48.0%),median-age 12(range 1-17)]. Hp-infection at baseline was reported in 7(9.2%) and 18(12.2%)IBD and non-IBD patients, respectively(p\u2009=\u20090.5065). The 7 IBD patients with Hp infection were compared to 69 IBD patients without Hp-infection at baseline evaluation, and no significant differences were reported considering CAI and ESS in these two groups. At 1-year FU, after ET, IBD patients with Hp infection improved, both for CAI and ESS, but statistical significance was not reached. CONCLUSION: The occurrence of Hp-infection did not differ between IBD and no-IBD patients. No differences in CAI or ESS were observed at the diagnosis, and after ET no worsening of CAI or ESS was noted at one-year FU, between Hp-positive and -negative IBD patients.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28198364", + "title": "Interleukin-22 drives nitric oxide-dependent DNA damage and dysplasia in a murine model of colitis-associated cancer.", + "year": 2017, + "journal": "Mucosal immunology", + "authors": [ + "Wang C", + "Gong G", + "Sheh A", + "Muthupalani S", + "Bryant EM", + "Puglisi DA", + "Holcombe H", + "Conaway EA", + "Parry NAP", + "Bakthavatchalu V", + "Short SP", + "Williams CS", + "Wogan GN", + "Tannenbaum SR", + "Fox JG", + "Horwitz BH" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.7131590458276423, + "mesh_terms": [ + "Animals", + "Antibodies, Blocking", + "Colitis, Ulcerative", + "Colon", + "Colonic Neoplasms", + "DNA Breaks, Double-Stranded", + "DNA-Binding Proteins", + "Disease Models, Animal", + "Helicobacter Infections", + "Helicobacter hepaticus", + "Humans", + "Inflammation", + "Interleukins", + "Macrophages, Peritoneal", + "Mice", + "Mice, 129 Strain", + "Mice, Knockout", + "Neoplasms", + "Nitric Oxide", + "Nitric Oxide Synthase Type II", + "Interleukin-22" + ], + "raw_abstract": "The risk of colon cancer is increased in patients with Crohn's disease and ulcerative colitis. Inflammation-induced DNA damage could be an important link between inflammation and cancer, although the pathways that link inflammation and DNA damage are incompletely defined. RAG2-deficient mice infected with Helicobacter hepaticus (Hh) develop colitis that progresses to lower bowel cancer. This process depends on nitric oxide (NO), a molecule with known mutagenic potential. We have previously hypothesized that production of NO by macrophages could be essential for Hh-driven carcinogenesis, however, whether Hh infection induces DNA damage in this model and whether this depends on NO has not been determined. Here we demonstrate that Hh infection of RAG2-deficient mice rapidly induces expression of iNOS and the development of DNA double-stranded breaks (DSBs) specifically in proliferating crypt epithelial cells. Generation of DSBs depended on iNOS activity, and further, induction of iNOS, the generation of DSBs, and the subsequent development of dysplasia were inhibited by depletion of the Hh-induced cytokine IL-22. These results demonstrate a strong association between Hh-induced DNA damage and the development of dysplasia, and further suggest that IL-22-dependent induction of iNOS within crypt epithelial cells rather than macrophages is a driving force in this process.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29603881", + "title": "Decreased risk for microscopic colitis and inflammatory bowel disease among patients with reflux disease.", + "year": 2018, + "journal": "Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland", + "authors": [ + "Sonnenberg A", + "Turner KO", + "Genta RM" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.6740123479275548, + "mesh_terms": [ + "Adult", + "Age Distribution", + "Aged", + "Biopsy, Needle", + "Case-Control Studies", + "Colitis, Microscopic", + "Comorbidity", + "Databases, Factual", + "Female", + "Gastroesophageal Reflux", + "Humans", + "Immunohistochemistry", + "Inflammatory Bowel Diseases", + "Logistic Models", + "Male", + "Middle Aged", + "Multivariate Analysis", + "Prevalence", + "Prognosis", + "Registries", + "Severity of Illness Index", + "Sex Distribution", + "United States" + ], + "raw_abstract": "AIM: Previous studies have found an increased risk for microscopic colitis (MC) associated with proton pump inhibitors. In patients with ulcerative colitis (UC) or Crohn's disease (CD), proton pump inhibitors have been associated with an increased risk for IBD flares and impaired outcomes. The aim of this study was to test the epidemiological associations between gastro-oesophageal reflux disease (GERD) and MC, UC or CD in a large database. METHOD: The Miraca Life Sciences Database is a national electronic repository of histopathological records of patients distributed throughout the entire USA. A case-control study evaluated whether the presence of Barrett's metaplasia, erosive oesophagitis on endoscopy or histological signs of reflux oesophagitis, clinical diagnosis of GERD or any GERD type affected the occurrence of MC, UC or CD among 228\u00a0506 subjects undergoing bidirectional endoscopy. Multivariate logistic regression analyses were used to calculate ORs and their 95% CI for the risk of MC, UC or CD associated with various types of GERD and were adjusted for age, sex and presence of Helicobacter pylori. RESULTS: The analysis revealed an inverse relationship between GERD and different types of inflammatory bowel disease. The inverse relationships applied similarly to MC (mean\u00a0=\u00a00.62, 95% CI: 0.58-0.66), UC (mean\u00a0=\u00a00.89, 95% CI: 0.81-0.97) and CD (mean\u00a0=\u00a00.76, 95% CI: 0.69-0.85). It also applied to different forms of GERD, with a trend towards more pronounced inverse relationships associated with Barrett's metaplasia or erosive oesophagitis than clinical diagnosis of GERD. CONCLUSION: Gastro-oesophageal reflux disease is inversely associated with all forms of inflammatory bowel disease, such as MC, UC, or CD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39326396", + "title": "Rosacea and Gastrointestinal Diseases: A Case-Control Study in the All of Us Database.", + "year": 2024, + "journal": "Dermatology (Basel, Switzerland)", + "authors": [ + "Piontkowski AJ", + "Sharma D", + "Ungar B" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.6720609801385199, + "mesh_terms": [ + "Humans", + "Rosacea", + "Case-Control Studies", + "Male", + "Female", + "Middle Aged", + "Adult", + "United States", + "Databases, Factual", + "Gastrointestinal Diseases", + "Aged", + "Irritable Bowel Syndrome", + "Celiac Disease", + "Helicobacter Infections", + "Crohn Disease", + "Colitis, Ulcerative", + "Young Adult", + "Colitis, Microscopic", + "Gastroesophageal Reflux", + "Adolescent", + "Logistic Models" + ], + "raw_abstract": "INTRODUCTION: Recent reports have suggested a link between rosacea and several gastrointestinal diseases, although the evidence has largely been limited to European and Asian populations. This study seeks to confirm and expand upon the connection between rosacea and gastrointestinal conditions using the diverse All of Us database. METHODS: We identified 8,319 rosacea patients and selected 4:1 controls matched (n = 33,276) based on age, race, gender, smoking status, insurance status, annual income, education, and alcohol use. Conditional logistic regression was then performed on the matched cohort to assess the relationship between rosacea and Crohn's disease (CD), microscopic colitis, ulcerative colitis (UC), celiac disease (CED), irritable bowel syndrome (IBS), Helicobacter-associated disease, and gastroesophageal reflux disease (GERD). RESULTS: On logistic regression, rosacea patients were significantly more likely than matched controls to be diagnosed with IBS (odds ratio [OR]: 2.35, 95% confidence interval [CI]: 2.18-2.53, p < 0.001), CD (OR: 1.82, 95% CI: 1.53-2.15, p < 0.001), UC (OR: 1.70, 95% CI: 1.44-2.02, p < 0.001), CED (OR: 1.93, 95% CI: 1.59-2.34, p < 0.001), Helicobacter-associated disease (OR: 1.79, 95% CI: 1.50-2.14, p < 0.001), and GERD (OR: 2.07, 95% CI: 1.97-2.18, p < 0.001). However, there was no statistically significant association between rosacea and microscopic colitis (OR: 1.47, 95% CI: 0.91-2.37, p = 0.12). CONCLUSION: This study highlights the presence of notable gastrointestinal comorbidities among individuals with rosacea in a diverse cohort. Consequently, more targeted monitoring of gastrointestinal diseases in rosacea patients may be warranted, as well as potential further investigation into the gut-skin axis in terms of rosacea pathophysiology.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32265456", + "title": "Seasonal changes of circulating 25-hydroxyvitamin D correlate with the lower gut microbiome composition in inflammatory bowel disease patients.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Soltys K", + "Stuchlikova M", + "Hlavaty T", + "Gaalova B", + "Budis J", + "Gazdarica J", + "Krajcovicova A", + "Zelinkova Z", + "Szemes T", + "Kuba D", + "Drahovska H", + "Turna J", + "Stuchlik S" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.6560260020108714, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteria", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Seasons", + "Vitamin D", + "Young Adult" + ], + "raw_abstract": "Higher probability of the development of Crohn's disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/Shigella spp.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33711050", + "title": "The prevalence of Helicobacter pylori infection in inflammatory bowel disease in China: A case-control study.", + "year": 2021, + "journal": "PloS one", + "authors": [ + "Ding ZH", + "Xu XP", + "Wang TR", + "Liang X", + "Ran ZH", + "Lu H" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.6219187177068851, + "mesh_terms": [ + "Adult", + "China", + "Colitis, Ulcerative", + "Crohn Disease", + "Female", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Male", + "Middle Aged", + "Prevalence", + "Retrospective Studies" + ], + "raw_abstract": "BACKGROUND & AIMS: Helicobacter pylori (H. pylori) infection remains high in China though the incidence of inflammatory bowel disease (IBD) has increased. Our aim was to investigate the relationship between the prevalence of H. pylori and inflammatory bowel disease. METHODS: Hospitalized IBD patients including Crohn's disease (CD) and ulcerative colitis (UC) who had tested H. pylori antibody were enrolled. Controls were chose from age- and sex- matched healthy physical examination people who had H. pylori antibody test in a 1:2 fashion (IBD patients:controls). IBD medical history was recorded. All patients were typed by the Montreal classification. Mayo Clinic score and the Harvey-Bradshaw Severity Index were used to evaluate their disease activity. Patients and controls that had H. pylori eradication therapy before were excluded. RESULTS: Two hundred and sixty IBD patients including 213 CD patients and 47 UC patients, and 520 controls were involved in this study. The prevalence of H. pylori infection in IBD patients (9.6%, 25/260) and IBD newly diagnosed patients (12.1%, 8/66), as well as CD patients (8.9%, 19/213) including CD newly diagnosed patients (10.6%, 5/47) and UC patients (12.8%, 6/47) was significantly lower than controls (29.8%, 155/520) (p = 2.796*10-10, 0.007, 5.723*10-9, 0.016, 0.014), while there was no statistically difference between UC newly diagnosed patients and the controls, and IBD patients with different disease type, disease activity and treatment history. CONCLUSIONS: H. pylori infection had a negative association with IBD, especially CD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26508508", + "title": "Dual role of Helicobacter and Campylobacter species in IBD: a systematic review and meta-analysis.", + "year": 2017, + "journal": "Gut", + "authors": [ + "Casta\u00f1o-Rodr\u00edguez N", + "Kaakoush NO", + "Lee WS", + "Mitchell HM" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5724453660376028, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Campylobacter", + "Campylobacter Infections", + "Colitis, Ulcerative", + "Crohn Disease", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Protective Factors", + "Risk Factors", + "Stomach Diseases" + ], + "raw_abstract": "OBJECTIVE: To conduct a comprehensive global systematic review and meta-analysis on the association between Helicobacter pylori infection and IBD. As bacterial antigen cross-reactivity has been postulated to be involved in this association, published data on enterohepatic Helicobacter spp (EHS) and Campylobacter spp and IBD was also analysed. DESIGN: Electronic databases were searched up to July 2015 for all case-control studies on H. pylori infection/EHS/Campylobacter spp and IBD. Pooled ORs (P-OR) and 95% CIs were obtained using the random effects model. Heterogeneity, sensitivity and stratified analyses were performed. RESULTS: Analyses comprising patients with Crohn's disease (CD), UC and IBD unclassified (IBDU), showed a consistent negative association between gastric H. pylori infection and IBD (P-OR: 0.43, p value <1e-10). This association appears to be stronger in patients with CD (P-OR: 0.38, p value <1e-10) and IBDU (P-OR: 0.43, p value=0.008) than UC (P-OR: 0.53, p value <1e-10). Stratification by age, ethnicity and medications showed significant results. In contrast to gastric H. pylori, non H. pylori-EHS (P-OR: 2.62, p value=0.001) and Campylobacter spp, in particular C. concisus (P-OR: 3.76, p value=0.006) and C. showae (P-OR: 2.39, p value=0.027), increase IBD risk. CONCLUSIONS: H. pylori infection is negatively associated with IBD regardless of ethnicity, age, H. pylori detection methods and previous use of aminosalicylates and corticosteroids. Antibiotics influenced the magnitude of this association. Closely related bacteria including EHS and Campylobacter spp increase the risk of IBD. These results infer that H. pylori might exert an immunomodulatory effect in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34758726", + "title": "Ulcerative colitis relapse after Helicobacter pylori eradication in a 12-year-old boy with duodenal ulcer.", + "year": 2021, + "journal": "BMC gastroenterology", + "authors": [ + "Fujita Y", + "Tominaga K", + "Tanaka T", + "Sugaya T", + "Yoshihara S" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.569213285023311, + "mesh_terms": [ + "Amoxicillin", + "Anti-Bacterial Agents", + "Child", + "Clarithromycin", + "Colitis, Ulcerative", + "Drug Therapy, Combination", + "Duodenal Ulcer", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Male", + "Recurrence" + ], + "raw_abstract": "BACKGROUND: Helicobacter pylori (H. pylori) prevalence is lower in patients with inflammatory bowel disease (IBD) than in those without IBD, suggesting that H. pylori plays a protective role in IBD. It has been reported that IBD may occur due to H. pylori eradication; however, it is unclear whether H. pylori eradication increases the incidence of IBD. Moreover, the effect of H. pylori eradication on IBD activity is unclear. CASE PRESENTATION: An 11-year-old boy diagnosed with ulcerative colitis (UC) was in clinical remission, with treatment involving 5-aminosalicylic acid. Fecal calprotectin (FC) level had decreased to 33.2\u00a0mg/kg, indicating mucosal healing. At age 12, he experienced epigastric pain on an empty stomach, which was relieved with dietary intake. His FC level was elevated without UC symptoms, such as diarrhea and bloody stools. He was diagnosed with H. pylori duodenal ulcer. H. pylori eradication (clarithromycin and amoxicillin for 7\u00a0days and a proton-pump inhibitor) led to symptom improvement the day after treatment initiation. However, he developed diarrhea and his FC level remained high despite improvement in duodenal ulcer symptoms and endoscopic findings of H. pylori eradication. Colonoscopy results indicated UC relapse. CONCLUSIONS: H. pylori eradication may worsen UC activity. However, further studies are required as this case report involved only one pediatric patient with increased UC activity after H. pylori eradication.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "25742401", + "title": "Helicobacter pylori-specific protection against inflammatory bowel disease requires the NLRP3 inflammasome and IL-18.", + "year": 2015, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Engler DB", + "Leonardi I", + "Hartung ML", + "Kyburz A", + "Spath S", + "Becher B", + "Rogler G", + "M\u00fcller A" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.554166456466124, + "mesh_terms": [ + "Animals", + "Carrier Proteins", + "Colitis", + "Dextran Sulfate", + "Diabetes Mellitus, Experimental", + "Diabetes Mellitus, Type 1", + "Disease Models, Animal", + "Encephalomyelitis, Autoimmune, Experimental", + "Helicobacter Infections", + "Helicobacter pylori", + "Interleukin-18", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Mice, Inbred NOD", + "Mucin-2", + "NLR Family, Pyrin Domain-Containing 3 Protein", + "Signal Transduction", + "T-Lymphocytes", + "Transcriptional Activation", + "Up-Regulation" + ], + "raw_abstract": "BACKGROUND: The Gram-negative bacterium Helicobacter pylori is a constituent of the human gastric microbiota. Chronic infection with H. pylori causes gastritis and predisposes to gastric carcinoma but has also been inversely linked to various allergic and chronic inflammatory conditions. In particular, large meta-analyses have documented an inverse association between H. pylori infection and the risk of developing ulcerative colitis and Crohn's disease. METHODS: We investigated possible protective effects of experimental H. pylori infection and of regular treatment with H. pylori extract in 2 mouse models of colitis and in mouse models of type I diabetes and multiple sclerosis. The mechanism of protection was examined in mouse strains lacking specific innate immune recognition pathways and cytokines. RESULTS: We show here that experimental infection with H. pylori and administration of regular doses of H. pylori extract both alleviate the clinical and histopathological features of dextran sodium sulfate-induced chronic colitis and of T-cell transfer-induced colitis. High resolution endoscopy of the protected animals revealed the accumulation of large amounts of colonic mucus upon H. pylori exposure, which could be attributed to transcriptional activation of the mucin 2 gene. The protection against dextran sodium sulfate-induced colitis was dependent on the NLRP3 inflammasome and interleukin-18 signaling. Other autoimmune diseases, i.e., experimental autoimmune encephalomyelitis and type I diabetes, were not controlled by H. pylori. CONCLUSIONS: In summary, we propose here that the immunomodulatory activity of an ancient constituent of the gut microbiota, H. pylori, may be exploited for the prevention and/or treatment of inflammatory bowel diseases.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31014995", + "title": "Environmental Risk Factors for Inflammatory Bowel Diseases: An Umbrella Review of Meta-analyses.", + "year": 2019, + "journal": "Gastroenterology", + "authors": [ + "Piovani D", + "Danese S", + "Peyrin-Biroulet L", + "Nikolopoulos GK", + "Lytras T", + "Bonovas S" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5477086187946159, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Drug-Related Side Effects and Adverse Reactions", + "Environment", + "Environmental Exposure", + "Humans", + "Hygiene", + "Life Style", + "Protective Factors", + "Risk Assessment", + "Risk Factors", + "Surgical Procedures, Operative", + "Vaccination" + ], + "raw_abstract": "BACKGROUND & AIMS: Multiple environmental factors have been associated with the development of inflammatory bowel diseases (IBDs). We performed an umbrella review of meta-analyses to summarize available epidemiologic evidence and assess its credibility. METHODS: We systematically identified and appraised meta-analyses of observational studies examining environmental factors and risk of IBD (Crohn's disease [CD] or ulcerative colitis [UC]). For each meta-analysis, we considered the random effects estimate, its 95% confidence interval, the estimates of heterogeneity, and small-study effects, and we graded the evidence according to prespecified criteria. Methodologic quality was assessed with AMSTAR (ie, A Measurement Tool to Assess Systematic Reviews)\u00a02. RESULTS: We examined 183 estimates in 53 meta-analyses of 71 environmental factors related to lifestyles and hygiene, surgeries, drug exposures, diet, microorganisms, and vaccinations. We identified 9 factors that increase risk of IBD: smoking (CD), urban living (CD and IBD), appendectomy (CD), tonsillectomy (CD), antibiotic exposure (IBD), oral contraceptive use (IBD), consumption of soft drinks (UC), vitamin D deficiency (IBD), and non-Helicobacter pylori-like enterohepatic Helicobacter species (IBD). We identified 7 factors that reduce risk of IBD: physical activity (CD), breastfeeding (IBD), bed sharing (CD), tea consumption (UC), high levels of folate (IBD), high levels of vitamin D (CD), and H pylori infection (CD, UC, and IBD). Epidemiologic evidence for all of these associations was of high to moderate strength; we identified another 11 factors associated with increased risk and 16 factors associated with reduced risk with weak credibility. Methodologic quality varied considerably among meta-analyses. Several associations were based on findings from retrospective studies, so it is not possible to determine if these are effects of IBD or the results of recall bias. CONCLUSIONS: In an umbrella review of meta-analyses, we found varying levels of evidence for associations of different environmental factors with risk of IBD. High-quality prospective studies with analyses of samples from patients with recent diagnoses of IBD are needed to determine whether these factors cause or are results of IBD and their pathogenic mechanisms.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27245408", + "title": "Helicobacter saguini, a Novel Helicobacter Isolated from Cotton-Top Tamarins with Ulcerative Colitis, Has Proinflammatory Properties and Induces Typhlocolitis and Dysplasia in Gnotobiotic IL-10-/- Mice.", + "year": 2016, + "journal": "Infection and immunity", + "authors": [ + "Shen Z", + "Mannion A", + "Whary MT", + "Muthupalani S", + "Sheh A", + "Feng Y", + "Gong G", + "Vandamme P", + "Holcombe HR", + "Paster BJ", + "Fox JG" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5456032577279222, + "mesh_terms": [ + "Animals", + "Antibodies, Bacterial", + "Cell Line", + "Colitis", + "Colitis, Ulcerative", + "Cytokines", + "Disease Models, Animal", + "Feces", + "Gene Expression", + "Genome, Bacterial", + "Helicobacter", + "Histones", + "Humans", + "Inflammation Mediators", + "Interleukin-10", + "Mice", + "Mice, Knockout", + "Monkey Diseases", + "Phylogeny", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "A urease-negative, fusiform, novel bacterium named Helicobacter saguini was isolated from the intestines and feces of cotton-top tamarins (CTTs) with chronic colitis. Helicobacter sp. was detected in 69% of feces or intestinal samples from 116 CTTs. The draft genome sequence, obtained by Illumina MiSeq sequencing, for H. saguini isolate MIT 97-6194-5, consisting of \u223c2.9 Mb with a G+C content of 35% and 2,704 genes, was annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline. H. saguini contains homologous genes of known virulence factors found in other enterohepatic helicobacter species (EHS) and H. pylori These include flagellin, \u03b3-glutamyl transpeptidase (ggt), collagenase, the secreted serine protease htrA, and components of a type VI secretion system, but the genome does not harbor genes for cytolethal distending toxin (cdt). H. saguini MIT 97-6194-5 induced significant levels of interleukin-8 (IL-8) in HT-29 cell culture supernatants by 4 h, which increased through 24 h. mRNAs for the proinflammatory cytokines IL-1\u03b2, tumor necrosis factor alpha (TNF-\u03b1), IL-10, and IL-6 and the chemokine CXCL1 were upregulated in cocultured HT-29 cells at 4 h compared to levels in control cells. At 3 months postinfection, all H. saguini-monoassociated gnotobiotic C57BL/129 IL-10(-/-) mice were colonized and had seroconverted to H. saguini antigen with a significant Th1-associated increase in IgG2c (P < 0.0001). H. saguini induced a significant typhlocolitis, associated epithelial defects, mucosa-associated lymphoid tissue (MALT) hyperplasia, and dysplasia. Inflammatory cytokines IL-22, IL-17a, IL-1\u03b2, gamma interferon (IFN-\u03b3), and TNF-\u03b1, as well as inducible nitric oxide synthase (iNOS) were significantly upregulated in the cecal tissues of infected mice. The expression of the DNA damage response molecule \u03b3-H2AX was significantly higher in the ceca of H. saguini-infected gnotobiotic mice than in the controls. This model using a nonhuman primate Helicobacter sp. can be used to study the pathogenic potential of EHS isolated from primates with naturally occurring inflammatory bowel disease (IBD) and colon cancer.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27057685", + "title": "Prevalence of Upper Gastrointestinal Lesions at Primary Diagnosis in Adults with Inflammatory Bowel Disease.", + "year": 2016, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Horjus Talabur Horje CS", + "Meijer J", + "Rovers L", + "van Lochem EG", + "Groenen MJ", + "Wahab PJ" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5252399251697438, + "mesh_terms": [ + "Adolescent", + "Adult", + "Biopsy", + "Colitis, Ulcerative", + "Crohn Disease", + "Duodenal Diseases", + "Endoscopy, Gastrointestinal", + "Female", + "Gastritis", + "Granuloma", + "Humans", + "Male", + "Prospective Studies", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The prevalence of upper gastrointestinal (GI) involvement in adult inflammatory bowel disease has mostly been studied in patients with long-standing disease. The aim of this study was to prospectively evaluate the prevalence of upper GI involvement in a consecutive series of newly diagnosed, treatment-naive adult patients with inflammatory bowel disease, irrespective of upper GI tract symptoms. METHODS: Consecutive patients with suspected inflammatory bowel disease underwent combined ileocolonoscopy and upper endoscopy with biopsies. Patients diagnosed with either Crohn's disease (CD) or ulcerative colitis (UC), denying use of nonsteroidal anti-inflammatory drug, were included in the study. Helicobacter pylori infection was diagnosed histologically and positive patients were excluded from the analysis. Endoscopic and histologic lesions in the stomach and duodenum were recorded. Upper GI location (+L4) was defined as a combination of endoscopic and histological lesions. RESULTS: A total of 152 patients (108 CD and 44 UC) were analyzed. Endoscopic lesions were only seen in patients with CD (60 of 108, 55%). Histological lesions were present in both patients with CD and patients with UC: focally enhanced gastritis in 58 CD (54%) and 10 UC (23%), granulomas in 30 CD (28%). Upper GI disease location was diagnosed in 44 patients with CD (41%) and no patients with UC. Upper GI tract symptoms were reported in 14 of 44 patients (32%) with upper GI location. CONCLUSIONS: A high prevalence of upper GI involvement was observed in newly diagnosed patients with CD, with a majority of the patients being asymptomatic. Focally enhanced gastritis was common in both patients with CD and patients with UC, whereas granulomatous inflammation was restricted to patients with CD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38012477", + "title": "Integrated Metabolomics and Gut Microbiome Analysis Reveals the Efficacy of a Phytochemical Constituent in the Management of Ulcerative Colitis.", + "year": 2024, + "journal": "Molecular nutrition & food research", + "authors": [ + "Zhang K", + "Ji J", + "Li N", + "Yin Z", + "Fan G" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5184782244216902, + "mesh_terms": [ + "Rats", + "Animals", + "Mice", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Bacteria", + "Inflammation", + "Phytochemicals", + "Dextran Sulfate", + "Disease Models, Animal", + "Colitis", + "Colon", + "Mice, Inbred C57BL" + ], + "raw_abstract": "SCOPE: Cinnamaldehyde (CAH), a phytochemical constituent isolated from cinnamon, is gaining attention due to its nutritional and medicinal benefits. This study aimed to investigate the potential role of CAH in the treatment of ulcerative colitis (UC). METHODS AND RESULTS: Integrated metabolomics and gut microbiome analysis are performed for 2,4,6-trinitrobenzenesulfonic acid (TNBS) induced UC rats. The effect of CAH on colonic inflammation, lipid peroxidation, metabolic profiles, and gut microbiota is systematically explored. It finds that CAH improves the colitis-related symptoms, decreases disease activity index, increases the colon length and body weight, and alleviates histologic inflammation of UC rats. These therapeutic effects of CAH are due to suppression of inflammation and lipid peroxidation. Moreover, multi-omics analysis reveals that CAH treatment cause changes in plasma metabolome and gut microbiome in UC rats. CAH regulates lipid metabolic processes, especially phosphatidylcholines, lysophosphatidylcholines, and polyunsaturated fatty acids. Meanwhile, CAH modulates the gut microbial structure by restraining pathogenic bacteria (such as Helicobacter) and increasing probiotic bacteria (such as Bifidobacterium and Lactobacillus). CONCLUSIONS: These results indicate that CAH exerts a beneficial role in UC by synergistic modulating the balance in gut microbiota and the associated metabolites, and highlights the nutritional and medicinal value of CAH in UC management.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38428658", + "title": "Gegen Qinlian decoction ameliorates TNBS-induced ulcerative colitis by regulating Th2/Th1 and Tregs/Th17\u00a0cells balance, inhibiting NLRP3 inflammasome activation and reshaping gut microbiota.", + "year": 2024, + "journal": "Journal of ethnopharmacology", + "authors": [ + "Hu Y", + "Tang J", + "Xie Y", + "Xu W", + "Zhu W", + "Xia L", + "Fang J", + "Yu D", + "Liu J", + "Zheng Z", + "Zhou Q", + "Shou Q", + "Zhang W" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5154108139017193, + "mesh_terms": [ + "Humans", + "Mice", + "Animals", + "Colitis, Ulcerative", + "Drugs, Chinese Herbal", + "Inflammasomes", + "Interleukin-18", + "Gastrointestinal Microbiome", + "NLR Family, Pyrin Domain-Containing 3 Protein", + "Th17 Cells", + "Occludin", + "RNA, Ribosomal, 16S", + "Mice, Inbred CBA", + "Colitis", + "Cytokines", + "Trinitrobenzenes", + "Anti-Inflammatory Agents", + "Body Weight", + "Caspases", + "Disease Models, Animal", + "Colon" + ], + "raw_abstract": "ETHNOPHARMACOLOGICAL RELEVANCE: Chinese herbal medicine Gegen Qinlian Decoction (GQD) has been clinically shown to be an effective treatment of ulcerative colitis (UC) in China. However, the underlying mechanism of GQD's anti-ulcerative colitis properties and its effect on gut microbiota still deserve further exploration. AIM OF THE STUDY: This study observed the regulatory effects of GQD on Th2/Th1 and Tregs/Th17\u00a0cells balance, the NOD-like receptor family pyrin domain containing 3 (NLRP3) infammasome and gut microbiota in TNBS-induced UC in BALB/c mice. MATERIALS AND METHODS: 61 main chemical compounds in the GQD were determined by UPLC-Q-TOF/MS. The UC BALB/c model was established by intrarectal administration of trinitrobenzene sulfonic acid (TNBS), and GQD was orally administered at low and high dosages of 2.96 and 11.83\u00a0g/kg/day, respectively. The anti-inflammatory effects of GQD for ulcerative colitis were evaluated by survival rate, body weight, disease activity index (DAI) score, colonic weight and index, spleen index, hematoxylin-eosin (HE) staining and histopathological scores. Flow cytometry was used to detect the percentage of CD4, Th1, Th2, Th17 and Tregs cells. The levels of Th1-/Th2-/Th17-/Tregs-related inflammatory cytokines and additional proinflammatory cytokines (IL-1\u03b2, IL-18) were detected by CBA, ELISA, and RT-PCR. The expressions of GATA3, T-bet, NLRP3, Caspase-1, IL-I\u03b2, Occludin and Zonula occludens-1 (ZO-1) on colon tissues were detected by Western blot and RT-PCR. Transcriptome sequencing was performed using colon tissue and 16S rRNA gene sequencing was performed on intestinal contents. Fecal microbiota transplantation (FMT) was employed to assess the contribution of intestinal microbiota and its correlation with CD4 T cells and the NLRP3 inflammasome. RESULTS: GQD increased the survival rate of TNBS-induced UC in BALB/c mice, and significantly improved their body weight, DAI score, colonic weight and index, spleen index, and histological characteristics. The intestinal barrier dysfunction was repaired after GQD administration through promoting the expression of tight junction proteins (Occludin and ZO-1). GQD restored the balance of Th2/Th1 and Tregs/Th17\u00a0cells immune response of colitis mice, primarily inhibiting the increase in Th2/Th1 ratio and their transcription factor production (GATA3 and T-bet). Morever, GQD changed the secretion of Th1-/Th2-/Th17-/Tregs-related cytokines (IL-2, IL-12, IL-5, IL-13, IL-6, IL-10, and IL-17A) and reduced the expressions of IL-1\u03b2, IL-18. Transcriptome results suggested that GQD could also remodel the immune inflammatory response of colitis by inhibiting NOD-like receptor signaling pathway, and Western blot, immunohistochemistry and RT-PCR further revealed that GQD exerted anti-inflammatory effects by inhibiting the NLRP3 inflammasome, such as down-regulating the expression of NLRP3, Caspase-1 and IL-1\u03b2. More interestingly, GQD regulated gut microbiota dysbiosis, suppressed the overgrowth of conditional pathogenic gut bacteria like Helicobacter, Proteobacteria, and Mucispirillum, while the probiotic gut microbiota, such as Lactobacillus, Muribaculaceae, Ruminiclostridium_6, Akkermansia, and Ruminococcaceae_unclassified were increased. We further confirmed that GQD-treated gut microbiota was sufficient to relieve TNBS-induced colitis by FMT, involving the modulation of Th2/Th1 and Tregs/Th17 balance, inhibition of NLRP3 inflammasome activation, and enhancement of colonic barrier function. CONCLUSIONS: GQD might alleviate TNBS-induced UC via regulating Th2/Th1 and Tregs/Th17 cells Balance, inhibiting NLRP3 inflammasome and reshaping gut microbiota, which may provide a novel strategy for patients with colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27438510", + "title": "Modulation of PD-L1 and CD8 Activity in Idiopathic and Infectious Chronic Inflammatory Conditions.", + "year": 2017, + "journal": "Applied immunohistochemistry & molecular morphology : AIMM", + "authors": [ + "Mezache L", + "Magro C", + "Hofmeister C", + "Pichiorri F", + "Sborov D", + "Nuovo GJ" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.514895260980597, + "mesh_terms": [ + "Animals", + "B7-H1 Antigen", + "CD8-Positive T-Lymphocytes", + "Cell Line, Tumor", + "Chronic Disease", + "Female", + "Humans", + "Infections", + "Inflammation", + "Male", + "Mice", + "Mice, Inbred C57BL", + "T-Lymphocytes, Regulatory" + ], + "raw_abstract": "Programmed death-ligand 1 (PD-L1) can reduce the immune response by inhibiting CD8 T-cell proliferation and cytotoxic activity. We studied a series of human viral (molloscum, human papillomavirus, herpes simplex, cytomegalovirus, Epstein-Barr virus, smallpox) and bacterial infections (Helicobacter pylori) for the in situ expression of PD-L1, mononuclear cell infiltration, and CD8 activity and compared this to noninfectious idiopathic inflammatory conditions to better define which immune responses may be more highly correlated with an infectious agent. Each viral and bacterial infection showed an increased PD-L1 expression that was most prominent in the mononuclear cell/CD8+ infiltrate surrounding the infection. However, the CD8 cells were mostly quiescent as evidenced by the low Ki67 index and minimal granzyme expression. Using a melanoma mouse model, acute reovirus infection increased PD-L1 expression, but decreased CD8 cytotoxic activity and Treg (FOXP3) cell numbers. In comparison, idiopathic noninfectious chronic inflammatory processes including lichen sclerosis, eczema, Sjogren's disease, and ulcerative colitis showed a comparable strong PD-L1 expression in the mononuclear cell infiltrates but much greater Treg infiltration. However, this strong immunosuppressor profile was ineffective as evidenced by strong CD8 proliferation and granzyme expression. These data suggest that viral and bacterial infections induce a PD-L1 response that, unlike noninfectious chronic inflammatory conditions, dampens the activity of the recruited CD8 cells which, in turn, may enhance the ability of anti-PD-L1 therapy to eliminate the infectious agent.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37612374", + "title": "Association between dietary acid load and the odds of ulcerative colitis: a case-control study.", + "year": 2023, + "journal": "Scientific reports", + "authors": [ + "Movahedian M", + "Emamat H", + "Tangestani H", + "Rashvand S", + "Ghalandari H", + "Somi MH", + "Hekmatdoost A" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5034819535276216, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Case-Control Studies", + "Helicobacter Infections", + "Helicobacter pylori", + "Diet" + ], + "raw_abstract": "Ulcerative colitis (UC) is one of the two types of inflammatory bowel disease (IBDs), which have a pivotal role in weakening the quality of lives of suffering patients. According to some recent studies, significant changes in dietary patterns may have contributed to the increased prevalence of UC. Potential renal acid load (PRAL) is an index used to estimate dietary acid load of the diet. The aim of the current study is to investigate the association between PRAL and odds of UC. The current case-control study included 62 newly diagnosed cases of UC and 124 healthy controls. Dietary habits of participants in the last year were collected with a valid food frequency questionnaire (FFQ). Thereafter, PRAL score was calculated based on a formula containing the dietary intake of protein, phosphorus, potassium, calcium, and magnesium. Participants were categorized according to quartiles of PRAL. Multivariable logistic regression models were used to estimate the odds' ratio (OR) with 95% confidence intervals (CIs) of UC across quartiles of PRAL. The results of the current study indicated that in the crude model, participants in the fourth quartile of PRAL had 2.51 time higher odds of UC compared with those in the first quartile of the PRAL [(OR 2.51; 95% CI 1.03-6.14), (P\u2009=\u20090.043)]. After adjustment for age and biological gender, this positive association remained significant [(OR 2.99; 95% CI 1.16-7.72), (P\u2009=\u20090.023)]. In the final model, after further adjustment for BMI, current smoking, education, Helicobacter pylori infection, and dietary intakes of total energy, omega-3 fatty acids, trans-fatty acids, and total dietary fiber, the odds of UC in the highest quartile of PRAL was significantly higher compared to the lowest quartile [(OR 3.08; 95% CI 1.01-9.39), (P\u2009=\u20090.048)]. So, we observed that higher dietary acid load assessed by PRAL score is associated with greater odds of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30580094", + "title": "Effects of Anti-Helicobacter pylori Therapy on Incidence of Autoimmune Diseases, Including Inflammatory Bowel Diseases.", + "year": 2019, + "journal": "Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association", + "authors": [ + "Lin KD", + "Chiu GF", + "Waljee AK", + "Owyang SY", + "El-Zaatari M", + "Bishu S", + "Grasberger H", + "Zhang M", + "Wu DC", + "Kao JY" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.4749434910824371, + "mesh_terms": [ + "Adult", + "Aged", + "Anti-Bacterial Agents", + "Arthritis, Rheumatoid", + "Autoimmune Diseases", + "Case-Control Studies", + "Cephalosporins", + "Colitis, Ulcerative", + "Crohn Disease", + "Dermatomyositis", + "Female", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Incidence", + "Inflammatory Bowel Diseases", + "Lupus Erythematosus, Systemic", + "Male", + "Middle Aged", + "Mortality", + "Pemphigus", + "Peptic Ulcer", + "Polymyositis", + "Proportional Hazards Models", + "Scleroderma, Systemic", + "Sjogren's Syndrome", + "Taiwan", + "Urinary Tract Infections", + "Vasculitis" + ], + "raw_abstract": "BACKGROUND & AIMS: Helicobacter pylori induces immune tolerance and is associated with a lower risk for immune-mediated disorders, such as autoimmune and inflammatory bowel diseases (IBD). We aimed to determine the effects of treatment for H pylori infection on the incidence of autoimmune disease and IBD. METHODS: We collected data from the National Health Insurance Research Database in Taiwan on patients younger than 18 years old without a prior diagnosis of autoimmune disease or IBD. Patients with peptic ulcer disease (PUD) with treatment of H pylori infection (PUD+HPRx), PUD without H pylori treatment (PUD-HPRx), a urinary tract infection (UTI) treated with cephalosporin, or without PUD (controls) were matched for age, sex, insurance, and Charlson's comorbidity index score. RESULTS: Of the 1 million patients we collected data from in 2005, we included 79,181 patients in the study. We compared the effects of treatment for H pylori infection on the risk of autoimmunity or IBD and found that PUD+HPRx has the highest adjusted hazard risk (aHR) for autoimmunity or IBD (aHR, 2.36), compared to PUD-HPRx (aHR, 1.91) or UTI (aHRs, 1.71) (P < .001). The increased risk of autoimmune disease was not completely accounted for by antibiotic therapy alone, because PUD+HPRx had a higher aHR than UTI (P < .001). A small but significant increase in mortality was observed in the PUD+HPRx cohort (aHR, 1.11; P = .001). CONCLUSION: In an analysis of data from the National Health Insurance Research Database in Taiwan, we found that treatment for H pylori infection is associated with a significant increase in the risk for autoimmune disease, including IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37682136", + "title": "The association between Helicobacter pylori infection and inflammatory bowel disease in children: A systematic review with meta-analysis.", + "year": 2023, + "journal": "Medicine", + "authors": [ + "Kong G", + "Liu Z", + "Lu Y", + "Li M", + "Guo H" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.4698957751971568, + "mesh_terms": [ + "Adult", + "Child", + "Humans", + "Helicobacter pylori", + "Helicobacter Infections", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Colitis, Ulcerative" + ], + "raw_abstract": "BACKGROUND: Available literature has reported the association of Helicobacter pylori (H pylori) infection with inflammatory bowel disease (IBD) in adults. However, only a few studies have addressed the disease in children. AIM: To ascertain the correlation of H pylori infection with IBD among children. METHODS: The aim of this systematic review and meta-analysis is to assess the association between H pylori infection and IBD in children. We searched databases including Cochrane, EMBASE, Google Scholar, PubMed, Medline, and Web of Science to select relevant studies. Ultimately, based on predetermined inclusion criteria, we included 6 studies that met the requirements. Review Manager and Stata software were used to extract and analyze the data from the relevant studies. In the methods, we employed both qualitative and quantitative approaches for comprehensive analysis. Qualitative analysis involved describing study designs, sample characteristics, and results, while quantitative analysis involved statistical tests such as calculating pooled risk ratios and 95% confidence intervals to evaluate the association between H pylori infection and IBD in children. Lastly, by combining the results of the individual studies, our objective is to provide a comprehensive understanding of the relationship between H pylori infection and IBD in children. RESULTS: In totality, we involved 2236 participants that were recruited in 6 studies. We detected no significant difference in H pylori prevalence (9.8% vs 12.7%, P = .12) by comparing the children IBD group to controls. Among the IBD children, we estimated odds ratio (OR) of H pylori infection to 0.62 [(95% confidence interval (CI) of 0.34-1.12)]. In children suffering from ulcerative colitis (UC) and Crohn disease (CD), the H pylori infection rates were higher than in those with IBD-unclassified (IBDU).When analyzed stratified by disease of study design, In CD group [OR = 1.42, 95% CI: 0.72-2.80)] (I2 = 0%, P = .64). but no significant difference in CD group. CONCLUSIONS: No correlation was found between H pylori infection and the occurrence of IBD in children.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28000477", + "title": "Probiotic: effectiveness nutrition in cancer treatment and prevention.", + "year": 2016, + "journal": "Nutricion hospitalaria", + "authors": [ + "Kich DM", + "Vincenzi A", + "Majolo F", + "Volken de Souza CF", + "Goettert MI" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.4648884517457694, + "mesh_terms": [ + "Animals", + "Humans", + "Neoplasms", + "Probiotics" + ], + "raw_abstract": "Among the neoplasias, colorectal cancer is one of the leading causes of cancer death in men and women. The increasing incidence of this type\u00a0of cancer is due to the increase in the population's life expectancy, by the increase in chronic inflammatory bowel diseases, primarily ulcerative\u00a0colitis and Crohn's disease, and the change in eating habits. The American Cancer Society (2011) shows that diet might be responsible for\u00a0approximately 30% of cancer cases in developed countries, moreover when considering only colorectal cancer, the number can reach 30% to\u00a050%. Probiotics are effective in the prevention and treatment of many bowel diseases as inflammatory bowel disease (IBD), diarrhea, irritable\u00a0bowel syndrome, gluten intolerance, gastroenteritis, Helicobacter pyloriinfection, and colon cancer. Classical examples are strains from the\u00a0Lactobacillus, and Bifidobacteriumgenus that have probiotic proprieties with a potential use in the prophylaxis, as well as in the treatment of a\u00a0variety of gastrointestinal tract disorders. Researchers are focusing on extremely important studies regarding the possibility of using probiotics to\u00a0promote a balanced microbiota composition, and a sufficient immunological surveillance system as a way to prevent cancer. Considering the fact\u00a0that the human intestines host 100 trillion bacteria, including more than 1,000 species, there is still need to perform more in depth investigations\u00a0in order to find probiotics with potential to prevent, and treat cancerous diseases, adding a very promising effect to this already successful panorama. This revision aims to conduct a review of the most recent studies correlating probiotics and its cancer preventing and treatment potential.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "25799959", + "title": "The use of probiotics in pediatric gastroenterology: a review of the literature and recommendations by Latin-American experts.", + "year": 2015, + "journal": "Paediatric drugs", + "authors": [ + "Cruchet S", + "Furnes R", + "Maruy A", + "Hebel E", + "Palacios J", + "Medina F", + "Ramirez N", + "Orsi M", + "Rondon L", + "Sdepanian V", + "X\u00f3chihua L", + "Ybarra M", + "Zablah RA" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.4436360883935258, + "mesh_terms": [ + "Child", + "Diarrhea", + "Evidence-Based Medicine", + "Gastroenterology", + "Humans", + "Latin America", + "Probiotics" + ], + "raw_abstract": "OBJECTIVE: The stability and composition of intestinal flora plays a vital role in human wellbeing throughout life from as early as birth. Over the past 50 years, several studies have been conducted to evaluate the effect of probiotic administration in pediatric gastroenterology. This document aims to provide a recommendation score on probiotic utilization in pediatric gastroenterology, together with a review of current knowledge concerning its benefits, tolerability, and safety. STUDY DESIGN: Published literature was selected without study design restriction: clinical guidelines, meta-analyses, randomized controlled trials (RCTs), cohort studies, outcomes research and case-controlled studies were selected using the following MESH-validated terms: probiotics, diarrhea, acute diarrhea, antibiotic-associated diarrhea, traveler's diarrhea, bacterial diarrhea, nosocomial diarrhea, prophylactic diarrhea, Helicobacter pylori infection, colic, infantile colic, necrotizing enterocolitis (NEC), inflammatory bowel disease, constipation, and allergy. Once the validity and the quality of results were evaluated, a recommendation score and level of evidence were assigned for pediatric gastrointestinal-related conditions, according to the updated Evidence-Based Medicine guidelines: 1a for systematic review (SR) of RCTs, 1b for individual RCT, 1c for SR and individual RCT, 2a for SR of cohort studies, 2b for individual cohort studies, 2c for outcomes research, and 3a for SR of case-control studies. RESULTS AND CONCLUSIONS: The Latin American Expert group consensus recommends the use of the following probiotics for pediatric gastrointestinal conditions: prevention of acute infectious diarrhea (AID): 1b for Bifidobacterium lactis, Lactobacillus rhamnosus GG (LGG), and L. reuteri; prevention of nosocomial diarrhea: 1 b for B. lactis Bb12, B. bifidum, LGG and Streptococcus thermophiles; treatment of AID: 1a for LGG and S. boulardii, 1b for L. reuteri; prevention of antibiotic-associated diarrhea: 1b for LGG and S. boulardii; prevention of traveler's diarrhea: 1b for S. boulardii; prevention of infantile colic: 1a for L. reuteri DSM 17938; treatment of infantile colic: 1b for L. reuteri DSM 17938; prevention of NEC: 1a for B. breve, mixtures of Bifidobacterium and Streptococcus, LGG, L. acidophilus and L. reuteri DSM 17938; induction and maintenance of remission in ulcerative colitis: 1b for VSL#3; improving symptoms of irritable bowel syndrome: 2c for LGG and VSL#3.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "25914487", + "title": "Helicobacter pylori infection and inflammatory bowel disease in Asians: a meta-analysis.", + "year": 2015, + "journal": "World journal of gastroenterology", + "authors": [ + "Wu XW", + "Ji HZ", + "Yang MF", + "Wu L", + "Wang FY" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.44183967601003343, + "mesh_terms": [ + "Asia", + "Asian People", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Inflammatory Bowel Diseases", + "Protective Factors", + "Risk Factors" + ], + "raw_abstract": "AIM: To investigate the relationship between Helicobacter pylori infection and inflammatory bowel disease (IBD) in an Asian population. METHODS: The PubMed, EMBASE, and Cochrane Library databases were searched for observational studies published up until June 2014, without language restrictions. Additional references were obtained from reviewed articles. RESULTS: Ten studies involving 1299 IBD patients and 1817 controls were included in the meta-analysis (24.9% of IBD patients had H. pylori infection vs 48.3% of the controls). The pooled risk ratio for H. pylori infection in IBD patients compared with controls was 0.48 (95%CI: 0.43-0.54; P < 0.001). There was no significant heterogeneity in the included studies (I (2) = 21%). Egger's linear regression indicated that there was no significant publication bias (P = 0.203). CONCLUSION: The H. pylori infection rate in Asian IBD patients is significantly lower than in non-IBD patients, indicating that infection protects against the development of IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27501017", + "title": "Rosacea and gastrointestinal disorders: a population-based cohort study.", + "year": 2017, + "journal": "The British journal of dermatology", + "authors": [ + "Egeberg A", + "Weinstock LB", + "Thyssen EP", + "Gislason GH", + "Thyssen JP" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.43156846176592073, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Cohort Studies", + "Denmark", + "Female", + "Helicobacter Infections", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "Prevalence", + "Prognosis", + "Rosacea", + "Socioeconomic Factors", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Rosacea is a common inflammatory facial skin condition. Recent genetic and epidemiological studies have suggested pathogenic links between rosacea and gastrointestinal disorders, but data are limited. OBJECTIVES: The objective was to investigate the association between rosacea and coeliac disease (CeD), Crohn disease (CD), ulcerative colitis (UC), Helicobacter pylori infection (HPI), small intestinal bacterial overgrowth (SIBO) and irritable bowel syndrome (IBS), respectively. METHODS: We performed a nationwide cohort study. A total of 49 475 patients with rosacea and 4 312 213 general population controls were identified using nationwide administrative registers. We established the prevalence of the aforementioned disorders, and used Cox regression analysis to obtain hazard ratios (HRs) of the risk of new-onset CeD, CD, UC, HPI, SIBO and IBS, respectively, in patients with rosacea. RESULTS: The prevalence of CeD, CD, UC, HPI, SIBO and IBS, respectively, was higher among patients with rosacea when compared with the control subjects. Adjusted HRs revealed significant associations between rosacea and CeD (HR 1\u00b746, 1\u00b711-1\u00b793), CD (HR 1\u00b745, 1\u00b719-1\u00b777), UC (HR 1\u00b719, 1\u00b702-1\u00b739), and IBS (HR 1\u00b734, 1\u00b719-1\u00b750), respectively, but not HPI (HR 1\u00b704, 0\u00b796-1\u00b713) or SIBO (HR 0\u00b771, 0\u00b718-1\u00b786). CONCLUSIONS: Rosacea is associated with certain gastrointestinal diseases, but the possible pathogenic link is unknown. Gastrointestinal complaints in patients with rosacea should warrant clinical suspicion of disease.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34291601", + "title": "Migraine and gastrointestinal disorders in middle and old age: A UK Biobank study.", + "year": 2021, + "journal": "Brain and behavior", + "authors": [ + "Welander NZ", + "Olivo G", + "Pisanu C", + "Rukh G", + "Schi\u00f6th HB", + "Mwinyi J" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.368492009519305, + "mesh_terms": [ + "Biological Specimen Banks", + "Celiac Disease", + "Cross-Sectional Studies", + "Humans", + "Migraine Disorders", + "United Kingdom" + ], + "raw_abstract": "INTRODUCTION: Migraine is a prevalent condition causing a substantial level of disability worldwide. Despite this, the pathophysiological mechanisms are not fully understood. Migraine often co-occurs with gastrointestinal disorders, but the direction of a potential causal link is unclear. The aim of this project was to investigate the associations between migraine and several gastrointestinal disorders in the same cohort in order to determine the relative strengths of these associations. METHODS: This cross-sectional study examined whether migraine is associated with irritable bowel syndrome (IBS), peptic ulcers, Helicobacter pylori (HP) infections, celiac disease, Crohn's disease and ulcerative colitis. Baseline data covering 489,753 UK Biobank participants (migraine group: n = 14,180) were analyzed using Pearson's chi-square tests and adjusted binary logistic regression models. RESULTS: Migraine was significantly associated with IBS (odds ratio [OR] 2.24, 95% confidence interval [CI] 2.08-2.40, p <.001) and peptic ulcers (OR 1.55, 95% CI 1.35-1.77, p <.001). Migraine was not associated with HP infection (OR 1.34, 95% CI 1.04-1.73, p = .024), celiac disease (OR 1.29, 95% CI 1.04-1.60, p = .023), Crohn's disease (OR 1.08, 95% CI 0.80-1.45, p = .617) or ulcerative colitis (OR 1.00, 95% CI 0.79-1.27, p = .979) after adjusting for multiple testing. CONCLUSIONS: Migraine was associated with IBS and peptic ulcers in this large population-based cohort. The associations with HP infection, celiac disease, Crohn's disease, and ulcerative colitis did not reach significance, suggesting a weaker link between migraine and autoimmune gastrointestinal conditions or HP infection.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32918343", + "title": "Review: Extragastric diseases and Helicobacter pylori.", + "year": 2020, + "journal": "Helicobacter", + "authors": [ + "Pellicano R", + "Ianiro G", + "Fagoonee S", + "Settanni CR", + "Gasbarrini A" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.353005396220811, + "mesh_terms": [ + "Animals", + "Cardiovascular Diseases", + "Comorbidity", + "Digestive System Diseases", + "Helicobacter Infections", + "Humans", + "Immune System Diseases", + "Metabolic Diseases", + "Nervous System Diseases", + "Prevalence" + ], + "raw_abstract": "The involvement of Helicobacter pylori infection in many extra-gastroduodenal manifestations remains a fascinating field of investigation. However, for several of these supposed associations, the potential pathogenic mechanism remains unclear. The present review highlights the main associations of H\u00a0pylori with extra-gastroduodenal manifestations reported during the last year. We searched for the most relevant studies on this topic, published between April 2019 and March 2020, identified using the term \"Helicobacter\" in the MEDLINE/Pubmed database. Consistent data emerged from studies investigating metabolic syndrome and ischaemic cardiovascular diseases. Other reported fields of investigation were hepatology, especially focused on non-alcoholic steatohepatitis, neurology, including Parkinson's disease and Alzheimer's disease, as well as dermatology. Inflammatory bowel disease (IBD), that comprises Crohn's disease and ulcerative colitis, may originate from a dysregulation of the host's immune response to commensal bacteria in individuals with genetic predisposition. The reduction of biodiversity and other specific imbalances in the faecal microbiome composition of IBD patients compared to that of healthy controls support this hypothesis. In this context, an inverse correlation between H\u00a0pylori infection and IBD prevalence has been confirmed. Similar results were found in patients with kidney diseases and allergic manifestations. There are indications of the possible involvement of H\u00a0pylori infection in metabolic syndrome and ischaemic cardiovascular diseases. However, due to a series of factors linked to study designs and the multifactorial pathogenesis of some diseases, further studies are needed.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28104319", + "title": "The Mexican consensus on probiotics in gastroenterology.", + "year": 2017, + "journal": "Revista de gastroenterologia de Mexico", + "authors": [ + "Valdovinos MA", + "Montijo E", + "Abreu AT", + "Heller S", + "Gonz\u00e1lez-Garay A", + "Bacarreza D", + "Bielsa-Fern\u00e1ndez M", + "Boj\u00f3rquez-Ramos MC", + "Bosques-Padilla F", + "Burguete-Garc\u00eda AI", + "Carmona-S\u00e1nchez R", + "Consuelo-S\u00e1nchez A", + "Coss-Adame E", + "Ch\u00e1vez-Barrera JA", + "de Ari\u00f1o M", + "Flores-Calder\u00f3n J", + "G\u00f3mez-Escudero O", + "Gonz\u00e1lez-Huezo MS", + "Icaza-Ch\u00e1vez ME", + "Larrosa-Haro A", + "Morales-Ar\u00e1mbula M", + "Murata C", + "Ram\u00edrez-Mayans JA", + "Remes-Troche JM", + "Rizo-Robles T", + "Pel\u00e1ez-Luna M", + "Toro-Monjaraz EM", + "Torre A", + "Urquidi-Rivera ME", + "V\u00e1zquez R", + "Yamamoto-Furusho JK", + "Guarner F" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.3372061926729069, + "mesh_terms": [ + "Adult", + "Child", + "Consensus", + "Delphi Technique", + "Gastroenterology", + "Guidelines as Topic", + "Humans", + "Mexico", + "Probiotics" + ], + "raw_abstract": "INTRODUCTION: Probiotics are frequently prescribed in clinical practice. Their efficacy in treating gastrointestinal disorders is supported by a significant number of clinical trials. However, the correct prescription of these agents is hampered due to a lack of knowledge of the scientific evidence and to the different presentations and microbial compositions of the probiotics that are currently available. AIM: To provide the clinician with a consensus review of probiotics and recommendations for their use in gastroenterology. MATERIALS AND METHODS: Controlled clinical trials, meta-analyses, and systematic reviews published up to 2015 were selected, using the MESH terms: probiotics, gastrointestinal diseases, humans, adults, AND children. The Delphi method was employed. Eighteen gastroenterologists treating adult patients and 14 pediatric gastroenterologists formulated statements that were voted on until agreement>70% was reached. The level of evidence based on the GRADE system was evaluated for each statement. RESULTS AND CONCLUSIONS: Eleven statements on the general concepts of probiotics and 27 statements on the use of probiotics in gastrointestinal diseases in both adults and children were formulated. The consensus group recommends the use of probiotics under the following clinical conditions: the prevention of diarrhea associated with antibiotics, the treatment of acute infectious diarrhea, the prevention of Clostridium difficile infection and necrotizing enterocolitis, the reduction of adverse events from Helicobacter pylori eradication therapy, relief from irritable bowel syndrome symptoms, the treatment of functional constipation in the adult, and the induction and maintenance of remission in patients with ulcerative colitis and pouchitis, and the treatment of covert and overt hepatic encephalopathy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26443321", + "title": "Scientific evidence for health effects attributed to the consumption of probiotics and prebiotics: an update for current perspectives and future challenges.", + "year": 2015, + "journal": "The British journal of nutrition", + "authors": [ + "Martinez RC", + "Bedani R", + "Saad SM" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.33634792117654405, + "mesh_terms": [ + "Europe", + "Food Safety", + "Humans", + "Immune System", + "Microbiota", + "Prebiotics", + "Preventive Medicine", + "Probiotics" + ], + "raw_abstract": "Probiotics and prebiotics, mainly commercialised as food ingredients and also as supplements, are considered highly profitable niche markets. However, in recent years, the food industry has suffered from a series of health claim restrictions on probiotics and prebiotics in many parts of the world, including those made by the European Food Safety Authority. Therefore, we reviewed the core benefits of probiotic and prebiotic consumption on health. A number of studies have examined the prevention and/or management of intestinal infections, respiratory tract infections, CVD, osteoporosis, urogenital infections, cavities, periodontal disease and halitosis, allergic reactions, inflammatory bowel disease and irritable bowel syndrome and Helicobacter pylori gastric infections. In fact, a deeper understanding of the mechanisms involved in human microbiota and immune system modulation by probiotics and prebiotics relies on continuous efforts to establish suitable biomarkers of health and diseases risk factors for the design of clinical trials required for health claim approval. In spite of the promising results, the performance of large, long-term, well-planned, well-aligned clinical studies is crucial to provide more reliability and a more solid basis for the outcomes achieved and to support the potential use of probiotics and prebiotics in clinical practice.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29915396", + "title": "Probiotics in Gastroenterology: How Pro Is the Evidence in Adults?", + "year": 2018, + "journal": "The American journal of gastroenterology", + "authors": [ + "Koretz RL" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.3339767024547596, + "mesh_terms": [ + "Adult", + "Gastroenterology", + "Gastrointestinal Diseases", + "Humans", + "Practice Guidelines as Topic", + "Probiotics", + "Randomized Controlled Trials as Topic" + ], + "raw_abstract": "Probiotic usage has become popular with both medical practitioners and the community in general; patients commonly seek advice regarding what, if any, such preparation would be useful for their own diseases. Since such advice should be evidence-based, identified randomized clinical trials (RCTs) for a number of gastrointestinal conditions were reviewed; the data were organized by individual probiotic genera/species. Only trials in adults were considered. Most of the identified RCTs were small and low-quality, so any conclusions to be drawn will be limited at least by methodologic problems. Using the GRADE system to consider the reliability of the evidence generated from these RCTs, it did appear that the use of fecal microbial transplantation to treat recurrent Clostridium difficile infection is well justified. Given the methodologic issues, there was moderately good evidence for preventing antibiotic-associated diarrhea with Lactobacillus, Bifidobacterium, Streptococcus, or Saccharomyces boulardii and for using Lactobacillus, Bifidobacterium, or Saccharomyces as adjunct therapy in the treatment of Helicobacter pylori. There were other conditions for which some supportive evidence was available. These conditions include VSL#3 for maintaining remissions in patients with pouchitis or treating active ulcerative colitis (UC), fecal microbial transplantation for treating active UC, Bifidobacterium for treating patients with UC in remission, Lactobacillus in patients with painful diverticulosis, a variety of probiotics (Lactobacillus, Bifidobacterium, Streptococcus, or VSL#3) in patients with minimal hepatic encephalopathy, and providing synbiotics to patients postoperatively after liver transplantation. Unfortunately, other limitations in the evidence made it very likely that future research will have an effect on the estimated benefit; these interventions cannot yet be recommended for routine use.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26674958", + "title": "Diagnosis of Helicobacter Pylori Infection is Associated with Lower Prevalence and Subsequent Incidence of Crohn's Disease.", + "year": 2016, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Bartels LE", + "Jepsen P", + "Christensen LA", + "Gerdes LU", + "Vilstrup H", + "Dahlerup JF" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.3235485667001347, + "mesh_terms": [ + "Adult", + "Celiac Disease", + "Colitis, Ulcerative", + "Crohn Disease", + "Cross-Sectional Studies", + "Denmark", + "Female", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Incidence", + "Male", + "Middle Aged", + "Prevalence", + "Risk Factors" + ], + "raw_abstract": "BACKGROUND AND AIMS: Helicobacter pylori infection may protect against some chronic inflammatory diseases. This study examined H. pylori infection and its association with the prevalence of the gastrointestinal diseases Crohn's disease [CD], ulcerative colitis [UC], and coeliac disease [CeD]. Incident cases in a follow-up period after H. pylori testing were recorded to investigate if protective effects of H. pylori persisted after probable eradication. METHODS: This was a historical cohort study performed in the Central Denmark Region. Patients were enrolled consecutively from primary health care centres after a urea breath test [UBT] for H. pylori and were then followed for a median of 6 years. The patient's diseases, country of birth, and gender were acquired from nationwide administrative registries. We used logistic regression to compare the prevalences of CD, UC, and CeD and Cox regression to compare the incidences of CD, UC, and CeD between H. pylori-positive and H. pylori-negative patients, adjusting for confounding variables. RESULTS: We found a lower prevalence of CD in H. pylori-positive than in H. pylori-negative patients (odds ratio = 0.36 [0.17-0.75]). There were fewer incident cases of CD in H. pylori-positive than H. pylori-negative patients in the follow-up period (hazard ratio = 0.59 [0.36-0.96]). Similar trends were found for CeD but not for UC. CONCLUSIONS: H. pylori infection may be a protective factor against the development of CD. However, the incidence of CD is still reduced after UBT and probable H. pylori eradication; thus, H. pylori status may be a marker for other factors that protect against CD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36806052", + "title": "Pseudolymphoma to Lymphoma: A Case of Chronic Reactive Lymphoid Hyperplasia Transforming to Primary Cutaneous Marginal Zone Lymphoma.", + "year": 2023, + "journal": "The American Journal of dermatopathology", + "authors": [ + "Singh N", + "Fagan KK", + "Patel RT", + "Grider DJ" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.31648320290730664, + "mesh_terms": [ + "Humans", + "Middle Aged", + "Pseudolymphoma", + "Skin Neoplasms", + "Hyperplasia", + "Lymphoma", + "Lymphoma, B-Cell", + "Lymphoma, B-Cell, Marginal Zone" + ], + "raw_abstract": "Primary cutaneous marginal zone lymphoma (PCMZL) is a low-grade malignant B-cell lymphoma that originates from the skin. It often presents as erythematous solitary or multiple papules, nodules, and/or plaques. It is one of the 3 main subtypes of primary cutaneous B-cell lymphomas. PCMZLs are believed to develop from chronic antigenic stimulation such as from tick-borne bacteria, vaccines, tattoo pigment, or other foreign body. In addition, cutaneous lymphoid hyperplasia, a documented precursor to malignant PCMZL, often presents in response to areas of chronic inflammation. Cutaneous lymphoid hyperplasia and PCMZL share several clinical and histological similarities that require clinicopathologic suspicion, immunohistochemical ancillary studies, and histopathologic analysis to accurately differentiate the 2 entities. Although gene rearrangement studies have historically been of limited value in the diagnosis of PCMZL, recent studies investigating molecular markers have identified the presence of multiple genetic abnormalities that have helped to better characterize the disease and aid in diagnosis. In addition, newer studies have found associations between PCMZL and gastrointestinal disorders, including Helicobacter pylori and inflammatory bowel disorders. In this article, we describe a case of a 56-year-old patient with a history of ulcerative colitis presenting with chronic reactive lymphoid hyperplasia that transformed to primary cutaneous marginal zone lymphoma.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31953721", + "title": "Prevalence of gastrointestinal disorders having an impact on tablet levothyroxine absorption: should this formulation still be considered as the first-line therapy?", + "year": 2020, + "journal": "Endocrine", + "authors": [ + "Castellana M", + "Castellana C", + "Giovanella L", + "Trimboli P" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.2773530721271757, + "mesh_terms": [ + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Prevalence", + "Systematic Reviews as Topic", + "Tablets", + "Thyroxine" + ], + "raw_abstract": "PURPOSE: In patients with hypothyroidism, levothyroxine (LT4) is the treatment of choice, and tablets are the most commonly prescribed formulation. Despite multiple scenarios being reported in the literature with impaired tablet absorption and likely missed TSH targets, it is yet unclear what the implications are for clinical practice and the role of liquid solution (LS) and soft gel (SG) formulations. We have thus conducted a narrative review evaluating the prevalence within the general population of gastrointestinal disorders impacting tablet LT4 absorption. METHODS: PubMed and Google Scholar were searched until December 2019 for systematic reviews and meta-analyses on the topic. If they could not be retrieved, other types of manuscripts were searched. RESULTS: Lactose malabsorption and Helicobacter pylori infection represented the most common disorders, with a global prevalence of 68% and 48%, respectively. The prevalence of other conditions, including autoimmune gastritis, bariatric surgery, celiac disease, gastroparesis, giardiasis, liver cirrhosis, or ulcerative colitis, was lower than 20%. Data at regional and country levels were found to be heterogeneous, but at least one in five patients was diagnosed with one disorder. CONCLUSIONS: The worldwide prevalence of gastrointestinal disorders associated with tablet LT4 malabsorption, including lactose malabsorption and Helicobacter pylori infection, is high. Interactions with drugs or food can further increase this risk. Considering that all studies investigating the impact of switching patients from tablet to LS or SG found an improved thyroid balance, the latter formulations should be considered as first-line therapy for managing hypothyroidism.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34671932", + "title": "Factors influencing the levothyroxine dose in the hormone replacement therapy of primary hypothyroidism in adults.", + "year": 2022, + "journal": "Reviews in endocrine & metabolic disorders", + "authors": [ + "Caron P", + "Grunenwald S", + "Persani L", + "Borson-Chazot F", + "Leroy R", + "Duntas L" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.2690124125165972, + "mesh_terms": [ + "Adult", + "Helicobacter Infections", + "Helicobacter pylori", + "Hormone Replacement Therapy", + "Humans", + "Hypothyroidism", + "Thyrotropin", + "Thyroxine" + ], + "raw_abstract": "Levothyroxine (LT4) is a safe, effective means of hormone replacement therapy for hypothyroidism. Here, we review the pharmaceutical, pathophysiological and behavioural factors influencing the absorption, distribution, metabolism and excretion of LT4. Any factor that alters the state of the epithelium in the stomach or small intestine will reduce and/or slow absorption of LT4; these include ulcerative colitis, coeliac disease, bariatric surgery, Helicobacter pylori infection, food intolerance, gastritis, mineral supplements, dietary fibre, resins, and various drugs. Once in the circulation, LT4 is almost fully bound to plasma proteins. Although free T4 (FT4) and liothyronine concentrations are extensively buffered, it is possible that drug- or disorder-induced changes in plasma proteins levels can modify free hormone levels. The data on the clinical significance of genetic variants in deiodinase genes are contradictory, and wide-scale genotyping of hypothyroid patients is not currently justified. We developed a decision tree for the physician faced with an abnormally high thyroid-stimulating hormone (TSH) level in a patient reporting adequate compliance with the recommended LT4 dose. The physician should review medications, the medical history and the serum FT4 level and check for acute adrenal insufficiency, heterophilic anti-TSH antibodies, antibodies against gastric and intestinal components (gastric parietal cells, endomysium, and tissue transglutaminase 2), and Helicobacter pylori infection. The next step is an LT4 pharmacodynamic absorption test; poor LT4 absorption should prompt a consultation with a gastroenterologist and (depending on the findings) an increase in the LT4 dose level. An in-depth etiological investigation can reveal visceral disorders and, especially, digestive tract disorders.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27043835", + "title": "Onset of Ulcerative Colitis after Helicobacter pylori Eradication Therapy: A Case Report.", + "year": 2016, + "journal": "The Permanente journal", + "authors": [ + "Chiba M", + "Tsuji T", + "Takahashi K", + "Komatsu M", + "Sugawara T", + "Ono I" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.2592303864967239, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Colitis, Ulcerative", + "Drug Therapy, Combination", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Male", + "Middle Aged" + ], + "raw_abstract": "In Japan, Helicobacter pylori eradication has been approved since 2013 for treatment of H pylori-induced chronic gastritis, in an attempt to reduce the prevalence of gastric cancer, a leading cancer in Japan. H pylori infection affects more than 50% of the world's population. H pylori eradication therapy is generally safe. To our knowledge, no case of newly diagnosed ulcerative colitis occurring immediately after H pylori eradication therapy has previously been reported.A 63-year-old man received a diagnosis of chronic gastritis and H pylori infection. In early March 2014, primary H pylori eradication therapy was initiated; lansoprazole, amoxicillin, and clarithromycin were administered for 1 week. Beginning on the fourth day, he had watery diarrhea twice a day. From the 11th day, bloody stools and watery diarrhea increased to 6 times a day. Colonoscopy, performed on the 40th day after termination of drug therapy, revealed diffuse inflammation in the distal aspect of the colon, with histologic findings consistent with ulcerative colitis. He was admitted to the hospital and was provided with a semivegetarian diet and metronidazole. He noticed a gradual decrease in the amount of blood in his feces then a disappearance of the blood. A fecal occult blood test on the 11th hospital day recorded 337 ng/mL. Fecal occult blood test is not indicated during macroscopic bloody stool but is indicated after disappearance of bloody stool. Therefore, he achieved clinical remission by the 11th hospital day. He was in remission on discharge.New onset of ulcerative colitis should be added to a list of adverse events of H pylori eradication therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31123976", + "title": "Strongyloides stercoralis infection in a patient with rheumatoid arthritis and type 2 diabetes mellitus: a case-based review.", + "year": 2019, + "journal": "Clinical rheumatology", + "authors": [ + "Ashiri A", + "Beiromvand M", + "Khanzadeh A" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.24241124351898422, + "mesh_terms": [ + "Animals", + "Arthritis, Rheumatoid", + "Diabetes Mellitus, Type 2", + "Female", + "Humans", + "Middle Aged", + "Strongyloides stercoralis", + "Strongyloidiasis" + ], + "raw_abstract": "Strongyloides stercoralis (S. stercoralis), a human intestinal nematode, can lead to hyper/disseminated (HD) infection in patients treated with corticosteroids. Here, we report a case of strongyloidiasis in a 58-year-old female with a history of rheumatoid arthritis (RA) and type 2 diabetes mellitus (T2DM). The patient presented with abdominal pain and gastrointestinal (GI) bleeding. Stool was negative for parasitic agents in the first direct smear examination, and the patient with the probable diagnosis of Helicobacter pylori (H. pylori) infection or Crohn's disease received antibiotics and corticosteroids. Parasitic agents were not detected in further direct stool examinations, and the patient with the diagnosis of pneumonia, chronic kidney disease (CKD), ulcerative colitis, sepsis, and candidiasis received fungal, antibiotic, and corticosteroids medications. Low sensitivity of direct smear and the lack of using two methods in diagnosing intestinal parasitic infections led to delayed detection. In the fourth direct stool examination, rhabditiform larva of S. stercoralis was reported. The treatment of corticosteroids was discontinued and albendazole was started. A literature review was conducted by searching Medline, Embase, Scopus, and Web of Science with the keywords S. stercoralis, strongyloidiasis, RA, and T2DM. Our case indicates that screening S. stercoralis infection in high-risk groups, especially those who are candidates for corticosteroids medications, must be implemented using at least two diagnostic techniques.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32109493", + "title": "Impact of gastrointestinal physiology on drug absorption in special populations--An UNGAP review.", + "year": 2020, + "journal": "European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences", + "authors": [ + "Stillhart C", + "Vu\u010di\u0107evi\u0107 K", + "Augustijns P", + "Basit AW", + "Batchelor H", + "Flanagan TR", + "Gesquiere I", + "Greupink R", + "Keszthelyi D", + "Koskinen M", + "Madla CM", + "Matthys C", + "Milju\u0161 G", + "Mooij MG", + "Parrott N", + "Ungell AL", + "de Wildt SN", + "Orlu M", + "Klein S", + "M\u00fcllertz A" + ], + "bacteria": "Helicobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.22514422367891246, + "mesh_terms": [ + "Administration, Oral", + "Adult", + "Aged", + "Child", + "Drug Liberation", + "Gastrointestinal Absorption", + "Gastrointestinal Diseases", + "Gastrointestinal Tract", + "Humans" + ], + "raw_abstract": "The release and absorption profile of an oral medication is influenced by the physicochemical properties of the drug and its formulation, as well as by the anatomy and physiology of the gastrointestinal (GI) tract. During drug development the bioavailability of a new drug is typically assessed in early clinical studies in a healthy adult population. However, many disease conditions are associated with an alteration of the anatomy and/or physiology of the GI tract. The same holds true for some subpopulations, such as paediatric or elderly patients, or populations with different ethnicity. The variation in GI tract conditions compared to healthy adults can directly affect the kinetics of drug absorption, and thus, safety and efficacy of an oral medication. This review provides an overview of GI tract properties in special populations compared to healthy adults and discusses how drug absorption is affected by these conditions. Particular focus is directed towards non-disease dependent conditions (age, sex, ethnicity, genetic factors, obesity, pregnancy), GI diseases (ulcerative colitis and Crohn's disease, celiac disease, cancer in the GI tract, Roux-en-Y gastric bypass, lactose intolerance, Helicobacter pylori infection, and infectious diseases of the GI tract), as well as systemic diseases that change the GI tract conditions (cystic fibrosis, diabetes, Parkinson's disease, HIV enteropathy, and critical illness). The current knowledge about GI conditions in special populations and their impact on drug absorption is still limited. Further research is required to improve confidence in pharmacokinetic predictions and dosing recommendations in the targeted patient population, and thus to ensure safe and effective drug therapies.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32610889", + "title": "Whipple disease mimicking inflammatory bowel disease.", + "year": 2021, + "journal": "Intestinal research", + "authors": [ + "Tatsuki M", + "Ishige T", + "Igarashi Y", + "Hatori R", + "Hokama A", + "Hirato J", + "Muise A", + "Takizawa T", + "Arakawa H" + ], + "bacteria": "Tropheryma", + "condition": "ulcerative colitis", + "relevance_score": 0.2757891393977873, + "mesh_terms": [], + "raw_abstract": "Whipple disease is a systemic chronic infection caused by Tropheryma whipplei. Although chronic diarrhea is a common gastrointestinal symptom, diagnosis is often difficult because there are no specific endoscopic findings, and the pathogen is not detectable by stool culture. We present a female patient with Whipple disease who developed chronic bloody diarrhea and growth retardation at the age of 4 years. Colonoscopy showed a mildly edematous terminal ileum and marked erythema without vascular patterns throughout the sigmoid colon and rectum. Subsequently, a primary diagnosis of ulcerative colitis was made. Histopathological analysis of the terminal ileum showed the presence of foamy macrophages filled with periodic acidSchiff-positive particles. Polymerase chain reaction using DNA from a terminal ileum biopsy sample amplified a fragment of 16S rRNA from T. whipplei. Antibiotic treatment relieved the patient's symptoms. There was no evidence of immunodeficiency in the present case. Since Whipple disease worsens after anti-tumor necrosis factor inhibitor therapy, considering this infection in the differential diagnosis may be important in patients with inflammatory bowel disease, especially before initiation of immunotherapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32301754", + "title": "Gastrointestinal Malakoplakia: Clinicopathologic Analysis of 26 Cases.", + "year": 2020, + "journal": "The American journal of surgical pathology", + "authors": [ + "Zhang Y", + "Byrnes K", + "Lam-Himlin D", + "Pittman M", + "Pezhouh M", + "Gonzalez RS", + "Alruwaii Z", + "Larman T", + "Miller JA", + "Matoso A", + "Oshima K", + "Epstein JI", + "Montgomery EA", + "Voltaggio L" + ], + "bacteria": "Tropheryma", + "condition": "ulcerative colitis", + "relevance_score": 0.21850842122571232, + "mesh_terms": [ + "Adult", + "Aged", + "Aged, 80 and over", + "Biopsy", + "Female", + "Gastric Mucosa", + "Gastrointestinal Diseases", + "Gastrointestinal Tract", + "Humans", + "Incidental Findings", + "Intestinal Mucosa", + "Malacoplakia", + "Male", + "Middle Aged", + "Prognosis", + "Tropheryma", + "United States", + "Young Adult" + ], + "raw_abstract": "Malakoplakia is an inflammatory process related to defective macrophage response to bacterial infection. To further characterize the clinicopathologic manifestations of gastrointestinal malakoplakia, 26 cases were identified from 6 institutions. Hematoxylin and eosin-stained slides and available stains were reviewed, and pertinent clinicopathologic features analyzed. Sixteen patients were women (62%). Mean patient age was 64 (range: 24 to 83). Sites included the colorectum (n=23), appendix (n=1), and stomach (n=2). Clinical indications for tissue procurement included screening (n=14), tumor resection (n=5), diarrhea (n=1), adenoma surveillance (n=1), ulcerative colitis flare (n=1), abdominal pain (n=1), and appendicitis (1). All cases featured histiocytes with abundant, pale, eosinophilic cytoplasm focally containing Michaelis-Gutmann bodies. The process frequently involved the mucosa (n=19), with architectural distortion in 13 cases. Lymphoid aggregates were present in 18 cases, which were prominent or obscuring in 11 (all colon biopsies) and provoked concern for lymphoma in 2. Associated findings included adenocarcinoma (n=5), adenoma (n=2), gastric hyperplastic polyps (n=1), chemical gastritis (n=1), collagenous colitis (n=1), and active chronic colitis (n=2). In cases with available stains, Michaelis-Gutman bodies were highlighted by Periodic Acid-Schiff with diastase, Von Kossa, and iron stains. Although 2 cases were positive for Tropheryma whipplei antibody, no T. whipplei transcripts were detected on real-time polymerase chain reaction. All patients with available follow-up are alive and well with no additional instances of malakoplakia. Malakoplakia of the gastrointestinal tract is a benign, incidental finding. Although histologic features in the stomach and colon resections are similar to those at other sites, exuberant lymphocytic response in colon biopsies and immunoreactivity with T. whippleii antibody may provoke initial confusion and lead to unnecessary time and resource investment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38064857", + "title": "Fucoidan alleviated dextran sulfate sodium-induced ulcerative colitis with improved intestinal barrier, reshaped gut microbiota composition, and promoted autophagy in male C57BL/6 mice.", + "year": 2024, + "journal": "Nutrition research (New York, N.Y.)", + "authors": [ + "Li S", + "Qian Q", + "Yang H", + "Wu Z", + "Xie Y", + "Yin Y", + "Cui Y", + "Li X" + ], + "bacteria": "Escherichia-Shigella", + "condition": "ulcerative colitis", + "relevance_score": 0.7514056443071709, + "mesh_terms": [ + "Humans", + "Male", + "Animals", + "Mice", + "Mice, Inbred C57BL", + "Colitis, Ulcerative", + "Dextran Sulfate", + "Gastrointestinal Microbiome", + "Colon", + "Autophagy", + "Bacteroidetes", + "Clostridiales", + "Disease Models, Animal", + "Colitis", + "Polysaccharides" + ], + "raw_abstract": "Although previous research has unveiled the remedial effects of fucoidan, an extract from marine algae, on ulcerative colitis (UC), the precise mechanisms remain elusive. Animal studies have suggested a connection between autophagy and the beneficial influences of fucoidan intervention. We hypothesized that fucoidan's alleviative effects on dextran sulfate sodium (DSS)-induced UC could be ascribed to autophagy. For our study, we chose 36 male C57BL/6 mice and administered 100 or 400 mg/(kg/body weight/day) of fucoidan via gavage for 5 consecutive weeks. During the last week, the mice were given 3% DSS in drinking water to induce UC. In contrast to the DSS-induced UC model, fucoidan intervention prevented DSS-induced body weight loss, mitigated colon shortening, improved colon mucosa damage, enhanced the intestinal barrier, and reduced serum inflammatory factor concentrations. Furthermore, fucoidan intervention reshaped the gut microbiota compositions, increased the relative abundance of Bacteroidota, Muribaculaceae_unclassified, Clostridiales_unclassified, and Lachnospiraceae_NK4A136_group, and decreased the relative abundance of Firmicutes, Proteobacteria, and Escherichia-Shigella, which led to a lower Firmicutes/Bacteroidota ratio. Additionally, fucoidan treatment enhanced autophagy, as evidenced by upregulated protein expressions of BECLIN1, ATG5, ATG7, and an increased microtubule-associated-proteinlight-chain-3-II/microtubule-associated-proteinlight-chain-3-I ratio. Our findings corroborated the ameliorating effects of fucoidan intervention on DSS-induced UC through autophagy activation, reorganization of gut microbiota, and fortification of the intestinal barrier. This lends support to the therapeutic potential of fucoidan as a natural bioactive ingredient for future UC treatments in humans.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32858455", + "title": "Integrated study of metabolomics and gut metabolic activity from ulcerative colitis to colorectal cancer: The combined action of disordered gut microbiota and linoleic acid metabolic pathway might fuel cancer.", + "year": 2020, + "journal": "Journal of chromatography. A", + "authors": [ + "Tang Q", + "Cang S", + "Jiao J", + "Rong W", + "Xu H", + "Bi K", + "Li Q", + "Liu R" + ], + "bacteria": "Escherichia-Shigella", + "condition": "ulcerative colitis", + "relevance_score": 0.7161181578235164, + "mesh_terms": [ + "Animals", + "Chromatography, High Pressure Liquid", + "Colitis, Ulcerative", + "Colorectal Neoplasms", + "Discriminant Analysis", + "Escherichia coli", + "Feces", + "Gastrointestinal Microbiome", + "Least-Squares Analysis", + "Linoleic Acid", + "Male", + "Metabolomics", + "Principal Component Analysis", + "RNA, Ribosomal, 16S", + "Rats", + "Rats, Sprague-Dawley", + "Shigella", + "Tandem Mass Spectrometry" + ], + "raw_abstract": "Colorectal cancer (CRC) is one of the most serious complications of ulcerative colitis (UC). Altered gut microbiota is implicated in the development of CRC and metabolic perturbations are often associated with changes in the gut microbiome composition. Given the links between gut microbiome and the metabolic profiles in the body, an approach involving ultra-high-performance liquid chromatography combined with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UHPLC-Q-TOF-MS/MS) metabolomics and 16S rDNA sequencing technology was applied to trace the development UC into CRC in rats. The study identified 11 differential metabolites related to both UC and CRC, which mainly referred to the linoleic acid metabolism. Among these, linoleic acid and 12\u2011hydroxy\u20118,10-octadecadienoic acid could serve as key biomarkers for the development of UC into CRC. Besides, a significant change was observed in the microflora structure during the development from UC to CRC; this mainly involved a gradual increase in Escherichia-Shigella and a gradual decrease in Lactobacillus. In addition, Pearson's correlation analysis revealed strong correlations between intestinal microflora-related metabolites and specific intestinal microflora, which indicated both of them can promote the transition of UC to CRC. The results of the present study provided positive support for the involvement of intestinal microflora and host metabolism in the pathophysiological mechanism that is responsible for the development of UC into CRC. This information can help understand the risk for CRC that accompanies a diagnosis of UC and also provide different means of targeting these differential metabolites and intestinal microbiota to avoid UC-induced CRC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34087350", + "title": "Main active components of Jiawei Gegen Qinlian decoction protects against ulcerative colitis under different dietary environments in a gut microbiota-dependent manner.", + "year": 2021, + "journal": "Pharmacological research", + "authors": [ + "Li Q", + "Cui Y", + "Xu B", + "Wang Y", + "Lv F", + "Li Z", + "Li H", + "Chen X", + "Peng X", + "Chen Y", + "Wu E", + "Qu D", + "Jian Y", + "Si H" + ], + "bacteria": "Escherichia-Shigella", + "condition": "ulcerative colitis", + "relevance_score": 0.67684392224105, + "mesh_terms": [ + "Animals", + "Anti-Inflammatory Agents", + "Bacteria", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "Disease Models, Animal", + "Drugs, Chinese Herbal", + "Dysbiosis", + "Female", + "Gastrointestinal Agents", + "Gastrointestinal Microbiome", + "Inflammation Mediators", + "Male", + "Oxidative Stress", + "Rats, Sprague-Dawley", + "Rats" + ], + "raw_abstract": "As an effective drug against acute enteritis diarrhea, Gegen Qinlian decoction (GQD) has a history of 2000 years. However, the potential molecular mechanism through which GQD could protect intestinal barrier from ulcerative colitis (UC) still remains undefined. As an important part of the homeostasis of the colon, gut microbiota is closely related to the dynamic evolution of the surrounding environment and the adjustment of dietary structure. At present, the effectiveness and mechanism of Jiawei Gegen Qinlian decoction against UC in different dietary environments are not clear. Here, the main active components of Jiawei Gegen Qinlian Decoction (PBM), were selected to construct a reasonable and effective compound scheme. We adopted \"5% dextran sulfate sodium (DSS)\" and \"high temperature and humidity + high sugar and high fat + alcohol + 5%DSS\" to induce UC rat models in general environment and UC rat models in Lingnan area, respectively. Then, we examined the therapeutic effects of PBM (89.96\u00a0mg/kg and 179.92\u00a0mg/kg) on two kinds of UC rats. The role of gut microbiota in the anti-UC effect of PBM was identified by intestinal flora consumption and fecal microbiota transplantation (FMT) experiments. Subsequently, we monitored the alterations of gut microbiota and fecal metabolism in the rat colon by 16Sr DNA technique and targeted metabonomics, respectively. The colon inflammation of the PBM-treated and the FMT-treated rats both showed significant relief, as evidenced by a reduction in body weight loss, bloody stool, diarrhea, disease activity index (DAI) score, shortening of colon length as well as decreased colon histology damage. Interestingly enough, the depletion of intestinal flora took away the protective effect of PBM, confirming the importance of intestinal flora in the anti-UC effect of PBM. Then our findings suggested that PBM could not only regulate the gut microbiota by increasing Akkermansia and Romboutsia but also decrease Escherichia-Shigella. More importantly, PBM could increase the production of propionate and total short-chain fatty acids (SCFAs) in colitis rats, regulate medium and long chain fatty acids (M-LCFAs), maintain bile acids (BAs) homeostasis, and regulate amino acids (AAs) metabolism. The transformation of intestinal environment might be related to the upregulation of anti-inflammation, anti-oxidation and tight junction protein expression in colonic mucosa. In summary, PBM showed potential for anti-UC activity through gut microbiota dependence and was expected to be a complementary and alternative medicine herb therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33686049", + "title": "Effects of Pretreatment with Bifidobacterium bifidum Using 16S Ribosomal RNA Gene Sequencing in a Mouse Model of Acute Colitis Induced by Dextran Sulfate Sodium.", + "year": 2021, + "journal": "Medical science monitor : international medical journal of experimental and clinical research", + "authors": [ + "Weng YJ", + "Jiang DX", + "Liang J", + "Ye SC", + "Tan WK", + "Yu CY", + "Zhou Y" + ], + "bacteria": "Escherichia-Shigella", + "condition": "ulcerative colitis", + "relevance_score": 0.6743117575396589, + "mesh_terms": [ + "Animals", + "Bacteria", + "Bifidobacterium bifidum", + "Colitis", + "Colitis, Ulcerative", + "Colon", + "Dextran Sulfate", + "Disease Models, Animal", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Mice", + "Mice, Inbred C57BL", + "Probiotics", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND Bifidobacterium is a potentially effective and safe treatment for patients with inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease. However, information on the influence of B. bifidum on gut microbial diversity of treated and pretreated IBD patients is limited. MATERIAL AND METHODS Our study investigated therapeutic and preventive effects of B. bifidum ATCC 29521 on C57BL/6 mice with dextran sulfate sodium (DSS)-induced acute colitis via 16S ribosomal ribonucleic acid (rRNA) gene sequencing. RESULTS Treatment and pretreatment of mice with B. bifidum ATCC 29521 significantly alleviated the severity of acute colitis on the basis of clinical and pathologic indicators. 16S rRNA gene sequencing showed that administration of B. bifidum shifted composition of the gut microbiome in mice with DSS-induced colitis in both treated and pretreated groups. Mice pretreated with B. bifidum ATCC 29521 for 21 days exhibited a significant increase in diversity of the gut microbiome. Principal coordinate analysis showed that gut microbiota structure was shaped by different treatments and time points. On the basis of linear discriminant analysis of effect size, the abundance of the genus Escherichia-Shigella, belonging to the family Enterobacteriaceae, was reduced in the B. bifidum-treated group, indicating that pathogens were inhibited by the B. bifidum treatment. Furthermore, the genera Intestinimonas and Bacteroides were significantly associated with the B. bifidum-pretreated group. CONCLUSIONS 16S rRNA gene sequencing showed that pretreatment with B. bifidum ATCC 29521 reduced intestinal inflammation and altered the gut microbiota to favor the genera Intestinimonas and Bacteroides.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39390011", + "title": "Dysbiotic signatures and diagnostic potential of gut microbial markers for inflammatory bowel disease in Korean population.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Kim HS", + "Oh SJ", + "Kim BK", + "Kim JE", + "Kim BH", + "Park YK", + "Yang BG", + "Lee JY", + "Bae JW", + "Lee CK" + ], + "bacteria": "Escherichia-Shigella", + "condition": "ulcerative colitis", + "relevance_score": 0.6138099747205611, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Dysbiosis", + "Female", + "Male", + "Republic of Korea", + "Adult", + "Middle Aged", + "Biomarkers", + "RNA, Ribosomal, 16S", + "Feces", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Metagenomics", + "Crohn Disease", + "Case-Control Studies", + "Cross-Sectional Studies", + "Young Adult", + "Aged" + ], + "raw_abstract": "Fecal samples were collected from 640 individuals in Korea, including 523 patients with IBD (223 with Crohn's disease [CD] and 300 with ulcerative colitis [UC]) and 117 healthy controls. The samples were subjected to cross-sectional gut metagenomic analysis using 16\u00a0S rRNA sequencing and bioinformatics analysis. Patients with IBD, particularly those with CD, exhibited significantly lower alpha diversities than the healthy subjects. Differential abundance analysis revealed dysbiotic signatures, characterized by an expansion of the genus Escherichia-Shigella in patients with CD. Functional annotations showed that functional pathways related to bacterial pathogenesis and production of hydrogen sulfide (H", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36440681", + "title": "Colitis aggravated by Mrgprb2 knockout is associated with altered immune response, intestinal barrier function and gut microbiota.", + "year": 2023, + "journal": "Experimental physiology", + "authors": [ + "Shao M", + "Liu J", + "Luo H" + ], + "bacteria": "Escherichia-Shigella", + "condition": "ulcerative colitis", + "relevance_score": 0.6074390426562856, + "mesh_terms": [ + "Humans", + "Male", + "Mice", + "Animals", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Dextran Sulfate", + "Mice, Knockout", + "Colitis", + "Colon", + "Immunity", + "Disease Models, Animal", + "Mice, Inbred C57BL", + "Nerve Tissue Proteins", + "Receptors, Neuropeptide", + "Receptors, G-Protein-Coupled" + ], + "raw_abstract": "NEW FINDINGS: What is the central question of this study? What is the role of mas-related G protein-coupled receptor X2 (MRGPRX2/Mrgprb2) in ulcerative colitis in relation to the intestinal flora, intestinal barrier and immune response? What is the main finding and its importance? Knockout of mouse Mrgprb2 aggravates dextran sulfate sodium (DSS)-induced colitis, which is associated with altered gut microbiota and immune response and disruption of the intestinal barrier. MRGPRB2 may have a protective effect on DSS-induced colitis. ABSTRACT: Ulcerative colitis (UC) is a chronic immune-related disease, and changes in the intestinal microbiota and damage to the intestinal barrier contribute to its pathogenesis. Mast cells (MCs) are widely distributed in the gastrointestinal tract and are thought to be related to the pathogenesis of UC. Human mas-related G protein-coupled receptor X2 (MRGPRX2) and its mouse homologue, Mrgprb2, are selectively expressed on MCs to recruit immune cells and modulate host defence against microbial infection. To investigate the role of Mrgprb2 in UC in mice, we compared the differences between Mrgprb2 knockout (b2KO) male mice and wild-type (WT) male mice with dextran sulfate sodium (DSS)-induced colitis in the severity of clinical symptoms, inflammatory cell infiltration, degree of intestinal barrier damage and composition of the intestinal flora. The results showed that weight loss, disease activity index score, colon shortening and colonic pathological damage were significantly increased in b2KO mice while MC activation, cytokine and chemokine secretion, and inflammatory cell infiltration were decreased. In addition, the abundance and diversity of the intestinal microbiota were reduced in b2KO mice. B2KO mice also exhibited a reduction of probiotics such as norank_f_Muribaculaceae and Lactobacillus and increase of harmful bacteria like Escherichia-Shigella. Intestinal mucosal barrier damage of b2KO mice was more severe than that of WT mice due to the attenuated expression of mucin-2 and occludin. These results demonstrated that MRGPRB2 may have a protective effect on DSS-induced colitis by altering the intestinal flora, participating in barrier repair and recruiting inflammatory cells to eliminate pathogens.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31055592", + "title": "Combined Signature of the Fecal Microbiome and Plasma Metabolome in Patients with Ulcerative Colitis.", + "year": 2019, + "journal": "Medical science monitor : international medical journal of experimental and clinical research", + "authors": [ + "Sun M", + "Du B", + "Shi Y", + "Lu Y", + "Zhou Y", + "Liu B" + ], + "bacteria": "Escherichia-Shigella", + "condition": "ulcerative colitis", + "relevance_score": 0.6064671547438342, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metabolome", + "Methylamines", + "Microbiota", + "Middle Aged", + "Plasma", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND Ulcerative colitis is a chronic, idiopathic in\ufb02ammatory disease that destroys the colon structure. Nevertheless, the exact pathogenesis is not clear and needs to be fully elucidated. MATERIAL AND METHODS Stool and plasma samples were used for 16S ribosomal RNA sequencing and liquid chromatography mass spectrometry, respectively. In addition, we detected the level of trimethylamine N-oxide. Finally, we performed Pearson correlation analysis between the microbiome and the metabolome. RESULTS Twenty-three active ulcerative colitis, 25 inactive ulcerative colitis, and 30 control cases were included. Thirty-four significantly different metabolites were found between the active ulcerative colitis and control groups, 38 were found between the inactive ulcerative colitis and control groups, and only 1 was found between the active ulcerative colitis and inactive ulcerative colitis groups. The plasma trimethylamine N-oxide level of the inactive ulcerative colitis and active ulcerative colitis groups was significantly higher than that of the control group. Moreover, we identified significant changes in 24, 18, and 12 bacterial genera for active ulcerative colitis-control, inactive ulcerative colitis-control, and active ulcerative colitis-inactive ulcerative colitis, respectively. Cross-correlation indicated an association between sphingosine 1-phosphate and Roseburia, Klebsiella, and Escherichia-Shigella. Through the pathway analysis, we found sphingolipid metabolism was one of the most significantly increased pathways. CONCLUSIONS Although levels of trimethylamine N-oxide were higher in ulcerative colitis patients, they did not achieve statistical significance in active ulcerative colitis and inactive ulcerative colitis groups. Sphingosine 1-phosphate was increased in ulcerative colitis patients and there were several microbiota associated with it. Although further study is still needed, sphingosine 1-phosphate will probably become a new target for treatment of ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29385143", + "title": "Longitudinal microbiome analysis of single donor fecal microbiota transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis.", + "year": 2018, + "journal": "PloS one", + "authors": [ + "Mintz M", + "Khair S", + "Grewal S", + "LaComb JF", + "Park J", + "Channer B", + "Rajapakse R", + "Bucobo JC", + "Buscaglia JM", + "Monzur F", + "Chawla A", + "Yang J", + "Robertson CE", + "Frank DN", + "Li E" + ], + "bacteria": "Escherichia-Shigella", + "condition": "ulcerative colitis", + "relevance_score": 0.5131417467476894, + "mesh_terms": [ + "Clostridioides difficile", + "Clostridium Infections", + "Colitis, Ulcerative", + "Fecal Microbiota Transplantation", + "Feces", + "Humans", + "Longitudinal Studies", + "Microbiota", + "Polymerase Chain Reaction", + "Prospective Studies", + "Recurrence", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Studies of colonoscopic fecal microbiota transplant (FMT) in patients with recurrent CDI, indicate that this is a very effective treatment for preventing further relapses. In order to provide this service at Stony Brook University Hospital, we initiated an open-label prospective study of single colonoscopic FMT among patients with \u2265 2 recurrences of CDI, with the intention of monitoring microbial composition in the recipient before and after FMT, as compared with their respective donor. We also initiated a concurrent open label prospective trial of single colonoscopic FMT of patients with ulcerative colitis (UC) not responsive to therapy, after obtaining an IND permit (IND 15642). To characterize how FMT alters the fecal microbiota in patients with recurrent Clostridia difficile infections (CDI) and/or UC, we report the results of a pilot microbiome analysis of 11 recipients with a history of 2 or more recurrences of C. difficile infections without inflammatory bowel disease (CDI-only), 3 UC recipients with recurrent C. difficile infections (CDI + UC), and 5 UC recipients without a history of C. difficile infections (UC-only). METHOD: V3V4 Illumina 16S ribosomal RNA (rRNA) gene sequencing was performed on the pre-FMT, 1-week post-FMT, and 3-months post-FMT recipient fecal samples along with those collected from the healthy donors. Fitted linear mixed models were used to examine the effects of Group (CDI-only, CDI + UC, UC-only), timing of FMT (Donor, pre-FMT, 1-week post-FMT, 3-months post-FMT) and first order Group*FMT interactions on the diversity and composition of fecal microbiota. Pairwise comparisons were then carried out on the recipient vs. donor and between the pre-FMT, 1-week post-FMT, and 3-months post-FMT recipient samples within each group. RESULTS: Significant effects of FMT on overall microbiota composition (e.g., beta diversity) were observed for the CDI-only and CDI + UC groups. Marked decreases in the relative abundances of the strictly anaerobic Bacteroidetes phylum, and two Firmicutes sub-phyla associated with butyrate production (Ruminococcaceae and Lachnospiraceae) were observed between the CDI-only and CDI + UC recipient groups. There were corresponding increases in the microaerophilic Proteobacteria phylum and the Firmicutes/Bacilli group in the CDI-only and CDI + UC recipient groups. At a more granular level, significant effects of FMT were observed for 81 genus-level operational taxonomic units (OTUs) in at least one of the three recipient groups (p<0.00016 with Bonferroni correction). Pairwise comparisons of the estimated pre-FMT recipient/donor relative abundance ratios identified 6 Gammaproteobacteria OTUs, including the Escherichia-Shigella genus, and 2 Fusobacteria OTUs with significantly increased relative abundance in the pre-FMT samples of all three recipient groups (FDR < 0.05), however the magnitude of the fold change was much larger in the CDI-only and CDI + UC recipients than in the UC-only recipients. Depletion of butyrate producing OTUs, such as Faecalibacterium, in the CDI-only and CDI + UC recipients, were restored after FMT. CONCLUSION: The results from this pilot study suggest that the microbial imbalances in the CDI + UC recipients more closely resemble those of the CDI-only recipients than the UC-only recipients.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38499070", + "title": "Fecal microbiota transplant on Escherichia-Shigella gut composition and its potential role in the treatment of generalized anxiety disorder: A systematic review.", + "year": 2024, + "journal": "Journal of affective disorders", + "authors": [ + "Baske MM", + "Timmerman KC", + "Garmo LG", + "Freitas MN", + "McCollum KA", + "Ren TY" + ], + "bacteria": "Escherichia-Shigella", + "condition": "ulcerative colitis", + "relevance_score": 0.4799592631318192, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Gastrointestinal Microbiome", + "Anxiety Disorders", + "Brain-Gut Axis" + ], + "raw_abstract": "BACKGROUND: The gut-brain-axis has a role in mental health disorders. In people with generalized anxiety disorder, GAD, METHODS: A systematic review of literature was conducted on articles published in PubMed, CINAHL Plus, Scopus, Cochrane Library, and Wed of Science from 2000 to 2022 that analyzed FMT as a modality to alter the gut microbiome in which Escherichia-Shigella levels were quantified and reported. RESULTS: Of 1916 studies identified, 14 fit criteria and were included. Recipients undergoing FMT procedures had at least one enteric diagnosis and increased percentages of Escherichia-Shigella pre-FMT. Five studies on recurrent Clostridioides difficile infection, three irritable bowel syndrome, two ulcerative colitis, one ulcerative colitis and recurrent Clostridioides difficile infection, one acute intestinal and chronic graft-vs-host disease, one pouchitis, and one slow transit constipation. 10 articles (71.4\u00a0%) showed decreased levels of Escherichia-Shigella post-FMT compared to pre-FMT. Four studies claimed the results were significant (40\u00a0%). LIMITATIONS: Limitations include potential bias in study selection, study methods of analysis, and generalization of results. CONCLUSIONS: The gut-brain-axis has a role in GAD. Those with GAD have significantly higher Escherichia-Shigella compared to those without GAD. FMT has the potential to decrease Escherichia-Shigella in patients with GAD to positively alter the gut-brain-axis as a potential for future GAD treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36327509", + "title": "In vitro fermentation characteristics of the dietary fiber in bamboo (Phyllostachys edulis) shoots and its regulatory effects on the intestinal microbiota and metabolites.", + "year": 2023, + "journal": "Food chemistry", + "authors": [ + "Wu W", + "Li Q", + "Chen H", + "Fang X", + "Niu B", + "Liu R", + "Mu H", + "Gao H" + ], + "bacteria": "Escherichia-Shigella", + "condition": "ulcerative colitis", + "relevance_score": 0.33454070431332444, + "mesh_terms": [ + "Animals", + "Mice", + "Gastrointestinal Microbiome", + "Dextran Sulfate", + "Fermentation", + "Dietary Fiber", + "Colitis, Ulcerative", + "Colon", + "Poaceae", + "Disease Models, Animal", + "Colitis", + "Mice, Inbred C57BL" + ], + "raw_abstract": "The effects of bamboo (Phyllostachys edulis) shoot dietary fiber (BSDF-1) on ulcerative colitis (UC) are unclear. Therefore, we performed an in vitro glycolysis study of intestinal microbiota samples, based on 16S rDNA sequencing and determining the metabolites in non-targeted colonic fecal fermentation broth. After a 48\u00a0h fermentation, the pH of the fermentation broth decreased significantly (p\u00a0<\u00a00.05) with the dextran sulfate sodium group (referred to here as the Mod group). The carbohydrate utilization rate was 26.59\u00a0%, and the total short-chain fatty acid content was 16.46\u00a0\u00b1\u00a00.71\u00a0mmol/L. The abundances of Alistipes and Lactobacillus increased after BDSF-1 fermentation, whereas those of Escherichia-Shigella, Enterococcus, and Proteus significantly decreased. BSDF-1 altered the levels of 17 metabolites in the Mod group after fermentation for 48\u00a0h, which reduced the cadaverine increasing induced by DSS. These results indicate that BSDF-1 can regulate the metabolism of the intestinal microbiota and the host, suggesting its use as a promising therapeutic strategy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "25559083", + "title": "Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation.", + "year": 2015, + "journal": "Gut microbes", + "authors": [ + "Tang MS", + "Poles J", + "Leung JM", + "Wolff MJ", + "Davenport M", + "Lee SC", + "Lim YA", + "Chua KH", + "Loke P", + "Cho I" + ], + "bacteria": "Acinetobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.7020289648366351, + "mesh_terms": [ + "Biota", + "Colitis", + "Feces", + "Humans", + "Intestinal Mucosa", + "Male", + "Metabolic Networks and Pathways", + "Middle Aged" + ], + "raw_abstract": "The mucosal microbiota lives in close proximity with the intestinal epithelium and may interact more directly with the host immune system than the luminal/fecal bacteria. The availability of nutrients in the mucus layer of the epithelium is also very different from the gut lumen environment. Inferred metagenomic analysis for microbial function of the mucosal microbiota is possible by PICRUSt. We recently found that by using this approach, actively inflamed tissue of ulcerative colitis (UC) patients have mucosal communities enriched for genes involved in lipid and amino acid metabolism, and reduced for carbohydrate and nucleotide metabolism. Here, we find that the same bacterial taxa (e.g. Acinetobacter) and predicted microbial pathways enriched in actively inflamed colitis tissue are also enriched in the mucosa of subjects undergoing routine screening colonoscopies, when compared with paired samples of luminal/fecal bacteria. These results suggest that the mucosa of healthy individuals may be a reservoir of aerotolerant microbial communities expanded during colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31546058", + "title": "Association of Alterations in Intestinal Microbiota With Impaired Psychological Function in Patients With Inflammatory Bowel Diseases in Remission.", + "year": 2020, + "journal": "Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association", + "authors": [ + "Humbel F", + "Rieder JH", + "Franc Y", + "Juillerat P", + "Scharl M", + "Misselwitz B", + "Schreiner P", + "Begr\u00e9 S", + "Rogler G", + "von K\u00e4nel R", + "Yilmaz B", + "Biedermann L" + ], + "bacteria": "Lactococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.536965525003367, + "mesh_terms": [ + "Cohort Studies", + "Colitis, Ulcerative", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Prospective Studies", + "Quality of Life", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND & AIMS: Depression and anxiety are frequent comorbidities with inflammatory bowel diseases (IBD). Alterations to the intestinal microbiome promote not only intestinal inflammation but also psychologic function. We studied the interactions between the composition of\u00a0the intestinal microbiota and psychological outcomes in patients with IBD in Switzerland. METHODS: We performed a prospective study of psychological comorbidities and quality of life (QoL) in 171 participants in the Swiss IBD Cohort Study with IBD in remission. Participants complete the Hospital Anxiety and Depression Scale, Perceived Stress Questionnaire, the 36-Item Short Form Survey, and the IBD QoL Questionnaire. Microbes were collected from intestinal biopsies and analyzed by 16S rRNA high-throughput sequencing. RESULTS: Microbiomes of patients with higher perceived stress had significantly lower alpha diversity. Anxiety and depressive symptoms were significantly associated with beta diversity. We found a negative correlation between psychological distress and abundance of Clostridia, Bacilli, Bacteroidia, and Beta- and Gamma-proteobacteria. Psychological distress was also associated with decreases in operational taxonomic units from the lineages of Lachnospiraceae, Fusobacteriaceae, Ruminococcaceae, Veillonellaceae, Alcaligenaceae, Desulfovibrionaceae, and Bacteroidaceae families. The relative abundance of Bifidobacterium in patients with Crohn's disease and Desulfovibrio in patients with ulcerative colitis correlated with depression, whereas abundance of Sutterella, RF 32, and Lactococcus correlated with quality of life in patients with Crohn's disease. CONCLUSIONS: We identified correlations between the composition of the intestinal microbiota in patients with IBD and remission, psychological well-being, and QoL. Further studies should investigate how intestinal inflammation, the microbiome, and microbial metabolites affect psychological well-being and whether these components are mono- or bi-directionally linked.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Lactococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.505491338085921, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32122364", + "title": "An engineering probiotic producing defensin-5 ameliorating dextran sodium sulfate-induced mice colitis via Inhibiting NF-kB pathway.", + "year": 2020, + "journal": "Journal of translational medicine", + "authors": [ + "Zeng L", + "Tan J", + "Xue M", + "Liu L", + "Wang M", + "Liang L", + "Deng J", + "Chen W", + "Chen Y" + ], + "bacteria": "Lactococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.49491713542556864, + "mesh_terms": [ + "Animals", + "Caco-2 Cells", + "Colitis", + "Defensins", + "Dextran Sulfate", + "Disease Models, Animal", + "Humans", + "Intestinal Mucosa", + "Mice", + "Mice, Inbred C57BL", + "NF-kappa B", + "Probiotics", + "Sulfates" + ], + "raw_abstract": "BACKGROUND: Human defensin-5 (HD-5) is a key antimicrobial peptide which plays an important role in host immune defense, while the short half-life greatly limits its clinical application. The purpose of this study was to investigate the effects of an engineering probiotic producing HD-5 on intestinal barrier and explore its underlying mechanism METHODS: We constructed the pN8148-SHD-5 vector, and transfected this plasmid into Lactococcus lactis (L. lactis) to create the recombinant NZ9000SHD-5 strain, which continuously produces mature HD-5. NZ9000SHD-5 was administrated appropriately in a dextran sodium sulfate (DSS)-induced colitis model. Alterations in the wounded intestine were analyzed by hematoxylin-eosin staining. The changes of intestinal permeability were detected by FITC-dextran permeability test, the tight junction (TJ) proteins ZO-1 and occludin and cytokines were analyzed by western blotting or enzyme linked immunosorbent assay. In Caco-2 cell monolayers, the permeability were analyzed by transepithelial electrical resistance, and the TJ proteins were detected by western blotting and immunofluorescence. In addition, NF-\u03baB signaling pathway was investigated to further analyze the molecular mechanism of NZ9000SHD-5 treatment on inducing intestinal protection in vitro. RESULTS: We found oral administration with NZ9000SHD-5 significantly reduced colonic glandular structure destruction and inflammatory cell infiltration, downregulated expression of several inflammation-related molecules and preserved epithelial barrier integrity. The same protective effects were observed in in vitro experiments, and pretreatment of macrophages with NZ9000SHD-5 culture supernatants prior to LPS application significantly reduced the expression of phosphorylated nuclear transcription factor-kappa B (NF-\u03baB) p65 and its inhibitor I\u03baB\u03b1. CONCLUSIONS: These results indicate the NZ9000SHD-5 can alleviate DSS-induced mucosal damage by suppressing NF-\u03baB signaling pathway, and NZ9000SHD-5 may be a novel therapeutic means for ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30606251", + "title": "Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases.", + "year": 2019, + "journal": "Microbiome", + "authors": [ + "Armstrong H", + "Alipour M", + "Valcheva R", + "Bording-Jorgensen M", + "Jovel J", + "Zaidi D", + "Shah P", + "Lou Y", + "Ebeling C", + "Mason AL", + "Lafleur D", + "Jerasi J", + "Wong GK", + "Madsen K", + "Carroll MW", + "Huynh HQ", + "Dieleman LA", + "Wine E" + ], + "bacteria": "Flavonifractor", + "condition": "ulcerative colitis", + "relevance_score": 0.5827115292774536, + "mesh_terms": [ + "Adolescent", + "Bacteria", + "Child", + "Child, Preschool", + "Colonoscopy", + "Female", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Immunoglobulin G", + "In Situ Hybridization, Fluorescence", + "Inflammatory Bowel Diseases", + "Intestines", + "Male", + "Metagenomics", + "Phylogeny" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel diseases (IBD) are a group of complex and multifactorial disorders with unknown etiology. Chronic intestinal inflammation develops against resident intestinal bacteria in genetically susceptible hosts. We hypothesized that host intestinal immunoglobulin (Ig) G can be used to identify bacteria involved in IBD pathogenesis. RESULTS: IgG-bound and -unbound microorganisms were collected from 32 pediatric terminal ileum aspirate washes during colonoscopy [non-IBD (n\u2009=\u200910), Crohn disease (n\u2009=\u200915), and ulcerative colitis (n\u2009=\u20097)], and composition was assessed using the Illumina MiSeq platform. In vitro analysis of invasive capacity was evaluated by fluorescence in situ hybridization and gentamicin invasion assay; immune activation was measured by qPCR. Despite considerable inter-individual variations, IgG binding favored specific and unique mucosa-associated species in pediatric IBD patients. Burkholderia cepacia, Flavonifractor plautii, and Rumminococcus sp. demonstrated increased IgG binding, while Pseudomonas ST29 demonstrated reduced IgG binding, in IBD. In vitro validation confirmed that B. cepacia, F. plautii, and Rumminococcus display invasive potential while Pseudomonas protogens did not. CONCLUSION: Using IgG as a marker of pathobionts in larger patient cohorts to identify microbes and elucidate their role in IBD pathogenesis will potentially underpin new strategies to facilitate development of novel, targeted diagnostic, and therapeutic approaches. Interestingly, this method can be used beyond the scope of this manuscript to evaluate altered gut pathobionts in a number of diseases associated with altered microbiota including arthritis, obesity, diabetes mellitus, alcoholic liver disease, cirrhosis, metabolic syndrome, and carcinomas.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33947329", + "title": "Ecological and network analyses identify four microbial species with potential significance for the diagnosis/treatment of ulcerative colitis (UC).", + "year": 2021, + "journal": "BMC microbiology", + "authors": [ + "Li W", + "Sun Y", + "Dai L", + "Chen H", + "Yi B", + "Niu J", + "Wang L", + "Zhang F", + "Luo J", + "Wang K", + "Guo R", + "Li L", + "Zou Q", + "Ma ZS", + "Miao Y" + ], + "bacteria": "Flavonifractor", + "condition": "ulcerative colitis", + "relevance_score": 0.5553104396558273, + "mesh_terms": [ + "Bacteria", + "Biodiversity", + "China", + "Colitis, Ulcerative", + "DNA, Bacterial", + "Dysbiosis", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is one of the primary types of inflammatory bowel disease (IBD), the occurrence of which has been increasing worldwide. Although IBD is an intensively studied human microbiome-associated disease, research on Chinese populations remains relatively limited, particularly on the mucosal microbiome. The present study aimed to analyze the changes in the mucosal microbiome associated with UC from the perspectives of medical ecology and complex network analysis. RESULTS: In total, 56 mucosal microbiome samples were collected from 28 Chinese UC patients and their healthy family partners, followed by amplicon sequencing. Based on sequencing data, we analyzed species diversity, shared species, and inter-species interactions at the whole community, main phyla, and core/periphery species levels. We identified four opportunistic \"pathogens\" (i.e., Clostridium tertium, Odoribacter splanchnicus, Ruminococcus gnavus, and Flavonifractor plautii) with potential significance for the diagnosis and treatment of UC, which were inhibited in healthy individuals, but unrestricted in the UC patients. In addition, we also discovered in this study: (i) The positive-to-negative links (P/N) ratio, which measures the balance of species interactions or inhibition effects in microbiome networks, was significantly higher in UC patients, indicating loss of inhibition against potentially opportunistic \"pathogens\" associated with dysbiosis. (ii) Previous studies have reported conflicting evidence regarding species diversity and composition between UC patients and healthy controls. Here, significant differences were found at the major phylum and core/periphery scales, but not at the whole community level. Thus, we argue that the paradoxical results found in existing studies are due to the scale effect. CONCLUSIONS: Our results reveal changes in the ecology and network structure of the gut mucosal microbiome that might be associated with UC, and these changes might provide potential therapeutic mechanisms of UC. The four opportunistic pathogens that were identified in the present study deserve further investigation in future studies.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37095601", + "title": "A Mediterranean Diet Pattern Improves Intestinal Inflammation Concomitant with Reshaping of the Bacteriome in Ulcerative Colitis: A Randomised Controlled Trial.", + "year": 2023, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Haskey N", + "Estaki M", + "Ye J", + "Shim RK", + "Singh S", + "Dieleman LA", + "Jacobson K", + "Gibson DL" + ], + "bacteria": "Flavonifractor", + "condition": "ulcerative colitis", + "relevance_score": 0.5345849190962763, + "mesh_terms": [ + "Adult", + "Humans", + "Female", + "Middle Aged", + "Male", + "Colitis, Ulcerative", + "Diet, Mediterranean", + "Prospective Studies", + "RNA, Ribosomal, 16S", + "Canada", + "Inflammation", + "Feces", + "Butyric Acid", + "Leukocyte L1 Antigen Complex" + ], + "raw_abstract": "BACKGROUND AND AIMS: Dietary patterns are important in managing ulcerative colitis [UC], given their influence on gut microbiome-host symbiosis and inflammation. We investigated whether the Mediterranean Diet Pattern [MDP] vs the Canadian Habitual Diet Pattern [CHD] would affect disease activity, inflammation, and the gut microbiome in patients with quiescent UC. METHODS: We performed a prospective, randomised, controlled trial in adults [65% female; median age 47 years] with quiescent UC in an outpatient setting from 2017 to 2021. Participants were randomised to an MDP [n\u2005=\u200515] or CHD [n\u2005=\u200513] for 12 weeks. Disease activity [Simple Clinical Colitis Activity Index] and faecal calprotectin [FC] were measured at baseline and week 12. Stool samples were analysed by 16S rRNA gene amplicon sequencing. RESULTS: The diet was well tolerated by the MDP group. At week 12, 75% [9/12] of participants in the CHD had an FC\u2005>100 \u03bcg/g, vs 20% [3/15] of participants in the MDP group. The MDP group had higher levels of total faecal short chain fatty acids [SCFAs] [p\u2005=\u20050.01], acetic acid [p\u2005=\u20050.03], and butyric acid [p\u2005=\u20050.03] compared with the CHD. Furthermore, the MDP induced alterations in microbial species associated with a protective role in colitis [Alistipes finegoldii and Flavonifractor plautii], as well as the production of SCFAs [Ruminococcus bromii]. CONCLUSIONS: An MDP induces gut microbiome alterations associated with the maintenance of clinical remission and reduced FC in patients with quiescent UC. The data support that the MDP is a sustainable diet pattern that could be recommended as a maintenance diet and adjunctive therapy for UC patients in clinical remission. ClinicalTrials.gov no: NCT0305371.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38836628", + "title": "Gut Microbial Species and Endotypes Associate with Remission in Ulcerative Colitis Patients Treated with Anti-TNF or Anti-integrin Therapy.", + "year": 2024, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Tamburini FB", + "Tripathi A", + "Gold MP", + "Yang JC", + "Biancalani T", + "McBride JM", + "Keir ME", + "Gardenia Study Group" + ], + "bacteria": "Flavonifractor", + "condition": "ulcerative colitis", + "relevance_score": 0.5059967618256986, + "mesh_terms": [ + "Adult", + "Female", + "Humans", + "Male", + "Middle Aged", + "Antibodies, Monoclonal, Humanized", + "Colitis, Ulcerative", + "Feces", + "Gastrointestinal Agents", + "Gastrointestinal Microbiome", + "Infliximab", + "Remission Induction", + "Tumor Necrosis Factor Inhibitors" + ], + "raw_abstract": "BACKGROUND AND AIMS: The gut microbiota contributes to aberrant inflammation in inflammatory bowel disease, but the bacterial factors causing or exacerbating inflammation are not fully understood. Further, the predictive or prognostic value of gut microbial biomarkers for remission in response to biologic therapy is unclear. METHODS: We perform whole metagenomic sequencing of 550 stool samples from 287 ulcerative colitis patients from a large, phase 3, head-to-head study of infliximab and etrolizumab. RESULTS: We identify several bacterial species in baseline and/or post-treatment samples that associate with clinical remission. These include previously described associations [Faecalibacterium prausnitzii_F] as well as new associations with remission to biologic therapy [Flavonifractor plautii]. We build multivariate models and find that gut microbial species are better predictors for remission than clinical variables alone. Finally, we describe patient groups that differ in microbiome composition and remission rate after induction therapy, suggesting the potential utility of microbiome-based endotyping. CONCLUSIONS: In this large study of ulcerative colitis patients, we show that few individual species associate strongly with clinical remission, but multivariate models including microbiome can predict clinical remission and have better predictive power compared with clinical data alone.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38521930", + "title": "Human-derived bacterial strains mitigate colitis via modulating gut microbiota and repairing intestinal barrier function in mice.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Dai J", + "Jiang M", + "Wang X", + "Lang T", + "Wan L", + "Wang J" + ], + "bacteria": "Oscillibacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5951787363092838, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "Gastrointestinal Microbiome", + "Intestinal Barrier Function", + "RNA, Ribosomal, 16S", + "Colitis", + "Colitis, Ulcerative", + "Bacteroidetes", + "Enterococcus faecium", + "Escherichia coli", + "Mice, Inbred C57BL", + "Disease Models, Animal", + "Colon" + ], + "raw_abstract": "BACKGROUND: Unbalanced gut microbiota is considered as a pivotal etiological factor in colitis. Nevertheless, the precise influence of the endogenous gut microbiota composition on the therapeutic efficacy of probiotics in colitis remains largely unexplored. RESULTS: In this study, we isolated bacteria from fecal samples of a healthy donor and a patient with ulcerative colitis in remission. Subsequently, we identified three bacterial strains that exhibited a notable ability to ameliorate dextran sulfate sodium (DSS)-induced colitis, as evidenced by increased colon length, reduced disease activity index, and improved histological score. Further analysis revealed that each of Pediococcus acidilactici CGMCC NO.17,943, Enterococcus faecium CGMCC NO.17,944 and Escherichia coli CGMCC NO.17,945 significantly attenuated inflammatory responses and restored gut barrier dysfunction in mice. Mechanistically, bacterial 16S rRNA gene sequencing indicated that these three strains partially restored the overall structure of the gut microbiota disrupted by DSS. Specially, they promoted the growth of Faecalibaculum and Lactobacillus murinus, which were positively correlated with gut barrier function, while suppressing Odoribacter, Rikenella, Oscillibacter and Parasutterella, which were related to inflammation. Additionally, these strains modulated the composition of short chain fatty acids (SCFAs) in the cecal content, leading to an increase in acetate and a decrease in butyrate. Furthermore, the expression of metabolites related receptors, such as receptor G Protein-coupled receptor (GPR) 43, were also affected. Notably, the depletion of endogenous gut microbiota using broad-spectrum antibiotics completely abrogated these protective effects. CONCLUSIONS: Our findings suggest that selected human-derived bacterial strains alleviate experimental colitis and intestinal barrier dysfunction through mediating resident gut microbiota and their metabolites in mice. This study provides valuable insights into the potential therapeutic application of probiotics in the treatment of colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Oscillibacter", + "condition": "ulcerative colitis", + "relevance_score": 0.505491338085921, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Butyrivibrio", + "condition": "ulcerative colitis", + "relevance_score": 0.505491338085921, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29782507", + "title": "Paraclostridium bifermentans exacerbates pathosis in a mouse model of ulcerative colitis.", + "year": 2018, + "journal": "PloS one", + "authors": [ + "Kutsuna R", + "Tomida J", + "Morita Y", + "Kawamura Y" + ], + "bacteria": "Paraclostridium", + "condition": "ulcerative colitis", + "relevance_score": 0.767762271805429, + "mesh_terms": [ + "Animals", + "Clostridiales", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "Dextran Sulfate", + "Disease Models, Animal", + "Fatty Acids, Volatile", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation Mediators", + "Mice", + "Mice, Inbred C57BL", + "Peroxidase", + "RNA, Messenger" + ], + "raw_abstract": "Although it has been recognized that intestinal bacteria play an important role in the pathology of human ulcerative colitis (UC), specific pathogenic bacteria for UC have not been identified. We investigated the influence of Paraclostridium bifermentans PAGU1678 strain on the pathology of a UC mouse model and found it increased UC pathosis scores such as loose and bloody stools, reduced diversity of fecal flora, disappearance of the crypt structure of distal colon tissue, destruction of intestinal epithelial cells, and atrophy of the colon. Furthermore, we observed an increase in COX-2, TNF-\u03b1, IL-6, IL-1, and IL-17 expression and a decrease in Foxp3 and SOCS3 expression, as inflammation-related factors and inflammatory cytokines, a decrease in the concentration of short chain fatty acids (acetic acid, propionic acid, and butyric acid) in feces, and an increase of intestinal mucosal myeloperoxidase activity. These results suggest that P. bifermentans PAGU1678 is a pathology-exacerbating factor in a mouse model of UC. This study is the first to demonstrate exacerbation of the pathological condition in a mouse model of UC by a single bacterial strain.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33598970", + "title": "Adsorptive granulomonocytapheresis alters the gut bacterial microbiota in patients with active ulcerative colitis.", + "year": 2021, + "journal": "Journal of clinical apheresis", + "authors": [ + "Chen X", + "Lou L", + "Tang H", + "Tan X", + "Bi J", + "Wu H", + "Li N", + "Wang Y", + "Mao J" + ], + "bacteria": "Dialister", + "condition": "ulcerative colitis", + "relevance_score": 0.7228788005550831, + "mesh_terms": [ + "Adult", + "Colitis, Ulcerative", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Granulocytes", + "Humans", + "Leukapheresis", + "Male", + "Middle Aged", + "Monocytes", + "Prospective Studies" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is a refractory disease with unclear etiology. Studies have shown that UC is closely associated with gut microbiota dysbiosis. Adsorptive granulomonocytapheresis (GMA) using an Adacolumn has been found to treat UC effectively, but its underlying mechanism of treatment has not been fully elucidated. In this study, we aimed to investigate the influence of GMA on the gut microbiota in patients with active UC. METHODS: We conducted a single-center prospective analysis of patients with active UC who received GMA therapy and ultimately achieved clinical remission. Stool samples of healthy controls and patients before and after 5 or 10 sessions of GMA therapy were collected. Subsequently, high-throughput sequencing of the 16S rRNA V3 and V4 gene region of the stool was conducted and clustering of operational taxonomic units and species annotation were performed. RESULTS: Gut microbial profiles in patients with UC were characterized by low bacterial diversity. After 5 or 10 sessions of GMA therapy, the gut microbiota diversity in patients with UC increased and was similar to that of healthy controls. UC was further characterized by increased abundances of Proteobacteria and Bacteroides, as well as decreased abundances of Faecalibacterium, Roseburia, Firmicutes, and Dialister; however, after GMA therapy, the abundance of Bacteroides decreased, whereas those of Faecalibacterium, Roseburia, and Firmicutes increased. CONCLUSIONS: Active UC is associated with gut microbiota dysbiosis. GMA therapy exerts a strong regulatory effect on the gut microbiota in patients with UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35184056", + "title": "Preliminary Comparison of Endoscopic Brush and Net Catheters as the Sampling Tool to Analyze the Intestinal Mucus in the Rectum with Ulcerative Colitis Patients.", + "year": 2022, + "journal": "Digestion", + "authors": [ + "Nakamura M", + "Maeda K", + "Yamamoto K", + "Yamamura T", + "Sawada T", + "Ishikawa E", + "Kakushima N", + "Furukawa K", + "Iida T", + "Mizutani Y", + "Ishikawa T", + "Ohno E", + "Honda T", + "Ishigami M", + "Kawashima H" + ], + "bacteria": "Dialister", + "condition": "ulcerative colitis", + "relevance_score": 0.5484253849506656, + "mesh_terms": [ + "Catheters", + "Colitis, Ulcerative", + "Humans", + "Intestinal Mucosa", + "Mucus", + "RNA, Ribosomal, 16S", + "Rectum" + ], + "raw_abstract": "BACKGROUND: The pathophysiology of ulcerative colitis (UC) remains unclear, but early lesions on the colorectal mucosal surface may play an important role in its etiology. Intestinal mucus samples, including inner and outer layers, are collected by net or brush catheters, but the quality of the samples obtained by each method has not been fully investigated. OBJECTIVE: The purpose of this study was to compare the microbiome and protein content of intestinal mucus collected by net and brush catheters during colonoscopy. METHODS: Intestinal mucus samples from the lower rectum of 4 patients with UC were collected using a net catheter, a brush catheter, and intestinal fluid suction. Microbiome and protein content were analyzed using 16S rRNA gene sequencing and mass spectrometry. RESULTS: The patients demonstrated significant differences in microbiome alpha diversity (p < 0.05), but this difference was not observed between the sampling methods. Net catheter samples demonstrated higher total protein concentrations than brush catheter samples. The brush catheter group had more Lachnospira, a butyrate-producing bacterium, when compared to the net group. The brush catheter group also had more oral bacteria of Staphylococcus and Dialister in those with active phase when compared to the net group. CONCLUSIONS: Brush catheters are more likely to collect the intestinal mucus inner layer, whereas net catheters are more likely to collect larger samples that include the outer mucus layer, as well as the intestinal fluid. Two sampling methods with different types of collection of the mucosa may lead to different results among patients with mucosal vulnerabilities.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29311644", + "title": "Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.", + "year": 2018, + "journal": "Nature microbiology", + "authors": [ + "Schirmer M", + "Franzosa EA", + "Lloyd-Price J", + "McIver LJ", + "Schwager R", + "Poon TW", + "Ananthakrishnan AN", + "Andrews E", + "Barron G", + "Lake K", + "Prasad M", + "Sauk J", + "Stevens B", + "Wilson RG", + "Braun J", + "Denson LA", + "Kugathasan S", + "McGovern DPB", + "Vlamakis H", + "Xavier RJ", + "Huttenhower C" + ], + "bacteria": "Dialister", + "condition": "ulcerative colitis", + "relevance_score": 0.4825950383560378, + "mesh_terms": [ + "Adolescent", + "Adult", + "Child", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gene Expression Profiling", + "Humans", + "Inflammatory Bowel Diseases", + "Longitudinal Studies", + "Male", + "Metagenomics", + "Phenotype", + "Transcription, Genetic", + "Young Adult" + ], + "raw_abstract": "Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period. Here, we present the first results based on 78 paired faecal metagenomes\u00a0and\u00a0metatranscriptomes, and 222 additional metagenomes from 59 patients with Crohn's disease, 34 with ulcerative colitis and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, although many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microorganisms per host (for example, by Faecalibacterium prausnitzii). Thus, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Furthermore, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (for example, Dialister invisus). Last, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways that were predominantly expressed by different organisms in patients with IBD (for example, Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypical changes that are complementary to those linked to metagenomic abundances. The study's results highlight the strength of analysing both the activity and the presence of gut microorganisms to provide insight into the role of the microbiome in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28683448", + "title": "Gut Microbiota in Health, Diverticular Disease, Irritable Bowel Syndrome, and Inflammatory Bowel Diseases: Time for Microbial Marker of Gastrointestinal Disorders.", + "year": 2018, + "journal": "Digestive diseases (Basel, Switzerland)", + "authors": [ + "Lopetuso LR", + "Petito V", + "Graziani C", + "Schiavoni E", + "Paroni Sterbini F", + "Poscia A", + "Gaetani E", + "Franceschi F", + "Cammarota G", + "Sanguinetti M", + "Masucci L", + "Scaldaferri F", + "Gasbarrini A" + ], + "bacteria": "Dialister", + "condition": "ulcerative colitis", + "relevance_score": 0.4277484386282709, + "mesh_terms": [ + "Adult", + "Biomarkers", + "Diverticular Diseases", + "Female", + "Gastrointestinal Microbiome", + "Health", + "Humans", + "Inflammatory Bowel Diseases", + "Irritable Bowel Syndrome", + "Male", + "Middle Aged", + "Phylogeny", + "Principal Component Analysis", + "Species Specificity" + ], + "raw_abstract": "Few data exist on differences in gut microbiota composition among principal gastrointestinal (GI) diseases. We evaluated the differences in gut microbiota composition among uncomplicated diverticular disease (DD), irritable bowel syndrome (IBS) and inflammatory bowel diseases (IBD) patients. DD, IBS, and IBD patients along with healthy controls (CT) were enrolled in our Italian GI outpatient clinic. Stool samples were collected. Microbiota composition was evaluated through a metagenomic gene-targeted approach. GI pathology represented a continuous spectrum of diseases where IBD displayed one extreme, while CT displayed the other. Among Phyla, Biplot PC2/PC3 and dendogram plot showed major differences in samples from IBS and IBD. DD resembled species CT composition, but not for Bacteroides fragilis. In IBS, Dialister spp. and then Faecalibacterium prausnitzii were the most representative species. Ulcerative colitis showed a reduced concentration of Clostridium difficile and an increase of Bacteroides fragilis. In Crohn's disease, Parabacteroides distasonis was the most represented, while Faecalibacterium prausnitzii and Bacteroides fragilis were significantly reduced. Each disorder has its definite overall microbial signature, which produces a clear differentiation from the others. On the other hand, shared alterations constitute the \"core dysbiosis\" of GI diseases. The assessment of these microbial markers represents a parameter that may complete the diagnostic assessment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28852861", + "title": "Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.", + "year": 2018, + "journal": "Journal of gastroenterology", + "authors": [ + "Nishino K", + "Nishida A", + "Inoue R", + "Kawada Y", + "Ohno M", + "Sakai S", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Kawahara M", + "Naito Y", + "Andoh A" + ], + "bacteria": "Actinobacillus", + "condition": "ulcerative colitis", + "relevance_score": 0.7115498488149531, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Endoscopy, Gastrointestinal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. METHODS: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. RESULTS: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. \u03b1-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. CONCLUSIONS: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28842640", + "title": "Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients.", + "year": 2017, + "journal": "Scientific reports", + "authors": [ + "Santoru ML", + "Piras C", + "Murgia A", + "Palmas V", + "Camboni T", + "Liggi S", + "Ibba I", + "Lai MA", + "Orr\u00f9 S", + "Blois S", + "Loizedda AL", + "Griffin JL", + "Usai P", + "Caboni P", + "Atzori L", + "Manzin A" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7986079588356289, + "mesh_terms": [], + "raw_abstract": "Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract of uncertain origin, which includes ulcerative colitis (UC) and Crohn's disease (CD). The composition of gut microbiota may change in IBD affected individuals, but whether dysbiosis is the cause or the consequence of inflammatory processes in the intestinal tissue is still unclear. Here, the composition of the microbiota and the metabolites in stool of 183 subjects (82 UC, 50 CD, and 51 healthy controls) were determined. The metabolites content and the microbiological profiles were significantly different between IBD and healthy subjects. In the IBD group, Firmicutes, Proteobacteria, Verrucomicrobia, and Fusobacteria were significantly increased, whereas Bacteroidetes and Cyanobacteria were decreased. At genus level Escherichia, Faecalibacterium, Streptococcus, Sutterella and Veillonella were increased, whereas Bacteroides, Flavobacterium, and Oscillospira decreased. Various metabolites including biogenic amines, amino acids, lipids, were significantly increased in IBD, while others, such as two B group vitamins, were decreased in IBD compared to healthy subjects. This study underlines the potential role of an inter-omics approach in understanding the metabolic pathways involved in IBD. The combined evaluation of metabolites and fecal microbiome can be useful to discriminate between healthy subjects and patients with IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34404881", + "title": "Immunoglobulin subtype-coated bacteria are correlated with the disease activity of inflammatory bowel disease.", + "year": 2021, + "journal": "Scientific reports", + "authors": [ + "Masu Y", + "Kanazawa Y", + "Kakuta Y", + "Shimoyama Y", + "Onodera M", + "Naito T", + "Moroi R", + "Kuroha M", + "Kimura T", + "Shiga H", + "Kinouchi Y", + "Masamune A" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.776801588781772, + "mesh_terms": [ + "Adult", + "Antibodies, Bacterial", + "Bacteria", + "Feces", + "Female", + "Humans", + "Immunoglobulin A", + "Immunoglobulin G", + "Immunoglobulin Isotypes", + "Immunoglobulin M", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged" + ], + "raw_abstract": "Immune response involving various immunoglobulin (Ig) isotypes and subtypes to microbiome is involved in the pathogenesis and disease activity of inflammatory bowel diseases (IBDs). To clarify the presence of Ig-coated bacteria in the intestine and its association with disease activity in ulcerative colitis (UC) and Crohn's disease (CD), we extracted and classified Ig-coated bacteria from fecal samples of 42 patients with IBD and 12 healthy controls (HCs) using flow cytometry and 16S ribosomal RNA sequence analysis. The percentage of bacteria coated with IgA and IgM was higher in patients with IBD than in HCs, and IgG-coated bacteria were found only in patients with IBD. Moreover, the percentages of bacteria coated with IgG1, IgG2, IgG3, and IgM in UC samples and IgG3, IgG4, and IgM in CD samples were correlated with disease activities. The proportions of Bacteroides ovatus and Streptococcus increased during the active phase of CD. Hence, the detailed analysis of Ig-coated bacteria and Ig subtypes using flow cytometry could aid in developing useful indicators of disease activity and identifying more disease-related bacteria, which could become novel treatment targets for IBDs.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34111242", + "title": "Alteration in Urease-producing Bacteria in the Gut Microbiomes of Patients with Inflammatory Bowel Diseases.", + "year": 2021, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Ryvchin R", + "Dubinsky V", + "Rabinowitz K", + "Wasserberg N", + "Dotan I", + "Gophna U" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7544071644238234, + "mesh_terms": [ + "Case-Control Studies", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Streptococcus", + "Urease" + ], + "raw_abstract": "BACKGROUND AND AIMS: Bacterial urease is a major virulence factor of human pathogens, and murine models have shown that it can contribute to the pathogenesis of inflammatory bowel diseases [IBD]. METHODS: The distribution of urease-producing bacteria in IBD was assessed using public faecal metagenomic data from various cohorts, including non-IBD controls [n = 55], patients with Crohn's disease [n = 291] or ulcerative colitis [n = 214], and patients with a pouch [n = 53]. The ureA gene and the taxonomic markers gyrA, rpoB, and recA were used to estimate the percentage of urease producers in each sample. RESULTS: Levels of urease producers in patients with IBD and non-IBD controls were comparable. In non-IBD controls and most IBD patients, urease producers were primarily acetate-producing genera such as Blautia and Ruminococcus. A shift in the type of the dominant urease producers towards Proteobacteria and Bacilli was observed in a subset of all IBD subtypes, which correlated with faecal calprotectin levels in one cohort. Some patients with IBD had no detectable urease producers. In patients with a pouch, the probiotic-associated species Streptococcus thermophilus was more common as a main urease producer than in other IBD phenotypes, and it generally did not co-occur with other Bacilli or with Proteobacteria. CONCLUSIONS: Unlike all non-IBD controls, patients with IBD often showed a shift towards Bacilli or Proteobacteria or a complete loss of urease production. Probiotics containing the species S. thermophilus may have a protective effect against colonisation by undesirable urease-producing bacteria in a subset of patients with a pouch.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39026313", + "title": "Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease.", + "year": 2024, + "journal": "Microbiome", + "authors": [ + "Tian X", + "Li S", + "Wang C", + "Zhang Y", + "Feng X", + "Yan Q", + "Guo R", + "Wu F", + "Wu C", + "Wang Y", + "Huo X", + "Ma X" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7398748548914773, + "mesh_terms": [ + "Humans", + "Virome", + "Gastrointestinal Microbiome", + "Animals", + "Feces", + "Mice", + "Inflammatory Bowel Diseases", + "Female", + "Male", + "Adult", + "Middle Aged", + "Crohn Disease", + "Bacteriophages", + "Colitis, Ulcerative", + "Bacteria", + "China", + "Fecal Microbiota Transplantation", + "Case-Control Studies", + "Viruses" + ], + "raw_abstract": "BACKGROUND: The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS: In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella\u00a0species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS: Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33352216", + "title": "Changes in intestinal microbiota and correlation with TLRs in ulcerative colitis in the coastal area of northern China.", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Xu N", + "Bai X", + "Cao X", + "Yue W", + "Jiang W", + "Yu Z" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6704919320648388, + "mesh_terms": [ + "China", + "Colitis, Ulcerative", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: To investigate the communities of fecal microbiota and the role of Toll-like receptors in patients with ulcerative colitis in the coastal area of northern China. METHODS: Stool samples from 31 patients with ulcerative colitis and 12 healthy individuals were collected. The total bacterial genomic DNA was extracted, and the V3+V4 hypervariable region in the bacterial 16S rRNA gene sequence was amplified by polymerase chain reaction (PCR). High-throughput sequencing analysis was performed on the Illumina Hiseq platform. The expression of TLR2, TLR4, Tollip, PPAR-\u03b3, IL-6, and TNF-\u03b1 in the colonic mucosa was measured by Western blots. RESULTS: The diversity of the fecal microbiota in patients with ulcerative colitis was significantly less than that in healthy control individuals (p\u00a0<\u00a00.05). The proportion of Bacteroidetes was significantly reduced (p\u00a0<\u00a00.01), whereas Proteobacteria was prevalent (p\u00a0<\u00a00.01) in patients with ulcerative colitis. At the genus level, the relative abundance of Streptococcus and Anaerostipes was significantly increased (p\u00a0<\u00a00.05), whereas the proportion of Bacteroides, Lachnospira, Ruminococcus, Phascolarctobacterium, and Coprococcus was significantly decreased in patients with ulcerative colitis (p\u00a0<\u00a00.05). The diversity indexes of fecal microbiota in patients with ulcerative colitis were negatively correlated with disease severity (p\u00a0<\u00a00.05). The relative abundance of Enterobacteriaceae was positively correlated with disease severity, and the relative abundance of Phascolarctobacterium, Anaerostipes, Fusobacterium, Parabacteroides, Oscillospira, and Ochrobactrum were negatively correlated with disease severity. The expression levels of TLR2 and TLR4 in the intestinal mucosa were positively correlated with the relative abundance of Streptococcus and Enterobacteriaceae, respectively (r\u00a0=\u00a00.481, p\u00a0=\u00a00.007; r\u00a0=\u00a00.455, p\u00a0=\u00a00.017). CONCLUSION: There were significant changes in the diversity and composition of the fecal microbiota in patients with ulcerative colitis compared to healthy individuals. The dysbiosis of gut microbiota and correlation with TLRs might play important roles in the pathogenesis and progression of ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37696680", + "title": "Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Del Chierico F", + "Cardile S", + "Baldelli V", + "Alterio T", + "Reddel S", + "Bramuzzo M", + "Knafelz D", + "Lega S", + "Bracci F", + "Torre G", + "Maggiore G", + "Putignani L" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6497302845846373, + "mesh_terms": [ + "Humans", + "Child", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Cholangitis, Sclerosing", + "Dysbiosis", + "RNA, Ribosomal, 16S", + "Bacteria", + "Bacteroidetes", + "Italy" + ], + "raw_abstract": "BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis. METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs). RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients. CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC. In this study, we report the gut microbiota and mycobiota dysbiosis in pediatric patients affected by primary sclerosing cholangitis (PSC) associated with ulcerative colitis (UC), with an increase in pro-inflammatory pathobionts and a reduction in anti-inflammatory commensals.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29126267", + "title": "Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis.", + "year": 2017, + "journal": "FEMS microbiology ecology", + "authors": [ + "Mancabelli L", + "Milani C", + "Lugli GA", + "Turroni F", + "Cocconi D", + "van Sinderen D", + "Ventura M" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6374957297651715, + "mesh_terms": [ + "Bacteria", + "Biodiversity", + "Biomarkers", + "Colitis, Ulcerative", + "Crohn Disease", + "Enterocolitis, Pseudomembranous", + "Gastrointestinal Microbiome", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Intestines", + "Polymerase Chain Reaction", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Intestinal diseases, such as Crohn's disease (CD), ulcerative colitis (UC) and pseudomembranous colitis (CDI), are among the most common diseases in humans and may lead to more serious pathologies, e.g. colorectal cancer (CRC). Next generation sequencing has in recent years allowed the identification of correlations between intestinal bacteria and diseases, although the formulation of universal gut microbial biomarkers for such diseases is only in its infancy. In the current study, we selected and reanalyzed a total of 3048 public datasets obtained from 16S rRNA profiling of individuals affected by CD, UC, CDI and CRC. This meta-analysis revealed possible biases in the reconstruction of the gut microbiota composition due to the use of different primer pairs employed for PCR of 16S rRNA gene fragments. Notably, this approach also identified common features of individuals affected by gut diseases (DS), including lower biodiversity compared to control subjects. Moreover, potential universal intestinal disease microbial biomarkers were identified through cross-disease comparisons. In detail, CTRL showed high abundance of the genera Barnesiella, Ruminococcaceae UCG-005, Alistipes, Christensenellaceae R-7 group and unclassified member of Lachnospiraceae family, while DS exhibited high abundance of Lactobacillus, unclassified member of Erysipelotrichaceae family and Streptococcus genera.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34427649", + "title": "Antitumor Necrosis Factor-like Ligand 1A Therapy Targets Tissue Inflammation and Fibrosis Pathways and Reduces Gut Pathobionts in Ulcerative Colitis.", + "year": 2022, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Hassan-Zahraee M", + "Ye Z", + "Xi L", + "Baniecki ML", + "Li X", + "Hyde CL", + "Zhang J", + "Raha N", + "Karlsson F", + "Quan J", + "Ziemek D", + "Neelakantan S", + "Lepsy C", + "Allegretti JR", + "Romatowski J", + "Scherl EJ", + "Klopocka M", + "Danese S", + "Chandra DE", + "Schoenbeck U", + "Vincent MS", + "Longman R", + "Hung KE" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6337459224103871, + "mesh_terms": [ + "Colitis, Ulcerative", + "Fibrosis", + "Humans", + "Inflammation", + "Ligands", + "Necrosis", + "Proteomics", + "Tumor Necrosis Factor Ligand Superfamily Member 15" + ], + "raw_abstract": "BACKGROUND: The first-in-class treatment PF-06480605 targets the tumor necrosis factor-like ligand 1A (TL1A) molecule in humans. Results from the phase 2a TUSCANY trial highlighted the safety and efficacy of PF-06480605 in ulcerative colitis. Preclinical and in vitro models have identified a role for TL1A in both innate and adaptive immune responses, but the mechanisms underlying the efficacy of anti-TL1A treatment in inflammatory bowel disease (IBD) are not known. METHODS: Here, we provide analysis of tissue transcriptomic, peripheral blood proteomic, and fecal metagenomic data from the recently completed phase 2a TUSCANY trial and demonstrate endoscopic improvement post-treatment with PF-06480605 in participants with ulcerative colitis. RESULTS: Our results revealed robust TL1A target engagement in colonic tissue and a distinct colonic transcriptional response reflecting a reduction in inflammatory T helper 17 cell, macrophage, and fibrosis pathways in patients with endoscopic improvement. Proteomic analysis of peripheral blood revealed a corresponding decrease in inflammatory T-cell cytokines. Finally, microbiome analysis showed significant changes in IBD-associated pathobionts, Streptococcus salivarius, S. parasanguinis, and Haemophilus parainfluenzae post-therapy. CONCLUSIONS: The ability of PF-06480605 to engage and inhibit colonic TL1A, targeting inflammatory T cell and fibrosis pathways, provides the first-in-human mechanistic data to guide anti-TL1A therapy for the treatment of IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31333315", + "title": "Gut microbiota contributes to the distinction between two traditional Chinese medicine syndromes of ulcerative colitis.", + "year": 2019, + "journal": "World journal of gastroenterology", + "authors": [ + "Zhang YL", + "Cai LT", + "Qi JY", + "Lin YZ", + "Dai YC", + "Jiao N", + "Chen YL", + "Zheng L", + "Wang BB", + "Zhu LX", + "Tang ZP", + "Zhu RX" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.55876227166398, + "mesh_terms": [ + "Adult", + "Bacteria", + "Colitis, Ulcerative", + "Colon", + "DNA, Bacterial", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Male", + "Medicine, Chinese Traditional", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Retrospective Studies", + "Syndrome" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is considered to be closely associated with alteration of intestinal microorganisms. According to the traditional Chinese medicine (TCM) theory, UC can be divided into two disease syndromes called Pi-Xu-Shi-Yun (PXSY) and Da-Chang-Shi-Re (DCSR). The relationships among gut microbiota, TCM syndromes, and UC pathogenesis have not been well investigated. AIM: To investigate the role of gut microbiota in UC and the distinction of microbiota dysbiosis between PXSY and DCSR syndromes. METHODS: From May 2015 to February 2016, UC patients presenting to LongHua Hospital who met the established inclusion and exclusion criteria were enrolled in this retrospective study. Fresh stool specimens of UC patients with PXSY or DCSR were collected. The feces of the control group came from the health examination population of Longhua Hospital. The composition of gut bacterial communities in stool samples was determined by the pyrosequencing of 16S ribosomal RNA. The high-throughput sequencing reads were processed with QIIME, and biological functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. RESULTS: The composition of gut bacterial communities in 93 stool samples (30 healthy controls, 32 patients with PXSY syndrome, and 31 patients with DCSR syndrome) was determined by the pyrosequencing of 16S ribosomal RNA. Beta diversity showed that the composition of the microbiota was different among the three groups. At the family level, Porphyromonadaceae, Rikeneliaceae, and Lachnospiraceae significantly decreased while Enterococcus, Streptococcus, and other potential pathogens significantly increased in UC patients compared to healthy subjects. At the genus level, CONCLUSION: Our study suggests that the gut microbiota contributes to the distinction between the two TCM syndromes of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37280117", + "title": "Gut Microbiota Signatures Are Associated With Psychopathological Profiles in Patients With Ulcerative Colitis: Results From an Italian Tertiary IBD Center.", + "year": 2023, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Scaldaferri F", + "D'Onofrio AM", + "Calia R", + "Di Vincenzo F", + "Ferrajoli GF", + "Petito V", + "Maggio E", + "Pafundi PC", + "Napolitano D", + "Masi L", + "Schiavoni E", + "Fanali C", + "Puca P", + "Turchini L", + "Lopetuso LR", + "Del Chierico F", + "Putignani L", + "Gasbarrini A", + "Camardese AG" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5447925242892918, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Longitudinal Studies", + "Depressive Disorder, Major", + "Prospective Studies", + "Quality of Life", + "Bacteria" + ], + "raw_abstract": "BACKGROUND: Several patients with ulcerative colitis (UC) suffer from psychiatric disorders, such as major depressive disorder, anxiety, or bipolar disorder, and show specific personality traits. Despite this, there are few data about personality profiles' characterization in UC patients and about correlation of their psychopathological profile with their intestinal microbiota.The aim of our study is to analyze the psychopathological and personality profile of UC patients and correlate it with specific signatures of their gut microbiota. METHODS: This is a prospective interventional longitudinal cohort study. We enrolled consecutive patients affected by UC attending to the IBD Unit of Center for Digestive Disease of \"A. Gemelli\" IRCCS Hospital in Rome and a group of healthy subjects, matched for specific characteristics. Each patient was evaluated by a gastroenterologist and a psychiatrist. Moreover, all participants underwent psychological tests and a collection of stool samples. RESULTS: We recruited 39 UC patients and 37 healthy subjects. Most patients showed high level of alexithymia, anxiety symptoms, depressive symptoms, as well as neuroticism and hypochondria, with obsessive-compulsive features at the behavioral level, which significantly impaired their quality of life and abilities at work. Gut microbiota analysis in UC patients demonstrated an increase in actinobacteria, Proteobacteria and Saccharibacteria (TM7), with a reduction in verrucomicrobia, euryarchaeota and tenericutes. CONCLUSIONS: Our study confirmed the presence of high levels of psycho-emotional distress in UC patients, alongside alterations of the intestinal microbiota, and highlighted some families and genera of bacteria (Enterobacteriaceae, Streptococcus, Veillonella, Klebsiella, and Clostridiaceae) as potential markers of an altered gut-brain axis in these patients. Psychiatric disorders are more prevalent in IBD patients than in general population. In this prospective cohort study, we found a correlation between active UC, peculiar psychiatric distress (anxiety and depression above all), and specific taxonomic gut microbiota signatures.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31771630", + "title": "A distinct gut microbiota composition in patients with ankylosing spondylitis is associated with increased levels of fecal calprotectin.", + "year": 2019, + "journal": "Arthritis research & therapy", + "authors": [ + "Klingberg E", + "Magnusson MK", + "Strid H", + "Deminger A", + "St\u00e5hl A", + "Sundin J", + "Simr\u00e9n M", + "Carlsten H", + "\u00d6hman L", + "Forsblad-d'Elia H" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5059332859215979, + "mesh_terms": [ + "Adult", + "Bacteria", + "C-Reactive Protein", + "Colitis, Ulcerative", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Middle Aged", + "Population Dynamics", + "Spondylitis, Ankylosing", + "Surveys and Questionnaires", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Ankylosing spondylitis (AS) shares many characteristics with inflammatory bowel disease (IBD). Intestinal microbiota most likely plays an important role in the development of IBDs and may also be involved in the pathogenesis of AS. We aimed to define and compare the fecal microbiota composition in patients with AS, ulcerative colitis (UC), and healthy controls (HC) and to determine relationships between fecal microbiota, fecal calprotectin, and disease-related variables in AS. METHODS: Fecal microbiota composition was assessed with GA-map\u2122 Dysbiosis Test (Genetic Analysis, Oslo, Norway), which also reports the degree of deviation of the microbiota composition compared with a healthy control population, a Dysbiosis Index (DI) score 1-5. The AS patients were assessed with questionnaires, back mobility tests, fecal calprotectin, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP). RESULTS: Totally, 150 patients with AS (55% men, median age 55.5\u2009years, median BASDAI 3.2), 18 patients with UC (56% men, median age 30.5\u2009years), and 17 HC (65% men, median age 22\u2009years) were included. Principal component analysis showed highly separate clustering of fecal microbiota from the patients with AS, UC, and HC. Compared with HC, fecal microbiota in AS was characterized by a higher abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcus species, and Actinobacteria, but lower abundance of Bacteroides and Lachnospiraceae. Further, fecal microbiota composition differed between patients with normal (\u2264\u200950\u2009mg/kg, n\u2009=\u200957) and increased (\u2265\u2009200\u2009mg/kg, n\u2009=\u200936) fecal calprotectin. Patients with increased fecal calprotectin had lower abundance of bacteria with anti-inflammatory properties such as Faecalibacterium prausnitzii and Clostridium and higher abundance of the genus Streptococcus. No association was found between the fecal microbiota composition and HLAB27 status, disease activity, function, or medication. Dysbiosis (defined as DI\u2009\u2265\u20093) was found in 87% of AS patients. CONCLUSIONS: Patients with AS have a distinct fecal microbiota signature, which is linked to fecal calprotectin levels, a marker of intestinal inflammation, but not to other clinical parameters. These findings suggest a local interplay between intestinal microbiota and gut inflammation in AS. TRIAL REGISTRATION: ClinicalTrials.gov, NCT00858819. Registered March 9, 2009.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36634565", + "title": "The gut microbiota and metabolome are associated with diminished COVID-19 vaccine-induced antibody responses in immunosuppressed inflammatory bowel disease patients.", + "year": 2023, + "journal": "EBioMedicine", + "authors": [ + "Alexander JL", + "Mullish BH", + "Danckert NP", + "Liu Z", + "Olbei ML", + "Saifuddin A", + "Torkizadeh M", + "Ibraheim H", + "Blanco JM", + "Roberts LA", + "Bewshea CM", + "Nice R", + "Lin S", + "Prabhudev H", + "Sands C", + "Horneffer-van der Sluis V", + "Lewis M", + "Sebastian S", + "Lees CW", + "Teare JP", + "Hart A", + "Goodhand JR", + "Kennedy NA", + "Korcsmaros T", + "Marchesi JR", + "Ahmad T", + "Powell N" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.39013270817304896, + "mesh_terms": [ + "Humans", + "COVID-19 Vaccines", + "Antibody Formation", + "Gastrointestinal Microbiome", + "ChAdOx1 nCoV-19", + "BNT162 Vaccine", + "Infliximab", + "RNA, Ribosomal, 16S", + "Tumor Necrosis Factor Inhibitors", + "COVID-19", + "SARS-CoV-2", + "Inflammatory Bowel Diseases", + "Metabolome" + ], + "raw_abstract": "BACKGROUND: Patients with inflammatory bowel disease (IBD) treated with anti-TNF therapy exhibit attenuated humoral immune responses to vaccination against SARS-CoV-2. The gut microbiota and its functional metabolic output, which are perturbed in IBD, play an important role in shaping host immune responses. We explored whether the gut microbiota and metabolome could explain variation in anti-SARS-CoV-2 vaccination responses in immunosuppressed IBD patients. METHODS: Faecal and serum samples were prospectively collected from infliximab-treated patients with IBD in the CLARITY-IBD study undergoing vaccination against SARS-CoV-2. Antibody responses were measured following two doses of either ChAdOx1 nCoV-19 or BNT162b2 vaccine. Patients were classified as having responses above or below the geometric mean of the wider CLARITY-IBD cohort. 16S rRNA gene amplicon sequencing, nuclear magnetic resonance (NMR) spectroscopy and bile acid profiling with ultra-high-performance liquid chromatography mass spectrometry (UHPLC-MS) were performed on faecal samples. Univariate, multivariable and correlation analyses were performed to determine gut microbial and metabolomic predictors of response to vaccination. FINDINGS: Forty-three infliximab-treated patients with IBD were recruited (30 Crohn's disease, 12 ulcerative colitis, 1\u00a0IBD-unclassified; 26 with concomitant thiopurine therapy). Eight patients had evidence of prior SARS-CoV-2 infection. Seventeen patients (39.5%) had a serological response below the geometric mean. Gut microbiota diversity was lower in below average responders (p\u00a0=\u00a00.037). Bilophila abundance was associated with better serological response, while Streptococcus was associated with poorer response. The faecal metabolome was distinct between above and below average responders (OPLS-DA R INTERPRETATION: Our data suggest that there is an association between the gut microbiota and variable serological response to vaccination against SARS-CoV-2 in immunocompromised patients. Microbial metabolites including trimethylamine may be important in mitigating anti-TNF-induced attenuation of the immune response. FUNDING: JLA is the recipient of an NIHR Academic Clinical Lectureship (CL-2019-21-502), funded by Imperial College London and The Joyce and Norman Freed Charitable Trust. BHM is the recipient of an NIHR Academic Clinical Lectureship (CL-2019-21-002). The Division of Digestive Diseases at Imperial College London receives financial and infrastructure support from the NIHR Imperial Biomedical Research Centre (BRC) based at Imperial College Healthcare NHS Trust and Imperial College London. Metabolomics studies were performed at the MRC-NIHR National Phenome Centre at Imperial College London; this work was supported by the Medical Research Council (MRC), the National Institute of Health Research (NIHR) (grant number MC_PC_12025) and infrastructure support was provided by the NIHR Imperial Biomedical Research Centre (BRC). The NIHR Exeter Clinical Research Facility is a partnership between the University of Exeter Medical School College of Medicine and Health, and Royal Devon and Exeter NHS Foundation Trust. This project is supported by the National Institute for Health Research (NIHR) Exeter Clinical Research Facility. The views expressed are those of the authors and not necessarily those of the NIHR or the UK Department of Health and Social Care.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31605691", + "title": "Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy.", + "year": 2020, + "journal": "Gastroenterology", + "authors": [ + "Dubinsky V", + "Reshef L", + "Bar N", + "Keizer D", + "Golan N", + "Rabinowitz K", + "Godny L", + "Yadgar K", + "Zonensain K", + "Tulchinsky H", + "Gophna U", + "Dotan I" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.3791447419293631, + "mesh_terms": [ + "Adult", + "Anti-Bacterial Agents", + "Bacteria", + "Ciprofloxacin", + "Cytokines", + "Drug Resistance, Bacterial", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "HT29 Cells", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Metagenomics", + "Metronidazole", + "Middle Aged", + "Point Mutation", + "Pouchitis", + "Prospective Studies", + "Recurrence", + "Treatment Outcome", + "Virulence Factors", + "Young Adult" + ], + "raw_abstract": "BACKGROUND & AIMS: Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic-dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial factors associated with response to antibiotic treatment and development of antibiotic dependence in patients with pouchitis. METHODS: We performed a prospective study of 49 patients who had undergone pouch surgery at a tertiary center. Disease activity was determined based on clinical, endoscopic, and histologic criteria. Pouch phenotype was defined as recurrent-acute pouchitis (n\u00a0= 6), chronic pouchitis and Crohn's-like disease of the pouch (n\u00a0= 27), normal pouch from patient with ulcerative colitis (n\u00a0= 10), and normal pouch from patient with familial adenomatous polyposis (n\u00a0= 6). Fecal samples (n\u00a0= 234) were collected over time during or in the absence of antibiotic treatment (ciprofloxacin and/or metronidazole). Thirty-three patients were treated with antibiotics, for a median of 425 days of cumulative antibiotic therapy, during follow-up. Calprotectin was measured and fecal DNA was sequenced using shotgun metagenomics and analyzed with specifically designed bioinformatic pipelines. Bacterial strains were isolated from fecal samples. We assessed their ciprofloxacin resistance and ability to induce secretion of inflammatory cytokines by HT-29 intestinal epithelial cells. RESULTS: Most antibiotic-treated patients (79%) had a clinical response to each course of antibiotics; however, 89% of those who completed a 4-week course relapsed within 3 months. Median calprotectin levels decreased by 40% in response to antibiotics. Antibiotic treatment reduced disease-associated bacteria such as Clostridium perfringens, Ruminococcus gnavus, and Klebsiella pneumoniae, but also beneficial species, such as Faecalibacterium prausnitzii. The microbiomes of antibiotic-responsive patients were dominated by facultative anaerobic genera (Escherichia, Enterococcus, and Streptococcus), with multiple ciprofloxacin-resistance mutations in drug target genes and confirmed drug resistance. However, these strains had lower potential for virulence and did not induce secretion of inflammatory cytokines by epithelial cells. After antibiotic cessation, patients had an abrupt shift in microbiome composition, with blooms of oral and disease-associated bacteria. In addition, antibiotic treatment enriched for strains that acquired multidrug resistance loci, encoding enzymes that confer resistance to nonrelated antibiotics, including extended-spectrum beta-lactamases. CONCLUSIONS: The efficacy of antibiotic treatment of pouchitis might be attributed to the establishment of an antibiotic-resistant microbiome with low inflammatory potential. This microbiome might provide resistance against colonization by bacteria that promote inflammation. To avoid progression to antibiotic-dependent disease and its consequences, strategies such as short-term alternating antibiotics and nutrition- and microbiome-based interventions should be considered.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29915396", + "title": "Probiotics in Gastroenterology: How Pro Is the Evidence in Adults?", + "year": 2018, + "journal": "The American journal of gastroenterology", + "authors": [ + "Koretz RL" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.37540605325837434, + "mesh_terms": [ + "Adult", + "Gastroenterology", + "Gastrointestinal Diseases", + "Humans", + "Practice Guidelines as Topic", + "Probiotics", + "Randomized Controlled Trials as Topic" + ], + "raw_abstract": "Probiotic usage has become popular with both medical practitioners and the community in general; patients commonly seek advice regarding what, if any, such preparation would be useful for their own diseases. Since such advice should be evidence-based, identified randomized clinical trials (RCTs) for a number of gastrointestinal conditions were reviewed; the data were organized by individual probiotic genera/species. Only trials in adults were considered. Most of the identified RCTs were small and low-quality, so any conclusions to be drawn will be limited at least by methodologic problems. Using the GRADE system to consider the reliability of the evidence generated from these RCTs, it did appear that the use of fecal microbial transplantation to treat recurrent Clostridium difficile infection is well justified. Given the methodologic issues, there was moderately good evidence for preventing antibiotic-associated diarrhea with Lactobacillus, Bifidobacterium, Streptococcus, or Saccharomyces boulardii and for using Lactobacillus, Bifidobacterium, or Saccharomyces as adjunct therapy in the treatment of Helicobacter pylori. There were other conditions for which some supportive evidence was available. These conditions include VSL#3 for maintaining remissions in patients with pouchitis or treating active ulcerative colitis (UC), fecal microbial transplantation for treating active UC, Bifidobacterium for treating patients with UC in remission, Lactobacillus in patients with painful diverticulosis, a variety of probiotics (Lactobacillus, Bifidobacterium, Streptococcus, or VSL#3) in patients with minimal hepatic encephalopathy, and providing synbiotics to patients postoperatively after liver transplantation. Unfortunately, other limitations in the evidence made it very likely that future research will have an effect on the estimated benefit; these interventions cannot yet be recommended for routine use.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32017001", + "title": "Effects of mesalazine combined with bifid triple viable on intestinal flora, immunoglobulin and levels of cal, MMP-9, and MPO in feces of patients with ulcerative colitis.", + "year": 2020, + "journal": "European review for medical and pharmacological sciences", + "authors": [ + "Jiang XE", + "Yang SM", + "Zhou XJ", + "Zhang Y" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.2937316490716622, + "mesh_terms": [ + "Adult", + "Anti-Inflammatory Agents, Non-Steroidal", + "Colitis, Ulcerative", + "Combined Modality Therapy", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Immunity, Cellular", + "Immunoglobulins", + "Intestinal Mucosa", + "Leukocyte L1 Antigen Complex", + "Male", + "Matrix Metalloproteinase 9", + "Mesalamine", + "Middle Aged", + "Peroxidase", + "Probiotics", + "Treatment Outcome" + ], + "raw_abstract": "OBJECTIVE: Ulcerative colitis (UC) commonly occurs in young and middle-aged people and is characterized by frequent attacks and difficult cure. Mesalazine is often applied in the initial treatment of UC, but it can lead to serious adverse effects. Its combination with bifid triple viable could mitigate adverse effects. This study aims to explore the effects of mesalazine combined with bifid triple viable on the intestinal flora, immunoglobulin (Ig), and levels of calprotectin (Cal), matrix metalloproteinase-9 (MMP-9), myeloperoxidase (MPO) in feces of UC patients. PATIENTS AND METHODS: A total of 180 UC patients in our hospital were divided into two groups with 90 cases in each one. Patients in control group were treated with oral mesalazine (1.5 g/d), and those in the treatment group were treated with oral mesalazine (1.5 g/d) combined with bifid triple viable (1.26 g/d) for 2 months. Treatment effects in both groups following the therapeutic period were observed accordingly. Feces of patients in the two groups were collected for detecting intestinal microorganism and the levels of Cal, MMP-9, and MPO. Serum levels of IgG, IgA, and IgM in each patient were detected by enzyme-linked immunosorbent assay (ELISA). RESULTS: The overall response rate of the treatment group (91.11%) was significantly higher than that of control group (68.89%; p=0.000). The abundances of intestinal microflora, including Bifidobacterium, Actinomycetes, Rikenellaceae, Genus VI of Acidaminococcaceae, and Metascardovia in treatment group were remarkably higher than those in control group. The abundances of intestinal microorganisms such as Phocaeicola, Lawsonia intracelluaris, Streptococcus, Ruminococcaceae, and Clostridium in control group were significantly higher than those in treatment group. After treatment, serum levels of IgG and IgM of patients in treatment group were lower than those in control group, with IgG of (15.14\u00b10.98) (p=0.031) and IgM of (1.50\u00b10.18) (p=0.000). No statistical difference in IgG level was observed between treatment group and control group after treatment (p=0.871). After treatment, the levels of Cal and MMP-9 in feces of patients in treatment group were significantly lower than those in control group with Cal of (79.81\u00b15.42) (p=0.000) and MMP-9 of (4.89\u00b10.98) (p=0.000). There was no statistical difference in the MPO level between treatment group and control group after treatment (p=0.871). CONCLUSIONS: Mesalazine combined with bifid triple viable is able to enhance the curative effect for UC, improve the composition of intestinal flora, weaken the immune response, and reduce levels of Cal and MMP-9 in the intestinal tract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32383181", + "title": "A disease-specific decline of the relative abundance of Bifidobacterium in patients with autoimmune hepatitis.", + "year": 2020, + "journal": "Alimentary pharmacology & therapeutics", + "authors": [ + "Liwinski T", + "Casar C", + "Ruehlemann MC", + "Bang C", + "Sebode M", + "Hohenester S", + "Denk G", + "Lieb W", + "Lohse AW", + "Franke A", + "Schramm C" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.2794166419286227, + "mesh_terms": [ + "Adult", + "Aged", + "Bacterial Load", + "Bifidobacterium", + "Case-Control Studies", + "Cohort Studies", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Hepatitis, Autoimmune", + "Humans", + "Liver Cirrhosis, Biliary", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: The pathogenesis of autoimmune hepatitis (AIH) is poorly understood and little is known about enteric microbiota in AIH. AIM: To investigate disease-specific microbiome alterations in AIH. METHODS: The V1-V2 variable regions of the 16S rRNA gene were sequenced in faecal samples from 347 patients with AIH and controls (AIH n\u00a0=\u00a072, healthy controls (HC) n\u00a0=\u00a095, primary biliary cholangitis (PBC) n\u00a0=\u00a099 and ulcerative colitis (UC) n\u00a0=\u00a081). RESULTS: Biodiversity (Shannon entropy) was decreased in AIH patients compared to HC (P\u00a0=\u00a00.016), which was partially reversed by azathioprine (P\u00a0=\u00a00.011). Regarding between-sample diversity, AIH patients separated from HC, PBC and UC individuals (all P\u00a0=\u00a00.001). Compared to HC, decreased relative abundance of anaerobic genera such as Faecalibacterium and an increase of Veillonella and the facultative anaerobic genera Streptococcus and Lactobacillus were detected. Importantly, a disease-specific decline of relative abundance of Bifidobacterium was observed in AIH patients. Lack of Bifidobacterium was associated with failure to achieve remission of AIH (P\u00a0<\u00a00.001). Of potential therapeutic implication, Bifidobacterium abundance correlated with average protein intake (P\u00a0<\u00a00.001). Random forests classification between AIH and PBC on the microbiome signature yielded an area under receiver operating characteristic curve (AUC) of 0.787 in the training cohort, and an AUC of 0.849 in an external validation cohort. CONCLUSION: Disease-specific faecal microbial alterations were identified in patients with AIH. Intestinal dysbiosis in AIH was characterised by a decline of Bifidobacterium, which was associated with increased disease activity. These results point to the contribution of intestinal microbiota to AIH pathogenesis and to novel therapeutic targets.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26019464", + "title": "Effectiveness of probiotic therapy for the prevention of relapse in patients with inactive ulcerative colitis.", + "year": 2015, + "journal": "World journal of gastroenterology", + "authors": [ + "Yoshimatsu Y", + "Yamada A", + "Furukawa R", + "Sono K", + "Osamura A", + "Nakamura K", + "Aoki H", + "Tsuda Y", + "Hosoe N", + "Takada N", + "Suzuki Y" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.2749429112904593, + "mesh_terms": [ + "Adult", + "Bacillus", + "Chromatography, High Pressure Liquid", + "Clostridium butyricum", + "Cluster Analysis", + "Colitis, Ulcerative", + "Colon", + "DNA, Bacterial", + "Double-Blind Method", + "Enterococcus faecalis", + "Feces", + "Female", + "Humans", + "Japan", + "Kaplan-Meier Estimate", + "Male", + "Middle Aged", + "Probiotics", + "Recurrence", + "Remission Induction", + "Ribotyping", + "Time Factors", + "Treatment Outcome" + ], + "raw_abstract": "AIM: To evaluate the effectiveness of probiotic therapy for suppressing relapse in patients with inactive ulcerative colitis (UC). METHODS: Bio-Three tablets, each containing 2 mg of lactomin (Streptococcus faecalis T-110), 10 mg of Clostridium butyricum TO-A, and 10 mg of Bacillus mesentericus TO-A, were used as probiotic therapy. Sixty outpatients with UC in remission were randomly assigned to receive 9 Bio-Three tablets/day (Bio-Three group) or 9 placebo tablets/day (placebo group) for 12 mo in addition to their ongoing medications. Clinical symptoms were evaluated monthly or on the exacerbation of symptoms or need for additional medication. Fecal samples were collected to analyze bacterial DNA at baseline and 3-mo intervals. Terminal restriction fragment length polymorphism and cluster analyses were done to examine bacterial components of the fecal microflora. RESULTS: Forty-six patients, 23 in each group, completed the study, and 14 were excluded. The relapse rates in the Bio-Three and placebo groups were respectively 0.0% vs 17.4% at 3 mo (P = 0.036), 8.7% vs 26.1% at 6 mo (P = 0.119), and 21.7% vs 34.8% (P = 0.326) at 9 mo. At 12 mo, the remission rate was 69.5% in the Bio-Three group and 56.6% in the placebo group (P = 0.248). On cluster analysis of fecal flora, 7 patients belonged to cluster\u2005I, 32 to cluster II, and 7 to cluster III. CONCLUSION: Probiotics may be effective for maintaining clinical remission in patients with quiescent UC, especially those who belong to cluster\u2005I\u2005on fecal bacterial analysis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30529583", + "title": "Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis.", + "year": 2019, + "journal": "Gastroenterology", + "authors": [ + "Paramsothy S", + "Nielsen S", + "Kamm MA", + "Deshpande NP", + "Faith JJ", + "Clemente JC", + "Paramsothy R", + "Walsh AJ", + "van den Bogaerde J", + "Samuel D", + "Leong RWL", + "Connor S", + "Ng W", + "Lin E", + "Borody TJ", + "Wilkins MR", + "Colombel JF", + "Mitchell HM", + "Kaakoush NO" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.2678577146510703, + "mesh_terms": [ + "Bacteria", + "Biomarkers", + "Colitis, Ulcerative", + "Double-Blind Method", + "Fecal Microbiota Transplantation", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Metabolomics", + "New South Wales", + "Remission Induction", + "Ribotyping", + "Time Factors", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy. METHODS: We performed a double-blind trial of 81 patients with active UC randomly assigned to groups that received an initial colonoscopic infusion and then intensive multidonor FMT or placebo enemas, 5 d/wk for 8 weeks. Patients in the FMT group received blended homogenized stool from 3-7 unrelated donors. Patients in the placebo group were eligible to receive open-label FMT after the double-blind study period. We collected 314 fecal samples from the patients at screening, every 4 weeks during treatment, and 8 weeks after the blinded or open-label FMT therapy. We also collected 160 large-bowel biopsy samples from the patients at study entry, at completion of 8 weeks of blinded therapy, and at the end of open-label FMT, if applicable. We analyzed 105 fecal samples from the 14 individual donors (n\u00a0= 55), who in turn contributed to 21 multidonor batches (n\u00a0= 50). Bacteria in colonic and fecal samples were analyzed by both 16S ribosomal RNA gene and transcript amplicon sequencing; 285 fecal samples were analyzed by shotgun metagenomics, and 60 fecal samples were analyzed for metabolome features. RESULTS: FMT increased microbial diversity and altered composition, based on analyses of colon and fecal samples collected before vs after FMT. Diversity was greater in fecal and colon samples collected before and after FMT treatment from patients who achieved remission compared with patients who did not. Patients in remission after FMT had enrichment of Eubacterium hallii and Roseburia inulivorans compared with patients who did not achieve remission after FMT and had increased levels of short-chain fatty acid biosynthesis and secondary bile acids. Patients who did not achieve remission had enrichment of Fusobacterium gonidiaformans, Sutterella wadsworthensis, and Escherichia species and increased levels of heme and lipopolysaccharide biosynthesis. Bacteroides in donor stool were associated with remission in patients receiving FMT, and Streptococcus species in donor stool was associated with no response to FMT. CONCLUSIONS: In an analysis of fecal and colonic mucosa samples from patients receiving FMT for active UC and stool samples from donors, we associated specific bacteria and metabolic pathways with induction of remission. These findings may be of value in the design of microbe-based therapies for UC. ClinicalTrials.gov, Number NCT01896635.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37463118", + "title": "Prediction of Response to Systemic Corticosteroids in Active UC by Microbial Composition-A Prospective Multicenter Study.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Blesl A", + "Wurm P", + "Waschina S", + "Gr\u00f6chenig HP", + "Novacek G", + "Primas C", + "Reinisch W", + "Kutschera M", + "Illiasch C", + "Hennlich B", + "Steiner P", + "Koch R", + "Tillinger W", + "Haas T", + "Reicht G", + "Mayer A", + "Ludwiczek O", + "Miehsler W", + "Steidl K", + "Binder L", + "Reider S", + "Watschinger C", + "F\u00fcrst S", + "Kump P", + "Moschen A", + "Aden K", + "Gorkiewicz G", + "H\u00f6genauer C" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.24187317587685042, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "RNA, Ribosomal, 16S", + "Prospective Studies", + "Feces", + "Adrenal Cortex Hormones", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Corticosteroids are used for induction of remission in patients with moderately to severely active ulcerative colitis. However, up to one-third of patients fail to this therapy. We investigated if fecal microbial composition or its metabolic capacity are associated with response to systemic corticosteroids. METHODS: In this prospective, multicenter study, patients with active ulcerative colitis (Lichtiger score \u22654) receiving systemic corticosteroids were eligible. Data were assessed and fecal samples collected before and after 4 weeks of treatment. Patients were divided into responders (decrease of Lichtiger Score \u226550%) and nonresponders. The fecal microbiome was assessed by the 16S rRNA gene marker and analyzed with QIIME 2. Microbial metabolic pathways were predicted using parsimonious flux balance analysis. RESULTS: Among 93 included patients, 69 (74%) patients responded to corticosteroids after 4 weeks. At baseline, responders could not be distinguished from nonresponders by microbial diversity and composition, except for a subgroup of biologic-na\u00efve patients. Within 4 weeks of treatment, responders experienced changes in beta diversity with enrichment of ascribed beneficial taxa, including Blautia, Anaerostipes, and Bifidobacterium, as well as an increase in predicted butyrate synthesis. Nonresponders had only minor longitudinal taxonomic changes with a significant increase of Streptococcus salivarius and a microbial composition shifting away from responders. CONCLUSION: Baseline microbial diversity and composition seem to be of limited use to predict response to systemic corticosteroids in active ulcerative colitis. Response is longitudinally associated with restoration of microbial composition and its metabolic capacity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30545401", + "title": "A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?", + "year": 2018, + "journal": "Microbiome", + "authors": [ + "Forbes JD", + "Chen CY", + "Knox NC", + "Marrie RA", + "El-Gabalawy H", + "de Kievit T", + "Alfa M", + "Bernstein CN", + "Van Domselaar G" + ], + "bacteria": "Streptococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.2132820813105585, + "mesh_terms": [ + "Adult", + "Arthritis, Rheumatoid", + "Bacteria", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "DNA, Bacterial", + "DNA, Ribosomal", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Machine Learning", + "Male", + "Metagenomics", + "Middle Aged", + "Multiple Sclerosis", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "BACKGROUND: Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology is common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of the gut microbiome in IMIDs. This study used 16S rRNA gene amplicon sequencing to compare the gut microbiota of patients with Crohn's disease (CD; N\u2009=\u200920), ulcerative colitis (UC; N\u2009=\u200919), multiple sclerosis (MS; N\u2009=\u200919), and rheumatoid arthritis (RA; N\u2009=\u200921) versus healthy controls (HC; N\u2009=\u200923). Biological replicates were collected from participants within a 2-month interval. This study aimed to identify common (or unique) taxonomic biomarkers of IMIDs using both differential abundance testing and a machine learning approach. RESULTS: Significant microbial community differences between cohorts were observed (pseudo F\u2009=\u20094.56; p\u2009=\u20090.01). Richness and diversity were significantly different between cohorts (pFDR <\u20090.001) and were lowest in CD while highest in HC. Abundances of Actinomyces, Eggerthella, Clostridium III, Faecalicoccus, and Streptococcus (pFDR <\u20090.001) were significantly higher in all disease cohorts relative to HC, whereas significantly lower abundances were observed for Gemmiger, Lachnospira, and Sporobacter (pFDR <\u20090.001). Several taxa were found to be differentially abundant in IMIDs versus HC including significantly higher abundances of Intestinibacter in CD, Bifidobacterium in UC, and unclassified Erysipelotrichaceae in MS and significantly lower abundances of Coprococcus in CD, Dialister in MS, and Roseburia in RA. A machine learning approach to classify disease versus HC was highest for CD (AUC\u2009=\u20090.93 and AUC\u2009=\u20090.95 for OTU and genus features, respectively) followed by MS, RA, and UC. Gemmiger and Faecalicoccus were identified as important features for classification of subjects to CD and HC. In general, features identified by differential abundance testing were consistent with machine learning feature importance. CONCLUSIONS: This study identified several gut microbial taxa with differential abundance patterns common to IMIDs. We also found differentially abundant taxa between IMIDs. These taxa may serve as biomarkers for the detection and diagnosis of IMIDs and suggest there may be a common component to IMID etiology.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26309350", + "title": "Oral Campylobacter species: Initiators of a subgroup of inflammatory bowel disease?", + "year": 2015, + "journal": "World journal of gastroenterology", + "authors": [ + "Zhang L" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.7699462224194341, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Campylobacter", + "Campylobacter Infections", + "Colitis, Ulcerative", + "Crohn Disease", + "Host-Pathogen Interactions", + "Humans", + "Intestines", + "Mouth", + "Risk Factors", + "Virulence" + ], + "raw_abstract": "In recent years, a number of studies detected a significantly higher prevalence of Campylobacter species such as Campylobacter concisus (C. concisus) in intestinal biopsies and fecal samples collected from patients with inflammatory bowel disease (IBD) compared to controls. Most of these Campylobacter species are not of zoonotic origin but are human oral Campylobacter species. Bacterial species usually cause diseases in the location where they colonize. However, C. concisus and other oral Campylobacter species are associated with IBD occurring at the lower parts of the gastrointestinal tract, suggesting that these Campylobacter species may have unique virulence factors that are expressed in the lower parts of the gastrointestinal tract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37946238", + "title": "The oral bacterial microbiota facilitates the stratification for ulcerative colitis patients with oral ulcers.", + "year": 2023, + "journal": "Annals of clinical microbiology and antimicrobials", + "authors": [ + "Xu J", + "Zhang Y", + "Fang XH", + "Liu Y", + "Huang YB", + "Ke ZL", + "Wang Y", + "Zhang YF", + "Zhang Y", + "Zhou JH", + "Su HT", + "Chen N", + "Liu YL" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.7553721693404465, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Oral Ulcer", + "RNA, Ribosomal, 16S", + "Gastrointestinal Microbiome", + "Microbiota", + "Inflammatory Bowel Diseases", + "Bacteria", + "Feces", + "Mesalamine" + ], + "raw_abstract": "BACKGROUND: Clinically, a large part of inflammatory bowel disease (IBD) patients is complicated by oral lesions. Although previous studies proved oral microbial dysbiosis in IBD patients, the bacterial community in the gastrointestinal (GI) tract of those IBD patients combined with oral ulcers has not been profiled yet. METHODS: In this study, we enrolled four groups of subjects, including healthy controls (CON), oral ulcer patients (OU), and ulcerative colitis patients with (UC_OU) and without (UC) oral ulcers. Bio-samples from three GI niches containing salivary, buccal, and fecal samples, were collected for 16S rRNA V3-V4 region sequencing. Bacterial abundance and related bio-functions were compared, and data showed that the fecal microbiota was more potent than salivary and buccal microbes in shaping the host immune system.\u2009~\u200922 UC and 10 UC_OU 5-aminosalicylate (5-ASA) routine treated patients were followed-up for six months; according to their treatment response (a decrease in the endoscopic Mayo score), they were further sub-grouped as responding and non-responding patients. RESULTS: We found those UC patients complicated with oral ulcers presented weaker treatment response, and three oral bacterial genera, i.e., Fusobacterium, Oribacterium, and Campylobacter, might be connected with treatment responding. Additionally, the salivary microbiome could be an indicator of treatment responding in 5-ASA routine treatment rather than buccal or fecal ones. CONCLUSIONS: The fecal microbiota had a strong effect on the host's immune indices, while the oral bacterial microbiota could help stratification for ulcerative colitis patients with oral ulcers. Additionally, the oral microbiota had the potential role in reflecting the treatment response of UC patients. Three oral bacteria genera (Fusobacterium, Oribacterium, and Campylobacter) might be involved in UC patients with oral ulcers lacking treatment responses, and monitoring oral microbiota may be meaningful in assessing the therapeutic response in UC patients.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30389589", + "title": "Gastrointestinal Infection Increases Odds of Inflammatory Bowel Disease in a Nationwide Case-Control Study.", + "year": 2019, + "journal": "Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association", + "authors": [ + "Axelrad JE", + "Ol\u00e9n O", + "Askling J", + "Lebwohl B", + "Khalili H", + "Sachs MC", + "Ludvigsson JF" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.7263502686184847, + "mesh_terms": [ + "Adult", + "Female", + "Follow-Up Studies", + "Gastroenteritis", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "Morbidity", + "Population Surveillance", + "Prognosis", + "Registries", + "Retrospective Studies", + "Sweden", + "Young Adult" + ], + "raw_abstract": "BACKGROUND & AIMS: Gastrointestinal infections have been associated with later development of inflammatory bowel diseases (IBD). However, studies have produced conflicting results. We performed a nationwide case-control study in Sweden to determine whether gastroenteritis is associated with the development of Crohn's disease (CD) or ulcerative colitis (UC). METHODS: Using the Swedish National Patient Register, we identified 44,214 patients with IBD (26,450 with UC; 13,387 with CD; and 4377 with IBD-unclassified) from 2002 to 2014 and matched them with 436,507 individuals in the general population (control subjects). We then identified patients and control subjects with reported episodes of gastroenteritis (from 1964 to 2014) and type of pathogen associated. We collected medical and demographic data and used logistic regression to estimate odds ratios (ORs) for IBD associated with enteric infection. RESULTS: Of the patients with IBD, 3105 (7.0%) (1672 with UC, 1050 with CD, and 383 with IBD-unclassified) had a record of previous gastroenteritis compared with 17,685 control subjects (4.1%). IBD cases had higher odds for an antecedent episode of gastrointestinal infection (aOR, 1.64; 1.57-1.71), bacterial gastrointestinal infection (aOR, 2.02; 1.82-2.24), parasitic gastrointestinal infection (aOR, 1.55; 1.03-2.33), and viral gastrointestinal infection (aOR, 1.55; 1.34-1.79). Patients with UC had higher odds of previous infection with Salmonella, Escherichia coli, Campylobacter, or Clostridium difficile compared to control subjects. Patients with CD had higher odds of previous infection with Salmonella, Campylobacter, Yersinia enterocolitica, C\u00a0difficile, amoeba, or norovirus compared to control subjects. Increasing numbers of gastroenteritis episodes were associated with increased odds of IBD, and a previous episode of gastroenteritis remained associated with odds for IBD more than 10 years later (aOR, 1.26; 1.19-1.33). CONCLUSIONS: In an analysis of the Swedish National Patient Register, we found previous episodes of gastroenteritis to increase odds of later development of IBD. Although we cannot formally exclude misclassification bias, enteric infections might induce microbial dysbiosis that contributes to the development of IBD in susceptible individuals.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26994772", + "title": "Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India.", + "year": 2016, + "journal": "Journal of gastroenterology", + "authors": [ + "Kedia S", + "Rampal R", + "Paul J", + "Ahuja V" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.6380925576201456, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Dysentery, Amebic", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "India", + "Intestinal Mucosa" + ], + "raw_abstract": "The disease profile in the Indian population provides a unique opportunity for studying the host microbiome interaction in both infectious (amebiasis) and autoimmune diseases\u00a0like inflammatory bowel disease (IBD) from a similar environment and genetic background. Analysis of fecal samples from untreated amebic liver abscess (ALA) patients, Entamoeba histolytica (Eh)-negative and -positive asymptomatic individuals, and pus samples from naive ALA patients revealed a significant reduction in Lactobacillus in asymptomatic individuals (Eh +ve) and ALA patients. Two anaerobic genera, namely Bacteroides and Peptostreptococcus, were detected in naive ALA pus samples. Analysis of fecal samples from amoebic colitis patients showed a significant decline in population of Bacteroides, Clostridium coccoides and leptum subgroup, Lactobacillus, Campylobacter, and Eubacterium, whereas a significant increase in Bifidobacterium was observed. Mucosa-associated bacterial flora analysis from IBD patients and healthy controls revealed a significant difference in concentration of bacteria among predominating and subdominating genera between ulcerative colitis (UC), Crohn's disease (CD) patients, and controls. In contrast to the mucosal studies, we found a significant increase in lactobacilli population in fecal samples of active UC patients. Another study revealed a significant decrease of Clostridium coccoides and leptum clusters in fecal samples of active UC patients along with decreased concentrations of fecal SCFAs, especially of n-butyrate, iso-butyrate, and acetate. We therefore found similar perturbations in gut microbiome in both infectious and autoimmune diseases, indicating inflammation to be the major driver for changes in gut microbiome.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26508508", + "title": "Dual role of Helicobacter and Campylobacter species in IBD: a systematic review and meta-analysis.", + "year": 2017, + "journal": "Gut", + "authors": [ + "Casta\u00f1o-Rodr\u00edguez N", + "Kaakoush NO", + "Lee WS", + "Mitchell HM" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.6302759850592, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Campylobacter", + "Campylobacter Infections", + "Colitis, Ulcerative", + "Crohn Disease", + "Helicobacter Infections", + "Helicobacter pylori", + "Humans", + "Protective Factors", + "Risk Factors", + "Stomach Diseases" + ], + "raw_abstract": "OBJECTIVE: To conduct a comprehensive global systematic review and meta-analysis on the association between Helicobacter pylori infection and IBD. As bacterial antigen cross-reactivity has been postulated to be involved in this association, published data on enterohepatic Helicobacter spp (EHS) and Campylobacter spp and IBD was also analysed. DESIGN: Electronic databases were searched up to July 2015 for all case-control studies on H. pylori infection/EHS/Campylobacter spp and IBD. Pooled ORs (P-OR) and 95% CIs were obtained using the random effects model. Heterogeneity, sensitivity and stratified analyses were performed. RESULTS: Analyses comprising patients with Crohn's disease (CD), UC and IBD unclassified (IBDU), showed a consistent negative association between gastric H. pylori infection and IBD (P-OR: 0.43, p value <1e-10). This association appears to be stronger in patients with CD (P-OR: 0.38, p value <1e-10) and IBDU (P-OR: 0.43, p value=0.008) than UC (P-OR: 0.53, p value <1e-10). Stratification by age, ethnicity and medications showed significant results. In contrast to gastric H. pylori, non H. pylori-EHS (P-OR: 2.62, p value=0.001) and Campylobacter spp, in particular C. concisus (P-OR: 3.76, p value=0.006) and C. showae (P-OR: 2.39, p value=0.027), increase IBD risk. CONCLUSIONS: H. pylori infection is negatively associated with IBD regardless of ethnicity, age, H. pylori detection methods and previous use of aminosalicylates and corticosteroids. Antibiotics influenced the magnitude of this association. Closely related bacteria including EHS and Campylobacter spp increase the risk of IBD. These results infer that H. pylori might exert an immunomodulatory effect in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30072777", + "title": "Enteric Infections Are Common in Patients with Flares of Inflammatory Bowel Disease.", + "year": 2018, + "journal": "The American journal of gastroenterology", + "authors": [ + "Axelrad JE", + "Joelson A", + "Green PHR", + "Lawlor G", + "Lichtiger S", + "Cadwell K", + "Lebwohl B" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.6285956471632719, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Bacterial Infections", + "Campylobacter", + "Colitis, Ulcerative", + "Crohn Disease", + "Cross-Sectional Studies", + "Endoscopy, Gastrointestinal", + "Enterocolitis", + "Escherichia coli", + "Feces", + "Female", + "Humans", + "Intestines", + "Male", + "Middle Aged", + "Norovirus", + "Plesiomonas", + "Prevalence", + "Severity of Illness Index", + "Symptom Flare Up", + "Young Adult" + ], + "raw_abstract": "OBJECTIVES: Few studies have examined the role of non-Clostridium difficile enteric infections in flares of inflammatory bowel disease (IBD). Our objective was to investigate enteric infection detected by multiplex PCR stool testing in patients with IBD. METHODS: We performed a cross-sectional analysis of 9403 patients who underwent 13,231 stool tests with a gastrointestinal pathogen PCR panel during a diarrheal illness from March 2015 to May 2017. Our primary outcome was the presence of an infection. Secondary outcomes included endoscopic and histologic predictors of infection, and IBD outcomes following testing. RESULTS: A total of 277 patients with Crohn's disease (CD), 300 patients with ulcerative colitis (UC), and 8826 patients without IBD underwent 454, 503, and 12,275 tests, respectively. Compared to patients without IBD, patients with IBD were less likely to test positive (CD 18.1%, UC 16.1%, no IBD 26.6%, p\u2009<\u20090.001). Compared to patients without IBD, CD had a higher prevalence of norovirus (p\u2009=\u20090.05) and Campylobacter (p\u2009=\u20090.043), whereas UC had a lower prevalence of norovirus (p\u2009=\u20090.001) and a higher prevalence of Campylobacter (p\u2009=\u20090.013), Plesiomonas (p\u2009=\u20090.049), and Escherichia coli species (p\u2009<\u20090.001). Of 77 patients who underwent endoscopy, there were no major endoscopic or histologic predictors of a positive test. Patients who tested negative were more likely to have IBD therapy escalated (p\u2009=\u20090.004). Enteric infection did not impact IBD outcomes following testing (log-rank 0.224). CONCLUSIONS: Non-Clostridium difficile enteric infections were identified in 17% of symptomatic patients with IBD. Endoscopic and histologic findings may not differentiate flare from infection. Norovirus and E.coli may play an important role in flare of IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29037938", + "title": "Non-Clostridium difficile Bacterial Infections Are Rare in Patients With Flares of Inflammatory Bowel Disease.", + "year": 2018, + "journal": "Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association", + "authors": [ + "Hanada Y", + "Khanna S", + "Loftus EV", + "Raffals LE", + "Pardi DS" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5331229587209485, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Aged, 80 and over", + "Bacteria", + "Bacterial Infections", + "Bacteriological Techniques", + "Feces", + "Female", + "Follow-Up Studies", + "Hospitalization", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "Polymerase Chain Reaction", + "Retrospective Studies", + "Young Adult" + ], + "raw_abstract": "BACKGROUND & AIMS: Clostridium difficile infection (CDI) causes flares in patients with inflammatory bowel disease (IBD). We investigated the frequency and outcomes of non-CDI bacterial enteric infections in symptomatic patients with IBD. METHODS: We performed a retrospective study of patients with ulcerative colitis (UC) or Crohn's disease (CD) from whom stool samples were collected and analyzed by PCR or culture for bacterial pathogens (Campylobacter jejuni or C coli, Salmonella species, Shigella species, enteroinvasive Escherichia coli, shiga toxin-producing E coli, or Yersinia species) from November 19, 2011, through June 30, 2014. Patients were excluded if they had nonbacterial infections or no symptoms. Data were collected from medical records on IBD duration, treatment, age at diagnosis, and presence of concurrent CDI. Patients were followed for 1 year after the date of infection resolution or until date of last follow-up in the health record. Each patient with an enteric infection was matched with 2 patients with IBD flares and negative results from stool tests (non-infected control) and 2 patients with IBD and CDI (CDI control), adjusted for age (within 5 years at the time of stool test), sex, and IBD subtype. Outcome measures included IBD therapy escalation and hospitalization. RESULTS: Of 9247 patients with IBD seen during the study period, stool samples were tested from 1345 patients (50% with UC and 50% with CD). There were 3 positive results (detection of bacterial pathogens) from 339 PCR analyses of stool samples from 296 patients with UC (0.88%) and 12 positive results from 486 cultures of stool samples from 418 patients with UC (2.5%). There was 1 positive result from 355 PCR analyses of stool samples from 311 patients with CD (0.28%) and 9 positive results from 496 cultures of stool samples from 413 patients with CD (1.8%). Of the 19 patients followed beyond infection, 9 patients required escalation of their IBD therapy (47%)-most commonly addition of an immunomodulator (5 patients) or a biological agent (3 patients)-compared with 34% of CDI controls and 66% of non-infected controls (P\u00a0<\u00a0.001). Higher proportions of patients with non-CDI bacterial infections were in remission 1 year after their infection (89%) than patients with CDI (55%) or negative results of stool tests (63%; P\u00a0= .04). We did not observe differences in hospitalization, emergency department visits, or surgical interventions among groups. CONCLUSIONS: In a retrospective study of patients with an IBD flare, we detected non-CDI bacterial infections in fewer than 3% of those who were tested. Higher proportions of patients with non-CDI bacterial infections were in remission in the year after their infection than patients with CDI.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.505491338085921, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "25517595", + "title": "Aeromonas species: an opportunistic enteropathogen in patients with inflammatory bowel diseases? A single center cohort study.", + "year": 2015, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Lobat\u00f3n T", + "Hoffman I", + "Vermeire S", + "Ferrante M", + "Verhaegen J", + "Van Assche G" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.4873703544227165, + "mesh_terms": [ + "Adult", + "Aeromonas", + "Aged", + "Belgium", + "Female", + "Follow-Up Studies", + "Gram-Negative Bacterial Infections", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "Prevalence", + "Prognosis", + "Retrospective Studies", + "Risk Factors" + ], + "raw_abstract": "BACKGROUND: The role of Aeromonas species as an enteropathogen in patients with and without inflammatory bowel disease (IBD) is still debated. The aim was to explore the significance of positive Aeromonas stool cultures in IBD and patients without IBD. METHODS: Observational retrospective study including all patients with a stool culture positive for Aeromonas between January 2011 and October 2013 at the Leuven University Hospitals. Demographics, clinical, and endoscopic outcomes and laboratory results were analyzed. RESULTS: A total of 77 patients (11 IBD) were identified. In 37 cases, Aeromonas caused a mild self-limited gastrointestinal infection. Among the 40 patients needing antibiotics, 22 presented a mild-to-moderate gastrointestinal infection; 4 suffered from extraintestinal complications; and 4 were coinfected by Campylobacter spp. A. veronii caused more frequently severe infection than the other species (25% versus 5%; P = 0.046). In 2 patients with ulcerative colitis, Aeromonas triggered a moderate-to-severe flare and 2 cases appeared in the context of de novo Crohn's disease. In contrast, in 1 patient with ulcerative colitis and 2 patients with Crohn's disease, Aeromonas caused a mild gastrointestinal infection not worsening the disease activity and in 4 patients with Crohn's disease, it presented in the context of active disease with no clear pathogenic role. Patients with IBD were treated more often with antibiotics (82 versus 41%, P = 0.012) and had more complications (46 versus 14%, P = 0.024). CONCLUSIONS: Aeromonas caused mostly mild infections but also moderate and severe infections. A. veronii was more prevalent in patients with IBD and was associated with worse clinical outcomes. Aeromonas caused milder infections in patients without IBD. Other risk factors for severe infection were not found.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35426646", + "title": "Ulcerative Colitis: Rapid Evidence Review.", + "year": 2022, + "journal": "American family physician", + "authors": [ + "Adams SM", + "Close ED", + "Shreenath AP" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.4486179701424387, + "mesh_terms": [ + "Antibodies, Anti-Idiotypic", + "Colitis, Ulcerative", + "Fecal Microbiota Transplantation", + "Humans", + "Inflammation", + "Leukocyte L1 Antigen Complex" + ], + "raw_abstract": "Ulcerative colitis is a relapsing and remitting inflammatory bowel disease of the large intestine. Risk factors include recent Salmonella or Campylobacter infection and a family history of ulcerative colitis. Diagnosis is suspected based on symptoms of urgency, tenesmus, and hematochezia and is confirmed with endoscopic findings of continuous inflammation from the rectum to more proximal colon, depending on the extent of disease. Fecal calprotectin may be used to assess disease activity and relapse. Medications available to treat the inflammation include 5-aminosalicylic acid, corticosteroids, tumor necrosis factor-alpha antibodies, anti-integrin antibodies, anti-interleukin-12 and -23 antibodies, and Janus kinase inhibitors. Choice of medication and method of delivery depend on the location and severity of mucosal inflammation. Other treatments such as fecal microbiota transplantation are considered experimental, and complementary therapies such as probiotics and curcumin have mixed data. Surgical treatment may be needed for fulminant or refractory disease. Increased risk of colorectal cancer and use of immunosuppressive therapies affect the preventive care needs for these patients.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29432367", + "title": "The possible relationship between Campylobacter spp./Arcobacter spp. and patients with ulcerative colitis.", + "year": 2018, + "journal": "European journal of gastroenterology & hepatology", + "authors": [ + "Akar M", + "Aydin F", + "Yurci MA", + "Abay S", + "Ate\u015f \u0130", + "Deniz K" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.4472263626012101, + "mesh_terms": [ + "Adult", + "Anti-Bacterial Agents", + "Arcobacter", + "Bacterial Typing Techniques", + "Campylobacter", + "Campylobacter Infections", + "Case-Control Studies", + "Colitis, Ulcerative", + "Colonoscopy", + "Drug Resistance, Multiple, Bacterial", + "Feces", + "Female", + "Follow-Up Studies", + "Gram-Negative Bacterial Infections", + "Humans", + "Male", + "Microbial Sensitivity Tests", + "Middle Aged", + "Severity of Illness Index" + ], + "raw_abstract": "BACKGROUND AND AIMS: The role of bacterial infection in the pathogenesis of ulcerative colitis (UC) is under investigation. This study aims to (i) determine the prevalence of Campylobacter spp. and Arcobacter spp. in patients with UC, (ii) identify the antibiotic susceptibility of isolated agents, and (iii) investigate the role of these microorganisms in the pathogenesis and/or activation of UC. PATIENTS AND METHODS: Eighty patients with UC and 40 healthy individuals were included in the study. Stool samples were used for cultural examination. Direct plating, membrane filtration, and enrichment methods were used for isolation. 16s rRNA sequence analysis was used for definitive identification of isolates that were identified phenotypically. RESULTS: In the UC group, 20 (25%) patients had proctitis, 40 (50%) patients had left-type involvement, and 20 (25%) patients had extensive involvement. Campylobacter spp. were isolated from four (5%) patients in the UC group and isolates were identified as C. curvus, C. concisus, C. sputorum, and C. jejuni. C. concisus and C. jejuni were found to be resistant to ciprofloxacin, levofloxacin, and trimethoprim-sulfamethoxazole. C. jejuni was also resistant to tetracycline. All samples were negative for Arcobacter spp. The samples from the control group neither showed the presence of Campylobacter spp. nor Arcobacter spp. CONCLUSION: Given the clinical, endoscopic, and bacteriological examination results, it is believed that Campylobacter spp. are agents that cause flare-up clinically by being superimposed on the primary disease, rather than agents that initiate the disease in patients with UC. Arcobacter spp., which are known to cause acute gastroenteritis, were not found to be associated with UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32445725", + "title": "Incidence, risk factors, and health service burden of sequelae of campylobacter and non-typhoidal salmonella infections in England, 2000-2015: A retrospective cohort study using linked electronic health records.", + "year": 2020, + "journal": "The Journal of infection", + "authors": [ + "Esan OB", + "Perera R", + "McCarthy N", + "Violato M", + "Fanshawe TR" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.44168346703268563, + "mesh_terms": [ + "Campylobacter", + "Campylobacter Infections", + "Electronic Health Records", + "England", + "Health Services", + "Humans", + "Incidence", + "Retrospective Studies", + "Risk Factors", + "Salmonella Infections" + ], + "raw_abstract": "BACKGROUND: Reactive arthritis, irritable bowel syndrome (IBS), Guillain-Barr\u00e9 syndrome, ulcerative colitis, and Crohn's disease may be sequelae of Campylobacter or non-typhoidal Salmonella (NTS) infections. Proton pump inhibitors (PPI) and antibiotics may increase the risk of gastrointestinal infections (GII); however, their impact on sequelae onset is unclear. We investigated the incidence of sequelae, their association with antibiotics and PPI prescription, and assessed the economic impact on the NHS. METHODS: Data from the Clinical Practice Research Datalink for patients consulting their GP for Campylobacter or NTS infection, during 2000-2015, were linked to hospital, mortality, and Index of Multiple Deprivation data. We estimated the incidence of sequelae and deaths in the 12 months following GII. We conducted logistic regression modelling for the adjusted association with prescriptions. We compared differences in resource use and costs pre- and post-infection amongst patients with and without sequelae. FINDINGS: Of 20,471 patients with GII (Campylobacter 17,838), less than 2% (347) developed sequelae, with IBS (268) most common. Amongst Campylobacter patients, those with prescriptions for PPI within 12 months before and cephalosporins within 7-days before/after infection had elevated risk of IBS (adjusted odds ratio [aOR] 2.1, 1.5-2.9) and (aOR 3.6, 1.1-11.7) respectively. Campylobacter sequelae led to \u223c \u00a31.3 million, (\u00a3750,000, \u00a31.7 million) in additional annual NHS expenditure. INTERPRETATION: Sequelae of Campylobacter and NTS infections are rare but associated with increased NHS costs. Prior prescription of PPI may be a modifiable risk factor. Incidence of sequelae, healthcare resource use and costs are essential parameters for future burden of disease studies.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26185088", + "title": "The Roles of Inflammation, Nutrient Availability and the Commensal Microbiota in Enteric Pathogen Infection.", + "year": 2015, + "journal": "Microbiology spectrum", + "authors": [ + "Stecher B" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.3744471766076153, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Enterobacteriaceae", + "Enterobacteriaceae Infections", + "Gastrointestinal Diseases", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Intestinal Mucosa", + "Intestines", + "Symbiosis" + ], + "raw_abstract": "The healthy human intestine is colonized by as many as 1014 bacteria belonging to more than 500 different species forming a microbial ecosystem of unsurpassed diversity, termed the microbiota. The microbiota's various bacterial members engage in a physiological network of cooperation and competition within several layers of complexity. Within the last 10 years, technological progress in the field of next-generation sequencing technologies has tremendously advanced our understanding of the wide variety of physiological and pathological processes that are influenced by the commensal microbiota (1, 2). An increasing number of human disease conditions, such as inflammatory bowel diseases (IBD), type 2 diabetes, obesity, allergies and colorectal cancer are linked with altered microbiota composition (3). Moreover, a clearer picture is emerging of the composition of the human microbiota in healthy individuals, its variability over time and between different persons and how the microbiota is shaped by environmental factors (i.e., diet) and the host's genetic background (4). A general feature of a normal, healthy gut microbiota can generate conditions in the gut that disfavor colonization of enteric pathogens. This is termed colonization-resistance (CR). Upon disturbance of the microbiota, CR can be transiently disrupted, and pathogens can gain the opportunity to grow to high levels. This disruption can be caused by exposure to antibiotics (5, 6), changes in diet (7, 8), application of probiotics and drugs (9), and a variety of diseases (3). Breakdown of CR can boost colonization by intrinsic pathogens or increase susceptibility to infections (10). One consequence of pathogen expansion is the triggering of inflammatory host responses and pathogen-mediated disease. Interestingly, human enteric pathogens are part of a small group of bacterial families that belong to the Proteobacteria: the Enterobacteriaceae (E. coli, Yersinia spp., Salmonella spp., Shigella spp.), the Vibrionaceae (Vibrio cholerae) and the Campylobacteriaceae (Campylobacter spp.). In general, members of these families (be it commensals or pathogens) only constitute a minority of the intestinal microbiota. However, proteobacterial \"blooms\" are a characteristic trait of an abnormal microbiota such as in the course of antibiotic therapy, dietary changes or inflammation (11). It has become clear that the gut microbiota not only plays a major role in priming and regulating mucosal and systemic immunity, but that the immune system also contributes to host control over microbiota composition. These two ways of mutual communication between the microbiota and the immune system were coined as \"outside-in\" and \"inside-out,\" respectively (12). The significance of those interactions for human health is particularly evident in Crohn's disease (CD) and Ulcerative Colitis (UC). The symptoms of these recurrent, chronic types of gut inflammation are caused by an excessive immune response against one's own commensal microbiota (13). It is assumed that deregulated immune responses can be caused by a genetic predisposition, leading to, for example, the impairment of intestinal barrier function or disruption of mucosal T-cell homeostasis. In CD or UC patients, an abnormally composed microbiota, referred to as \"dysbiosis,\" is commonly observed (discussed later). This is often characterized by an increased relative abundance of facultative anaerobic bacteria (e.g., Enterobacteriaeceae, Bacilli) and, at the same time, depletion of obligate anaerobic bacteria of the classes Bacteroidia and Clostridia. So far, it is unclear whether dysbiosis is a cause or a consequence of inflammatory bowel disease (IBD). In fact, both scenarios are equally conceivable. Recent work suggests that inflammatory immune responses in the gut (both IBD and pathogen-induced) can alter the gut luminal milieu in a way that favors dysbiosis (14). In this chapter, I present a survey on our current state of understanding of the characteristics and mechanisms underlying gut inflammation-associated dysbiosis. The role of dysbiosis in enteric infections and human IBD is discussed. In addition, I will focus on competition of enteric pathogens and the gut microbiota in the inflamed gut and the role of dysbiotic microbiota alterations (e.g., \"Enterobacterial blooms\" (11)) for the evolution of pathogenicity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35697847", + "title": "Mapping of etiologies of computed tomography-proven acute colitis: a prospective cohort study.", + "year": 2022, + "journal": "Scientific reports", + "authors": [ + "Meyer J", + "Schrenzel J", + "Balaphas A", + "Delaune V", + "Abbas M", + "Morel P", + "Puppa G", + "Rubbia-Brandt L", + "Bichard P", + "Frossard JL", + "Toso C", + "Buchs NC", + "Ris F" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.35773593835571454, + "mesh_terms": [ + "Biomarkers", + "Colitis", + "Colitis, Ischemic", + "Colitis, Ulcerative", + "Colonoscopy", + "Feces", + "Humans", + "Inflammatory Bowel Diseases", + "Leukocyte L1 Antigen Complex", + "Prospective Studies", + "Salmonella", + "Tomography", + "Tomography, X-Ray Computed" + ], + "raw_abstract": "Our objective was to describe the etiologies of acute colitis and to identify patients who require diagnostic endoscopy. Patients with symptoms of gastrointestinal infection and colonic inflammation on CT were prospectively included. Those immunosuppressed, with history of colorectal cancer or inflammatory bowel disease (IBD), were excluded. Microbiological analysis of the feces was performed using PCR assays BD-Max and FilmArray (GI panel,) and fecal cultures. Fecal calprotectin was determined. Patients with negative BD-Max underwent colonoscopy. One hundred and seventy-nine patients were included. BD-Max was positive in 93 patients (52%) and FilmArray in 108 patients (60.3%). Patients with infectious colitis (n\u2009=\u2009103, 57.5%) were positive for Campylobacter spp. (n\u2009=\u200957, 55.3%), Escherichia coli spp. (n\u2009=\u20098, 7.8%), Clostridioides difficile (n\u2009=\u200923, 22.3%), Salmonella spp. (n\u2009=\u20099, 8.7%), viruses (n\u2009=\u20097, 6.8%), Shigella spp. (n\u2009=\u20096, 5.8%), Entamoeba histolytica (n\u2009=\u20092, 1.9%) and others (n\u2009=\u20094, 3.9%). Eighty-six patients underwent colonoscopy, which was compatible with ischemic colitis in 18 patients (10.1%) and IBD in 4 patients (2.2%). Fecal calprotectin was elevated in all patients, with a mean concentration of 1922.1\u2009\u00b1\u20092895.6\u00a0\u03bcg/g, and was the highest in patients with IBD (8511\u2009\u00b1\u20099438\u00a0\u03bcg/g, p\u2009<\u20090.001). After exclusion of patients with infectious etiology, a fecal calprotectin\u2009>\u2009625\u00a0\u03bcg/g allowed identifying patients with IBD with an area under ROC curve of 85.1%. To conclude, computed tomography-proven colitis was of infectious etiology in 57.5% of patients. The main pathogens identified were Campylobacter spp. (55.3%), Clostridioides difficile (22.3%) and Salmonella spp. (8.7%). Ischemic colitis (10.1%) and IBD (2.2%) were seldom represented. No colorectal cancer was found.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29636463", + "title": "Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn's disease.", + "year": 2018, + "journal": "Emerging microbes & infections", + "authors": [ + "Liu F", + "Ma R", + "Tay CYA", + "Octavia S", + "Lan R", + "Chung HKL", + "Riordan SM", + "Grimm MC", + "Leong RW", + "Tanaka MM", + "Connor S", + "Zhang L" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.30655373943896846, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Bacterial Proteins", + "Campylobacter", + "Campylobacter Infections", + "Child, Preschool", + "Chromosomes, Bacterial", + "Crohn Disease", + "Female", + "Genetic Markers", + "Genome, Bacterial", + "Genomics", + "Humans", + "Male", + "Middle Aged", + "Mouth", + "Symbiosis", + "Whole Genome Sequencing", + "Young Adult" + ], + "raw_abstract": "Campylobacter concisus is an oral bacterium that is associated with inflammatory bowel disease (IBD) including Crohn's disease (CD) and ulcerative colitis (UC). C. concisus consists of two genomospecies (GS) and diverse strains. This study aimed to identify molecular markers to differentiate commensal and IBD-associated C. concisus strains. The genomes of 63 oral C. concisus strains isolated from patients with IBD and healthy controls were examined, of which 38 genomes were sequenced in this study. We identified a novel secreted enterotoxin B homologue, Csep1. The csep1 gene was found in 56% of GS2 C. concisus strains, presented in the plasmid pICON or the chromosome. A six-nucleotide insertion at the position 654-659\u2009bp in csep1 (csep1-6bpi) was found. The presence of csep1-6bpi in oral C. concisus strains isolated from patients with active CD (47%, 7/15) was significantly higher than that in strains from healthy controls (0/29, P\u2009=\u20090.0002), and the prevalence of csep1-6bpi positive C. concisus strains was significantly higher in patients with active CD (67%, 4/6) as compared to healthy controls (0/23, P\u2009=\u20090.0006). Proteomics analysis detected the Csep1 protein. A csep1 gene hot spot in the chromosome of different C. concisus strains was found. The pICON plasmid was only found in GS2 strains isolated from the two relapsed CD patients with small bowel complications. This study reports a C. concisus molecular marker (csep1-6bpi) that is associated with active CD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26548336", + "title": "Probiotics: a proactive approach to health. A symposium report.", + "year": 2015, + "journal": "The British journal of nutrition", + "authors": [ + "Thomas LV", + "Suzuki K", + "Zhao J" + ], + "bacteria": "Campylobacter", + "condition": "ulcerative colitis", + "relevance_score": 0.2645465952450497, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Bacteria", + "Bacterial Infections", + "Child", + "Diarrhea", + "Gastrointestinal Diseases", + "HIV Infections", + "Humans", + "Integrative Medicine", + "Intestinal Mucosa", + "Metabolic Diseases", + "Microbiota", + "Neoplasms", + "Practice Guidelines as Topic", + "Probiotics" + ], + "raw_abstract": "This report summarises talks given at the 8th International Yakult Symposium, held on 23-24 April 2015 in Berlin. Two presentations explored different aspects of probiotic intervention: the small intestine as a probiotic target and inclusion of probiotics into integrative approaches to gastroenterology. Probiotic recommendations in gastroenterology guidelines and current data on probiotic efficacy in paediatric patients were reviewed. Updates were given on probiotic and gut microbiota research in obesity and obesity-related diseases, the gut-brain axis and development of psychobiotics, and the protective effects of equol-producing strains for prostate cancer. Recent studies were presented on probiotic benefit for antibiotic-associated diarrhoea and people with HIV, as well as protection against the adverse effects of a short-term high-fat diet. Aspects of probiotic mechanisms of activity were discussed, including immunomodulatory mechanisms and metabolite effects, the anti-inflammatory properties of Faecalibacterium prausnitzii, the relationship between periodontitis, microbial production of butyrate in the oral cavity and ageing, and the pathogenic mechanisms of Campylobacter. Finally, an insight was given on a recent expert meeting, which re-examined the probiotic definition, advised on the appropriate use and scope of the term and outlined different probiotic categories and the prevalence of different mechanisms of activity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27684872", + "title": "Increased Enterococcus faecalis infection is associated with clinically active Crohn disease.", + "year": 2016, + "journal": "Medicine", + "authors": [ + "Zhou Y", + "Chen H", + "He H", + "Du Y", + "Hu J", + "Li Y", + "Li Y", + "Zhou Y", + "Wang H", + "Chen Y", + "Nie Y" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7792572102506696, + "mesh_terms": [ + "Adult", + "China", + "Crohn Disease", + "DNA, Bacterial", + "Enterococcus faecalis", + "Feces", + "Female", + "Gram-Positive Bacterial Infections", + "Humans", + "Incidence", + "Male", + "Real-Time Polymerase Chain Reaction", + "Young Adult" + ], + "raw_abstract": "This study was performed to investigate the relationship between the abundance of pathogenic gut microbes in Chinese patients with inflammatory bowel disease (IBD) and disease severity.We collected clinical data and fecal samples from 47 therapy-naive Chinese patients with ulcerative colitis (UC), 67 patients with Crohn disease (CD), and 48 healthy volunteers. Bacteria levels of Fusobacterium species (spp), enterotoxigenic Bacteroides fragilis (B fragilis), enteropathogenic Escherichia coli (E coli), and Enterococcus faecalis (E faecalis) were assessed by quantitative real-time PCR (qRT-PCR). Spearman correlation coefficients were calculated to test associations between bacterial content and clinical parameters.Compared to healthy controls, the levels of both Fusobacterium spp and E faecalis were significantly increased in the feces of patients with IBD (P\u200a<\u200a0.01). B fragilis levels were higher (P\u200a<\u200a0.05) and E faecalis levels lower (P\u200a<\u200a0.05) in patients with CD compared to those with UC. Increased E faecalis colonization in CD associated positively with disease activity (P = 0.015), Crohn disease activity index (CDAI; R = 0.3118, P = 0.0108), and fecal calprotectin (P = 0.016).E faecalis and Fusobacterium spp are significantly enriched in patients with IBD, and increased E faecalis infection is associated with clinically active CD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35882645", + "title": "Patient-derived Enterococcus faecium with inflammatory genotypes promote colitis.", + "year": 2022, + "journal": "Journal of gastroenterology", + "authors": [ + "Wang Z", + "Iida N", + "Seishima J", + "Okafuji H", + "Yutani M", + "Fujinaga Y", + "Hashimoto Y", + "Tomita H", + "Mizukoshi E", + "Kaneko S" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7788044531574998, + "mesh_terms": [ + "Animals", + "Antioxidants", + "Colitis", + "Colitis, Ulcerative", + "Dysbiosis", + "Enterococcus faecium", + "Genotype", + "Humans", + "Interleukin-10", + "Mice", + "Probiotics", + "Reactive Oxygen Species", + "Thioctic Acid" + ], + "raw_abstract": "BACKGROUND: Dysbiosis of gut microbiota promotes colitis in ulcerative colitis (UC). Enterococcus faecium is an important constituent of dysbiotic microbiota. However, the mechanisms underlying E. faecium-induced colitis remain unclear. METHODS: Overall, 23 E. faecium strains isolated from human feces and 3 commercial strains were inoculated into Il10 RESULTS: Inoculation of E. faecium derived from patients with UC resulted in colitis in Il10 CONCLUSIONS: Enterococcus faecium strains in the inflammatory cluster promoted colitis with higher production of ROS than the strains in the probiotic cluster.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39026313", + "title": "Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease.", + "year": 2024, + "journal": "Microbiome", + "authors": [ + "Tian X", + "Li S", + "Wang C", + "Zhang Y", + "Feng X", + "Yan Q", + "Guo R", + "Wu F", + "Wu C", + "Wang Y", + "Huo X", + "Ma X" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7381481005944613, + "mesh_terms": [ + "Humans", + "Virome", + "Gastrointestinal Microbiome", + "Animals", + "Feces", + "Mice", + "Inflammatory Bowel Diseases", + "Female", + "Male", + "Adult", + "Middle Aged", + "Crohn Disease", + "Bacteriophages", + "Colitis, Ulcerative", + "Bacteria", + "China", + "Fecal Microbiota Transplantation", + "Case-Control Studies", + "Viruses" + ], + "raw_abstract": "BACKGROUND: The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS: In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella\u00a0species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS: Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33871395", + "title": "Fecal microbiota profile in patients with inflammatory bowel disease in Taiwan.", + "year": 2021, + "journal": "Journal of the Chinese Medical Association : JCMA", + "authors": [ + "Chang TE", + "Luo JC", + "Yang UC", + "Huang YH", + "Hou MC", + "Lee FY" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7212587404993733, + "mesh_terms": [ + "Adult", + "Cross-Sectional Studies", + "Feces", + "Female", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Microbiota", + "Middle Aged", + "Taiwan" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with complicated interaction between immune, gut microbiota, and environmental factors in a genetically vulnerable host. Dysbiosis is often seen in patients with IBD. We aimed to investigate the fecal microbiota in patients with IBD and compared them with a control group in Taiwan. METHODS: In this cross-sectional study, we investigated fecal microbiota in 20 patients with IBD and 48 healthy controls. Fecal samples from both IBD patients and controls were analyzed by the next-generation sequencing method and relevant software. RESULTS: The IBD group showed lower bacterial richness and diversity compared with the control group. The principal coordinate analysis also revealed the significant structural differences between the IBD group and the control group. These findings were consistent whether the analysis was based on an operational taxonomic unit or amplicon sequence variant. However, no significant difference was found when comparing the composition of fecal microbiota between ulcerative colitis (UC) and Crohn's disease (CD). Further analysis showed that Lactobacillus, Enterococcus, and Bifidobacterium were dominant in the IBD group, whereas Faecalibacterium and Subdoligranulum were dominant in the control group at the genus level. When comparing UC, CD, and control group, Lactobacillus, Bifidobacterium, and Enterococcus were identified as dominant genera in the UC group. Fusobacterium and Escherichia_Shigella were dominant in the CD group. CONCLUSION: Compared with the healthy control, the IBD group showed dysbiosis with a significant decrease in both richness and diversity of gut microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36677307", + "title": "Gluten Degradation by the Gut Microbiota of Ulcerative Colitis Patients.", + "year": 2022, + "journal": "Microorganisms", + "authors": [ + "Harringer EOS", + "Durack J", + "Piceno Y", + "Andersen V", + "Lynch SV" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7199078049798318, + "mesh_terms": [], + "raw_abstract": "Several studies have reported improved disease symptomatology in ulcerative colitis (UC) patients consuming a gluten free diet. This observation coupled with diversity depletion in the gut microbiota of UC patients led us to hypothesize that UC-associated enteric microbes differentially metabolize dietary gluten to produce immunogenic products that promote inflammation. Gluten concentration in stool was determined using gluten-specific ELISA, and gluten intake was assessed by food frequency questionnaire (FFQ) in UC (n = 12) and healthy controls (HC; n = 13). Gluten-metabolizing bacteria were isolated on minimal media supplemented with 1% gluten from UC and HC and identified by 16S rRNA profiling. Cell-free culture media from gluten metabolizing gut bacterial isolates was assessed for immunogenicity in vitro using HT29 colonocytes. Compared to HC, UC patients did not consume gluten differently (Mann\u2212Whitney; p > 0.10) and exhibited equivalent levels of gluten in their feces (Mann\u2212Whitney; p = 0.163). The profile of gluten-degrading bacteria isolated from UC stool was distinct (Chi-square; p \u2264 0.0001). Compared with Enterococcus isolates, products of gluten degradation by Bacillus strains induced higher IL8 and lower occludin (Mann\u2212Whitney; p = 0.002 and p = 0.059, respectively) gene expression in colonocytes irrespective of whether they originated from UC or healthy gut. Members of HC and UC microbiota exhibit gluten-degrading ability, metabolites of which influence genes involved in inflammation and barrier function in enteric colonocyte cultures. Preliminary findings of this study warrant further investigations into the mechanisms by which gut microbiota contribute to UC pathogenesis through gluten degradation.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28852861", + "title": "Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.", + "year": 2018, + "journal": "Journal of gastroenterology", + "authors": [ + "Nishino K", + "Nishida A", + "Inoue R", + "Kawada Y", + "Ohno M", + "Sakai S", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Kawahara M", + "Naito Y", + "Andoh A" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7115498488149531, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Endoscopy, Gastrointestinal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. METHODS: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. RESULTS: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. \u03b1-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. CONCLUSIONS: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39337688", + "title": "Follicular Skin Disorders, Inflammatory Bowel Disease, and the Microbiome: A Systematic Review.", + "year": 2024, + "journal": "International journal of molecular sciences", + "authors": [ + "Fleshner L", + "Roster K", + "Farabi B", + "Hirani R", + "Tepper K", + "Pitchumoni CS", + "Safai B", + "Marmon S" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.710147300228024, + "mesh_terms": [ + "Humans", + "Dysbiosis", + "Gastrointestinal Microbiome", + "Hidradenitis Suppurativa", + "Inflammatory Bowel Diseases", + "Microbiota", + "Skin", + "Skin Diseases" + ], + "raw_abstract": "Follicular skin disorders, including hidradenitis suppurativa (HS), frequently coexist with systemic autoinflammatory diseases, such as inflammatory bowel disease (IBD) and its subtypes, Crohn's disease and ulcerative colitis. Previous studies suggest that dysbiosis of the human gut microbiome may serve as a pathogenic link between HS and IBD. However, the role of the microbiome (gut, skin, and blood) in the context of IBD and various follicular disorders remains underexplored. Here, we performed a systematic review to investigate the relationship between follicular skin disorders, IBD, and the microbiome. Of the sixteen included studies, four evaluated the impact of diet on the microbiome in HS patients, highlighting a possible link between gut dysbiosis and yeast-exclusion diets. Ten studies explored bacterial colonization and HS severity with specific gut and skin microbiota, including Enterococcus and Veillonella. Two studies reported on immunological or serological biomarkers in HS patients with autoinflammatory disease, including IBD, and identified common markers including elevated cytokines and T-lymphocytes. Six studies investigated HS and IBD patients concurrently. Our systematic literature review highlights the complex interplay between the human microbiome, IBD, and follicular disorders with a particular focus on HS. The results indicate that dietary modifications hold promise as a therapeutic intervention to mitigate the burden of HS and IBD. Microbiota analyses and the identification of key serological biomarkers are crucial for a deeper understanding of the impact of dysbiosis in these conditions. Future research is needed to more thoroughly delineate the causal versus associative roles of dysbiosis in patients with both follicular disorders and IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39574001", + "title": "Changes in amino acid concentrations and the gut microbiota composition are implicated in the mucosal healing of ulcerative colitis and can be used as noninvasive diagnostic biomarkers.", + "year": 2024, + "journal": "Clinical proteomics", + "authors": [ + "Wu J", + "Li M", + "Zhou C", + "Rong J", + "Zhang F", + "Wen Y", + "Qu J", + "Wu R", + "Miao Y", + "Niu J" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6911426965077664, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Mucosal healing is the therapeutic target for ulcerative colitis (UC). While amino acids (AAs) and the gut microbiota are known to be involved in the pathogenesis of UC, their specific roles in mucosal healing have not been fully defined. OBJECTIVES: To longitudinally assess the changes in AA concentrations and the gut microbiota composition in the context of mucosal healing in UC patients, with the aim of identifying new biomarkers with predictive value for mucosal healing in UC patients and providing a new theoretical basis for dietary therapy. METHODS: A total of 15 UC patients with infliximab-induced mucosal healing were enrolled. Serum and fecal AA concentrations before and after mucosal healing were determined via targeted metabolomics. A receiver operating characteristic (ROC) curve was plotted to evaluate the value of different AAs in predicting mucosal healing in UC patients. The changes in the composition of the fecal gut microbiota were analyzed via metagenomics, and bioinformatics was used to analyze the functional genes and metabolic pathways associated with different bacterial species. Spearman correlation analyses of fecal AAs with significantly different concentrations and the differentially abundant bacterial species before and after mucosal healing were performed. RESULTS: 1. The fecal concentrations of alanine, aspartic acid, glutamic acid, glutamine, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine were significantly decreased after mucosal healing. The serum concentrations of alanine, cysteine and valine significantly increased, whereas that of aspartic acid significantly decreased. Glutamic acid, leucine, lysine, methionine and threonine could accurately predict mucosal healing in UC patients, and the area under the curve (AUC) was >\u20090.9. After combining the 5 amino acids, the AUC reached 0.96. 2. There were significant differences in the gut microbiota composition before and after mucosal healing in UC, characterized by an increase in the abundance of beneficial microbiota (Faecalibacterium prausnitzii and Bacteroides fragilis) and a decrease in the abundance of harmful microbiota (Enterococcus faecalis). LEfSe analysis identified 57 species that could predict mucosal healing, and the AUC was 0.7846. 3. Amino acid metabolic pathways were enriched in samples after mucosal healing, was associated with the abundance of multiple species, such as Faecalibacterium prausnitzi, Bacteroides fragilis, Bacteroides vulgatus and Alistipes putredinis. 4. The fecal concentrations of several AAs were negatively correlated with the abundance of a variety of beneficial strains, such as Bacteroides fragilis, uncultured Clostridium sp., Firmicutes bacterium CAG:103, Adlercreutzia equolifaciens, Coprococcus comes and positively correlated with the abundance of several harmful strains, such as Citrobacter freundii, Enterococcus faecalis, Klebsiella aerogenes, Salmonella enterica. CONCLUSION: Altered concentrations of amino acids and their associations with the gut microbiota are implicated in the mucosal healing of UC patients and can serve as noninvasive diagnostic biomarkers.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26026389", + "title": "Pouch Inflammation Is Associated With a Decrease in Specific Bacterial Taxa.", + "year": 2015, + "journal": "Gastroenterology", + "authors": [ + "Reshef L", + "Kovacs A", + "Ofer A", + "Yahav L", + "Maharshak N", + "Keren N", + "Konikoff FM", + "Tulchinsky H", + "Gophna U", + "Dotan I" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6556776481254082, + "mesh_terms": [ + "Adult", + "Aged", + "Anti-Bacterial Agents", + "Bacteria", + "C-Reactive Protein", + "Case-Control Studies", + "Colitis, Ulcerative", + "Colonic Pouches", + "Dysbiosis", + "Feces", + "Female", + "Humans", + "Immunologic Factors", + "Inflammation Mediators", + "Israel", + "Male", + "Microbiota", + "Middle Aged", + "Pouchitis", + "Proctocolectomy, Restorative", + "Prospective Studies", + "RNA, Bacterial", + "RNA, Ribosomal, 16S", + "Ribotyping", + "Risk Factors", + "Severity of Illness Index", + "Young Adult" + ], + "raw_abstract": "BACKGROUND & AIMS: Pouchitis is a common long-term complication in patients with ulcerative colitis (UC) undergoing proctocolectomy with ileal pouch-anal anastomosis. Because the inflammation occurs in a previously normal small bowel, studies of this process might provide information about the development of Crohn's disease. Little is known about the intestinal microbiome of patients with pouchitis. We investigated whether specific bacterial populations correlate with the pouch disease phenotype and inflammatory activity. METHODS: We performed a prospective study of patients with UC who underwent pouch surgery (N = 131) from 1981 through 2012 and were followed at Tel Aviv Medical Center. Patients were assigned to groups based on their degree and type of pouch inflammation. Patients with familial adenomatous polyposis after pouch surgery (n = 9), individuals with intact colons undergoing surveillance colonoscopy (n = 10), and patients with UC who did not undergo surgery (n = 9) served as controls. We collected demographic and disease activity data (based on the Pouchitis Disease Activity Index) and measured levels of C-reactive protein. Fecal samples were collected, levels of calprotectin were measured, and microbiota were analyzed by 16S ribosomal RNA gene amplicon pyrosequencing. RESULTS: Increased proportions of the Fusobacteriaceae family correlated with increased disease activity and levels of C-reactive protein in patients with UC who underwent pouch surgery. In contrast, proportions of Faecalibacterium were reduced in patients with pouchitis vs controls; there was a negative correlation between proportion of Faecalibacterium and level of C-reactive protein. There was an association between antibiotic treatment, but not biologic or immunomodulatory therapy, with reduced proportions of 11 genera and with increased proportions of Enterococcus and Enterobacteriaceae. CONCLUSIONS: Reductions in protective bacteria and increases in inflammatory bacteria are associated with pouch inflammation in patients with UC who underwent pouch surgery. The finding that antibiotics exacerbate dysbiosis indicates that these drugs might not provide long-term benefit for patients with pouchitis. Additional studies of this form of dysbiosis could provide information about the pathogenesis of Crohn's disease.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37696680", + "title": "Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Del Chierico F", + "Cardile S", + "Baldelli V", + "Alterio T", + "Reddel S", + "Bramuzzo M", + "Knafelz D", + "Lega S", + "Bracci F", + "Torre G", + "Maggiore G", + "Putignani L" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6157648362160162, + "mesh_terms": [ + "Humans", + "Child", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Cholangitis, Sclerosing", + "Dysbiosis", + "RNA, Ribosomal, 16S", + "Bacteria", + "Bacteroidetes", + "Italy" + ], + "raw_abstract": "BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis. METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs). RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients. CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC. In this study, we report the gut microbiota and mycobiota dysbiosis in pediatric patients affected by primary sclerosing cholangitis (PSC) associated with ulcerative colitis (UC), with an increase in pro-inflammatory pathobionts and a reduction in anti-inflammatory commensals.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35184054", + "title": "Oral Corticosteroids Impair Mucin Production and Alter the Posttransplantation Microbiota in the Gut.", + "year": 2022, + "journal": "Digestion", + "authors": [ + "Okafuji H", + "Iida N", + "Kitamura K", + "Seishima J", + "Wang Z", + "Yutani M", + "Yoshio T", + "Yamashita T", + "Sakai Y", + "Honda M", + "Yamashita T", + "Fujinaga Y", + "Shinkura R", + "Hamaguchi Y", + "Mizukoshi E", + "Kaneko S" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5985788849523144, + "mesh_terms": [ + "Adrenal Cortex Hormones", + "Animals", + "Colitis, Ulcerative", + "Feces", + "Inflammation", + "Mice", + "Microbiota", + "Mucins", + "RNA, Ribosomal, 16S", + "Treatment Outcome" + ], + "raw_abstract": "INTRODUCTION: Gut microbiota alterations cause inflammation in patients with ulcerative colitis (UC). Fecal microbiota transplantation (FMT) enables manipulating the microbiota's composition, but the mechanisms underlying colonization of the posttransplantation microbiota are poorly understood. METHODS: In this open-label, nonrandomized study, the FMT efficacy and changes in the gut microbiota were evaluated in 8 UC patients with mild-to-moderately active endoscopic colonic lesions. Compositional changes in the fecal and mucosal microbiotas between donors and recipients were examined via 16S rRNA-based sequencing. To investigate the effects of oral corticosteroids on microbiota colonization, FMT was performed in germ-free prednisolone (PSL)-administered mice to examine the factors determining colonization. RESULTS: Four UC patients achieved clinical remission (CR) after FMT, and 3 also achieved endoscopic remission. The fecal microbiotas of the CR patients changed similar to those of the donors after FMT. The mucin-coding gene, MUC2, was less expressed in the colons of the PSL-dependent patients than in the PSL-free patients. In the mice, PSL treatment decreased the fecal mucin production and altered the posttransplantation fecal microbiota composition. Adding either exogenous mucin or the mucin secretagogue, rebamipide, partially alleviated the PSL-induced dysbiosis of the gut microbiota. Administering rebamipide with FMT from healthy donors relieved inflammation in mice with Enterococcus faecium-induced colitis. CONCLUSION: Colonic mucin controlled the gut microbiota composition, and oral corticosteroid treatment modified the gut microbiota partly by reducing the colonic mucin.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38521930", + "title": "Human-derived bacterial strains mitigate colitis via modulating gut microbiota and repairing intestinal barrier function in mice.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Dai J", + "Jiang M", + "Wang X", + "Lang T", + "Wan L", + "Wang J" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5951787363092838, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "Gastrointestinal Microbiome", + "Intestinal Barrier Function", + "RNA, Ribosomal, 16S", + "Colitis", + "Colitis, Ulcerative", + "Bacteroidetes", + "Enterococcus faecium", + "Escherichia coli", + "Mice, Inbred C57BL", + "Disease Models, Animal", + "Colon" + ], + "raw_abstract": "BACKGROUND: Unbalanced gut microbiota is considered as a pivotal etiological factor in colitis. Nevertheless, the precise influence of the endogenous gut microbiota composition on the therapeutic efficacy of probiotics in colitis remains largely unexplored. RESULTS: In this study, we isolated bacteria from fecal samples of a healthy donor and a patient with ulcerative colitis in remission. Subsequently, we identified three bacterial strains that exhibited a notable ability to ameliorate dextran sulfate sodium (DSS)-induced colitis, as evidenced by increased colon length, reduced disease activity index, and improved histological score. Further analysis revealed that each of Pediococcus acidilactici CGMCC NO.17,943, Enterococcus faecium CGMCC NO.17,944 and Escherichia coli CGMCC NO.17,945 significantly attenuated inflammatory responses and restored gut barrier dysfunction in mice. Mechanistically, bacterial 16S rRNA gene sequencing indicated that these three strains partially restored the overall structure of the gut microbiota disrupted by DSS. Specially, they promoted the growth of Faecalibaculum and Lactobacillus murinus, which were positively correlated with gut barrier function, while suppressing Odoribacter, Rikenella, Oscillibacter and Parasutterella, which were related to inflammation. Additionally, these strains modulated the composition of short chain fatty acids (SCFAs) in the cecal content, leading to an increase in acetate and a decrease in butyrate. Furthermore, the expression of metabolites related receptors, such as receptor G Protein-coupled receptor (GPR) 43, were also affected. Notably, the depletion of endogenous gut microbiota using broad-spectrum antibiotics completely abrogated these protective effects. CONCLUSIONS: Our findings suggest that selected human-derived bacterial strains alleviate experimental colitis and intestinal barrier dysfunction through mediating resident gut microbiota and their metabolites in mice. This study provides valuable insights into the potential therapeutic application of probiotics in the treatment of colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31333315", + "title": "Gut microbiota contributes to the distinction between two traditional Chinese medicine syndromes of ulcerative colitis.", + "year": 2019, + "journal": "World journal of gastroenterology", + "authors": [ + "Zhang YL", + "Cai LT", + "Qi JY", + "Lin YZ", + "Dai YC", + "Jiao N", + "Chen YL", + "Zheng L", + "Wang BB", + "Zhu LX", + "Tang ZP", + "Zhu RX" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.55876227166398, + "mesh_terms": [ + "Adult", + "Bacteria", + "Colitis, Ulcerative", + "Colon", + "DNA, Bacterial", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Male", + "Medicine, Chinese Traditional", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Retrospective Studies", + "Syndrome" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is considered to be closely associated with alteration of intestinal microorganisms. According to the traditional Chinese medicine (TCM) theory, UC can be divided into two disease syndromes called Pi-Xu-Shi-Yun (PXSY) and Da-Chang-Shi-Re (DCSR). The relationships among gut microbiota, TCM syndromes, and UC pathogenesis have not been well investigated. AIM: To investigate the role of gut microbiota in UC and the distinction of microbiota dysbiosis between PXSY and DCSR syndromes. METHODS: From May 2015 to February 2016, UC patients presenting to LongHua Hospital who met the established inclusion and exclusion criteria were enrolled in this retrospective study. Fresh stool specimens of UC patients with PXSY or DCSR were collected. The feces of the control group came from the health examination population of Longhua Hospital. The composition of gut bacterial communities in stool samples was determined by the pyrosequencing of 16S ribosomal RNA. The high-throughput sequencing reads were processed with QIIME, and biological functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. RESULTS: The composition of gut bacterial communities in 93 stool samples (30 healthy controls, 32 patients with PXSY syndrome, and 31 patients with DCSR syndrome) was determined by the pyrosequencing of 16S ribosomal RNA. Beta diversity showed that the composition of the microbiota was different among the three groups. At the family level, Porphyromonadaceae, Rikeneliaceae, and Lachnospiraceae significantly decreased while Enterococcus, Streptococcus, and other potential pathogens significantly increased in UC patients compared to healthy subjects. At the genus level, CONCLUSION: Our study suggests that the gut microbiota contributes to the distinction between the two TCM syndromes of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39938966", + "title": "Outcomes of oral vancomycin therapy in children with atypical ulcerative colitis with or without confirmed primary sclerosing cholangitis: a real-world observational study.", + "year": 2025, + "journal": "BMJ open gastroenterology", + "authors": [ + "R\u00e4is\u00e4nen L", + "Balouch F", + "McLaren-Kennedy A", + "Clark JE", + "Lewindon P" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5093577935935384, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Cholangitis, Sclerosing", + "Female", + "Male", + "Retrospective Studies", + "Child", + "Vancomycin", + "Administration, Oral", + "Treatment Outcome", + "Anti-Bacterial Agents", + "Adolescent", + "Recurrence", + "Colonoscopy", + "Australia", + "Leukocyte L1 Antigen Complex", + "Severity of Illness Index" + ], + "raw_abstract": "OBJECTIVES: Atypical ulcerative colitis (UC) presenting reverse gradient colitis, backwash ileitis, or rectal sparing and/or positive atypical antineutrophil cytoplasmic antibody serology is often associated with primary sclerosing cholangitis (PSC) and can be resistant to conventional medical therapies (CMT) for inflammatory bowel diseases. We report short-term and long-term outcomes of oral vancomycin therapy (OVT) in children with atypical UC and confirmed PSC in imaging/biopsy (PSC-UC) or treatment-resistant atypical UC without detectable PSC (aUC-non-PSC). METHODS: In this retrospective real-world observational study from a tertiary paediatric centre in Brisbane, Australia, 44 children with aUC (29 PSC-UC, 15 aUC-non-PSC) received 79 OVT courses between 2014 and 2023. Pre-post-OVT characteristics were compared and relapses/repeated courses were recorded. RESULTS: Pre-OVT, all had active colitis by Paediatric Ulcerative Colitis Activity Index (PUCAI), Feacal Calprotectin (FC) and/or colonoscopy. Post-OVT, PUCAI reduced from 15 (IQR 5-33) to 0 (IQR 0-5); 85% of children with pre-OVT PUCAI \u226510 achieved clinical remission (100% PSC-UC vs 64% aUC-non-PSC, p=0.019). FC reduced from 995 (IQR 319-1825) to 44 (IQR 16-79)\u2009\u00b5g/g; 83% of children with pre-OVT FC \u2265100\u2009\u00b5g/g achieved biochemical remission (92% PSC-UC vs 64% aUC-non-PSC, p=0.063). Colonoscopy confirmed Mayo 0 healing in 62% (67% PSC-UC vs 54% aUC-non-PSC, p=0.443) and 46% achieved pan-colonic histological remission (54% PSC-UC vs 31% aUC-non-PSC, p=0.173). All pre-post-OVT changes in these four markers were significant in both groups. After ceasing first OVT, 25/44 relapsed within 8.2 (IQR 1.9-14.5) months. Recommencing OVT regained biomarker remission in 13/25. During 3.8 (IQR 2.0-5.3) years of follow-up, 79 OVT courses in conjunction with CMT maintained deep remission in 67%. Routine stool testing (n=138) detected no vancomycin-resistant Enterococcus (VRE). CONCLUSIONS: OVT induced and reinduced remission in children with atypical UC. Relapse often followed ceasing vancomycin, half responded to reinduction. No VRE was developed.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "25916983", + "title": "Enterococcus faecalis Gelatinase Mediates Intestinal Permeability via Protease-Activated Receptor 2.", + "year": 2015, + "journal": "Infection and immunity", + "authors": [ + "Maharshak N", + "Huh EY", + "Paiboonrungruang C", + "Shanahan M", + "Thurlow L", + "Herzog J", + "Djukic Z", + "Orlando R", + "Pawlinski R", + "Ellermann M", + "Borst L", + "Patel S", + "Dotan I", + "Sartor RB", + "Carroll IM" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.4963102749051029, + "mesh_terms": [ + "Animals", + "Cell Line", + "Colon", + "Culture Media, Conditioned", + "Enterococcus faecalis", + "Epithelial Cells", + "Gelatinases", + "Humans", + "Intestinal Mucosa", + "Mice, Inbred C57BL", + "Mice, Knockout", + "Permeability", + "Receptor, PAR-2" + ], + "raw_abstract": "Microbial protease-mediated disruption of the intestinal epithelium is a potential mechanism whereby a dysbiotic enteric microbiota can lead to disease. This mechanism was investigated using the colitogenic, protease-secreting enteric microbe Enterococcus faecalis. Caco-2 and T-84 epithelial cell monolayers and the mouse colonic epithelium were exposed to concentrated conditioned media (CCM) from E. faecalis V583 and E. faecalis lacking the gelatinase gene (gelE). The flux of fluorescein isothiocyanate (FITC)-labeled dextran across monolayers or the mouse epithelium following exposure to CCM from parental or mutant E. faecalis strains indicated paracellular permeability. A protease-activated receptor 2 (PAR2) antagonist and PAR2-deficient (PAR2(-/-)) mice were used to investigate the role of this receptor in E. faecalis-induced permeability. Gelatinase (GelE) purified from E. faecalis V583 was used to confirm the ability of this protease to induce epithelial cell permeability and activate PAR2. The protease-mediated permeability of colonic epithelia from wild-type (WT) and PAR2(-/-) mice by fecal supernatants from ulcerative colitis patients was assessed. Secreted E. faecalis proteins induced permeability in epithelial cell monolayers, which was reduced in the absence of gelE or by blocking PAR2 activity. Secreted E. faecalis proteins induced permeability in the colonic epithelia of WT mice that was absent in tissues from PAR2(-/-) mice. Purified GelE confirmed the ability of this protease to induce epithelial cell permeability via PAR2 activation. Fecal supernatants from ulcerative colitis patients induced permeability in the colonic epithelia of WT mice that was reduced in tissues from PAR2(-/-) mice. Our investigations demonstrate that GelE from E. faecalis can regulate enteric epithelial permeability via PAR2.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39604394", + "title": "Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease.", + "year": 2024, + "journal": "Nature communications", + "authors": [ + "Akiyama S", + "Nishijima S", + "Kojima Y", + "Kimura M", + "Ohsugi M", + "Ueki K", + "Mizokami M", + "Hattori M", + "Tsuchiya K", + "Uemura N", + "Kawai T", + "Bork P", + "Nagata N" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.482130594685921, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Crohn Disease", + "Gastrointestinal Microbiome", + "Feces", + "Male", + "Metagenomics", + "Female", + "Bacteriophages", + "Adult", + "Escherichia coli", + "Middle Aged", + "Japan", + "Fungi", + "Bacteria", + "Metagenome", + "Saccharomyces cerevisiae", + "Bifidobacterium", + "Virome", + "Enterococcus faecium", + "Fatty Acids, Volatile", + "Young Adult", + "China", + "Case-Control Studies" + ], + "raw_abstract": "The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39661894", + "title": "Differentiated approach to management of patients with irritable bowel syndrome and ulcerative colitis in non-alcoholic fatty liver disease.", + "year": 2024, + "journal": "Wiadomosci lekarskie (Warsaw, Poland : 1960)", + "authors": [ + "Sirchak YS", + "Kornash VV", + "Dutko OO", + "Lopit MM", + "Ustych OV", + "Griga VI" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.4539399079031216, + "mesh_terms": [ + "Adult", + "Female", + "Humans", + "Male", + "Middle Aged", + "alpha 1-Antitrypsin", + "Bifidobacterium", + "Biomarkers", + "Colitis, Ulcerative", + "Diagnosis, Differential", + "Dysbiosis", + "Early Diagnosis", + "Enterococcus", + "Escherichia coli", + "Feces", + "Gastrointestinal Microbiome", + "Irritable Bowel Syndrome", + "Lactobacillus", + "Leukocyte L1 Antigen Complex", + "Non-alcoholic Fatty Liver Disease", + "Severity of Illness Index", + "Case-Control Studies" + ], + "raw_abstract": "OBJECTIVE: Aim: To determine the main clinical and laboratory features and severity of colon dysbiosis in irritable bowel syndrome (IBS) and IBD in patients with NAFLD. PATIENTS AND METHODS: Materials and Methods: 80 patients with NAFLD were examined. Patients were divided into two groups. Group 1 (n=40) included patients with NAFLD in combination with ulcerative colitis (UC), and group 2 (n=40) included patients with NAFLD and IBS (clinically manifested by diarrhoea). At patients diagnosed the level of faecal calprotectin (FC) and a1-antirpsin (a1-AT). Changes in the quantitative and qualitative composition of the colon microflora were assessed. RESULTS: Results: In both groups of examined patients, a decrease of Bifidobacteria and Lactobacilli, as well as Enterococcus and E. coli with normal enzymatic properties was found compared with the control group. In patients with NAFLD and IBD, an increase in the level of FC was found in 23.8 times compared with the control group. As expected, there was an increase in the level of a1-AT in the blood serum, faeces and its clearance in patients of group 1. CONCLUSION: Conclusions: In patients with NAFLD, both UC and \u0406BS have similar clinical symptoms. An effective biomarker for differentiating and choosing treatment tactics in patients with NAFLD and UC is the determination of the level of FC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34103031", + "title": "Effect of the standard herbal preparation, STW5, treatment on dysbiosis induced by dextran sodium sulfate in experimental colitis.", + "year": 2021, + "journal": "BMC complementary medicine and therapies", + "authors": [ + "Mohamed SS", + "Abdeltawab NF", + "Wadie W", + "Ahmed LA", + "Ammar RM", + "Rabini S", + "Abdel-Aziz H", + "Khayyal MT" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.4514413256165948, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Dextran Sulfate", + "Disease Models, Animal", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Plant Extracts", + "Rats, Wistar", + "Rats" + ], + "raw_abstract": "BACKGROUND: The standardized herbal preparation, STW 5, is effective clinically in functional gastrointestinal disorders and experimentally in ulcerative colitis (UC). The present study explores whether the beneficial effect of STW 5 involves influencing the intestinal microbiota. METHODS: UC was induced in Wistar rats by feeding them 5% dextran sodium sulfate (DSS) in drinking water for 7\u2009days. Rats were treated concurrently with STW 5 and sacrificed 24\u2009h after last drug administration. Fecal samples were used to determine changes in the abundance of selected microbial phyla and genera using real-time PCR. RESULTS: Induction of UC led to dysbiosis and changes in the gut microbiota. The changes included an increase in some genera of the Firmicutes, namely Enterococcus, and a decrease in others, namely Blautia, Clostridium, and Lactobacillus. DSS further induced a marked increase in the abundance of Bacteroidetes and Proteobacteria as well as in the relative abundance of Actinobacteria and its genus Bifidobacterium. Methanobrevibacter levels (phylum Euryarchaeota) were also increased. Microbial dysbiosis was associated with changes in various parameters of colonic inflammation. STW 5 effectively guarded against those changes and significantly affected the indices of edema and inflammation in the UC model. Changes in colon length, colon mass index, inflammatory and apoptotic markers, and histological changes induced by DSS were also prevented. CONCLUSIONS: Dysbiosis plays a contributing role in the development of DSS-induced UC. Derangements in the microbial flora and associated inflammatory processes were largely prevented by STW 5, suggesting that this effect might contribute towards its beneficial usefulness in this condition.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29135456", + "title": "Probiotics and Their Use in Inflammatory Bowel Disease.", + "year": 2018, + "journal": "Alternative therapies in health and medicine", + "authors": [ + "Amer M", + "Nadeem M", + "Nazir SUR", + "Fakhar M", + "Abid F", + "Ain QU", + "Asif E" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.42407637200730647, + "mesh_terms": [ + "Humans", + "Inflammatory Bowel Diseases", + "Lactobacillus", + "Pakistan", + "Probiotics" + ], + "raw_abstract": "Context \u2022 Crohn's disease and ulcerative colitis result in similar gastrointestinal (GI) symptoms, including pain, diarrhea, stools with mucus or blood, and ulceration or tissue damage within the alimentary canal. Gut microbiota play a crucial role in triggering, maintaining, and exacerbating inflammatory bowel disease (IBD). Probiotics might help to rebalance the gut flora in a positive way, shifting from pro- to anti-inflammatory. Objectives \u2022 The study intended to investigate the safety and use of probiotics and the biological effects of probiotic bacteria on IBD. Design \u2022 The research team performed a literature review. The team conducted a database search in April 2015 using Google Scholar and PubMed to find studies relevant to probiotics and their use in IBD. Only papers that were published in English were considered, and all available years in each database were searched. The initial search identified 38 published articles, for which the research team obtained full texts and independently read them in full to identify those papers suitable for inclusion in the review. Setting \u2022 The study took place in the main library of the University of Lahore (Islamabad, Pakistan). Results \u2022 Many strains of probiotics exist, but the most common strains available today are (1) the Bifidobacterium species, (2) Enterococcus faecium, (4) the Lactobacillus strains, (4) Saccharomyces boulardii, (5) the Bacillus species, and (6) Pediococcus, all used to produce beneficial health effects. These species showed their beneficial effects on the host using different mechanisms involving (1) production of proteins, quorum sensing signaling inhibitors, butyrate, immunoglobulin A, and short-chain fatty acids; (2) decreased production of tumor necrosis factor alpha and interleukin 8; (3) increased expression of mucin 2; and (4) increased upregulation of defensin. Conclusions \u2022 Studies on probiotics in animal models of IBD are promising, and clinical results in IBD patients are encouraging; however, the data are limited, and few studies are placebo controlled. Additional placebo-controlled, double-blind studies in IBD are required before recommendations can be offered for routine use of probiotics in IBD. Additional organisms may eventually be developed through genetic engineering. The current evidence also indicates that probiotic effects are strain specific; they do not act through the same mechanisms nor are all probiotics indicated for the same health conditions. More research is needed to determine what strains and at what dose probiotics become more useful as part of a clinical intervention.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31605691", + "title": "Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy.", + "year": 2020, + "journal": "Gastroenterology", + "authors": [ + "Dubinsky V", + "Reshef L", + "Bar N", + "Keizer D", + "Golan N", + "Rabinowitz K", + "Godny L", + "Yadgar K", + "Zonensain K", + "Tulchinsky H", + "Gophna U", + "Dotan I" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.3791447419293631, + "mesh_terms": [ + "Adult", + "Anti-Bacterial Agents", + "Bacteria", + "Ciprofloxacin", + "Cytokines", + "Drug Resistance, Bacterial", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "HT29 Cells", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Metagenomics", + "Metronidazole", + "Middle Aged", + "Point Mutation", + "Pouchitis", + "Prospective Studies", + "Recurrence", + "Treatment Outcome", + "Virulence Factors", + "Young Adult" + ], + "raw_abstract": "BACKGROUND & AIMS: Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic-dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial factors associated with response to antibiotic treatment and development of antibiotic dependence in patients with pouchitis. METHODS: We performed a prospective study of 49 patients who had undergone pouch surgery at a tertiary center. Disease activity was determined based on clinical, endoscopic, and histologic criteria. Pouch phenotype was defined as recurrent-acute pouchitis (n\u00a0= 6), chronic pouchitis and Crohn's-like disease of the pouch (n\u00a0= 27), normal pouch from patient with ulcerative colitis (n\u00a0= 10), and normal pouch from patient with familial adenomatous polyposis (n\u00a0= 6). Fecal samples (n\u00a0= 234) were collected over time during or in the absence of antibiotic treatment (ciprofloxacin and/or metronidazole). Thirty-three patients were treated with antibiotics, for a median of 425 days of cumulative antibiotic therapy, during follow-up. Calprotectin was measured and fecal DNA was sequenced using shotgun metagenomics and analyzed with specifically designed bioinformatic pipelines. Bacterial strains were isolated from fecal samples. We assessed their ciprofloxacin resistance and ability to induce secretion of inflammatory cytokines by HT-29 intestinal epithelial cells. RESULTS: Most antibiotic-treated patients (79%) had a clinical response to each course of antibiotics; however, 89% of those who completed a 4-week course relapsed within 3 months. Median calprotectin levels decreased by 40% in response to antibiotics. Antibiotic treatment reduced disease-associated bacteria such as Clostridium perfringens, Ruminococcus gnavus, and Klebsiella pneumoniae, but also beneficial species, such as Faecalibacterium prausnitzii. The microbiomes of antibiotic-responsive patients were dominated by facultative anaerobic genera (Escherichia, Enterococcus, and Streptococcus), with multiple ciprofloxacin-resistance mutations in drug target genes and confirmed drug resistance. However, these strains had lower potential for virulence and did not induce secretion of inflammatory cytokines by epithelial cells. After antibiotic cessation, patients had an abrupt shift in microbiome composition, with blooms of oral and disease-associated bacteria. In addition, antibiotic treatment enriched for strains that acquired multidrug resistance loci, encoding enzymes that confer resistance to nonrelated antibiotics, including extended-spectrum beta-lactamases. CONCLUSIONS: The efficacy of antibiotic treatment of pouchitis might be attributed to the establishment of an antibiotic-resistant microbiome with low inflammatory potential. This microbiome might provide resistance against colonization by bacteria that promote inflammation. To avoid progression to antibiotic-dependent disease and its consequences, strategies such as short-term alternating antibiotics and nutrition- and microbiome-based interventions should be considered.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36327509", + "title": "In vitro fermentation characteristics of the dietary fiber in bamboo (Phyllostachys edulis) shoots and its regulatory effects on the intestinal microbiota and metabolites.", + "year": 2023, + "journal": "Food chemistry", + "authors": [ + "Wu W", + "Li Q", + "Chen H", + "Fang X", + "Niu B", + "Liu R", + "Mu H", + "Gao H" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.33098025404675113, + "mesh_terms": [ + "Animals", + "Mice", + "Gastrointestinal Microbiome", + "Dextran Sulfate", + "Fermentation", + "Dietary Fiber", + "Colitis, Ulcerative", + "Colon", + "Poaceae", + "Disease Models, Animal", + "Colitis", + "Mice, Inbred C57BL" + ], + "raw_abstract": "The effects of bamboo (Phyllostachys edulis) shoot dietary fiber (BSDF-1) on ulcerative colitis (UC) are unclear. Therefore, we performed an in vitro glycolysis study of intestinal microbiota samples, based on 16S rDNA sequencing and determining the metabolites in non-targeted colonic fecal fermentation broth. After a 48\u00a0h fermentation, the pH of the fermentation broth decreased significantly (p\u00a0<\u00a00.05) with the dextran sulfate sodium group (referred to here as the Mod group). The carbohydrate utilization rate was 26.59\u00a0%, and the total short-chain fatty acid content was 16.46\u00a0\u00b1\u00a00.71\u00a0mmol/L. The abundances of Alistipes and Lactobacillus increased after BDSF-1 fermentation, whereas those of Escherichia-Shigella, Enterococcus, and Proteus significantly decreased. BSDF-1 altered the levels of 17 metabolites in the Mod group after fermentation for 48\u00a0h, which reduced the cadaverine increasing induced by DSS. These results indicate that BSDF-1 can regulate the metabolism of the intestinal microbiota and the host, suggesting its use as a promising therapeutic strategy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29361092", + "title": "Safety, Clinical Response, and Microbiome Findings Following Fecal Microbiota Transplant in Children With Inflammatory Bowel Disease.", + "year": 2018, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Goyal A", + "Yeh A", + "Bush BR", + "Firek BA", + "Siebold LM", + "Rogers MB", + "Kufen AD", + "Morowitz MJ" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.3176443507922425, + "mesh_terms": [ + "Adolescent", + "Bacteria", + "Biomarkers", + "Child", + "Fecal Microbiota Transplantation", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Prospective Studies", + "Remission Induction", + "Severity of Illness Index" + ], + "raw_abstract": "BACKGROUND: The role of fecal microbiota transplant (FMT) in the treatment of pediatric inflammatory bowel disease (IBD) is unknown. The aims of this study were to assess safety, clinical response, and gut microbiome alterations in children with Crohn's disease (CD), ulcerative colitis (UC), or indeterminate colitis (IC). METHODS: In this open-label, single-center prospective trial, patients with IBD refractory to medical therapy underwent a single FMT by upper and lower endoscopy. Adverse events, clinical response, gut microbiome, and biomarkers were assessed at baseline, 1 week, 1 month, and 6 months following FMT. RESULTS: Twenty-one subjects were analyzed, with a median age of 12 years, of whom 57% and 28% demonstrated clinical response at 1 and 6 months post-FMT, respectively. Two CD patients were in remission at 6 months. Adverse events attributable to FMT were mild to moderate and self-limited. Patients prior to FMT showed decreased species diversity and significant microbiome compositional differences characterized by increased Enterobacteriaceae, Enterococcus, Haemophilus, and Fusobacterium compared with donors and demonstrated increased species diversity at 30 days post-FMT. At 6 months, these changes shifted toward baseline. Clinical responders had a higher relative abundance of Fusobacterium and a lower diversity at baseline, as well as a greater shift toward donor-like microbiome after FMT compared with nonresponders. CONCLUSIONS: A single FMT is relatively safe and can result in a short-term response in young patients with active IBD. Responders possessed increased Fusobacterium prior to FMT and demonstrated more significant microbiome changes compared with nonresponders after FMT. Microbiome characteristics may help in predicting response.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37770177", + "title": "Phage therapy in gut microbiome.", + "year": 2023, + "journal": "Progress in molecular biology and translational science", + "authors": [ + "Chen X", + "Mendes BG", + "Alves BS", + "Duan Y" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.2803441522492126, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Phage Therapy", + "Gastrointestinal Tract", + "Bacteria", + "Microbiota", + "Anti-Bacterial Agents" + ], + "raw_abstract": "Phage therapy, the use of bacteriophage viruses for bacterial infection treatment, has been around for almost a century, but with the increase in antibiotic use, its importance has declined rapidly. There has been renewed interest in revisiting this practice due to the general decline in the effectiveness of antibiotics, combined with improved understanding of human microbiota and advances in sequencing technologies. Phage therapy has been proposed as a clinical alternative to restore the gut microbiota in the absence of an effective treatment. That is due to its immunomodulatory and bactericidal effects against its target bacteria. In the gastrointestinal diseases field, phage therapy has been studied mainly as a promising tool in infectious diseases treatment, such as cholera and diarrhea. However, many studies have been conducted in non-communicable diseases, such as the targeting of adherent invasive Escherichia coli in Crohn's disease, the treatment of Clostridioides difficile in ulcerative colitis, the eradication of Fusobacterium nucleatum in colorectal cancer, the targeting of alcohol-producing Klebsiella pneumoniae in non-alcoholic fatty liver disease, or Enterococcus faecalis in alcohol-associated hepatitis. This review will summarize the changes in the gut microbiota and the phageome in association with some gastrointestinal and liver diseases and highlight the recent scientific advances in phage therapy as a therapeutic tool for their treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34627158", + "title": "Stool preparation under anaerobic conditions contributes to retention of obligate anaerobes: potential improvement for fecal microbiota transplantation.", + "year": 2021, + "journal": "BMC microbiology", + "authors": [ + "Shimizu H", + "Arai K", + "Asahara T", + "Takahashi T", + "Tsuji H", + "Matsumoto S", + "Takeuchi I", + "Kyodo R", + "Yamashiro Y" + ], + "bacteria": "Enterococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.23346626192971684, + "mesh_terms": [ + "Anaerobiosis", + "Bacteria, Anaerobic", + "Fecal Microbiota Transplantation", + "Feces", + "Humans", + "RNA, Ribosomal, 16S", + "RNA, Ribosomal, 23S", + "Specimen Handling" + ], + "raw_abstract": "BACKGROUND: Fecal microbiota transplantation (FMT) in patients with ulcerative colitis has shown variable efficacy depending on the protocol used. A previous randomized controlled trial reported that anaerobic preparation of donor stool contributes to improved efficacy. Despite the suggestion that viable obligate anaerobes would be decreased through aerobic handling, there have been only a limited number of reports on how these aerobic or anaerobic procedures affect the composition of viable microbiota in the fecal slurries used for FMT. METHODS: We adopted 16S and 23S rRNA-targeted reverse transcription-quantitative polymerase chain reaction to quantify viable bacteria in fecal slurries. This study utilized specific primers designed to detect obligate anaerobes (including Clostridium coccoides group, C. leptum subgroup, Bacteroides fragilis group, Bifidobacterium, Atopobium cluster, and Prevotella) and facultative anaerobes (including total lactobacilli, Enterobacteriaceae, Enterococcus, Streptococcus, and Staphylococcus). We then calculated the ratio change (RC) between before and after mixing, and compared the resulting values between anaerobic-prep and aerobic-prep in samples fixed immediately after blending (RC RESULTS: For most obligate anaerobes, the median RC tended to be less than 1, indicating that the number of obligate anaerobes was decreased by the blending procedure. However, in samples maintained for 1\u2009h after blending, anaerobic-prep counteracted the decrease otherwise seen for the C. coccoides group and B. fragilis groups (P\u2009<\u20090.01 for both). The C. leptum subgroup also tended to show higher RC by anaerobic-prep than by aerobic-prep, although this effect was not statistically significant. Among facultative anaerobes, Enterobacteriaceae, Enterococcus, and Staphylococcus showed median RC values of more than 1, indicating that these organisms survived and even grew after mixing. Moreover, oxygen exposure had no significant influence on the survival of the facultative anaerobes. CONCLUSIONS: The conditions under which the blending procedure was performed affected the proportion of live anaerobes in fecal slurries. The obligate anaerobes tended to be decreased by blending processes, but anaerobic-prep significantly mitigated this effect. Anaerobic-prep may improve the efficacy of FMT by permitting the efficient transfer of obligate anaerobes to patients with ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38029703", + "title": "Altered metabolome and microbiome features provide clues in predicting recurrence of ulcerative colitis.", + "year": 2024, + "journal": "Journal of pharmaceutical and biomedical analysis", + "authors": [ + "Liu H", + "Feng X", + "Wang D", + "Liu L", + "Liu Y", + "Liu B", + "Zhu L", + "Zhang C", + "Yang W" + ], + "bacteria": "UCG-005", + "condition": "ulcerative colitis", + "relevance_score": 0.7356759877050981, + "mesh_terms": [ + "Humans", + "Animals", + "Colitis, Ulcerative", + "Chromatography, Liquid", + "RNA, Ribosomal, 16S", + "Tandem Mass Spectrometry", + "Microbiota", + "Metabolome", + "Biomarkers", + "Dextran Sulfate", + "Disease Models, Animal" + ], + "raw_abstract": "PURPOSE: Many studies have shown that the imbalance of the intestinal flora and metabolite can lead to the development of ulcerative colitis (UC), but their role in recurrent-UC is still unclear. We studied the intestinal flora and metabolites associated with recurrent-UC to elucidate the mechanism and biomarkers of recurrent-UC. METHODS: Ulcerative colitis (UC) models in active, remission, and recurrence stages were established, and the abundance of intestinal flora was determined by 16\u00a0S rRNA sequencing. The changes in the metabolites present in feces and serum were analyzed by UPLC-MS/MS. RESULTS: We identified 24 metabolites in feces and serum, which might be used as diagnostic and predictive biomarkers of recurrent-UC. The dominant flora of recurrent-UC included Romboutsia, UCG-005, etc. The results of a network analysis found that long-chain fatty acids and phenylalanine were strongly correlated with Firmicutes and Proteobacteria, which indicated that the recurrence of UC might be closely related to metabolites and microorganisms. CONCLUSION: The changes in intestinal microbiota and metabolites are closely related to the development of UC. Microbiota is an important inducer of UC, which can regulate metabolites through the 'microorganism-gut-metabolite' axis. It may provide a new method for the prediction and treatment of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29126267", + "title": "Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis.", + "year": 2017, + "journal": "FEMS microbiology ecology", + "authors": [ + "Mancabelli L", + "Milani C", + "Lugli GA", + "Turroni F", + "Cocconi D", + "van Sinderen D", + "Ventura M" + ], + "bacteria": "UCG-005", + "condition": "ulcerative colitis", + "relevance_score": 0.6404522721417891, + "mesh_terms": [ + "Bacteria", + "Biodiversity", + "Biomarkers", + "Colitis, Ulcerative", + "Crohn Disease", + "Enterocolitis, Pseudomembranous", + "Gastrointestinal Microbiome", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Intestines", + "Polymerase Chain Reaction", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Intestinal diseases, such as Crohn's disease (CD), ulcerative colitis (UC) and pseudomembranous colitis (CDI), are among the most common diseases in humans and may lead to more serious pathologies, e.g. colorectal cancer (CRC). Next generation sequencing has in recent years allowed the identification of correlations between intestinal bacteria and diseases, although the formulation of universal gut microbial biomarkers for such diseases is only in its infancy. In the current study, we selected and reanalyzed a total of 3048 public datasets obtained from 16S rRNA profiling of individuals affected by CD, UC, CDI and CRC. This meta-analysis revealed possible biases in the reconstruction of the gut microbiota composition due to the use of different primer pairs employed for PCR of 16S rRNA gene fragments. Notably, this approach also identified common features of individuals affected by gut diseases (DS), including lower biodiversity compared to control subjects. Moreover, potential universal intestinal disease microbial biomarkers were identified through cross-disease comparisons. In detail, CTRL showed high abundance of the genera Barnesiella, Ruminococcaceae UCG-005, Alistipes, Christensenellaceae R-7 group and unclassified member of Lachnospiraceae family, while DS exhibited high abundance of Lactobacillus, unclassified member of Erysipelotrichaceae family and Streptococcus genera.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37946238", + "title": "The oral bacterial microbiota facilitates the stratification for ulcerative colitis patients with oral ulcers.", + "year": 2023, + "journal": "Annals of clinical microbiology and antimicrobials", + "authors": [ + "Xu J", + "Zhang Y", + "Fang XH", + "Liu Y", + "Huang YB", + "Ke ZL", + "Wang Y", + "Zhang YF", + "Zhang Y", + "Zhou JH", + "Su HT", + "Chen N", + "Liu YL" + ], + "bacteria": "Oribacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7553721693404465, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Oral Ulcer", + "RNA, Ribosomal, 16S", + "Gastrointestinal Microbiome", + "Microbiota", + "Inflammatory Bowel Diseases", + "Bacteria", + "Feces", + "Mesalamine" + ], + "raw_abstract": "BACKGROUND: Clinically, a large part of inflammatory bowel disease (IBD) patients is complicated by oral lesions. Although previous studies proved oral microbial dysbiosis in IBD patients, the bacterial community in the gastrointestinal (GI) tract of those IBD patients combined with oral ulcers has not been profiled yet. METHODS: In this study, we enrolled four groups of subjects, including healthy controls (CON), oral ulcer patients (OU), and ulcerative colitis patients with (UC_OU) and without (UC) oral ulcers. Bio-samples from three GI niches containing salivary, buccal, and fecal samples, were collected for 16S rRNA V3-V4 region sequencing. Bacterial abundance and related bio-functions were compared, and data showed that the fecal microbiota was more potent than salivary and buccal microbes in shaping the host immune system.\u2009~\u200922 UC and 10 UC_OU 5-aminosalicylate (5-ASA) routine treated patients were followed-up for six months; according to their treatment response (a decrease in the endoscopic Mayo score), they were further sub-grouped as responding and non-responding patients. RESULTS: We found those UC patients complicated with oral ulcers presented weaker treatment response, and three oral bacterial genera, i.e., Fusobacterium, Oribacterium, and Campylobacter, might be connected with treatment responding. Additionally, the salivary microbiome could be an indicator of treatment responding in 5-ASA routine treatment rather than buccal or fecal ones. CONCLUSIONS: The fecal microbiota had a strong effect on the host's immune indices, while the oral bacterial microbiota could help stratification for ulcerative colitis patients with oral ulcers. Additionally, the oral microbiota had the potential role in reflecting the treatment response of UC patients. Three oral bacteria genera (Fusobacterium, Oribacterium, and Campylobacter) might be involved in UC patients with oral ulcers lacking treatment responses, and monitoring oral microbiota may be meaningful in assessing the therapeutic response in UC patients.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29615776", + "title": "Dysbiosis of the salivary microbiota in pediatric-onset primary sclerosing cholangitis and its potential as a biomarker.", + "year": 2018, + "journal": "Scientific reports", + "authors": [ + "Iwasawa K", + "Suda W", + "Tsunoda T", + "Oikawa-Kawamoto M", + "Umetsu S", + "Takayasu L", + "Inui A", + "Fujisawa T", + "Morita H", + "Sogo T", + "Hattori M" + ], + "bacteria": "Oribacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.7004462988893462, + "mesh_terms": [ + "Adolescent", + "Biomarkers", + "Case-Control Studies", + "Child", + "Cholangitis, Sclerosing", + "Dysbiosis", + "Female", + "Humans", + "Male", + "Phenotype", + "RNA, Ribosomal, 16S", + "Saliva" + ], + "raw_abstract": "Primary sclerosing cholangitis (PSC) is a liver disease known for its frequent concurrence with inflammatory bowel disease. Dysbiosis of the gut microbiota in PSC was reported in several studies, but the microbiological features of the salivary microbiota in PSC have not been established. Here we compared the salivary microbial communities of 24 pediatric-onset PSC patients, 16 age-matched ulcerative colitis (UC) patients, and 24 healthy controls (HCs) by analyzing the bacterial 16S rRNA gene sequence data. The species-richness (\u03b1-diversity) showed no significant between-group differences, whereas the overall salivary microbiota structure (\u03b2-diversity) showed significant differences among the three groups. Taxonomic assignment revealed that the PSC salivary microbiota were characterized by significant decreases in the abundance of Rothia and Haemophilus compared to the HC group, and significantly decreased Haemophilus and increased Oribacterium compared to the UC group. By combining the genera selected by the random forest algorithm in machine learning, followed by confirmation with 10-fold cross-validation, we were able to distinguish the PSC group from the HC group with the area under the curve (AUC) of 0.7423, and from the UC group with the AUC of 0.8756. Our results indicate the potential of salivary microbiota as biomarkers for a noninvasive diagnosis of PSC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37507685", + "title": "Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population.", + "year": 2023, + "journal": "BMC gastroenterology", + "authors": [ + "Alsulaiman RM", + "Al-Quorain AA", + "Al-Muhanna FA", + "Piotrowski S", + "Kurdi EA", + "Vatte C", + "Alquorain AA", + "Alfaraj NH", + "Alrezuk AM", + "Robinson F", + "Dowdell AK", + "Alamri TA", + "Hamilton L", + "Lad H", + "Gao H", + "Gandla D", + "Keating BJ", + "Meng R", + "Piening B", + "Al-Ali AK" + ], + "bacteria": "Harryflintia", + "condition": "ulcerative colitis", + "relevance_score": 0.6427295074351848, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Saudi Arabia", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Crohn Disease" + ], + "raw_abstract": "BACKGROUND: Crohn's diseases and ulcerative colitis, both of which are chronic immune-mediated disorders of the gastrointestinal tract are major contributors to the overarching Inflammatory bowel diseases. It has become increasingly evident that the pathological processes of IBDs results from interactions between genetic and environmental factors, which can skew immune responses against normal intestinal flora. METHODS: The aim of this study is to assess and analyze the taxa diversity and relative abundances in CD and UC in the Saudi population. We utilized a sequencing strategy that targets all variable regions in the 16\u00a0S rRNA gene using the Swift Amplicon 16\u00a0S rRNA Panel on Illumina NovaSeq 6000. RESULTS: The composition of stool 16\u00a0S rRNA was analyzed from 219 patients with inflammatory bowel disease and from 124 healthy controls. We quantified the abundance of microbial communities to examine any significant differences between subpopulations of samples. At the genus level, two genera in particular, Veillonella and Lachnoclostridium showed significant association with CD versus controls. There were significant differences between subjects with CD versus UC, with the top differential genera spanning Akkermansia, Harryflintia, Maegamonas and Phascolarctobacterium. Furthermore, statistically significant taxa diversity in microbiome composition was observed within the UC and CD groups. CONCLUSIONS: In conclusion we have shown that there are significant differences in gut microbiota between UC, CD and controls in a Saudi Arabian inflammatory bowel disease cohort. This reinforces the need for further studies in large populations that are ethnically and geographically diverse. In addition, our results show the potential to develop classifiers that may have add additional richness of context to clinical diagnosis of UC and CD with larger inflammatory bowel disease cohorts.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33970546", + "title": "Gut dysbiosis and clinical phases of pancolitis in patients with ulcerative colitis.", + "year": 2021, + "journal": "MicrobiologyOpen", + "authors": [ + "Maldonado-Arriaga B", + "Sandoval-Jim\u00e9nez S", + "Rodr\u00edguez-Silverio J", + "Lizeth Alcar\u00e1z-Estrada S", + "Cort\u00e9s-Espinosa T", + "P\u00e9rez-Cabeza de Vaca R", + "Licona-Cassani C", + "G\u00e1mez-Valdez JS", + "Shaw J", + "Mondrag\u00f3n-Ter\u00e1n P", + "Hern\u00e1ndez-Cortez C", + "Su\u00e1rez-Cuenca JA", + "Castro-Escarpulli G" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.7576783819583092, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biodiversity", + "Colitis", + "Colitis, Ulcerative", + "DNA, Bacterial", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "RNA, Ribosomal, 16S", + "Severity of Illness Index" + ], + "raw_abstract": "Ulcerative colitis (UC) is a frequent type of inflammatory bowel disease, characterized by periods of remission and exacerbation. Gut dysbiosis may influence pathophysiology and clinical response in UC. The purpose of this study was to evaluate whether gut microbiota is related to the active and remission phases of pancolitis in patients with UC as well as in healthy participants. Fecal samples were obtained from 18 patients with UC and clinical-endoscopic evidenced pancolitis (active phase n\u00a0=\u00a09 and remission phase n\u00a0=\u00a09), as well as 15 healthy participants. After fecal DNA extraction, the 16S rRNA gene was amplified and sequenced (Illumina MiSeq), operational taxonomic units were analyzed with the QIIME software. Gut microbiota composition revealed a higher abundance of the phyla Proteobacteria and Fusobacteria in active pancolitis, as compared with remission and healthy participants. Likewise, a marked abundance of the genus Bilophila and Fusobacteria were present in active pancolitis, whereas a higher abundance of Faecalibacterium characterized both remission and healthy participants. LEfSe analysis showed that the genus\u00a0Roseburia\u00a0and Faecalibacterium were enriched in remission pancolitis, and genera\u00a0Bilophila\u00a0and\u00a0Fusobacterium\u00a0were enriched in active pancolitis. The relative abundance of Fecalibacterium and Roseburia showed a higher correlation with fecal calprotectin, while Bilophila and Fusobacterium showed AUCs (area under the curve) of 0.917 and 0.988 for active vs. remission pancolitis. The results of our study highlight the relation of gut dysbiosis with clinically relevant phases of pancolitis in patients with UC. Particularly, Fecalibacterium, Roseburia, Bilophila, and Fusobacterium were identified as genera highly related to the different clinical phases of pancolitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28852861", + "title": "Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.", + "year": 2018, + "journal": "Journal of gastroenterology", + "authors": [ + "Nishino K", + "Nishida A", + "Inoue R", + "Kawada Y", + "Ohno M", + "Sakai S", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Kawahara M", + "Naito Y", + "Andoh A" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.7404425867634223, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Endoscopy, Gastrointestinal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. METHODS: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. RESULTS: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. \u03b1-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. CONCLUSIONS: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33598970", + "title": "Adsorptive granulomonocytapheresis alters the gut bacterial microbiota in patients with active ulcerative colitis.", + "year": 2021, + "journal": "Journal of clinical apheresis", + "authors": [ + "Chen X", + "Lou L", + "Tang H", + "Tan X", + "Bi J", + "Wu H", + "Li N", + "Wang Y", + "Mao J" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.7241981999644483, + "mesh_terms": [ + "Adult", + "Colitis, Ulcerative", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Granulocytes", + "Humans", + "Leukapheresis", + "Male", + "Middle Aged", + "Monocytes", + "Prospective Studies" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is a refractory disease with unclear etiology. Studies have shown that UC is closely associated with gut microbiota dysbiosis. Adsorptive granulomonocytapheresis (GMA) using an Adacolumn has been found to treat UC effectively, but its underlying mechanism of treatment has not been fully elucidated. In this study, we aimed to investigate the influence of GMA on the gut microbiota in patients with active UC. METHODS: We conducted a single-center prospective analysis of patients with active UC who received GMA therapy and ultimately achieved clinical remission. Stool samples of healthy controls and patients before and after 5 or 10 sessions of GMA therapy were collected. Subsequently, high-throughput sequencing of the 16S rRNA V3 and V4 gene region of the stool was conducted and clustering of operational taxonomic units and species annotation were performed. RESULTS: Gut microbial profiles in patients with UC were characterized by low bacterial diversity. After 5 or 10 sessions of GMA therapy, the gut microbiota diversity in patients with UC increased and was similar to that of healthy controls. UC was further characterized by increased abundances of Proteobacteria and Bacteroides, as well as decreased abundances of Faecalibacterium, Roseburia, Firmicutes, and Dialister; however, after GMA therapy, the abundance of Bacteroides decreased, whereas those of Faecalibacterium, Roseburia, and Firmicutes increased. CONCLUSIONS: Active UC is associated with gut microbiota dysbiosis. GMA therapy exerts a strong regulatory effect on the gut microbiota in patients with UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38367851", + "title": "Microbiome and its relevance to indigenous inflammatory bowel diseases in China.", + "year": 2024, + "journal": "Gene", + "authors": [ + "Han A", + "Yang M", + "Chen B", + "Cao G", + "Xu J", + "Meng T", + "Liu Y", + "Wang Z", + "Zhou Y", + "Xu N", + "Han W", + "Sun H", + "Mei Q", + "Zhu L", + "Xiong M" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.6950034090466982, + "mesh_terms": [ + "Humans", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Colitis, Ulcerative", + "Microbiota", + "Feces", + "Dysbiosis" + ], + "raw_abstract": "BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract with an unknown etiology. Although dysbiosis is implicated in its pathogenesis, deep sequencing and oral microbiota study in Chinese IBD patients is absent. AIM: To explore the role of oral / intestinal microbiota in patients with IBD and the potential associations therein. METHODS: Clinical data, fecal and saliva samples were harvested from 80 patients with IBD (Crohn's disease, CD, n\u00a0=\u00a069; Ulcerative colitis, UC, n\u00a0=\u00a011) and 24 normal controls. Microbiomics (16S rRNA sequencing and 16S rRNA full-length sequencing) were used to detect and analyze the difference between IBD patients and normal control. RESULTS: Compared with normal controls, a higher abundance of the intestinal Shigella spp. (Shigella flexneri and Shigella sonnei, which were positively relate to the severity of IBD), lower abundance of intestinal probiotics (Prevotella, Faecalibacterium and Roseburia), and higher abundance of oral Neisseria were present in IBD patients with microbiome. The higher inflammation-related markers, impaired hepatic and renal function, and dyslipidaemia were present in patients with IBD. A higher intake of red meat and increased abundance of Clostridium in the gut were found in CD patients, while the elevated abundance of Ruminococcus in the gut was showed in UC ones. The bacterial composition of saliva and fecal samples was completely different, yet there was some correlation in the distribution of dominant probiotics. CONCLUSION: Enteric dysbacteriosis and the infections of pathogenic bacteria (Shigella) may associate with the occurrence or development of IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33977948", + "title": "No Title", + "year": 2021, + "journal": "Food & function", + "authors": [ + "Pang B", + "Jin H", + "Liao N", + "Li J", + "Jiang C", + "Shao D", + "Shi J" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.6306895291173065, + "mesh_terms": [ + "Animals", + "Mice", + "Anti-Inflammatory Agents", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "Disease Models, Animal", + "Fatty Acids, Volatile", + "Feces", + "Gastrointestinal Microbiome", + "Intestines", + "Lacticaseibacillus rhamnosus", + "Mice, Inbred C57BL", + "Milk, Human", + "RNA, Ribosomal, 16S", + "Tight Junction Proteins" + ], + "raw_abstract": "Gut microbiota imbalance is one of the major causes of ulcerative colitis (UC). L. rhamnosus SHA113 (LRS), a strain isolated from healthy human milk, influences the regulation of gut flora. This study aims to determine whether this strain can ameliorate UC by modulating gut microbiota. Mouse models of UC were established using C57BL/6Cnc mice with intragastric administration of 3.0% (w/v) dextran sodium sulfate (DSS). LRS was used to treat the mouse models of UC with 109 cfu mL-1 cell suspension via intragastric administration. To verify the effect of gut microbiota on UC, fecal microbiota collected from the mice after the treatment with LRS were also used to treat the UC mouse models (FMT). The severity of UC was evaluated based on body weight, colon length, disease activity index (DAI), and hematoxylin-eosin staining. The microbial composition was analyzed by 16S rRNA sequencing. The mRNA expression levels of cytokines, mucins, tight junction proteins, and antimicrobial peptides in the gastrointestinal tract were detected by quantitative real-time polymerase chain reaction. The short-chain fatty acid (SCFAs) in the cecal contents of all mice were quantitatively detected by gas chromatography and mass spectrometry. Both LRS and FMT exerted excellent therapeutic effects on UC, as evidenced by the reduction in body weight loss, colon length, and colon structural integrity, as well as the increase in the DAI (disease activity index). LRS and FMT treatments showed similar effects: (1) an increase of total SCFA production in the cecal contents and the abundance of gut microbial diversity and flora composition; (2) decreases in two genera (Parabacteroides and Escherichia/Shigella) related to the DAI and the enhancement of SCFAs and IL-10 positively related genera in the gut microbiota (Bilophila, Roseburia, Akkermansia, and Bifidobacterium); (3) downregulation of the expression of tumor necrosis factor-\u03b1, interleukin IL-6, and IL-1\u03b2, and upregulation of the expression of the anti-inflammatory cytokine IL-10; and (4) upregulation of the expression of mucins (Muc1-4) and tight junction protein ZO-1. Overall, L. rhamnosus SHA113 relieves UC via the regulation of gut microbiota: increases in SCFA-producing genera and decreases in UC-related genera. In addition, a single strain is sufficient to induce a significant change in the gut microbiota and exert therapeutic effects on UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31055592", + "title": "Combined Signature of the Fecal Microbiome and Plasma Metabolome in Patients with Ulcerative Colitis.", + "year": 2019, + "journal": "Medical science monitor : international medical journal of experimental and clinical research", + "authors": [ + "Sun M", + "Du B", + "Shi Y", + "Lu Y", + "Zhou Y", + "Liu B" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.6053761928385026, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metabolome", + "Methylamines", + "Microbiota", + "Middle Aged", + "Plasma", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND Ulcerative colitis is a chronic, idiopathic in\ufb02ammatory disease that destroys the colon structure. Nevertheless, the exact pathogenesis is not clear and needs to be fully elucidated. MATERIAL AND METHODS Stool and plasma samples were used for 16S ribosomal RNA sequencing and liquid chromatography mass spectrometry, respectively. In addition, we detected the level of trimethylamine N-oxide. Finally, we performed Pearson correlation analysis between the microbiome and the metabolome. RESULTS Twenty-three active ulcerative colitis, 25 inactive ulcerative colitis, and 30 control cases were included. Thirty-four significantly different metabolites were found between the active ulcerative colitis and control groups, 38 were found between the inactive ulcerative colitis and control groups, and only 1 was found between the active ulcerative colitis and inactive ulcerative colitis groups. The plasma trimethylamine N-oxide level of the inactive ulcerative colitis and active ulcerative colitis groups was significantly higher than that of the control group. Moreover, we identified significant changes in 24, 18, and 12 bacterial genera for active ulcerative colitis-control, inactive ulcerative colitis-control, and active ulcerative colitis-inactive ulcerative colitis, respectively. Cross-correlation indicated an association between sphingosine 1-phosphate and Roseburia, Klebsiella, and Escherichia-Shigella. Through the pathway analysis, we found sphingolipid metabolism was one of the most significantly increased pathways. CONCLUSIONS Although levels of trimethylamine N-oxide were higher in ulcerative colitis patients, they did not achieve statistical significance in active ulcerative colitis and inactive ulcerative colitis groups. Sphingosine 1-phosphate was increased in ulcerative colitis patients and there were several microbiota associated with it. Although further study is still needed, sphingosine 1-phosphate will probably become a new target for treatment of ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35104755", + "title": "Integrated microbiome-metabolomics analysis reveals the potential therapeutic mechanism of Zuo-Jin-Wan in ulcerative colitis.", + "year": 2022, + "journal": "Phytomedicine : international journal of phytotherapy and phytopharmacology", + "authors": [ + "Cai Y", + "Li S", + "Zhang X", + "Cao X", + "Liu D", + "Zhu Y", + "Ye S", + "Xu Z", + "Liao Q", + "Hong Y", + "Xie Z" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.5814548368548027, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Dysregulation in gut microbiota and host cometabolome contributes to the complicated pathology of ulcerative colitis (UC), while Zuo-Jin-Wan (ZJW), a traditional Chinese medicine has shown therapeutic effects against UC with its underlying mechanism remains elusive. PURPOSE: This study utilized an integrated analysis combining gut microbiome and host cometabolism to disclose the potential therapeutic mechanism of ZJW on dextran sulfate sodium (DSS)-induced UC in rats. METHODS: We first evaluated the therapeutic effects of ZJW treatment in DSS-induced rat model. 16S rRNA sequencing, RESULTS: Our results showed that UC symptoms in ZJW rats were significantly attenuated. Marked decline in microbial diversity in ZJW group was accompanied by its correspondent function adjustment. Specific enrichment of genus Bacteroides, Sutterella, Akkermansia and Roseburia along with the major varying amino acid metabolism and lipid metabolism were observed meantime. Metabolic data further corroborated that ZJW-related metabolic changes were basically gathered in amino acid metabolism, carbohydrate/energy metabolism and lipid metabolism. Of note, some biochemical parameters were deeply implicated with the discriminative microbial genera and metabolites involved in tricarboxylic acid (TCA) cycle and amino acid metabolism, indicating the microbiome-metabolome association in gut microbiota-metabolite-phenotype axis during UC treatment of ZJW. CONCLUSION: For the first time, integrated microbiome-metabolome analysis depicted that ZJW could alleviate DSS-induced UC in rats via a crosstalk between gut microbiota and host cometabolites.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32576228", + "title": "Effects of soy milk consumption on gut microbiota, inflammatory markers, and disease severity in patients with ulcerative colitis: a study protocol for a randomized clinical trial.", + "year": 2020, + "journal": "Trials", + "authors": [ + "Sadeghi O", + "Milajerdi A", + "Siadat SD", + "Keshavarz SA", + "Sima AR", + "Vahedi H", + "Adibi P", + "Esmaillzadeh A" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.5496370877772266, + "mesh_terms": [ + "Adult", + "Anti-Inflammatory Agents", + "Biomarkers", + "Colitis, Ulcerative", + "Eating", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Iran", + "Male", + "Middle Aged", + "Phytoestrogens", + "Quality of Life", + "Randomized Controlled Trials as Topic", + "Severity of Illness Index", + "Soy Milk", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Several strategies are recommended to alleviate clinical symptoms of ulcerative colitis (UC). Soy milk may affect UC through its anti-inflammatory properties. However, no study has examined the effects of soy milk consumption on gut microbiota and inflammatory biomarkers in patients with UC. The current study will be done to examine the effects of soy milk consumption on UC symptoms, inflammation, and gut microbiota in patients with UC. METHODS: This study is a randomized clinical trial, in which thirty patients with mild to moderate severity of UC will be randomly allocated to receive either 250\u2009mL/day soy milk plus routine treatments (n\u2009=\u200915) or only routine treatments (n\u2009=\u200915) for 4\u2009weeks. Assessment of anthropometric measures and biochemical indicators including serum concentrations of high-sensitivity C-reactive protein (hs-CRP), tumor necrosis factor-\u03b1 (TNF-\u03b1), interleukin-1\u03b2 (IL-1\u03b2), and interferon gamma (IFN-\u03b3) will be done at the study baseline and end of trial. In addition, the quantity of butyrate-producing bacteria including Clostridium cluster IV, Faecalibacterium prausnitzii, and Roseburia spp.; prebiotic bacteria including Lactobacillus spp. and Bifidobacteria spp.; and mucus-degrading bacteria including Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., as well as calprotectin and lactoferrin levels, will be explored in fecal samples. Also, the Firmicutes to Bacteroidetes ratio which is of significant relevance in human gut microbiota composition will be assessed. DISCUSSION: Altered gut microbiota has been reported as an important contributing factor to inflammation in patients with inflammatory bowel disease (IBD). Soy milk contains several components such as phytoestrogens with potential anti-inflammatory properties. This product might affect gut microbiota through its protein and fiber content. Therefore, soy milk might beneficially affect systemic inflammation, gut microbiota, and then clinical symptoms in patients with UC. TRIAL REGISTRATION: Iranian Registry of Clinical Trials (www.irct.ir) IRCT20181205041859N1. Registered on 27 January 2019.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26423113", + "title": "Specific members of the predominant gut microbiota predict pouchitis following colectomy and IPAA in UC.", + "year": 2017, + "journal": "Gut", + "authors": [ + "Machiels K", + "Sabino J", + "Vandermosten L", + "Joossens M", + "Arijs I", + "de Bruyn M", + "Eeckhaut V", + "Van Assche G", + "Ferrante M", + "Verhaegen J", + "Van Steen K", + "Van Immerseel F", + "Huys G", + "Verbeke K", + "Wolthuis A", + "de Buck Van Overstraeten A", + "D'Hoore A", + "Rutgeerts P", + "Vermeire S" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.5120829768694797, + "mesh_terms": [ + "Adult", + "Bacteroidetes", + "Clostridium perfringens", + "Cluster Analysis", + "Colitis, Ulcerative", + "Colonic Pouches", + "DNA, Bacterial", + "Fatty Acids, Volatile", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Middle Aged", + "Pouchitis", + "Predictive Value of Tests", + "Preoperative Period", + "Proctocolectomy, Restorative", + "Prospective Studies", + "Ruminococcus", + "Time Factors" + ], + "raw_abstract": "OBJECTIVE: Pouchitis is the most common complication after colectomy with ileal pouch-anal anastomosis (IPAA) for UC and the risk is the highest within the 1st year after surgery. The pathogenesis is not completely understood but clinical response to antibiotics suggests a role for gut microbiota. We hypothesised that the risk for pouchitis can be predicted based on the faecal microbial composition before colectomy. DESIGN: Faecal samples from 21 patients with UC undergoing IPAA were prospectively collected before colectomy and at predefined clinical visits at 1 month, 3 months, 6 months and 12\u2005months after IPAA. The predominant microbiota was analysed using community profiling with denaturing gradient gel electrophoresis followed by quantitative real-time PCR validation. RESULTS: Cluster analysis before colectomy distinguished patients with pouchitis from those with normal pouch during the 1st year of follow-up. In patients developing pouchitis, an increase of Ruminococcus gnavus (p<0.001), Bacteroides vulgatus (p=0.043), Clostridium perfringens (p=0.011) and a reduction of two Lachnospiraceae genera (Blautia (p=0.04), Roseburia (p=0.008)) was observed. A score combining these five bacterial risk factors was calculated and presence of at least two risk factors showed a sensitivity and specificity of 100% and 63.6%, respectively. CONCLUSIONS: Presence of R. gnavus, B. vulgatus and C. perfringens and absence of Blautia and Roseburia in faecal samples of patients with UC before surgery is associated with a higher risk of pouchitis after IPAA. Our findings suggest new predictive and therapeutic strategies in patients undergoing colectomy with IPAA.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32322944", + "title": "Protective effect of baicalin on the regulation of Treg/Th17 balance, gut microbiota and short-chain fatty acids in rats with ulcerative colitis.", + "year": 2020, + "journal": "Applied microbiology and biotechnology", + "authors": [ + "Zhu L", + "Xu LZ", + "Zhao S", + "Shen ZF", + "Shen H", + "Zhan LB" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.5073693749337005, + "mesh_terms": [ + "Animals", + "Butyrates", + "Colitis, Ulcerative", + "Disease Models, Animal", + "Dysbiosis", + "Fatty Acids, Volatile", + "Flavonoids", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Prebiotics", + "Rats", + "T-Lymphocytes, Regulatory", + "Th17 Cells", + "Trinitrobenzenesulfonic Acid" + ], + "raw_abstract": "Baicalin is reported as an effective drug for ulcerative colitis (UC). However, its effect on gut microbiota and short-chain fatty acids (SCFAs) remains unknown. In this study, we investigated the role of baicalin on Th17/Treg balance, gut microbiota community, and SCFAs levels in trinitrobenzene sulphonic acid (TNBS)-induced UC rat model. We found the DAI scores were significantly increased in the TNBS-treated rats, while reduced in the baicalin-treated group in a dose-dependent manner, accompanied with the alleviation of mucosal injury, the reduction of ZO-1, Occludin, and MUC2 expression. At the meanwhile, baicalin repressed the increased levels of reactive oxygen species (ROS) and MDA, while deceased the GSH and SOD levels in colon tissue of rats treated with TNBS. On the other hand, administration of baicalin attenuated the TNBS-induced upregulations of Th17/Treg ratio, indicating a strong amelioration in the colorectal inflammation. More importantly, pyrosequencing of the V4 regions of 16S rRNA genes in rat feces revealed a deviation of the gut microbiota in response to baicalin treatment. In particular, the decreased Firmicutes-to-Bacteroidetes ratios and endotoxin-bearing Proteobacteria levels indicated that baicalin reversed TNBS-induced gut dysbiosis OTUs. In addition, we further investigated the fecal levels of major SCFAs in rats and found that baicalin significantly resorted the fecal butyrate levels in rats treated with TNBS. The increased butyrate levels were in consistent with the higher abundance of butyrate-producing species such as Butyricimonas spp., Roseburia spp., Subdoligranulum spp., and Eubacteriu spp. in baicalin-treated group. In conclusion, our findings suggest that baicalin possibly protected rats against ulcerative colitis by regulation of Th17/Treg balance, and modulation of both gut microbiota and SCFAs. Baicalin may be used as a prebiotic agent to treat ulcerative colitis-associated inflammation and gut dysbiosis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28494241", + "title": "Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases.", + "year": 2017, + "journal": "Cell host & microbe", + "authors": [ + "Ananthakrishnan AN", + "Luo C", + "Yajnik V", + "Khalili H", + "Garber JJ", + "Stevens BW", + "Cleland T", + "Xavier RJ" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.45996211684769084, + "mesh_terms": [ + "Antibodies, Monoclonal, Humanized", + "Biological Therapy", + "Butyrates", + "Colitis, Ulcerative", + "Crohn Disease", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Integrins", + "Metagenome", + "Prospective Studies", + "Treatment Outcome" + ], + "raw_abstract": "The gut microbiome plays a central role in inflammatory bowel diseases (IBDs) pathogenesis and propagation. To determine whether the gut microbiome may predict responses to IBD therapy, we conducted a prospective study with Crohn's disease (CD) or ulcerative colitis (UC) patients initiating anti-integrin therapy (vedolizumab). Disease activity and stool metagenomes at baseline, and weeks 14, 30, and 54\u00a0after therapy initiation were assessed. Community \u03b1-diversity was significantly higher, and Roseburia inulinivorans and a Burkholderiales species were more abundant at baseline among CD patients achieving week 14 remission. Several significant associations were identified with microbial function; 13\u00a0pathways including branched chain amino acid synthesis were significantly enriched in baseline samples from CD patients achieving remission. A\u00a0neural network algorithm, vedoNet, incorporating microbiome and clinical data, provided highest classifying power for clinical remission. We hypothesize that the trajectory of early microbiome changes may be a marker of response to IBD treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32184182", + "title": "Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases.", + "year": 2021, + "journal": "Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association", + "authors": [ + "Borren NZ", + "Plichta D", + "Joshi AD", + "Bonilla G", + "Peng V", + "Colizzo FP", + "Luther J", + "Khalili H", + "Garber JJ", + "Janneke van der Woude C", + "Sadreyev R", + "Vlamakis H", + "Xavier RJ", + "Ananthakrishnan AN" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.44987113945563206, + "mesh_terms": [ + "Adult", + "Clostridiales", + "Colitis, Ulcerative", + "Fatigue", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Metabolome", + "Proteomics" + ], + "raw_abstract": "BACKGROUND & AIMS: Fatigue is frequent and disabling in patients with inflammatory bowel diseases (IBD) but its mechanisms are poorly understood. We investigated alterations in fecal microbiomes and serum metabolomes and proteomes in patients with quiescent IBD, with vs without fatigue. METHODS: We performed a prospective observational study of patients (44% women; mean age, 39.8 y) with clinically and endoscopically quiescent Crohn's disease (n\u00a0= 106) or ulcerative colitis (n\u00a0=\u00a060) at a tertiary hospital, from March 2016 through December 2018. Fatigue was assessed using the functional assessment of chronic illness therapy-fatigue scoring system and defined as a score of 43 or less. We performed metabolomic analysis of serum samples using liquid chromatography-mass spectrometry methods and proteomic analysis using multiplex proximity extension assay (PEA) technology. Stool samples were obtained from 50 patients and analyzed by shotgun metagenomic sequencing on Illumina HiSeq platform. RESULTS: Of the 166 study participants, 91 (55%) were fatigued. Serum samples from patients with fatigue (n\u00a0= 59) did not have significant increases in levels of inflammatory cytokines compared with serum samples from nonfatigued patients (n\u00a0= 72). We found a statistically significant difference in a cluster of 18 serum metabolites between patients with fatigue (n\u00a0= 84) vs without fatigue (n\u00a0= 72) (P = .033); serum samples from patients with fatigue had significant reductions in levels of methionine (P = .020), tryptophan (P = .042), proline (P = .017), and sarcosine (P = .047). Fecal samples from patients with fatigue had a less diverse gut microbiome, with significant reductions in butyrate-producing bacteria, including Faecalibacterium prausnitzii (P = .0002, q =.007) and\u00a0Roseburia hominis (P = .0079, q = 0.105). This fatigue-like microbiome was associated with fatigue scales and correlated with progressive depletion of metabolites from serum samples. CONCLUSIONS: In an analysis of fecal and serum samples from 166 patients with IBD, we found alterations in serum metabolites and fecal microbes that were associated with fatigue.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34761733", + "title": "Attributes of intestinal microbiota composition and their correlation with clinical primary non-response to anti-TNF-\u03b1 agents in inflammatory bowel disease patients.", + "year": 2022, + "journal": "Bosnian journal of basic medical sciences", + "authors": [ + "Alatawi H", + "Mosli M", + "Saadah OI", + "Annese V", + "Al-Hindi R", + "Alatawy M", + "Al-Amrah H", + "Alshehri D", + "Bahieldin A", + "Edris S" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.31943079819820963, + "mesh_terms": [ + "Bacteria", + "Biomarkers", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "RNA, Ribosomal, 16S", + "Tumor Necrosis Factor Inhibitors" + ], + "raw_abstract": "The largest microbial aggregation in the human body exists in the gastrointestinal tract. The microbiota in the host gastrointestinal tract comprises a diverse ecosystem, and the intestinal microbiota plays a vital role in maintaining gut homeostasis. This study aims to examine whether the gut microbiota influences unresponsiveness to anti-TNF-\u03b1 treatments in primary nonresponder patients, and consequently identify the responsible microbes as biomarkers of unresponsiveness. Stool samples were collected from a cohort of patients with an established diagnosis of IBD, either ulcerative colitis (UC) or Crohn's disease (CD), following completion of the induction phase of anti TNF therapy. 16S rRNA sequencing analysis was used to examine the pattern of microbiota communities in fecal samples. The quality and quantity of fecal microbiota were compared in responder and primary nonresponder IBD patients following anti-TNF-\u03b1 therapy. As per our hypothesis, a difference in gut microbiome composition between the two patient subgroups was observed. A decreased abundance of short-chain fatty acid (SCFA)-producing bacteria, including Anaerostipes, Coprococcus, Lachnospira, Roseburia, and Ruminococcus, was detected in non-responsive patients, which was the hallmark of dysbiosis. Biomarkers of dysbiosis that were identified as predictors of clinical nonresponse, included Klebsiella, Eubacteriaceae, RF32, Bifidobacterium_animalis, and Muribaculaceae-previously known as S24-7. Signature biomarkers showed dramatic alteration in the composition of gut microbiota in patients who demonstrated primary nonresponse to anti-TNF-\u03b1 agents. Dysbiosis, with features including a dropped biodiversity, augmentation in opportunistic pathogenic microbiota, and a lack of SCFA-producing bacteria, is a prominent feature of the microbiome of primary nonresponders to anti-TNF-\u03b1 therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30529583", + "title": "Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis.", + "year": 2019, + "journal": "Gastroenterology", + "authors": [ + "Paramsothy S", + "Nielsen S", + "Kamm MA", + "Deshpande NP", + "Faith JJ", + "Clemente JC", + "Paramsothy R", + "Walsh AJ", + "van den Bogaerde J", + "Samuel D", + "Leong RWL", + "Connor S", + "Ng W", + "Lin E", + "Borody TJ", + "Wilkins MR", + "Colombel JF", + "Mitchell HM", + "Kaakoush NO" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.2678577146510703, + "mesh_terms": [ + "Bacteria", + "Biomarkers", + "Colitis, Ulcerative", + "Double-Blind Method", + "Fecal Microbiota Transplantation", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Metabolomics", + "New South Wales", + "Remission Induction", + "Ribotyping", + "Time Factors", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy. METHODS: We performed a double-blind trial of 81 patients with active UC randomly assigned to groups that received an initial colonoscopic infusion and then intensive multidonor FMT or placebo enemas, 5 d/wk for 8 weeks. Patients in the FMT group received blended homogenized stool from 3-7 unrelated donors. Patients in the placebo group were eligible to receive open-label FMT after the double-blind study period. We collected 314 fecal samples from the patients at screening, every 4 weeks during treatment, and 8 weeks after the blinded or open-label FMT therapy. We also collected 160 large-bowel biopsy samples from the patients at study entry, at completion of 8 weeks of blinded therapy, and at the end of open-label FMT, if applicable. We analyzed 105 fecal samples from the 14 individual donors (n\u00a0= 55), who in turn contributed to 21 multidonor batches (n\u00a0= 50). Bacteria in colonic and fecal samples were analyzed by both 16S ribosomal RNA gene and transcript amplicon sequencing; 285 fecal samples were analyzed by shotgun metagenomics, and 60 fecal samples were analyzed for metabolome features. RESULTS: FMT increased microbial diversity and altered composition, based on analyses of colon and fecal samples collected before vs after FMT. Diversity was greater in fecal and colon samples collected before and after FMT treatment from patients who achieved remission compared with patients who did not. Patients in remission after FMT had enrichment of Eubacterium hallii and Roseburia inulivorans compared with patients who did not achieve remission after FMT and had increased levels of short-chain fatty acid biosynthesis and secondary bile acids. Patients who did not achieve remission had enrichment of Fusobacterium gonidiaformans, Sutterella wadsworthensis, and Escherichia species and increased levels of heme and lipopolysaccharide biosynthesis. Bacteroides in donor stool were associated with remission in patients receiving FMT, and Streptococcus species in donor stool was associated with no response to FMT. CONCLUSIONS: In an analysis of fecal and colonic mucosa samples from patients receiving FMT for active UC and stool samples from donors, we associated specific bacteria and metabolic pathways with induction of remission. These findings may be of value in the design of microbe-based therapies for UC. ClinicalTrials.gov, Number NCT01896635.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37859536", + "title": "Baizhu-Baishao herb pair ameliorates functional constipation and intestinal microflora disorder in rats.", + "year": 2023, + "journal": "Animal models and experimental medicine", + "authors": [ + "Li X", + "Wang X", + "Wang Z", + "Guan J" + ], + "bacteria": "Roseburia", + "condition": "ulcerative colitis", + "relevance_score": 0.2518166578057637, + "mesh_terms": [ + "Rats", + "Animals", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Serotonin", + "Constipation", + "Vasoactive Intestinal Peptide", + "Substance P" + ], + "raw_abstract": "BACKGROUND: In China, Rhizoma atractylodis macrocephalae-Paeonia lactiflora Pall (Biazhu-Baishao, BZBS) is a classic herb pair used to treat intestinal stress syndrome, ulcerative colitis and other diseases. However, the mechanism of BZBS in the treatment of functional constipation (FC) has been little studied and remains unclear. In this study, a behavioral investigation, colon tissue morphology, enzyme-linked immunosorbent assay (Elisa) and intestinal microflora analysis have been used to illuminate the potential mechanism of the effects of BZBS on FC in a rat model. METHODS: A FC rat model was constructed and BZBS was given as treatment. Observations and recordings were made of the fecal moisture content, the defecation time of the first black stool, and the rate of intestinal propulsion. Elisa was used to detect the expression levels of substance P (SP), vasoactive intestinal peptide (VIP), 5-hydroxytryptamine (5-HT) in the colon. To ascertain the composition of the microbial community, a high throughput 16S ribosomal RNA (16S rRNA) gene sequencing technique was employed. RESULTS: Oral administration of BZBS significantly ameliorated several key excretion parameters, including the time to first black stool defecation, stool water content, and the propulsion rate in the small intestine in FC rats. It increased the expression of SP, VIP and 5-HT in the colon. 16S rRNA gene sequencing results showed that BZBS changed the microbial community structure, decreased the Bacteroidetes/Firmicutes ratio, increased the relative abundance of Blautia and Fusicatenibacter, and decreased the relative abundance of Ruminococcus and Roseburia. CONCLUSIONS: BZBS effectively alleviates FC and improves dysbacteriosis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29049404", + "title": "Low-complexity microbiota in the duodenum of children with newly diagnosed ulcerative colitis.", + "year": 2017, + "journal": "PloS one", + "authors": [ + "Sj\u00f6berg F", + "Barkman C", + "Nookaew I", + "\u00d6stman S", + "Adlerberth I", + "Saalman R", + "Wold AE" + ], + "bacteria": "Collinsella", + "condition": "ulcerative colitis", + "relevance_score": 0.700455933695068, + "mesh_terms": [ + "Adolescent", + "Case-Control Studies", + "Child", + "Colitis, Ulcerative", + "Duodenum", + "Female", + "Humans", + "Male", + "Microbiota", + "Pilot Projects" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is characterized by gut dysbiosis. To date, the large bowel microbiota has been in focus. However, the microbiota of the small intestine may also be of importance, as the small bowel is a site for the induction and control of mucosal immune responses, which can be modulated by constituents of the local microbiota. METHODS: Duodenal fluids were collected during diagnostic work-up of treatment-na\u00efve children who were suspected of having IBD. The duodenal fluids were analyzed by pyrosequencing (average of 32,000 reads/sample, read length of 500 nucleotides). After diagnosis, the duodenal microbiota of subjects with ulcerative colitis (N = 8) or Crohn's disease (N = 5), and non-IBD controls (N = 8) were compared. RESULTS: Pyrosequencing revealed that the duodenal microbiota of children with ulcerative colitis contained fewer Operational Taxonomic Units (OTUs) per individual than the duodenal microbiota of the controls (P = 0.005). This reduction in richness of the duodenal microbiota was seen for three major phyla: Firmicutes, Actinobacteria, and Bacteroidetes. Several bacterial genera were detected less frequently in the children with ulcerative colitis than in the non-IBD controls, including Collinsella (P = 0.001), Lactobacillus (P = 0.007), and Bacillus (P = 0.007), as well as a non-identified member of the order Sphingobacteriales (P = 0.007). CONCLUSIONS: In this pilot study, we show that the duodenal microbiota of children with ulcerative colitis exhibits reduced overall richness, despite the fact that the inflammation is primarily localized to the colon. These results should be corroborated in a larger study.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32265456", + "title": "Seasonal changes of circulating 25-hydroxyvitamin D correlate with the lower gut microbiome composition in inflammatory bowel disease patients.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Soltys K", + "Stuchlikova M", + "Hlavaty T", + "Gaalova B", + "Budis J", + "Gazdarica J", + "Krajcovicova A", + "Zelinkova Z", + "Szemes T", + "Kuba D", + "Drahovska H", + "Turna J", + "Stuchlik S" + ], + "bacteria": "Collinsella", + "condition": "ulcerative colitis", + "relevance_score": 0.6560260020108714, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteria", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Seasons", + "Vitamin D", + "Young Adult" + ], + "raw_abstract": "Higher probability of the development of Crohn's disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/Shigella spp.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37696680", + "title": "Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Del Chierico F", + "Cardile S", + "Baldelli V", + "Alterio T", + "Reddel S", + "Bramuzzo M", + "Knafelz D", + "Lega S", + "Bracci F", + "Torre G", + "Maggiore G", + "Putignani L" + ], + "bacteria": "Collinsella", + "condition": "ulcerative colitis", + "relevance_score": 0.6157648362160162, + "mesh_terms": [ + "Humans", + "Child", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Cholangitis, Sclerosing", + "Dysbiosis", + "RNA, Ribosomal, 16S", + "Bacteria", + "Bacteroidetes", + "Italy" + ], + "raw_abstract": "BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis. METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs). RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients. CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC. In this study, we report the gut microbiota and mycobiota dysbiosis in pediatric patients affected by primary sclerosing cholangitis (PSC) associated with ulcerative colitis (UC), with an increase in pro-inflammatory pathobionts and a reduction in anti-inflammatory commensals.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35444617", + "title": "Fecal Microbiota Transplantation Ameliorates Active Ulcerative Colitis by Downregulating Pro-inflammatory Cytokines in Mucosa and Serum.", + "year": 2022, + "journal": "Frontiers in microbiology", + "authors": [ + "Zhang WH", + "Jin ZY", + "Yang ZH", + "Zhang JY", + "Ma XH", + "Guan J", + "Sun BL", + "Chen X" + ], + "bacteria": "Collinsella", + "condition": "ulcerative colitis", + "relevance_score": 0.44525956655354704, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is a multi-factor disease characterized by alternating remission periods and repeated occurrence. It has been shown that fecal microbiota transplantation (FMT) is an emerging and effective approach for UC treatment. Since most existing studies chose adults as donors for fecal microbiota, we conducted this study to determine the long-term efficacy and safety of the microbiota from young UC patient donors and illustrate its specific physiological effects. METHODS: Thirty active UC patients were enrolled and FMT were administered with the first colonoscopy and two subsequent enema/transendoscopic enteral tubing (TET) practical regimens in The First Affiliated Hospital of Anhui Medical University in China. Disease activity and inflammatory biomarkers were assessed 6\u2009weeks/over 1\u2009year after treatment. The occurrence of adverse events was also recorded. The samples from blood and mucosa were collected to detect the changes of inflammatory biomarkers and cytokines. The composition of gut and oral microbiota were also sampled and sequenced to confirm the alteration of microbial composition. RESULTS: Twenty-seven patients completed the treatment, among which 16 (59.3%) achieved efficacious clinical response and 11 (40.7%) clinical remission. Full Mayo score and calprotectin dropped significantly and remained stable over 1\u2009year. FMT also significantly reduced the levels of C-reactive protein (CRP), interleukin-1 beta (IL-1\u03b2), and interleukin-6 (IL-6). The gut microbiota altered significantly with increased bacterial diversity and decreased metabolic diversity in responsive patients. The pro-inflammatory enterobacteria decreased after FMT and the abundance of Collinsella increased. Accordingly, the altered metabolic functions, including antigen synthesis, amino acids metabolism, short chain fatty acid production, and vitamin K synthesis of microbiota, were also corrected by FMT. CONCLUSION: Fecal microbiota transplantation seems to be safe and effective for active UC patients who are nonresponsive to mesalazine or prednisone in the long-term. FMT could efficiently downregulate pro-inflammatory cytokines to ameliorate the inflammation.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29796862", + "title": "Molecular profiling of mucosal tissue associated microbiota in patients manifesting acute exacerbations and remission stage of ulcerative colitis.", + "year": 2018, + "journal": "World journal of microbiology & biotechnology", + "authors": [ + "Walujkar SA", + "Kumbhare SV", + "Marathe NP", + "Patangia DV", + "Lawate PS", + "Bharadwaj RS", + "Shouche YS" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.753774227138873, + "mesh_terms": [ + "Adult", + "Bacteria", + "Bacterial Load", + "Bacteroidetes", + "Biodiversity", + "Colitis, Ulcerative", + "DNA, Bacterial", + "Dysbiosis", + "Female", + "Firmicutes", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Male", + "Microbial Consortia", + "Middle Aged", + "Phylogeny", + "Proteobacteria", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Dysbiosis of intestinal microflora has been postulated in ulcerative colitis (UC), which is characterized by imbalance of mucosal tissue associated bacterial communities. However, the specific changes in mucosal microflora during different stages of UC are still unknown. The aim of the current study was to investigate the changes in mucosal tissue associated microbiota during acute exacerbations and remission stages of UC. The mucosal microbiota associated with colon biopsy of 12 patients suffering from UC (exacerbated stage) and the follow-up samples from the same patients (remission stage) as well as non-IBD subjects was studied using 16S rRNA gene-based sequencing and quantitative PCR. The total bacterial count in patients suffering from exacerbated phase of UC was observed to be two fold lower compared to that of the non-IBD subjects (p\u2009=\u20090.0049, Wilcox on matched-pairs signed rank tests). Bacterial genera including Stenotrophomonas, Parabacteroides, Elizabethkingia, Pseudomonas, Micrococcus, Ochrobactrum and Achromobacter were significantly higher in abundance during exacerbated phase of UC as compared to remission phase. The alterations in bacterial diversity with an increase in the abnormal microbial communities signify the extent of dysbiosis in mucosal microbiota in patients suffering from UC. Our study helps in identifying the specific genera dominating the microbiota during the disease and thus lays a basis for further investigation of the possible role of these bacteria in pathogenesis of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36759757", + "title": "Integrating the serum proteomic and fecal metaproteomic to analyze the impacts of overweight/obesity on IBD: a pilot investigation.", + "year": 2023, + "journal": "Clinical proteomics", + "authors": [ + "Yan P", + "Sun Y", + "Luo J", + "Liu X", + "Wu J", + "Miao Y" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.684074031696057, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) encompasses a group of chronic relapsing disorders which include ulcerative colitis (UC) and Crohn's disease (CD). The incidences of IBD and overweight/obesity are increasing in parallel. Here, we investigated alterations in proteomic in serum and metaproteomic in feces of IBD patients with overweight/obesity and aimed to explore the effect of overweight/ obesity on IBD and the underlying mechanism. METHODS: This prospective observational study (n\u2009=\u200964) comprised 26 health control subjects (HC, 13 with overweight/obesity) and 38 IBD patients (19 with overweight/obesity) at a tertiary hospital. Overweight/obesity was evaluated by body mass index (BMI) and defined as a BMI greater than 24\u00a0kg/m RESULTS: UC and CD presented similar serum molecular profiles but distinct gut microbiota. UC and CD serum exhibited higher levels of cytoskeleton organization- associated and inflammatory response-related proteins than the HC serum. Compared the serum proteome of UC and CD without overweight/obesity, inflammatory response-associated proteins were dramatically decreased in UC and CD with overweight/obesity. Fecal metaproteome identified 66 species in the feces. Among them, Parasutterella excrementihominis was increased in CD compared with that in HC. UC group had a significant enrichment of Moniliophthora roreri, but had dramatically decreased abundances of Alistipes indistinctus, Clostridium methylpentosum, Bacteroides vulgatus, and Schizochytrium aggregatum. In addition, overweight/obesity could improve the microbial diversity of UC. Specifically, the UC patients with overweight/obesity had increased abundance of some probiotics in contrast to those without overweight/obesity, including Parabacteroides distasonis, Alistipes indistincus, and Ruminococcus bromii. CONCLUSION: This study provided high-quality multi-omics data of IBD serum and fecal samples, which enabled deciphering the molecular bases of clinical phenotypes of IBD, revealing the impacts of microbiota on IBD, and emphasizing the important role of overweight/obesity in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37696680", + "title": "Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Del Chierico F", + "Cardile S", + "Baldelli V", + "Alterio T", + "Reddel S", + "Bramuzzo M", + "Knafelz D", + "Lega S", + "Bracci F", + "Torre G", + "Maggiore G", + "Putignani L" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.68245755731191, + "mesh_terms": [ + "Humans", + "Child", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Cholangitis, Sclerosing", + "Dysbiosis", + "RNA, Ribosomal, 16S", + "Bacteria", + "Bacteroidetes", + "Italy" + ], + "raw_abstract": "BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis. METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs). RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients. CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC. In this study, we report the gut microbiota and mycobiota dysbiosis in pediatric patients affected by primary sclerosing cholangitis (PSC) associated with ulcerative colitis (UC), with an increase in pro-inflammatory pathobionts and a reduction in anti-inflammatory commensals.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33352216", + "title": "Changes in intestinal microbiota and correlation with TLRs in ulcerative colitis in the coastal area of northern China.", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Xu N", + "Bai X", + "Cao X", + "Yue W", + "Jiang W", + "Yu Z" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6692808597856181, + "mesh_terms": [ + "China", + "Colitis, Ulcerative", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: To investigate the communities of fecal microbiota and the role of Toll-like receptors in patients with ulcerative colitis in the coastal area of northern China. METHODS: Stool samples from 31 patients with ulcerative colitis and 12 healthy individuals were collected. The total bacterial genomic DNA was extracted, and the V3+V4 hypervariable region in the bacterial 16S rRNA gene sequence was amplified by polymerase chain reaction (PCR). High-throughput sequencing analysis was performed on the Illumina Hiseq platform. The expression of TLR2, TLR4, Tollip, PPAR-\u03b3, IL-6, and TNF-\u03b1 in the colonic mucosa was measured by Western blots. RESULTS: The diversity of the fecal microbiota in patients with ulcerative colitis was significantly less than that in healthy control individuals (p\u00a0<\u00a00.05). The proportion of Bacteroidetes was significantly reduced (p\u00a0<\u00a00.01), whereas Proteobacteria was prevalent (p\u00a0<\u00a00.01) in patients with ulcerative colitis. At the genus level, the relative abundance of Streptococcus and Anaerostipes was significantly increased (p\u00a0<\u00a00.05), whereas the proportion of Bacteroides, Lachnospira, Ruminococcus, Phascolarctobacterium, and Coprococcus was significantly decreased in patients with ulcerative colitis (p\u00a0<\u00a00.05). The diversity indexes of fecal microbiota in patients with ulcerative colitis were negatively correlated with disease severity (p\u00a0<\u00a00.05). The relative abundance of Enterobacteriaceae was positively correlated with disease severity, and the relative abundance of Phascolarctobacterium, Anaerostipes, Fusobacterium, Parabacteroides, Oscillospira, and Ochrobactrum were negatively correlated with disease severity. The expression levels of TLR2 and TLR4 in the intestinal mucosa were positively correlated with the relative abundance of Streptococcus and Enterobacteriaceae, respectively (r\u00a0=\u00a00.481, p\u00a0=\u00a00.007; r\u00a0=\u00a00.455, p\u00a0=\u00a00.017). CONCLUSION: There were significant changes in the diversity and composition of the fecal microbiota in patients with ulcerative colitis compared to healthy individuals. The dysbiosis of gut microbiota and correlation with TLRs might play important roles in the pathogenesis and progression of ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33977948", + "title": "No Title", + "year": 2021, + "journal": "Food & function", + "authors": [ + "Pang B", + "Jin H", + "Liao N", + "Li J", + "Jiang C", + "Shao D", + "Shi J" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6306895291173065, + "mesh_terms": [ + "Animals", + "Mice", + "Anti-Inflammatory Agents", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "Disease Models, Animal", + "Fatty Acids, Volatile", + "Feces", + "Gastrointestinal Microbiome", + "Intestines", + "Lacticaseibacillus rhamnosus", + "Mice, Inbred C57BL", + "Milk, Human", + "RNA, Ribosomal, 16S", + "Tight Junction Proteins" + ], + "raw_abstract": "Gut microbiota imbalance is one of the major causes of ulcerative colitis (UC). L. rhamnosus SHA113 (LRS), a strain isolated from healthy human milk, influences the regulation of gut flora. This study aims to determine whether this strain can ameliorate UC by modulating gut microbiota. Mouse models of UC were established using C57BL/6Cnc mice with intragastric administration of 3.0% (w/v) dextran sodium sulfate (DSS). LRS was used to treat the mouse models of UC with 109 cfu mL-1 cell suspension via intragastric administration. To verify the effect of gut microbiota on UC, fecal microbiota collected from the mice after the treatment with LRS were also used to treat the UC mouse models (FMT). The severity of UC was evaluated based on body weight, colon length, disease activity index (DAI), and hematoxylin-eosin staining. The microbial composition was analyzed by 16S rRNA sequencing. The mRNA expression levels of cytokines, mucins, tight junction proteins, and antimicrobial peptides in the gastrointestinal tract were detected by quantitative real-time polymerase chain reaction. The short-chain fatty acid (SCFAs) in the cecal contents of all mice were quantitatively detected by gas chromatography and mass spectrometry. Both LRS and FMT exerted excellent therapeutic effects on UC, as evidenced by the reduction in body weight loss, colon length, and colon structural integrity, as well as the increase in the DAI (disease activity index). LRS and FMT treatments showed similar effects: (1) an increase of total SCFA production in the cecal contents and the abundance of gut microbial diversity and flora composition; (2) decreases in two genera (Parabacteroides and Escherichia/Shigella) related to the DAI and the enhancement of SCFAs and IL-10 positively related genera in the gut microbiota (Bilophila, Roseburia, Akkermansia, and Bifidobacterium); (3) downregulation of the expression of tumor necrosis factor-\u03b1, interleukin IL-6, and IL-1\u03b2, and upregulation of the expression of the anti-inflammatory cytokine IL-10; and (4) upregulation of the expression of mucins (Muc1-4) and tight junction protein ZO-1. Overall, L. rhamnosus SHA113 relieves UC via the regulation of gut microbiota: increases in SCFA-producing genera and decreases in UC-related genera. In addition, a single strain is sufficient to induce a significant change in the gut microbiota and exert therapeutic effects on UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35662877", + "title": "Zingiber officinale and Panax ginseng ameliorate ulcerative colitis in mice via modulating gut microbiota and its metabolites.", + "year": 2022, + "journal": "Journal of chromatography. B, Analytical technologies in the biomedical and life sciences", + "authors": [ + "Wan Y", + "Yang L", + "Li H", + "Ren H", + "Zhu K", + "Dong Z", + "Jiang S", + "Shang E", + "Qian D", + "Duan J" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.5981279443355652, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Zingiber officinale", + "Mice", + "Panax", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Zingiber officinale and Panax ginseng, as well-known traditional Chinese medicines, have been used together to clinically treat ulcerative colitis with synergistic effects for thousands of years. However, their compatibility mechanism remains unclear. In this study, the shift of gut microbiome and fecal metabolic profiles were monitored by 16S rRNA sequencing technology and ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry analysis, respectively, which aimed to reveal the synergistic mechanism of Zingiber officinale and Panax ginseng on the amelioration of ulcerative colitis. The results showed that the relative abundance of beneficial bacteria (such as Muribaculaceae_norank, Lachnospiraceae NK4A136 group and Akkermansia) was significantly increased and the abundance of pathogenic bacteria (such as Bacteroides, Parabacteroides and Desulfovibrio) was markedly decreased after the intervention of Zingiber officinale-Panax ginseng herb pair. And a total of 16 differential metabolites related to ulcerative colitis were identified by the metabolomics analysis, which were majorly associated with the metabolic pathways, including arachidonic acid metabolism, tryptophan metabolism, and steroid biosynthesis. Based on these findings, it was suggested that the regulation of the gut microbiota-metabolite axis might be a potential target for the synergistic mechanism of Zingiber officinale-Panax ginseng herb pair in the treatment of ulcerative colitis. Furthermore, the integrated analysis of microbiome and metabolomics used in this study could also serve as a useful template for exploring the mechanism of other drugs.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.505491338085921, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35151255", + "title": "Gut microbiome alterations in colitis rats after moxibustion at bilateral Tianshu acupoints.", + "year": 2022, + "journal": "BMC gastroenterology", + "authors": [ + "Qi Q", + "Liu YN", + "Lv SY", + "Wu HG", + "Zhang LS", + "Cao Z", + "Liu HR", + "Wang XM", + "Wu LY" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.4767693447749241, + "mesh_terms": [ + "Acupuncture Points", + "Animals", + "Colitis", + "Colitis, Ulcerative", + "Dextran Sulfate", + "Disease Models, Animal", + "Gastrointestinal Microbiome", + "Male", + "Moxibustion", + "Rats" + ], + "raw_abstract": "BACKGROUND: The pathogenesis of ulcerative colitis (UC) is closely related to the gut microbiota. Moxibustion has been used to improve the inflammation and gastrointestinal dysfunctions in gastrointestinal\u00a0disorders such as UC. In this study, we investigated whether moxibustion could improve the gut microbial dysbiosis induced by dextran sulphate sodium. METHODS: Twenty-five male rats were randomly assigned into five groups. The UC rat model was established by administering DSS solution. The rats in the moxibustion and normal rats with moxibustion groups were treated with moxibustion at Tianshu (bilateral, ST25) points, and the mesalazine group rats were treated with mesalazine once daily for 7 consecutive days. Disease activity index (DAI) and haematoxylin and eosin staining were used to evaluate the effect of moxibustion. Gut microbiota profiling was conducted by metagenomic high throughput sequencing technology. The gut microbiota composition, diversity and function were analyzed and compared using metagenomics methodologies. RESULTS: The DAI scores and histopathology scores in the moxibustion and mesalazine groups were significantly decreased compared with the UC group (P\u2009<\u20090.01). Moxibustion treatment increased abundance levels of Bacteroidetes, Actinobacteria, Ascomycota, Synergistetes and decreased abundance of Firmicutes, Proteobacteria. At the genus level, the abundance of Bacteroides, Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2, were increased and Bacteroides_bacterium_H3, Parabacteroides, Porphyromonas, Alistipes, Parasutterella were decreased in the UC group in comparsion with those in the NG group. Moxibustion increased the abundance of Bacteroides and Bacteroides_bacterium_H3 and decreased Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2. In UC group, the specie Bacteroides_massiliensis was negatively (P\u2009<\u20090.05) correlated with IL-23, Bacteroides_eggerthii_CAG109 and Bacteroides_eggerthii were negatively (P\u2009<\u20090.05) correlated with TGF-\u03b2. And the species Prevotella_sp_CAG1031 and Bacteroides_bacterium_H2 were significant positively (P\u2009<\u20090.05) correlated with IL-23. In addition, compare with the normal group, genes involved in certain metabolic pathways, such as energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, were under-represented in the UC group, and these changes in the metabolic pathways could be reversed by moxibustion treatment and mesalazine treatment. CONCLUSIONS: Our findings suggest that moxibustion treatment may protect the host from mucosal inflammation by modulating the intestinal microbiota community.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28683448", + "title": "Gut Microbiota in Health, Diverticular Disease, Irritable Bowel Syndrome, and Inflammatory Bowel Diseases: Time for Microbial Marker of Gastrointestinal Disorders.", + "year": 2018, + "journal": "Digestive diseases (Basel, Switzerland)", + "authors": [ + "Lopetuso LR", + "Petito V", + "Graziani C", + "Schiavoni E", + "Paroni Sterbini F", + "Poscia A", + "Gaetani E", + "Franceschi F", + "Cammarota G", + "Sanguinetti M", + "Masucci L", + "Scaldaferri F", + "Gasbarrini A" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.40374843862827087, + "mesh_terms": [ + "Adult", + "Biomarkers", + "Diverticular Diseases", + "Female", + "Gastrointestinal Microbiome", + "Health", + "Humans", + "Inflammatory Bowel Diseases", + "Irritable Bowel Syndrome", + "Male", + "Middle Aged", + "Phylogeny", + "Principal Component Analysis", + "Species Specificity" + ], + "raw_abstract": "Few data exist on differences in gut microbiota composition among principal gastrointestinal (GI) diseases. We evaluated the differences in gut microbiota composition among uncomplicated diverticular disease (DD), irritable bowel syndrome (IBS) and inflammatory bowel diseases (IBD) patients. DD, IBS, and IBD patients along with healthy controls (CT) were enrolled in our Italian GI outpatient clinic. Stool samples were collected. Microbiota composition was evaluated through a metagenomic gene-targeted approach. GI pathology represented a continuous spectrum of diseases where IBD displayed one extreme, while CT displayed the other. Among Phyla, Biplot PC2/PC3 and dendogram plot showed major differences in samples from IBS and IBD. DD resembled species CT composition, but not for Bacteroides fragilis. In IBS, Dialister spp. and then Faecalibacterium prausnitzii were the most representative species. Ulcerative colitis showed a reduced concentration of Clostridium difficile and an increase of Bacteroides fragilis. In Crohn's disease, Parabacteroides distasonis was the most represented, while Faecalibacterium prausnitzii and Bacteroides fragilis were significantly reduced. Each disorder has its definite overall microbial signature, which produces a clear differentiation from the others. On the other hand, shared alterations constitute the \"core dysbiosis\" of GI diseases. The assessment of these microbial markers represents a parameter that may complete the diagnostic assessment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39740381", + "title": "Gingerols: Preparation, encapsulation, and bioactivities focusing gut microbiome modulation and attenuation of disease symptoms.", + "year": 2025, + "journal": "Phytomedicine : international journal of phytotherapy and phytopharmacology", + "authors": [ + "Abdullah", + "Ahmad N", + "Xiao J", + "Tian W", + "Khan NU", + "Hussain M", + "Ahsan HM", + "Hamed YS", + "Zhong H", + "Guan R" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.3958667585459114, + "mesh_terms": [ + "Gastrointestinal Microbiome", + "Humans", + "Catechols", + "Fatty Alcohols", + "Animals", + "Zingiber officinale", + "Phytochemicals", + "Dysbiosis", + "Anti-Inflammatory Agents" + ], + "raw_abstract": "BACKGROUND: Gut dysbiosis, chronic diseases, and microbial recurrent infections concerns have driven the researchers to explore phytochemicals from medicinal and food homologous plants to modulate gut microbiota, mitigate diseases, and inhibit pathogens. Gingerols have attracted attention as therapeutic agents due to their diverse biological activities like gut microbiome regulation, gastro-protective, anti-inflammatory, anti-microbial, and anti-oxidative effects. PURPOSE: This review aimed to summarize the gingerols health-promoting potential, specifically focusing on the regulation of gut microbiome, attenuation of disease symptoms, mechanisms of action, and signaling pathways involved. METHOD: Research findings from experimental and clinical studies have been summarized regarding gingerols effects on the modulation of gut microbiome and its metabolites, and attenuation of disease symptoms. RESULTS: Gingerols are phenolic compounds characterized by a common 3-methoxy-4-hydroxyphenyl moiety in their chemical structures, and further divided into different gingerol types, including gingerols (major), shogaols, paradols, gingerdiols, gingerdiones, and zingerones (minor). Advanced extraction techniques (e.g., ionic liquid-based-, enzyme-assisted-, microwave-assisted-, pressurized liquid-, ultrasound-assisted-, and supercritical fluid extractions) were reported as optimal alternatives to conventional methods for gingerols extraction. Research studies reported that gingerols positively modulated the composition of gut microbiome that helped to combat disease symptoms (e.g., obesity by decreasing weight gain- (Lactobacillus reuteri and Lachnospiraceae) and increasing weight loss associated-bacteria (Akkermansia, Muribaculaceae, and Alloprevotella). Gingerols intervention also ameliorated ulcerative colitis by increasing relative abundance of the beneficial bacteria (Akkermansia, Lachnospiraceae NK4A136, and Muribaculaceae_norank), and decreasing pathogenic microorganisms (Bacteroides, Parabacteroides, and Desulfovibrio). Emerging delivery systems (e.g., microcapsules, nanoparticles, nanostructured lipid carriers, nanoemulsions, and nanoliposomes) can enhance the bioavailability and therapeutic efficacy of gingerols by preserving their inherent properties and addressing challenges of stability, solubility, and absorption. CONCLUSION: Gingerols are promising therapeutic agents to modulate gut microbiome (increase beneficial bacteria and inhibit pathogenic microbes), and attenuate chronic disease symptoms such as diabetes, colitis, obesity, oxidative stress, and cancer. Despite significant progress, challenges persist in transforming research findings into industrial applications, such as stability and solubility during processing and low bioavailability in the distal gut to impart desirable health benefits.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31250469", + "title": "Consistent alterations in faecal microbiomes of patients with primary sclerosing cholangitis independent of associated colitis.", + "year": 2019, + "journal": "Alimentary pharmacology & therapeutics", + "authors": [ + "R\u00fchlemann M", + "Liwinski T", + "Heinsen FA", + "Bang C", + "Zenouzi R", + "Kummen M", + "Thingholm L", + "Tempel M", + "Lieb W", + "Karlsen T", + "Lohse A", + "Hov J", + "Denk G", + "Lammert F", + "Krawczyk M", + "Schramm C", + "Franke A" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.3810086496957726, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cholangitis, Sclerosing", + "Cohort Studies", + "Colitis, Ulcerative", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Germany", + "Humans", + "Male", + "Middle Aged", + "Norway", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Single-centre studies reported alterations of faecal microbiota in patients with primary sclerosing cholangitis (PSC). As regional factors may affect microbial communities, it is unclear if a microbial signature of PSC exists across different geographical regions. AIM: To identify a robust microbial signature of PSC independent of geography and environmental influences. METHODS: We included 388 individuals (median age, 47\u00a0years; range, 15-78) from Germany and Norway in the study, 137 patients with PSC (n\u00a0=\u00a075 with colitis), 118 with ulcerative colitis (UC) and 133 healthy controls. Faecal microbiomes were analysed by 16S rRNA gene sequencing (V1-V2). Differences in relative abundances of single taxa were subjected to a meta-analysis. RESULTS: In both cohorts, microbiota composition (beta-diversity) differed between PSC patients and controls (P\u00a0<\u00a00.001). Random forests classification discriminated PSC patients from controls in both geographical cohorts with an average area under the curve of 0.88. Compared to healthy controls, many new cohort-spanning alterations were identified in PSC, such as an increase of Proteobacteria and the bile-tolerant genus Parabacteroides, which were detected independent from geographical region. Associated colitis only had minor effects on microbiota composition, suggesting that PSC itself drives the faecal microbiota changes observed. CONCLUSION: Compared to healthy controls, numerous microbiota alterations are reproducible in PSC patients across geographical regions, clearly pointing towards a microbiota composition that is shaped by the disease itself and not by environmental factors. These reproducibly altered microbial populations might provide future insights into the pathophysiology of PSC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27585552", + "title": "In\u00a0vitro analysis of partially hydrolyzed guar gum fermentation on identified gut microbiota.", + "year": 2016, + "journal": "Anaerobe", + "authors": [ + "Carlson J", + "Gould T", + "Slavin J" + ], + "bacteria": "Parabacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.3369667353713552, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteroidetes", + "Colon", + "Culture Media", + "Dietary Fiber", + "Feces", + "Female", + "Fermentation", + "Galactans", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Hydrolysis", + "Male", + "Mannans", + "Middle Aged", + "Plant Gums", + "Prebiotics" + ], + "raw_abstract": "BACKGROUND: Prebiotic dietary fibers resist digestion in the upper gastrointestinal tract and allow for stimulation of bacteria in the distal intestine and colon. Stimulation of bacteria among different individuals varies greatly, depending on a wide range of variables. OBJECTIVE: To determine the range of differences in response between individuals, a preclinical in\u00a0vitro fermentation was conducted with six fecal donors. The primary objective was to compare the fecal microbiota of six individuals at baseline, 12\u00a0h and 24\u00a0h post-exposure to partially hydrolyzed guar gum (PHGG). METHOD: Fecal donations were collected from six healthy individuals consuming a non-specific Western diet, free of antibiotic treatments in the past year, not affected by any GI diseases and not consuming any probiotic or prebiotic supplements. Fecal samples were exposed to 0.5\u00a0g of PHGG and measured for bacterial changes at 0, 12 and 24\u00a0h based on 16S rRNA sequencing. RESULTS: Parabacteroides increased from 3.48% of sequence reads to 10.62% of sequence reads after 24\u00a0h (p\u00a0=\u00a00.0181) and Bacteroidetes increased from 45.89% of sequence reads to 50.29% of sequence reads (p\u00a0=\u00a00.0008). CONCLUSIONS: PHGG stimulates growth of Parabacteroides, a genus of bacteria that have been inversely associated with IBS and ulcerative colitis. PHGG provides stimulation of beneficial Bacteroidetes (Bacteroides and Parabacteroides), which may be correlated with many positive health markers and outcomes. PHGG is a prebiotic dietary fiber that is readily fermentable.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36858036", + "title": "The Role of Fecal Microbiota Transplantation in the Induction of Remission in Ulcerative Colitis.", + "year": 2023, + "journal": "Digestive diseases (Basel, Switzerland)", + "authors": [ + "Saleh A", + "Parsa S", + "Garza M", + "Quigley EMM", + "Abraham BP" + ], + "bacteria": "Odoribacter", + "condition": "ulcerative colitis", + "relevance_score": 0.7229807234485702, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Colitis, Ulcerative", + "Feces", + "Inflammatory Bowel Diseases", + "Remission Induction", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Considerable research supports an important role for the microbiome and/or microbiome-host immune system interactions in the pathogenesis of inflammatory bowel disease (IBD). Consequently, microbiota-modulating interventions, such as fecal microbiota transplantation (FMT), have attracted interest in the management of IBD, including ulcerative colitis (UC). SUMMARY: While the clinical response to FMT in UC has varied between different studies, results to date may offer guidance toward optimal use of FMT. Thus, increased microbiome biodiversity, the presence of short-chain fatty acid-producing bacteria, Clostridium clusters IV and XIVa, Odoribacter splanchnicus, and reduced levels of Caudovirales bacteriophages have been identified as characteristics of the donor microbiome that predict a positive response. However, inconsistency in FMT protocol between studies confounds their interpretation, so it is currently difficult to predict response and premature to recommend FMT, in general, as a treatment for UC. Additional randomized controlled trials designed based on previous findings and employing a standardized protocol are needed to define the role of FMT in the management of UC. KEY MESSAGES: There is a well-developed rationale for the use of microbiome-modulating interventions in UC. Despite variations in study protocol and limitations in study design that confound their interpretation, FMT seems to benefit patients with UC, overall. Available data identify factors predicting FMT response and should lead to the development of optimal FMT study protocols.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38905376", + "title": "Inflammatory proteins may mediate the causal relationship between gut microbiota and inflammatory bowel disease: A mediation and multivariable Mendelian randomization study.", + "year": 2024, + "journal": "Medicine", + "authors": [ + "Huang YL", + "Zheng JM", + "Shi ZY", + "Chen HH", + "Wang XT", + "Kong FB" + ], + "bacteria": "Odoribacter", + "condition": "ulcerative colitis", + "relevance_score": 0.7158731629680425, + "mesh_terms": [ + "Mendelian Randomization Analysis", + "Humans", + "Gastrointestinal Microbiome", + "Crohn Disease", + "Colitis, Ulcerative", + "Inflammatory Bowel Diseases" + ], + "raw_abstract": "This research investigates the causal relationships among gut microbiota, inflammatory proteins, and inflammatory bowel disease (IBD), including crohn disease (CD) and ulcerative colitis (UC), and identifies the role of inflammatory proteins as potential mediators. Our study analyzed gut microbiome data from 13,266 samples collected by the MiBioGen alliance, along with inflammatory protein data from recent research by Zhao et al, and genetic data on CD and UC from the International Inflammatory Bowel Disease Genetics Consortium (IIBDGC). We used Mendelian randomization (MR) to explore the associations, complemented by replication, meta-analysis, and multivariable MR techniques for enhanced accuracy and robustness. Our analysis employed several statistical methods, including inverse-variance weighting, MR-Egger, and the weighted median method, ensuring comprehensive and precise evaluation. After MR analysis, replication and meta-analysis, we revealed significant associations between 11 types of gut microbiota and 17 inflammatory proteins were associated with CD and UC. Mediator MR analysis and multivariable MR analysis showed that in CD, the CD40L receptor mediated the causal effect of Defluviitaleaceae UCG-011 on CD (mediation ratio 8.3%), and the Hepatocyte growth factor mediated the causal effect of Odoribacter on CD (mediation ratio 18%). In UC, the C-C motif chemokine 4 mediated the causal effect of Ruminococcus2 on UC (mediation ratio 4%). This research demonstrates the interactions between specific gut microbiota, inflammatory proteins, and CD and UC. Furthermore, the CD40L receptor may mediate the relationship between Defluviitaleaceae UCG-011 and CD; the Hepatocyte growth factor may mediate the relationship between Odoribacter and CD; and the C-C motif chemokine 4 may mediate the relationship between Ruminococcus2 and UC. The identified associations and mediation effects offer insights into potential therapeutic approaches targeting the gut microbiome for managing CD and UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38521930", + "title": "Human-derived bacterial strains mitigate colitis via modulating gut microbiota and repairing intestinal barrier function in mice.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Dai J", + "Jiang M", + "Wang X", + "Lang T", + "Wan L", + "Wang J" + ], + "bacteria": "Odoribacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5951787363092838, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "Gastrointestinal Microbiome", + "Intestinal Barrier Function", + "RNA, Ribosomal, 16S", + "Colitis", + "Colitis, Ulcerative", + "Bacteroidetes", + "Enterococcus faecium", + "Escherichia coli", + "Mice, Inbred C57BL", + "Disease Models, Animal", + "Colon" + ], + "raw_abstract": "BACKGROUND: Unbalanced gut microbiota is considered as a pivotal etiological factor in colitis. Nevertheless, the precise influence of the endogenous gut microbiota composition on the therapeutic efficacy of probiotics in colitis remains largely unexplored. RESULTS: In this study, we isolated bacteria from fecal samples of a healthy donor and a patient with ulcerative colitis in remission. Subsequently, we identified three bacterial strains that exhibited a notable ability to ameliorate dextran sulfate sodium (DSS)-induced colitis, as evidenced by increased colon length, reduced disease activity index, and improved histological score. Further analysis revealed that each of Pediococcus acidilactici CGMCC NO.17,943, Enterococcus faecium CGMCC NO.17,944 and Escherichia coli CGMCC NO.17,945 significantly attenuated inflammatory responses and restored gut barrier dysfunction in mice. Mechanistically, bacterial 16S rRNA gene sequencing indicated that these three strains partially restored the overall structure of the gut microbiota disrupted by DSS. Specially, they promoted the growth of Faecalibaculum and Lactobacillus murinus, which were positively correlated with gut barrier function, while suppressing Odoribacter, Rikenella, Oscillibacter and Parasutterella, which were related to inflammation. Additionally, these strains modulated the composition of short chain fatty acids (SCFAs) in the cecal content, leading to an increase in acetate and a decrease in butyrate. Furthermore, the expression of metabolites related receptors, such as receptor G Protein-coupled receptor (GPR) 43, were also affected. Notably, the depletion of endogenous gut microbiota using broad-spectrum antibiotics completely abrogated these protective effects. CONCLUSIONS: Our findings suggest that selected human-derived bacterial strains alleviate experimental colitis and intestinal barrier dysfunction through mediating resident gut microbiota and their metabolites in mice. This study provides valuable insights into the potential therapeutic application of probiotics in the treatment of colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34606847", + "title": "Transferable Immunoglobulin A-Coated Odoribacter splanchnicus in Responders to Fecal Microbiota Transplantation for Ulcerative Colitis Limits Colonic Inflammation.", + "year": 2022, + "journal": "Gastroenterology", + "authors": [ + "Lima SF", + "Gogokhia L", + "Viladomiu M", + "Chou L", + "Putzel G", + "Jin WB", + "Pires S", + "Guo CJ", + "Gerardin Y", + "Crawford CV", + "Jacob V", + "Scherl E", + "Brown SE", + "Hambor J", + "Longman RS" + ], + "bacteria": "Odoribacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5658003262321126, + "mesh_terms": [ + "Animals", + "Bacteroidetes", + "Clinical Trials as Topic", + "Colitis", + "Colitis, Ulcerative", + "Colon", + "Disease Models, Animal", + "Fecal Microbiota Transplantation", + "Forkhead Transcription Factors", + "Gastrointestinal Microbiome", + "Germ-Free Life", + "Humans", + "Immunity, Mucosal", + "Immunoglobulin A", + "Intestinal Mucosa", + "Intraepithelial Lymphocytes", + "Metagenome", + "Metagenomics", + "Mice, Inbred C57BL", + "Mice, Knockout", + "Nuclear Receptor Subfamily 1, Group F, Member 3", + "T-Lymphocytes, Regulatory", + "Treatment Outcome", + "Mice" + ], + "raw_abstract": "BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) is an emerging treatment modality for ulcerative colitis (UC). Several randomized controlled trials have shown efficacy for FMT in the treatment of UC, but a better understanding of the transferable microbiota and their immune impact is needed to develop more efficient microbiome-based therapies for UC. METHODS: Metagenomic analysis and strain tracking was performed on 60 donor and recipient samples receiving FMT for active UC. Sorting and sequencing of immunoglobulin (Ig) A-coated microbiota (called IgA-seq) was used to define immune-reactive microbiota. Colonization of germ-free or genetically engineered mice with patient-derived strains was performed to determine the mechanism of microbial impact on intestinal immunity. RESULTS: Metagenomic analysis defined a core set of donor-derived transferable bacterial strains in UC subjects achieving clinical response, which predicted response in an independent trial of FMT for UC. IgA-seq of FMT recipient samples and gnotobiotic mice colonized with donor microbiota identified Odoribacter splanchnicus as a transferable strain shaping mucosal immunity, which correlated with clinical response and the induction of mucosal regulatory T cells. Colonization of mice with O splanchnicus led to an increase in Foxp3 CONCLUSIONS: This work provides the first evidence of transferable, donor-derived strains that correlate with clinical response to FMT in UC and reveals O splanchnicus as a key component promoting both metabolic and immune cell protection from colitis. These mechanistic features will help\u00a0enable strategies to enhance the efficacy of\u00a0microbial therapy for UC. Clinicaltrials.gov ID NCT02516384.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33947329", + "title": "Ecological and network analyses identify four microbial species with potential significance for the diagnosis/treatment of ulcerative colitis (UC).", + "year": 2021, + "journal": "BMC microbiology", + "authors": [ + "Li W", + "Sun Y", + "Dai L", + "Chen H", + "Yi B", + "Niu J", + "Wang L", + "Zhang F", + "Luo J", + "Wang K", + "Guo R", + "Li L", + "Zou Q", + "Ma ZS", + "Miao Y" + ], + "bacteria": "Odoribacter", + "condition": "ulcerative colitis", + "relevance_score": 0.5553104396558273, + "mesh_terms": [ + "Bacteria", + "Biodiversity", + "China", + "Colitis, Ulcerative", + "DNA, Bacterial", + "Dysbiosis", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is one of the primary types of inflammatory bowel disease (IBD), the occurrence of which has been increasing worldwide. Although IBD is an intensively studied human microbiome-associated disease, research on Chinese populations remains relatively limited, particularly on the mucosal microbiome. The present study aimed to analyze the changes in the mucosal microbiome associated with UC from the perspectives of medical ecology and complex network analysis. RESULTS: In total, 56 mucosal microbiome samples were collected from 28 Chinese UC patients and their healthy family partners, followed by amplicon sequencing. Based on sequencing data, we analyzed species diversity, shared species, and inter-species interactions at the whole community, main phyla, and core/periphery species levels. We identified four opportunistic \"pathogens\" (i.e., Clostridium tertium, Odoribacter splanchnicus, Ruminococcus gnavus, and Flavonifractor plautii) with potential significance for the diagnosis and treatment of UC, which were inhibited in healthy individuals, but unrestricted in the UC patients. In addition, we also discovered in this study: (i) The positive-to-negative links (P/N) ratio, which measures the balance of species interactions or inhibition effects in microbiome networks, was significantly higher in UC patients, indicating loss of inhibition against potentially opportunistic \"pathogens\" associated with dysbiosis. (ii) Previous studies have reported conflicting evidence regarding species diversity and composition between UC patients and healthy controls. Here, significant differences were found at the major phylum and core/periphery scales, but not at the whole community level. Thus, we argue that the paradoxical results found in existing studies are due to the scale effect. CONCLUSIONS: Our results reveal changes in the ecology and network structure of the gut mucosal microbiome that might be associated with UC, and these changes might provide potential therapeutic mechanisms of UC. The four opportunistic pathogens that were identified in the present study deserve further investigation in future studies.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32048723", + "title": "Aging Increases the Severity of Colitis and the Related Changes to the Gut Barrier and Gut Microbiota in Humans and Mice.", + "year": 2020, + "journal": "The journals of gerontology. Series A, Biological sciences and medical sciences", + "authors": [ + "Liu A", + "Lv H", + "Wang H", + "Yang H", + "Li Y", + "Qian J" + ], + "bacteria": "Odoribacter", + "condition": "ulcerative colitis", + "relevance_score": 0.42065181675976, + "mesh_terms": [ + "Adult", + "Age Factors", + "Aged", + "Aging", + "Animals", + "Cadherins", + "Case-Control Studies", + "Colitis, Ulcerative", + "Disease Models, Animal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Middle Aged", + "Occludin", + "Severity of Illness Index" + ], + "raw_abstract": "This study aims to compare intestinal mucosal barrier function in older and young ulcerative colitis (UC) patients and the healthy population, and to explore the possible mechanisms through which aging increases the severity of colitis in mice. The old healthy group showed discontinued tight junction (TJ) strand. The E-cadherin and occludin protein expressions in the colonic tissue of the old healthy subjects were lower than those in the younger healthy people. The protein expressions of E-cadherin and occludin were lower in the old UC patients than in the younger UC patients. In mice, disease activity indexes induced by inflammatory stimulus differed as a function of age. Weight loss level, histological scores, and expression of proinflammatory factors were higher in the dextran sulfate sodium (DSS)-induced group of aged mice than in the young DSS-induced mice. Compared with the results observed in the young DSS-induced mice, the protein expressions of E-cadherin and occludin in the aged DSS-induced mice were lower. Furthermore, significant differences were observed in the composition of the gut microbiota between the young and aged mice. In the aged mice, the fraction of beneficial bacteria (Lactobacillus) was lower before the DSS treatment, while the fraction of the harmful bacteria (Turicibacter, Parasutterella) was higher than that observed in the young mice. After the DSS treatment in the aged mice, the fraction of beneficial bacteria (Odoribacter and Alistipes) was lower, while the fraction of harmful bacteria (Turicibacter) was higher than in the young mice. We demonstrate that the aging of the human colon is characterized by an impairment of the intestinal barrier. Aging leads to more severe disease following DSS challenge. Age-related deterioration of gastrointestinal barrier function and gut microbial dysbiosis may be involved in the pathogenesis of colitis in the aged mice.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34111242", + "title": "Alteration in Urease-producing Bacteria in the Gut Microbiomes of Patients with Inflammatory Bowel Diseases.", + "year": 2021, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Ryvchin R", + "Dubinsky V", + "Rabinowitz K", + "Wasserberg N", + "Dotan I", + "Gophna U" + ], + "bacteria": "Blautia", + "condition": "ulcerative colitis", + "relevance_score": 0.7544071644238234, + "mesh_terms": [ + "Case-Control Studies", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Streptococcus", + "Urease" + ], + "raw_abstract": "BACKGROUND AND AIMS: Bacterial urease is a major virulence factor of human pathogens, and murine models have shown that it can contribute to the pathogenesis of inflammatory bowel diseases [IBD]. METHODS: The distribution of urease-producing bacteria in IBD was assessed using public faecal metagenomic data from various cohorts, including non-IBD controls [n = 55], patients with Crohn's disease [n = 291] or ulcerative colitis [n = 214], and patients with a pouch [n = 53]. The ureA gene and the taxonomic markers gyrA, rpoB, and recA were used to estimate the percentage of urease producers in each sample. RESULTS: Levels of urease producers in patients with IBD and non-IBD controls were comparable. In non-IBD controls and most IBD patients, urease producers were primarily acetate-producing genera such as Blautia and Ruminococcus. A shift in the type of the dominant urease producers towards Proteobacteria and Bacilli was observed in a subset of all IBD subtypes, which correlated with faecal calprotectin levels in one cohort. Some patients with IBD had no detectable urease producers. In patients with a pouch, the probiotic-associated species Streptococcus thermophilus was more common as a main urease producer than in other IBD phenotypes, and it generally did not co-occur with other Bacilli or with Proteobacteria. CONCLUSIONS: Unlike all non-IBD controls, patients with IBD often showed a shift towards Bacilli or Proteobacteria or a complete loss of urease production. Probiotics containing the species S. thermophilus may have a protective effect against colonisation by undesirable urease-producing bacteria in a subset of patients with a pouch.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34397940", + "title": "Intestinal flora differences between patients with ulcerative colitis of different ethnic groups in China.", + "year": 2021, + "journal": "Medicine", + "authors": [ + "Liu H", + "Liu W", + "Huang X", + "Feng Y", + "Lu J", + "Gao F" + ], + "bacteria": "Blautia", + "condition": "ulcerative colitis", + "relevance_score": 0.7443901830789369, + "mesh_terms": [ + "Adult", + "Bacteria", + "China", + "Colitis, Ulcerative", + "Ethnicity", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Incidence", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Retrospective Studies", + "Young Adult" + ], + "raw_abstract": "To determine the differences in intestinal flora between Uygur and Han patients with ulcerative colitis (UC).Microbial diversity and structural composition of fecal bacteria from patients with UC and their matched healthy spouses or first-degree relatives were analyzed using high-throughput sequencing technology.The fecal microbial diversity and abundance index of Uygur patients with UC (UUC) were significantly lower compared with the Uygur normal control group, while there was no significant difference between the Han UC patients (HUC) and the Han normal control group (HN). Compared with their respective control groups, Uygur UC patients and Han UC patients had a different main composition of human intestinal flora (P\u200a<\u200a.05). The abundance of Burkholderia, Caballeronia, Paraburkholderia in the UUC group were higher compared with the HUC group, while Faecalibacterium, Bifidobacterium, and Blautia in the HUC group were higher than those in the UUC group (P\u200a<\u200a.05). Veillonella in the UUC group was higher than that in the Uygur normal control group group, while Subdoligranulum and Ruminococcaceae_UCG-002 were significantly lower (P\u200a<\u200a.05). Prevotella_9 in the HUC group was significantly higher than that in HN group, while Blautia, Anaerostipes, and [Eubacterium]_hallii_group were significantly lower. Moreover, the top 6 species in order of importance were Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella.The difference in intestinal microflora structure may be one of the reasons for the clinical heterogeneity between Uygur and Han patients with UC. Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella could be used as potential biomarkers for predicting UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39026313", + "title": "Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease.", + "year": 2024, + "journal": "Microbiome", + "authors": [ + "Tian X", + "Li S", + "Wang C", + "Zhang Y", + "Feng X", + "Yan Q", + "Guo R", + "Wu F", + "Wu C", + "Wang Y", + "Huo X", + "Ma X" + ], + "bacteria": "Blautia", + "condition": "ulcerative colitis", + "relevance_score": 0.7398748548914773, + "mesh_terms": [ + "Humans", + "Virome", + "Gastrointestinal Microbiome", + "Animals", + "Feces", + "Mice", + "Inflammatory Bowel Diseases", + "Female", + "Male", + "Adult", + "Middle Aged", + "Crohn Disease", + "Bacteriophages", + "Colitis, Ulcerative", + "Bacteria", + "China", + "Fecal Microbiota Transplantation", + "Case-Control Studies", + "Viruses" + ], + "raw_abstract": "BACKGROUND: The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS: In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella\u00a0species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS: Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38457570", + "title": "Gut microbiota-based discriminative model for patients with ulcerative colitis: A meta-analysis and real-world study.", + "year": 2024, + "journal": "Medicine", + "authors": [ + "Zhang R", + "Chen J", + "Liu L", + "Li X", + "Qiu C" + ], + "bacteria": "Blautia", + "condition": "ulcerative colitis", + "relevance_score": 0.7141947235198892, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Bacteria", + "Feces", + "Intestinal Mucosa", + "Firmicutes", + "Clostridiales", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Gut microbiota directly interacts with intestinal epithelium and is a significant factor in the pathogenesis of ulcerative colitis (UC). A meta-analysis was performed to investigate gut microbiota composition of patients with UC in the United States. We also collected fecal samples from Chinese patients with UC and healthy individuals. Gut microbiota was tested using 16S ribosomal RNA gene sequencing. Meta-analysis and 16S ribosomal RNA sequencing revealed significant differences in gut bacterial composition between UC patients and healthy subjects. The Chinese UC group had the highest scores for Firmicutes, Clostridia, Clostridiales, Streptococcaceae, and Blautia, while healthy cohort had the highest scores for P-Bacteroidetes, Bacteroidia, Bacteroidales, Prevotellaceae, and Prevotella_9. A gut microbiota-based discriminative model trained on an American cohort achieved a discrimination efficiency of 0.928 when applied to identify the Chinese UC cohort, resulting in a discrimination efficiency of 0.759. Additionally, a differentiation model was created based on gut microbiota of a Chinese cohort, resulting in an area under the receiver operating characteristic curve of 0.998. Next, we applied the model established for the Chinese UC cohort to analyze the American cohort. Our findings suggest that the diagnostic efficiency ranged from 0.8794 to 0.9497. Furthermore, a combined analysis using data from both the Chinese and US cohorts resulted in a model with a diagnostic efficacy of 0.896. In summary, we found significant differences in gut bacteria between UC individuals and healthy subjects. Notably, the model from the Chinese cohort performed better at diagnosing UC patients compared to healthy subjects. These results highlight the promise of personalized and region-specific approaches using gut microbiota data for UC diagnosis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28852861", + "title": "Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.", + "year": 2018, + "journal": "Journal of gastroenterology", + "authors": [ + "Nishino K", + "Nishida A", + "Inoue R", + "Kawada Y", + "Ohno M", + "Sakai S", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Kawahara M", + "Naito Y", + "Andoh A" + ], + "bacteria": "Blautia", + "condition": "ulcerative colitis", + "relevance_score": 0.6838575411226454, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Endoscopy, Gastrointestinal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. METHODS: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. RESULTS: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. \u03b1-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. CONCLUSIONS: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39126385", + "title": "Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis.", + "year": 2025, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Jangi S", + "Zhao N", + "Hsia K", + "Park YS", + "Michaud DS", + "Yoon H" + ], + "bacteria": "Blautia", + "condition": "ulcerative colitis", + "relevance_score": 0.5505885116520582, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Male", + "Adult", + "Female", + "Prospective Studies", + "Middle Aged", + "Clostridiales", + "Candida", + "Republic of Korea", + "Feces" + ], + "raw_abstract": "BACKGROUND AND AIMS: While there is increasing interest in microbiome-directed therapies for patients with ulcerative colitis (UC), the identification of microbial targets remains elusive, underlining the need for novel approaches. METHODS: Utilizing metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation, we used a tree-based dichotomous approach to assemble distinct clusters of species-level bacterial co-abundance groups (CAGs). We evaluated the abundance of bacterial CAGs and fungal taxa during remission (n\u2005=\u2005166) and activity (n\u2005=\u200546). We examined if the bacterial CAGs identified in our cohorts were conserved in 2 healthy cohorts and a Korean UC cohort. RESULTS: CAG3 and CAG8, dominated by bacteria from the family Lachnospiraceae, were associated with remission. Low abundance of CAG8 and elevated abundance of Candida genus were predictive of active UC. Constituents from CAG8 were influential hub species of the remission-associated microbial UC network, including Ruminococcus gnavus, Erysipelatoclostridium ramosum, Blautia, and Dorea species. These hub species interactions were preserved in 2 healthy cohorts and were partially recapitulated in a Korean UC cohort. CAG8 abundance correlated with the secondary bile acid production pathway. Bacterial CAGs did not correlate with Candida; however, Bifidobacterium adolescentis and Alistipes putredinis were negatively associated with Candida. CONCLUSIONS: Lachnospiraceae-dominated bacterial CAGs were associated with remission in UC, with key bacterial interactions within the CAG also observed in 2 healthy cohorts and a Korean UC cohort. Bacterial CAG-based analyses may aid in designing candidate consortia for microbiome-based therapeutics.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26423113", + "title": "Specific members of the predominant gut microbiota predict pouchitis following colectomy and IPAA in UC.", + "year": 2017, + "journal": "Gut", + "authors": [ + "Machiels K", + "Sabino J", + "Vandermosten L", + "Joossens M", + "Arijs I", + "de Bruyn M", + "Eeckhaut V", + "Van Assche G", + "Ferrante M", + "Verhaegen J", + "Van Steen K", + "Van Immerseel F", + "Huys G", + "Verbeke K", + "Wolthuis A", + "de Buck Van Overstraeten A", + "D'Hoore A", + "Rutgeerts P", + "Vermeire S" + ], + "bacteria": "Blautia", + "condition": "ulcerative colitis", + "relevance_score": 0.5120829768694797, + "mesh_terms": [ + "Adult", + "Bacteroidetes", + "Clostridium perfringens", + "Cluster Analysis", + "Colitis, Ulcerative", + "Colonic Pouches", + "DNA, Bacterial", + "Fatty Acids, Volatile", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Middle Aged", + "Pouchitis", + "Predictive Value of Tests", + "Preoperative Period", + "Proctocolectomy, Restorative", + "Prospective Studies", + "Ruminococcus", + "Time Factors" + ], + "raw_abstract": "OBJECTIVE: Pouchitis is the most common complication after colectomy with ileal pouch-anal anastomosis (IPAA) for UC and the risk is the highest within the 1st year after surgery. The pathogenesis is not completely understood but clinical response to antibiotics suggests a role for gut microbiota. We hypothesised that the risk for pouchitis can be predicted based on the faecal microbial composition before colectomy. DESIGN: Faecal samples from 21 patients with UC undergoing IPAA were prospectively collected before colectomy and at predefined clinical visits at 1 month, 3 months, 6 months and 12\u2005months after IPAA. The predominant microbiota was analysed using community profiling with denaturing gradient gel electrophoresis followed by quantitative real-time PCR validation. RESULTS: Cluster analysis before colectomy distinguished patients with pouchitis from those with normal pouch during the 1st year of follow-up. In patients developing pouchitis, an increase of Ruminococcus gnavus (p<0.001), Bacteroides vulgatus (p=0.043), Clostridium perfringens (p=0.011) and a reduction of two Lachnospiraceae genera (Blautia (p=0.04), Roseburia (p=0.008)) was observed. A score combining these five bacterial risk factors was calculated and presence of at least two risk factors showed a sensitivity and specificity of 100% and 63.6%, respectively. CONCLUSIONS: Presence of R. gnavus, B. vulgatus and C. perfringens and absence of Blautia and Roseburia in faecal samples of patients with UC before surgery is associated with a higher risk of pouchitis after IPAA. Our findings suggest new predictive and therapeutic strategies in patients undergoing colectomy with IPAA.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34103031", + "title": "Effect of the standard herbal preparation, STW5, treatment on dysbiosis induced by dextran sodium sulfate in experimental colitis.", + "year": 2021, + "journal": "BMC complementary medicine and therapies", + "authors": [ + "Mohamed SS", + "Abdeltawab NF", + "Wadie W", + "Ahmed LA", + "Ammar RM", + "Rabini S", + "Abdel-Aziz H", + "Khayyal MT" + ], + "bacteria": "Blautia", + "condition": "ulcerative colitis", + "relevance_score": 0.4514413256165948, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Dextran Sulfate", + "Disease Models, Animal", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Plant Extracts", + "Rats, Wistar", + "Rats" + ], + "raw_abstract": "BACKGROUND: The standardized herbal preparation, STW 5, is effective clinically in functional gastrointestinal disorders and experimentally in ulcerative colitis (UC). The present study explores whether the beneficial effect of STW 5 involves influencing the intestinal microbiota. METHODS: UC was induced in Wistar rats by feeding them 5% dextran sodium sulfate (DSS) in drinking water for 7\u2009days. Rats were treated concurrently with STW 5 and sacrificed 24\u2009h after last drug administration. Fecal samples were used to determine changes in the abundance of selected microbial phyla and genera using real-time PCR. RESULTS: Induction of UC led to dysbiosis and changes in the gut microbiota. The changes included an increase in some genera of the Firmicutes, namely Enterococcus, and a decrease in others, namely Blautia, Clostridium, and Lactobacillus. DSS further induced a marked increase in the abundance of Bacteroidetes and Proteobacteria as well as in the relative abundance of Actinobacteria and its genus Bifidobacterium. Methanobrevibacter levels (phylum Euryarchaeota) were also increased. Microbial dysbiosis was associated with changes in various parameters of colonic inflammation. STW 5 effectively guarded against those changes and significantly affected the indices of edema and inflammation in the UC model. Changes in colon length, colon mass index, inflammatory and apoptotic markers, and histological changes induced by DSS were also prevented. CONCLUSIONS: Dysbiosis plays a contributing role in the development of DSS-induced UC. Derangements in the microbial flora and associated inflammatory processes were largely prevented by STW 5, suggesting that this effect might contribute towards its beneficial usefulness in this condition.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35999575", + "title": "Location-specific signatures of Crohn's disease at a multi-omics scale.", + "year": 2022, + "journal": "Microbiome", + "authors": [ + "Gonzalez CG", + "Mills RH", + "Zhu Q", + "Sauceda C", + "Knight R", + "Dulai PS", + "Gonzalez DJ" + ], + "bacteria": "Blautia", + "condition": "ulcerative colitis", + "relevance_score": 0.3530891007040926, + "mesh_terms": [ + "Bile Acids and Salts", + "Crohn Disease", + "Cross-Sectional Studies", + "Feces", + "Humans", + "Metagenomics", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Crohn's disease (CD), an inflammatory bowel disease (IBD) subtype, results from pathologic interactions between host cells and its resident gut microbes. CD manifests in both isolated disease locations (ileum or colon) or a combination of locations (ileocolonic). To date, a comprehensive understanding of how isolated CD subtypes influence molecular profiles remains outstanding. To address this, we sought to define CD location signatures by leveraging a large cross-sectional feature set captured from the stool of over 200 IBD patients and healthy controls using metaproteomics, shotgun metagenomics, 16S rRNA sequencing, metabolomic profiling, and host genetics paired with clinical endoscopic assessments. RESULTS: Neither metagenomic nor host genetics alone distinguished CD location subtypes. In contrast, ileal and colonic CD were distinguished using mass spectrometry-based methods (metabolomics or metaproteomics) or a combined multi-omic feature set. This multi-omic feature set revealed colonic CD was strongly associated with neutrophil-related proteins. Additionally, colonic CD displayed a disease-severity-related association with Bacteroides vulgatus. Colonic CD and ulcerative colitis profiles harbored strikingly similar feature enrichments compared to ileal CD, including neutrophil-related protein enrichments. Compared to colonic CD, ileal CD profiles displayed increased primary and secondary bile acid levels and concomitant shifts in taxa with noted sensitivities such as Faecalibacterium prausnitzii or affinities for bile acid-rich environments, including Gammaproteobacteria and Blautia sp. Having shown robust molecular and microbial distinctions tied to CD locations, we leveraged these profiles to generate location-specific disease severity biomarkers that surpass the performance of Calprotectin. CONCLUSIONS: When compared using multi-omics features, colonic- and ileal-isolated CD subtypes display striking differences that suggest separate location-specific pathologies. Colonic CD's strong similarity to ulcerative colitis, including neutrophil and Bacteroides vulgatus involvement, is also evidence of a shared pathology for colonic-isolated IBD subtypes, while ileal CD maintains a unique, bile acid-driven profile. More broadly, this study demonstrates the power of multi-omics approaches for IBD biomarker discovery and elucidating the underlying biology. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37859536", + "title": "Baizhu-Baishao herb pair ameliorates functional constipation and intestinal microflora disorder in rats.", + "year": 2023, + "journal": "Animal models and experimental medicine", + "authors": [ + "Li X", + "Wang X", + "Wang Z", + "Guan J" + ], + "bacteria": "Blautia", + "condition": "ulcerative colitis", + "relevance_score": 0.2518166578057637, + "mesh_terms": [ + "Rats", + "Animals", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Serotonin", + "Constipation", + "Vasoactive Intestinal Peptide", + "Substance P" + ], + "raw_abstract": "BACKGROUND: In China, Rhizoma atractylodis macrocephalae-Paeonia lactiflora Pall (Biazhu-Baishao, BZBS) is a classic herb pair used to treat intestinal stress syndrome, ulcerative colitis and other diseases. However, the mechanism of BZBS in the treatment of functional constipation (FC) has been little studied and remains unclear. In this study, a behavioral investigation, colon tissue morphology, enzyme-linked immunosorbent assay (Elisa) and intestinal microflora analysis have been used to illuminate the potential mechanism of the effects of BZBS on FC in a rat model. METHODS: A FC rat model was constructed and BZBS was given as treatment. Observations and recordings were made of the fecal moisture content, the defecation time of the first black stool, and the rate of intestinal propulsion. Elisa was used to detect the expression levels of substance P (SP), vasoactive intestinal peptide (VIP), 5-hydroxytryptamine (5-HT) in the colon. To ascertain the composition of the microbial community, a high throughput 16S ribosomal RNA (16S rRNA) gene sequencing technique was employed. RESULTS: Oral administration of BZBS significantly ameliorated several key excretion parameters, including the time to first black stool defecation, stool water content, and the propulsion rate in the small intestine in FC rats. It increased the expression of SP, VIP and 5-HT in the colon. 16S rRNA gene sequencing results showed that BZBS changed the microbial community structure, decreased the Bacteroidetes/Firmicutes ratio, increased the relative abundance of Blautia and Fusicatenibacter, and decreased the relative abundance of Ruminococcus and Roseburia. CONCLUSIONS: BZBS effectively alleviates FC and improves dysbacteriosis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37463118", + "title": "Prediction of Response to Systemic Corticosteroids in Active UC by Microbial Composition-A Prospective Multicenter Study.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Blesl A", + "Wurm P", + "Waschina S", + "Gr\u00f6chenig HP", + "Novacek G", + "Primas C", + "Reinisch W", + "Kutschera M", + "Illiasch C", + "Hennlich B", + "Steiner P", + "Koch R", + "Tillinger W", + "Haas T", + "Reicht G", + "Mayer A", + "Ludwiczek O", + "Miehsler W", + "Steidl K", + "Binder L", + "Reider S", + "Watschinger C", + "F\u00fcrst S", + "Kump P", + "Moschen A", + "Aden K", + "Gorkiewicz G", + "H\u00f6genauer C" + ], + "bacteria": "Blautia", + "condition": "ulcerative colitis", + "relevance_score": 0.24187317587685042, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "RNA, Ribosomal, 16S", + "Prospective Studies", + "Feces", + "Adrenal Cortex Hormones", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Corticosteroids are used for induction of remission in patients with moderately to severely active ulcerative colitis. However, up to one-third of patients fail to this therapy. We investigated if fecal microbial composition or its metabolic capacity are associated with response to systemic corticosteroids. METHODS: In this prospective, multicenter study, patients with active ulcerative colitis (Lichtiger score \u22654) receiving systemic corticosteroids were eligible. Data were assessed and fecal samples collected before and after 4 weeks of treatment. Patients were divided into responders (decrease of Lichtiger Score \u226550%) and nonresponders. The fecal microbiome was assessed by the 16S rRNA gene marker and analyzed with QIIME 2. Microbial metabolic pathways were predicted using parsimonious flux balance analysis. RESULTS: Among 93 included patients, 69 (74%) patients responded to corticosteroids after 4 weeks. At baseline, responders could not be distinguished from nonresponders by microbial diversity and composition, except for a subgroup of biologic-na\u00efve patients. Within 4 weeks of treatment, responders experienced changes in beta diversity with enrichment of ascribed beneficial taxa, including Blautia, Anaerostipes, and Bifidobacterium, as well as an increase in predicted butyrate synthesis. Nonresponders had only minor longitudinal taxonomic changes with a significant increase of Streptococcus salivarius and a microbial composition shifting away from responders. CONCLUSION: Baseline microbial diversity and composition seem to be of limited use to predict response to systemic corticosteroids in active ulcerative colitis. Response is longitudinally associated with restoration of microbial composition and its metabolic capacity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33470709", + "title": "Fecal and mucosal microbiota profiling in pediatric inflammatory bowel diseases.", + "year": 2021, + "journal": "European journal of gastroenterology & hepatology", + "authors": [ + "Putignani L", + "Oliva S", + "Isoldi S", + "Del Chierico F", + "Carissimi C", + "Laudadio I", + "Cucchiara S", + "Stronati L" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7780324462517223, + "mesh_terms": [ + "Adult", + "Child", + "Colitis, Ulcerative", + "Feces", + "Humans", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Microbiota", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: An altered gut microbiota profile has been widely documented in inflammatory bowel diseases (IBD). The intestinal microbial community has been more frequently investigated in the stools than at the level of the mucosa, while most of the studies have been performed in adults. We aimed to define the gut microbiota profile either by assessing fecal and colonic mucosa samples (inflamed or not) from pediatric IBD patients. PATIENTS AND METHODS: Fecal and colonic samples from pediatric IBD (Crohn's disease or ulcerative colitis) and controls were analyzed. The relative abundance of bacteria at phylum and genus/species levels and bacterial diversity were determined through 16S rRNA sequence-based of fecal and mucosal microbiota analysis. RESULTS: A total of 59 children with IBD (26 Crohn's disease, 33 ulcerative colitis) and 39 controls were analyzed. A clear separation between IBD and controls in the overall composition of fecal and mucosal microbiota was found, as well as a reduced bacterial richness in the fecal microbiota of IBD. At the phylum level, abundance of Proteobacteria and Actinobacteria occurred in fecal microbiota of IBD, while species with anti-inflammatory properties (i.e., Ruminococcus) were reduced. Fusobacterium prevailed in inflamed IBD areas in comparison to noninflamed and controls samples. CONCLUSION: Significant alterations in gut microbiota profile were shown in our IBD pediatric patients, in whom an abundance of species with a proinflammatory mucosal activity was clearly detected. An analysis of gut microbiota could be incorporated in designing personalized IBD treatment scenarios in future.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35906158", + "title": "Study of the gut microbiome in Egyptian patients with active ulcerative colitis.", + "year": 2023, + "journal": "Revista de gastroenterologia de Mexico (English)", + "authors": [ + "Ahmed EA", + "Ahmed SM", + "Zakaria NH", + "Baddour NM", + "Header DA" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7744841040992952, + "mesh_terms": [], + "raw_abstract": "INTRODUCTION AND AIM: Ulcerative colitis (UC) is characterized by chronic, uncontrolled inflammation of the intestinal mucosa. Gut microbiota dysbiosis was reported to be a factor in intestinal inflammation. The aim of the present study was to study changes in the gut microbiome in Egyptian patients with active UC. MATERIALS AND METHODS: In this cross-sectional study, the gut bacterial microbiome of 21 UC patients and 20 control subjects was analyzed using the quantitative SYBR Green real-time PCR technique, targeting the 16S rRNA gene of selected bacterial phyla/genera and/or species. RESULTS: UC patients showed marked dysbiosis evidenced by a significant decrease in the Firmicutes and F. prausnitzii anti-inflammatory bacteria. The Firmicutes/Bacteroidetes ratio was also lower in the UC cases (1.65), compared with the healthy controls (2.93). In addition, the UC cases showed a statistically significant decrease in Ruminococcus, compared with the control group. However, there were no statistically significant differences between UC patients and the controls, regarding A. muciniphila, Bifidobacterium, Lactobacillus, Bacteroides, and Prevotella. One UC case was positive for the pathogenic bacterium, Clostridioides difficile, with low relative abundance. CONCLUSION: The current study showed differences in the gut microbiome of UC patients, compared with healthy controls. This may help in identifying the gut microbiome and specific bacterial changes that can be targeted for treatment of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34111242", + "title": "Alteration in Urease-producing Bacteria in the Gut Microbiomes of Patients with Inflammatory Bowel Diseases.", + "year": 2021, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Ryvchin R", + "Dubinsky V", + "Rabinowitz K", + "Wasserberg N", + "Dotan I", + "Gophna U" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7544071644238234, + "mesh_terms": [ + "Case-Control Studies", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Streptococcus", + "Urease" + ], + "raw_abstract": "BACKGROUND AND AIMS: Bacterial urease is a major virulence factor of human pathogens, and murine models have shown that it can contribute to the pathogenesis of inflammatory bowel diseases [IBD]. METHODS: The distribution of urease-producing bacteria in IBD was assessed using public faecal metagenomic data from various cohorts, including non-IBD controls [n = 55], patients with Crohn's disease [n = 291] or ulcerative colitis [n = 214], and patients with a pouch [n = 53]. The ureA gene and the taxonomic markers gyrA, rpoB, and recA were used to estimate the percentage of urease producers in each sample. RESULTS: Levels of urease producers in patients with IBD and non-IBD controls were comparable. In non-IBD controls and most IBD patients, urease producers were primarily acetate-producing genera such as Blautia and Ruminococcus. A shift in the type of the dominant urease producers towards Proteobacteria and Bacilli was observed in a subset of all IBD subtypes, which correlated with faecal calprotectin levels in one cohort. Some patients with IBD had no detectable urease producers. In patients with a pouch, the probiotic-associated species Streptococcus thermophilus was more common as a main urease producer than in other IBD phenotypes, and it generally did not co-occur with other Bacilli or with Proteobacteria. CONCLUSIONS: Unlike all non-IBD controls, patients with IBD often showed a shift towards Bacilli or Proteobacteria or a complete loss of urease production. Probiotics containing the species S. thermophilus may have a protective effect against colonisation by undesirable urease-producing bacteria in a subset of patients with a pouch.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28852861", + "title": "Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.", + "year": 2018, + "journal": "Journal of gastroenterology", + "authors": [ + "Nishino K", + "Nishida A", + "Inoue R", + "Kawada Y", + "Ohno M", + "Sakai S", + "Inatomi O", + "Bamba S", + "Sugimoto M", + "Kawahara M", + "Naito Y", + "Andoh A" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7404425867634223, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Endoscopy, Gastrointestinal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. METHODS: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. RESULTS: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. \u03b1-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. CONCLUSIONS: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39026313", + "title": "Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease.", + "year": 2024, + "journal": "Microbiome", + "authors": [ + "Tian X", + "Li S", + "Wang C", + "Zhang Y", + "Feng X", + "Yan Q", + "Guo R", + "Wu F", + "Wu C", + "Wang Y", + "Huo X", + "Ma X" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7381481005944613, + "mesh_terms": [ + "Humans", + "Virome", + "Gastrointestinal Microbiome", + "Animals", + "Feces", + "Mice", + "Inflammatory Bowel Diseases", + "Female", + "Male", + "Adult", + "Middle Aged", + "Crohn Disease", + "Bacteriophages", + "Colitis, Ulcerative", + "Bacteria", + "China", + "Fecal Microbiota Transplantation", + "Case-Control Studies", + "Viruses" + ], + "raw_abstract": "BACKGROUND: The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS: In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella\u00a0species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS: Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37652126", + "title": "Fermentation patterns of prebiotics fructooligosaccharides-SCFA esters inoculated with fecal microbiota from ulcerative colitis patients.", + "year": 2023, + "journal": "Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association", + "authors": [ + "Chen W", + "Tan D", + "Yang Z", + "Tang J", + "Bai W", + "Tian L" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.7251184336916032, + "mesh_terms": [ + "Inflammation", + "Fatty Acids, Volatile", + "Humans", + "Microbiota", + "Prebiotics", + "Colitis, Ulcerative", + "Fermentation", + "Feces", + "Clostridiales" + ], + "raw_abstract": "Ulcerative colitis (UC) is believed to arise from an imbalance between the intestinal microbiota and mucosal immunity, leading to excessive intestinal inflammation. Modulating the gut microbial community through dietary components presents a valuable strategy in aiding the treatment of UC. In this study, esters formed by binding of well-known prebiotics, fructooligosaccharides (FOS), with short chain fatty acids (SCFAs) via both enzymatic and chemical methods were evaluated for their impact on the gut microbiota of UC patients. An in vitro human colonic fermentation model was employed to monitor changes in total carbohydrates and SCFAs production during the fermentation of these esters by microbiota from patients with active and remission UC. The results showed that pronounced abundance of [Ruminococcus]_gnavus_group, Escherichia_Shigella, Lachnoclostridium, Klebsiella and other potential pathogens were detected in the fecal samples from UC patients, with a milder condition observed during the remission phase. Significant higher levels of corresponding SCFA were observed in the groups with addition of FOS-SCFAs esters during fermentation. Butyrylated fructooligosaccharides (B-FOS) and propionylated fructooligosaccharides (P-FOS) by enzymatic synthesis successfully promoted the proliferation of Bifidobacterium and inhibited Clostridium_sensu_stricto_1 and Klebsiella. Overall, B-FOS and P-FOS exhibit promising potential for restoring intestinal homeostasis and alleviating intestinal inflammation in individuals with UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38367851", + "title": "Microbiome and its relevance to indigenous inflammatory bowel diseases in China.", + "year": 2024, + "journal": "Gene", + "authors": [ + "Han A", + "Yang M", + "Chen B", + "Cao G", + "Xu J", + "Meng T", + "Liu Y", + "Wang Z", + "Zhou Y", + "Xu N", + "Han W", + "Sun H", + "Mei Q", + "Zhu L", + "Xiong M" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6950034090466982, + "mesh_terms": [ + "Humans", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Colitis, Ulcerative", + "Microbiota", + "Feces", + "Dysbiosis" + ], + "raw_abstract": "BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract with an unknown etiology. Although dysbiosis is implicated in its pathogenesis, deep sequencing and oral microbiota study in Chinese IBD patients is absent. AIM: To explore the role of oral / intestinal microbiota in patients with IBD and the potential associations therein. METHODS: Clinical data, fecal and saliva samples were harvested from 80 patients with IBD (Crohn's disease, CD, n\u00a0=\u00a069; Ulcerative colitis, UC, n\u00a0=\u00a011) and 24 normal controls. Microbiomics (16S rRNA sequencing and 16S rRNA full-length sequencing) were used to detect and analyze the difference between IBD patients and normal control. RESULTS: Compared with normal controls, a higher abundance of the intestinal Shigella spp. (Shigella flexneri and Shigella sonnei, which were positively relate to the severity of IBD), lower abundance of intestinal probiotics (Prevotella, Faecalibacterium and Roseburia), and higher abundance of oral Neisseria were present in IBD patients with microbiome. The higher inflammation-related markers, impaired hepatic and renal function, and dyslipidaemia were present in patients with IBD. A higher intake of red meat and increased abundance of Clostridium in the gut were found in CD patients, while the elevated abundance of Ruminococcus in the gut was showed in UC ones. The bacterial composition of saliva and fecal samples was completely different, yet there was some correlation in the distribution of dominant probiotics. CONCLUSION: Enteric dysbacteriosis and the infections of pathogenic bacteria (Shigella) may associate with the occurrence or development of IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36759757", + "title": "Integrating the serum proteomic and fecal metaproteomic to analyze the impacts of overweight/obesity on IBD: a pilot investigation.", + "year": 2023, + "journal": "Clinical proteomics", + "authors": [ + "Yan P", + "Sun Y", + "Luo J", + "Liu X", + "Wu J", + "Miao Y" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.684074031696057, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) encompasses a group of chronic relapsing disorders which include ulcerative colitis (UC) and Crohn's disease (CD). The incidences of IBD and overweight/obesity are increasing in parallel. Here, we investigated alterations in proteomic in serum and metaproteomic in feces of IBD patients with overweight/obesity and aimed to explore the effect of overweight/ obesity on IBD and the underlying mechanism. METHODS: This prospective observational study (n\u2009=\u200964) comprised 26 health control subjects (HC, 13 with overweight/obesity) and 38 IBD patients (19 with overweight/obesity) at a tertiary hospital. Overweight/obesity was evaluated by body mass index (BMI) and defined as a BMI greater than 24\u00a0kg/m RESULTS: UC and CD presented similar serum molecular profiles but distinct gut microbiota. UC and CD serum exhibited higher levels of cytoskeleton organization- associated and inflammatory response-related proteins than the HC serum. Compared the serum proteome of UC and CD without overweight/obesity, inflammatory response-associated proteins were dramatically decreased in UC and CD with overweight/obesity. Fecal metaproteome identified 66 species in the feces. Among them, Parasutterella excrementihominis was increased in CD compared with that in HC. UC group had a significant enrichment of Moniliophthora roreri, but had dramatically decreased abundances of Alistipes indistinctus, Clostridium methylpentosum, Bacteroides vulgatus, and Schizochytrium aggregatum. In addition, overweight/obesity could improve the microbial diversity of UC. Specifically, the UC patients with overweight/obesity had increased abundance of some probiotics in contrast to those without overweight/obesity, including Parabacteroides distasonis, Alistipes indistincus, and Ruminococcus bromii. CONCLUSION: This study provided high-quality multi-omics data of IBD serum and fecal samples, which enabled deciphering the molecular bases of clinical phenotypes of IBD, revealing the impacts of microbiota on IBD, and emphasizing the important role of overweight/obesity in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39162211", + "title": "Washed microbiota transplantation improved the level of serum vitamin D in ulcerative colitis.", + "year": 2024, + "journal": "Journal of gastroenterology and hepatology", + "authors": [ + "Zhang H", + "Xiao Y", + "Wen Q", + "Zhang S", + "Li P", + "Marcella C", + "Hu B", + "Liu H", + "Zhang F", + "Cui B" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6665413533883564, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Male", + "Vitamin D", + "Female", + "Adult", + "Fecal Microbiota Transplantation", + "Middle Aged", + "Receptors, Calcitriol", + "Gastrointestinal Microbiome", + "Vitamin D Deficiency", + "Treatment Outcome", + "Mesalamine" + ], + "raw_abstract": "BACKGROUND AND AIM: Vitamin D (VD) deficiency was reported to correlate with ulcerative colitis (UC) activity, which might be closely related to gut microbiota dysbiosis. This study aims to investigate the effects of washed microbiota transplantation (WMT) on VD metabolism in UC. METHODS: The serum levels of 25-hdroxyvitamin D [25(OH)D] in 121 patients with UC and 53 healthy controls (HC) were detected. Subsequently, a non-randomized control trial (non-RCT) was conducted. Patients with UC were non-randomly assigned to undergo WMT (n\u00a0=\u00a028) vs. conventional treatment (5-aminosalicylic acid, 5-ASA, n\u00a0=\u00a010). Serum levels of 25(OH)D, fecal microbiota, and the expression of vitamin D receptor (VDR) in patients with UC were evaluated with a 3-month follow-up. RESULTS: Serum VD levels collected in the clinic practice indicated that patients with UC had significantly lower VD levels than HC (P\u00a0<\u00a00.001). In the non-RCT, serum 25(OH)D level and VDR expression significantly increased (P\u00a0=\u00a00.011, 0.026, respectively) in the WMT group, while no noticeable changes were observed in the non-WMT group. Microbiome profiling revealed that the increase in VD levels after WMT was positively associated with the abundances of Adlercreutzia_equolifaciens, Ruminococcus_obeum, and Dorea but negatively correlated with Escherichia. CONCLUSIONS: The study suggested that WMT increases the levels of VD with characteristic changes of specific microbiota, which indicated the association between the VD and the activity of UC might be regulated by gut microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28398347", + "title": "Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation.", + "year": 2017, + "journal": "The ISME journal", + "authors": [ + "Fuentes S", + "Rossen NG", + "van der Spek MJ", + "Hartman JH", + "Huuskonen L", + "Korpela K", + "Saloj\u00e4rvi J", + "Aalvink S", + "de Vos WM", + "D'Haens GR", + "Zoetendal EG", + "Ponsioen CY" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6662080340913457, + "mesh_terms": [ + "Adult", + "Bacteria", + "Chronic Disease", + "Colitis, Ulcerative", + "Fecal Microbiota Transplantation", + "Feces", + "Female", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Phylogeny" + ], + "raw_abstract": "Faecal microbiota transplantation (FMT) may contribute towards disease remission in ulcerative colitis (UC), but it is unknown which factors determine long-term effect of treatment. Here, we aimed to identify bacterial signatures associated with sustained remission. To this end, samples from healthy donors and UC patients-grouped into responders and non-responders at a primary end point (week 12) and further stratified by sustained clinical remission and relapse assessed at \u2a7e1-year follow-up were analysed, comparing the efficacy of FMT from either a healthy donor or autologous faeces. Microbiota composition was determined with a 16S rRNA gene-based phylogenetic microarray on faecal and mucosal samples, and functional profiles were predicted using PICRUSt with quantitative PCR verification of the butyrate production capacity; short-chain fatty acids were measured in faecal samples. At baseline, UC patients showed reduced amounts of bacterial groups from the Clostridium cluster XIVa, and significantly higher levels of Bacteroidetes as compared with donors. These differences were reduced after FMT mostly in responders. Sustained remission was associated with known butyrate producers and overall increased butyrate production capacity, while relapse was associated with Proteobacteria and Bacteroidetes. Ruminococcus gnavus was found at high levels in donors of failed FMT. A microbial ecosystem rich in Bacteroidetes and Proteobacteria and low in Clostridium clusters IV and XIVa observed in UC patients after FMT was predictive of poor sustained response, unless modified with a donor microbiota rich in specific members from the Clostridium clusters IV and XIVa. Additionally, sustained response was associated with restoration of the butyrate production capacity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37344396", + "title": "Differences in gut microbiota and fecal bile acids between Caucasian and Hispanic children and young adults with ulcerative colitis.", + "year": 2023, + "journal": "Physiological reports", + "authors": [ + "Aboud Syriani L", + "Parsana R", + "Durazo-Arvizu RA", + "Michail S" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6578299797023995, + "mesh_terms": [ + "Child", + "Humans", + "Young Adult", + "Bile Acids and Salts", + "Colitis, Ulcerative", + "Feces", + "Gastrointestinal Microbiome", + "Hispanic or Latino", + "Inflammatory Bowel Diseases", + "RNA, Ribosomal, 16S", + "White" + ], + "raw_abstract": "Ulcerative Colitis (UC) is an inflammatory bowel disease (IBD) that has been associated with gut dysbiosis. Changes in the gut microbiome lead to changes in bile acids (BA) metabolism, which changes the BA profiles in patients with UC. We conducted this study to investigate the differences in bile acids and gut microbiota between Hispanic and Caucasian children and young adults with UC. Twenty-seven Caucasian and 20 Hispanic children and young adults with UC were enrolled in the study. BAs were extracted from the subjects' stool samples and analyzed by liquid chromatography-mass spectrometry. Microbial DNA was also extracted from the stool samples to perform 16s rRNA amplicon sequencing. The median levels of cholic acid and taurolithocholic acid were found to be\u00a0significantly higher in Hispanic children and young adults with UC compared to their Caucasian counterparts. The abundance of the gut microbiota that metabolizes BAs such as Proteobacteria, Pseudomonadaceae, Pseudomonas, Ruminococcus gnavus, and Escherichia coli were also all significantly higher in Hispanic children and young adults as well. The distinct BA profile that we found in Hispanic children and young adults with UC, in addition to the unique composition of their gut microbiome, provide them with a protective gut environment against inflammation, which is contrary to the common believe that Hispanics have worse IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33352216", + "title": "Changes in intestinal microbiota and correlation with TLRs in ulcerative colitis in the coastal area of northern China.", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Xu N", + "Bai X", + "Cao X", + "Yue W", + "Jiang W", + "Yu Z" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6415885520933103, + "mesh_terms": [ + "China", + "Colitis, Ulcerative", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: To investigate the communities of fecal microbiota and the role of Toll-like receptors in patients with ulcerative colitis in the coastal area of northern China. METHODS: Stool samples from 31 patients with ulcerative colitis and 12 healthy individuals were collected. The total bacterial genomic DNA was extracted, and the V3+V4 hypervariable region in the bacterial 16S rRNA gene sequence was amplified by polymerase chain reaction (PCR). High-throughput sequencing analysis was performed on the Illumina Hiseq platform. The expression of TLR2, TLR4, Tollip, PPAR-\u03b3, IL-6, and TNF-\u03b1 in the colonic mucosa was measured by Western blots. RESULTS: The diversity of the fecal microbiota in patients with ulcerative colitis was significantly less than that in healthy control individuals (p\u00a0<\u00a00.05). The proportion of Bacteroidetes was significantly reduced (p\u00a0<\u00a00.01), whereas Proteobacteria was prevalent (p\u00a0<\u00a00.01) in patients with ulcerative colitis. At the genus level, the relative abundance of Streptococcus and Anaerostipes was significantly increased (p\u00a0<\u00a00.05), whereas the proportion of Bacteroides, Lachnospira, Ruminococcus, Phascolarctobacterium, and Coprococcus was significantly decreased in patients with ulcerative colitis (p\u00a0<\u00a00.05). The diversity indexes of fecal microbiota in patients with ulcerative colitis were negatively correlated with disease severity (p\u00a0<\u00a00.05). The relative abundance of Enterobacteriaceae was positively correlated with disease severity, and the relative abundance of Phascolarctobacterium, Anaerostipes, Fusobacterium, Parabacteroides, Oscillospira, and Ochrobactrum were negatively correlated with disease severity. The expression levels of TLR2 and TLR4 in the intestinal mucosa were positively correlated with the relative abundance of Streptococcus and Enterobacteriaceae, respectively (r\u00a0=\u00a00.481, p\u00a0=\u00a00.007; r\u00a0=\u00a00.455, p\u00a0=\u00a00.017). CONCLUSION: There were significant changes in the diversity and composition of the fecal microbiota in patients with ulcerative colitis compared to healthy individuals. The dysbiosis of gut microbiota and correlation with TLRs might play important roles in the pathogenesis and progression of ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32070388", + "title": "A randomized controlled trial investigating the effect of a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols on the intestinal microbiome and inflammation in patients with ulcerative colitis: study protocol for a randomized controlled trial.", + "year": 2020, + "journal": "Trials", + "authors": [ + "Milajerdi A", + "Sadeghi O", + "Siadat SD", + "Keshavarz SA", + "Sima A", + "Vahedi H", + "Adibi P", + "Esmaillzadeh A" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6263466957590321, + "mesh_terms": [ + "Adult", + "Biomarkers", + "Colitis, Ulcerative", + "Diet, Carbohydrate-Restricted", + "Dietary Sugars", + "Female", + "Fermentation", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Male", + "Middle Aged", + "Monosaccharides", + "Oligosaccharides", + "Polymers", + "Randomized Controlled Trials as Topic", + "Severity of Illness Index", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: No conclusive treatment is available for irritable bowel disease (IBD). Adherence to a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) might alleviate clinical symptoms of IBD. However, no study has investigated the effect of low FODMAPs diet on the intestinal microbiota and inflammatory biomarkers in patients with IBD. The aim of current study is to examine the effect a low FODMAP diet on IBD symptoms, inflammation, and the intestinal microbiota in patients with ulcerative colitis. METHODS AND ANALYSIS: This study is a randomized clinical trial. Thirty patients with mild to moderate ulcerative colitis will be randomly allocated to receive a low FODMAP diet (n\u2009=\u200915) or to continue their usual diet as control (n\u2009=\u200915), for 4\u2009weeks. The quantity of intestinal microbiota including Clostridium cluster IV, Faecalibacterium prausnitzii, Rosburia spp., Lactobacillus spp., Bifidobacteria spp., Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., and the Firmicutes to Bacteroidetes ratio and calprotectin and lactoferrin levels will be explored in fecal samples from patients. In addition, anthropometric measures and biochemical assessments including serum concentrations of highly sensitive-C reactive protein (hs-CRP), tumour necrosis factor-\u03b1 (TNF-\u03b1) and IL-1\u03b2 will be taken from patients at baseline and end of the study. The study has been registered in IRCT (IRCT20181126041763N1; registration date: 2019-01-18). DISCUSSION: Consumption of a low-FODMAP diet might decrease systemic and intestinal inflammation, change the bacterial population in the gut, and modulate clinical symptoms in patients with ulcerative colitis. Further studies investigating the effect of such a diet on other variables, including other bacterial species and inflammatory cytokines, are required to confirm future findings of this trial.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35692191", + "title": "Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease.", + "year": 2023, + "journal": "Intestinal research", + "authors": [ + "Shin SY", + "Kim Y", + "Kim WS", + "Moon JM", + "Lee KM", + "Jung SA", + "Park H", + "Huh EY", + "Kim BC", + "Lee SC", + "Choi CH" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.6102972168788905, + "mesh_terms": [], + "raw_abstract": "BACKGROUND/AIMS: The fecal microbiota of Korean patients with inflammatory bowel disease (IBD) was investigated with respect to disease phenotypes and taxonomic biomarkers for diagnosis and prognosis of IBD. METHODS: Fecal samples from 70 ulcerative colitis (UC) patients, 39 Crohn's disease (CD) patients, and 100 healthy control individuals (HC) were collected. The fecal samples were amplified via polymerase chain reaction and sequenced using Illumina MiSeq. The relationships between fecal bacteria and clinical phenotypes were analyzed using the EzBioCloud database and 16S microbiome pipeline. RESULTS: The alpha-diversity of fecal bacteria was significantly lower in UC and CD (P<0.05) compared to that in HC. Bacterial community compositions in UC and CD were significantly different from that of HC according to Bray-Curtis dissimilarities, and there was also a difference between community composition in UC and CD (P=0.01). In UC, alpha-diversity was further decreased when the disease was more severe and the extent of disease was greater, and community composition significantly differed depending on the extent of the disease. We identified 9 biomarkers of severity and 6 biomarkers of the extent of UC. We also identified 5 biomarkers of active disease and 3 biomarkers of ileocolonic involvement in CD. Lachnospiraceae and Ruminococcus gnavus were biomarkers for better prognosis in CD. CONCLUSIONS: The fecal microbiota profiles of IBD patients were different from those of HC, and several bacterial taxa may be used as biomarkers to determine disease phenotypes and prognosis. These data may also help discover new therapeutic targets for IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39073916", + "title": "Core microbiome-associated proteins associated with ulcerative colitis interact with cytokines for synergistic or antagonistic effects on gut bacteria.", + "year": 2024, + "journal": "The ISME journal", + "authors": [ + "Zhang T", + "Zhong H", + "Lin L", + "Zhang Z", + "Xue K", + "He F", + "Luo Y", + "Wang P", + "Zhao Z", + "Cong L", + "Pang P", + "Li X", + "Shan H", + "Yan Z" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5828772262635463, + "mesh_terms": [ + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Humans", + "Cytokines", + "Calgranulin B", + "Calgranulin A", + "Proteomics", + "Feces", + "Ruminococcus", + "Host Microbial Interactions", + "Clostridiales" + ], + "raw_abstract": "Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is associated with a loss or an imbalance of host-microorganism interactions. However, such interactions at protein levels remain largely unknown. Here, we applied a depletion-assisted metaproteomics approach to obtain in-depth host-microbiome association networks of IBD, where the core host proteins shifted from those maintaining mucosal homeostasis in controls to those involved in inflammation, proteolysis, and intestinal barrier in IBD. Microbial nodes such as short-chain fatty-acid producer-related host-microbial crosstalk were lost or suppressed by inflammatory proteins in IBD. Guided by protein-protein association networks, we employed proteomics and lipidomics to investigate the effects of UC-related core proteins S100A8, S100A9, and cytokines (IL-1\u03b2, IL-6, and TNF-\u03b1) on gut bacteria. These proteins suppressed purine nucleotide biosynthesis in stool-derived in vitro communities, which was also reduced in IBD stool samples. Single species study revealed that S100A8, S100A9, and cytokines can synergistically or antagonistically alter gut bacteria intracellular and secreted proteome, with combined S100A8 and S100A9 potently inhibiting beneficial Bifidobacterium adolescentis. Furthermore, these inflammatory proteins only altered the extracellular but not intracellular proteins of Ruminococcus gnavus. Generally, S100A8 induced more significant bacterial proteome changes than S100A9, IL-1\u03b2, IL-6, and TNF-\u03b1 but gut bacteria degrade significantly more S100A8 than S100A9 in the presence of both proteins. Among the investigated species, distinct lipid alterations were only observed in Bacteroides vulgatus treated with combined S100A8, S100A9, and cytokines. These results provided a valuable resource of inflammatory protein-centric host-microbial molecular interactions.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34264407", + "title": "A case-control study on the association of intestinal flora with ulcerative colitis.", + "year": 2021, + "journal": "AMB Express", + "authors": [ + "Tang YH", + "Liu HC", + "Song G", + "Wu TT", + "Zhao Y", + "Shi LJ" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5625006601305937, + "mesh_terms": [], + "raw_abstract": "The association between intestinal flora and ulcerative colitis (UC) was studied in order to provide a basis and method for clinical treatment. Fresh fecal samples were collected from 30 active UC patients and 10 healthy controls. The intestinal flora DNA from each sample was extracted and 16S rRNA gene sequencing was carried out using HiSeq platform to identify the intestinal flora in fecal samples. The richness and diversity of intestinal flora in UC patients were significantly lower than those in healthy control group (P\u2009<\u20090.05). Significant differences were observed between the intestinal flora-species of UC patients and healthy controls. Synergistetes (P\u2009<\u20090.01) and Firmicutes (P\u2009<\u20090.05), along with probiotics Veillonella (P\u2009<\u20090.01), Ruminococcus and Coprococcus (P\u2009<\u20090.05) in the UC patients were lower than that in the healthy controls significantly. Furthermore, compared with the control group, Tenericutes (P\u2009<\u20090.01) and intestinal pathogenic bacteria, including Bacteroides (P\u2009<\u20090.01), Escherichia and Sutterella (P\u2009<\u20090.05) were significantly increased. The incidence of UC is significantly associated with the changes in intestinal flora. Changes in intestinal flora may lead to a decrease in the diversity of intestinal flora or to the enrichment of a particular intestinal flora.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33947329", + "title": "Ecological and network analyses identify four microbial species with potential significance for the diagnosis/treatment of ulcerative colitis (UC).", + "year": 2021, + "journal": "BMC microbiology", + "authors": [ + "Li W", + "Sun Y", + "Dai L", + "Chen H", + "Yi B", + "Niu J", + "Wang L", + "Zhang F", + "Luo J", + "Wang K", + "Guo R", + "Li L", + "Zou Q", + "Ma ZS", + "Miao Y" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5553104396558273, + "mesh_terms": [ + "Bacteria", + "Biodiversity", + "China", + "Colitis, Ulcerative", + "DNA, Bacterial", + "Dysbiosis", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is one of the primary types of inflammatory bowel disease (IBD), the occurrence of which has been increasing worldwide. Although IBD is an intensively studied human microbiome-associated disease, research on Chinese populations remains relatively limited, particularly on the mucosal microbiome. The present study aimed to analyze the changes in the mucosal microbiome associated with UC from the perspectives of medical ecology and complex network analysis. RESULTS: In total, 56 mucosal microbiome samples were collected from 28 Chinese UC patients and their healthy family partners, followed by amplicon sequencing. Based on sequencing data, we analyzed species diversity, shared species, and inter-species interactions at the whole community, main phyla, and core/periphery species levels. We identified four opportunistic \"pathogens\" (i.e., Clostridium tertium, Odoribacter splanchnicus, Ruminococcus gnavus, and Flavonifractor plautii) with potential significance for the diagnosis and treatment of UC, which were inhibited in healthy individuals, but unrestricted in the UC patients. In addition, we also discovered in this study: (i) The positive-to-negative links (P/N) ratio, which measures the balance of species interactions or inhibition effects in microbiome networks, was significantly higher in UC patients, indicating loss of inhibition against potentially opportunistic \"pathogens\" associated with dysbiosis. (ii) Previous studies have reported conflicting evidence regarding species diversity and composition between UC patients and healthy controls. Here, significant differences were found at the major phylum and core/periphery scales, but not at the whole community level. Thus, we argue that the paradoxical results found in existing studies are due to the scale effect. CONCLUSIONS: Our results reveal changes in the ecology and network structure of the gut mucosal microbiome that might be associated with UC, and these changes might provide potential therapeutic mechanisms of UC. The four opportunistic pathogens that were identified in the present study deserve further investigation in future studies.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39126385", + "title": "Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis.", + "year": 2025, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Jangi S", + "Zhao N", + "Hsia K", + "Park YS", + "Michaud DS", + "Yoon H" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5505885116520582, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Male", + "Adult", + "Female", + "Prospective Studies", + "Middle Aged", + "Clostridiales", + "Candida", + "Republic of Korea", + "Feces" + ], + "raw_abstract": "BACKGROUND AND AIMS: While there is increasing interest in microbiome-directed therapies for patients with ulcerative colitis (UC), the identification of microbial targets remains elusive, underlining the need for novel approaches. METHODS: Utilizing metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation, we used a tree-based dichotomous approach to assemble distinct clusters of species-level bacterial co-abundance groups (CAGs). We evaluated the abundance of bacterial CAGs and fungal taxa during remission (n\u2005=\u2005166) and activity (n\u2005=\u200546). We examined if the bacterial CAGs identified in our cohorts were conserved in 2 healthy cohorts and a Korean UC cohort. RESULTS: CAG3 and CAG8, dominated by bacteria from the family Lachnospiraceae, were associated with remission. Low abundance of CAG8 and elevated abundance of Candida genus were predictive of active UC. Constituents from CAG8 were influential hub species of the remission-associated microbial UC network, including Ruminococcus gnavus, Erysipelatoclostridium ramosum, Blautia, and Dorea species. These hub species interactions were preserved in 2 healthy cohorts and were partially recapitulated in a Korean UC cohort. CAG8 abundance correlated with the secondary bile acid production pathway. Bacterial CAGs did not correlate with Candida; however, Bifidobacterium adolescentis and Alistipes putredinis were negatively associated with Candida. CONCLUSIONS: Lachnospiraceae-dominated bacterial CAGs were associated with remission in UC, with key bacterial interactions within the CAG also observed in 2 healthy cohorts and a Korean UC cohort. Bacterial CAG-based analyses may aid in designing candidate consortia for microbiome-based therapeutics.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32576228", + "title": "Effects of soy milk consumption on gut microbiota, inflammatory markers, and disease severity in patients with ulcerative colitis: a study protocol for a randomized clinical trial.", + "year": 2020, + "journal": "Trials", + "authors": [ + "Sadeghi O", + "Milajerdi A", + "Siadat SD", + "Keshavarz SA", + "Sima AR", + "Vahedi H", + "Adibi P", + "Esmaillzadeh A" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5496370877772266, + "mesh_terms": [ + "Adult", + "Anti-Inflammatory Agents", + "Biomarkers", + "Colitis, Ulcerative", + "Eating", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Iran", + "Male", + "Middle Aged", + "Phytoestrogens", + "Quality of Life", + "Randomized Controlled Trials as Topic", + "Severity of Illness Index", + "Soy Milk", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Several strategies are recommended to alleviate clinical symptoms of ulcerative colitis (UC). Soy milk may affect UC through its anti-inflammatory properties. However, no study has examined the effects of soy milk consumption on gut microbiota and inflammatory biomarkers in patients with UC. The current study will be done to examine the effects of soy milk consumption on UC symptoms, inflammation, and gut microbiota in patients with UC. METHODS: This study is a randomized clinical trial, in which thirty patients with mild to moderate severity of UC will be randomly allocated to receive either 250\u2009mL/day soy milk plus routine treatments (n\u2009=\u200915) or only routine treatments (n\u2009=\u200915) for 4\u2009weeks. Assessment of anthropometric measures and biochemical indicators including serum concentrations of high-sensitivity C-reactive protein (hs-CRP), tumor necrosis factor-\u03b1 (TNF-\u03b1), interleukin-1\u03b2 (IL-1\u03b2), and interferon gamma (IFN-\u03b3) will be done at the study baseline and end of trial. In addition, the quantity of butyrate-producing bacteria including Clostridium cluster IV, Faecalibacterium prausnitzii, and Roseburia spp.; prebiotic bacteria including Lactobacillus spp. and Bifidobacteria spp.; and mucus-degrading bacteria including Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., as well as calprotectin and lactoferrin levels, will be explored in fecal samples. Also, the Firmicutes to Bacteroidetes ratio which is of significant relevance in human gut microbiota composition will be assessed. DISCUSSION: Altered gut microbiota has been reported as an important contributing factor to inflammation in patients with inflammatory bowel disease (IBD). Soy milk contains several components such as phytoestrogens with potential anti-inflammatory properties. This product might affect gut microbiota through its protein and fiber content. Therefore, soy milk might beneficially affect systemic inflammation, gut microbiota, and then clinical symptoms in patients with UC. TRIAL REGISTRATION: Iranian Registry of Clinical Trials (www.irct.ir) IRCT20181205041859N1. Registered on 27 January 2019.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37095601", + "title": "A Mediterranean Diet Pattern Improves Intestinal Inflammation Concomitant with Reshaping of the Bacteriome in Ulcerative Colitis: A Randomised Controlled Trial.", + "year": 2023, + "journal": "Journal of Crohn's & colitis", + "authors": [ + "Haskey N", + "Estaki M", + "Ye J", + "Shim RK", + "Singh S", + "Dieleman LA", + "Jacobson K", + "Gibson DL" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5345849190962763, + "mesh_terms": [ + "Adult", + "Humans", + "Female", + "Middle Aged", + "Male", + "Colitis, Ulcerative", + "Diet, Mediterranean", + "Prospective Studies", + "RNA, Ribosomal, 16S", + "Canada", + "Inflammation", + "Feces", + "Butyric Acid", + "Leukocyte L1 Antigen Complex" + ], + "raw_abstract": "BACKGROUND AND AIMS: Dietary patterns are important in managing ulcerative colitis [UC], given their influence on gut microbiome-host symbiosis and inflammation. We investigated whether the Mediterranean Diet Pattern [MDP] vs the Canadian Habitual Diet Pattern [CHD] would affect disease activity, inflammation, and the gut microbiome in patients with quiescent UC. METHODS: We performed a prospective, randomised, controlled trial in adults [65% female; median age 47 years] with quiescent UC in an outpatient setting from 2017 to 2021. Participants were randomised to an MDP [n\u2005=\u200515] or CHD [n\u2005=\u200513] for 12 weeks. Disease activity [Simple Clinical Colitis Activity Index] and faecal calprotectin [FC] were measured at baseline and week 12. Stool samples were analysed by 16S rRNA gene amplicon sequencing. RESULTS: The diet was well tolerated by the MDP group. At week 12, 75% [9/12] of participants in the CHD had an FC\u2005>100 \u03bcg/g, vs 20% [3/15] of participants in the MDP group. The MDP group had higher levels of total faecal short chain fatty acids [SCFAs] [p\u2005=\u20050.01], acetic acid [p\u2005=\u20050.03], and butyric acid [p\u2005=\u20050.03] compared with the CHD. Furthermore, the MDP induced alterations in microbial species associated with a protective role in colitis [Alistipes finegoldii and Flavonifractor plautii], as well as the production of SCFAs [Ruminococcus bromii]. CONCLUSIONS: An MDP induces gut microbiome alterations associated with the maintenance of clinical remission and reduced FC in patients with quiescent UC. The data support that the MDP is a sustainable diet pattern that could be recommended as a maintenance diet and adjunctive therapy for UC patients in clinical remission. ClinicalTrials.gov no: NCT0305371.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31094471", + "title": "Markers of dysbiosis in patients with ulcerative colitis and Crohn's disease.", + "year": 2019, + "journal": "Terapevticheskii arkhiv", + "authors": [ + "Danilova NA", + "Abdulkhakov SR", + "Grigoryeva TV", + "Markelova MI", + "Vasilyev IY", + "Boulygina EA", + "Ardatskaya MD", + "Pavlenko AV", + "Tyakht AV", + "Odintsova AK", + "Abdulkhakov RA" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.5211650934273171, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans" + ], + "raw_abstract": "AIM: The aim of the study was to study the taxonomic and functional composition of the gut microbiota in ulcerative colitis (UC) and Crohn's disease (CD) patients to identify key markers of dysbiosis in IBD. MATERIALS AND METHODS: Fecal samples obtained from 95 IBD patients (78 UC and 17 CD) as well as 96 healthy volunteers were used for whole-genome sequencing carried out on the SOLiD 5500 W platform. Taxonomic profiling was performed by aligning the reeds, not maped on hg19, on MetaPhlAn2 reference database. Reeds were mapped using the HUNAnN2 algorithm to the ChocoPhlAn database to assess the representation of microbial metabolic pathways. Short-chain fatty acids (SCFA) level were measured in fecal samples by gas-liquid chromatographic analysis. RESULTS: Changes in IBD patients gut microbiota were characterized by an increase in the representation of Proteobacteria and Bacteroidetes phyla bacteria and decrease in the number of Firmicutes phylum bacteria and Euryarchaeota phylum archaea; a decrease in the alpha-diversity index, relative representation of butyrate-producing, hydrogen-utilizing bacteria, and Methanobrevibacter smithii; increase in the relative representation of Ruminococcus gnavus in UC and CD patients and Akkermansia muciniphila in CD patients. Reduction of Butyryl-CoA: acetate CoA transferase gene relative representation in CD patients, decrease of absolute content of SCFA total number as well as particular SCFAs and main SCFAs ratio in IBD patients may indicate inhibition of functional activity and number of anaerobic microflora and/or an change in SCFA utilization by colonocytes. CONCLUSION: the revealed changes can be considered as typical signs of dysbiosis in IBD patients and can be used as potential targets for IBD patients personalized treatment development.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36649193", + "title": "Microbiota DNA Translocation Into Mesentery Lymph Nodes Is Associated With Early Development of Pouchitis After IPAA for Ulcerative Colitis.", + "year": 2023, + "journal": "Diseases of the colon and rectum", + "authors": [ + "Zhao L", + "Zhu F", + "Chen J", + "Wang Z", + "Zhang T", + "Yu Z", + "Xu Y", + "Ding C", + "Gong J" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.4902748462943649, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Pouchitis", + "Proctocolectomy, Restorative", + "Mesentery", + "Male", + "Female", + "Adult", + "Bacterial Translocation", + "Lymph Nodes", + "Prospective Studies", + "Gastrointestinal Microbiome", + "Case-Control Studies", + "DNA, Bacterial", + "Middle Aged", + "Postoperative Complications" + ], + "raw_abstract": "BACKGROUND: The role of bacterial translocation in Crohn's disease has been extensively studied. However, data regarding bacterial translocation into the mesentery in patients with ulcerative colitis were scarce. OBJECTIVE: This study aimed to explore the relationship between bacterial translocation and postoperative outcome by comparing the microbiome profile of different anatomical sites in patients with ulcerative colitis who underwent proctocolectomy and IPAA. DESIGN: A prospective study. SETTING: This study was conducted at the Jinling Hospital from August 2017 to May 2018. PATIENTS: Samples of 27 patients with ulcerative colitis who had IPAA and 15 healthy controls who underwent routine colonoscopy were collected. MAIN OUTCOME MEASURES: The microbiome profile of different tissue sites and short- and long-term outcomes after IPAA in patients with ulcerative colitis. RESULTS: Bacterial DNA was detected in mesenteric lymph nodes of 51.9% of patients with ulcerative colitis (14/27) and in mesenteric adipose tissue of 66.7% of patients (18/27). The microbiome in mesenteric lymph nodes and mesenteric adipose tissue resembled the mucosal microbiome to a greater extent than the fecal microbiome. Positive bacterial DNA in mesenteric lymph nodes (8/14 vs 0/13; p = 0.002) was associated with pouchitis within 12 months after IPAA, whereas Bray-Curtis distance in mesenteric lymph nodes was significantly different between patients with pouchitis and without ( p = 0.009). LIMITATIONS: This study was limited by its small sample size and lacked situ experiment to confirm the true bacterial translation. CONCLUSIONS: Bacterial translocation was highly prevalent in patients with ulcerative colitis. The translocated bacteria DNA in mesenteric adipose tissue and mesenteric lymph nodes was highly correlated and more likely to originate from mucosal than fecal microbiome. Also, the extent of bacterial translocation and translocation of certain bacteria might be associated with the early development of pouchitis after IPAA. This might represent an unprecedented technique to predict pouchitis using mesenteric lymph node bacterial profiles. See Video Abstract at http://links.lww.com/DCR/C119 . LA TRANSLOCACIN DEL ADN DE LA MICROBIOTA EN LOS GANGLIOS LINFTICOS DEL MESENTERIO SE ASOCIA CON EL DESARROLLO TEMPRANO DE POUCHITIS DESPUS DE IPAA PARA LA COLITIS ULCEROSA: ANTECEDENTES:El papel de la translocaci\u00f3n bacteriana en la enfermedad de Crohn se ha estudiado ampliamente en los \u00faltimos a\u00f1os. Sin embargo, los datos sobre la translocaci\u00f3n bacteriana en el mesenterio en pacientes con colitis ulcerosa fueron escasos.OBJETIVO:El objetivo de este estudio fue explorar la relaci\u00f3n entre la translocaci\u00f3n bacteriana y el resultado postoperatorio comparando el perfil del microbioma de diferentes sitios anat\u00f3micos en pacientes con colitis ulcerosa que se sometieron a proctocolectom\u00eda y anastomosis ileoanal con bolsa.DISE\u00d1O:Estudio prospectivo.AJUSTE:Este estudio se realiz\u00f3 en el Hospital Jinling desde agosto de 2017 hasta mayo de 2018.PACIENTES:Se recogieron muestras de 27 pacientes con colitis ulcerosa que ten\u00edan anastomosis de bolsa ileoanal y 15 controles sanos que se sometieron a una colonoscopia de rutina.PRINCIPALES MEDIDAS DE RESULTADO:El perfil del microbioma de diferentes sitios de tejido y los resultados a corto y largo plazo despu\u00e9s de la anastomosis ileoanal con bolsa en pacientes con colitis ulcerosa.RESULTADOS:Se detect\u00f3 ADN bacteriano en los ganglios linf\u00e1ticos mesent\u00e9ricos del 51,9 % (14/27) de los pacientes con colitis ulcerosa y en el tejido adiposo mesent\u00e9rico del 66,7 % (18/27) de los pacientes, respectivamente. El microbioma en los ganglios linf\u00e1ticos mesent\u00e9ricos y el tejido adiposo mesent\u00e9rico se parec\u00eda m\u00e1s al microbioma de la mucosa que al microbioma fecal. El ADN bacteriano translocado en los ganglios linf\u00e1ticos mesent\u00e9ricos y el tejido adiposo mesent\u00e9rico estaban altamente correlacionados. El ADN bacteriano positivo en los ganglios linf\u00e1ticos mesent\u00e9ricos (8/14 frente a 0/13, p = 0,002) se asoci\u00f3 con reservoritis dentro de los 12 meses posteriores a la anastomosis ileoanal con reservorio, mientras que la distancia de Bray-Curtis en los ganglios linf\u00e1ticos mesent\u00e9ricos fue significativamente diferente entre reservoritis y no reservorios. -pacientes con reservorio (p = 0,009). Ruminococcus, Bacteroides y Clostridiales se encontraron exclusivamente en los ganglios linf\u00e1ticos mesent\u00e9ricos de pacientes con reservoritis.LIMITACI\u00d3N:Este estudio estuvo limitado por el peque\u00f1o tama\u00f1o de la muestra y la falta de un experimento in situ para confirmar la verdadera traducci\u00f3n bacteriana.CONCLUSI\u00d3N:La translocaci\u00f3n bacteriana fue altamente prevalente en pacientes con colitis ulcerosa. El ADN bacteriano translocado en el tejido adiposo mesent\u00e9rico y los ganglios linf\u00e1ticos mesent\u00e9ricos estaba altamente correlacionado y era m\u00e1s probable que se originara en el microbioma de la mucosa que en el fecal. Adem\u00e1s, la extensi\u00f3n de la translocaci\u00f3n bacteriana y la translocaci\u00f3n de ciertas bacterias podr\u00eda estar asociada con el desarrollo temprano de reservoritis despu\u00e9s de la anastomosis del reservorio ileoanal. Esto podr\u00eda representar una t\u00e9cnica sin precedentes para predecir la reservoritis utilizando perfiles bacterianos de los ganglios linf\u00e1ticos mesent\u00e9ricos. Consulte Video Resumen en. http://links.lww.com/DCR/C119(Traducci\u00f3n-Dr. Felipe Bellolio ).", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29052237", + "title": "The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis.", + "year": 2018, + "journal": "Alimentary pharmacology & therapeutics", + "authors": [ + "Kump P", + "Wurm P", + "Gr\u00f6chenig HP", + "Wenzl H", + "Petritsch W", + "Halwachs B", + "Wagner M", + "Stadlbauer V", + "Eherer A", + "Hoffmann KM", + "Deutschmann A", + "Reicht G", + "Reiter L", + "Slawitsch P", + "Gorkiewicz G", + "H\u00f6genauer C" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.4848185506562907, + "mesh_terms": [ + "Adult", + "Anti-Bacterial Agents", + "Colitis, Ulcerative", + "Fecal Microbiota Transplantation", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Microbiota", + "Middle Aged", + "Prospective Studies", + "Remission Induction", + "Ruminococcus", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Faecal microbiota transplantation is an experimental approach for the treatment of patients with ulcerative colitis. Although there is growing evidence that faecal microbiota transplantation is effective in this disease, factors affecting its response are unknown. AIMS: To establish a faecal microbiota transplantation treatment protocol in ulcerative colitis patients, and to investigate which patient or donor factors are responsible for the treatment success. METHODS: This is an open controlled trial of repeated faecal microbiota transplantation after antibiotic pre-treatment (FMT-group, n\u00a0=\u00a017) vs antibiotic pre-treatment only (AB-group, n\u00a0=\u00a010) in 27 therapy refractory ulcerative colitis patients over 90\u00a0days. Faecal samples of donors and patients were analysed by 16SrRNA gene-based microbiota analysis. RESULTS: In the FMT-group, 10/17 (59%) of patients showed a response and 4/17 (24%) a remission to faecal microbiota transplantation. Response to faecal microbiota transplantation was mainly influenced by the taxonomic composition of the donor's microbiota. Stool of donors with a high bacterial richness (observed species remission 946\u00a0\u00b1\u00a093 vs no response 797\u00a0\u00b1\u00a0181 at 15367\u00a0rps) and a high relative abundance of Akkermansia muciniphila (3.3\u00a0\u00b1\u00a03.1% vs 0.1\u00a0\u00b1\u00a00.2%), unclassified Ruminococcaceae (13.8\u00a0\u00b1\u00a05.0% vs 7.5\u00a0\u00b1\u00a03.7%), and Ruminococcus spp. (4.9\u00a0\u00b1\u00a03.5% vs 1.0\u00a0\u00b1\u00a00.7%) were more likely to induce remission. In contrast antibiotic treatment alone (AB-group) was poorly tolerated, probably because of a sustained decrease of intestinal microbial richness. CONCLUSIONS: The taxonomic composition of the donor's intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in ulcerative colitis patients. The design of specific microbial preparation might lead to new treatments for ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26423113", + "title": "Specific members of the predominant gut microbiota predict pouchitis following colectomy and IPAA in UC.", + "year": 2017, + "journal": "Gut", + "authors": [ + "Machiels K", + "Sabino J", + "Vandermosten L", + "Joossens M", + "Arijs I", + "de Bruyn M", + "Eeckhaut V", + "Van Assche G", + "Ferrante M", + "Verhaegen J", + "Van Steen K", + "Van Immerseel F", + "Huys G", + "Verbeke K", + "Wolthuis A", + "de Buck Van Overstraeten A", + "D'Hoore A", + "Rutgeerts P", + "Vermeire S" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.4747223301240291, + "mesh_terms": [ + "Adult", + "Bacteroidetes", + "Clostridium perfringens", + "Cluster Analysis", + "Colitis, Ulcerative", + "Colonic Pouches", + "DNA, Bacterial", + "Fatty Acids, Volatile", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Middle Aged", + "Pouchitis", + "Predictive Value of Tests", + "Preoperative Period", + "Proctocolectomy, Restorative", + "Prospective Studies", + "Ruminococcus", + "Time Factors" + ], + "raw_abstract": "OBJECTIVE: Pouchitis is the most common complication after colectomy with ileal pouch-anal anastomosis (IPAA) for UC and the risk is the highest within the 1st year after surgery. The pathogenesis is not completely understood but clinical response to antibiotics suggests a role for gut microbiota. We hypothesised that the risk for pouchitis can be predicted based on the faecal microbial composition before colectomy. DESIGN: Faecal samples from 21 patients with UC undergoing IPAA were prospectively collected before colectomy and at predefined clinical visits at 1 month, 3 months, 6 months and 12\u2005months after IPAA. The predominant microbiota was analysed using community profiling with denaturing gradient gel electrophoresis followed by quantitative real-time PCR validation. RESULTS: Cluster analysis before colectomy distinguished patients with pouchitis from those with normal pouch during the 1st year of follow-up. In patients developing pouchitis, an increase of Ruminococcus gnavus (p<0.001), Bacteroides vulgatus (p=0.043), Clostridium perfringens (p=0.011) and a reduction of two Lachnospiraceae genera (Blautia (p=0.04), Roseburia (p=0.008)) was observed. A score combining these five bacterial risk factors was calculated and presence of at least two risk factors showed a sensitivity and specificity of 100% and 63.6%, respectively. CONCLUSIONS: Presence of R. gnavus, B. vulgatus and C. perfringens and absence of Blautia and Roseburia in faecal samples of patients with UC before surgery is associated with a higher risk of pouchitis after IPAA. Our findings suggest new predictive and therapeutic strategies in patients undergoing colectomy with IPAA.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34146566", + "title": "Mucosal Biofilms Are an Endoscopic Feature of Irritable Bowel Syndrome and Ulcerative Colitis.", + "year": 2021, + "journal": "Gastroenterology", + "authors": [ + "Baumgartner M", + "Lang M", + "Holley H", + "Crepaz D", + "Hausmann B", + "Pjevac P", + "Moser D", + "Haller F", + "Hof F", + "Beer A", + "Orgler E", + "Frick A", + "Khare V", + "Evstatiev R", + "Strohmaier S", + "Primas C", + "Dolak W", + "K\u00f6cher T", + "Klavins K", + "Rath T", + "Neurath MF", + "Berry D", + "Makristathis A", + "Muttenthaler M", + "Gasche C" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.4710280281627119, + "mesh_terms": [ + "Austria", + "Bacteria", + "Biofilms", + "Case-Control Studies", + "Colitis, Ulcerative", + "Colon", + "Colonoscopy", + "Deep Learning", + "Gastrointestinal Microbiome", + "Germany", + "Humans", + "Image Interpretation, Computer-Assisted", + "Intestinal Mucosa", + "Irritable Bowel Syndrome", + "Metabolomics", + "Microscopy, Confocal", + "Microscopy, Electron, Scanning", + "Predictive Value of Tests", + "Ribotyping" + ], + "raw_abstract": "BACKGROUND & AIMS: Irritable bowel syndrome (IBS) and inflammatory bowel diseases result in a substantial reduction in quality of life and a considerable socioeconomic impact. In IBS, diagnosis and treatment options are limited, but evidence for involvement of the gut microbiome in disease pathophysiology is emerging. Here we analyzed the prevalence of endoscopically visible mucosal biofilms in gastrointestinal disease and associated changes in microbiome composition and metabolism. METHODS: The presence of mucosal biofilms was assessed in 1426 patients at 2 European university-based endoscopy centers. One-hundred and seventeen patients were selected for in-depth molecular and microscopic analysis using 16S ribosomal RNA gene amplicon-sequencing of colonic biopsies and fecal samples, confocal microscopy with deep learning-based image analysis, scanning electron microscopy, metabolomics, and in\u00a0vitro biofilm formation assays. RESULTS: Biofilms were present in 57% of patients with IBS and 34% of patients with ulcerative colitis compared with 6% of controls (P < .001). These yellow-green adherent layers of the ileum and right-sided colon were microscopically confirmed to be dense bacterial biofilms. 16S-sequencing links the presence of biofilms to a dysbiotic gut microbiome, including overgrowth of Escherichia coli and Ruminococcus gnavus. R. gnavus isolates cultivated from patient biofilms also formed biofilms in\u00a0vitro. Metabolomic analysis found an accumulation of bile acids within biofilms that correlated with fecal bile acid excretion, linking this phenotype with a mechanism of diarrhea. CONCLUSIONS: The presence of mucosal biofilms is an endoscopic feature in a subgroup of IBS and ulcerative colitis with disrupted bile acid metabolism and bacterial dysbiosis. They provide novel insight into the pathophysiology of IBS and ulcerative colitis, illustrating that biofilm can be seen as a tipping point in the development of dysbiosis and disease.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32955197", + "title": "Fecal Microbiota Transplantation for Ulcerative Colitis: The Optimum Timing and Gut Microbiota as Predictors for Long-Term Clinical Outcomes.", + "year": 2020, + "journal": "Clinical and translational gastroenterology", + "authors": [ + "Li Q", + "Ding X", + "Liu K", + "Marcella C", + "Liu X", + "Zhang T", + "Liu Y", + "Li P", + "Xiang L", + "Cui B", + "Wang J", + "Bai J", + "Zhang F" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.4465861642905628, + "mesh_terms": [ + "Adolescent", + "Adult", + "Child", + "Colitis, Ulcerative", + "DNA, Bacterial", + "Fecal Microbiota Transplantation", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged", + "Prognosis", + "Prospective Studies", + "RNA, Ribosomal, 16S", + "Remission Induction", + "Retreatment", + "Time-to-Treatment", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "INTRODUCTION: The previous researches aimed to evaluate the efficacy and safety of fecal microbiota transplantation (FMT) for ulcerative colitis (UC) in a short-term observation. The present study aimed to explore the optimum timing of FMT for maintaining the long-term clinical benefits and to target the gut microbiota that may help to predict the long-term success or failure of FMT in UC. METHODS: Two hundred two patients with UC were recruited from November 2012 to September 2018. The primary endpoint of this study was the maintaining time of the first and second courses of FMT. Relapse was defined as partial Mayo score \u22652 after achieving clinical remission and an increase of partial Mayo score \u22651 after achieving clinical response. The stool samples were analyzed by 16S rRNA gene sequencing. RESULTS: The median maintaining time of the efficacy was 120 days (IQR, 45-180) and 182.5 days (IQR, 105-311.25) from the first course and second course of FMT, respectively. No FMT-related serious adverse events were observed. The differences of the relative abundance in Eggerthella, Lactobacillus, and Ruminococcus between pre-FMT and 5 days post-FMT were remarkably correlated with the long-term clinical remission (P < 0.05). DISCUSSION: This study demonstrated that patients with UC should undergo the second course of FMT within 4 months after the first course of FMT for maintaining the long-term clinical benefits. The short-term alterations of microbiota after FMT may be conducive to predicting the long-term efficacy of FMT in UC (see Visual Abstract, Supplementary Digital Content, http://links.lww.com/CTG/A363).", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39442743", + "title": "Gut Microbiota Features in Relation to Fecal Microbiota Transplantation Outcome in Ulcerative Colitis: A Systematic Review and Meta-Analysis.", + "year": 2024, + "journal": "Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association", + "authors": [ + "B\u00e9nard MV", + "de Goffau MC", + "Blonk J", + "Hugenholtz F", + "van Buuren J", + "Paramsothy S", + "Kaakoush NO", + "D'Haens GRAM", + "Borody TJ", + "Kamm MA", + "Ponsioen CY" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.3829949186510492, + "mesh_terms": [], + "raw_abstract": "BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis, yet its efficacy needs improvement. We conducted a comprehensive evaluation of the current literature on microbial factors affecting outcome, as well as a meta-analysis on some of the largest datasets regarding composition. METHODS: MEDLINE, Embase, and Cochrane were systematically searched through August 2024 for relevant studies. The quality of studies was analyzed with JBI tools and a composite critical appraisal score. Additionally, species-level data from 2 landmark FMT trials (the Transplantation of Feces in Ulcerative Colitis; Returning Nature's Homeostasis [TURN] and Fecal Microbiota Transplantation for Chronic Active Ulcerative Colitis [FOCUS] trials) were reanalyzed from a compositional perspective. RESULTS: Out of 3755 citations identified, 56 met the inclusion criteria, of which 29 fulfilled quality standards. Higher microbial \u03b1-diversity, either in donors or recipients (at baseline or following FMT treatment), was associated with better clinical response rates. Engraftment of the donors' microbiota could not be clearly linked with clinical response, possibly because not every donor has an ideal microbiome. Butyrate-producing species from the Lachnospiraceae and Oscillospiraceae families were often related with response, whereas the reverse was true for Fusobacteria, many Proteobacteria, and Ruminococcus gnavus. Compositional analyses showed that clinical response is associated with a shift from a low-diversity, often Bacteroides-dominant composition to one with higher diversity, either dominated by various butyrate producers, the Christensenellaceae-Methanobrevibacter trophic network, or a moderate/high-diversity composition with abundant but not excessive levels of Prevotella copri. CONCLUSIONS: This systematic review/meta-analysis yielded a coherent picture from a compositional perspective, which may help identify beneficial donor profiles and guide personalized FMT approaches.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39030520", + "title": "Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Joo M", + "Nam S" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.3668337016421349, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Adolescent", + "RNA, Ribosomal, 16S", + "Obesity", + "Female", + "Male", + "Bacteria", + "Phylogeny", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Colitis, Ulcerative", + "Dysbiosis", + "Prevotella", + "Faecalibacterium prausnitzii", + "Feces" + ], + "raw_abstract": "BACKGROUND: Recently, there has been an increase in the number of studies focusing on the association between the gut microbiome and obesity or inflammatory diseases, especially in adults. However, there is a lack of studies investigating the association between gut microbiome and gastrointestinal (GI) diseases in adolescents. METHOD: We obtained 16S rRNA-seq datasets for gut microbiome analysis from 202 adolescents, comprising ulcerative colitis (UC), Crohn's disease (CD), obesity (Ob), and healthy controls (HC). We utilized Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to acquire Operational Taxonomic Units (OTUs). Subsequently, we analyzed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) terms and pathway enrichment for the identified OTUs. RESULTS: In this study, we investigated the difference between the gut microbiomes in adolescents with GI diseases and those in healthy adolescents using 202 samples of 16S rRNA sequencing data. The distribution of the six main gut microbiota (i.e., unclassified Dorea, unclassified Lachnospiraceae, unclassified Ruminococcus, Faecalibacterium prausnitzii, Prevotella copri, unclassified Sutterella) was different based on the status of obesity and inflammatory diseases. Dysbiosis was observed within Lachnospiraceae in adolescents with inflammatory diseases (i.e., UC and CD), and in adolescents with obesity within Prevotella and Sutterella. More specifically, our results showed that the relative abundance of Faecalibacterium prausnitzii and unclassified Lachnospiraceae was more than 10% and 8% higher, respectively, in the UC group compared to the CD, Ob, and HC groups. Additionally, the Ob group had over 20% and over 3% higher levels of Prevotella copri and unclassified Sutterella, respectively, compared to the UC, CD, and HC groups. Also, inspecting associations between the six specific microbiota and KO terms, we found that the six microbiota -relating KO terms were associated with NOD-like receptor signaling. These six taxa differences may affect the immune system and inflammatory response by affecting NOD-like receptor signaling in the host during critical adolescence. CONCLUSION: In this study, we discovered that dysbiosis of the microbial community had varying degrees of influence on the inflammatory and immune response pathways in adolescents with inflammatory diseases and obesity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31605691", + "title": "Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy.", + "year": 2020, + "journal": "Gastroenterology", + "authors": [ + "Dubinsky V", + "Reshef L", + "Bar N", + "Keizer D", + "Golan N", + "Rabinowitz K", + "Godny L", + "Yadgar K", + "Zonensain K", + "Tulchinsky H", + "Gophna U", + "Dotan I" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.36200188478650597, + "mesh_terms": [ + "Adult", + "Anti-Bacterial Agents", + "Bacteria", + "Ciprofloxacin", + "Cytokines", + "Drug Resistance, Bacterial", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "HT29 Cells", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Metagenomics", + "Metronidazole", + "Middle Aged", + "Point Mutation", + "Pouchitis", + "Prospective Studies", + "Recurrence", + "Treatment Outcome", + "Virulence Factors", + "Young Adult" + ], + "raw_abstract": "BACKGROUND & AIMS: Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic-dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial factors associated with response to antibiotic treatment and development of antibiotic dependence in patients with pouchitis. METHODS: We performed a prospective study of 49 patients who had undergone pouch surgery at a tertiary center. Disease activity was determined based on clinical, endoscopic, and histologic criteria. Pouch phenotype was defined as recurrent-acute pouchitis (n\u00a0= 6), chronic pouchitis and Crohn's-like disease of the pouch (n\u00a0= 27), normal pouch from patient with ulcerative colitis (n\u00a0= 10), and normal pouch from patient with familial adenomatous polyposis (n\u00a0= 6). Fecal samples (n\u00a0= 234) were collected over time during or in the absence of antibiotic treatment (ciprofloxacin and/or metronidazole). Thirty-three patients were treated with antibiotics, for a median of 425 days of cumulative antibiotic therapy, during follow-up. Calprotectin was measured and fecal DNA was sequenced using shotgun metagenomics and analyzed with specifically designed bioinformatic pipelines. Bacterial strains were isolated from fecal samples. We assessed their ciprofloxacin resistance and ability to induce secretion of inflammatory cytokines by HT-29 intestinal epithelial cells. RESULTS: Most antibiotic-treated patients (79%) had a clinical response to each course of antibiotics; however, 89% of those who completed a 4-week course relapsed within 3 months. Median calprotectin levels decreased by 40% in response to antibiotics. Antibiotic treatment reduced disease-associated bacteria such as Clostridium perfringens, Ruminococcus gnavus, and Klebsiella pneumoniae, but also beneficial species, such as Faecalibacterium prausnitzii. The microbiomes of antibiotic-responsive patients were dominated by facultative anaerobic genera (Escherichia, Enterococcus, and Streptococcus), with multiple ciprofloxacin-resistance mutations in drug target genes and confirmed drug resistance. However, these strains had lower potential for virulence and did not induce secretion of inflammatory cytokines by epithelial cells. After antibiotic cessation, patients had an abrupt shift in microbiome composition, with blooms of oral and disease-associated bacteria. In addition, antibiotic treatment enriched for strains that acquired multidrug resistance loci, encoding enzymes that confer resistance to nonrelated antibiotics, including extended-spectrum beta-lactamases. CONCLUSIONS: The efficacy of antibiotic treatment of pouchitis might be attributed to the establishment of an antibiotic-resistant microbiome with low inflammatory potential. This microbiome might provide resistance against colonization by bacteria that promote inflammation. To avoid progression to antibiotic-dependent disease and its consequences, strategies such as short-term alternating antibiotics and nutrition- and microbiome-based interventions should be considered.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39731099", + "title": "Reduced gut microbiota diversity in ulcerative colitis patients with latent tuberculosis infection during vedolizumab therapy: insights on prophylactic anti-tuberculosis effects.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Hu Y", + "Wu Z", + "Yang X", + "Ding J", + "Wang Q", + "Fang H", + "Zhu L", + "Hu M" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.3485323861254706, + "mesh_terms": [ + "Humans", + "Male", + "Female", + "Adult", + "Aged", + "Gastrointestinal Agents", + "Gastrointestinal Microbiome", + "Biodiversity", + "Latent Tuberculosis", + "Colitis, Ulcerative", + "RNA, Ribosomal, 16S", + "Antitubercular Agents", + "Cohort Studies", + "Isoniazid", + "Antibiotic Prophylaxis", + "Antibodies, Monoclonal, Humanized" + ], + "raw_abstract": "BACKGROUND: The gut microbiota plays a pivotal role in ulcerative colitis (UC) development. This study explores the impact of latent tuberculosis infection (LTBI) on the gut microbiota in UC and assesses changes during vedolizumab treatment, investigating prophylactic anti-tuberculosis therapy. RESULTS: This cohort study included adult patients with UC receiving vedolizumab treatment at Jinhua Hospital, Zhejiang University from April 2021 to December 2022. Patients were divided into LTBI (n\u2009=\u200924) and non-LTBI (n\u2009=\u200921) groups. Patients in the LTBI group were further subdivided into prophylactic (n\u2009=\u200913) and non-prophylactic (n\u2009=\u200911) groups. Clinical and fecal samples were collected pre- and post-vedolizumab treatment for the LTBI groups and pre-treatment for the non-LTBI group. The gut microbiota was analyzed using 16\u00a0S rRNA sequencing. Patients in the non-LTBI group exhibited higher diversity indices. Vedolizumab demonstrated efficacy in the LTBI group, with clinical response and remission rates of 83.3% and 75.0%, respectively. The gut microbiota diversity in the LTBI group increased post-vedolizumab treatment, and receiving prophylactic isoniazid showed no significant difference in vedolizumab treatment response compared to not receiving prophylactic isoniazid. Microbiota changes were similar between groups, with an increase in [Ruminococcus] expression after vedolizumab treatment. CONCLUSIONS: This cohort study, conducted at a single center, highlights that LTBI can reduce gut microbiota diversity among adult patient with UC. The observed efficacy of vedolizumab treatment in the LTBI group indicates a potential association with microbiota changes. However, mono-isoniazid exhibited limited impact, underscoring the potential of vedolizumab as a promising candidate for prophylactic anti-tuberculosis treatment in the context of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26130823", + "title": "A retrospective metagenomics approach to studying Blastocystis.", + "year": 2015, + "journal": "FEMS microbiology ecology", + "authors": [ + "Andersen LO", + "Bonde I", + "Nielsen HB", + "Stensvold CR" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.34815727161910853, + "mesh_terms": [ + "Adult", + "Bacteroides", + "Blastocystis", + "Colitis, Ulcerative", + "Crohn Disease", + "Feces", + "Female", + "Humans", + "Male", + "Metagenomics", + "Middle Aged", + "Retrospective Studies" + ], + "raw_abstract": "Blastocystis is a common single-celled intestinal parasitic genus, comprising several subtypes. Here, we screened data obtained by metagenomic analysis of faecal DNA for Blastocystis by searching for subtype-specific genes in coabundance gene groups, which are groups of genes that covary across a selection of 316 human faecal samples, hence representing genes originating from a single subtype. The 316 faecal samples were from 236 healthy individuals, 13 patients with Crohn's disease (CD) and 67 patients with ulcerative colitis (UC). The prevalence of Blastocystis was 20.3% in the healthy individuals and 14.9% in patients with UC. Meanwhile, Blastocystis was absent in patients with CD. Individuals with intestinal microbiota dominated by Bacteroides were much less prone to having Blastocystis-positive stool (Matthew's correlation coefficient = -0.25, P < 0.0001) than individuals with Ruminococcus- and Prevotella-driven enterotypes. This is the first study to investigate the relationship between Blastocystis and communities of gut bacteria using a metagenomics approach. The study serves as an example of how it is possible to retrospectively investigate microbial eukaryotic communities in the gut using metagenomic datasets targeting the bacterial component of the intestinal microbiome and the interplay between these microbial communities.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34761733", + "title": "Attributes of intestinal microbiota composition and their correlation with clinical primary non-response to anti-TNF-\u03b1 agents in inflammatory bowel disease patients.", + "year": 2022, + "journal": "Bosnian journal of basic medical sciences", + "authors": [ + "Alatawi H", + "Mosli M", + "Saadah OI", + "Annese V", + "Al-Hindi R", + "Alatawy M", + "Al-Amrah H", + "Alshehri D", + "Bahieldin A", + "Edris S" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.31943079819820963, + "mesh_terms": [ + "Bacteria", + "Biomarkers", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "RNA, Ribosomal, 16S", + "Tumor Necrosis Factor Inhibitors" + ], + "raw_abstract": "The largest microbial aggregation in the human body exists in the gastrointestinal tract. The microbiota in the host gastrointestinal tract comprises a diverse ecosystem, and the intestinal microbiota plays a vital role in maintaining gut homeostasis. This study aims to examine whether the gut microbiota influences unresponsiveness to anti-TNF-\u03b1 treatments in primary nonresponder patients, and consequently identify the responsible microbes as biomarkers of unresponsiveness. Stool samples were collected from a cohort of patients with an established diagnosis of IBD, either ulcerative colitis (UC) or Crohn's disease (CD), following completion of the induction phase of anti TNF therapy. 16S rRNA sequencing analysis was used to examine the pattern of microbiota communities in fecal samples. The quality and quantity of fecal microbiota were compared in responder and primary nonresponder IBD patients following anti-TNF-\u03b1 therapy. As per our hypothesis, a difference in gut microbiome composition between the two patient subgroups was observed. A decreased abundance of short-chain fatty acid (SCFA)-producing bacteria, including Anaerostipes, Coprococcus, Lachnospira, Roseburia, and Ruminococcus, was detected in non-responsive patients, which was the hallmark of dysbiosis. Biomarkers of dysbiosis that were identified as predictors of clinical nonresponse, included Klebsiella, Eubacteriaceae, RF32, Bifidobacterium_animalis, and Muribaculaceae-previously known as S24-7. Signature biomarkers showed dramatic alteration in the composition of gut microbiota in patients who demonstrated primary nonresponse to anti-TNF-\u03b1 agents. Dysbiosis, with features including a dropped biodiversity, augmentation in opportunistic pathogenic microbiota, and a lack of SCFA-producing bacteria, is a prominent feature of the microbiome of primary nonresponders to anti-TNF-\u03b1 therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37859536", + "title": "Baizhu-Baishao herb pair ameliorates functional constipation and intestinal microflora disorder in rats.", + "year": 2023, + "journal": "Animal models and experimental medicine", + "authors": [ + "Li X", + "Wang X", + "Wang Z", + "Guan J" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.2518166578057637, + "mesh_terms": [ + "Rats", + "Animals", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Serotonin", + "Constipation", + "Vasoactive Intestinal Peptide", + "Substance P" + ], + "raw_abstract": "BACKGROUND: In China, Rhizoma atractylodis macrocephalae-Paeonia lactiflora Pall (Biazhu-Baishao, BZBS) is a classic herb pair used to treat intestinal stress syndrome, ulcerative colitis and other diseases. However, the mechanism of BZBS in the treatment of functional constipation (FC) has been little studied and remains unclear. In this study, a behavioral investigation, colon tissue morphology, enzyme-linked immunosorbent assay (Elisa) and intestinal microflora analysis have been used to illuminate the potential mechanism of the effects of BZBS on FC in a rat model. METHODS: A FC rat model was constructed and BZBS was given as treatment. Observations and recordings were made of the fecal moisture content, the defecation time of the first black stool, and the rate of intestinal propulsion. Elisa was used to detect the expression levels of substance P (SP), vasoactive intestinal peptide (VIP), 5-hydroxytryptamine (5-HT) in the colon. To ascertain the composition of the microbial community, a high throughput 16S ribosomal RNA (16S rRNA) gene sequencing technique was employed. RESULTS: Oral administration of BZBS significantly ameliorated several key excretion parameters, including the time to first black stool defecation, stool water content, and the propulsion rate in the small intestine in FC rats. It increased the expression of SP, VIP and 5-HT in the colon. 16S rRNA gene sequencing results showed that BZBS changed the microbial community structure, decreased the Bacteroidetes/Firmicutes ratio, increased the relative abundance of Blautia and Fusicatenibacter, and decreased the relative abundance of Ruminococcus and Roseburia. CONCLUSIONS: BZBS effectively alleviates FC and improves dysbacteriosis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26024217", + "title": "The effect of sampling and storage on the fecal microbiota composition in healthy and diseased subjects.", + "year": 2015, + "journal": "PloS one", + "authors": [ + "Tedjo DI", + "Jonkers DM", + "Savelkoul PH", + "Masclee AA", + "van Best N", + "Pierik MJ", + "Penders J" + ], + "bacteria": "Ruminococcus", + "condition": "ulcerative colitis", + "relevance_score": 0.22097449197202915, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Bacteria", + "Biodiversity", + "Colitis, Ulcerative", + "Crohn Disease", + "Feces", + "Female", + "Humans", + "Irritable Bowel Syndrome", + "Male", + "Microbiota", + "Middle Aged", + "Specimen Handling" + ], + "raw_abstract": "Large-scale cohort studies are currently being designed to investigate the human microbiome in health and disease. Adequate sampling strategies are required to limit bias due to shifts in microbial communities during sampling and storage. Therefore, we examined the impact of different sampling and storage conditions on the stability of fecal microbial communities in healthy and diseased subjects. Fecal samples from 10 healthy controls, 10 irritable bowel syndrome and 8 inflammatory bowel disease patients were collected on site, aliquoted immediately after defecation and stored at -80 \u00b0C, -20 \u00b0C for 1 week, at +4\u00b0C or room temperature for 24 hours. Fecal transport swabs (FecalSwab, Copan) were collected and stored for 48-72 hours at room temperature. We used pyrosequencing of the 16S gene to investigate the stability of microbial communities. Alpha diversity did not differ between all storage methods and -80 \u00b0C, except for the fecal swabs. UPGMA clustering and principal coordinate analysis showed significant clustering by test subject (p < 0.001) but not by storage method. Bray-Curtis dissimilarity and (un)weighted UniFrac showed a significant higher distance between fecal swabs and -80 \u00b0C versus the other methods and -80 \u00b0C samples (p < 0.009). The relative abundance of Ruminococcus and Enterobacteriaceae did not differ between the storage methods versus -80 \u00b0C, but was higher in fecal swabs (p < 0.05). Storage up to 24 hours (at +4 \u00b0C or room temperature) or freezing at -20 \u00b0C did not significantly alter the fecal microbial community structure compared to direct freezing of samples from healthy subjects and patients with gastrointestinal disorders.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Abiotrophia", + "condition": "ulcerative colitis", + "relevance_score": 0.505491338085921, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36327509", + "title": "In vitro fermentation characteristics of the dietary fiber in bamboo (Phyllostachys edulis) shoots and its regulatory effects on the intestinal microbiota and metabolites.", + "year": 2023, + "journal": "Food chemistry", + "authors": [ + "Wu W", + "Li Q", + "Chen H", + "Fang X", + "Niu B", + "Liu R", + "Mu H", + "Gao H" + ], + "bacteria": "Proteus", + "condition": "ulcerative colitis", + "relevance_score": 0.33098025404675113, + "mesh_terms": [ + "Animals", + "Mice", + "Gastrointestinal Microbiome", + "Dextran Sulfate", + "Fermentation", + "Dietary Fiber", + "Colitis, Ulcerative", + "Colon", + "Poaceae", + "Disease Models, Animal", + "Colitis", + "Mice, Inbred C57BL" + ], + "raw_abstract": "The effects of bamboo (Phyllostachys edulis) shoot dietary fiber (BSDF-1) on ulcerative colitis (UC) are unclear. Therefore, we performed an in vitro glycolysis study of intestinal microbiota samples, based on 16S rDNA sequencing and determining the metabolites in non-targeted colonic fecal fermentation broth. After a 48\u00a0h fermentation, the pH of the fermentation broth decreased significantly (p\u00a0<\u00a00.05) with the dextran sulfate sodium group (referred to here as the Mod group). The carbohydrate utilization rate was 26.59\u00a0%, and the total short-chain fatty acid content was 16.46\u00a0\u00b1\u00a00.71\u00a0mmol/L. The abundances of Alistipes and Lactobacillus increased after BDSF-1 fermentation, whereas those of Escherichia-Shigella, Enterococcus, and Proteus significantly decreased. BSDF-1 altered the levels of 17 metabolites in the Mod group after fermentation for 48\u00a0h, which reduced the cadaverine increasing induced by DSS. These results indicate that BSDF-1 can regulate the metabolism of the intestinal microbiota and the host, suggesting its use as a promising therapeutic strategy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34397940", + "title": "Intestinal flora differences between patients with ulcerative colitis of different ethnic groups in China.", + "year": 2021, + "journal": "Medicine", + "authors": [ + "Liu H", + "Liu W", + "Huang X", + "Feng Y", + "Lu J", + "Gao F" + ], + "bacteria": "Haemophilus", + "condition": "ulcerative colitis", + "relevance_score": 0.7443901830789369, + "mesh_terms": [ + "Adult", + "Bacteria", + "China", + "Colitis, Ulcerative", + "Ethnicity", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Incidence", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Retrospective Studies", + "Young Adult" + ], + "raw_abstract": "To determine the differences in intestinal flora between Uygur and Han patients with ulcerative colitis (UC).Microbial diversity and structural composition of fecal bacteria from patients with UC and their matched healthy spouses or first-degree relatives were analyzed using high-throughput sequencing technology.The fecal microbial diversity and abundance index of Uygur patients with UC (UUC) were significantly lower compared with the Uygur normal control group, while there was no significant difference between the Han UC patients (HUC) and the Han normal control group (HN). Compared with their respective control groups, Uygur UC patients and Han UC patients had a different main composition of human intestinal flora (P\u200a<\u200a.05). The abundance of Burkholderia, Caballeronia, Paraburkholderia in the UUC group were higher compared with the HUC group, while Faecalibacterium, Bifidobacterium, and Blautia in the HUC group were higher than those in the UUC group (P\u200a<\u200a.05). Veillonella in the UUC group was higher than that in the Uygur normal control group group, while Subdoligranulum and Ruminococcaceae_UCG-002 were significantly lower (P\u200a<\u200a.05). Prevotella_9 in the HUC group was significantly higher than that in HN group, while Blautia, Anaerostipes, and [Eubacterium]_hallii_group were significantly lower. Moreover, the top 6 species in order of importance were Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella.The difference in intestinal microflora structure may be one of the reasons for the clinical heterogeneity between Uygur and Han patients with UC. Christensenellaceae_R_7_group, Ruminococcae_ucg_005, Ruminococcae_ucg_010, Ruminococcae_ucg_013, Haemophilus, and Ezakiella could be used as potential biomarkers for predicting UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29615776", + "title": "Dysbiosis of the salivary microbiota in pediatric-onset primary sclerosing cholangitis and its potential as a biomarker.", + "year": 2018, + "journal": "Scientific reports", + "authors": [ + "Iwasawa K", + "Suda W", + "Tsunoda T", + "Oikawa-Kawamoto M", + "Umetsu S", + "Takayasu L", + "Inui A", + "Fujisawa T", + "Morita H", + "Sogo T", + "Hattori M" + ], + "bacteria": "Haemophilus", + "condition": "ulcerative colitis", + "relevance_score": 0.7020934245640779, + "mesh_terms": [ + "Adolescent", + "Biomarkers", + "Case-Control Studies", + "Child", + "Cholangitis, Sclerosing", + "Dysbiosis", + "Female", + "Humans", + "Male", + "Phenotype", + "RNA, Ribosomal, 16S", + "Saliva" + ], + "raw_abstract": "Primary sclerosing cholangitis (PSC) is a liver disease known for its frequent concurrence with inflammatory bowel disease. Dysbiosis of the gut microbiota in PSC was reported in several studies, but the microbiological features of the salivary microbiota in PSC have not been established. Here we compared the salivary microbial communities of 24 pediatric-onset PSC patients, 16 age-matched ulcerative colitis (UC) patients, and 24 healthy controls (HCs) by analyzing the bacterial 16S rRNA gene sequence data. The species-richness (\u03b1-diversity) showed no significant between-group differences, whereas the overall salivary microbiota structure (\u03b2-diversity) showed significant differences among the three groups. Taxonomic assignment revealed that the PSC salivary microbiota were characterized by significant decreases in the abundance of Rothia and Haemophilus compared to the HC group, and significantly decreased Haemophilus and increased Oribacterium compared to the UC group. By combining the genera selected by the random forest algorithm in machine learning, followed by confirmation with 10-fold cross-validation, we were able to distinguish the PSC group from the HC group with the area under the curve (AUC) of 0.7423, and from the UC group with the AUC of 0.8756. Our results indicate the potential of salivary microbiota as biomarkers for a noninvasive diagnosis of PSC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34427649", + "title": "Antitumor Necrosis Factor-like Ligand 1A Therapy Targets Tissue Inflammation and Fibrosis Pathways and Reduces Gut Pathobionts in Ulcerative Colitis.", + "year": 2022, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Hassan-Zahraee M", + "Ye Z", + "Xi L", + "Baniecki ML", + "Li X", + "Hyde CL", + "Zhang J", + "Raha N", + "Karlsson F", + "Quan J", + "Ziemek D", + "Neelakantan S", + "Lepsy C", + "Allegretti JR", + "Romatowski J", + "Scherl EJ", + "Klopocka M", + "Danese S", + "Chandra DE", + "Schoenbeck U", + "Vincent MS", + "Longman R", + "Hung KE" + ], + "bacteria": "Haemophilus", + "condition": "ulcerative colitis", + "relevance_score": 0.6337459224103871, + "mesh_terms": [ + "Colitis, Ulcerative", + "Fibrosis", + "Humans", + "Inflammation", + "Ligands", + "Necrosis", + "Proteomics", + "Tumor Necrosis Factor Ligand Superfamily Member 15" + ], + "raw_abstract": "BACKGROUND: The first-in-class treatment PF-06480605 targets the tumor necrosis factor-like ligand 1A (TL1A) molecule in humans. Results from the phase 2a TUSCANY trial highlighted the safety and efficacy of PF-06480605 in ulcerative colitis. Preclinical and in vitro models have identified a role for TL1A in both innate and adaptive immune responses, but the mechanisms underlying the efficacy of anti-TL1A treatment in inflammatory bowel disease (IBD) are not known. METHODS: Here, we provide analysis of tissue transcriptomic, peripheral blood proteomic, and fecal metagenomic data from the recently completed phase 2a TUSCANY trial and demonstrate endoscopic improvement post-treatment with PF-06480605 in participants with ulcerative colitis. RESULTS: Our results revealed robust TL1A target engagement in colonic tissue and a distinct colonic transcriptional response reflecting a reduction in inflammatory T helper 17 cell, macrophage, and fibrosis pathways in patients with endoscopic improvement. Proteomic analysis of peripheral blood revealed a corresponding decrease in inflammatory T-cell cytokines. Finally, microbiome analysis showed significant changes in IBD-associated pathobionts, Streptococcus salivarius, S. parasanguinis, and Haemophilus parainfluenzae post-therapy. CONCLUSIONS: The ability of PF-06480605 to engage and inhibit colonic TL1A, targeting inflammatory T cell and fibrosis pathways, provides the first-in-human mechanistic data to guide anti-TL1A therapy for the treatment of IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37696680", + "title": "Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Del Chierico F", + "Cardile S", + "Baldelli V", + "Alterio T", + "Reddel S", + "Bramuzzo M", + "Knafelz D", + "Lega S", + "Bracci F", + "Torre G", + "Maggiore G", + "Putignani L" + ], + "bacteria": "Haemophilus", + "condition": "ulcerative colitis", + "relevance_score": 0.6157648362160162, + "mesh_terms": [ + "Humans", + "Child", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Cholangitis, Sclerosing", + "Dysbiosis", + "RNA, Ribosomal, 16S", + "Bacteria", + "Bacteroidetes", + "Italy" + ], + "raw_abstract": "BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis. METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs). RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients. CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC. In this study, we report the gut microbiota and mycobiota dysbiosis in pediatric patients affected by primary sclerosing cholangitis (PSC) associated with ulcerative colitis (UC), with an increase in pro-inflammatory pathobionts and a reduction in anti-inflammatory commensals.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35972440", + "title": "Patient-Reported Outcomes Correlate With Microbial Community Composition Independent of Mucosal Inflammation in Pediatric Inflammatory Bowel Disease.", + "year": 2023, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Hellmann J", + "Ta A", + "Ollberding NJ", + "Bezold R", + "Lake K", + "Jackson K", + "Dirksing K", + "Bonkowski E", + "Haslam DB", + "Denson LA" + ], + "bacteria": "Haemophilus", + "condition": "ulcerative colitis", + "relevance_score": 0.6100886713980962, + "mesh_terms": [ + "Humans", + "Child", + "Prospective Studies", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Crohn Disease", + "Microbiota", + "Feces", + "Leukocyte L1 Antigen Complex", + "Inflammation", + "Abdominal Pain", + "Patient Reported Outcome Measures" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel diseases (IBDs) involve an aberrant host response to intestinal microbiota causing mucosal inflammation and gastrointestinal symptoms. Patient-reported outcomes (PROs) are increasingly important in clinical care and research. Our aim was to examine associations between PROs and fecal microbiota in patients 0 to 22 years of age with IBD. METHODS: A longitudinal, prospective, single-center study tested for associations between microbial community composition via shotgun metagenomics and PROs including stool frequency and rectal bleeding in ulcerative colitis (UC) and abdominal pain and stool frequency in Crohn's disease (CD). Mucosal inflammation was assessed with fecal calprotectin. A negative binomial mixed-effects model including clinical characteristics and fecal calprotectin tested for differentially abundant species and metabolic pathways by PROs. RESULTS: In 70 CD patients with 244 stool samples, abdominal pain correlated with increased relative abundance of Haemophilus and reduced Clostridium spp. There were no differences relative to calprotectin level. In 23 UC patients with 76 samples, both rectal bleeding and increased stool frequency correlated with increased Klebsiella and reduced Bacteroides spp. Conversely, UC patients with lower calprotectin had reduced Klebsiella. Both UC and CD patients with active symptoms exhibited less longitudinal microbial community stability. No differences in metabolic pathways were observed in CD. Increased sulfoglycolysis and ornithine biosynthesis correlated with symptomatic UC. CONCLUSIONS: Microbial community composition correlated with PROs in both CD and UC. Metabolic pathways differed relative to PROs in UC, but not CD. Data suggest that microbiota may contribute to patient symptoms in IBD, in addition to effects of mucosal inflammation.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31689349", + "title": "Vaccinations and Immunization Status in Pediatric Inflammatory Bowel Disease: A Multicenter Study From the Pediatric IBD Porto Group of the ESPGHAN.", + "year": 2020, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Martinelli M", + "Giugliano FP", + "Strisciuglio C", + "Urbonas V", + "Serban DE", + "Banaszkiewicz A", + "Assa A", + "Hojsak I", + "Lerchova T", + "Navas-L\u00f3pez VM", + "Romano C", + "Sladek M", + "Veres G", + "Aloi M", + "Kucinskiene R", + "Miele E" + ], + "bacteria": "Haemophilus", + "condition": "ulcerative colitis", + "relevance_score": 0.3525399923656662, + "mesh_terms": [ + "Child", + "Colitis, Ulcerative", + "Crohn Disease", + "Epstein-Barr Virus Infections", + "Female", + "Guideline Adherence", + "Herpesvirus 4, Human", + "Humans", + "Immunization Schedule", + "Immunosuppressive Agents", + "Inflammatory Bowel Diseases", + "Latent Tuberculosis", + "Male", + "Mycobacterium tuberculosis", + "Opportunistic Infections", + "Retrospective Studies", + "Vaccination" + ], + "raw_abstract": "BACKGROUND: Vaccine-preventable diseases and opportunistic infections in pediatric inflammatory bowel disease (IBD) are increasingly recognized issues. The aims of this study were to evaluate vaccinations, immunization status, and consequent therapeutic management in children with IBD and to analyze the differences among patients diagnosed before (Group 1) and after June 2012 (Group 2). METHODS: This was a multicenter, retrospective cohort investigation. Between July 2016 and July 2017, 430 children with IBD were enrolled in 13 centers. Diagnosis, therapeutic history, vaccinations, and immunization status screening at diagnosis and at immunosuppressant (IM)/biologic initiation and reasons for incomplete immunization were retrieved. RESULTS: Vaccination rates at diagnosis were unsatisfactory for measles, mumps, and rubella (89.3%), Haemophilus influenzae (81.9%), meningococcus C (23.5%), chickenpox (18.4%), pneumococcus (18.6%), papillomavirus (5.9%), and rotavirus (1.9%). Complete immunization was recorded in 38/430 (8.8%) children, but specific vaccines were recommended in 79/430 patients (18.6%), without differences between the 2 groups. At IM start, 22% of children were tested for Epstein-Barr virus (EBV) status, with 96.2% of EBV-na\u00efve patients starting azathioprine, without differences between Groups 1 and 2. Screening for latent tuberculosis (TB) before start of biologics was performed in 175/190 (92.1%), with up to 9 different screening strategies and numerous inconsistencies. CONCLUSIONS: We demonstrated a poor immunization status at diagnosis in children with IBD, which was not followed by proper vaccination catch-up. EBV status before IM initiation and latent TB before biologics were not adequately assessed. Thus, the overall impact of the current guidelines seems unsatisfactory.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29361092", + "title": "Safety, Clinical Response, and Microbiome Findings Following Fecal Microbiota Transplant in Children With Inflammatory Bowel Disease.", + "year": 2018, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Goyal A", + "Yeh A", + "Bush BR", + "Firek BA", + "Siebold LM", + "Rogers MB", + "Kufen AD", + "Morowitz MJ" + ], + "bacteria": "Haemophilus", + "condition": "ulcerative colitis", + "relevance_score": 0.3176443507922425, + "mesh_terms": [ + "Adolescent", + "Bacteria", + "Biomarkers", + "Child", + "Fecal Microbiota Transplantation", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Prospective Studies", + "Remission Induction", + "Severity of Illness Index" + ], + "raw_abstract": "BACKGROUND: The role of fecal microbiota transplant (FMT) in the treatment of pediatric inflammatory bowel disease (IBD) is unknown. The aims of this study were to assess safety, clinical response, and gut microbiome alterations in children with Crohn's disease (CD), ulcerative colitis (UC), or indeterminate colitis (IC). METHODS: In this open-label, single-center prospective trial, patients with IBD refractory to medical therapy underwent a single FMT by upper and lower endoscopy. Adverse events, clinical response, gut microbiome, and biomarkers were assessed at baseline, 1 week, 1 month, and 6 months following FMT. RESULTS: Twenty-one subjects were analyzed, with a median age of 12 years, of whom 57% and 28% demonstrated clinical response at 1 and 6 months post-FMT, respectively. Two CD patients were in remission at 6 months. Adverse events attributable to FMT were mild to moderate and self-limited. Patients prior to FMT showed decreased species diversity and significant microbiome compositional differences characterized by increased Enterobacteriaceae, Enterococcus, Haemophilus, and Fusobacterium compared with donors and demonstrated increased species diversity at 30 days post-FMT. At 6 months, these changes shifted toward baseline. Clinical responders had a higher relative abundance of Fusobacterium and a lower diversity at baseline, as well as a greater shift toward donor-like microbiome after FMT compared with nonresponders. CONCLUSIONS: A single FMT is relatively safe and can result in a short-term response in young patients with active IBD. Responders possessed increased Fusobacterium prior to FMT and demonstrated more significant microbiome changes compared with nonresponders after FMT. Microbiome characteristics may help in predicting response.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29126267", + "title": "Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis.", + "year": 2017, + "journal": "FEMS microbiology ecology", + "authors": [ + "Mancabelli L", + "Milani C", + "Lugli GA", + "Turroni F", + "Cocconi D", + "van Sinderen D", + "Ventura M" + ], + "bacteria": "Barnesiella", + "condition": "ulcerative colitis", + "relevance_score": 0.6374957297651715, + "mesh_terms": [ + "Bacteria", + "Biodiversity", + "Biomarkers", + "Colitis, Ulcerative", + "Crohn Disease", + "Enterocolitis, Pseudomembranous", + "Gastrointestinal Microbiome", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Intestines", + "Polymerase Chain Reaction", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Intestinal diseases, such as Crohn's disease (CD), ulcerative colitis (UC) and pseudomembranous colitis (CDI), are among the most common diseases in humans and may lead to more serious pathologies, e.g. colorectal cancer (CRC). Next generation sequencing has in recent years allowed the identification of correlations between intestinal bacteria and diseases, although the formulation of universal gut microbial biomarkers for such diseases is only in its infancy. In the current study, we selected and reanalyzed a total of 3048 public datasets obtained from 16S rRNA profiling of individuals affected by CD, UC, CDI and CRC. This meta-analysis revealed possible biases in the reconstruction of the gut microbiota composition due to the use of different primer pairs employed for PCR of 16S rRNA gene fragments. Notably, this approach also identified common features of individuals affected by gut diseases (DS), including lower biodiversity compared to control subjects. Moreover, potential universal intestinal disease microbial biomarkers were identified through cross-disease comparisons. In detail, CTRL showed high abundance of the genera Barnesiella, Ruminococcaceae UCG-005, Alistipes, Christensenellaceae R-7 group and unclassified member of Lachnospiraceae family, while DS exhibited high abundance of Lactobacillus, unclassified member of Erysipelotrichaceae family and Streptococcus genera.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39468026", + "title": "Galactooligosaccharides and Limosilactobacillus reuteri synergistically alleviate gut inflammation and barrier dysfunction by enriching Bacteroides acidifaciens for pentadecanoic acid biosynthesis.", + "year": 2024, + "journal": "Nature communications", + "authors": [ + "Wu Y", + "Zhang X", + "Liu X", + "Zhao Z", + "Tao S", + "Xu Q", + "Zhao J", + "Dai Z", + "Zhang G", + "Han D", + "Wang J" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.8223300898653814, + "mesh_terms": [ + "Animals", + "Humans", + "Oligosaccharides", + "Mice", + "Limosilactobacillus reuteri", + "Bacteroides", + "Synbiotics", + "Swine", + "Disease Models, Animal", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Mice, Inbred C57BL", + "Feces", + "Male", + "NF-kappa B", + "Inflammation", + "Tight Junctions" + ], + "raw_abstract": "Ulcerative colitis (UC) is a debilitating inflammatory bowel disease characterized by intestinal inflammation, barrier dysfunction, and dysbiosis, with limited treatment options available. This study systematically investigates the therapeutic potential of a synbiotic composed of galactooligosaccharides (GOS) and Limosilactobacillus reuteri in a murine model of colitis, revealing that GOS and L. reuteri synergistically protect against intestinal inflammation and barrier dysfunction by promoting the synthesis of pentadecanoic acid, an odd-chain fatty acid, from Bacteroides acidifaciens. Notably, the synbiotic, B. acidifaciens, and pentadecanoic acid are each capable of suppressing intestinal inflammation and enhancing tight junction by inhibiting NF-\u03baB activation. Furthermore, similar reduction in B. acidifaciens and pentadecanoic acid levels are also observed in the feces from both human UC patients and lipopolysaccharide-induced intestinal inflammation in pigs. Our findings elucidate the protective mechanism of the synbiotic and highlight its therapeutic potential, along with B. acidifaciens and pentadecanoic acid, for UC and other intestinal inflammatory disorders.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28842640", + "title": "Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients.", + "year": 2017, + "journal": "Scientific reports", + "authors": [ + "Santoru ML", + "Piras C", + "Murgia A", + "Palmas V", + "Camboni T", + "Liggi S", + "Ibba I", + "Lai MA", + "Orr\u00f9 S", + "Blois S", + "Loizedda AL", + "Griffin JL", + "Usai P", + "Caboni P", + "Atzori L", + "Manzin A" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7986079588356289, + "mesh_terms": [], + "raw_abstract": "Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract of uncertain origin, which includes ulcerative colitis (UC) and Crohn's disease (CD). The composition of gut microbiota may change in IBD affected individuals, but whether dysbiosis is the cause or the consequence of inflammatory processes in the intestinal tissue is still unclear. Here, the composition of the microbiota and the metabolites in stool of 183 subjects (82 UC, 50 CD, and 51 healthy controls) were determined. The metabolites content and the microbiological profiles were significantly different between IBD and healthy subjects. In the IBD group, Firmicutes, Proteobacteria, Verrucomicrobia, and Fusobacteria were significantly increased, whereas Bacteroidetes and Cyanobacteria were decreased. At genus level Escherichia, Faecalibacterium, Streptococcus, Sutterella and Veillonella were increased, whereas Bacteroides, Flavobacterium, and Oscillospira decreased. Various metabolites including biogenic amines, amino acids, lipids, were significantly increased in IBD, while others, such as two B group vitamins, were decreased in IBD compared to healthy subjects. This study underlines the potential role of an inter-omics approach in understanding the metabolic pathways involved in IBD. The combined evaluation of metabolites and fecal microbiome can be useful to discriminate between healthy subjects and patients with IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35087228", + "title": "Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity.", + "year": 2022, + "journal": "Nature microbiology", + "authors": [ + "Mills RH", + "Dulai PS", + "V\u00e1zquez-Baeza Y", + "Sauceda C", + "Daniel N", + "Gerner RR", + "Batachari LE", + "Malfavon M", + "Zhu Q", + "Weldon K", + "Humphrey G", + "Carrillo-Terrazas M", + "Goldasich LD", + "Bryant M", + "Raffatellu M", + "Quinn RA", + "Gewirtz AT", + "Chassaing B", + "Chu H", + "Sandborn WJ", + "Dorrestein PC", + "Knight R", + "Gonzalez DJ" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7902963198752916, + "mesh_terms": [ + "Adult", + "Animals", + "Bacterial Proteins", + "Bacteroides", + "Cohort Studies", + "Colitis, Ulcerative", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Longitudinal Studies", + "Male", + "Metagenome", + "Metagenomics", + "Mice", + "Middle Aged", + "Peptide Hydrolases", + "Proteomics", + "Severity of Illness Index" + ], + "raw_abstract": "Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn's disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27684872", + "title": "Increased Enterococcus faecalis infection is associated with clinically active Crohn disease.", + "year": 2016, + "journal": "Medicine", + "authors": [ + "Zhou Y", + "Chen H", + "He H", + "Du Y", + "Hu J", + "Li Y", + "Li Y", + "Zhou Y", + "Wang H", + "Chen Y", + "Nie Y" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7792572102506696, + "mesh_terms": [ + "Adult", + "China", + "Crohn Disease", + "DNA, Bacterial", + "Enterococcus faecalis", + "Feces", + "Female", + "Gram-Positive Bacterial Infections", + "Humans", + "Incidence", + "Male", + "Real-Time Polymerase Chain Reaction", + "Young Adult" + ], + "raw_abstract": "This study was performed to investigate the relationship between the abundance of pathogenic gut microbes in Chinese patients with inflammatory bowel disease (IBD) and disease severity.We collected clinical data and fecal samples from 47 therapy-naive Chinese patients with ulcerative colitis (UC), 67 patients with Crohn disease (CD), and 48 healthy volunteers. Bacteria levels of Fusobacterium species (spp), enterotoxigenic Bacteroides fragilis (B fragilis), enteropathogenic Escherichia coli (E coli), and Enterococcus faecalis (E faecalis) were assessed by quantitative real-time PCR (qRT-PCR). Spearman correlation coefficients were calculated to test associations between bacterial content and clinical parameters.Compared to healthy controls, the levels of both Fusobacterium spp and E faecalis were significantly increased in the feces of patients with IBD (P\u200a<\u200a0.01). B fragilis levels were higher (P\u200a<\u200a0.05) and E faecalis levels lower (P\u200a<\u200a0.05) in patients with CD compared to those with UC. Increased E faecalis colonization in CD associated positively with disease activity (P = 0.015), Crohn disease activity index (CDAI; R = 0.3118, P = 0.0108), and fecal calprotectin (P = 0.016).E faecalis and Fusobacterium spp are significantly enriched in patients with IBD, and increased E faecalis infection is associated with clinically active CD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37734419", + "title": "Pathobionts in Inflammatory Bowel Disease: Origins, Underlying Mechanisms, and Implications for Clinical Care.", + "year": 2024, + "journal": "Gastroenterology", + "authors": [ + "Gilliland A", + "Chan JJ", + "De Wolfe TJ", + "Yang H", + "Vallance BA" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7777405561638909, + "mesh_terms": [ + "Humans", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Crohn Disease", + "Intestines", + "Feces" + ], + "raw_abstract": "The gut microbiota plays a significant role in the pathogenesis of both forms of inflammatory bowel disease (IBD), namely, Crohn's disease (CD) and ulcerative colitis (UC). Although evidence suggests dysbiosis and loss of beneficial microbial species can exacerbate IBD, many new studies have identified microbes with pathogenic qualities, termed \"pathobionts,\" within the intestines of patients with IBD. The concept of pathobionts initiating or driving the chronicity of IBD has largely focused on the putative aggravating role that adherent invasive Escherichia coli may play in CD. However, recent studies have identified additional bacterial and fungal pathobionts in patients with CD and UC. This review will highlight the characteristics of these pathobionts and their implications for IBD treatment. Beyond exploring the origins of pathobionts, we discuss those associated with specific clinical features and the potential mechanisms involved, such as creeping fat (Clostridium innocuum) and impaired wound healing (Debaryomyces hansenii) in patients with CD as well as the increased fecal proteolytic activity (Bacteroides vulgatus) seen as a biomarker for UC severity. Finally, we examine the potential impact of pathobionts on current IBD therapies, and several new approaches to target pathobionts currently in the early stages of development. Despite recognizing that pathobionts likely contribute to the pathogenesis of IBD, more work is needed to define their modes of action. Determining whether causal relationships exist between pathobionts and specific disease characteristics could pave the way for improved care for patients, particularly for those not responding to current IBD therapies.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34404881", + "title": "Immunoglobulin subtype-coated bacteria are correlated with the disease activity of inflammatory bowel disease.", + "year": 2021, + "journal": "Scientific reports", + "authors": [ + "Masu Y", + "Kanazawa Y", + "Kakuta Y", + "Shimoyama Y", + "Onodera M", + "Naito T", + "Moroi R", + "Kuroha M", + "Kimura T", + "Shiga H", + "Kinouchi Y", + "Masamune A" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.776801588781772, + "mesh_terms": [ + "Adult", + "Antibodies, Bacterial", + "Bacteria", + "Feces", + "Female", + "Humans", + "Immunoglobulin A", + "Immunoglobulin G", + "Immunoglobulin Isotypes", + "Immunoglobulin M", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged" + ], + "raw_abstract": "Immune response involving various immunoglobulin (Ig) isotypes and subtypes to microbiome is involved in the pathogenesis and disease activity of inflammatory bowel diseases (IBDs). To clarify the presence of Ig-coated bacteria in the intestine and its association with disease activity in ulcerative colitis (UC) and Crohn's disease (CD), we extracted and classified Ig-coated bacteria from fecal samples of 42 patients with IBD and 12 healthy controls (HCs) using flow cytometry and 16S ribosomal RNA sequence analysis. The percentage of bacteria coated with IgA and IgM was higher in patients with IBD than in HCs, and IgG-coated bacteria were found only in patients with IBD. Moreover, the percentages of bacteria coated with IgG1, IgG2, IgG3, and IgM in UC samples and IgG3, IgG4, and IgM in CD samples were correlated with disease activities. The proportions of Bacteroides ovatus and Streptococcus increased during the active phase of CD. Hence, the detailed analysis of Ig-coated bacteria and Ig subtypes using flow cytometry could aid in developing useful indicators of disease activity and identifying more disease-related bacteria, which could become novel treatment targets for IBDs.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35906158", + "title": "Study of the gut microbiome in Egyptian patients with active ulcerative colitis.", + "year": 2023, + "journal": "Revista de gastroenterologia de Mexico (English)", + "authors": [ + "Ahmed EA", + "Ahmed SM", + "Zakaria NH", + "Baddour NM", + "Header DA" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7744841040992952, + "mesh_terms": [], + "raw_abstract": "INTRODUCTION AND AIM: Ulcerative colitis (UC) is characterized by chronic, uncontrolled inflammation of the intestinal mucosa. Gut microbiota dysbiosis was reported to be a factor in intestinal inflammation. The aim of the present study was to study changes in the gut microbiome in Egyptian patients with active UC. MATERIALS AND METHODS: In this cross-sectional study, the gut bacterial microbiome of 21 UC patients and 20 control subjects was analyzed using the quantitative SYBR Green real-time PCR technique, targeting the 16S rRNA gene of selected bacterial phyla/genera and/or species. RESULTS: UC patients showed marked dysbiosis evidenced by a significant decrease in the Firmicutes and F. prausnitzii anti-inflammatory bacteria. The Firmicutes/Bacteroidetes ratio was also lower in the UC cases (1.65), compared with the healthy controls (2.93). In addition, the UC cases showed a statistically significant decrease in Ruminococcus, compared with the control group. However, there were no statistically significant differences between UC patients and the controls, regarding A. muciniphila, Bifidobacterium, Lactobacillus, Bacteroides, and Prevotella. One UC case was positive for the pathogenic bacterium, Clostridioides difficile, with low relative abundance. CONCLUSION: The current study showed differences in the gut microbiome of UC patients, compared with healthy controls. This may help in identifying the gut microbiome and specific bacterial changes that can be targeted for treatment of UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31240835", + "title": "Correlation of diet, microbiota and metabolite networks in inflammatory bowel disease.", + "year": 2019, + "journal": "Journal of digestive diseases", + "authors": [ + "Weng YJ", + "Gan HY", + "Li X", + "Huang Y", + "Li ZC", + "Deng HM", + "Chen SZ", + "Zhou Y", + "Wang LS", + "Han YP", + "Tan YF", + "Song YJ", + "Du ZM", + "Liu YY", + "Wang Y", + "Qin N", + "Bai Y", + "Yang RF", + "Bi YJ", + "Zhi FC" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.773269869614341, + "mesh_terms": [ + "Adult", + "Biopsy", + "Body Mass Index", + "Case-Control Studies", + "Diet", + "Dysbiosis", + "Feces", + "Female", + "Food Preferences", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Male", + "Metabolic Networks and Pathways", + "Metagenomics", + "Middle Aged", + "Nutrition Assessment", + "Young Adult" + ], + "raw_abstract": "OBJECTIVES: Microbiota dysbiosis in inflammatory bowel disease (IBD) has been widely reported. The gut microbiota connect diet to the metabolism by producing small molecules via diverse metabolic pathways. In this study we aimed to investigate the dietary preferences of IBD patients, and to explore the interactions among gut microbiota composition, dietary components, and metabolites in relation to IBD. METHODS: Dietary preferences of IBD patients (including those with ulcerative colitis [UC] and Crohn's disease [CD]) and health controls were investigated, and their gut microbiota were analyzed using 16S rRNA gene sequencing and metagenomic analyses of fecal and biopsy samples. The metabolite profiles of the samples were then analyzed using gas and liquid chromatography-mass spectrometry analyses. RESULTS: The daily intake of folic acid, niacin, vitamins C and D, calcium, and selenium differed significantly between patients with IBD and healthy controls. A decrease in long-chain (such as arachidic, and oleic acid) and medium-chain fatty acids (sebacic acid and isocaproic acid) as well as bile acid was observed in patients with IBD. Compared with healthy controls, 22 microbial species (including Sulfolobus acidocaldarius, and Clostridium clostridioforme CAG132) in the UC group and 37 microbial species (such as Bacteroides fragilis and Fusobacterium nucleatum) in the CD group were found to be correlated to diet and metabolites. Bacteroides fragilis was enriched in patients with IBD and associated with multi-nutrients, and 21 metabolites including 25-hydroxyvitamin D CONCLUSIONS: This study provides an interaction network to identify key micronutrients, microbiota components and metabolites that contribute to IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26261163", + "title": "Alterations of mucosal microbiota in the colon of patients with inflammatory bowel disease revealed by real time polymerase chain reaction amplification of 16S ribosomal ribonucleic acid.", + "year": 2015, + "journal": "The Indian journal of medical research", + "authors": [ + "Kabeerdoss J", + "Jayakanthan P", + "Pugazhendhi S", + "Ramakrishna BS" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7701345166982795, + "mesh_terms": [ + "Adult", + "Bacteroidetes", + "Colitis, Ulcerative", + "Colon", + "Crohn Disease", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Male", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND & OBJECTIVES: Alterations in microbial communities closely associated with the intestinal mucosa are likely to be important in the pathogenesis of inflammatory bowel disease (IBD). We examined the abundance of specific microbial populations in colonic mucosa of patients with ulcerative colitis (UC), Crohn's disease (CD) and controls using reverse transcription quantitative polymerase chain reaction (RT-qPCR) amplification of 16S ribosomal ribonucleic acid (16S rRNA). METHODS: RNA was extracted from colonic mucosal biopsies of patients with UC (32), CD (28) and patients undergoing screening colonoscopy (controls), and subjected to RT-qPCR using primers targeted at 16S rRNA sequences specific to selected microbial populations. RESULTS: Bacteroides-Prevotella-Porphyromonas group and Enterobacteriaceae were the most abundant mucosal microbiota. Bacteroides and Lactobacillus abundance was greater in UC patients compared with controls or CD. Escherichia coli abundance was increased in UC compared with controls. Clostridium coccoides group and C. leptum group abundances were reduced in CD compared with controls. Microbial population did not differ between diseased and adjacent normal mucosa, or between untreated patients and those already on medical treatment. The Firmicutes to Bacteroidetes ratio was significantly decreased in both UC and CD compared with controls, indicative of a dysbiosis in both conditions. INTERPRETATION & CONCLUSIONS: Dysbiosis appears to be a primary feature in both CD and UC. Microbiome-directed interventions are likely to be appropriate in therapy of IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29210899", + "title": "Distinct Microbial Populations Exist in the Mucosa-associated Microbiota of Diarrhea Predominant Irritable Bowel Syndrome and Ulcerative Colitis.", + "year": 2019, + "journal": "Journal of clinical gastroenterology", + "authors": [ + "Zhong W", + "Lu X", + "Shi H", + "Zhao G", + "Song Y", + "Wang Y", + "Zhang J", + "Jin Y", + "Wang S" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7503379559085429, + "mesh_terms": [ + "Adult", + "Bacteria", + "Case-Control Studies", + "Colitis, Ulcerative", + "Colonoscopy", + "Diarrhea", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "In Situ Hybridization, Fluorescence", + "Intestinal Mucosa", + "Irritable Bowel Syndrome", + "Male", + "Middle Aged" + ], + "raw_abstract": "GOALS: The goal of this study was to observe the bacterial colonization in the intestinal mucosa in the patients with diarrhea predominant irritable bowel syndrome (IBS-D) and ulcerative colitis (UC), and compare the mucosa-associated microbiota among the IBS-D patients, UC patients and the healthy control, and explore the correlation of the mucosa-associated microbiota with clinical manifestations. STUDY: A total of 20 IBS-D patients, 28 patients with UC (16 active, 12 inactive) and 16 healthy subjects were enrolled in the study. They all underwent colonoscopies in the Gastrointestinal Endoscopy Center in the Second Affiliated Hospital of Xi'an Jiaotong University from June 2016 to October 2016. The mucosa specimens were taken at the junction of rectum and sigmoid colon for fluorescent in situ hybridization (FISH). Then the observed mucosa-associated microbiota was counted and compared. RESULTS: (1) In the IBS-D patients, the mucosa-associated bacteria were found to colonize in the surface of mucosa and the adjacent mucin layer. And in active UC, Escherichia coli, and Bacteroides were found in the lamina propria, in addition to bacterial colonization in the above-mentioned areas. (2) The total count of mucosa-associated bacteria and the individual counts of E. coli, Clostridium, and Bacteroides were significantly increased, and Bifidobacteria significantly decreased (P<0.05) in the IBS-D patients and UC patients. Counts of Lactobacillus were decreased only in UC patients compared with the healthy control. And a significantly larger variation of the above-mentioned bacterial counts was found in the patients with UC, particularly in those with active UC, compared with those with IBS-D (P<0.05); the counts in the UC group were 1.3 to 5.3 times more or less than those in the IBS-D group. (3) Compared with healthy controls and IBS-D, the total count of bacteria and the individual counts of E. coli and Bacteroides in the lamina propria in active UC were significantly increased (P<0.05). (4) A significant negative correlation of the counts of Lactobacillus and Bifidobacteria with the defecation frequency and fecal characteristics (P<0.05) was found in the IBS-D patients; in those with UC, both the total count of bacteria and the individual counts of E. coli, Clostridium, Bacteroides, Lactobacillus, and Bifidobacteria were significantly correlated, positively or negatively, with the related clinical manifestations and the activity of the disease (P<0.05). CONCLUSIONS: Compared with the healthy control, intestinal microecology was changed most obviously in UC with much smaller differences though in the same direction in IBS-D. The translocation of some bacteria into the lamina propria was found in UC, particularly in active UC. The changes of mucosa-associated microbiota were related more or less to some clinical manifestations in IBS-D and UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33686049", + "title": "Effects of Pretreatment with Bifidobacterium bifidum Using 16S Ribosomal RNA Gene Sequencing in a Mouse Model of Acute Colitis Induced by Dextran Sulfate Sodium.", + "year": 2021, + "journal": "Medical science monitor : international medical journal of experimental and clinical research", + "authors": [ + "Weng YJ", + "Jiang DX", + "Liang J", + "Ye SC", + "Tan WK", + "Yu CY", + "Zhou Y" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7456826701320471, + "mesh_terms": [ + "Animals", + "Bacteria", + "Bifidobacterium bifidum", + "Colitis", + "Colitis, Ulcerative", + "Colon", + "Dextran Sulfate", + "Disease Models, Animal", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Mice", + "Mice, Inbred C57BL", + "Probiotics", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND Bifidobacterium is a potentially effective and safe treatment for patients with inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease. However, information on the influence of B. bifidum on gut microbial diversity of treated and pretreated IBD patients is limited. MATERIAL AND METHODS Our study investigated therapeutic and preventive effects of B. bifidum ATCC 29521 on C57BL/6 mice with dextran sulfate sodium (DSS)-induced acute colitis via 16S ribosomal ribonucleic acid (rRNA) gene sequencing. RESULTS Treatment and pretreatment of mice with B. bifidum ATCC 29521 significantly alleviated the severity of acute colitis on the basis of clinical and pathologic indicators. 16S rRNA gene sequencing showed that administration of B. bifidum shifted composition of the gut microbiome in mice with DSS-induced colitis in both treated and pretreated groups. Mice pretreated with B. bifidum ATCC 29521 for 21 days exhibited a significant increase in diversity of the gut microbiome. Principal coordinate analysis showed that gut microbiota structure was shaped by different treatments and time points. On the basis of linear discriminant analysis of effect size, the abundance of the genus Escherichia-Shigella, belonging to the family Enterobacteriaceae, was reduced in the B. bifidum-treated group, indicating that pathogens were inhibited by the B. bifidum treatment. Furthermore, the genera Intestinimonas and Bacteroides were significantly associated with the B. bifidum-pretreated group. CONCLUSIONS 16S rRNA gene sequencing showed that pretreatment with B. bifidum ATCC 29521 reduced intestinal inflammation and altered the gut microbiota to favor the genera Intestinimonas and Bacteroides.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26994772", + "title": "Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India.", + "year": 2016, + "journal": "Journal of gastroenterology", + "authors": [ + "Kedia S", + "Rampal R", + "Paul J", + "Ahuja V" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7295391277973537, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Dysentery, Amebic", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "India", + "Intestinal Mucosa" + ], + "raw_abstract": "The disease profile in the Indian population provides a unique opportunity for studying the host microbiome interaction in both infectious (amebiasis) and autoimmune diseases\u00a0like inflammatory bowel disease (IBD) from a similar environment and genetic background. Analysis of fecal samples from untreated amebic liver abscess (ALA) patients, Entamoeba histolytica (Eh)-negative and -positive asymptomatic individuals, and pus samples from naive ALA patients revealed a significant reduction in Lactobacillus in asymptomatic individuals (Eh +ve) and ALA patients. Two anaerobic genera, namely Bacteroides and Peptostreptococcus, were detected in naive ALA pus samples. Analysis of fecal samples from amoebic colitis patients showed a significant decline in population of Bacteroides, Clostridium coccoides and leptum subgroup, Lactobacillus, Campylobacter, and Eubacterium, whereas a significant increase in Bifidobacterium was observed. Mucosa-associated bacterial flora analysis from IBD patients and healthy controls revealed a significant difference in concentration of bacteria among predominating and subdominating genera between ulcerative colitis (UC), Crohn's disease (CD) patients, and controls. In contrast to the mucosal studies, we found a significant increase in lactobacilli population in fecal samples of active UC patients. Another study revealed a significant decrease of Clostridium coccoides and leptum clusters in fecal samples of active UC patients along with decreased concentrations of fecal SCFAs, especially of n-butyrate, iso-butyrate, and acetate. We therefore found similar perturbations in gut microbiome in both infectious and autoimmune diseases, indicating inflammation to be the major driver for changes in gut microbiome.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33598970", + "title": "Adsorptive granulomonocytapheresis alters the gut bacterial microbiota in patients with active ulcerative colitis.", + "year": 2021, + "journal": "Journal of clinical apheresis", + "authors": [ + "Chen X", + "Lou L", + "Tang H", + "Tan X", + "Bi J", + "Wu H", + "Li N", + "Wang Y", + "Mao J" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7241981999644483, + "mesh_terms": [ + "Adult", + "Colitis, Ulcerative", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Granulocytes", + "Humans", + "Leukapheresis", + "Male", + "Middle Aged", + "Monocytes", + "Prospective Studies" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is a refractory disease with unclear etiology. Studies have shown that UC is closely associated with gut microbiota dysbiosis. Adsorptive granulomonocytapheresis (GMA) using an Adacolumn has been found to treat UC effectively, but its underlying mechanism of treatment has not been fully elucidated. In this study, we aimed to investigate the influence of GMA on the gut microbiota in patients with active UC. METHODS: We conducted a single-center prospective analysis of patients with active UC who received GMA therapy and ultimately achieved clinical remission. Stool samples of healthy controls and patients before and after 5 or 10 sessions of GMA therapy were collected. Subsequently, high-throughput sequencing of the 16S rRNA V3 and V4 gene region of the stool was conducted and clustering of operational taxonomic units and species annotation were performed. RESULTS: Gut microbial profiles in patients with UC were characterized by low bacterial diversity. After 5 or 10 sessions of GMA therapy, the gut microbiota diversity in patients with UC increased and was similar to that of healthy controls. UC was further characterized by increased abundances of Proteobacteria and Bacteroides, as well as decreased abundances of Faecalibacterium, Roseburia, Firmicutes, and Dialister; however, after GMA therapy, the abundance of Bacteroides decreased, whereas those of Faecalibacterium, Roseburia, and Firmicutes increased. CONCLUSIONS: Active UC is associated with gut microbiota dysbiosis. GMA therapy exerts a strong regulatory effect on the gut microbiota in patients with UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36344781", + "title": "Impact of gut Microbiome alteration in Ulcerative Colitis patients on disease severity and outcome.", + "year": 2023, + "journal": "Clinical and experimental medicine", + "authors": [ + "Basha OM", + "Hafez RA", + "Salem SM", + "Anis RH", + "Hanafy AS" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7190738573741547, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Patient Acuity", + "Recurrence" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis is a heterogeneous disease in terms of disease course, location, and therapeutic response. The current study was done to assess the alteration of the gut microbiome in UC patients and its relationship to severity, response to therapy, and outcome. PATIENTS AND METHODS: The study included 96 participants who were divided into a case group (n\u2009=\u200948, recent onset, treatment naive ulcerative colitis patients who were subdivided into mild, moderate, and severe subgroups based on Truelove-Witts and endoscopic severity) and a healthy control group (n\u2009=\u200948). All were subjected to a thorough history, clinical examination, colonoscopy, routine laboratory tests, and quantitative real-time PCR to quantify Bacteroides, Lactobacilli, Faecalibacterium prausnitzii, Veillonella, and Hemophilus in fecal samples at baseline and 6\u00a0months after treatment. RESULTS: Bacterial 16S rRNA gene sequencing revealed a significant reduction in the phylum Firmicutes in UC patients, with a significant predominance of the phylum Bacteriodetes. F. prausnitzii and lactobacilli were inversely proportional to disease severity, whereas Bacteroides, Hemophilus, and Veillonella were directly proportional to it. Six months after therapy, a statistically significant increase in F. prausnitzii and lactobacilli was observed, with a decrease in the levels of other bacteria. Lower baseline F. praustinizii (<\u20098.5) increased the risk of relapse; however, lower ESR (<\u200910), lower post-treatment CRP (<\u20096), lower Bacteroides (<\u200910.6) indefinitely protect against relapse. CONCLUSION: The gut microbiome of recently diagnosed UC showed lower levels of Lactobacilli, Faecalibacterium, and higher levels of Bacteroides and Veillonella, and the change in their levels can be used to predict response to therapy.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39574001", + "title": "Changes in amino acid concentrations and the gut microbiota composition are implicated in the mucosal healing of ulcerative colitis and can be used as noninvasive diagnostic biomarkers.", + "year": 2024, + "journal": "Clinical proteomics", + "authors": [ + "Wu J", + "Li M", + "Zhou C", + "Rong J", + "Zhang F", + "Wen Y", + "Qu J", + "Wu R", + "Miao Y", + "Niu J" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7151500422502697, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Mucosal healing is the therapeutic target for ulcerative colitis (UC). While amino acids (AAs) and the gut microbiota are known to be involved in the pathogenesis of UC, their specific roles in mucosal healing have not been fully defined. OBJECTIVES: To longitudinally assess the changes in AA concentrations and the gut microbiota composition in the context of mucosal healing in UC patients, with the aim of identifying new biomarkers with predictive value for mucosal healing in UC patients and providing a new theoretical basis for dietary therapy. METHODS: A total of 15 UC patients with infliximab-induced mucosal healing were enrolled. Serum and fecal AA concentrations before and after mucosal healing were determined via targeted metabolomics. A receiver operating characteristic (ROC) curve was plotted to evaluate the value of different AAs in predicting mucosal healing in UC patients. The changes in the composition of the fecal gut microbiota were analyzed via metagenomics, and bioinformatics was used to analyze the functional genes and metabolic pathways associated with different bacterial species. Spearman correlation analyses of fecal AAs with significantly different concentrations and the differentially abundant bacterial species before and after mucosal healing were performed. RESULTS: 1. The fecal concentrations of alanine, aspartic acid, glutamic acid, glutamine, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine were significantly decreased after mucosal healing. The serum concentrations of alanine, cysteine and valine significantly increased, whereas that of aspartic acid significantly decreased. Glutamic acid, leucine, lysine, methionine and threonine could accurately predict mucosal healing in UC patients, and the area under the curve (AUC) was >\u20090.9. After combining the 5 amino acids, the AUC reached 0.96. 2. There were significant differences in the gut microbiota composition before and after mucosal healing in UC, characterized by an increase in the abundance of beneficial microbiota (Faecalibacterium prausnitzii and Bacteroides fragilis) and a decrease in the abundance of harmful microbiota (Enterococcus faecalis). LEfSe analysis identified 57 species that could predict mucosal healing, and the AUC was 0.7846. 3. Amino acid metabolic pathways were enriched in samples after mucosal healing, was associated with the abundance of multiple species, such as Faecalibacterium prausnitzi, Bacteroides fragilis, Bacteroides vulgatus and Alistipes putredinis. 4. The fecal concentrations of several AAs were negatively correlated with the abundance of a variety of beneficial strains, such as Bacteroides fragilis, uncultured Clostridium sp., Firmicutes bacterium CAG:103, Adlercreutzia equolifaciens, Coprococcus comes and positively correlated with the abundance of several harmful strains, such as Citrobacter freundii, Enterococcus faecalis, Klebsiella aerogenes, Salmonella enterica. CONCLUSION: Altered concentrations of amino acids and their associations with the gut microbiota are implicated in the mucosal healing of UC patients and can serve as noninvasive diagnostic biomarkers.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36759757", + "title": "Integrating the serum proteomic and fecal metaproteomic to analyze the impacts of overweight/obesity on IBD: a pilot investigation.", + "year": 2023, + "journal": "Clinical proteomics", + "authors": [ + "Yan P", + "Sun Y", + "Luo J", + "Liu X", + "Wu J", + "Miao Y" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.7117663393883649, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) encompasses a group of chronic relapsing disorders which include ulcerative colitis (UC) and Crohn's disease (CD). The incidences of IBD and overweight/obesity are increasing in parallel. Here, we investigated alterations in proteomic in serum and metaproteomic in feces of IBD patients with overweight/obesity and aimed to explore the effect of overweight/ obesity on IBD and the underlying mechanism. METHODS: This prospective observational study (n\u2009=\u200964) comprised 26 health control subjects (HC, 13 with overweight/obesity) and 38 IBD patients (19 with overweight/obesity) at a tertiary hospital. Overweight/obesity was evaluated by body mass index (BMI) and defined as a BMI greater than 24\u00a0kg/m RESULTS: UC and CD presented similar serum molecular profiles but distinct gut microbiota. UC and CD serum exhibited higher levels of cytoskeleton organization- associated and inflammatory response-related proteins than the HC serum. Compared the serum proteome of UC and CD without overweight/obesity, inflammatory response-associated proteins were dramatically decreased in UC and CD with overweight/obesity. Fecal metaproteome identified 66 species in the feces. Among them, Parasutterella excrementihominis was increased in CD compared with that in HC. UC group had a significant enrichment of Moniliophthora roreri, but had dramatically decreased abundances of Alistipes indistinctus, Clostridium methylpentosum, Bacteroides vulgatus, and Schizochytrium aggregatum. In addition, overweight/obesity could improve the microbial diversity of UC. Specifically, the UC patients with overweight/obesity had increased abundance of some probiotics in contrast to those without overweight/obesity, including Parabacteroides distasonis, Alistipes indistincus, and Ruminococcus bromii. CONCLUSION: This study provided high-quality multi-omics data of IBD serum and fecal samples, which enabled deciphering the molecular bases of clinical phenotypes of IBD, revealing the impacts of microbiota on IBD, and emphasizing the important role of overweight/obesity in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33352216", + "title": "Changes in intestinal microbiota and correlation with TLRs in ulcerative colitis in the coastal area of northern China.", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Xu N", + "Bai X", + "Cao X", + "Yue W", + "Jiang W", + "Yu Z" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6969731674779258, + "mesh_terms": [ + "China", + "Colitis, Ulcerative", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: To investigate the communities of fecal microbiota and the role of Toll-like receptors in patients with ulcerative colitis in the coastal area of northern China. METHODS: Stool samples from 31 patients with ulcerative colitis and 12 healthy individuals were collected. The total bacterial genomic DNA was extracted, and the V3+V4 hypervariable region in the bacterial 16S rRNA gene sequence was amplified by polymerase chain reaction (PCR). High-throughput sequencing analysis was performed on the Illumina Hiseq platform. The expression of TLR2, TLR4, Tollip, PPAR-\u03b3, IL-6, and TNF-\u03b1 in the colonic mucosa was measured by Western blots. RESULTS: The diversity of the fecal microbiota in patients with ulcerative colitis was significantly less than that in healthy control individuals (p\u00a0<\u00a00.05). The proportion of Bacteroidetes was significantly reduced (p\u00a0<\u00a00.01), whereas Proteobacteria was prevalent (p\u00a0<\u00a00.01) in patients with ulcerative colitis. At the genus level, the relative abundance of Streptococcus and Anaerostipes was significantly increased (p\u00a0<\u00a00.05), whereas the proportion of Bacteroides, Lachnospira, Ruminococcus, Phascolarctobacterium, and Coprococcus was significantly decreased in patients with ulcerative colitis (p\u00a0<\u00a00.05). The diversity indexes of fecal microbiota in patients with ulcerative colitis were negatively correlated with disease severity (p\u00a0<\u00a00.05). The relative abundance of Enterobacteriaceae was positively correlated with disease severity, and the relative abundance of Phascolarctobacterium, Anaerostipes, Fusobacterium, Parabacteroides, Oscillospira, and Ochrobactrum were negatively correlated with disease severity. The expression levels of TLR2 and TLR4 in the intestinal mucosa were positively correlated with the relative abundance of Streptococcus and Enterobacteriaceae, respectively (r\u00a0=\u00a00.481, p\u00a0=\u00a00.007; r\u00a0=\u00a00.455, p\u00a0=\u00a00.017). CONCLUSION: There were significant changes in the diversity and composition of the fecal microbiota in patients with ulcerative colitis compared to healthy individuals. The dysbiosis of gut microbiota and correlation with TLRs might play important roles in the pathogenesis and progression of ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38928402", + "title": "Integrated Analysis of Microbiome and Metabolome Reveals Disease-Specific Profiles in Inflammatory Bowel Diseases and Intestinal Beh\u00e7et's Disease.", + "year": 2024, + "journal": "International journal of molecular sciences", + "authors": [ + "Park Y", + "Ahn JB", + "Kim DH", + "Park IS", + "Son M", + "Kim JH", + "Ma HW", + "Kim SW", + "Cheon JH" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6891700614806541, + "mesh_terms": [ + "Humans", + "Behcet Syndrome", + "Metabolome", + "Gastrointestinal Microbiome", + "Male", + "Female", + "Adult", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Crohn Disease", + "Metabolomics", + "Inflammatory Bowel Diseases", + "Biomarkers", + "Feces", + "Colitis, Ulcerative", + "Case-Control Studies" + ], + "raw_abstract": "The gut microbial and metabolic characteristics of intestinal Beh\u00e7et's disease (BD), a condition sharing many clinical similarities with ulcerative colitis (UC) and Crohn's disease (CD), are largely unexplored. This study investigated the gut microbial and metabolic characteristics of intestinal BD as well as potential biomarkers, comparing them with those in UC, CD, and healthy controls. Colon tissue and stool samples from 100 patients (35 UC, 30 CD, and 35 intestinal BD) and 41 healthy volunteers were analyzed using 16S ribosomal RNA sequencing to assess microbial diversity, taxonomic composition, and functional profiling. Plasma metabolomic analyses were performed using gas chromatography and ultra-performance liquid chromatography-mass spectrometry. Results indicated reduced microbial diversity in CD but not in intestinal BD, with intestinal BD showing fewer changes compared to controls yet distinct taxonomic features from UC, CD, and controls. Common alterations across all diseases included a reduction in beneficial bacteria producing short-chain fatty acids. Intestinal BD-specific changes featured a decreased abundance of Bacteroides fragilis. Metabolomic profiles in intestinal BD were similar to those in CD but distinct from those in UC, displaying significant changes in energy metabolism and genetic information processing. This integrative analysis revealed both shared and unique profiles in intestinal BD compared with UC, CD, and controls, advancing our understanding of the distinctive features of these diseases.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26811648", + "title": "Role of antibiotics for treatment of inflammatory bowel disease.", + "year": 2016, + "journal": "World journal of gastroenterology", + "authors": [ + "Nitzan O", + "Elias M", + "Peretz A", + "Saliba W" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6838991101363793, + "mesh_terms": [ + "Animals", + "Anti-Bacterial Agents", + "Bacteria", + "Colitis, Ulcerative", + "Crohn Disease", + "Gastrointestinal Microbiome", + "Host-Pathogen Interactions", + "Humans", + "Intestines", + "Practice Guidelines as Topic", + "Treatment Outcome" + ], + "raw_abstract": "Inflammatory bowel disease is thought to be caused by an aberrant immune response to gut bacteria in a genetically susceptible host. The gut microbiota plays an important role in the pathogenesis and complications of the two main inflammatory bowel diseases: Crohn's disease (CD) and ulcerative colitis. Alterations in gut microbiota, and specifically reduced intestinal microbial diversity, have been found to be associated with chronic gut inflammation in these disorders. Specific bacterial pathogens, such as virulent Escherichia coli strains, Bacteroides spp, and Mycobacterium avium subspecies paratuberculosis, have been linked to the pathogenesis of inflammatory bowel disease. Antibiotics may influence the course of these diseases by decreasing concentrations of bacteria in the gut lumen and altering the composition of intestinal microbiota. Different antibiotics, including ciprofloxacin, metronidazole, the combination of both, rifaximin, and anti-tuberculous regimens have been evaluated in clinical trials for the treatment of inflammatory bowel disease. For the treatment of active luminal CD, antibiotics may have a modest effect in decreasing disease activity and achieving remission, and are more effective in patients with disease involving the colon. Rifamixin, a non absorbable rifamycin has shown promising results. Treatment of suppurative complications of CD such as abscesses and fistulas, includes drainage and antibiotic therapy, most often ciprofloxacin, metronidazole, or a combination of both. Antibiotics might also play a role in maintenance of remission and prevention of post operative recurrence of CD. Data is more sparse for ulcerative colitis, and mostly consists of small trials evaluating ciprofloxacin, metronidazole and rifaximin. Most trials did not show a benefit for the treatment of active ulcerative colitis with antibiotics, though 2 meta-analyses concluded that antibiotic therapy is associated with a modest improvement in clinical symptoms. Antibiotics show a clinical benefit when used for the treatment of pouchitis. The downsides of antibiotic treatment, especially with recurrent or prolonged courses such as used in inflammatory bowel disease, are significant side effects that often cause intolerance to treatment, Clostridium dificile infection, and increasing antibiotic resistance. More studies are needed to define the exact role of antibiotics in inflammatory bowel diseases.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37696680", + "title": "Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Del Chierico F", + "Cardile S", + "Baldelli V", + "Alterio T", + "Reddel S", + "Bramuzzo M", + "Knafelz D", + "Lega S", + "Bracci F", + "Torre G", + "Maggiore G", + "Putignani L" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.68245755731191, + "mesh_terms": [ + "Humans", + "Child", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Cholangitis, Sclerosing", + "Dysbiosis", + "RNA, Ribosomal, 16S", + "Bacteria", + "Bacteroidetes", + "Italy" + ], + "raw_abstract": "BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis. METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs). RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients. CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC. In this study, we report the gut microbiota and mycobiota dysbiosis in pediatric patients affected by primary sclerosing cholangitis (PSC) associated with ulcerative colitis (UC), with an increase in pro-inflammatory pathobionts and a reduction in anti-inflammatory commensals.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38387133", + "title": "Gut microbiota-based discovery of Houttuyniae Herba as a novel prebiotic of Bacteroides thetaiotaomicron with anti-colitis activity.", + "year": 2024, + "journal": "Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie", + "authors": [ + "Zou LE", + "Yang YN", + "Zhan J", + "Cheng J", + "Fu Y", + "Cao Y", + "Yan X", + "Wang Y", + "Wu C" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6823884375989377, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "Bacteroides thetaiotaomicron", + "Gastrointestinal Microbiome", + "Colitis", + "Colitis, Ulcerative", + "Bacteroides", + "Prebiotics" + ], + "raw_abstract": "Ulcerative colitis (UC) represents an inflammatory disease characterized by fluctuations in severity, posing substantial challenges in treatment. The gut microbiota plays a pivotal role in the pathogenesis of UC. This study sought to identify drugs specifically targeting the gut microbiota to mitigate UC. We initiated a meta-analysis on gut microbiota in UC patients to identify UC-associated bacterial strains. Subsequently, we screened 164 dietary herbal medicines in vitro to identify potential prebiotics for the UC-associated bacterium, Bacteroides thetaiotaomicron. The DSS-induced colitis mouse model was utilized to evaluate the anti-colitis efficacy of the identified dietary herbal medicine. Full-length 16\u202fS rRNA amplicon sequencing was employed to observe changes in gut microbiota following dietary herbal medicine intervention. The relative abundance of Bacteroides was notably diminished in UC patients compared to their healthy counterparts. B. thetaiotaomicron exhibited an inverse relationship with UC symptoms, indicating its potential as an anti-colitis agent. In vitro assessments revealed that H. Herba significantly bolstered the proliferation of B. thetaiotaomicron. Further experiments showed that treating DSS-induced mice with an aqueous extract of H. Herba considerably alleviated colitis indicators such as weight loss, colon shortening, disease activity score (DAI), and systemic inflammation. Microbial analysis revealed B. thetaiotaomicron as the sole bacterium substantially augmented by H. Herba in vivo. Overall H. Herba emerges as a promising prebiotic for B. thetaiotaomicron, offering significant anti-colitis benefits. Employing a gut microbiota-centric approach proves valuable in the quest for drug discovery.This study provides a new paradigm for drug discovery that targets the gut microbiota to treat UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32265456", + "title": "Seasonal changes of circulating 25-hydroxyvitamin D correlate with the lower gut microbiome composition in inflammatory bowel disease patients.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Soltys K", + "Stuchlikova M", + "Hlavaty T", + "Gaalova B", + "Budis J", + "Gazdarica J", + "Krajcovicova A", + "Zelinkova Z", + "Szemes T", + "Kuba D", + "Drahovska H", + "Turna J", + "Stuchlik S" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6560260020108714, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteria", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Seasons", + "Vitamin D", + "Young Adult" + ], + "raw_abstract": "Higher probability of the development of Crohn's disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/Shigella spp.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29788382", + "title": "Colonic Inhibition of Phosphatase and Tensin Homolog Increases Colitogenic Bacteria, Causing Development of Colitis in Il10-/- Mice.", + "year": 2018, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Mitchell J", + "Kim SJ", + "Koukos G", + "Seelmann A", + "Veit B", + "Shepard B", + "Blumer-Schuette S", + "Winter HS", + "Iliopoulos D", + "Pothoulakis C", + "Im E", + "Rhee SH" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6519030248558214, + "mesh_terms": [ + "Animals", + "Colitis", + "Colitis, Ulcerative", + "Colon", + "Disease Models, Animal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Interleukin-10", + "Intestinal Mucosa", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Mice, Knockout", + "Organometallic Compounds", + "PTEN Phosphohydrolase" + ], + "raw_abstract": "BACKGROUND: Phosphatase and tensin homolog (Pten) is capable of mediating microbe-induced immune responses in the gut. Thus, Pten deficiency in the intestine accelerates colitis development in Il10-/- mice. As some ambient pollutants inhibit Pten function and exposure to ambient pollutants may increase inflammatory bowel disease (IBD) incidence, it is of interest to examine how Pten inhibition could affect colitis development in genetically susceptible hosts. METHODS: With human colonic mucosa biopsies from pediatric ulcerative colitis and non-IBD control subjects, we assessed the mRNA levels of the PTEN gene and the gene involved in IL10 responses. The data from the human tissues were corroborated by treating Il10-/-, Il10rb-/-, and wild-type C57BL/6 mice with Pten-specific inhibitor VO-OHpic. We evaluated the severity of mouse colitis by investigating the tissue histology and cytokine production. The gut microbiome was investigated by analyzing the 16S ribosomal RNA gene sequence with mouse fecal samples. RESULTS: PTEN and IL10RB mRNA levels were reduced in the human colonic mucosa of pediatric ulcerative colitis compared with non-IBD subjects. Intracolonic treatment of the Pten inhibitor induced colitis in Il10-/- mice, characterized by reduced body weight, marked colonic damage, and increased production of inflammatory cytokines, whereas Il10rb-/- and wild-type C57BL/6 mice treated with the inhibitor did not develop colitis. Pten inhibitor treatment changed the fecal microbiome, with increased abundance of colitogenic bacteria Bacteroides and Akkermansia in Il10-/- mice. CONCLUSIONS: Loss of Pten function increases the levels of colitogenic bacteria in the gut, thereby inducing deleterious colitis in an Il10-deficient condition.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37820918", + "title": "Scytosiphon lomentaria fucoidan ameliorates DSS-induced colitis in dietary fiber-deficient mice via modulating the gut microbiota and inhibiting the TLR4/NF-\u03baB/MLCK pathway.", + "year": 2023, + "journal": "International journal of biological macromolecules", + "authors": [ + "Jia J", + "Zheng W", + "Tang S", + "Song S", + "Ai C" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6420246914011817, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "NF-kappa B", + "Toll-Like Receptor 4", + "Gastrointestinal Microbiome", + "Myosin-Light-Chain Kinase", + "Polysaccharides", + "Colitis", + "Colitis, Ulcerative", + "Dietary Fiber", + "Colon", + "Dextran Sulfate", + "Disease Models, Animal", + "Mice, Inbred C57BL" + ], + "raw_abstract": "The prevalence of ulcerative colitis (UC) poses a serious threat to human health. This study showed that fiber-deficient diet (FD) increased the susceptibility of mice to low dosage of DSS-induced UC, and a UC model was established by feeding mice with DSS and FD to evaluate the effect of Scytosiphon lomentaria fucoidan (SLF) on UC. SLF ameliorated the symptoms of UC, as evidenced by increases in colon length, goblet cells and glycoprotein and reduction in inflammatory cell infiltration and intestinal epithelial injury. SLF alleviated oxidative stress and inhibited colonic inflammation by reducing the levels of lipopolysaccharides and pro-inflammatory cytokines and suppressing the activation of nuclear factor kappa B pathway. SLF protected tight junction integrity by reducing the level of myosin light chain kinase and increasing the levels of claudin, zonula occludens-1 and occludin. SLF improved serum metabolites profile and affected multiple metabolic pathways that are crucial to human health, e.g. butanoate metabolism. The underlying mechanism can be associated with modulation of the gut microbiota and metabolites, including increases in short chain fatty acids and reduction in Proteobacteria, Bacteroides and Romboutsia. It suggests that SLF could be developed as a prebiotic polysaccharide to benefit human health by improving intestinal microecology.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38423015", + "title": "Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota.", + "year": 2024, + "journal": "Cell host & microbe", + "authors": [ + "Carasso S", + "Zaatry R", + "Hajjo H", + "Kadosh-Kariti D", + "Ben-Assa N", + "Naddaf R", + "Mandelbaum N", + "Pressman S", + "Chowers Y", + "Gefen T", + "Jeffrey KL", + "Jofre J", + "Coyne MJ", + "Comstock LE", + "Sharon I", + "Geva-Zatorsky N" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6416281419684179, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "Gastrointestinal Microbiome", + "Colitis", + "Inflammatory Bowel Diseases", + "Inflammation", + "DNA" + ], + "raw_abstract": "Reversible genomic DNA inversions control the expression of numerous gut bacterial molecules, but how this impacts disease remains uncertain. By analyzing metagenomic samples from inflammatory bowel disease (IBD) cohorts, we identified multiple invertible regions where a particular orientation correlated with disease. These include the promoter of polysaccharide A (PSA) of Bacteroides fragilis, which induces regulatory T\u00a0cells (Tregs) and ameliorates experimental colitis. The PSA promoter was mostly oriented \"OFF\" in IBD patients, which correlated with increased B.\u00a0fragilis-associated bacteriophages. Similarly, in mice colonized with a healthy human microbiota and B.\u00a0fragilis, induction of colitis caused a decline of PSA in the \"ON\" orientation that reversed as inflammation resolved. Monocolonization of mice with B.\u00a0fragilis revealed that bacteriophage infection increased the frequency of PSA in the \"OFF\" orientation, causing reduced PSA expression and decreased Treg cells. Altogether, we reveal dynamic bacterial phase variations driven by bacteriophages and host inflammation, signifying bacterial functional plasticity during disease.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39155343", + "title": "Bacteroides fragilis in saliva: investigating links with ulcerative colitis.", + "year": 2024, + "journal": "Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]", + "authors": [ + "Zamani S", + "Besharat S", + "Behnampour N", + "Behnam A", + "Asgari N", + "Mortazavi N" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6413924958101966, + "mesh_terms": [ + "Humans", + "Bacteroides fragilis", + "Female", + "Male", + "Saliva", + "Colitis, Ulcerative", + "Adult", + "Iran", + "Middle Aged", + "Young Adult", + "Bacteroides Infections", + "Case-Control Studies" + ], + "raw_abstract": "BACKGROUND: Ulcerative colitis (UC) is a long-term bowel inflammation of unknown cause. Recent research points to gut microbiota, especially Enterotoxigenic Bacteroides fragilis (ETBF), in UC's development. This study examined the presence of Bacteroides fragilis (B. fragilis) and ETBF in the saliva of UC patients and Healthy Controls (HCs) in Iran. METHODS: A total of 40 UC patients and 40 healthy controls were included in the study. Saliva samples were collected and analyzed for the presence of B. fragilis and ETBF using real-time polymerase chain reaction (PCR). RESULTS: B. fragilis was more prevalent in HCs (70%) than UC patients (67.5%), but not significantly (p\u2009=\u20090.809). ETBF was significantly more prevalent in UC patients (50%) than HCs (10%) (p\u2009<\u20090.0001). The mean count of B. fragilis was higher in UC patients, but not significantly (p\u2009=\u20090.47). However, the mean count of ETBF was significantly higher in UC patients (p\u2009=\u20090.000089). In terms of gender, the number of B. fragilis in women was not significant (p\u2009=\u20090.16), but the number of ETBF was significantly higher in women with UC (p\u2009=\u20090.000458). For men, no significant differences were observed. CONCLUSIONS: The present study suggest a higher prevalence of B. fragilis observed in UC patients compared to HCs. Further research is needed to confirm these findings and explore potential mechanisms underlying this association.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32070388", + "title": "A randomized controlled trial investigating the effect of a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols on the intestinal microbiome and inflammation in patients with ulcerative colitis: study protocol for a randomized controlled trial.", + "year": 2020, + "journal": "Trials", + "authors": [ + "Milajerdi A", + "Sadeghi O", + "Siadat SD", + "Keshavarz SA", + "Sima A", + "Vahedi H", + "Adibi P", + "Esmaillzadeh A" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6263466957590321, + "mesh_terms": [ + "Adult", + "Biomarkers", + "Colitis, Ulcerative", + "Diet, Carbohydrate-Restricted", + "Dietary Sugars", + "Female", + "Fermentation", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Male", + "Middle Aged", + "Monosaccharides", + "Oligosaccharides", + "Polymers", + "Randomized Controlled Trials as Topic", + "Severity of Illness Index", + "Treatment Outcome", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: No conclusive treatment is available for irritable bowel disease (IBD). Adherence to a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) might alleviate clinical symptoms of IBD. However, no study has investigated the effect of low FODMAPs diet on the intestinal microbiota and inflammatory biomarkers in patients with IBD. The aim of current study is to examine the effect a low FODMAP diet on IBD symptoms, inflammation, and the intestinal microbiota in patients with ulcerative colitis. METHODS AND ANALYSIS: This study is a randomized clinical trial. Thirty patients with mild to moderate ulcerative colitis will be randomly allocated to receive a low FODMAP diet (n\u2009=\u200915) or to continue their usual diet as control (n\u2009=\u200915), for 4\u2009weeks. The quantity of intestinal microbiota including Clostridium cluster IV, Faecalibacterium prausnitzii, Rosburia spp., Lactobacillus spp., Bifidobacteria spp., Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., and the Firmicutes to Bacteroidetes ratio and calprotectin and lactoferrin levels will be explored in fecal samples from patients. In addition, anthropometric measures and biochemical assessments including serum concentrations of highly sensitive-C reactive protein (hs-CRP), tumour necrosis factor-\u03b1 (TNF-\u03b1) and IL-1\u03b2 will be taken from patients at baseline and end of the study. The study has been registered in IRCT (IRCT20181126041763N1; registration date: 2019-01-18). DISCUSSION: Consumption of a low-FODMAP diet might decrease systemic and intestinal inflammation, change the bacterial population in the gut, and modulate clinical symptoms in patients with ulcerative colitis. Further studies investigating the effect of such a diet on other variables, including other bacterial species and inflammatory cytokines, are required to confirm future findings of this trial.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39122767", + "title": "Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Zhang B", + "Magnaye KM", + "Stryker E", + "Moltzau-Anderson J", + "Porsche CE", + "Hertz S", + "McCauley KE", + "Smith BJ", + "Zydek M", + "Pollard KS", + "Ma A", + "El-Nachef N", + "Lynch SV" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6159114247017194, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Fecal Microbiota Transplantation", + "Male", + "Female", + "Feces", + "Bacteroides", + "Adult", + "Intestinal Mucosa", + "Middle Aged", + "Gastrointestinal Microbiome", + "Treatment Failure", + "RNA, Ribosomal, 16S", + "Metabolome" + ], + "raw_abstract": "Fecal microbial transplantation (FMT) offers promise for treating ulcerative colitis (UC), though the mechanisms underlying treatment failure are unknown. This study harnessed longitudinally collected colonic biopsies (n\u2009=\u200938) and fecal samples (n\u2009=\u2009179) from 19 adults with mild-to-moderate UC undergoing serial FMT in which antimicrobial pre-treatment and delivery mode (capsules versus enema) were assessed for clinical response (\u2265\u20093 points decrease from the pre-treatment Mayo score). Colonic biopsies underwent dual RNA-Seq; fecal samples underwent parallel 16S rRNA\u00a0and shotgun metagenomic sequencing as well as untargeted metabolomic analyses. Pre-FMT, the colonic mucosa of non-responsive (NR) patients harbored an increased burden of bacteria, including Bacteroides, that expressed more antimicrobial resistance genes compared to responsive (R) patients. NR patients also exhibited muted mucosal expression of innate immune antimicrobial response genes. Post-FMT, NR and R fecal microbiomes and metabolomes exhibited significant divergence. NR metabolomes had elevated concentrations of immunostimulatory compounds including sphingomyelins, lysophospholipids and taurine. NR fecal microbiomes were enriched for Bacteroides fragilis and Bacteroides salyersiae strains that encoded genes capable of taurine production. These findings suggest that both effective mucosal microbial clearance and reintroduction of bacteria that reshape luminal metabolism associate with FMT success\u00a0and that persistent mucosal and fecal colonization by antimicrobial-resistant Bacteroides species may contribute to FMT failure.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35972440", + "title": "Patient-Reported Outcomes Correlate With Microbial Community Composition Independent of Mucosal Inflammation in Pediatric Inflammatory Bowel Disease.", + "year": 2023, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Hellmann J", + "Ta A", + "Ollberding NJ", + "Bezold R", + "Lake K", + "Jackson K", + "Dirksing K", + "Bonkowski E", + "Haslam DB", + "Denson LA" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6100886713980962, + "mesh_terms": [ + "Humans", + "Child", + "Prospective Studies", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Crohn Disease", + "Microbiota", + "Feces", + "Leukocyte L1 Antigen Complex", + "Inflammation", + "Abdominal Pain", + "Patient Reported Outcome Measures" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel diseases (IBDs) involve an aberrant host response to intestinal microbiota causing mucosal inflammation and gastrointestinal symptoms. Patient-reported outcomes (PROs) are increasingly important in clinical care and research. Our aim was to examine associations between PROs and fecal microbiota in patients 0 to 22 years of age with IBD. METHODS: A longitudinal, prospective, single-center study tested for associations between microbial community composition via shotgun metagenomics and PROs including stool frequency and rectal bleeding in ulcerative colitis (UC) and abdominal pain and stool frequency in Crohn's disease (CD). Mucosal inflammation was assessed with fecal calprotectin. A negative binomial mixed-effects model including clinical characteristics and fecal calprotectin tested for differentially abundant species and metabolic pathways by PROs. RESULTS: In 70 CD patients with 244 stool samples, abdominal pain correlated with increased relative abundance of Haemophilus and reduced Clostridium spp. There were no differences relative to calprotectin level. In 23 UC patients with 76 samples, both rectal bleeding and increased stool frequency correlated with increased Klebsiella and reduced Bacteroides spp. Conversely, UC patients with lower calprotectin had reduced Klebsiella. Both UC and CD patients with active symptoms exhibited less longitudinal microbial community stability. No differences in metabolic pathways were observed in CD. Increased sulfoglycolysis and ornithine biosynthesis correlated with symptomatic UC. CONCLUSIONS: Microbial community composition correlated with PROs in both CD and UC. Metabolic pathways differed relative to PROs in UC, but not CD. Data suggest that microbiota may contribute to patient symptoms in IBD, in addition to effects of mucosal inflammation.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34264407", + "title": "A case-control study on the association of intestinal flora with ulcerative colitis.", + "year": 2021, + "journal": "AMB Express", + "authors": [ + "Tang YH", + "Liu HC", + "Song G", + "Wu TT", + "Zhao Y", + "Shi LJ" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.6025006601305938, + "mesh_terms": [], + "raw_abstract": "The association between intestinal flora and ulcerative colitis (UC) was studied in order to provide a basis and method for clinical treatment. Fresh fecal samples were collected from 30 active UC patients and 10 healthy controls. The intestinal flora DNA from each sample was extracted and 16S rRNA gene sequencing was carried out using HiSeq platform to identify the intestinal flora in fecal samples. The richness and diversity of intestinal flora in UC patients were significantly lower than those in healthy control group (P\u2009<\u20090.05). Significant differences were observed between the intestinal flora-species of UC patients and healthy controls. Synergistetes (P\u2009<\u20090.01) and Firmicutes (P\u2009<\u20090.05), along with probiotics Veillonella (P\u2009<\u20090.01), Ruminococcus and Coprococcus (P\u2009<\u20090.05) in the UC patients were lower than that in the healthy controls significantly. Furthermore, compared with the control group, Tenericutes (P\u2009<\u20090.01) and intestinal pathogenic bacteria, including Bacteroides (P\u2009<\u20090.01), Escherichia and Sutterella (P\u2009<\u20090.05) were significantly increased. The incidence of UC is significantly associated with the changes in intestinal flora. Changes in intestinal flora may lead to a decrease in the diversity of intestinal flora or to the enrichment of a particular intestinal flora.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35662877", + "title": "Zingiber officinale and Panax ginseng ameliorate ulcerative colitis in mice via modulating gut microbiota and its metabolites.", + "year": 2022, + "journal": "Journal of chromatography. B, Analytical technologies in the biomedical and life sciences", + "authors": [ + "Wan Y", + "Yang L", + "Li H", + "Ren H", + "Zhu K", + "Dong Z", + "Jiang S", + "Shang E", + "Qian D", + "Duan J" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.5981279443355652, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Zingiber officinale", + "Mice", + "Panax", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "Zingiber officinale and Panax ginseng, as well-known traditional Chinese medicines, have been used together to clinically treat ulcerative colitis with synergistic effects for thousands of years. However, their compatibility mechanism remains unclear. In this study, the shift of gut microbiome and fecal metabolic profiles were monitored by 16S rRNA sequencing technology and ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry analysis, respectively, which aimed to reveal the synergistic mechanism of Zingiber officinale and Panax ginseng on the amelioration of ulcerative colitis. The results showed that the relative abundance of beneficial bacteria (such as Muribaculaceae_norank, Lachnospiraceae NK4A136 group and Akkermansia) was significantly increased and the abundance of pathogenic bacteria (such as Bacteroides, Parabacteroides and Desulfovibrio) was markedly decreased after the intervention of Zingiber officinale-Panax ginseng herb pair. And a total of 16 differential metabolites related to ulcerative colitis were identified by the metabolomics analysis, which were majorly associated with the metabolic pathways, including arachidonic acid metabolism, tryptophan metabolism, and steroid biosynthesis. Based on these findings, it was suggested that the regulation of the gut microbiota-metabolite axis might be a potential target for the synergistic mechanism of Zingiber officinale-Panax ginseng herb pair in the treatment of ulcerative colitis. Furthermore, the integrated analysis of microbiome and metabolomics used in this study could also serve as a useful template for exploring the mechanism of other drugs.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36401221", + "title": "Triclosan exposure induced disturbance of gut microbiota and exaggerated experimental colitis in mice.", + "year": 2022, + "journal": "BMC gastroenterology", + "authors": [ + "Liu J", + "Tao Y", + "Haikun W", + "Lanfang Y", + "Jingyi L", + "Ping Y" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.5954623770482104, + "mesh_terms": [ + "Humans", + "Mice", + "Animals", + "Gastrointestinal Microbiome", + "Triclosan", + "Dextran Sulfate", + "Colitis, Ulcerative", + "Occludin", + "Mice, Inbred C57BL", + "Colitis", + "Sulfates", + "Butyrates" + ], + "raw_abstract": "BACKGROUND: Triclosan, an antimicrobial agent in personal care products, could be absorbed into the human body through the digestive tract. This animal experiment aimed to clarify the effects of triclosan exposure on the microbiome and intestinal immune functions in healthy and ulcerative colitis models. METHODS: Balb/c mice were maintained on an AIN-93G diet containing 80ppm triclosan dissolved in polyethylene as vehicle or vehicle alone for 1 week or 4 weeks. In the end, the mice were sacrificed, blood samples and colon tissues were collected for analysis of inflammation, and fecal samples were collected for 16\u00a0S rRNA sequencing of gut microbiota. To establish ulcerative colitis mice model, at the beginning of the 4th week, mice maintained on the diet with or without triclosan were treated with 2% Dextran sulfate sodium(DSS) in drinking water for 1 week. Then mice were sacrificed for analysis of colitis and gut microbiota. RESULTS: Triclosan exposure to common mice enhanced the levels of p-NF-\u03bab and Toll-like receptor 4 (TLR4), and decreased the Occludin in the colon. Triclosan exposure to DSS-induced mice increased the level of inflammatory cytokines, reduced the levels of Occludin, and exacerbated the degree of damage to intestinal mucosa and crypt, infiltration of inflammatory cells and atypia of glandular cells. Low-grade intraepithelial neoplasia appeared. Both in common and DSS-induced mice, triclosan exposure changed the diversity and composition of gut microbiota. Fecal samples showed higher enrichment of sulfate-reducing bacteria and Bacteroides, and less butyrate-producing bacteria. CONCLUSION: Triclosan exposure induced disturbance of gut microbiota and exaggerated experimental colitis in mice. And changes in the composition of gut microbiota were characterized by the increase of harmful bacteria, including sulfate-reducing bacteria and Bacteroides, and the reduction of protective probiotics, butyrate-producing bacteria.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39984099", + "title": "\u03b2-1,3-glucans from Euglena Gracilis protects against ulcerative colitis via modulating the gut barrier, T-cell immunity and gut microbiota.", + "year": 2025, + "journal": "International journal of biological macromolecules", + "authors": [ + "Guo B", + "Zhang W", + "Zou J", + "Sun L", + "Dong N", + "Liu B" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.585730985247043, + "mesh_terms": [], + "raw_abstract": "Ulcerative colitis (UC) is characterized by impaired gut barrier, dysregulated immune responses and pronounced gut dysbiosis. Euglena gracilis (EG), rich in \u03b2-1,3-glucan (EGP), exhibits immunomodulatory properties, yet its effects on colitis and EGP's role as a core bioactive component are unclear. The aim of this study was to investigate the protective effects of EGP against UC by targeting gut barrier, T-cell immunity and gut microbiota. Results indicated that EG and EGP effectively improved the body weight, colon growth and reduced disease activity index of the DSS-induced mice. Both treatments also significantly suppressed the level of TNF-\u03b1 and IL-6, restored gut barrier by upregulating ZO-1 and balanced Th17/Treg cells ratio. Microbiota analysis revealed EG and EGP reshaped gut microbiota composition, with an increase in beneficial strains, particularly within the Bacteroidota phylum. Metabolomics linked these changes to enhanced amino acid metabolism. Bacteroides fragilis, a Bacteroidota member, displayed similar anti-colitis bioactivity. In vitro fermentation with fecal samples from UC patients confirmed EGP's role in reshaping gut microbiota, increasing beneficial families such as Clostridiaceae and Lactobacillaceae, while enhancing tryptophan metabolism with anti-inflammatory indoles. These findings identify EGP as the core active component of EG, highlighting its potential in UC prevention through microbiota modulation, gut barrier support and immune regulation.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35151255", + "title": "Gut microbiome alterations in colitis rats after moxibustion at bilateral Tianshu acupoints.", + "year": 2022, + "journal": "BMC gastroenterology", + "authors": [ + "Qi Q", + "Liu YN", + "Lv SY", + "Wu HG", + "Zhang LS", + "Cao Z", + "Liu HR", + "Wang XM", + "Wu LY" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.5837953957639432, + "mesh_terms": [ + "Acupuncture Points", + "Animals", + "Colitis", + "Colitis, Ulcerative", + "Dextran Sulfate", + "Disease Models, Animal", + "Gastrointestinal Microbiome", + "Male", + "Moxibustion", + "Rats" + ], + "raw_abstract": "BACKGROUND: The pathogenesis of ulcerative colitis (UC) is closely related to the gut microbiota. Moxibustion has been used to improve the inflammation and gastrointestinal dysfunctions in gastrointestinal\u00a0disorders such as UC. In this study, we investigated whether moxibustion could improve the gut microbial dysbiosis induced by dextran sulphate sodium. METHODS: Twenty-five male rats were randomly assigned into five groups. The UC rat model was established by administering DSS solution. The rats in the moxibustion and normal rats with moxibustion groups were treated with moxibustion at Tianshu (bilateral, ST25) points, and the mesalazine group rats were treated with mesalazine once daily for 7 consecutive days. Disease activity index (DAI) and haematoxylin and eosin staining were used to evaluate the effect of moxibustion. Gut microbiota profiling was conducted by metagenomic high throughput sequencing technology. The gut microbiota composition, diversity and function were analyzed and compared using metagenomics methodologies. RESULTS: The DAI scores and histopathology scores in the moxibustion and mesalazine groups were significantly decreased compared with the UC group (P\u2009<\u20090.01). Moxibustion treatment increased abundance levels of Bacteroidetes, Actinobacteria, Ascomycota, Synergistetes and decreased abundance of Firmicutes, Proteobacteria. At the genus level, the abundance of Bacteroides, Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2, were increased and Bacteroides_bacterium_H3, Parabacteroides, Porphyromonas, Alistipes, Parasutterella were decreased in the UC group in comparsion with those in the NG group. Moxibustion increased the abundance of Bacteroides and Bacteroides_bacterium_H3 and decreased Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2. In UC group, the specie Bacteroides_massiliensis was negatively (P\u2009<\u20090.05) correlated with IL-23, Bacteroides_eggerthii_CAG109 and Bacteroides_eggerthii were negatively (P\u2009<\u20090.05) correlated with TGF-\u03b2. And the species Prevotella_sp_CAG1031 and Bacteroides_bacterium_H2 were significant positively (P\u2009<\u20090.05) correlated with IL-23. In addition, compare with the normal group, genes involved in certain metabolic pathways, such as energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, were under-represented in the UC group, and these changes in the metabolic pathways could be reversed by moxibustion treatment and mesalazine treatment. CONCLUSIONS: Our findings suggest that moxibustion treatment may protect the host from mucosal inflammation by modulating the intestinal microbiota community.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39073916", + "title": "Core microbiome-associated proteins associated with ulcerative colitis interact with cytokines for synergistic or antagonistic effects on gut bacteria.", + "year": 2024, + "journal": "The ISME journal", + "authors": [ + "Zhang T", + "Zhong H", + "Lin L", + "Zhang Z", + "Xue K", + "He F", + "Luo Y", + "Wang P", + "Zhao Z", + "Cong L", + "Pang P", + "Li X", + "Shan H", + "Yan Z" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.5828772262635463, + "mesh_terms": [ + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Humans", + "Cytokines", + "Calgranulin B", + "Calgranulin A", + "Proteomics", + "Feces", + "Ruminococcus", + "Host Microbial Interactions", + "Clostridiales" + ], + "raw_abstract": "Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is associated with a loss or an imbalance of host-microorganism interactions. However, such interactions at protein levels remain largely unknown. Here, we applied a depletion-assisted metaproteomics approach to obtain in-depth host-microbiome association networks of IBD, where the core host proteins shifted from those maintaining mucosal homeostasis in controls to those involved in inflammation, proteolysis, and intestinal barrier in IBD. Microbial nodes such as short-chain fatty-acid producer-related host-microbial crosstalk were lost or suppressed by inflammatory proteins in IBD. Guided by protein-protein association networks, we employed proteomics and lipidomics to investigate the effects of UC-related core proteins S100A8, S100A9, and cytokines (IL-1\u03b2, IL-6, and TNF-\u03b1) on gut bacteria. These proteins suppressed purine nucleotide biosynthesis in stool-derived in vitro communities, which was also reduced in IBD stool samples. Single species study revealed that S100A8, S100A9, and cytokines can synergistically or antagonistically alter gut bacteria intracellular and secreted proteome, with combined S100A8 and S100A9 potently inhibiting beneficial Bifidobacterium adolescentis. Furthermore, these inflammatory proteins only altered the extracellular but not intracellular proteins of Ruminococcus gnavus. Generally, S100A8 induced more significant bacterial proteome changes than S100A9, IL-1\u03b2, IL-6, and TNF-\u03b1 but gut bacteria degrade significantly more S100A8 than S100A9 in the presence of both proteins. Among the investigated species, distinct lipid alterations were only observed in Bacteroides vulgatus treated with combined S100A8, S100A9, and cytokines. These results provided a valuable resource of inflammatory protein-centric host-microbial molecular interactions.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35104755", + "title": "Integrated microbiome-metabolomics analysis reveals the potential therapeutic mechanism of Zuo-Jin-Wan in ulcerative colitis.", + "year": 2022, + "journal": "Phytomedicine : international journal of phytotherapy and phytopharmacology", + "authors": [ + "Cai Y", + "Li S", + "Zhang X", + "Cao X", + "Liu D", + "Zhu Y", + "Ye S", + "Xu Z", + "Liao Q", + "Hong Y", + "Xie Z" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.5814548368548027, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Dysregulation in gut microbiota and host cometabolome contributes to the complicated pathology of ulcerative colitis (UC), while Zuo-Jin-Wan (ZJW), a traditional Chinese medicine has shown therapeutic effects against UC with its underlying mechanism remains elusive. PURPOSE: This study utilized an integrated analysis combining gut microbiome and host cometabolism to disclose the potential therapeutic mechanism of ZJW on dextran sulfate sodium (DSS)-induced UC in rats. METHODS: We first evaluated the therapeutic effects of ZJW treatment in DSS-induced rat model. 16S rRNA sequencing, RESULTS: Our results showed that UC symptoms in ZJW rats were significantly attenuated. Marked decline in microbial diversity in ZJW group was accompanied by its correspondent function adjustment. Specific enrichment of genus Bacteroides, Sutterella, Akkermansia and Roseburia along with the major varying amino acid metabolism and lipid metabolism were observed meantime. Metabolic data further corroborated that ZJW-related metabolic changes were basically gathered in amino acid metabolism, carbohydrate/energy metabolism and lipid metabolism. Of note, some biochemical parameters were deeply implicated with the discriminative microbial genera and metabolites involved in tricarboxylic acid (TCA) cycle and amino acid metabolism, indicating the microbiome-metabolome association in gut microbiota-metabolite-phenotype axis during UC treatment of ZJW. CONCLUSION: For the first time, integrated microbiome-metabolome analysis depicted that ZJW could alleviate DSS-induced UC in rats via a crosstalk between gut microbiota and host cometabolites.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34215773", + "title": "Mucosa-associated gut microbiota reflects clinical course of ulcerative colitis.", + "year": 2021, + "journal": "Scientific reports", + "authors": [ + "Nishihara Y", + "Ogino H", + "Tanaka M", + "Ihara E", + "Fukaura K", + "Nishioka K", + "Chinen T", + "Tanaka Y", + "Nakayama J", + "Kang D", + "Ogawa Y" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.5603967412610934, + "mesh_terms": [ + "Adult", + "Bacteroides", + "Clostridiales", + "Colitis, Ulcerative", + "Colon", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Longitudinal Studies", + "Male", + "Middle Aged", + "Prevotella", + "RNA, Ribosomal, 16S", + "Recurrence" + ], + "raw_abstract": "This longitudinal study was designed to elucidate whether gut microbiota is associated with relapse and treatment response in ulcerative colitis (UC) patients. Fifty-one patients with UC were enrolled between 2012 and 2017, and followed up through 2020. Colon mucosal biopsy were obtained at enrollment, and 16S ribosomal RNA sequencing was performed using extracted RNA. Of the 51 patients, 24 were in remission and 27 had active UC at enrollment. Of the 24 patients in remission, 17 maintained remission and 7 developed relapse during follow-up. The 7 patients with relapse showed lower diversity, with a lower proportion of Clostridiales (p\u2009=\u20090.0043), and a higher proportion of Bacteroides (p\u2009=\u20090.047) at enrollment than those without relapse. The 27 patients with active UC were classified into response (n\u2009=\u20096), refractory (n\u2009=\u200913), and non-response (n\u2009=\u20098) groups according to their treatment response in 6\u00a0months. The refractory and non-response groups showed lower diversity with a lower proportion of Prevotella (p\u2009=\u20090.048 and 0.043) at enrollment than the response group. This study is the first demonstration that reduced diversity and particular microbes are associated with the later clinical course of relapse events and treatment response in UC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33548121", + "title": "Gut microbiota changes in inflammatory bowel diseases and ankylosing spondilytis.", + "year": 2021, + "journal": "Journal of gastrointestinal and liver diseases : JGLD", + "authors": [ + "Cardoneanu A", + "Mihai C", + "Rezus E", + "Burlui A", + "Popa I", + "Cijevschi Prelipcean C" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.5579199206439506, + "mesh_terms": [ + "Bacteria", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Escherichia coli", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases" + ], + "raw_abstract": "BACKGROUND AND AIMS: Both inflammatory bowel diseases (IBD) and ankylosing spondylitis (AS) can be considered chronic immune disorders sharing common etiopathogenetic mechanisms. Changes in the composition of the intestinal microbiota, which can lead to an abnormal mucosal response, could be the missing link between these two diseases. Our study evaluate the composition of intestinal microbiota and to characterize gut dysbiosis in patients with IBD and AS. METHODS: We conducted a prospective case-control study that enrolled 124 patients [20 Crohn's disease (CD), 27 ulcerative colitis (UC), 28 AS, 17 IBD + AS and 32 controls). Intestinal microbiota analysis was performed by real-time polymerase chain reaction in stool samples. RESULTS: The total quantity of bacteria was decreased in all investigated groups compared to the control group. In studied groups, we noticed an increased percentage of Bacteroides and Escherichia coli (E.coli) and a decreased percentage of Clostridium coccoides, Clostridium leptum, and Faecalibacterium prausnitzii compared to the control group. The percentages of Bifidobacterium (p=0.010) as well as Lactobacillus group (p=0.023) were higher in the L3 form of CD patients. In the E2 form of UC, the quantity of Bacteroides was much higher compared to the E3 form (p=0.004). In AS patients, significant correlations were observed only for the Bifidobacterium species, significantly increased in the axial form compared to peripheral disease (p=0.035). Statistically significant correlations were demonstrated between the Crohn Disease Activity Index score and the total bacterial group (p=0.023, r=-0.507), respectively Bacteroides (p=0.021, r=-0.511) and between the Mayo score and Lactobacillus (p=0.001), respectively E. coli (p=0.001). In IBD + AS group, the Crohn Disease Activity Index score was inversely correlated with the total bacterial group (p=0.010) and directly correlated with Lactobacillus (p=0.047). CONCLUSIONS: Intestinal dysbiosis is associated with both IBD and AS. In the association of IBD with AS, dysbiosis is intermediate, but it is associated with the more severe articular disease. Bifidobacterium and Lactobacillus (commonly used as probiotics!) were found to be increased in the association between active IBD and active AS. Further studies are needed to understand how dysbiosis regulates the gut immune system and contributes to intestinal and articular inflammation.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32576228", + "title": "Effects of soy milk consumption on gut microbiota, inflammatory markers, and disease severity in patients with ulcerative colitis: a study protocol for a randomized clinical trial.", + "year": 2020, + "journal": "Trials", + "authors": [ + "Sadeghi O", + "Milajerdi A", + "Siadat SD", + "Keshavarz SA", + "Sima AR", + "Vahedi H", + "Adibi P", + "Esmaillzadeh A" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.5496370877772266, + "mesh_terms": [ + "Adult", + "Anti-Inflammatory Agents", + "Biomarkers", + "Colitis, Ulcerative", + "Eating", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Iran", + "Male", + "Middle Aged", + "Phytoestrogens", + "Quality of Life", + "Randomized Controlled Trials as Topic", + "Severity of Illness Index", + "Soy Milk", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Several strategies are recommended to alleviate clinical symptoms of ulcerative colitis (UC). Soy milk may affect UC through its anti-inflammatory properties. However, no study has examined the effects of soy milk consumption on gut microbiota and inflammatory biomarkers in patients with UC. The current study will be done to examine the effects of soy milk consumption on UC symptoms, inflammation, and gut microbiota in patients with UC. METHODS: This study is a randomized clinical trial, in which thirty patients with mild to moderate severity of UC will be randomly allocated to receive either 250\u2009mL/day soy milk plus routine treatments (n\u2009=\u200915) or only routine treatments (n\u2009=\u200915) for 4\u2009weeks. Assessment of anthropometric measures and biochemical indicators including serum concentrations of high-sensitivity C-reactive protein (hs-CRP), tumor necrosis factor-\u03b1 (TNF-\u03b1), interleukin-1\u03b2 (IL-1\u03b2), and interferon gamma (IFN-\u03b3) will be done at the study baseline and end of trial. In addition, the quantity of butyrate-producing bacteria including Clostridium cluster IV, Faecalibacterium prausnitzii, and Roseburia spp.; prebiotic bacteria including Lactobacillus spp. and Bifidobacteria spp.; and mucus-degrading bacteria including Akkermansia muciniphila, Bacteroides fragilis, and Ruminococcus spp., as well as calprotectin and lactoferrin levels, will be explored in fecal samples. Also, the Firmicutes to Bacteroidetes ratio which is of significant relevance in human gut microbiota composition will be assessed. DISCUSSION: Altered gut microbiota has been reported as an important contributing factor to inflammation in patients with inflammatory bowel disease (IBD). Soy milk contains several components such as phytoestrogens with potential anti-inflammatory properties. This product might affect gut microbiota through its protein and fiber content. Therefore, soy milk might beneficially affect systemic inflammation, gut microbiota, and then clinical symptoms in patients with UC. TRIAL REGISTRATION: Iranian Registry of Clinical Trials (www.irct.ir) IRCT20181205041859N1. Registered on 27 January 2019.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36484910", + "title": "Dark-purple rice extract modulates gut microbiota composition in acetic acid- and indomethacin-induced inflammatory bowel disease in rats.", + "year": 2023, + "journal": "International microbiology : the official journal of the Spanish Society for Microbiology", + "authors": [ + "Thipart K", + "Gruneck L", + "Phunikhom K", + "Sharpton TJ", + "Sattayasai J", + "Popluechai S" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.5448053773469497, + "mesh_terms": [ + "Animals", + "Rats", + "Oryza", + "Gastrointestinal Microbiome", + "Acetic Acid", + "Indomethacin", + "RNA, Ribosomal, 16S", + "Anthocyanins", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Colitis, Ulcerative", + "Bacteria" + ], + "raw_abstract": "Ulcerative colitis (UC) and Crohn's disease (CD) are two major forms of inflammatory bowel disease (IBD). The disease has been linked with gut microbiota dysbiosis in which the balance of commensal communities is disrupted. Accumulating evidence demonstrates that treatment with biologically active compounds can modulate gut microbiota composition in animal models. Our previous work has also shown the beneficial effect of Luem Pua (LP) rice extract, which is rich in anthocyanins, on inflammation. However, its effect on gut microbiota is yet to be explored. In this study, we profiled fecal microbiota of acetic acid (AA)-induced UC and indomethacin (ID)-induced CD rat models with and without pretreatment with LP rice extract by 16S rRNA gene sequencing. The results showed that gut microbiota communities of rats were altered by both AA-induced UC and ID-induced CD. The relative abundances of beneficial bacteria, especially the Lachnospiraceae NK4A136 group and Lactobacillus, were decreased in the AA-induced UC model, while some opportunistic pathogens (Bacteroides, Escherichia/Shigella, Fusobacterium, and Veillonella) were raised by ID-induced CD. Interestingly, pretreatment with LP rice extract before AA-inducing UC in rats increased the proportion of the butyrate-producing bacteria (Lachnospiraceae NK4A136 group). The abundances of these beneficial bacteria and other SCFA-producing bacteria were unaffected by the indomethacin treatment with LP. Overall, our study revealed different impacts of AA-induced UC and ID-induced CD on changes in community composition and hinted at how LP may protect against UC by modifying the gut microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26839545", + "title": "Quantitative Analysis of Intestinal Flora of Uygur and Han Ethnic Chinese Patients with Ulcerative Colitis.", + "year": 2016, + "journal": "Gastroenterology research and practice", + "authors": [ + "Yao P", + "Cui M", + "Wang H", + "Gao H", + "Wang L", + "Yang T", + "Cheng Y" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.5239886563650639, + "mesh_terms": [], + "raw_abstract": "Aim. To study the correlation between intestinal flora and ulcerative colitis by analyzing the abundance of Bacteroides, Fusobacterium, Clostridium, Bifidobacterium spp., and Faecalibacterium prausnitzii in the intestinal of ulcerative colitis (UC) patients and healthy controls with Uygur and Han ethnic. Methods. Bacterial genomic DNA was extracted from fecal samples and analyzed with real-time fluorescence quantitative polymerase chain reaction (PCR) to identify the abundance of Bacteroides, Fusobacterium, Clostridium, Bifidobacterium spp., and Faecalibacterium prausnitzii. Results. The samples from UC patients, Uygur and Han ethnic combined, had higher abundance of Bacteroides (P = 0.026) but lower Clostridium (P = 0.004), Bifidobacterium spp. (P = 0.009), and Faecalibacterium prausnitzii (P = 0.008) than those from healthy controls. Among UC patients, Bacteroides population was raised in acute UC patients (P \u2264 0.05), while the abundance of Clostridium, Bifidobacterium spp., Fusobacterium, and Faecalibacterium prausnitzii decreased (P \u2264 0.05) compared with the remission. In both UC patients group and control group, no difference was observed in the abundance of these 5 bacteria between the Han and the Uygur group. Conclusions. Variations in the abundance of these five bacterial strains in intestines may be associated with the occurrence of UC in Uygur and Han populations; however, these variations were not associated with ethnic difference.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30763538", + "title": "Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis.", + "year": 2019, + "journal": "Cell host & microbe", + "authors": [ + "Gogokhia L", + "Buhrke K", + "Bell R", + "Hoffman B", + "Brown DG", + "Hanke-Gogokhia C", + "Ajami NJ", + "Wong MC", + "Ghazaryan A", + "Valentine JF", + "Porter N", + "Martens E", + "O'Connell R", + "Jacob V", + "Scherl E", + "Crawford C", + "Stephens WZ", + "Casjens SR", + "Longman RS", + "Round JL" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.4966259174852292, + "mesh_terms": [ + "Animals", + "Bacteria", + "Bacteriophages", + "CD4-Positive T-Lymphocytes", + "Colitis, Ulcerative", + "Colorectal Neoplasms", + "Disease Models, Animal", + "Fecal Microbiota Transplantation", + "Gastrointestinal Microbiome", + "Humans", + "Interferon-gamma", + "Intestinal Mucosa", + "Mice", + "Mice, Inbred C57BL", + "Mice, Knockout", + "Pilot Projects", + "Prospective Studies", + "Specific Pathogen-Free Organisms" + ], + "raw_abstract": "Bacteriophages are the most abundant members of the microbiota and have the potential to shape gut bacterial communities. Changes to bacteriophage composition are associated with disease, but how phages impact mammalian health remains unclear. We noted an induction of host immunity when experimentally treating bacterially driven cancer, leading us to test whether bacteriophages alter immune responses. Treating germ-free mice with bacteriophages leads to immune cell expansion in the gut. Lactobacillus, Escherichia, and Bacteroides bacteriophages and phage DNA stimulated IFN-\u03b3 via the nucleotide-sensing receptor TLR9. The resultant immune responses were both phage and bacteria specific. Additionally, increasing bacteriophage levels exacerbated colitis via TLR9 and IFN-\u03b3. Similarly, ulcerative colitis (UC) patients responsive to fecal microbiota transplantation (FMT) have reduced phages compared to non-responders, and mucosal IFN-\u03b3 positively correlates with bacteriophage levels. Bacteriophages from active UC patients induced more IFN-\u03b3 compared to healthy individuals. Collectively, these results indicate that bacteriophages can alter mucosal immunity to impact mammalian health.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35568112", + "title": "Study on the mechanism of Huangqin Decoction on rats with ulcerative colitis of damp-heat type base on mtDNA, TLR4, p-PI3K, p-Akt protein expression and microbiota.", + "year": 2022, + "journal": "Journal of ethnopharmacology", + "authors": [ + "Zheng Y", + "Liang C", + "Li Z", + "Chen J", + "Chen Z", + "Jiang Y", + "Dong Q", + "Xiao Y", + "Fu C", + "Liao W", + "Yuan X" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.4914754087088629, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "DNA, Mitochondrial", + "Dextran Sulfate", + "Disease Models, Animal", + "Gastrointestinal Microbiome", + "Hot Temperature", + "Interleukin-17", + "Interleukin-23", + "Interleukin-6", + "Phosphatidylinositol 3-Kinases", + "Proto-Oncogene Proteins c-akt", + "Rats", + "Scutellaria baicalensis", + "Toll-Like Receptor 4" + ], + "raw_abstract": "ETHNOPHARMACOLOGICAL RELEVANCE: Huangqin decoction (HQD), composed of Scutellaria(Huangqin), Peony(Shaoyao), Liquorice(Gancao) and Jujube(Dazao), is a traditional Chinese medicine prescription, originated from treatise on Febrile Diseases, has the functions of clearing heat, stopping benefits and relieving pain. It is the original prescription for treating heat and relieving dysentery, and is commonly used in clinic for diarrhea and other diseases. In ulcerative colitis, damp-heat syndrome is the most common. However, its mechanism of action is not completely clear. AIMS OF THE REVIEW: The purpose of the research is to investigate the protective effect of HQD on ulcerative colitis rats and the regulation effect of mitochondrial DNA, TLR4, p-Akt, p-PI3K protein and microbiota. MATERIALS AND METHODS: The effects of HQD anti-UC were investigated by fluorescence quantitative PCR, cytokine level and histopathological analysis in DSS-induced ulcerative colitis (UC) rats. The content of mtDNA in colon epithelial cells of rats in each group was detected by fluorescence quantitative PCR, p-PI3K, p-Akt and TLR4 protein expressions in colon tissues of rats in each group were detected by Western blotting. IL-6, IL-17 and IL-23 inflammatory factors were detected by ELISA. The effect of HQD on intestinal microbiota of rats with ulcerative colitis was studied by high-throughput sequencing technology, and the correlation between mtDNA level and inflammatory factors as well as protein expression in colonic epithelium of rats with ulcerative colitis was analyzed by SPSS23.0. RESULTS: HQD significantly alleviated UC symptoms by improving the mucosal intestinal epithelial cell structure, mental state, hair gloss, fecal occult blood, lamina propria intestinal glands and inflammatory cell infiltration. And HQD reduced the pro-inflammatory cytokines in the colonic epithelium of UC rats Production of IL-6, IL-17 and IL-23. The HE stained section of colon tissue showed a complete intestinal epithelial mucosal layer structure. The structure of epithelial cells was more normal and abundant. There were more goblet cells in lamina propria adenoma, which improved the infiltration of inflammatory cells. HQD significantly inhibited the mtDNA content in rat colonic epithelial tissue, and significantly inhibited the expression of TLR4, p-PI3K and p-Akt inflammatory signaling pathways. The results of the microbiota experiment showed that the abundance of HQD in the phylum Firmicutes increased, and the number of Bacteroides phylum decreased (p\u00a0<\u00a00.05). At the genus level, HQD significantly increased Lactobacillus and Firmicutes Bacteroides, while Treponema and Bacteroides were significantly reduced (p\u00a0<\u00a00.05). CONCLUSION: HQD has a certain protective effect on rats with damp heat ulcerative colitis. Its mechanism may be related to regulating the expression of p-PI3K, p-Akt and TLR4 proteins, mitochondrial DNA as well as microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36649193", + "title": "Microbiota DNA Translocation Into Mesentery Lymph Nodes Is Associated With Early Development of Pouchitis After IPAA for Ulcerative Colitis.", + "year": 2023, + "journal": "Diseases of the colon and rectum", + "authors": [ + "Zhao L", + "Zhu F", + "Chen J", + "Wang Z", + "Zhang T", + "Yu Z", + "Xu Y", + "Ding C", + "Gong J" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.4902748462943649, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Pouchitis", + "Proctocolectomy, Restorative", + "Mesentery", + "Male", + "Female", + "Adult", + "Bacterial Translocation", + "Lymph Nodes", + "Prospective Studies", + "Gastrointestinal Microbiome", + "Case-Control Studies", + "DNA, Bacterial", + "Middle Aged", + "Postoperative Complications" + ], + "raw_abstract": "BACKGROUND: The role of bacterial translocation in Crohn's disease has been extensively studied. However, data regarding bacterial translocation into the mesentery in patients with ulcerative colitis were scarce. OBJECTIVE: This study aimed to explore the relationship between bacterial translocation and postoperative outcome by comparing the microbiome profile of different anatomical sites in patients with ulcerative colitis who underwent proctocolectomy and IPAA. DESIGN: A prospective study. SETTING: This study was conducted at the Jinling Hospital from August 2017 to May 2018. PATIENTS: Samples of 27 patients with ulcerative colitis who had IPAA and 15 healthy controls who underwent routine colonoscopy were collected. MAIN OUTCOME MEASURES: The microbiome profile of different tissue sites and short- and long-term outcomes after IPAA in patients with ulcerative colitis. RESULTS: Bacterial DNA was detected in mesenteric lymph nodes of 51.9% of patients with ulcerative colitis (14/27) and in mesenteric adipose tissue of 66.7% of patients (18/27). The microbiome in mesenteric lymph nodes and mesenteric adipose tissue resembled the mucosal microbiome to a greater extent than the fecal microbiome. Positive bacterial DNA in mesenteric lymph nodes (8/14 vs 0/13; p = 0.002) was associated with pouchitis within 12 months after IPAA, whereas Bray-Curtis distance in mesenteric lymph nodes was significantly different between patients with pouchitis and without ( p = 0.009). LIMITATIONS: This study was limited by its small sample size and lacked situ experiment to confirm the true bacterial translation. CONCLUSIONS: Bacterial translocation was highly prevalent in patients with ulcerative colitis. The translocated bacteria DNA in mesenteric adipose tissue and mesenteric lymph nodes was highly correlated and more likely to originate from mucosal than fecal microbiome. Also, the extent of bacterial translocation and translocation of certain bacteria might be associated with the early development of pouchitis after IPAA. This might represent an unprecedented technique to predict pouchitis using mesenteric lymph node bacterial profiles. See Video Abstract at http://links.lww.com/DCR/C119 . LA TRANSLOCACIN DEL ADN DE LA MICROBIOTA EN LOS GANGLIOS LINFTICOS DEL MESENTERIO SE ASOCIA CON EL DESARROLLO TEMPRANO DE POUCHITIS DESPUS DE IPAA PARA LA COLITIS ULCEROSA: ANTECEDENTES:El papel de la translocaci\u00f3n bacteriana en la enfermedad de Crohn se ha estudiado ampliamente en los \u00faltimos a\u00f1os. Sin embargo, los datos sobre la translocaci\u00f3n bacteriana en el mesenterio en pacientes con colitis ulcerosa fueron escasos.OBJETIVO:El objetivo de este estudio fue explorar la relaci\u00f3n entre la translocaci\u00f3n bacteriana y el resultado postoperatorio comparando el perfil del microbioma de diferentes sitios anat\u00f3micos en pacientes con colitis ulcerosa que se sometieron a proctocolectom\u00eda y anastomosis ileoanal con bolsa.DISE\u00d1O:Estudio prospectivo.AJUSTE:Este estudio se realiz\u00f3 en el Hospital Jinling desde agosto de 2017 hasta mayo de 2018.PACIENTES:Se recogieron muestras de 27 pacientes con colitis ulcerosa que ten\u00edan anastomosis de bolsa ileoanal y 15 controles sanos que se sometieron a una colonoscopia de rutina.PRINCIPALES MEDIDAS DE RESULTADO:El perfil del microbioma de diferentes sitios de tejido y los resultados a corto y largo plazo despu\u00e9s de la anastomosis ileoanal con bolsa en pacientes con colitis ulcerosa.RESULTADOS:Se detect\u00f3 ADN bacteriano en los ganglios linf\u00e1ticos mesent\u00e9ricos del 51,9 % (14/27) de los pacientes con colitis ulcerosa y en el tejido adiposo mesent\u00e9rico del 66,7 % (18/27) de los pacientes, respectivamente. El microbioma en los ganglios linf\u00e1ticos mesent\u00e9ricos y el tejido adiposo mesent\u00e9rico se parec\u00eda m\u00e1s al microbioma de la mucosa que al microbioma fecal. El ADN bacteriano translocado en los ganglios linf\u00e1ticos mesent\u00e9ricos y el tejido adiposo mesent\u00e9rico estaban altamente correlacionados. El ADN bacteriano positivo en los ganglios linf\u00e1ticos mesent\u00e9ricos (8/14 frente a 0/13, p = 0,002) se asoci\u00f3 con reservoritis dentro de los 12 meses posteriores a la anastomosis ileoanal con reservorio, mientras que la distancia de Bray-Curtis en los ganglios linf\u00e1ticos mesent\u00e9ricos fue significativamente diferente entre reservoritis y no reservorios. -pacientes con reservorio (p = 0,009). Ruminococcus, Bacteroides y Clostridiales se encontraron exclusivamente en los ganglios linf\u00e1ticos mesent\u00e9ricos de pacientes con reservoritis.LIMITACI\u00d3N:Este estudio estuvo limitado por el peque\u00f1o tama\u00f1o de la muestra y la falta de un experimento in situ para confirmar la verdadera traducci\u00f3n bacteriana.CONCLUSI\u00d3N:La translocaci\u00f3n bacteriana fue altamente prevalente en pacientes con colitis ulcerosa. El ADN bacteriano translocado en el tejido adiposo mesent\u00e9rico y los ganglios linf\u00e1ticos mesent\u00e9ricos estaba altamente correlacionado y era m\u00e1s probable que se originara en el microbioma de la mucosa que en el fecal. Adem\u00e1s, la extensi\u00f3n de la translocaci\u00f3n bacteriana y la translocaci\u00f3n de ciertas bacterias podr\u00eda estar asociada con el desarrollo temprano de reservoritis despu\u00e9s de la anastomosis del reservorio ileoanal. Esto podr\u00eda representar una t\u00e9cnica sin precedentes para predecir la reservoritis utilizando perfiles bacterianos de los ganglios linf\u00e1ticos mesent\u00e9ricos. Consulte Video Resumen en. http://links.lww.com/DCR/C119(Traducci\u00f3n-Dr. Felipe Bellolio ).", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31771630", + "title": "A distinct gut microbiota composition in patients with ankylosing spondylitis is associated with increased levels of fecal calprotectin.", + "year": 2019, + "journal": "Arthritis research & therapy", + "authors": [ + "Klingberg E", + "Magnusson MK", + "Strid H", + "Deminger A", + "St\u00e5hl A", + "Sundin J", + "Simr\u00e9n M", + "Carlsten H", + "\u00d6hman L", + "Forsblad-d'Elia H" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.48085006894621674, + "mesh_terms": [ + "Adult", + "Bacteria", + "C-Reactive Protein", + "Colitis, Ulcerative", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Middle Aged", + "Population Dynamics", + "Spondylitis, Ankylosing", + "Surveys and Questionnaires", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Ankylosing spondylitis (AS) shares many characteristics with inflammatory bowel disease (IBD). Intestinal microbiota most likely plays an important role in the development of IBDs and may also be involved in the pathogenesis of AS. We aimed to define and compare the fecal microbiota composition in patients with AS, ulcerative colitis (UC), and healthy controls (HC) and to determine relationships between fecal microbiota, fecal calprotectin, and disease-related variables in AS. METHODS: Fecal microbiota composition was assessed with GA-map\u2122 Dysbiosis Test (Genetic Analysis, Oslo, Norway), which also reports the degree of deviation of the microbiota composition compared with a healthy control population, a Dysbiosis Index (DI) score 1-5. The AS patients were assessed with questionnaires, back mobility tests, fecal calprotectin, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP). RESULTS: Totally, 150 patients with AS (55% men, median age 55.5\u2009years, median BASDAI 3.2), 18 patients with UC (56% men, median age 30.5\u2009years), and 17 HC (65% men, median age 22\u2009years) were included. Principal component analysis showed highly separate clustering of fecal microbiota from the patients with AS, UC, and HC. Compared with HC, fecal microbiota in AS was characterized by a higher abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcus species, and Actinobacteria, but lower abundance of Bacteroides and Lachnospiraceae. Further, fecal microbiota composition differed between patients with normal (\u2264\u200950\u2009mg/kg, n\u2009=\u200957) and increased (\u2265\u2009200\u2009mg/kg, n\u2009=\u200936) fecal calprotectin. Patients with increased fecal calprotectin had lower abundance of bacteria with anti-inflammatory properties such as Faecalibacterium prausnitzii and Clostridium and higher abundance of the genus Streptococcus. No association was found between the fecal microbiota composition and HLAB27 status, disease activity, function, or medication. Dysbiosis (defined as DI\u2009\u2265\u20093) was found in 87% of AS patients. CONCLUSIONS: Patients with AS have a distinct fecal microbiota signature, which is linked to fecal calprotectin levels, a marker of intestinal inflammation, but not to other clinical parameters. These findings suggest a local interplay between intestinal microbiota and gut inflammation in AS. TRIAL REGISTRATION: ClinicalTrials.gov, NCT00858819. Registered March 9, 2009.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28683448", + "title": "Gut Microbiota in Health, Diverticular Disease, Irritable Bowel Syndrome, and Inflammatory Bowel Diseases: Time for Microbial Marker of Gastrointestinal Disorders.", + "year": 2018, + "journal": "Digestive diseases (Basel, Switzerland)", + "authors": [ + "Lopetuso LR", + "Petito V", + "Graziani C", + "Schiavoni E", + "Paroni Sterbini F", + "Poscia A", + "Gaetani E", + "Franceschi F", + "Cammarota G", + "Sanguinetti M", + "Masucci L", + "Scaldaferri F", + "Gasbarrini A" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.47915727452760515, + "mesh_terms": [ + "Adult", + "Biomarkers", + "Diverticular Diseases", + "Female", + "Gastrointestinal Microbiome", + "Health", + "Humans", + "Inflammatory Bowel Diseases", + "Irritable Bowel Syndrome", + "Male", + "Middle Aged", + "Phylogeny", + "Principal Component Analysis", + "Species Specificity" + ], + "raw_abstract": "Few data exist on differences in gut microbiota composition among principal gastrointestinal (GI) diseases. We evaluated the differences in gut microbiota composition among uncomplicated diverticular disease (DD), irritable bowel syndrome (IBS) and inflammatory bowel diseases (IBD) patients. DD, IBS, and IBD patients along with healthy controls (CT) were enrolled in our Italian GI outpatient clinic. Stool samples were collected. Microbiota composition was evaluated through a metagenomic gene-targeted approach. GI pathology represented a continuous spectrum of diseases where IBD displayed one extreme, while CT displayed the other. Among Phyla, Biplot PC2/PC3 and dendogram plot showed major differences in samples from IBS and IBD. DD resembled species CT composition, but not for Bacteroides fragilis. In IBS, Dialister spp. and then Faecalibacterium prausnitzii were the most representative species. Ulcerative colitis showed a reduced concentration of Clostridium difficile and an increase of Bacteroides fragilis. In Crohn's disease, Parabacteroides distasonis was the most represented, while Faecalibacterium prausnitzii and Bacteroides fragilis were significantly reduced. Each disorder has its definite overall microbial signature, which produces a clear differentiation from the others. On the other hand, shared alterations constitute the \"core dysbiosis\" of GI diseases. The assessment of these microbial markers represents a parameter that may complete the diagnostic assessment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26423113", + "title": "Specific members of the predominant gut microbiota predict pouchitis following colectomy and IPAA in UC.", + "year": 2017, + "journal": "Gut", + "authors": [ + "Machiels K", + "Sabino J", + "Vandermosten L", + "Joossens M", + "Arijs I", + "de Bruyn M", + "Eeckhaut V", + "Van Assche G", + "Ferrante M", + "Verhaegen J", + "Van Steen K", + "Van Immerseel F", + "Huys G", + "Verbeke K", + "Wolthuis A", + "de Buck Van Overstraeten A", + "D'Hoore A", + "Rutgeerts P", + "Vermeire S" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.4747223301240291, + "mesh_terms": [ + "Adult", + "Bacteroidetes", + "Clostridium perfringens", + "Cluster Analysis", + "Colitis, Ulcerative", + "Colonic Pouches", + "DNA, Bacterial", + "Fatty Acids, Volatile", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "Middle Aged", + "Pouchitis", + "Predictive Value of Tests", + "Preoperative Period", + "Proctocolectomy, Restorative", + "Prospective Studies", + "Ruminococcus", + "Time Factors" + ], + "raw_abstract": "OBJECTIVE: Pouchitis is the most common complication after colectomy with ileal pouch-anal anastomosis (IPAA) for UC and the risk is the highest within the 1st year after surgery. The pathogenesis is not completely understood but clinical response to antibiotics suggests a role for gut microbiota. We hypothesised that the risk for pouchitis can be predicted based on the faecal microbial composition before colectomy. DESIGN: Faecal samples from 21 patients with UC undergoing IPAA were prospectively collected before colectomy and at predefined clinical visits at 1 month, 3 months, 6 months and 12\u2005months after IPAA. The predominant microbiota was analysed using community profiling with denaturing gradient gel electrophoresis followed by quantitative real-time PCR validation. RESULTS: Cluster analysis before colectomy distinguished patients with pouchitis from those with normal pouch during the 1st year of follow-up. In patients developing pouchitis, an increase of Ruminococcus gnavus (p<0.001), Bacteroides vulgatus (p=0.043), Clostridium perfringens (p=0.011) and a reduction of two Lachnospiraceae genera (Blautia (p=0.04), Roseburia (p=0.008)) was observed. A score combining these five bacterial risk factors was calculated and presence of at least two risk factors showed a sensitivity and specificity of 100% and 63.6%, respectively. CONCLUSIONS: Presence of R. gnavus, B. vulgatus and C. perfringens and absence of Blautia and Roseburia in faecal samples of patients with UC before surgery is associated with a higher risk of pouchitis after IPAA. Our findings suggest new predictive and therapeutic strategies in patients undergoing colectomy with IPAA.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35660786", + "title": "Systematic review of donor and recipient predictive biomarkers of response to faecal microbiota transplantation in patients with ulcerative colitis.", + "year": 2022, + "journal": "EBioMedicine", + "authors": [ + "Rees NP", + "Shaheen W", + "Quince C", + "Tselepis C", + "Horniblow RD", + "Sharma N", + "Beggs AD", + "Iqbal TH", + "Quraishi MN" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.4658834842330747, + "mesh_terms": [ + "Biomarkers", + "Colitis, Ulcerative", + "Fecal Microbiota Transplantation", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND: Faecal microbiota transplantation (FMT) has previously been explored as a treatment for ulcerative colitis (UC) however, biomarkers that predict and / or are associated with clinical response are poorly defined. The aim of this systematic review was to identify donor and recipient clinical, microbial and metabolomic predictive biomarkers of response to FMT in UC. METHODS: A systematic search of the relevant literature of studies exploring FMT in UC was conducted. Data on microbial diversity, taxonomic changes, metabolic changes, donor and recipient microbiota relationship and baseline predictors was examined. FINDINGS: 2852 studies were screened, and 25 papers were included in this systematic review. Following FMT, alpha diversity was seen to increase in responders along with increases in the abundance of Clostridiales clusters (order) and Bacteroides genus. Metabolomic analysis revealed short chain fatty acid (SCFA) production as a marker of FMT success. Donors or FMT batches with higher microbial alpha diversity and a greater abundance of taxa belonging to certain Bacteroides and Clostridia clusters were associated with clinical response to FMT. Baseline clinical predictors of response in patients with UC included younger age, less severe disease and possibly shorter disease duration. Baseline recipient microbial predictors at response consisted of higher faecal species richness, greater abundance of Candida and donor microbial profile similarity. INTERPRETATION: Distinct changes in gut microbiota profiles post-FMT indicate that certain baseline characteristics along with specific microbial and metabolomic alterations may predispose patients towards a successful therapeutic outcome. Opportunities towards a biomarker led precision medicine approach with FMT should be explored in future clinical studies. FUNDING: There no specific funding to declare.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34627951", + "title": "Bacteroides fragilis restricts colitis-associated cancer via negative regulation of the NLRP3 axis.", + "year": 2021, + "journal": "Cancer letters", + "authors": [ + "Shao X", + "Sun S", + "Zhou Y", + "Wang H", + "Yu Y", + "Hu T", + "Yao Y", + "Zhou C" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.456572977057962, + "mesh_terms": [ + "Animals", + "Bacteroides fragilis", + "Butyrates", + "Colitis, Ulcerative", + "Colitis-Associated Neoplasms", + "Dysbiosis", + "Fatty Acids, Volatile", + "Gastrointestinal Microbiome", + "Humans", + "Macrophages", + "Male", + "Mice", + "Mice, Inbred C57BL", + "NLR Family, Pyrin Domain-Containing 3 Protein" + ], + "raw_abstract": "Patients with persistent ulcerative colitis (UC) are at a higher risk of developing colitis-associated cancer (CAC). Previous studies have reported that intestinal microbiota disturbance plays an important role in the process of CAC development in patients with UC, indicating that targeted intervention of intestinal microbiota and its metabolites may be a potential therapeutic strategy. Gut microbiota in the process of colorectal cancer development in UC patients was analyzed using the gutMEGA database and verified in fecal samples. The abundance of Bacteroides fragilis reduced significantly in the process of colitis associated cancer development. Broad-spectrum antibiotics (BSAB) intervene with the intestinal microbiota of mice and accelerate the process of colon cancer development. However, gavage transplantation with B. fragilis can effectively reverse the effects of BSAB. In the intestinal tract, B. fragilis promotes the secretion of short-chain fatty acids (SCFAs). Subsequently, SCFAs, especially butyrate, negatively regulate the inflammatory signaling pathway mediated by NLRP3 to inhibit the activation of macrophages and the secretion of proinflammatory mediators such as IL-18 and IL-1\u03b2, reducing the level of intestinal inflammation and restricting CAC development. In conclusion, colonization with B. fragilis has been shown to be effective in ameliorating intestinal epithelial damage caused by chronic inflammation and preventing the development of colonic tumors. Thus, it can be a therapeutic intervention strategy with good clinical application prospects.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "29311644", + "title": "Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.", + "year": 2018, + "journal": "Nature microbiology", + "authors": [ + "Schirmer M", + "Franzosa EA", + "Lloyd-Price J", + "McIver LJ", + "Schwager R", + "Poon TW", + "Ananthakrishnan AN", + "Andrews E", + "Barron G", + "Lake K", + "Prasad M", + "Sauk J", + "Stevens B", + "Wilson RG", + "Braun J", + "Denson LA", + "Kugathasan S", + "McGovern DPB", + "Vlamakis H", + "Xavier RJ", + "Huttenhower C" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.45259503835603765, + "mesh_terms": [ + "Adolescent", + "Adult", + "Child", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Gene Expression Profiling", + "Humans", + "Inflammatory Bowel Diseases", + "Longitudinal Studies", + "Male", + "Metagenomics", + "Phenotype", + "Transcription, Genetic", + "Young Adult" + ], + "raw_abstract": "Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Genetic, environmental and microbial factors have been implicated in the onset and exacerbation of IBD. However, the mechanisms associating gut microbial dysbioses and aberrant immune responses remain largely unknown. The integrative Human Microbiome Project seeks to close these gaps by examining the dynamics of microbiome functionality in disease by profiling the gut microbiomes of >100 individuals sampled over a 1-year period. Here, we present the first results based on 78 paired faecal metagenomes\u00a0and\u00a0metatranscriptomes, and 222 additional metagenomes from 59 patients with Crohn's disease, 34 with ulcerative colitis and 24 non-IBD control patients. We demonstrate several cases in which measures of microbial gene expression in the inflamed gut can be informative relative to metagenomic profiles of functional potential. First, although many microbial organisms exhibited concordant DNA and RNA abundances, we also detected species-specific biases in transcriptional activity, revealing predominant transcription of pathways by individual microorganisms per host (for example, by Faecalibacterium prausnitzii). Thus, a loss of these organisms in disease may have more far-reaching consequences than suggested by their genomic abundances. Furthermore, we identified organisms that were metagenomically abundant but inactive or dormant in the gut with little or no expression (for example, Dialister invisus). Last, certain disease-specific microbial characteristics were more pronounced or only detectable at the transcript level, such as pathways that were predominantly expressed by different organisms in patients with IBD (for example, Bacteroides vulgatus and Alistipes putredinis). This provides potential insights into gut microbial pathway transcription that can vary over time, inducing phenotypical changes that are complementary to those linked to metagenomic abundances. The study's results highlight the strength of analysing both the activity and the presence of gut microorganisms to provide insight into the role of the microbiome in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37940667", + "title": "Inflammatory bowel disease biomarkers revealed by the human gut microbiome network.", + "year": 2023, + "journal": "Scientific reports", + "authors": [ + "Hu M", + "Caldarelli G", + "Gili T" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.43620764460829736, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Crohn Disease", + "Microbiota", + "Colitis, Ulcerative", + "Biomarkers", + "Escherichia coli" + ], + "raw_abstract": "Inflammatory bowel diseases (IBDs) are complex medical conditions in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when exposed to yet unclear environmental factors. The complexity of this class of diseases makes them suitable to be represented and studied with network science. In this paper, the metagenomic data of control, Crohn's disease, and ulcerative colitis subjects' gut microbiota were investigated by representing this data as correlation networks and co-expression networks. We obtained correlation networks by calculating Pearson's correlation between gene expression across subjects. A percolation-based procedure was used to threshold and binarize the adjacency matrices. In contrast, co-expression networks involved the construction of the bipartite subjects-genes networks and the monopartite genes-genes projection after binarization of the biadjacency matrix. Centrality measures and community detection were used on the so-built networks to mine data complexity and highlight possible biomarkers of the diseases. The main results were about the modules of Bacteroides, which were connected in the control subjects' correlation network, Faecalibacterium prausnitzii, where co-enzyme A became central in IBD correlation networks and Escherichia coli, whose module has different patterns of integration within the whole network in the different diagnoses.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35999575", + "title": "Location-specific signatures of Crohn's disease at a multi-omics scale.", + "year": 2022, + "journal": "Microbiome", + "authors": [ + "Gonzalez CG", + "Mills RH", + "Zhu Q", + "Sauceda C", + "Knight R", + "Dulai PS", + "Gonzalez DJ" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.40210338415399577, + "mesh_terms": [ + "Bile Acids and Salts", + "Crohn Disease", + "Cross-Sectional Studies", + "Feces", + "Humans", + "Metagenomics", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Crohn's disease (CD), an inflammatory bowel disease (IBD) subtype, results from pathologic interactions between host cells and its resident gut microbes. CD manifests in both isolated disease locations (ileum or colon) or a combination of locations (ileocolonic). To date, a comprehensive understanding of how isolated CD subtypes influence molecular profiles remains outstanding. To address this, we sought to define CD location signatures by leveraging a large cross-sectional feature set captured from the stool of over 200 IBD patients and healthy controls using metaproteomics, shotgun metagenomics, 16S rRNA sequencing, metabolomic profiling, and host genetics paired with clinical endoscopic assessments. RESULTS: Neither metagenomic nor host genetics alone distinguished CD location subtypes. In contrast, ileal and colonic CD were distinguished using mass spectrometry-based methods (metabolomics or metaproteomics) or a combined multi-omic feature set. This multi-omic feature set revealed colonic CD was strongly associated with neutrophil-related proteins. Additionally, colonic CD displayed a disease-severity-related association with Bacteroides vulgatus. Colonic CD and ulcerative colitis profiles harbored strikingly similar feature enrichments compared to ileal CD, including neutrophil-related protein enrichments. Compared to colonic CD, ileal CD profiles displayed increased primary and secondary bile acid levels and concomitant shifts in taxa with noted sensitivities such as Faecalibacterium prausnitzii or affinities for bile acid-rich environments, including Gammaproteobacteria and Blautia sp. Having shown robust molecular and microbial distinctions tied to CD locations, we leveraged these profiles to generate location-specific disease severity biomarkers that surpass the performance of Calprotectin. CONCLUSIONS: When compared using multi-omics features, colonic- and ileal-isolated CD subtypes display striking differences that suggest separate location-specific pathologies. Colonic CD's strong similarity to ulcerative colitis, including neutrophil and Bacteroides vulgatus involvement, is also evidence of a shared pathology for colonic-isolated IBD subtypes, while ileal CD maintains a unique, bile acid-driven profile. More broadly, this study demonstrates the power of multi-omics approaches for IBD biomarker discovery and elucidating the underlying biology. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39740381", + "title": "Gingerols: Preparation, encapsulation, and bioactivities focusing gut microbiome modulation and attenuation of disease symptoms.", + "year": 2025, + "journal": "Phytomedicine : international journal of phytotherapy and phytopharmacology", + "authors": [ + "Abdullah", + "Ahmad N", + "Xiao J", + "Tian W", + "Khan NU", + "Hussain M", + "Ahsan HM", + "Hamed YS", + "Zhong H", + "Guan R" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.3958667585459114, + "mesh_terms": [ + "Gastrointestinal Microbiome", + "Humans", + "Catechols", + "Fatty Alcohols", + "Animals", + "Zingiber officinale", + "Phytochemicals", + "Dysbiosis", + "Anti-Inflammatory Agents" + ], + "raw_abstract": "BACKGROUND: Gut dysbiosis, chronic diseases, and microbial recurrent infections concerns have driven the researchers to explore phytochemicals from medicinal and food homologous plants to modulate gut microbiota, mitigate diseases, and inhibit pathogens. Gingerols have attracted attention as therapeutic agents due to their diverse biological activities like gut microbiome regulation, gastro-protective, anti-inflammatory, anti-microbial, and anti-oxidative effects. PURPOSE: This review aimed to summarize the gingerols health-promoting potential, specifically focusing on the regulation of gut microbiome, attenuation of disease symptoms, mechanisms of action, and signaling pathways involved. METHOD: Research findings from experimental and clinical studies have been summarized regarding gingerols effects on the modulation of gut microbiome and its metabolites, and attenuation of disease symptoms. RESULTS: Gingerols are phenolic compounds characterized by a common 3-methoxy-4-hydroxyphenyl moiety in their chemical structures, and further divided into different gingerol types, including gingerols (major), shogaols, paradols, gingerdiols, gingerdiones, and zingerones (minor). Advanced extraction techniques (e.g., ionic liquid-based-, enzyme-assisted-, microwave-assisted-, pressurized liquid-, ultrasound-assisted-, and supercritical fluid extractions) were reported as optimal alternatives to conventional methods for gingerols extraction. Research studies reported that gingerols positively modulated the composition of gut microbiome that helped to combat disease symptoms (e.g., obesity by decreasing weight gain- (Lactobacillus reuteri and Lachnospiraceae) and increasing weight loss associated-bacteria (Akkermansia, Muribaculaceae, and Alloprevotella). Gingerols intervention also ameliorated ulcerative colitis by increasing relative abundance of the beneficial bacteria (Akkermansia, Lachnospiraceae NK4A136, and Muribaculaceae_norank), and decreasing pathogenic microorganisms (Bacteroides, Parabacteroides, and Desulfovibrio). Emerging delivery systems (e.g., microcapsules, nanoparticles, nanostructured lipid carriers, nanoemulsions, and nanoliposomes) can enhance the bioavailability and therapeutic efficacy of gingerols by preserving their inherent properties and addressing challenges of stability, solubility, and absorption. CONCLUSION: Gingerols are promising therapeutic agents to modulate gut microbiome (increase beneficial bacteria and inhibit pathogenic microbes), and attenuate chronic disease symptoms such as diabetes, colitis, obesity, oxidative stress, and cancer. Despite significant progress, challenges persist in transforming research findings into industrial applications, such as stability and solubility during processing and low bioavailability in the distal gut to impart desirable health benefits.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39442743", + "title": "Gut Microbiota Features in Relation to Fecal Microbiota Transplantation Outcome in Ulcerative Colitis: A Systematic Review and Meta-Analysis.", + "year": 2024, + "journal": "Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association", + "authors": [ + "B\u00e9nard MV", + "de Goffau MC", + "Blonk J", + "Hugenholtz F", + "van Buuren J", + "Paramsothy S", + "Kaakoush NO", + "D'Haens GRAM", + "Borody TJ", + "Kamm MA", + "Ponsioen CY" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.3829949186510492, + "mesh_terms": [], + "raw_abstract": "BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis, yet its efficacy needs improvement. We conducted a comprehensive evaluation of the current literature on microbial factors affecting outcome, as well as a meta-analysis on some of the largest datasets regarding composition. METHODS: MEDLINE, Embase, and Cochrane were systematically searched through August 2024 for relevant studies. The quality of studies was analyzed with JBI tools and a composite critical appraisal score. Additionally, species-level data from 2 landmark FMT trials (the Transplantation of Feces in Ulcerative Colitis; Returning Nature's Homeostasis [TURN] and Fecal Microbiota Transplantation for Chronic Active Ulcerative Colitis [FOCUS] trials) were reanalyzed from a compositional perspective. RESULTS: Out of 3755 citations identified, 56 met the inclusion criteria, of which 29 fulfilled quality standards. Higher microbial \u03b1-diversity, either in donors or recipients (at baseline or following FMT treatment), was associated with better clinical response rates. Engraftment of the donors' microbiota could not be clearly linked with clinical response, possibly because not every donor has an ideal microbiome. Butyrate-producing species from the Lachnospiraceae and Oscillospiraceae families were often related with response, whereas the reverse was true for Fusobacteria, many Proteobacteria, and Ruminococcus gnavus. Compositional analyses showed that clinical response is associated with a shift from a low-diversity, often Bacteroides-dominant composition to one with higher diversity, either dominated by various butyrate producers, the Christensenellaceae-Methanobrevibacter trophic network, or a moderate/high-diversity composition with abundant but not excessive levels of Prevotella copri. CONCLUSIONS: This systematic review/meta-analysis yielded a coherent picture from a compositional perspective, which may help identify beneficial donor profiles and guide personalized FMT approaches.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "26130823", + "title": "A retrospective metagenomics approach to studying Blastocystis.", + "year": 2015, + "journal": "FEMS microbiology ecology", + "authors": [ + "Andersen LO", + "Bonde I", + "Nielsen HB", + "Stensvold CR" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.34815727161910853, + "mesh_terms": [ + "Adult", + "Bacteroides", + "Blastocystis", + "Colitis, Ulcerative", + "Crohn Disease", + "Feces", + "Female", + "Humans", + "Male", + "Metagenomics", + "Middle Aged", + "Retrospective Studies" + ], + "raw_abstract": "Blastocystis is a common single-celled intestinal parasitic genus, comprising several subtypes. Here, we screened data obtained by metagenomic analysis of faecal DNA for Blastocystis by searching for subtype-specific genes in coabundance gene groups, which are groups of genes that covary across a selection of 316 human faecal samples, hence representing genes originating from a single subtype. The 316 faecal samples were from 236 healthy individuals, 13 patients with Crohn's disease (CD) and 67 patients with ulcerative colitis (UC). The prevalence of Blastocystis was 20.3% in the healthy individuals and 14.9% in patients with UC. Meanwhile, Blastocystis was absent in patients with CD. Individuals with intestinal microbiota dominated by Bacteroides were much less prone to having Blastocystis-positive stool (Matthew's correlation coefficient = -0.25, P < 0.0001) than individuals with Ruminococcus- and Prevotella-driven enterotypes. This is the first study to investigate the relationship between Blastocystis and communities of gut bacteria using a metagenomics approach. The study serves as an example of how it is possible to retrospectively investigate microbial eukaryotic communities in the gut using metagenomic datasets targeting the bacterial component of the intestinal microbiome and the interplay between these microbial communities.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38215655", + "title": "A metabolomics-driven model for early remission prediction following vedolizumab treatment in patients with moderate-to-severe active ulcerative colitis.", + "year": 2024, + "journal": "International immunopharmacology", + "authors": [ + "Jiang L", + "Liu X", + "Su Y", + "Chen Y", + "Yang S", + "Ke X", + "Yao K", + "Guo Z" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.3396844219774742, + "mesh_terms": [ + "Humans", + "Colitis, Ulcerative", + "Putrescine", + "Gastrointestinal Agents", + "Treatment Outcome", + "Remission Induction", + "Acetamides", + "Taurine", + "Retrospective Studies", + "Antibodies, Monoclonal, Humanized" + ], + "raw_abstract": "To predict early remission following anti-integrin therapy (vedolizumab [VDZ]) in patients with moderate-to-severe active ulcerative colitis (UC) using non-invasive biomarkers. The clinical data of a cohort of 33 patients with moderate-to-severe active UC admitted to the Department of Gastroenterology at Suzhou Municipal Hospital between January 2021 and December 2022 were collected. Of these, 9 patients declined VDZ treatment, and 21 received VDZ at doses of 300\u00a0mg\u00a0weeks 0, 2, and 6, each administered within a 30-minute infusion period. The treatment regimen aimed to induce remission of clinical symptoms; hence, the same dose was administered every 8\u00a0weeks. At weeks 0 and 14, serum C-reactive protein (CRP) and erythrocyte sedimentation rate were measured using a modified Mayo score. In addition to clinical assessment, stool samples at baseline and weeks 14 were collected and evaluated using 16SrRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS). Clinical remission was determined based on the clinical symptoms and partial Mayo scores. In patients who received VDZ, the strains of bifidobacterium longum (P\u00a0=\u00a00.022) and bacteroides sartorii (P\u00a0=\u00a00.039) significantly increased after treatment than before treatment. GC-MS analysis showed that taurine (P\u00a0=\u00a00.047) and putrescine (P\u00a0=\u00a00.035) significantly decreased after treatment. Furthermore, while acetamide exhibited a notable increase (P\u00a0=\u00a00.001), arachidic acid (P\u00a0<\u00a00.001) and behenic acid (P\u00a0=\u00a00.005) demonstrated statistically significant elevations. The combined prediction model of acetamide, taurine, and putrescine demonstrated a high predictive value of early remission in patients with moderate-to-severe active UC following VDZ treatment (area under the curve\u00a0=\u00a00.911, P\u00a0=\u00a00.014).", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27585552", + "title": "In\u00a0vitro analysis of partially hydrolyzed guar gum fermentation on identified gut microbiota.", + "year": 2016, + "journal": "Anaerobe", + "authors": [ + "Carlson J", + "Gould T", + "Slavin J" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.3340267679753812, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteroidetes", + "Colon", + "Culture Media", + "Dietary Fiber", + "Feces", + "Female", + "Fermentation", + "Galactans", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Hydrolysis", + "Male", + "Mannans", + "Middle Aged", + "Plant Gums", + "Prebiotics" + ], + "raw_abstract": "BACKGROUND: Prebiotic dietary fibers resist digestion in the upper gastrointestinal tract and allow for stimulation of bacteria in the distal intestine and colon. Stimulation of bacteria among different individuals varies greatly, depending on a wide range of variables. OBJECTIVE: To determine the range of differences in response between individuals, a preclinical in\u00a0vitro fermentation was conducted with six fecal donors. The primary objective was to compare the fecal microbiota of six individuals at baseline, 12\u00a0h and 24\u00a0h post-exposure to partially hydrolyzed guar gum (PHGG). METHOD: Fecal donations were collected from six healthy individuals consuming a non-specific Western diet, free of antibiotic treatments in the past year, not affected by any GI diseases and not consuming any probiotic or prebiotic supplements. Fecal samples were exposed to 0.5\u00a0g of PHGG and measured for bacterial changes at 0, 12 and 24\u00a0h based on 16S rRNA sequencing. RESULTS: Parabacteroides increased from 3.48% of sequence reads to 10.62% of sequence reads after 24\u00a0h (p\u00a0=\u00a00.0181) and Bacteroidetes increased from 45.89% of sequence reads to 50.29% of sequence reads (p\u00a0=\u00a00.0008). CONCLUSIONS: PHGG stimulates growth of Parabacteroides, a genus of bacteria that have been inversely associated with IBS and ulcerative colitis. PHGG provides stimulation of beneficial Bacteroidetes (Bacteroides and Parabacteroides), which may be correlated with many positive health markers and outcomes. PHGG is a prebiotic dietary fiber that is readily fermentable.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38735707", + "title": "Changes in intestinal microbiota and biochemical parameters in patients with inflammatory bowel disease and irritable bowel syndrome induced by the prolonged addition of soluble fibers to usual drug therapy.", + "year": 2024, + "journal": "The journal of medical investigation : JMI", + "authors": [ + "Watanabe H", + "Inoue T", + "Miyamoto L", + "Ono Y", + "Matsumoto K", + "Takeda M", + "Tsuchiya K" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.33287717576051185, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Irritable Bowel Syndrome", + "Male", + "Female", + "Dietary Fiber", + "Adult", + "Middle Aged", + "Mannans", + "Plant Gums", + "Galactans", + "Inflammatory Bowel Diseases", + "Feces", + "Fatty Acids, Volatile" + ], + "raw_abstract": "OBJECTIVES: Partially hydrolyzed guar gum (PHGG) is a soluble dietary fiber;in addition to improving bowel movements, it maintains intestinal health by producing short-chain fatty acids. However, majority of clinical studies on PHGG have been concluded within a month and excluded usual drug therapy. Hence, this study aimed to determine the effects of long-term consumption of PHGG, in combination with drug therapy, on gut bacteria ratios, laboratory values for inflammatory response, and fecal characteristics. METHODS AND RESULTS: The study was performed in patients with irritable bowel syndrome (IBS), Crohn's disease (CD), and ulcerative colitis (UC), by the administration of PHGG for six months while they continued their usual treatment. PHGG treatment caused significant changes in patients with IBS, including an increase in the abundance of short-chain fatty acid-producing bacteria, a significant decrease in Bacteroides abundance, and normalization of the Bristol scale of stool. In patients with UC, non-significant normalization of soft stools and decrease in fecal calprotectin were observed. Adverse events were not observed in any of the groups. CONCLUSION: Thus, it would be beneficial to include PHGG in the usual drug therapies of patients with IBS. J. Med. Invest. 71 : 121-128, February, 2024.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35273972", + "title": "A Randomized Placebo-Controlled Trial of Combination Therapy With Post-triple-antibiotic-therapy Fecal Microbiota Transplantation and Alginate for Ulcerative Colitis: Protocol.", + "year": 2022, + "journal": "Frontiers in medicine", + "authors": [ + "Ishikawa D", + "Zhang X", + "Nomura K", + "Seki N", + "Haraikawa M", + "Haga K", + "Shibuya T", + "Kim YG", + "Nagahara A" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.3303247347750435, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Fecal microbiota transplantation (FMT) has been widely performed for ulcerative colitis (UC) treatment at the clinical trial stage. Previous reports have used multiple FMT methods to enhance the colonization of healthy donor microbiota in the recipient's intestines. FMT following triple antibiotic therapy with amoxicillin, fosfomycin, and metronidazole (A-FMT) is not only effective but also requires only one FMT, which improves dysbiosis caused by reduced Bacteroidetes diversity in patients with UC. Alginate and its derivatives have the potential to induce the growth of intestinal bacteria including Bacteroides members and produce short-chain fatty acids (SCFAs), which are beneficial in regulating overactive autoimmunity. Our trial aims to investigate whether post-intervention with alginate, which can improve the intestinal environment, will enhance the therapeutic effect of A-FMT in UC and increase the long-term remission rate. METHODS AND ANALYSIS: This trial is a double-blinded, randomized, placebo-controlled, parallel assignment trial. Patients with UC and fecal donation candidates will undergo strict screening before being involved in the trial. Eligible patients are randomly divided into two groups: one group will drink one bottle of alginate twice a day for 8 consecutive weeks after A-FMT, while the other group will take a placebo instead of the alginate drink. The primary endpoints are the changes in the Total Mayo Score at 8 weeks after study initiation and A-FMT from baseline. The secondary endpoint is the comparison of clinical features, microbiota, and metabolomic analysis before and after 8 weeks of study food intake. Changes at 6, 12, 18, and 24 months after A-FMT will be assessed. Finally, a subpopulation analysis of the relationship between patients and donors is an exploratory endpoint. DISCUSSION: The FMT post-treatment used in this study is an oral alginate drink that is easily accepted by patients. If the regimen achieves the desired results, it can further improve the A-FMT regimen and provide evidence for clinical practice guidelines for UC. CLINICAL TRIAL REGISTRATION: https://jrct.niph.go.jp/latest-detail/jRCTs031200103, identifier: jRCTs031200103.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28583864", + "title": "The gut bacterium and pathobiont Bacteroides vulgatus activates NF-\u03baB in a human gut epithelial cell line in a strain and growth phase dependent manner.", + "year": 2017, + "journal": "Anaerobe", + "authors": [ + "\u00d3 Cu\u00edv P", + "de Wouters T", + "Giri R", + "Mondot S", + "Smith WJ", + "Blotti\u00e8re HM", + "Begun J", + "Morrison M" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.3288384606517788, + "mesh_terms": [ + "Bacteroides", + "Cell Line", + "Chemokine CCL2", + "Chemokine CXCL10", + "Epithelial Cells", + "Gastrointestinal Tract", + "Gene Expression", + "Host-Pathogen Interactions", + "Humans", + "Interleukin-6", + "Interleukin-8", + "NF-kappa B", + "Protein Transport", + "Up-Regulation" + ], + "raw_abstract": "The gut microbiota is increasingly implicated in the pathogenesis of Crohn's disease (CD) and ulcerative colitis (UC) although the identity of the bacteria that underpin these diseases has remained elusive. The pathobiont Bacteroides vulgatus has been associated with both diseases although relatively little is known about how its growth and functional activity might drive the host inflammatory response. We identified an ATP Binding Cassette (ABC) export system and lipoprotein in B.\u00a0vulgatus ATCC 8482 and B.\u00a0vulgatus PC510 that displayed significant sequence similarity to an NF-\u03baB immunomodulatory regulon previously identified on a CD-derived metagenomic fosmid clone. Interestingly, the ABC export system was specifically enriched in CD subjects suggesting that it may be important for colonization and persistence in the CD gut environment. Both B.\u00a0vulgatus ATCC 8482 and PC510 activated NF-\u03baB in a strain and growth phase specific manner in a HT-29/kb-seap-25 enterocyte like cell line. B.\u00a0vulgatus ATCC 8482 also activated NF-\u03baB in a Caco-2-NF-\u03baBluc enterocyte like and an LS174T-NF-\u03baBluc goblet cell like cell lines, and induced NF-\u03baB-p65 subunit nuclear translocation and IL-6, IL-8, CXCL-10 and MCP-1 gene expression. Despite this, NF-\u03baB activation was not coincident with maximal expression of the ABC exporter or lipoprotein in B.\u00a0vulgatus PC510 suggesting that the regulon may be necessary but not sufficient for the immunomodulatory effects.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38788915", + "title": "Rigorous Donor Selection for Fecal Microbiota Transplantation in Active Ulcerative Colitis: Key Lessons From a Randomized Controlled Trial Halted for Futility.", + "year": 2025, + "journal": "Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association", + "authors": [ + "Caenepeel C", + "Deleu S", + "Vazquez Castellanos JF", + "Arnauts K", + "Braekeleire S", + "Machiels K", + "Baert F", + "Mana F", + "Pouillon L", + "Hindryckx P", + "Lobaton T", + "Louis E", + "Franchimont D", + "Verstockt B", + "Ferrante M", + "Sabino J", + "Vieira-Silva S", + "Falony G", + "Raes J", + "Vermeire S" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.3123502380681619, + "mesh_terms": [ + "Humans", + "Fecal Microbiota Transplantation", + "Colitis, Ulcerative", + "Male", + "Female", + "Middle Aged", + "Adult", + "Double-Blind Method", + "Donor Selection", + "Treatment Outcome", + "Aged", + "Young Adult", + "Medical Futility" + ], + "raw_abstract": "BACKGROUND & AIMS: Rigorous donor preselection on microbiota level, strict anaerobic processing, and repeated fecal microbiota transplantation (FMT) administration were hypothesized to improve FMT induction of remission in ulcerative colitis (UC). METHODS: The RESTORE-UC trial was a multi-centric, double-blind, sham-controlled, randomized trial. Patients with moderate to severe UC (defined by total Mayo 4-10) were randomly allocated to receive 4 anaerobic-prepared allogenic or autologous donor FMTs. Allogenic donor material was selected after a rigorous screening based on microbial cell count, enterotype, and the abundance of specific genera. The primary endpoint was steroid-free clinical remission (total Mayo \u22642, no sub-score >1) at week 8. A pre-planned futility analysis was performed after 66% (n\u00a0= 72) of intended inclusions (n\u00a0= 108). Quantitative microbiome profiling (n\u00a0= 44) was performed at weeks 0 and\u00a08. RESULTS: In total, 72 patients were included, of which 66 received at least 1 FMT (allogenic FMT, n\u00a0= 30 and autologous FMT, n\u00a0= 36). At week 8, respectively, 3 and 5 patients reached the primary endpoint of steroid-free clinical remission (P\u00a0= .72), indicating no treatment difference of at least 5% in favor of allogenic FMT. Hence, the study was stopped due to futility. Microbiome analysis showed numerically more enterotype transitions upon allogenic FMT compared with autologous FMT, and more transitions were observed when patients were treated with a different enterotype than their own at baseline (P\u00a0= .01). Primary response was associated with lower total Mayo scores, lower bacterial cell counts, and higher Bacteroides 2 prevalence at baseline. CONCLUSION: The RESTORE-UC trial did not meet its primary endpoint of increased steroid-free clinical remission at week 8. Further research should additionally consider patient selection, sterilized sham-control, increased frequency, density, and viability of FMT prior to administration. CLINICALTRIALS: gov, Number: NCT03110289.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30529583", + "title": "Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis.", + "year": 2019, + "journal": "Gastroenterology", + "authors": [ + "Paramsothy S", + "Nielsen S", + "Kamm MA", + "Deshpande NP", + "Faith JJ", + "Clemente JC", + "Paramsothy R", + "Walsh AJ", + "van den Bogaerde J", + "Samuel D", + "Leong RWL", + "Connor S", + "Ng W", + "Lin E", + "Borody TJ", + "Wilkins MR", + "Colombel JF", + "Mitchell HM", + "Kaakoush NO" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.2678577146510703, + "mesh_terms": [ + "Bacteria", + "Biomarkers", + "Colitis, Ulcerative", + "Double-Blind Method", + "Fecal Microbiota Transplantation", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Metabolomics", + "New South Wales", + "Remission Induction", + "Ribotyping", + "Time Factors", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND & AIMS: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy. METHODS: We performed a double-blind trial of 81 patients with active UC randomly assigned to groups that received an initial colonoscopic infusion and then intensive multidonor FMT or placebo enemas, 5 d/wk for 8 weeks. Patients in the FMT group received blended homogenized stool from 3-7 unrelated donors. Patients in the placebo group were eligible to receive open-label FMT after the double-blind study period. We collected 314 fecal samples from the patients at screening, every 4 weeks during treatment, and 8 weeks after the blinded or open-label FMT therapy. We also collected 160 large-bowel biopsy samples from the patients at study entry, at completion of 8 weeks of blinded therapy, and at the end of open-label FMT, if applicable. We analyzed 105 fecal samples from the 14 individual donors (n\u00a0= 55), who in turn contributed to 21 multidonor batches (n\u00a0= 50). Bacteria in colonic and fecal samples were analyzed by both 16S ribosomal RNA gene and transcript amplicon sequencing; 285 fecal samples were analyzed by shotgun metagenomics, and 60 fecal samples were analyzed for metabolome features. RESULTS: FMT increased microbial diversity and altered composition, based on analyses of colon and fecal samples collected before vs after FMT. Diversity was greater in fecal and colon samples collected before and after FMT treatment from patients who achieved remission compared with patients who did not. Patients in remission after FMT had enrichment of Eubacterium hallii and Roseburia inulivorans compared with patients who did not achieve remission after FMT and had increased levels of short-chain fatty acid biosynthesis and secondary bile acids. Patients who did not achieve remission had enrichment of Fusobacterium gonidiaformans, Sutterella wadsworthensis, and Escherichia species and increased levels of heme and lipopolysaccharide biosynthesis. Bacteroides in donor stool were associated with remission in patients receiving FMT, and Streptococcus species in donor stool was associated with no response to FMT. CONCLUSIONS: In an analysis of fecal and colonic mucosa samples from patients receiving FMT for active UC and stool samples from donors, we associated specific bacteria and metabolic pathways with induction of remission. These findings may be of value in the design of microbe-based therapies for UC. ClinicalTrials.gov, Number NCT01896635.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30076785", + "title": "Antigenic mimicry of ubiquitin by the gut bacterium Bacteroides fragilis: a potential link with autoimmune disease.", + "year": 2018, + "journal": "Clinical and experimental immunology", + "authors": [ + "Stewart L", + "D M Edgar J", + "Blakely G", + "Patrick S" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.25504823570362234, + "mesh_terms": [ + "Adult", + "Antibody Specificity", + "Antigens, Bacterial", + "Autoantibodies", + "Autoimmune Diseases", + "Autoimmunity", + "Bacteroides fragilis", + "Cross Reactions", + "Gastrointestinal Microbiome", + "Gene Transfer, Horizontal", + "Humans", + "Middle Aged", + "Models, Molecular", + "Molecular Conformation", + "Molecular Mimicry", + "Structure-Activity Relationship", + "Ubiquitin" + ], + "raw_abstract": "Ubiquitin is highly conserved across eukaryotes and is essential for normal eukaryotic cell function. The bacterium Bacteroides fragilis is a member of the normal human gut microbiota, and the only bacterium known to encode a homologue of eukaryotic ubiquitin. The B. fragilis gene sequence indicates a past horizontal gene transfer event from a eukaryotic source. It encodes a protein (BfUbb) with 63% identity to human ubiquitin which is exported from the bacterial cell. The aim of this study was (i) to determine if there was antigenic cross-reactivity between B. fragilis ubiquitin and human ubiquitin and (ii) to determine if humans produced antibodies to BfUbb. Molecular model comparisons of BfUbb and human ubiquitin predicted a high level (99\u00b78% confidence) of structural similarity. Linear epitope mapping identified epitopes in BfUbb and human ubiquitin that cross-react. BfUbb also has epitope(s) that do not cross-react with human ubiquitin. The reaction of human serum (n = 474) to BfUbb and human ubiquitin from the following four groups of subjects was compared by enzyme-linked immunosorbent assay (ELISA): (1) newly autoantibody-positive patients, (2) allergen-specific immunoglobulin (Ig)E-negative patients, (3) ulcerative colitis patients and (4) healthy volunteers. We show that the immune system of some individuals has been exposed to BfUbb which has resulted in the generation of IgG antibodies. Serum from patients referred for first-time testing to an immunology laboratory for autoimmune disease are more likely to have a high level of antibodies to BfUbb than healthy volunteers. Molecular mimicry of human ubiquitin by BfUbb could be a trigger for autoimmune disease.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38413544", + "title": "CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker.", + "year": 2024, + "journal": "Food and environmental virology", + "authors": [ + "Remesh AT", + "Viswanathan R" + ], + "bacteria": "Bacteroides", + "condition": "ulcerative colitis", + "relevance_score": 0.23279133371726343, + "mesh_terms": [ + "Humans", + "Feces", + "Bacteriophages", + "Gastrointestinal Microbiome", + "Metagenome", + "Bacteria", + "Metagenomics" + ], + "raw_abstract": "CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Treponema", + "condition": "ulcerative colitis", + "relevance_score": 0.505491338085921, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35568112", + "title": "Study on the mechanism of Huangqin Decoction on rats with ulcerative colitis of damp-heat type base on mtDNA, TLR4, p-PI3K, p-Akt protein expression and microbiota.", + "year": 2022, + "journal": "Journal of ethnopharmacology", + "authors": [ + "Zheng Y", + "Liang C", + "Li Z", + "Chen J", + "Chen Z", + "Jiang Y", + "Dong Q", + "Xiao Y", + "Fu C", + "Liao W", + "Yuan X" + ], + "bacteria": "Treponema", + "condition": "ulcerative colitis", + "relevance_score": 0.4516348019056029, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Colon", + "Cytokines", + "DNA, Mitochondrial", + "Dextran Sulfate", + "Disease Models, Animal", + "Gastrointestinal Microbiome", + "Hot Temperature", + "Interleukin-17", + "Interleukin-23", + "Interleukin-6", + "Phosphatidylinositol 3-Kinases", + "Proto-Oncogene Proteins c-akt", + "Rats", + "Scutellaria baicalensis", + "Toll-Like Receptor 4" + ], + "raw_abstract": "ETHNOPHARMACOLOGICAL RELEVANCE: Huangqin decoction (HQD), composed of Scutellaria(Huangqin), Peony(Shaoyao), Liquorice(Gancao) and Jujube(Dazao), is a traditional Chinese medicine prescription, originated from treatise on Febrile Diseases, has the functions of clearing heat, stopping benefits and relieving pain. It is the original prescription for treating heat and relieving dysentery, and is commonly used in clinic for diarrhea and other diseases. In ulcerative colitis, damp-heat syndrome is the most common. However, its mechanism of action is not completely clear. AIMS OF THE REVIEW: The purpose of the research is to investigate the protective effect of HQD on ulcerative colitis rats and the regulation effect of mitochondrial DNA, TLR4, p-Akt, p-PI3K protein and microbiota. MATERIALS AND METHODS: The effects of HQD anti-UC were investigated by fluorescence quantitative PCR, cytokine level and histopathological analysis in DSS-induced ulcerative colitis (UC) rats. The content of mtDNA in colon epithelial cells of rats in each group was detected by fluorescence quantitative PCR, p-PI3K, p-Akt and TLR4 protein expressions in colon tissues of rats in each group were detected by Western blotting. IL-6, IL-17 and IL-23 inflammatory factors were detected by ELISA. The effect of HQD on intestinal microbiota of rats with ulcerative colitis was studied by high-throughput sequencing technology, and the correlation between mtDNA level and inflammatory factors as well as protein expression in colonic epithelium of rats with ulcerative colitis was analyzed by SPSS23.0. RESULTS: HQD significantly alleviated UC symptoms by improving the mucosal intestinal epithelial cell structure, mental state, hair gloss, fecal occult blood, lamina propria intestinal glands and inflammatory cell infiltration. And HQD reduced the pro-inflammatory cytokines in the colonic epithelium of UC rats Production of IL-6, IL-17 and IL-23. The HE stained section of colon tissue showed a complete intestinal epithelial mucosal layer structure. The structure of epithelial cells was more normal and abundant. There were more goblet cells in lamina propria adenoma, which improved the infiltration of inflammatory cells. HQD significantly inhibited the mtDNA content in rat colonic epithelial tissue, and significantly inhibited the expression of TLR4, p-PI3K and p-Akt inflammatory signaling pathways. The results of the microbiota experiment showed that the abundance of HQD in the phylum Firmicutes increased, and the number of Bacteroides phylum decreased (p\u00a0<\u00a00.05). At the genus level, HQD significantly increased Lactobacillus and Firmicutes Bacteroides, while Treponema and Bacteroides were significantly reduced (p\u00a0<\u00a00.05). CONCLUSION: HQD has a certain protective effect on rats with damp heat ulcerative colitis. Its mechanism may be related to regulating the expression of p-PI3K, p-Akt and TLR4 proteins, mitochondrial DNA as well as microbiota.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39087657", + "title": "Intestinal spirochetosis: four cases with different clinical presentations.", + "year": 2024, + "journal": "Revista espanola de enfermedades digestivas", + "authors": [ + "Boix Clemente C", + "Navarro Peir\u00f3 C", + "Moreno Torres B", + "Alemany P\u00e9rez G", + "P\u00e9rez Zahonero MD", + "Olcina Dom\u00ednguez P", + "Mart\u00ed Romero L", + "Gonz\u00e1lez Gonz\u00e1lez L" + ], + "bacteria": "Treponema", + "condition": "ulcerative colitis", + "relevance_score": 0.2676171476345338, + "mesh_terms": [ + "Adult", + "Humans", + "Male", + "Middle Aged", + "Colonoscopy", + "Diarrhea", + "Spirochaetales Infections", + "Aged" + ], + "raw_abstract": "We present 4 clinical cases of intestinal spirochetosis. The first one presents with chronic diarrhea, and spirochetes are detected in random biopsies. The second is homosexual, HIV+, presents rectal bleeding, colonoscopy shows a straight ulcer and spirochete biopsies show negative treponema PCR. The third was also homosexual, HIV+, asymptomatic, with a chance finding of spirochetosis. The last case is also a chance histological diagnosis in a patient with inactive ulcerative colitis without lesions. Intestinal spirochetosis appears to be transmitted sexually and by consumption of contaminated water. The majority are asymptomatic cases but could cause lesions including ulcerations and symptoms. Treatment is only recommended in symptomatic or immunosuppressed patients. It must be distinguished from lesions caused by Treponema pallidum.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "28163288", + "title": "[Clinical significance of human intestinal spirochetosis: a retrospective study].", + "year": 2017, + "journal": "Nihon Shokakibyo Gakkai zasshi = The Japanese journal of gastro-enterology", + "authors": [ + "Umeda S", + "Serizawa H", + "Kobayashi T", + "Toyonaga T", + "Saito E", + "Nakano M", + "Higuchi H", + "Tsunematsu S", + "Watanabe N", + "Hibi T", + "Morinaga S" + ], + "bacteria": "Treponema", + "condition": "ulcerative colitis", + "relevance_score": 0.24059131914862328, + "mesh_terms": [ + "Biopsy", + "Colitis", + "Colonoscopy", + "Female", + "Humans", + "Male", + "Middle Aged", + "Retrospective Studies", + "Spirochaetales Infections" + ], + "raw_abstract": "The clinical and pathological features of human intestinal spirochetosis (HIS) are not well known. Here we report 55 patients with HIS who were diagnosed at our institution during the past 5 years. Seven patients presented with symptoms such as abdominal pain or diarrhea, while the others were incidentally diagnosed during screening colonoscopy. Most patients had non-specific endoscopic findings, including intestinal edema or erosion. The diagnosis of HIS was histologically confirmed via hematoxylin and eosin staining, periodic acid-Schiff staining, and/or immunohistochemistry using anti-Treponema pallidum antibody. Among the 55 patients, five were diagnosed with diseases other than HIS (amoebic colitis, three;ulcerative colitis, one). Sixteen patients were treated with either amoxicillin or metronidazole;only metronidazole proved to be effective. The clinical significance of asymptomatic HIS remains unknown. Some case reports suggest a risk for increased severity in patients with immunodeficiency and/or sexually transmitted diseases. Therefore, aggressive treatment for HIS should be considered, particularly in high-risk patients.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38608475", + "title": "Turtle peptide and its derivative peptide ameliorated DSS-induced ulcerative colitis by inhibiting inflammation and modulating the composition of the gut microbiota.", + "year": 2024, + "journal": "International immunopharmacology", + "authors": [ + "Guo HX", + "Wang BB", + "Wu HY", + "Feng HY", + "Zhang HY", + "Gao W", + "Yuan B" + ], + "bacteria": "Parasutterella", + "condition": "ulcerative colitis", + "relevance_score": 0.7362113372008529, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Dextran Sulfate", + "Mice", + "Peptides", + "Anti-Inflammatory Agents", + "Turtles", + "Male", + "Mice, Inbred C57BL", + "Toll-Like Receptor 4", + "NF-kappa B", + "Disease Models, Animal", + "Intestinal Mucosa", + "Colon", + "Humans", + "Oxidative Stress", + "Signal Transduction" + ], + "raw_abstract": "Ulcerative colitis (UC) is a recurrent intestinal disease with an increasing incidence worldwide that seriously affects the life of patients. Turtle peptide (TP) is a bioactive peptide extracted from turtles that has anti-inflammatory, antioxidant and anti-aging properties. However, studies investigating the effect of TP on the progression of UC are lacking. The aim of this study was to investigate effects and underlying mechanisms of TP and its derivative peptide GPAGPIGPV (GP-9) in alleviating UC in mice. The results showed that 500\u00a0mg/kg TP treatment significantly ameliorated colitis symptoms and oxidative stress in UC mice. TP alleviated intestinal barrier damage in UC mice by promoting mucosal repair and increasing the expression of tight junction proteins (ZO1, occludin and claudin-1). TP also modulated the composition of the gut microbiota by increasing the abundance of the beneficial bacteria Anaerotignum, Prevotellaceae_UCG-001, Alistipes, and Lachno-spiraceae_NK4A136_group and decreasing the abundance of the harmful bacteria Prevotella_9 and Parasutterella. Furthermore, we characterized the peptide composition of TP and found that GP-9 ameliorated the symptoms of dextran sodium sulfate (DSS)-induced colitis in mice by inhibiting the TLR4/NF-\u03baB signaling pathway. In conclusion, TP and its derivative peptides ameliorated DSS-induced ulcerative colitis by inhibiting the expression of inflammatory factors and modulating the composition of the intestinal microbiota; this study provides a theoretical basis for the application of TP and its derivative peptides for their anti-inflammatory activity.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36759757", + "title": "Integrating the serum proteomic and fecal metaproteomic to analyze the impacts of overweight/obesity on IBD: a pilot investigation.", + "year": 2023, + "journal": "Clinical proteomics", + "authors": [ + "Yan P", + "Sun Y", + "Luo J", + "Liu X", + "Wu J", + "Miao Y" + ], + "bacteria": "Parasutterella", + "condition": "ulcerative colitis", + "relevance_score": 0.7117663393883649, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) encompasses a group of chronic relapsing disorders which include ulcerative colitis (UC) and Crohn's disease (CD). The incidences of IBD and overweight/obesity are increasing in parallel. Here, we investigated alterations in proteomic in serum and metaproteomic in feces of IBD patients with overweight/obesity and aimed to explore the effect of overweight/ obesity on IBD and the underlying mechanism. METHODS: This prospective observational study (n\u2009=\u200964) comprised 26 health control subjects (HC, 13 with overweight/obesity) and 38 IBD patients (19 with overweight/obesity) at a tertiary hospital. Overweight/obesity was evaluated by body mass index (BMI) and defined as a BMI greater than 24\u00a0kg/m RESULTS: UC and CD presented similar serum molecular profiles but distinct gut microbiota. UC and CD serum exhibited higher levels of cytoskeleton organization- associated and inflammatory response-related proteins than the HC serum. Compared the serum proteome of UC and CD without overweight/obesity, inflammatory response-associated proteins were dramatically decreased in UC and CD with overweight/obesity. Fecal metaproteome identified 66 species in the feces. Among them, Parasutterella excrementihominis was increased in CD compared with that in HC. UC group had a significant enrichment of Moniliophthora roreri, but had dramatically decreased abundances of Alistipes indistinctus, Clostridium methylpentosum, Bacteroides vulgatus, and Schizochytrium aggregatum. In addition, overweight/obesity could improve the microbial diversity of UC. Specifically, the UC patients with overweight/obesity had increased abundance of some probiotics in contrast to those without overweight/obesity, including Parabacteroides distasonis, Alistipes indistincus, and Ruminococcus bromii. CONCLUSION: This study provided high-quality multi-omics data of IBD serum and fecal samples, which enabled deciphering the molecular bases of clinical phenotypes of IBD, revealing the impacts of microbiota on IBD, and emphasizing the important role of overweight/obesity in IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "38521930", + "title": "Human-derived bacterial strains mitigate colitis via modulating gut microbiota and repairing intestinal barrier function in mice.", + "year": 2024, + "journal": "BMC microbiology", + "authors": [ + "Dai J", + "Jiang M", + "Wang X", + "Lang T", + "Wan L", + "Wang J" + ], + "bacteria": "Parasutterella", + "condition": "ulcerative colitis", + "relevance_score": 0.5951787363092838, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "Gastrointestinal Microbiome", + "Intestinal Barrier Function", + "RNA, Ribosomal, 16S", + "Colitis", + "Colitis, Ulcerative", + "Bacteroidetes", + "Enterococcus faecium", + "Escherichia coli", + "Mice, Inbred C57BL", + "Disease Models, Animal", + "Colon" + ], + "raw_abstract": "BACKGROUND: Unbalanced gut microbiota is considered as a pivotal etiological factor in colitis. Nevertheless, the precise influence of the endogenous gut microbiota composition on the therapeutic efficacy of probiotics in colitis remains largely unexplored. RESULTS: In this study, we isolated bacteria from fecal samples of a healthy donor and a patient with ulcerative colitis in remission. Subsequently, we identified three bacterial strains that exhibited a notable ability to ameliorate dextran sulfate sodium (DSS)-induced colitis, as evidenced by increased colon length, reduced disease activity index, and improved histological score. Further analysis revealed that each of Pediococcus acidilactici CGMCC NO.17,943, Enterococcus faecium CGMCC NO.17,944 and Escherichia coli CGMCC NO.17,945 significantly attenuated inflammatory responses and restored gut barrier dysfunction in mice. Mechanistically, bacterial 16S rRNA gene sequencing indicated that these three strains partially restored the overall structure of the gut microbiota disrupted by DSS. Specially, they promoted the growth of Faecalibaculum and Lactobacillus murinus, which were positively correlated with gut barrier function, while suppressing Odoribacter, Rikenella, Oscillibacter and Parasutterella, which were related to inflammation. Additionally, these strains modulated the composition of short chain fatty acids (SCFAs) in the cecal content, leading to an increase in acetate and a decrease in butyrate. Furthermore, the expression of metabolites related receptors, such as receptor G Protein-coupled receptor (GPR) 43, were also affected. Notably, the depletion of endogenous gut microbiota using broad-spectrum antibiotics completely abrogated these protective effects. CONCLUSIONS: Our findings suggest that selected human-derived bacterial strains alleviate experimental colitis and intestinal barrier dysfunction through mediating resident gut microbiota and their metabolites in mice. This study provides valuable insights into the potential therapeutic application of probiotics in the treatment of colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31293117", + "title": "Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia.", + "year": 2019, + "journal": "Minerva gastroenterologica e dietologica", + "authors": [ + "Masoodi I", + "Alshanqeeti AS", + "Ahmad S", + "Alyamani EJ", + "Al-Lehibi AA", + "Qutub AN", + "Alsayari KN", + "Alomair AO" + ], + "bacteria": "Parasutterella", + "condition": "ulcerative colitis", + "relevance_score": 0.505491338085921, + "mesh_terms": [ + "Adolescent", + "Adult", + "Aged", + "Cohort Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Metagenome", + "Middle Aged", + "Saudi Arabia", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS: Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS: The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19\u00b110.67 years. There were 50 UC patient (28 females) mean age of 34.42\u00b112.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS: A significant dysbiosis was found in UC and CD patients compared to controls.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35151255", + "title": "Gut microbiome alterations in colitis rats after moxibustion at bilateral Tianshu acupoints.", + "year": 2022, + "journal": "BMC gastroenterology", + "authors": [ + "Qi Q", + "Liu YN", + "Lv SY", + "Wu HG", + "Zhang LS", + "Cao Z", + "Liu HR", + "Wang XM", + "Wu LY" + ], + "bacteria": "Parasutterella", + "condition": "ulcerative colitis", + "relevance_score": 0.4767693447749241, + "mesh_terms": [ + "Acupuncture Points", + "Animals", + "Colitis", + "Colitis, Ulcerative", + "Dextran Sulfate", + "Disease Models, Animal", + "Gastrointestinal Microbiome", + "Male", + "Moxibustion", + "Rats" + ], + "raw_abstract": "BACKGROUND: The pathogenesis of ulcerative colitis (UC) is closely related to the gut microbiota. Moxibustion has been used to improve the inflammation and gastrointestinal dysfunctions in gastrointestinal\u00a0disorders such as UC. In this study, we investigated whether moxibustion could improve the gut microbial dysbiosis induced by dextran sulphate sodium. METHODS: Twenty-five male rats were randomly assigned into five groups. The UC rat model was established by administering DSS solution. The rats in the moxibustion and normal rats with moxibustion groups were treated with moxibustion at Tianshu (bilateral, ST25) points, and the mesalazine group rats were treated with mesalazine once daily for 7 consecutive days. Disease activity index (DAI) and haematoxylin and eosin staining were used to evaluate the effect of moxibustion. Gut microbiota profiling was conducted by metagenomic high throughput sequencing technology. The gut microbiota composition, diversity and function were analyzed and compared using metagenomics methodologies. RESULTS: The DAI scores and histopathology scores in the moxibustion and mesalazine groups were significantly decreased compared with the UC group (P\u2009<\u20090.01). Moxibustion treatment increased abundance levels of Bacteroidetes, Actinobacteria, Ascomycota, Synergistetes and decreased abundance of Firmicutes, Proteobacteria. At the genus level, the abundance of Bacteroides, Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2, were increased and Bacteroides_bacterium_H3, Parabacteroides, Porphyromonas, Alistipes, Parasutterella were decreased in the UC group in comparsion with those in the NG group. Moxibustion increased the abundance of Bacteroides and Bacteroides_bacterium_H3 and decreased Bacteroides_bacterium_M7, Prevotella, Bacteroidales_bacterium_H2. In UC group, the specie Bacteroides_massiliensis was negatively (P\u2009<\u20090.05) correlated with IL-23, Bacteroides_eggerthii_CAG109 and Bacteroides_eggerthii were negatively (P\u2009<\u20090.05) correlated with TGF-\u03b2. And the species Prevotella_sp_CAG1031 and Bacteroides_bacterium_H2 were significant positively (P\u2009<\u20090.05) correlated with IL-23. In addition, compare with the normal group, genes involved in certain metabolic pathways, such as energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, were under-represented in the UC group, and these changes in the metabolic pathways could be reversed by moxibustion treatment and mesalazine treatment. CONCLUSIONS: Our findings suggest that moxibustion treatment may protect the host from mucosal inflammation by modulating the intestinal microbiota community.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39666667", + "title": "Gut microbiota diversity repeatedly diminishes over time following maintenance infliximab infusions in paediatric IBD patients.", + "year": 2024, + "journal": "PloS one", + "authors": [ + "Carlsen K", + "Thingholm LB", + "Dempfle A", + "Malham M", + "Bang C", + "Franke A", + "Wewer V" + ], + "bacteria": "Parasutterella", + "condition": "ulcerative colitis", + "relevance_score": 0.4664166543273229, + "mesh_terms": [ + "Humans", + "Infliximab", + "Gastrointestinal Microbiome", + "Adolescent", + "Child", + "Female", + "Male", + "Feces", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Gastrointestinal Agents", + "Colitis, Ulcerative", + "Crohn Disease", + "Leukocyte L1 Antigen Complex", + "Biodiversity" + ], + "raw_abstract": "BACKGROUND: The gut microbiome plays a crucial role in the pathogenesis and progression of inflammatory bowel disease (IBD). Understanding the dynamics of the gut microbiome in relation to treatment can provide valuable insights into disease management and therapy strategies. The aim of this study is to investigate if diversity and composition of the gut microbiome correlate with time since treatment and disease activity during maintenance infliximab (IFX) therapy among children with IBD. METHODS: Data was collected from IBD patients aged 10-17 participating in an IFX-eHealth study. IFX infusions were administered in 4-12-week intervals based on weekly faecal calprotectin (FC) combined with symptom scores. Excess stool samples underwent microbiome profiling using 16S rRNA gene sequencing. Microbiome features, including alpha diversity and single taxa, were analysed for three key variables: 1) weeks-since-treatment, 2) FC, and 3) symptom score. RESULTS: From 25 patients (median age 14.4 years) diagnosed with Crohn\u00b4s Disease (n = 16) or ulcerative colitis (n = 9), microbiota were analysed in 671 faecal samples collected across 15 treatment intervals. A significant decrease over time in Shannon diversity, following the initial increase within four weeks of treatment, was found across patients. FC levels showed no association with alpha diversity (p>0.1), while symptom scores showed a negative association with Shannon and observed diversity in patients with UC. At the genus level, a lower abundance of the genera Anaerostipes and Fusicatenibacter (Firmicutes), and a greater abundance of the genus Parasutterella (Proteobacteria), were associated (p.adj<0.05) with the time elapsed since last infusion in UC specifically, while only Parasutterella was associated across the full cohort (p.adj = 1e-10). CONCLUSIONS: We found a recurring reduction over time in alpha diversity following the initial increase in diversity after an IFX infusion. Changes in an individual's microbiome may be an early sign of increasing disease activity that precedes clinical symptoms and increased FC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32048723", + "title": "Aging Increases the Severity of Colitis and the Related Changes to the Gut Barrier and Gut Microbiota in Humans and Mice.", + "year": 2020, + "journal": "The journals of gerontology. Series A, Biological sciences and medical sciences", + "authors": [ + "Liu A", + "Lv H", + "Wang H", + "Yang H", + "Li Y", + "Qian J" + ], + "bacteria": "Parasutterella", + "condition": "ulcerative colitis", + "relevance_score": 0.42065181675976, + "mesh_terms": [ + "Adult", + "Age Factors", + "Aged", + "Aging", + "Animals", + "Cadherins", + "Case-Control Studies", + "Colitis, Ulcerative", + "Disease Models, Animal", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Middle Aged", + "Occludin", + "Severity of Illness Index" + ], + "raw_abstract": "This study aims to compare intestinal mucosal barrier function in older and young ulcerative colitis (UC) patients and the healthy population, and to explore the possible mechanisms through which aging increases the severity of colitis in mice. The old healthy group showed discontinued tight junction (TJ) strand. The E-cadherin and occludin protein expressions in the colonic tissue of the old healthy subjects were lower than those in the younger healthy people. The protein expressions of E-cadherin and occludin were lower in the old UC patients than in the younger UC patients. In mice, disease activity indexes induced by inflammatory stimulus differed as a function of age. Weight loss level, histological scores, and expression of proinflammatory factors were higher in the dextran sulfate sodium (DSS)-induced group of aged mice than in the young DSS-induced mice. Compared with the results observed in the young DSS-induced mice, the protein expressions of E-cadherin and occludin in the aged DSS-induced mice were lower. Furthermore, significant differences were observed in the composition of the gut microbiota between the young and aged mice. In the aged mice, the fraction of beneficial bacteria (Lactobacillus) was lower before the DSS treatment, while the fraction of the harmful bacteria (Turicibacter, Parasutterella) was higher than that observed in the young mice. After the DSS treatment in the aged mice, the fraction of beneficial bacteria (Odoribacter and Alistipes) was lower, while the fraction of harmful bacteria (Turicibacter) was higher than in the young mice. We demonstrate that the aging of the human colon is characterized by an impairment of the intestinal barrier. Aging leads to more severe disease following DSS challenge. Age-related deterioration of gastrointestinal barrier function and gut microbial dysbiosis may be involved in the pathogenesis of colitis in the aged mice.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36195889", + "title": "Understanding the tonifying and the detoxifying properties of Chinese medicines from their impacts on gut microbiota and host metabolism: a case study with four medicinal herbs in experimental colitis rat model.", + "year": 2022, + "journal": "Chinese medicine", + "authors": [ + "Li T", + "Gao X", + "Yan Z", + "Wai TS", + "Yang W", + "Chen J", + "Yan R" + ], + "bacteria": "Parasutterella", + "condition": "ulcerative colitis", + "relevance_score": 0.339913374634281, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: Chinese medicines (CMs) have emerged as an alternative therapy for ulcerative colitis through reinforcing the vital qi and/or eliminating the pathogenic factors according to the traditional Chinese medicinal theory. Presystemic interactions of CMs with gut microbiota and the associated metabolic network shift are believed to be essential to achieve their holistic health benefits in traditional oral application. METHODS: This study first employed 16S rDNA-based microbial profiling and mass spectrometry-based urinary metabolomics to simultaneously evaluate four\u00a0single CMs frequently prescribed as main constituent herbs for alleviating UC, the tonic ginseng and Astragali Radix (AR) and the detoxifying Scutellaria Radix (SR) and Rhubarb, on a dextran sodium sulfate (DSS)-induced colitis rat model, with aims to understanding the tonifying or detoxifying properties of CMs through clinical phenotypes, the common features and herb-specific signatures in gut microbial alterations and the associated host metabolic shifts. Colitis was induced in rats receiving 5% DSS for consecutive 7 days. Control group received water alone. Herbal groups received 5% DSS and respective herbal preparation by gavage once daily. Body weight, stool consistency, and rectal bleeding were recorded daily. Feces and urine were freshly collected at multiple time points. On day 7, blood and colon tissues were collected to determine anti-/pro-inflammatory cytokines levels, colonic myeloperoxidase activity, and histopathologic alterations. RESULTS: Gut microbiome was more prone to herb intervention than metabolome and displayed increasing associations with metabolic dynamics. Although both the tonic and the detoxifying herbs alleviated colitis and caused some similar changes in DSS-induced microbiome and metabolome disturbance, the tonic herbs were more effective and shared more common microbial and metabolic signatures. The detoxifying herbs elicited herb-specific changes. Rhubarb uniquely affected phenylalanine metabolism and established high correlations between Akkermansia muciniphila and Parasutterella and hydroxyphenylacetylglycine and phenylbutyrylglycine, while SR caused significant elevation of steroidal glucuronides dehydropregnenolone glucuronide and estriol glucuronide, both displaying exclusive correlations with genus Acetatifactor. CONCLUSION: Both tonic and detoxifying herbs tested ameliorated experimental colitis and elicited alternative microbial and host metabolic reprogramming. The findings highlight the importance of presystemic interactions with gut microbiota to host metabolic shifts and promote modern translation of tonic\u00a0and detoxifying properties of CMs.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "36040412", + "title": "Quantitative Fecal Microbiota Profiles Relate to Therapy Response During Induction With Tumor Necrosis Factor \u03b1 Antagonist Infliximab in Pediatric Inflammatory Bowel Disease.", + "year": 2023, + "journal": "Inflammatory bowel diseases", + "authors": [ + "H\u00f6yhty\u00e4 M", + "Korpela K", + "Saqib S", + "Junkkari S", + "Nissil\u00e4 E", + "Nikkonen A", + "Dikareva E", + "Salonen A", + "de Vos WM", + "Kolho KL" + ], + "bacteria": "Parasutterella", + "condition": "ulcerative colitis", + "relevance_score": 0.329445186548022, + "mesh_terms": [ + "Humans", + "Child", + "Infliximab", + "Tumor Necrosis Factor-alpha", + "Tumor Necrosis Factor Inhibitors", + "Inflammatory Bowel Diseases", + "Feces", + "Microbiota", + "Leukocyte L1 Antigen Complex" + ], + "raw_abstract": "BACKGROUND: The role of intestinal microbiota in inflammatory bowel diseases is intensively researched. Pediatric studies on the relation between microbiota and treatment response are sparse. We aimed to determine whether absolute abundances of gut microbes characterize the response to infliximab induction in pediatric inflammatory bowel disease. METHODS: We recruited pediatric patients with inflammatory bowel disease introduced to infliximab at Children's Hospital, University of Helsinki. Stool samples were collected at 0, 2, and 6 weeks for microbiota and calprotectin analyses. We defined treatment response as fecal calprotectin value <100 \u00b5g/g at week 6. Intestinal microbiota were analyzed by 16S ribosomal RNA gene amplicon sequencing using the Illumina MiSeq platform. We analyzed total bacterial counts using quantitative polymerase chain reaction and transformed the relative abundances into absolute abundances based on the total counts. RESULTS: At baseline, the intestinal microbiota in the treatment responsive group (n\u2005=\u200510) showed a higher absolute abundance of Bifidobacteriales and a lower absolute abundance of Actinomycetales than nonresponders (n\u2005=\u200519). The level of inflammation according to fecal calprotectin showed no statistically significant association with the absolute abundances of fecal microbiota. The results on relative abundances differed from the absolute abundances. At the genus level, the responders had an increased relative abundance of Anaerosporobacter but a reduced relative abundance of Parasutterella at baseline. CONCLUSIONS: High absolute abundance of Bifidobacteriales in the gut microbiota of pediatric patients reflects anti-inflammatory characteristics associated with rapid response to therapy. This warrants further studies on whether modification of pretreatment microbiota might improve the outcomes. We studied absolute and relative abundances of fecal microbiota in relation to response to induction therapy with infliximab in pediatric inflammatory bowel disease. We discovered that a high absolute abundance of anti-inflammatory Bifidobacteriales at baseline associated with response.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33233306", + "title": "Weissella paramesenteroides WpK4 plays an immunobiotic role in gut-brain axis, reducing gut permeability, anxiety-like and depressive-like behaviors in murine models of colitis and chronic stress.", + "year": 2020, + "journal": "Food research international (Ottawa, Ont.)", + "authors": [ + "Sandes S", + "Figueiredo N", + "Pedroso S", + "Sant'Anna F", + "Acurcio L", + "Abatemarco Junior M", + "Barros P", + "Oliveira F", + "Cardoso V", + "Generoso S", + "Caliari M", + "Nicoli J", + "Neumann E", + "Nunes \u00c1" + ], + "bacteria": "Weissella", + "condition": "ulcerative colitis", + "relevance_score": 0.6739609717712325, + "mesh_terms": [ + "Animals", + "Anxiety", + "Brain", + "Colitis", + "Disease Models, Animal", + "Humans", + "Mice", + "Permeability", + "Weissella" + ], + "raw_abstract": "The relationship between inflammatory bowel disease (IBD) and mood disorders is complex and involves overlapping metabolic pathways, which may determine comorbidity. Several studies have been shown that this comorbidity could worsen IBD clinical course. The treatment of ulcerative colitis is complex, and involves traditional therapy to promote the function of epithelial barrier, reducing exacerbated inflammatory responses. Recently, it has been shown that some probiotic strains could modulate gut-brain axis, reducing depressive and anxiety scores in humans, including IBD patients. Accordingly, this study aimed to evaluate the role of Weissella paramesenteroides WpK4 in murine models of ulcerative colitis and chronic stress. It was observed that bacterium ingestion improved health of colitis mice, reducing intestinal permeability, besides improving colon histopathological appearance. In stressed mice, bacterial consumption was associated with a reduced anxiety-like and depressive-like behaviors. In both assays, the beneficial role of W. paramesenteroides WpK4 was related to its immunomodulatory feature. It is possible to state that W. paramesenteroides WpK4 exerted their beneficial roles in gut-brain axis through their immunomodulatory effects with consequences in several metabolic pathways related to intestinal permeability and hippocampal physiology.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "34600098", + "title": "Probiotic potential of Lactobacillus isolated from horses and its therapeutic effect on DSS-induced colitis in mice.", + "year": 2022, + "journal": "Microbial pathogenesis", + "authors": [ + "Qin S", + "Huang Z", + "Wang Y", + "Pei L", + "Shen Y" + ], + "bacteria": "Weissella", + "condition": "ulcerative colitis", + "relevance_score": 0.403603708266476, + "mesh_terms": [ + "Animals", + "Anti-Bacterial Agents", + "Caco-2 Cells", + "Colitis", + "Dextran Sulfate", + "Disease Models, Animal", + "Horses", + "Humans", + "Inflammatory Bowel Diseases", + "Lactobacillus", + "Lactobacillus plantarum", + "Lipopolysaccharides", + "Male", + "Mice", + "Phylogeny", + "Probiotics" + ], + "raw_abstract": "Inflammatory bowel disease (IBD) is a refractory disease that endangers both humans and animals. In recent times, Lactobacillus have been used to treat animal diseases. It may be a good choice to try to isolate Lactobacillus with probiotic potential to treat IBD. Equine, as a kind of hindgut fermentation animal has rich intestinal microflora, but data regarding this is scarce. The isolation of Lactobacillus with probiotic potential from equine may become a new method for the treatment of IBD. Four isolates of Lactobacillus were isolated from fresh feces of healthy male adult horses and analyzed their biological characteristics. According to the phylogenetic analysis, A2.5 and A7.1 were identified as Pediococcus pentosaceus, A3 as Lactobacillus plantarum, and B8.2 as Weissella cibaria. All four isolates showed tolerance to the environment of acid, bile salt concentration and simulated artificial gastrointestinal fluid. The hydrophobic rate and self-aggregation rate of A3 were close to 100%, and the adhesion rate was 28.85\u00a0\u00b1\u00a00.74%. Four isolates were negative in hemolysis test and sensitive to common antibiotics and different isolates had different sensitivity to antibiotics. The four isolates had antibacterial and antioxidant activities which can reflect their probiotic potential. Furthermore, they could regulate the LPS (Lipopolysaccharides) stimulated Caco-2\u00a0cells. We chose A3 as the treatment strain to intervene Dextran sulfate sodium salt (DSS)-induced mice. The results showed that compared with DSS group, DSS\u00a0+\u00a0A3 group exhibited reduced Disease activity index (DAI), increased colon length, reduced pathological score and regulated cytokine secretion at the level of gene expression. In this study, four isolates of Lactobacillus with probiotic potential were isolated, and Lactobacillus plantarum A3 with reduced ulcerative colitis in mice was screened. It might provide a potential treatment for IBD.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "27824645", + "title": "A Single Species of Clostridium Subcluster XIVa Decreased in Ulcerative Colitis Patients.", + "year": 2016, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Takeshita K", + "Mizuno S", + "Mikami Y", + "Sujino T", + "Saigusa K", + "Matsuoka K", + "Naganuma M", + "Sato T", + "Takada T", + "Tsuji H", + "Kushiro A", + "Nomoto K", + "Kanai T" + ], + "bacteria": "Fusicatenibacter", + "condition": "ulcerative colitis", + "relevance_score": 0.8374867316424249, + "mesh_terms": [ + "Adult", + "Aged", + "Animals", + "Case-Control Studies", + "Clostridium", + "Colitis, Ulcerative", + "Disease Progression", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Intestinal Mucosa", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Middle Aged", + "Mucous Membrane", + "RNA, Ribosomal, 16S", + "Species Specificity", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Imbalance of the intestinal microbiota is associated with gastrointestinal disease and autoimmune disease and metabolic syndrome. Analysis of the intestinal microbiota has recently progressed, and the association with inflammatory bowel disease has been reported at the species level. Such findings suggest that the recovery of homeostasis in the intestinal microbiota could cure inflammatory bowel disease. We aimed to search new probiotic candidates for inflammatory bowel disease through translational research by analysis of ulcerative colitis (UC) patients' intestinal microbiota and clarify the effects of them on inflammation. Here, we focused on Fusicatenibacter saccharivorans, which belongs to Clostridium subcluster XIVa and was successfully isolated and cultured in 2013. We analyzed the association of F. saccharivorans to UC patients' activity and inflammation for the first time. METHODS: Feces from UC patients and healthy controls were analyzed by 16S ribosomal RNA gene sequences. F. saccharivorans was administered to murine colitis model. Colitic lamina propria mononuclear cells from UC patients and mice were stimulated with F. saccharivorans. RESULTS: The whole fecal bacteria in active UC patients were less than that in quiescent UC patients. Furthermore, F. saccharivorans was decreased in active UC patients and increased in quiescent. The administration of F. saccharivorans improved murine colitis. F. saccharivorans induced interleukin 10 production by lamina propria mononuclear cells from not only colitis model mice but also UC patients. CONCLUSIONS: F. saccharivorans decreased in correlation to UC activity and suppresses intestinal inflammation. These results suggest that F. saccharivorans could lead to a novel UC treatment.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "39666667", + "title": "Gut microbiota diversity repeatedly diminishes over time following maintenance infliximab infusions in paediatric IBD patients.", + "year": 2024, + "journal": "PloS one", + "authors": [ + "Carlsen K", + "Thingholm LB", + "Dempfle A", + "Malham M", + "Bang C", + "Franke A", + "Wewer V" + ], + "bacteria": "Fusicatenibacter", + "condition": "ulcerative colitis", + "relevance_score": 0.4650687475584419, + "mesh_terms": [ + "Humans", + "Infliximab", + "Gastrointestinal Microbiome", + "Adolescent", + "Child", + "Female", + "Male", + "Feces", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Gastrointestinal Agents", + "Colitis, Ulcerative", + "Crohn Disease", + "Leukocyte L1 Antigen Complex", + "Biodiversity" + ], + "raw_abstract": "BACKGROUND: The gut microbiome plays a crucial role in the pathogenesis and progression of inflammatory bowel disease (IBD). Understanding the dynamics of the gut microbiome in relation to treatment can provide valuable insights into disease management and therapy strategies. The aim of this study is to investigate if diversity and composition of the gut microbiome correlate with time since treatment and disease activity during maintenance infliximab (IFX) therapy among children with IBD. METHODS: Data was collected from IBD patients aged 10-17 participating in an IFX-eHealth study. IFX infusions were administered in 4-12-week intervals based on weekly faecal calprotectin (FC) combined with symptom scores. Excess stool samples underwent microbiome profiling using 16S rRNA gene sequencing. Microbiome features, including alpha diversity and single taxa, were analysed for three key variables: 1) weeks-since-treatment, 2) FC, and 3) symptom score. RESULTS: From 25 patients (median age 14.4 years) diagnosed with Crohn\u00b4s Disease (n = 16) or ulcerative colitis (n = 9), microbiota were analysed in 671 faecal samples collected across 15 treatment intervals. A significant decrease over time in Shannon diversity, following the initial increase within four weeks of treatment, was found across patients. FC levels showed no association with alpha diversity (p>0.1), while symptom scores showed a negative association with Shannon and observed diversity in patients with UC. At the genus level, a lower abundance of the genera Anaerostipes and Fusicatenibacter (Firmicutes), and a greater abundance of the genus Parasutterella (Proteobacteria), were associated (p.adj<0.05) with the time elapsed since last infusion in UC specifically, while only Parasutterella was associated across the full cohort (p.adj = 1e-10). CONCLUSIONS: We found a recurring reduction over time in alpha diversity following the initial increase in diversity after an IFX infusion. Changes in an individual's microbiome may be an early sign of increasing disease activity that precedes clinical symptoms and increased FC.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37859536", + "title": "Baizhu-Baishao herb pair ameliorates functional constipation and intestinal microflora disorder in rats.", + "year": 2023, + "journal": "Animal models and experimental medicine", + "authors": [ + "Li X", + "Wang X", + "Wang Z", + "Guan J" + ], + "bacteria": "Fusicatenibacter", + "condition": "ulcerative colitis", + "relevance_score": 0.2518166578057637, + "mesh_terms": [ + "Rats", + "Animals", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Serotonin", + "Constipation", + "Vasoactive Intestinal Peptide", + "Substance P" + ], + "raw_abstract": "BACKGROUND: In China, Rhizoma atractylodis macrocephalae-Paeonia lactiflora Pall (Biazhu-Baishao, BZBS) is a classic herb pair used to treat intestinal stress syndrome, ulcerative colitis and other diseases. However, the mechanism of BZBS in the treatment of functional constipation (FC) has been little studied and remains unclear. In this study, a behavioral investigation, colon tissue morphology, enzyme-linked immunosorbent assay (Elisa) and intestinal microflora analysis have been used to illuminate the potential mechanism of the effects of BZBS on FC in a rat model. METHODS: A FC rat model was constructed and BZBS was given as treatment. Observations and recordings were made of the fecal moisture content, the defecation time of the first black stool, and the rate of intestinal propulsion. Elisa was used to detect the expression levels of substance P (SP), vasoactive intestinal peptide (VIP), 5-hydroxytryptamine (5-HT) in the colon. To ascertain the composition of the microbial community, a high throughput 16S ribosomal RNA (16S rRNA) gene sequencing technique was employed. RESULTS: Oral administration of BZBS significantly ameliorated several key excretion parameters, including the time to first black stool defecation, stool water content, and the propulsion rate in the small intestine in FC rats. It increased the expression of SP, VIP and 5-HT in the colon. 16S rRNA gene sequencing results showed that BZBS changed the microbial community structure, decreased the Bacteroidetes/Firmicutes ratio, increased the relative abundance of Blautia and Fusicatenibacter, and decreased the relative abundance of Ruminococcus and Roseburia. CONCLUSIONS: BZBS effectively alleviates FC and improves dysbacteriosis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37071621", + "title": "Seasonal variations in gut microbiota and disease course in patients with inflammatory bowel disease.", + "year": 2023, + "journal": "PloS one", + "authors": [ + "Tani M", + "Shinzaki S", + "Asakura A", + "Tashiro T", + "Amano T", + "Otake-Kasamoto Y", + "Yoshihara T", + "Yoshii S", + "Tsujii Y", + "Hayashi Y", + "Inoue T", + "Motooka D", + "Nakamura S", + "Iijima H", + "Takehara T" + ], + "bacteria": "Actinomyces", + "condition": "ulcerative colitis", + "relevance_score": 0.7707719518857965, + "mesh_terms": [ + "Humans", + "Seasons", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Crohn Disease", + "Bacteria", + "Disease Progression", + "Feces" + ], + "raw_abstract": "BACKGROUND AND AIM: Environmental factors are associated with onset and course of inflammatory bowel disease (IBD). Our previous study by about 1,100 IBD patients revealed half of the patients experienced seasonal exacerbation of disease. We investigated the seasonality of fecal microbiota composition of IBD patients. METHODS: Fecal samples were consecutively collected in each season from IBD outpatients and healthy controls between November 2015 and April 2019. Participants who were treated with full elemental diet or antibiotics within 6 months or had ostomates were excluded. Bacterial profiles were analyzed by 16S rRNA sequencing, and the changes between the diseases and seasons were compared. RESULTS: A total of 188 fecal samples were analyzed from 47 participants comprising 19 Crohn's disease (CD) patients, 20 ulcerative colitis (UC) patients, and 8 healthy controls (HC). In CD patients, the phylum Actinobacteria and TM7 were both significantly more abundant in autumn than in spring and winter, but not in UC patients and HC. Moreover, the genera Actinomyces, a member of Actinobacteria, and c_TM7-3;o_;f_;g_ (TM7-3), that of TM7, were significantly more abundant in autumn than in spring, and the abundance of Actinomyces was significantly correlated with that of TM7-3 throughout the year in CD patients, but not in UC patients and HC. CD patients with high abundance of TM7-3 in the autumn required significantly fewer therapeutic intervention than those without seasonal fluctuation. CONCLUSIONS: Oral commensals Actinomyces and its symbiont TM7-3 were correlatively fluctuated in the feces of CD patients by season, which could affect the disease course.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "35351021", + "title": "Disseminated cutaneous Actinomyces bovis infection in an immunocompromised host: case report and review of the literature.", + "year": 2022, + "journal": "BMC infectious diseases", + "authors": [ + "Cunha F", + "Sousa DL", + "Trindade L", + "Duque V" + ], + "bacteria": "Actinomyces", + "condition": "ulcerative colitis", + "relevance_score": 0.5315288478665698, + "mesh_terms": [ + "Actinomyces", + "Actinomycosis", + "Aged", + "Female", + "Humans", + "Immunocompromised Host", + "Quality of Life" + ], + "raw_abstract": "BACKGROUND: Actinomycosis is an uncommon endogenous bacterial infection caused by Actinomyces species, characterized by the development of abscesses, tissue fibrosis, and fistulisation. It remains a diagnostic challenge, due to its similarities with diverse aetiologies' presentation, such as neoplasms, tuberculosis, or fungal infections. Actinomyces bovis is a microorganism rarely reported as a cause of human disease. Cutaneous involvement is sporadic. In this case, Actinomyces bovis was responsible for disseminated cutaneous disease in an immunosuppressed patient. CASE PRESENTATION: We report the case of a 69-year-old female with multiple skin masses, under immunosuppressive therapy due to ulcerative colitis. Imaging exams were compatible with multiple cutaneous abscesses in the cervicofacial region and limbs. Actinomyces bovis was isolated in culture after abscess drainage. Antimicrobial therapy with parenteral penicillin G and oral amoxicillin was administered for 6\u00a0months, with complete resolution of cutaneous lesions and no relapse of the infection. CONCLUSIONS: Considering actinomycosis as a possible diagnosis in the presence of subacute/chronic recurrent mass-like cutaneous lesions, especially in the setting of immunosuppression, may reduce the burden associated with delayed diagnosis and incorrect treatment and provide better outcomes and improvement of patient's quality of life.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "31812509", + "title": "Differences in Gut Microbiota in Patients With vs Without Inflammatory Bowel Diseases: A Systematic Review.", + "year": 2020, + "journal": "Gastroenterology", + "authors": [ + "Pittayanon R", + "Lau JT", + "Leontiadis GI", + "Tse F", + "Yuan Y", + "Surette M", + "Moayyedi P" + ], + "bacteria": "Actinomyces", + "condition": "ulcerative colitis", + "relevance_score": 0.4864845058822719, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestines" + ], + "raw_abstract": "BACKGROUND & AIMS: Altering the intestinal microbiota has been proposed as a treatment for inflammatory bowel diseases (IBDs), but there are no established associations between specific microbes and IBD. We performed a systematic review to identify frequent associations. METHODS: We searched the MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, and Cochrane Central Register of Controlled Trials databases, through April 2, 2018 for studies that compared intestinal microbiota (from fecal or colonic or ileal tissue samples) among patients (adult or pediatric) with IBD vs healthy individuals (controls). The primary outcome was difference in specific taxa in fecal or intestinal tissue samples from patients with IBD vs controls. We used the Newcastle-Ottawa scale to assess the quality of studies included in the review. RESULTS: We identified 2631 citations; 48 studies from 45 articles were included in the analysis. Most studies evaluated adults with Crohn's disease or ulcerative colitis. All 3 studies of Christensenellaceae and Coriobacteriaceae and 6 of 11 studies of Faecalibacterium prausnitzii reported a decreased amount of those organisms compared with controls, whereas 2 studies each of Actinomyces, Veillonella, and Escherichia coli revealed an increased amount in patients with Crohn's disease. For patients with ulcerative colitis, Eubacterium rectale and Akkermansia were decreased in all 3 studies, whereas E coli was increased in 4 of 9 studies. The microbiota diversity was either decreased or not different in patients with IBD vs controls. Fewer than 50% of the studies stated comparable sexes and ages of cases and controls. CONCLUSIONS: In a systematic review, we found evidence for differences in abundances of some bacteria in patients with IBD vs controls, but we cannot make conclusions due to inconsistent results and methods among studies. Further large-scale studies, with better methods of assessing microbe populations, are needed.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "30545401", + "title": "A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?", + "year": 2018, + "journal": "Microbiome", + "authors": [ + "Forbes JD", + "Chen CY", + "Knox NC", + "Marrie RA", + "El-Gabalawy H", + "de Kievit T", + "Alfa M", + "Bernstein CN", + "Van Domselaar G" + ], + "bacteria": "Actinomyces", + "condition": "ulcerative colitis", + "relevance_score": 0.2132820813105585, + "mesh_terms": [ + "Adult", + "Arthritis, Rheumatoid", + "Bacteria", + "Case-Control Studies", + "Colitis, Ulcerative", + "Crohn Disease", + "DNA, Bacterial", + "DNA, Ribosomal", + "Dysbiosis", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Machine Learning", + "Male", + "Metagenomics", + "Middle Aged", + "Multiple Sclerosis", + "Phylogeny", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA" + ], + "raw_abstract": "BACKGROUND: Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology is common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of the gut microbiome in IMIDs. This study used 16S rRNA gene amplicon sequencing to compare the gut microbiota of patients with Crohn's disease (CD; N\u2009=\u200920), ulcerative colitis (UC; N\u2009=\u200919), multiple sclerosis (MS; N\u2009=\u200919), and rheumatoid arthritis (RA; N\u2009=\u200921) versus healthy controls (HC; N\u2009=\u200923). Biological replicates were collected from participants within a 2-month interval. This study aimed to identify common (or unique) taxonomic biomarkers of IMIDs using both differential abundance testing and a machine learning approach. RESULTS: Significant microbial community differences between cohorts were observed (pseudo F\u2009=\u20094.56; p\u2009=\u20090.01). Richness and diversity were significantly different between cohorts (pFDR <\u20090.001) and were lowest in CD while highest in HC. Abundances of Actinomyces, Eggerthella, Clostridium III, Faecalicoccus, and Streptococcus (pFDR <\u20090.001) were significantly higher in all disease cohorts relative to HC, whereas significantly lower abundances were observed for Gemmiger, Lachnospira, and Sporobacter (pFDR <\u20090.001). Several taxa were found to be differentially abundant in IMIDs versus HC including significantly higher abundances of Intestinibacter in CD, Bifidobacterium in UC, and unclassified Erysipelotrichaceae in MS and significantly lower abundances of Coprococcus in CD, Dialister in MS, and Roseburia in RA. A machine learning approach to classify disease versus HC was highest for CD (AUC\u2009=\u20090.93 and AUC\u2009=\u20090.95 for OTU and genus features, respectively) followed by MS, RA, and UC. Gemmiger and Faecalicoccus were identified as important features for classification of subjects to CD and HC. In general, features identified by differential abundance testing were consistent with machine learning feature importance. CONCLUSIONS: This study identified several gut microbial taxa with differential abundance patterns common to IMIDs. We also found differentially abundant taxa between IMIDs. These taxa may serve as biomarkers for the detection and diagnosis of IMIDs and suggest there may be a common component to IMID etiology.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "33352216", + "title": "Changes in intestinal microbiota and correlation with TLRs in ulcerative colitis in the coastal area of northern China.", + "year": 2021, + "journal": "Microbial pathogenesis", + "authors": [ + "Xu N", + "Bai X", + "Cao X", + "Yue W", + "Jiang W", + "Yu Z" + ], + "bacteria": "Phascolarctobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6981842397571464, + "mesh_terms": [ + "China", + "Colitis, Ulcerative", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: To investigate the communities of fecal microbiota and the role of Toll-like receptors in patients with ulcerative colitis in the coastal area of northern China. METHODS: Stool samples from 31 patients with ulcerative colitis and 12 healthy individuals were collected. The total bacterial genomic DNA was extracted, and the V3+V4 hypervariable region in the bacterial 16S rRNA gene sequence was amplified by polymerase chain reaction (PCR). High-throughput sequencing analysis was performed on the Illumina Hiseq platform. The expression of TLR2, TLR4, Tollip, PPAR-\u03b3, IL-6, and TNF-\u03b1 in the colonic mucosa was measured by Western blots. RESULTS: The diversity of the fecal microbiota in patients with ulcerative colitis was significantly less than that in healthy control individuals (p\u00a0<\u00a00.05). The proportion of Bacteroidetes was significantly reduced (p\u00a0<\u00a00.01), whereas Proteobacteria was prevalent (p\u00a0<\u00a00.01) in patients with ulcerative colitis. At the genus level, the relative abundance of Streptococcus and Anaerostipes was significantly increased (p\u00a0<\u00a00.05), whereas the proportion of Bacteroides, Lachnospira, Ruminococcus, Phascolarctobacterium, and Coprococcus was significantly decreased in patients with ulcerative colitis (p\u00a0<\u00a00.05). The diversity indexes of fecal microbiota in patients with ulcerative colitis were negatively correlated with disease severity (p\u00a0<\u00a00.05). The relative abundance of Enterobacteriaceae was positively correlated with disease severity, and the relative abundance of Phascolarctobacterium, Anaerostipes, Fusobacterium, Parabacteroides, Oscillospira, and Ochrobactrum were negatively correlated with disease severity. The expression levels of TLR2 and TLR4 in the intestinal mucosa were positively correlated with the relative abundance of Streptococcus and Enterobacteriaceae, respectively (r\u00a0=\u00a00.481, p\u00a0=\u00a00.007; r\u00a0=\u00a00.455, p\u00a0=\u00a00.017). CONCLUSION: There were significant changes in the diversity and composition of the fecal microbiota in patients with ulcerative colitis compared to healthy individuals. The dysbiosis of gut microbiota and correlation with TLRs might play important roles in the pathogenesis and progression of ulcerative colitis.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37507685", + "title": "Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population.", + "year": 2023, + "journal": "BMC gastroenterology", + "authors": [ + "Alsulaiman RM", + "Al-Quorain AA", + "Al-Muhanna FA", + "Piotrowski S", + "Kurdi EA", + "Vatte C", + "Alquorain AA", + "Alfaraj NH", + "Alrezuk AM", + "Robinson F", + "Dowdell AK", + "Alamri TA", + "Hamilton L", + "Lad H", + "Gao H", + "Gandla D", + "Keating BJ", + "Meng R", + "Piening B", + "Al-Ali AK" + ], + "bacteria": "Phascolarctobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6427295074351848, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Saudi Arabia", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Crohn Disease" + ], + "raw_abstract": "BACKGROUND: Crohn's diseases and ulcerative colitis, both of which are chronic immune-mediated disorders of the gastrointestinal tract are major contributors to the overarching Inflammatory bowel diseases. It has become increasingly evident that the pathological processes of IBDs results from interactions between genetic and environmental factors, which can skew immune responses against normal intestinal flora. METHODS: The aim of this study is to assess and analyze the taxa diversity and relative abundances in CD and UC in the Saudi population. We utilized a sequencing strategy that targets all variable regions in the 16\u00a0S rRNA gene using the Swift Amplicon 16\u00a0S rRNA Panel on Illumina NovaSeq 6000. RESULTS: The composition of stool 16\u00a0S rRNA was analyzed from 219 patients with inflammatory bowel disease and from 124 healthy controls. We quantified the abundance of microbial communities to examine any significant differences between subpopulations of samples. At the genus level, two genera in particular, Veillonella and Lachnoclostridium showed significant association with CD versus controls. There were significant differences between subjects with CD versus UC, with the top differential genera spanning Akkermansia, Harryflintia, Maegamonas and Phascolarctobacterium. Furthermore, statistically significant taxa diversity in microbiome composition was observed within the UC and CD groups. CONCLUSIONS: In conclusion we have shown that there are significant differences in gut microbiota between UC, CD and controls in a Saudi Arabian inflammatory bowel disease cohort. This reinforces the need for further studies in large populations that are ethnically and geographically diverse. In addition, our results show the potential to develop classifiers that may have add additional richness of context to clinical diagnosis of UC and CD with larger inflammatory bowel disease cohorts.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "32066975", + "title": "Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota.", + "year": 2020, + "journal": "Nature medicine", + "authors": [ + "Nagao-Kitamoto H", + "Leslie JL", + "Kitamoto S", + "Jin C", + "Thomsson KA", + "Gillilland MG", + "Kuffa P", + "Goto Y", + "Jenq RR", + "Ishii C", + "Hirayama A", + "Seekatz AM", + "Martens EC", + "Eaton KA", + "Kao JY", + "Fukuda S", + "Higgins PDR", + "Karlsson NG", + "Young VB", + "Kamada N" + ], + "bacteria": "Phascolarctobacterium", + "condition": "ulcerative colitis", + "relevance_score": 0.6070612520808287, + "mesh_terms": [ + "Animals", + "Bacteria", + "Clostridioides difficile", + "Clostridium Infections", + "Enterocolitis, Pseudomembranous", + "Female", + "Gastrointestinal Microbiome", + "Glycosylation", + "Host Microbial Interactions", + "Humans", + "Interleukins", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Mice, Knockout", + "Veillonellaceae", + "Interleukin-22" + ], + "raw_abstract": "The involvement of host immunity in the gut microbiota-mediated colonization resistance to Clostridioides difficile infection (CDI) is incompletely understood. Here, we show that interleukin (IL)-22, induced by colonization of the gut microbiota, is crucial for the prevention of CDI in human microbiota-associated (HMA) mice. IL-22 signaling in HMA mice regulated host glycosylation, which enabled the growth of succinate-consuming bacteria Phascolarctobacterium spp. within the gut microbiome. Phascolarctobacterium reduced the availability of luminal succinate, a crucial metabolite for the growth of C. difficile, and therefore prevented the growth of C. difficile. IL-22-mediated host N-glycosylation is likely impaired in patients with ulcerative colitis (UC) and renders UC-HMA mice more susceptible to CDI. Transplantation of healthy human-derived microbiota or Phascolarctobacterium reduced luminal succinate levels and restored colonization resistance in UC-HMA mice. IL-22-mediated host glycosylation thus fosters the growth of commensal bacteria that compete with C. difficile for the nutritional niche.", + "condition_dir": "microbiome-uc-ibd/ulcerative_colitis" + }, + { + "pmid": "37507685", + "title": "Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population.", + "year": 2023, + "journal": "BMC gastroenterology", + "authors": [ + "Alsulaiman RM", + "Al-Quorain AA", + "Al-Muhanna FA", + "Piotrowski S", + "Kurdi EA", + "Vatte C", + "Alquorain AA", + "Alfaraj NH", + "Alrezuk AM", + "Robinson F", + "Dowdell AK", + "Alamri TA", + "Hamilton L", + "Lad H", + "Gao H", + "Gandla D", + "Keating BJ", + "Meng R", + "Piening B", + "Al-Ali AK" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.438669192088716, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Saudi Arabia", + "Inflammatory Bowel Diseases", + "Colitis, Ulcerative", + "Crohn Disease" + ], + "raw_abstract": "BACKGROUND: Crohn's diseases and ulcerative colitis, both of which are chronic immune-mediated disorders of the gastrointestinal tract are major contributors to the overarching Inflammatory bowel diseases. It has become increasingly evident that the pathological processes of IBDs results from interactions between genetic and environmental factors, which can skew immune responses against normal intestinal flora. METHODS: The aim of this study is to assess and analyze the taxa diversity and relative abundances in CD and UC in the Saudi population. We utilized a sequencing strategy that targets all variable regions in the 16\u00a0S rRNA gene using the Swift Amplicon 16\u00a0S rRNA Panel on Illumina NovaSeq 6000. RESULTS: The composition of stool 16\u00a0S rRNA was analyzed from 219 patients with inflammatory bowel disease and from 124 healthy controls. We quantified the abundance of microbial communities to examine any significant differences between subpopulations of samples. At the genus level, two genera in particular, Veillonella and Lachnoclostridium showed significant association with CD versus controls. There were significant differences between subjects with CD versus UC, with the top differential genera spanning Akkermansia, Harryflintia, Maegamonas and Phascolarctobacterium. Furthermore, statistically significant taxa diversity in microbiome composition was observed within the UC and CD groups. CONCLUSIONS: In conclusion we have shown that there are significant differences in gut microbiota between UC, CD and controls in a Saudi Arabian inflammatory bowel disease cohort. This reinforces the need for further studies in large populations that are ethnically and geographically diverse. In addition, our results show the potential to develop classifiers that may have add additional richness of context to clinical diagnosis of UC and CD with larger inflammatory bowel disease cohorts.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "31892611", + "title": "The Effect of Various Doses of Oral Vitamin D", + "year": 2020, + "journal": "Anticancer research", + "authors": [ + "Charoenngam N", + "Shirvani A", + "Kalajian TA", + "Song A", + "Holick MF" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.4002082630622424, + "mesh_terms": [ + "Administration, Oral", + "Adult", + "Bacteria", + "Cholecalciferol", + "Dietary Supplements", + "Dose-Response Relationship, Drug", + "Double-Blind Method", + "Gastrointestinal Microbiome", + "Humans" + ], + "raw_abstract": "BACKGROUND/AIM: To investigate the effects of vitamin D PATIENTS AND METHODS: Twenty adults with vitamin D insufficiency/deficiency [25(OH)D <30 ng/ml] were enrolled and given 600, 4,000 or 10,000 IUs/day of oral vitamin D RESULTS: Baseline serum 25(OH)D was associated with increased relative abundance of Akkermansia and decreased relative abundance of Porphyromonas (p<0.05). After the intervention, we observed a dose-dependent increase in relative abundance of Bacteroides with a significant difference between the 600 IUs and the 10,000 IUs groups (p=0.027), and Parabacteroides with a significant difference between the 600 IUs and the 4,000 IUs groups (p=0.039). CONCLUSION: Increased serum 25(OH)D was associated with increased beneficial bacteria and decreased pathogenic bacteria. A dose-dependent increase in bacteria associated with decreased inflammatory bowel disease activity was observed after vitamin D", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "30958298", + "title": "FEATURES OF MICROBIOTA IN PSORIATIC DISEASE: FROM SKIN AND GUT PERSPECTIVES (REVIEW).", + "year": 2019, + "journal": "Georgian medical news", + "authors": [ + "Algazina T", + "Yermekbayeva B", + "Batpenova G", + "Kushugulova A" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.3426615538847056, + "mesh_terms": [ + "Arthritis, Psoriatic", + "Dermatitis, Atopic", + "Humans", + "Microbiota", + "Psoriasis", + "Skin" + ], + "raw_abstract": "Psoriatic disease is a chronic inflammatory disease characterized by skin lesions. Psoriasis development has been associated both with genetic and environmental factors. Though skin and gut microbiota has been implicated in number of pathologies including atopic dermatitis, inflammatory bowel disease, Crohn's disease, allergy, and obesity, its role has been poorly studied in psoriatic disease, which incorporates both psoriasis and psoriatic arthritis. This literature review summarizes the most recent and major findings on microbiota features in psoriatic disease. Despite conflicting findings, psoriasis patients were frequently found to have distinct microbial composition in both skin and guts especially in the major bacterial phyla, Firmicutes, Bacteroidetes, and genus Akkermansia. Furthermore, bacterial DNA has been found in psoriatic patients both locally and systemically, and altogether suggesting a crucial role of bacteria in psoriatic disease and future studies in this field.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "35640610", + "title": "Interspecies commensal interactions have nonlinear impacts on host immunity.", + "year": 2022, + "journal": "Cell host & microbe", + "authors": [ + "Rice TA", + "Bielecka AA", + "Nguyen MT", + "Rosen CE", + "Song D", + "Sonnert ND", + "Yang Y", + "Cao Y", + "Khetrapal V", + "Catanzaro JR", + "Martin AL", + "Rashed SA", + "Leopold SR", + "Hao L", + "Yu X", + "van Dijk D", + "Ring AM", + "Flavell RA", + "de Zoete MR", + "Palm NW" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.2973499063238952, + "mesh_terms": [ + "Animals", + "Colitis", + "Germ-Free Life", + "Humans", + "Inflammatory Bowel Diseases", + "Intestines", + "Mice", + "Verrucomicrobia" + ], + "raw_abstract": "The impacts of individual commensal microbes on immunity and disease can differ dramatically depending on the surrounding microbial context; however, the specific bacterial combinations that dictate divergent immunological outcomes remain largely undefined. Here, we characterize an immunostimulatory Allobaculum species from an inflammatory bowel disease patient that exacerbates colitis in gnotobiotic mice. Allobaculum inversely associates with the taxonomically divergent immunostimulatory species Akkermansia muciniphila in human-microbiota-associated mice and human cohorts. Co-colonization with A.\u00a0muciniphila ameliorates Allobaculum-induced intestinal epithelial cell activation and colitis in mice, whereas Allobaculum blunts the A.muciniphila-specific systemic antibody response and reprograms the immunological milieu in mesenteric lymph nodes by blocking A.muciniphila-induced dendritic cell activation and T\u00a0cell expansion. These studies thus identify a pairwise reciprocal interaction between human gut bacteria that dictates divergent immunological outcomes. Furthermore, they establish a generalizable framework to define the contextual cues contributing to the \"incomplete penetrance\" of microbial impacts on human disease.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "31599433", + "title": "Akkermansia muciniphila: key player in metabolic and gastrointestinal disorders.", + "year": 2019, + "journal": "European review for medical and pharmacological sciences", + "authors": [ + "Macchione IG", + "Lopetuso LR", + "Ianiro G", + "Napoli M", + "Gibiino G", + "Rizzatti G", + "Petito V", + "Gasbarrini A", + "Scaldaferri F" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.2735616150113266, + "mesh_terms": [ + "Akkermansia", + "Animals", + "Diabetes Mellitus, Type 2", + "Dysbiosis", + "Dyslipidemias", + "Gastrointestinal Diseases", + "Gastrointestinal Microbiome", + "Glucose", + "Humans", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Lipid Metabolism", + "Obesity", + "Permeability", + "Verrucomicrobia" + ], + "raw_abstract": "OBJECTIVE: Gut microbiota has a key role in host metabolic regulation and immune response, and its dysbiosis represents one of the main causes of gastrointestinal diseases. In this scenario, Akkermansia muciniphila is a crucial player in keeping the integrity of the gastrointestinal tract. MATERIALS AND METHODS: This review focuses on the correlation between gut microbiota and intestinal homeostasis, primarily exploring A. muciniphila and its involvement in the development of metabolic disorders and gastrointestinal diseases. RESULTS: Akkermansia muciniphila belongs to the Verrucomicrobia phylum, and it colonizes the mucus layer in the gastrointestinal tract, representing 1 to 4% of the fecal microbiota. It stimulates mucosal microbial networks, and it improves intestinal barrier function, providing crucial host immunological responses. Several studies have demonstrated the possible involvement of A. muciniphila in the development of intestinal and metabolic disorders. Indeed, adipose and glucose metabolisms are influenced by A. muciniphila, and its levels inversely correlate to inflammatory conditions, such as inflammatory bowel disease, obesity, and diabetes. Conversely, its therapeutic administration decreases their development. CONCLUSIONS: A. muciniphila exerts a key role in the maintenance of intestinal health and in host metabolic modulation. Future studies could open new horizons towards its potential therapeutic applications in gastrointestinal and extra-intestinal diseases.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "38531966", + "title": "Lacidophilin tablets alleviate constipation through regulation of intestinal microflora by promoting the colonization of Akkermansia sps.", + "year": 2024, + "journal": "Scientific reports", + "authors": [ + "Sun D", + "Yu J", + "Zhan Y", + "Cheng X", + "Zhang J", + "Li Y", + "Li Q", + "Xiong Y", + "Liu W" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.2555774811255009, + "mesh_terms": [ + "Rats", + "Animals", + "Gastrointestinal Microbiome", + "Akkermansia", + "Constipation", + "Intestines", + "Loperamide" + ], + "raw_abstract": "Constipation is a major health problem worldwide that requires effective and safe treatment options. Increasing evidence indicates that disturbances in gut microbiota may be a risk factor for constipation. Administration of lacidophilin tablets shows promising therapeutic potential in the treatment of inflammatory bowel disease owing to their immunomodulatory properties and regulation of the gut microbiota. The focus of this study was on investigating the ability of lacidophilin tablets to relieve constipation by modulating the gut microbiome. Rats with loperamide hydrochloride induced constipation were treated with lacidophilin tablets via intragastric administration for ten days. The laxative effect of lacidophilin tablets was then evaluated by investigating the regulation of intestinal microflora and the possible underlying molecular mechanism. Our results reveal that treatment with lacidophilin tablets increased the intestinal advancement rate, fecal moisture content, and colonic AQP3 protein expression. It also improved colonic microflora structure in the colonic contents of model rats mainly by increasing Akkermansia muciniphila and decreasing Clostridium_sensu_stricto_1. Transcriptome analysis indicated that treatment with lacidophilin tablets maintains the immune response in the intestine and promotes recovery of the intestinal mechanical barrier in the constipation model. Our study shows that lacidophilin tablets improve constipation, possibly by promoting Akkermansia colonization and by modulating the intestinal immune response.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "39560666", + "title": "Immunomolecular and reactivity landscapes of gut IgA subclasses in homeostasis and inflammatory bowel disease.", + "year": 2024, + "journal": "The Journal of experimental medicine", + "authors": [ + "Tejedor Vaquero S", + "Neuman H", + "Comerma L", + "Marcos-Fa X", + "Corral-Vazquez C", + "Uzzan M", + "Pybus M", + "Segura-Garz\u00f3n D", + "Guerra J", + "Perruzza L", + "Tach\u00f3-Pi\u00f1ot R", + "Sintes J", + "Rosenstein A", + "Grasset EK", + "Iglesias M", + "Gonzalez Farr\u00e9 M", + "Lop J", + "Patriaca-Amiano ME", + "Larrubia-Loring M", + "Santiago-Diaz P", + "Perera-Bel J", + "Berenguer-Molins P", + "Martinez Gallo M", + "Martin-Nalda A", + "Varela E", + "Garrido-Pontnou M", + "Grassi F", + "Guarner F", + "Mehandru S", + "M\u00e1rquez-Mosquera L", + "Mehr R", + "Cerutti A", + "Magri G" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.24500096167525925, + "mesh_terms": [ + "Inflammatory Bowel Diseases", + "Humans", + "Homeostasis", + "Immunoglobulin A", + "Gastrointestinal Microbiome", + "Plasma Cells", + "Immunoglobulin A, Secretory", + "Akkermansia", + "Female", + "Intestinal Mucosa", + "Adult", + "Male" + ], + "raw_abstract": "The human gut includes plasma cells (PCs) expressing immunoglobulin A1 (IgA1) or IgA2, two structurally distinct IgA subclasses with elusive regulation, function, and reactivity. We show here that intestinal IgA1+ and IgA2+ PCs co-emerged early in life, comparably accumulated somatic mutations, and were enriched within short-lived CD19+ and long-lived CD19- PC subsets, respectively. IgA2+ PCs were extensively clonally related to IgA1+ PCs and a subset of them presumably emerged from IgA1+ precursors. Of note, secretory IgA1 (SIgA1) and SIgA2 dually coated a large fraction of mucus-embedded bacteria, including Akkermansia muciniphila. Disruption of homeostasis by inflammatory bowel disease (IBD) was associated with an increase in actively proliferating IgA1+ plasmablasts, a depletion in long-lived IgA2+ PCs, and increased SIgA1+SIgA2+ gut microbiota. Such increase featured enhanced IgA1 reactivity to pathobionts, including Escherichia coli, combined with depletion of beneficial A. muciniphila. Thus, gut IgA1 and IgA2 emerge from clonally related PCs and show unique changes in both frequency and reactivity in IBD.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "32616190", + "title": "Panax notoginseng saponins prevent colitis-associated colorectal cancer development: the role of gut microbiota.", + "year": 2020, + "journal": "Chinese journal of natural medicines", + "authors": [ + "Chen L", + "Chen MY", + "Shao L", + "Zhang W", + "Rao T", + "Zhou HH", + "Huang WH" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.22974388666667767, + "mesh_terms": [ + "Animals", + "Colitis-Associated Neoplasms", + "Colorectal Neoplasms", + "Disease Models, Animal", + "Feces", + "Gastrointestinal Microbiome", + "Male", + "Mice", + "Panax notoginseng", + "RNA, Ribosomal, 16S", + "Saponins" + ], + "raw_abstract": "Gut microbiota dysbiosis is a risk factor for colorectal cancer (CRC) in inflammatory bowel disease (IBD). In this study, the effects of Panax notoginseng saponins (PNS) on colitis-associated CRC progression were evaluated on an azoxymethane (AOM)/dextran sulfate sodium (DSS) mouse model. In vivo, PNS significantly relieved AOM/DSS-induced colon tumorigenesis and development by reducing the disease activity index (DAI) scores and colon tumor load. The 16S rRNA data of fecal samples showed that the microbiome community was obviously destructed, while PNS could recover the richness and diversity of gut microbiota. Especially, PNS could increase the abundance of Akkermansia spp. which was significantly decreased in model group and negatively correlated with the progression of CRC. Moreover, ginsenoside compound K (GC-K) was evaluated on the effects of human CRC cells, which was the main bio-transformed metabolite of PNS by gut microbiota. Our data showed that PNS played important role in the prevention of the progression of CRC, due to their regulation on the microbiome balance and microbial bio-converted product with anti-CRC activity.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "39041890", + "title": "Biomimetic Supramolecular Assembly with IGF-1C Delivery Ameliorates Inflammatory Bowel Disease (IBD) by Restoring Intestinal Barrier Integrity.", + "year": 2024, + "journal": "Advanced science (Weinheim, Baden-Wurttemberg, Germany)", + "authors": [ + "Fu E", + "Qian M", + "He N", + "Yin Y", + "Liu Y", + "Han Z", + "Han Z", + "Zhao Q", + "Cao X", + "Li Z" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.22758945966893857, + "mesh_terms": [ + "Inflammatory Bowel Diseases", + "Insulin-Like Growth Factor I", + "Animals", + "Intestinal Mucosa", + "Mice", + "Disease Models, Animal", + "Biomimetics", + "beta-Cyclodextrins", + "Hyaluronic Acid", + "Drug Delivery Systems", + "Male", + "Gastrointestinal Microbiome", + "Biomimetic Materials", + "Humans" + ], + "raw_abstract": "The management of dysfunctional intestinal epithelium by promoting mucosal healing and modulating the gut microbiota represents a novel therapeutic strategy for inflammatory bowel disease (IBD). As a convenient and well-tolerated method of drug delivery, intrarectal administration may represent a viable alternative to oral administration for the treatment of IBD. Here, a biomimetic supramolecular assembly of hyaluronic acid (HA) and \u03b2-cyclodextrin (HA-\u03b2-CD) for the delivery of the C domain peptide of insulin-like growth factor-1 (IGF-1C), which gradually releases IGF-1C, is developed. It is identified that the supramolecular assembly of HA-\u03b2-CD enhances the stability and prolongs the release of IGF-1C. Furthermore, this biomimetic supramolecular assembly potently inhibits the inflammatory response, thereby restoring intestinal barrier integrity. Following HA-\u03b2-CD-IGF-1C administration, 16S rDNA sequencing reveals a significant increase in the abundance of the probiotic Akkermansia, suggesting enhanced intestinal microbiome homeostasis. In conclusion, the findings demonstrate the promise of the HA-based mimicking peptide delivery platform as a therapeutic approach for IBD. This biomimetic supramolecular assembly effectively ameliorates intestinal barrier function and intestinal microbiome homeostasis, suggesting its potential for treating IBD.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "39097746", + "title": "The influence of Akkermansia muciniphila on intestinal barrier function.", + "year": 2024, + "journal": "Gut pathogens", + "authors": [ + "Mo C", + "Lou X", + "Xue J", + "Shi Z", + "Zhao Y", + "Wang F", + "Chen G" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.2217143276079699, + "mesh_terms": [], + "raw_abstract": "Intestinal barriers play a crucial role in human physiology, both in homeostatic and pathological conditions. Disruption of the intestinal barrier is a significant factor in the pathogenesis of gastrointestinal inflammatory diseases, such as inflammatory bowel disease. The profound influence of the gut microbiota on intestinal diseases has sparked considerable interest in manipulating it through dietary interventions, probiotics, and fecal microbiota transplantation as potential approaches to enhance the integrity of the intestinal barrier. Numerous studies have underscored the protective effects of specific microbiota and their associated metabolites. In recent years, an increasing body of research has demonstrated that Akkermansia muciniphila (A. muciniphila, Am) plays a beneficial role in various diseases, including diabetes, obesity, aging, cancer, and metabolic syndrome. It is gaining popularity as a regulator that influences the intestinal flora and intestinal barrier and is recognized as a 'new generation of probiotics'. Consequently, it may represent a potential target and promising therapy option for intestinal diseases. This article systematically summarizes the role of Am in the gut. Specifically, we carefully discuss key scientific issues that need resolution in the future regarding beneficial bacteria represented by Am, which may provide insights for the application of drugs targeting Am in clinical treatment.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "36056902", + "title": "A shared mucosal gut microbiota signature in primary sclerosing cholangitis before and after liver transplantation.", + "year": 2023, + "journal": "Hepatology (Baltimore, Md.)", + "authors": [ + "Hole MJ", + "J\u00f8rgensen KK", + "Holm K", + "Braadland PR", + "Meyer-Myklestad MH", + "Medhus AW", + "Reikvam DH", + "G\u00f6tz A", + "Grzyb K", + "Boberg KM", + "Karlsen TH", + "Kummen M", + "Hov JR" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.2089569809244345, + "mesh_terms": [ + "Humans", + "Liver Transplantation", + "Cholangitis, Sclerosing", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Liver" + ], + "raw_abstract": "BACKGROUND AND AIMS: Several characteristic features of the fecal microbiota have been described in primary sclerosing cholangitis (PSC), whereas data on mucosal microbiota are less consistent. We aimed to use a large colonoscopy cohort to investigate key knowledge gaps, including the role of gut microbiota in PSC with inflammatory bowel disease (IBD), the effect of liver transplantation (LT), and whether recurrent PSC (rPSC) may be used to define consistent microbiota features in PSC irrespective of LT. APPROACH AND RESULTS: We included 84 PSC and 51 liver transplanted PSC patients (PSC-LT) and 40 healthy controls (HCs) and performed sequencing of the 16S ribosomal RNA gene (V3-V4) from ileocolonic biopsies. Intraindividual microbial diversity was reduced in both PSC and PSC-LT versus HCs. An expansion of Proteobacteria was more pronounced in PSC-LT (up to 19% relative abundance) than in PSC (up to 11%) and HCs (up to 8%; Q FDR \u2009<\u20090.05). When investigating PSC before (PSC vs. HC) and after LT (rPSC vs. no-rPSC), increased variability (dispersion) in the PSC group was found. Five genera were associated with PSC before and after LT. A dysbiosis index calculated from the five genera, and the presence of the potential pathobiont, Klebsiella , were associated with reduced LT-free survival. Concomitant IBD was associated with reduced Akkermansia . CONCLUSIONS: Consistent mucosal microbiota features associated with PSC, PSC-IBD, and disease severity, irrespective of LT status, highlight the usefulness of investigating PSC and rPSC in parallel, and suggest that the impact of gut microbiota on posttransplant liver health should be investigated further.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "39836282", + "title": "Evaluation of variations in predominant gut microbiota members in inflammatory bowel disease using real-time PCR.", + "year": 2025, + "journal": "Molecular biology reports", + "authors": [ + "Tasoujlu M", + "Sharifi Y", + "Ghahremani M", + "Alizadeh K", + "Babaie F", + "Hosseiniazar MM" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.2052806031424637, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Real-Time Polymerase Chain Reaction", + "Male", + "Adult", + "Female", + "Feces", + "Middle Aged", + "Akkermansia", + "Bifidobacterium", + "Bacteria", + "Case-Control Studies", + "Lactobacillus", + "Enterobacteriaceae" + ], + "raw_abstract": "Inflammatory Bowel Disease (IBD) is a persistent ailment that impacts many individuals worldwide. The interaction between the immune system and gut microbiome is thought to influence IBD development. This study aimed to assess some microbiota in IBD patients compared to healthy individuals. The investigation involved a selected group of twenty patients suffering from IBD and an equal number of healthy participants. Stool specimens were obtained and analyzed for Lactobacillus, Bifidobacterium, Bacteroides, Clostridium leptum, Akkermansia muciniphila, Fusobacterium and Enterobacteriaceae using real-time PCR. The findings indicated significantly higher levels of Bifidobacterium in IBD patients (Pv\u2009=\u20090.009) and lower levels of A. muciniphila (Pv\u2009=\u20090.003) healthy individuals. Other bacteria tested did not show significant differences. The study suggests that the progression of IBD patients could be influenced by the rising of Bifidobacterium and the declining of A. muciniphila. Targeting these bacteria could lead to improved treatments and quality of life for those with IBD.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "35882149", + "title": "Chitosan-modified Phellinus igniarius polysaccharide PLGA nanoparticles ameliorated inflammatory bowel disease.", + "year": 2022, + "journal": "Biomaterials advances", + "authors": [ + "Bai X", + "Feng Z", + "Peng S", + "Zhu T", + "Jiao L", + "Mao N", + "Gu P", + "Liu Z", + "Yang Y", + "Wang D" + ], + "bacteria": "Akkermansia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.20174129990244793, + "mesh_terms": [ + "Anti-Inflammatory Agents", + "Chitosan", + "Humans", + "Inflammatory Bowel Diseases", + "Nanoparticles", + "Phellinus", + "Polysaccharides" + ], + "raw_abstract": "In many clinical studies, prebiotics have been used as adjuvant therapy for inflammatory bowel disease (IBD). Phellinus igniarius polysaccharide (PIP) possesses great anti-inflammatory and prebiotic activities. Herein, we developed an orally deliverable PIP-loaded chitosan-modified PLGA nanomedicine (CS-PIPP) to investigate its anti-inflammatory effect in vitro and in vivo. Dextran sodium sulfate (DSS)-induced colitis model was established to evaluate the preventive effect of CS-PIPP on IBD. This study characterized that CS-PIPP had a size of 288.7\u00a0\u00b1\u00a05.49\u00a0nm, positive zeta potential, and showed good stability over four weeks. The in-vitro study suggested that CS-PIPP had enhanced phagocytosis by macrophages, which could further significantly inhibit M1-like macrophages phenotype and regulate lipopolysaccharide (LPS)-induced inflammatory cytokines. The in-vivo study revealed that CS-PIPP prominently prevented intestinal inflammatory damage and protected the integrity of the intestinal barrier. Moreover, CS-PIPP increased the contents of short-chain fatty acids (SCFAs) and positively regulated the gut microbiota. Specifically, CS-PIPP reduced enteropathogenic microorganisms while increasing the beneficial microbiota, including Lactobacillus and Akkermansia, which revealed the potential of CS-PIPP as prebiotics. Generally, CS-PIPP promoted the anti-inflammatory effect of PIP, so it could be regarded as a novel and potent nanoformulation to treat IBD.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "28786749", + "title": "Specificities of the intestinal microbiota in patients with inflammatory bowel disease and Clostridium difficile infection.", + "year": 2018, + "journal": "Gut microbes", + "authors": [ + "Sokol H", + "Jegou S", + "McQuitty C", + "Straub M", + "Leducq V", + "Landman C", + "Kirchgesner J", + "Le Gall G", + "Bourrier A", + "Nion-Larmurier I", + "Cosnes J", + "Seksik P", + "Richard ML", + "Beaugerie L" + ], + "bacteria": "Dorea", + "condition": "inflammatory bowel disease", + "relevance_score": 0.24285953538732621, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biodiversity", + "Clostridium Infections", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestines", + "Male", + "Middle Aged", + "Species Specificity", + "Young Adult" + ], + "raw_abstract": "Clostridium difficile infection (CDI) is a common complication in inflammatory bowel disease (IBD) and has been associated with poor IBD outcome. Intestinal microbiota composition in IBD patients with CDI has not been specifically evaluated to date. The fecal microbiota of 56 IBD patients, including 8 in flare with concomitant CDI, 24 in flare without CDI, and 24 in remission, as well as 24 healthy subjects, was studied using 16S sequencing. Analysis was performed using the Qiime pipeline. Compared to IBD patients without CDI, IBD patients with CDI had more pronounced dysbiosis with higher levels of Ruminococcus gnavus and Enterococcus operational taxonomic units (OTUs) and lower levels of Blautia and Dorea OTUs. Correlation network analysis suggested a disrupted ecosystem in IBD patients in flare, particularly in those with CDI. In patients with IBD, CDI is associated with a more pronounced intestinal dysbiosis with specific alterations in intestinal microorganisms.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "36695274", + "title": "Composition of the gut microbiota in patients with inflammatory bowel disease in Saudi Arabia: A pilot study.", + "year": 2023, + "journal": "Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association", + "authors": [ + "Al-Amrah H", + "Saadah OI", + "Mosli M", + "Annese V", + "Al-Hindi R", + "Edris S", + "Alshehri D", + "Alatawi H", + "Alatawy M", + "Bahieldin A" + ], + "bacteria": "Dorea", + "condition": "inflammatory bowel disease", + "relevance_score": 0.22672875939095624, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Pilot Projects", + "Saudi Arabia", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Feces" + ], + "raw_abstract": "CONCLUSIONS: The results of this study provide an overview of the variations in microbiota diversity present in Saudi IBD patients compared to healthy controls. RESULTS: The key finding was three negative bacterial biomarkers, Paraprevotellaceae, the Muribaculaceae families of Bacteroidetes phylum, and the Leuconostocaceae family of Firmicutes phylum, which had a higher relative abundance in healthy individuals compared to IBD patients. It was also found that primary microbiota signatures at certain genera and species levels, including Prevotella copri, Bifidobacterium adolescentis, Ruminococcus callidus, Coprococcus sp., Ruminococcus gnavus, Dorea formicigenerans, Leuconostoc, Dialister, Catenibacterium, Eubacterium biforme, and Lactobacillus mucosae, were absent in almost all IBD patients, while Veillonella dispar was absent in all healthy individuals. METHODS: After obtaining an informed consent, fecal samples were collected from 11 participants with IBD (patients) and 10 healthy individuals (controls). The bacterial components of the microbial population were identified by next-generation sequencing of partial 16S rRNA. Statistically significant dissimilarities were observed between samples for all metrics. BACKGROUND: Inflammatory bowel disease (IBD) is a chronic intestinal inflammatory condition attributed to a complex interaction between imbalances in the gut microbiome, environmental conditions, and a deregulated immune response. The aim of the study was to investigate the composition of the gut microbiome of Saudi patients with IBD.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "29401402", + "title": "Potential of Lactobacillus plantarum ZDY2013 and Bifidobacterium bifidum WBIN03 in relieving colitis by gut microbiota, immune, and anti-oxidative stress.", + "year": 2018, + "journal": "Canadian journal of microbiology", + "authors": [ + "Wang Y", + "Guo Y", + "Chen H", + "Wei H", + "Wan C" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.5695466994990738, + "mesh_terms": [ + "Animals", + "Bifidobacterium bifidum", + "Colitis", + "Cytokines", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "HT29 Cells", + "Humans", + "Hydrogen Peroxide", + "Lactobacillus plantarum", + "Mice", + "Mice, Inbred BALB C", + "Oxidative Stress", + "Probiotics" + ], + "raw_abstract": "Ulcerative colitis (UC) is an inflammatory bowel disease that is difficult to cure, with rising incidence in recent decades. Probiotics have become a new strategy for UC treatment. In this study, we chose 2 new multisource probiotics, Lactobacillus plantarum ZDY2013 from acid beans and Bifidobacterium bifidum WBIN03 from infant feces, and a mixture of both, to investigate the anti-inflammatory and antioxidant effect on H", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "30227219", + "title": "Bifidobacterium longum and VSL#3", + "year": 2019, + "journal": "Developmental and comparative immunology", + "authors": [ + "Chen X", + "Fu Y", + "Wang L", + "Qian W", + "Zheng F", + "Hou X" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.4226322068160306, + "mesh_terms": [ + "Animals", + "Bifidobacterium longum", + "Caco-2 Cells", + "Colitis", + "Colon", + "Disease Models, Animal", + "Electric Impedance", + "Feces", + "HMGB1 Protein", + "Humans", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Male", + "Mice", + "Mice, Inbred BALB C", + "Probiotics", + "Trinitrobenzenesulfonic Acid", + "Zonula Occludens-1 Protein" + ], + "raw_abstract": "Probiotics are a beneficial treatment for inflammatory bowel disease (IBD). However, studies comparing the effects of similar doses of single and mixed probiotics on IBD are scarce. High mobility group box 1 (HMGB1) is an important proinflammatory mediator involved IBD development. The present study assessed fecal HMGB1 levels in IBD patients and compared the effects of similar doses of Bifidobacterium longum (Bif) versus VSL#3", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "39836282", + "title": "Evaluation of variations in predominant gut microbiota members in inflammatory bowel disease using real-time PCR.", + "year": 2025, + "journal": "Molecular biology reports", + "authors": [ + "Tasoujlu M", + "Sharifi Y", + "Ghahremani M", + "Alizadeh K", + "Babaie F", + "Hosseiniazar MM" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.3682877947764988, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Real-Time Polymerase Chain Reaction", + "Male", + "Adult", + "Female", + "Feces", + "Middle Aged", + "Akkermansia", + "Bifidobacterium", + "Bacteria", + "Case-Control Studies", + "Lactobacillus", + "Enterobacteriaceae" + ], + "raw_abstract": "Inflammatory Bowel Disease (IBD) is a persistent ailment that impacts many individuals worldwide. The interaction between the immune system and gut microbiome is thought to influence IBD development. This study aimed to assess some microbiota in IBD patients compared to healthy individuals. The investigation involved a selected group of twenty patients suffering from IBD and an equal number of healthy participants. Stool specimens were obtained and analyzed for Lactobacillus, Bifidobacterium, Bacteroides, Clostridium leptum, Akkermansia muciniphila, Fusobacterium and Enterobacteriaceae using real-time PCR. The findings indicated significantly higher levels of Bifidobacterium in IBD patients (Pv\u2009=\u20090.009) and lower levels of A. muciniphila (Pv\u2009=\u20090.003) healthy individuals. Other bacteria tested did not show significant differences. The study suggests that the progression of IBD patients could be influenced by the rising of Bifidobacterium and the declining of A. muciniphila. Targeting these bacteria could lead to improved treatments and quality of life for those with IBD.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "37599322", + "title": "The Anti-Inflammatory Effect of a Probiotic Cocktail in Human Feces Induced-Mouse Model.", + "year": 2023, + "journal": "Inflammation", + "authors": [ + "Salimi A", + "Sepehr A", + "Hejazifar N", + "Talebi M", + "Rohani M", + "Pourshafie MR" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.3314012746646197, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "Feces", + "Inflammatory Bowel Diseases", + "Inflammation", + "Probiotics", + "Anti-Inflammatory Agents", + "Dextran Sulfate", + "Colitis", + "Disease Models, Animal", + "Mice, Inbred C57BL" + ], + "raw_abstract": "Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract due to altered interaction between the immune system and the gut microbiota. The aim of this study was to investigate the role of a probiotic cocktail in modulating immune dysregulation induced in mice. Mice were divided into 5 groups (n = 5/group), and inflammation was induced in two separate groups by fecal microbiota transplantation (FMT) from the stool of human with IBD and dextran sulfate sodium (DSS). In the other two groups, the cocktail of Lactobacillus spp. and Bifidobacterium spp. (10", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "26770128", + "title": "Part 2: Treatments for Chronic Gastrointestinal Disease and Gut Dysbiosis.", + "year": 2015, + "journal": "Integrative medicine (Encinitas, Calif.)", + "authors": [ + "Bull MJ", + "Plummer NT" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.3026385915301118, + "mesh_terms": [], + "raw_abstract": "Part 1 of this review discussed the connection between the human gut microbiota and health. Manipulation of the intestinal microbiota holds promise as a prospective therapy for gut dysbiosis, ameliorating symptoms of gastrointestinal and systemic diseases and restoring health. The concept of probiotics has existed for more than 100 y, and modern research methods have established sound scientific support for the perceived benefits of probiotic bacteria, which mainly include Lactobacillus and Bifidobacterium genera. On the basis of these evidence-based functional approaches, dietary interventions that supplement the normal diet with probiotics or prebiotics are now considered as potentially viable alternatives or adjuncts to the use of steroids, immunosuppressants, and/or surgical interventions. Studies investigating the impact on gastrointestinal disorders, such as diarrhea, inflammatory bowel disease (IBD), irritable bowel syndrome (IBS); and systemic metabolic diseases, such as type 2 diabetes and obesity, in response to the use of probiotics and prebiotics are reviewed. Further, fecal microbial transplantation (FMT) is discussed as an exciting development in the treatment of gut dysbiosis using microbes.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "25744647", + "title": "Evaluation of the probiotic properties of new Lactobacillus and Bifidobacterium strains and their in vitro effect.", + "year": 2015, + "journal": "Applied microbiology and biotechnology", + "authors": [ + "Presti I", + "D'Orazio G", + "Labra M", + "La Ferla B", + "Mezzasalma V", + "Bizzaro G", + "Giardina S", + "Michelotti A", + "Tursi F", + "Vassallo M", + "Di Gennaro P" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.2926967814532617, + "mesh_terms": [ + "Animals", + "Anti-Bacterial Agents", + "Antibiosis", + "Antioxidants", + "Bifidobacterium", + "Bile Acids and Salts", + "Cell Line", + "DNA, Bacterial", + "DNA, Ribosomal", + "Epithelial Cells", + "Fibroblasts", + "Humans", + "Hydrogen-Ion Concentration", + "Lactobacillus", + "Mice, Inbred BALB C", + "Molecular Sequence Data", + "Probiotics", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA", + "Vitamin B Complex" + ], + "raw_abstract": "Probiotic ingestion is recommended as a preventive approach to maintain the balance of the intestinal microbiota and to enhance the human well-being. During the whole life of each individual, the gut microbiota composition could be altered by lifestyle, diet, antibiotic therapies and other stress conditions, which may lead to acute and chronic disorders. Hence, probiotics can be administered for the prevention or treatment of some disorders, including lactose malabsorption, acute diarrhoea, irritable bowel syndrome, necrotizing enterocolitis and mild forms of inflammatory bowel disease. The probiotic-mediated effect is an important issue that needs to be addressed in relation to strain-specific probiotic properties. In this work, the probiotic properties of new Lactobacillus and Bifidobacterium strains were screened, and their effects in vitro were evaluated. They were screened for probiotic properties by determining their tolerance to low pH and to bile salts, antibiotic sensitivity, antimicrobial activity and vitamin B8, B9 and B12 production, and by considering their ability to increase the antioxidant potential and to modulate the inflammatory status of systemic-miming cell lines in vitro. Three out of the examined strains presenting the most performant probiotic properties, as Lactobacillus plantarum PBS067, Lactobacillus rhamnosus PBS070 and Bifidobacterium animalis subsp. lactis PBSO75, were evaluated for their effects also on human intestinal HT-29 cell line. The obtained results support the possibility to move to another level of study, that is, the oral administration of these probiotical strains to patients with acute and chronic gut disorders, by in vivo experiments.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "25896155", + "title": "Effects of Probiotics on Gut Microbiota in Patients with Inflammatory Bowel Disease: A Double-blind, Placebo-controlled Clinical Trial.", + "year": 2015, + "journal": "The Korean journal of gastroenterology = Taehan Sohwagi Hakhoe chi", + "authors": [ + "Shadnoush M", + "Hosseini RS", + "Khalilnezhad A", + "Navai L", + "Goudarzi H", + "Vaezjalali M" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.28314883527591767, + "mesh_terms": [ + "Adult", + "Bacteroides", + "Bifidobacterium", + "DNA, Bacterial", + "Double-Blind Method", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestines", + "Lactobacillus", + "Male", + "Middle Aged", + "Placebo Effect", + "Probiotics", + "Real-Time Polymerase Chain Reaction" + ], + "raw_abstract": "BACKGROUND/AIMS: Several clinical trials have revealed various advantages for probiotics in inflammatory bowel disease (IBD). The aim of this study was to further investigate the effects of probiotic yogurt consumption on gut microbiota in patients with this disease. METHODS: A total of 305 participants were divided into three groups; group A (IBD patients receiving probiotic yogurt; n=105), group B (IBD patients receiving placebo; n=105), and control group (healthy individuals receiving probiotic yogurt; n=95). Stool samples were collected both before and after 8 weeks of intervention; and population of Lactobacillus, Bifidobacterium and Bacteroides in the stool specimens was measured by Taqman real-time PCR method. RESULTS: By the end of the intervention, no significant variations in the mean weight and body mass index were observed between three groups (p>0.05). However, the mean numbers of Lactobacillus, Bifidobacterium, and Bacteroides in group A were significantly increased compared to group B (p<0.001, p<0.001, and p< 0.01, respectively). There were also significant differences in the mean numbers of either of three bacteria between group A and the healthy control group; however, these differences between two groups were observed both at baseline and the end of the intervention. CONCLUSIONS: Consumption of probiotic yogurt by patients with IBD may help to improve intestinal function by increasing the number of probiotic bacteria in the intestine and colon. However, many more studies are required in order to prove the concept.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "28233848", + "title": "Spray-drying process preserves the protective capacity of a breast milk-derived Bifidobacterium lactis strain on acute and chronic colitis in mice.", + "year": 2017, + "journal": "Scientific reports", + "authors": [ + "Burns P", + "Alard J", + "Hrd\u1ef3 J", + "Boutillier D", + "P\u00e1ez R", + "Reinheimer J", + "Pot B", + "Vinderola G", + "Grangette C" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.26017519633747055, + "mesh_terms": [ + "Animals", + "Argentina", + "Bacteriological Techniques", + "Bifidobacterium animalis", + "Colitis", + "Desiccation", + "Disease Models, Animal", + "Humans", + "Mice", + "Microbial Viability", + "Milk, Human", + "Probiotics", + "Technology, Pharmaceutical" + ], + "raw_abstract": "Gut microbiota dysbiosis plays a central role in the development and perpetuation of chronic inflammation in inflammatory bowel disease (IBD) and therefore is key target for interventions with high quality and functional probiotics. The local production of stable probiotic formulations at limited cost is considered an advantage as it reduces transportation cost and time, thereby increasing the effective period at the consumer side. In the present study, we compared the anti-inflammatory capacities of the Bifidobacterium animalis subsp. lactis (B. lactis) INL1, a probiotic strain isolated in Argentina from human breast milk, with the commercial strain B. animalis subsp. lactis BB12. The impact of spray-drying, a low-cost alternative of bacterial dehydration, on the functionality of both bifidobacteria was also investigated. We showed for both bacteria that the spray-drying process did not impact on bacterial survival nor on their protective capacities against acute and chronic colitis in mice, opening future perspectives for the use of strain INL1 in populations with IBD.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "31418411", + "title": "Effects of pentasa-combined probiotics on the microflora structure and prognosis of patients with inflammatory bowel disease.", + "year": 2019, + "journal": "The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology", + "authors": [ + "Fan H", + "Du J", + "Liu X", + "Zheng WW", + "Zhuang ZH", + "Wang CD", + "Gao R" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.25130381525279044, + "mesh_terms": [ + "Adult", + "Anti-Inflammatory Agents, Non-Steroidal", + "Cytokines", + "Drug Therapy, Combination", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Mesalamine", + "Middle Aged", + "Probiotics", + "Prognosis", + "Treatment Outcome" + ], + "raw_abstract": "BACKGROUND/AIMS: The aim of the present study was to investigate the effects of the combination treatment of pentasa and probiotics on the microflora composition and prognosis in patients with inflammatory bowel disease (IBD). MATERIALS AND METHODS: A total of 40 patients with IBD (19 control group and 21 observation group) were randomized. Patients in the control group were given pentasa, and patients in the observation group were given probiotics along with pentasa. The microflora composition, biochemical indices, inflammatory markers, and activity scores of the two groups were analyzed. RESULTS: After treatment, the number of enterobacteria, enterococci, saccharomyces, and bacteroides; the levels of fecal lactoferrin, 1-antitrypsin, \u03b22-microglobulin, high-sensitivity C-reactive protein, and interleukin (IL)-6; activity scores; and recurrence rate in the observation group were significantly lower than those in the control group. Bifidobacterium and lactobacillus counts and IL-4 levels were significantly higher in the observation group than in the control group. CONCLUSION: The combination of probiotics and pentasa can improve microflora composition in patients with IBD and reduce the level of inflammatory cytokines; therefore, it is worthy of further clinical validation.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "39026313", + "title": "Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease.", + "year": 2024, + "journal": "Microbiome", + "authors": [ + "Tian X", + "Li S", + "Wang C", + "Zhang Y", + "Feng X", + "Yan Q", + "Guo R", + "Wu F", + "Wu C", + "Wang Y", + "Huo X", + "Ma X" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.22740080050403583, + "mesh_terms": [ + "Humans", + "Virome", + "Gastrointestinal Microbiome", + "Animals", + "Feces", + "Mice", + "Inflammatory Bowel Diseases", + "Female", + "Male", + "Adult", + "Middle Aged", + "Crohn Disease", + "Bacteriophages", + "Colitis, Ulcerative", + "Bacteria", + "China", + "Fecal Microbiota Transplantation", + "Case-Control Studies", + "Viruses" + ], + "raw_abstract": "BACKGROUND: The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS: In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella\u00a0species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS: Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "36695274", + "title": "Composition of the gut microbiota in patients with inflammatory bowel disease in Saudi Arabia: A pilot study.", + "year": 2023, + "journal": "Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association", + "authors": [ + "Al-Amrah H", + "Saadah OI", + "Mosli M", + "Annese V", + "Al-Hindi R", + "Edris S", + "Alshehri D", + "Alatawi H", + "Alatawy M", + "Bahieldin A" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.22672875939095624, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Pilot Projects", + "Saudi Arabia", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Feces" + ], + "raw_abstract": "CONCLUSIONS: The results of this study provide an overview of the variations in microbiota diversity present in Saudi IBD patients compared to healthy controls. RESULTS: The key finding was three negative bacterial biomarkers, Paraprevotellaceae, the Muribaculaceae families of Bacteroidetes phylum, and the Leuconostocaceae family of Firmicutes phylum, which had a higher relative abundance in healthy individuals compared to IBD patients. It was also found that primary microbiota signatures at certain genera and species levels, including Prevotella copri, Bifidobacterium adolescentis, Ruminococcus callidus, Coprococcus sp., Ruminococcus gnavus, Dorea formicigenerans, Leuconostoc, Dialister, Catenibacterium, Eubacterium biforme, and Lactobacillus mucosae, were absent in almost all IBD patients, while Veillonella dispar was absent in all healthy individuals. METHODS: After obtaining an informed consent, fecal samples were collected from 11 participants with IBD (patients) and 10 healthy individuals (controls). The bacterial components of the microbial population were identified by next-generation sequencing of partial 16S rRNA. Statistically significant dissimilarities were observed between samples for all metrics. BACKGROUND: Inflammatory bowel disease (IBD) is a chronic intestinal inflammatory condition attributed to a complex interaction between imbalances in the gut microbiome, environmental conditions, and a deregulated immune response. The aim of the study was to investigate the composition of the gut microbiome of Saudi patients with IBD.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "26994772", + "title": "Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India.", + "year": 2016, + "journal": "Journal of gastroenterology", + "authors": [ + "Kedia S", + "Rampal R", + "Paul J", + "Ahuja V" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.22369811126401973, + "mesh_terms": [ + "Colitis, Ulcerative", + "Crohn Disease", + "Dysentery, Amebic", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "India", + "Intestinal Mucosa" + ], + "raw_abstract": "The disease profile in the Indian population provides a unique opportunity for studying the host microbiome interaction in both infectious (amebiasis) and autoimmune diseases\u00a0like inflammatory bowel disease (IBD) from a similar environment and genetic background. Analysis of fecal samples from untreated amebic liver abscess (ALA) patients, Entamoeba histolytica (Eh)-negative and -positive asymptomatic individuals, and pus samples from naive ALA patients revealed a significant reduction in Lactobacillus in asymptomatic individuals (Eh +ve) and ALA patients. Two anaerobic genera, namely Bacteroides and Peptostreptococcus, were detected in naive ALA pus samples. Analysis of fecal samples from amoebic colitis patients showed a significant decline in population of Bacteroides, Clostridium coccoides and leptum subgroup, Lactobacillus, Campylobacter, and Eubacterium, whereas a significant increase in Bifidobacterium was observed. Mucosa-associated bacterial flora analysis from IBD patients and healthy controls revealed a significant difference in concentration of bacteria among predominating and subdominating genera between ulcerative colitis (UC), Crohn's disease (CD) patients, and controls. In contrast to the mucosal studies, we found a significant increase in lactobacilli population in fecal samples of active UC patients. Another study revealed a significant decrease of Clostridium coccoides and leptum clusters in fecal samples of active UC patients along with decreased concentrations of fecal SCFAs, especially of n-butyrate, iso-butyrate, and acetate. We therefore found similar perturbations in gut microbiome in both infectious and autoimmune diseases, indicating inflammation to be the major driver for changes in gut microbiome.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "37741962", + "title": "Designing a microbial fermentation-functionalized alginate microsphere for targeted release of 5-ASA using nano dietary fiber carrier for inflammatory bowel disease treatment.", + "year": 2023, + "journal": "Journal of nanobiotechnology", + "authors": [ + "Qiu L", + "Shen R", + "Wei L", + "Xu S", + "Xia W", + "Hou Y", + "Cui J", + "Qu R", + "Luo J", + "Cao J", + "Yang J", + "Sun J", + "Ma R", + "Yu Q" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.22118114080404738, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "Microspheres", + "Fermentation", + "Irritable Bowel Syndrome", + "Inflammatory Bowel Diseases", + "Mesalamine", + "Alginates", + "Dietary Fiber" + ], + "raw_abstract": "Patients with inflammatory bowel disease (IBD) always suffer from severe abdominal pain and appear to be at high risk for colorectal cancer. Recently, the co-delivery of targeted drugs and gut microbiota has developed into an attractive strategy. A new strategy using gut microbiota fermentation to overcome the interspace diffuse resistance from the mucus layer to control drug release in inflammatory bowel sites (IBS sites) has not yet been available. Here, we designed an alginate hydrogel microsphere encapsulating bifidobacterium (Bac) and drug-modified nanoscale dietary fibers (NDFs). The hydrogel microsphere is responsible for protecting drugs from acidic and multi-enzymatic environments and delivering drugs to the colorectum. Subsequently, the fermentation of Bac by digesting NDFs and proteins as carbon and nitrogen sources can promote drug release and play a probiotic role in the gut microbiota. In vitro evidence indicated that small-sized NDF (NDF-1) could significantly promote short-chain fatty acid (SCFA) expression. Notably, NDF-1 hydrogel microspheres showed a boost release of 5-ASA in the IBS sites, resulting in the amelioration of gut inflammation and remodeling of gut microbiota in chronic colitis mice. This study developed a controlled release system based on microbial fermentation for the treatment of IBD.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "35381290", + "title": "Inulin fructans in diet: Role in gut homeostasis, immunity, health outcomes and potential therapeutics.", + "year": 2022, + "journal": "International journal of biological macromolecules", + "authors": [ + "Tawfick MM", + "Xie H", + "Zhao C", + "Shao P", + "Farag MA" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.21919009491410932, + "mesh_terms": [ + "Animals", + "Bacteria", + "Diabetes Mellitus, Type 2", + "Diet", + "Fructans", + "Homeostasis", + "Humans", + "Inulin", + "Mice", + "Outcome Assessment, Health Care", + "Prebiotics" + ], + "raw_abstract": "Inulin consumption in both humans and animal models is recognized for its prebiotic action with the most consistent change that lies in enhancing the growth and functionality of Bifidobacterium bacteria, as well as its effect on host gene expression and metabolism. Further, inulin-type fructans are utilized in the colon by bacterial fermentation to yield short-chain fatty acids (SCFAs), which play important role in its biological effects both locally inside the gut and in systemic actions. The gut symbiosis sustained by inulin supplementation among other dietary fibers exerts preventive and/or therapeutic options for many metabolic disorders including obesity, type 2 diabetes mellitus, cardiometabolic diseases, kidney diseases and hyperuricemia. Although, gastrointestinal negative effects due to inulin consumption were reported, such as gastrointestinal symptoms in humans and exacerbated inflammatory bowel disease (IBD) in mice. This comprehensive review aims to present the whole story of how inulin functions as a prebiotic at cellular levels and the interplay between physiological, functional and immunological responses inside the animal or human gut as influenced by inulin in diets, in context to its structural composition. Such review is of importance to identify management and feed strategies to optimize gut health, for instance, consumption of the tolerated doses to healthy adults of 10\u00a0g/day of native inulin or 5\u00a0g/day of naturally inulin-rich chicory extract. In addition, inulin-drug interactions should be further clarified particularly if used as a supplement for the treatment of degenerative diseases (e.g., diabetes) over a long period. The combined effect of probiotics and inulin appears more effective, and more research on this synergy is still needed.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "28902124", + "title": "Guanylate Cyclase C Activation Shapes the Intestinal Microbiota in Patients with Familial Diarrhea and Increased Susceptibility for Crohn's Disease.", + "year": 2017, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Tronstad RR", + "Kummen M", + "Holm K", + "von Volkmann HL", + "Anmarkrud JA", + "H\u00f8ivik ML", + "Moum B", + "Gilja OH", + "Hausken T", + "Baines J", + "Karlsen TH", + "Fiskerstrand T", + "Hov JR" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.21161480624222345, + "mesh_terms": [ + "Adult", + "Case-Control Studies", + "Crohn Disease", + "DNA, Bacterial", + "Diarrhea", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Genetic Linkage", + "Genetic Predisposition to Disease", + "Humans", + "Intestinal Mucosa", + "Male", + "Middle Aged", + "Mutation, Missense", + "Norway", + "RNA, Ribosomal, 16S", + "Receptors, Enterotoxin" + ], + "raw_abstract": "BACKGROUND: With 25% prevalence of Crohn's disease, Familial GUCY2C diarrhea syndrome (FGDS) is a monogenic disorder potentially suited to study initiating factors in inflammatory bowel disease (IBD). We aimed to characterize the impact of an activating GUCY2C mutation on the gut microbiota in patients with FGDS controlling for Crohn's disease status and to determine whether changes share features with those observed in unrelated patients with IBD. METHODS: Bacterial DNA from fecal samples collected from patients with FGDS (N = 20), healthy relatives (N = 11), unrelated healthy individuals (N = 263), and IBD controls (N = 46) was subjected to sequencing of the V3-V4 region of the 16S rRNA gene to determine gut microbiota composition. Food frequency questionnaires were obtained from patients with FGDS and their relatives. RESULTS: Compared with healthy controls, FGDS displayed prominent changes in many microbial lineages including increase in Enterobacteriaceae, loss of Bifidobacterium and Faecalibacterium prausnitzii but an unchanged intraindividual (alpha) diversity. The depletion of F. prausnitzii is in line with what is typically observed in Crohn's disease. There was no significant difference in the dietary profile between the patients and related controls. The gut microbiota in related and unrelated healthy controls was also similar, suggesting that diet and familial factors do not explain the gut microbiota alterations in FGDS. CONCLUSIONS: The findings support that the activating mutation in GUCY2C creates an intestinal environment with a major influence on the microbiota, which could contribute to the increased susceptibility to IBD in patients with FGDS.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "38553410", + "title": "Efficacy of probiotic supplementation and impact on fecal microbiota in patients with inflammatory bowel disease: a systematic review and meta-analysis of randomized controlled trials.", + "year": 2025, + "journal": "Nutrition reviews", + "authors": [ + "Xu M", + "Zhang W", + "Lin B", + "Lei Y", + "Zhang Y", + "Zhang Y", + "Chen B", + "Mao Q", + "Kim JJ", + "Cao Q" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.21077084215997757, + "mesh_terms": [ + "Humans", + "Bifidobacterium", + "Dietary Supplements", + "Feces", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Probiotics", + "Randomized Controlled Trials as Topic", + "Treatment Outcome" + ], + "raw_abstract": "UNLABELLED: Context: Research regarding the treatment of inflammatory bowel disease (IBD) with probiotics has not yielded consistent results. OBJECTIVE: The aim of this meta-analysis was to evaluate the efficacy of probiotics supplementation in patients with IBD. DATA SOURCES: Randomized controlled trials (RCTs) evaluating the efficacy of probiotics in patients with IBD were searched in PubMed, the Google Scholar database, Web of Science, and CrossRef for the period July 2003 to June 2023. DATA EXTRACTION: The RCTs were extracted, independently by 2 authors, according to the PICOS criteria. DATA ANALYSIS: Seven studies, including a total of 795 patients, met the study criteria. Five end points were selected to evaluate the efficacy. Of these, 3 indicators showed a statistically significant difference in efficacy: C-reactive protein (odds ratio [OR]: -2.45, 95% confidence interval [CI]: -3.16, -1.73, P\u2009<\u2009.01), the number of fecal Bifidobacterium (OR: 3.37, 95% CI: 3.28, 3.47, P\u2009<\u2009.01), and Lactobacillus(OR: 2.00, 95% CI: 1.91, 2.09, P\u2009<\u2009.01). The other 2 indicators (disease activity for Crohn's disease and for ulcerative colitis) showed no statistically significant difference, while the OR reflected a positive correlation. CONCLUSION: Probiotics supplementation may have a positive effect on IBD by reducing clinical symptoms, reducing the serological inflammatory markers, and increasing favorable gut flora in patients with IBD. Additional RCTs are needed to evaluate the therapeutic effect of probiotics in IBD.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "33871395", + "title": "Fecal microbiota profile in patients with inflammatory bowel disease in Taiwan.", + "year": 2021, + "journal": "Journal of the Chinese Medical Association : JCMA", + "authors": [ + "Chang TE", + "Luo JC", + "Yang UC", + "Huang YH", + "Hou MC", + "Lee FY" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.20922478087883653, + "mesh_terms": [ + "Adult", + "Cross-Sectional Studies", + "Feces", + "Female", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Microbiota", + "Middle Aged", + "Taiwan" + ], + "raw_abstract": "BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with complicated interaction between immune, gut microbiota, and environmental factors in a genetically vulnerable host. Dysbiosis is often seen in patients with IBD. We aimed to investigate the fecal microbiota in patients with IBD and compared them with a control group in Taiwan. METHODS: In this cross-sectional study, we investigated fecal microbiota in 20 patients with IBD and 48 healthy controls. Fecal samples from both IBD patients and controls were analyzed by the next-generation sequencing method and relevant software. RESULTS: The IBD group showed lower bacterial richness and diversity compared with the control group. The principal coordinate analysis also revealed the significant structural differences between the IBD group and the control group. These findings were consistent whether the analysis was based on an operational taxonomic unit or amplicon sequence variant. However, no significant difference was found when comparing the composition of fecal microbiota between ulcerative colitis (UC) and Crohn's disease (CD). Further analysis showed that Lactobacillus, Enterococcus, and Bifidobacterium were dominant in the IBD group, whereas Faecalibacterium and Subdoligranulum were dominant in the control group at the genus level. When comparing UC, CD, and control group, Lactobacillus, Bifidobacterium, and Enterococcus were identified as dominant genera in the UC group. Fusobacterium and Escherichia_Shigella were dominant in the CD group. CONCLUSION: Compared with the healthy control, the IBD group showed dysbiosis with a significant decrease in both richness and diversity of gut microbiota.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "29895146", + "title": "Camellia Oil ( Camellia oleifera Abel.) Modifies the Composition of Gut Microbiota and Alleviates Acetic Acid-Induced Colitis in Rats.", + "year": 2018, + "journal": "Journal of agricultural and food chemistry", + "authors": [ + "Lee WT", + "Tung YT", + "Wu CC", + "Tu PS", + "Yen GC" + ], + "bacteria": "Bifidobacterium", + "condition": "inflammatory bowel disease", + "relevance_score": 0.20295600763403143, + "mesh_terms": [ + "Acetic Acid", + "Animals", + "Bacteria", + "Camellia", + "Colitis", + "Gastrointestinal Microbiome", + "Humans", + "Intestinal Mucosa", + "Intestines", + "Male", + "Plant Oils", + "Rats" + ], + "raw_abstract": "Ulcerative colitis (UC), one type of chronic inflammatory bowel disease (IBD), is a chronic and recurrent disorder of the gastrointestinal (GI) tract. As camellia oil (CO) is traditionally used to treat GI disorders, this study investigated the role of CO on acetic acid-induced colitis in the rat. The composition of the gut microbial community is related to many diseases; thus, this study also investigated the effects of CO on the composition of the gut microbiota. The rats were fed a dose of 2 mL/kg body weight CO, olive oil (OO), or soybean oil (SO) once a day for 20 days, and the gut microbiota was analyzed using 16S rRNA gene sequencing. Results of the gut microbiota examination showed significant clustering of feces after treatment with CO and OO; however, individual differences with OO varied considerably. Compared to SO and OO, the intake of CO increased the ratio of Firmicutes/Bacteroidetes, the \u03b1-diversity, relative abundance of the Bifidobacterium, and reduced Prevotella of the gut microbiota. On day 21, colitis was induced by a single transrectal administration of 2 mL of 4% acetic acid. However, pretreatment of rats with CO or OO for 24 days slightly enhanced antioxidant and antioxidant enzyme activities and significantly reduced inflammatory damage and lipid peroxidation, thus ameliorating acetic acid-induced colitis. These results indicated that CO was better able to ameliorate impairment of the antioxidant system induced by acetic acid compared to OO and SO, which may have been due to CO modifying the composition of the gut microbiota or CO being a rich source of phytochemicals.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "34008889", + "title": "Combined analysis of metagenomic data revealed consistent changes of gut microbiome structure and function in inflammatory bowel disease.", + "year": 2021, + "journal": "Journal of applied microbiology", + "authors": [ + "Xia Y", + "Wang J", + "Fang X", + "Dou T", + "Han L", + "Yang C" + ], + "bacteria": "Subdoligranulum", + "condition": "inflammatory bowel disease", + "relevance_score": 0.32777973415843714, + "mesh_terms": [ + "Clostridiales", + "Escherichia coli", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Metagenome" + ], + "raw_abstract": "AIMS: To reveal the consistency and discrepancy in the gut microbial structure and function in inflammatory bowel disease (IBD) patients from different regions. METHODS AND RESULTS: Gut microbes, antibiotic resistance genes (ARGs) and virulence factors genes (VFGs) were analysed using metagenome data from three cohorts. The abundance of Escherichia coli extensively increased in IBD patients, whereas Subdoligranulum unclassified decreased dramatically in IBD patients from three countries. Escherichia coli showed a positive correlation with multiple ARGs and VFGs in cohorts from China and the United States, including multidrug-related resistance genes and Capsule and LOS-related virulence factors genes. Escherichia coli biofilm synthesis pathways significantly enriched in IBD patients from three different regions. Notably, Subdoligranulum unclassified and Eubacterium hallii were negatively related to ARGs and VFGs. CONCLUSIONS: Consistent changes of microbiome structure and function were observed in IBD patients from three different regions. As pathogenic bacteria, E.\u00a0coli may accelerate IBD progression through encapsulation in biofilms by upregulating antibiotic resistance in Crohn's disease patients. Subdoligranulum unclassified and E. hallii may be beneficial for IBD patients and could serve as potential probiotics for IBD treatment. SIGNIFICANCE AND IMPACT OF THE STUDY: This work dispels worries about the regional differences in gut microbial changes in IBD patients and provides useful guidance for more rational microbiome-based therapies.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "27390077", + "title": "Brief Report: Dialister as a Microbial Marker of Disease Activity in Spondyloarthritis.", + "year": 2017, + "journal": "Arthritis & rheumatology (Hoboken, N.J.)", + "authors": [ + "Tito RY", + "Cypers H", + "Joossens M", + "Varkas G", + "Van Praet L", + "Glorieus E", + "Van den Bosch F", + "De Vos M", + "Raes J", + "Elewaut D" + ], + "bacteria": "Dialister", + "condition": "inflammatory bowel disease", + "relevance_score": 0.32894043177690324, + "mesh_terms": [ + "Colon", + "Female", + "Humans", + "Ileum", + "Inflammation", + "Male", + "Spondylarthritis", + "Veillonellaceae" + ], + "raw_abstract": "OBJECTIVE: Dysbiosis of the intestinal microbiota has been widely established in inflammatory bowel disease (IBD). There is significant clinical and genetic overlap between spondyloarthritis (SpA) and IBD, and up to 50% of all patients with SpA exhibit microscopic signs of bowel inflammation, often bearing particular resemblance to early Crohn's disease, a subtype of IBD. This study was undertaken to assess the relationship between intestinal microbial composition, gut histology, and disease activity markers in SpA. METHODS: Gene analysis by 16S ribosomal RNA amplicon sequencing was used to compare the microbial composition in ileal and colonic biopsy specimens from 27 patients with SpA (14 with microscopic bowel inflammation, 13 without) and 15 healthy control subjects (ileal samples from all 15 subjects and colonic samples from 6). Spearman's rank correlation tests were used to assess correlations of the microbial composition with disease activity measures. RESULTS: The intestinal inflammation status (histologically normal versus acute or chronic inflammation) was strongly associated with the mucosal microbiota profile of patients with SpA. In inflamed biopsy tissue, the detected bacterial community composition clustered separately from that in noninflamed biopsy tissue (P\u2009<\u20090.05 by permutational multivariate analysis of variance, using hierarchical clustering on Bray-Curtis distances). Interestingly, abundance of the genus Dialister was found to be positively correlated with the Ankylosing Spondylitis Disease Activity Score (Spearman's rho\u2009=\u20090.62, false discovery rate-corrected q\u2009<\u20090.01). This finding was further supported by the low frequency of Dialister observed in noninflamed ileal and colonic biopsy tissue from patients with SpA and healthy controls. CONCLUSION: These findings demonstrate a significant difference in the intestinal microbial composition in patients with SpA who have microscopic gut inflammation compared to those without microscopic gut inflammation. Moreover, Dialister may represent a potential microbial marker of disease activity in SpA.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "36695274", + "title": "Composition of the gut microbiota in patients with inflammatory bowel disease in Saudi Arabia: A pilot study.", + "year": 2023, + "journal": "Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association", + "authors": [ + "Al-Amrah H", + "Saadah OI", + "Mosli M", + "Annese V", + "Al-Hindi R", + "Edris S", + "Alshehri D", + "Alatawi H", + "Alatawy M", + "Bahieldin A" + ], + "bacteria": "Dialister", + "condition": "inflammatory bowel disease", + "relevance_score": 0.22672875939095624, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Pilot Projects", + "Saudi Arabia", + "RNA, Ribosomal, 16S", + "Inflammatory Bowel Diseases", + "Feces" + ], + "raw_abstract": "CONCLUSIONS: The results of this study provide an overview of the variations in microbiota diversity present in Saudi IBD patients compared to healthy controls. RESULTS: The key finding was three negative bacterial biomarkers, Paraprevotellaceae, the Muribaculaceae families of Bacteroidetes phylum, and the Leuconostocaceae family of Firmicutes phylum, which had a higher relative abundance in healthy individuals compared to IBD patients. It was also found that primary microbiota signatures at certain genera and species levels, including Prevotella copri, Bifidobacterium adolescentis, Ruminococcus callidus, Coprococcus sp., Ruminococcus gnavus, Dorea formicigenerans, Leuconostoc, Dialister, Catenibacterium, Eubacterium biforme, and Lactobacillus mucosae, were absent in almost all IBD patients, while Veillonella dispar was absent in all healthy individuals. METHODS: After obtaining an informed consent, fecal samples were collected from 11 participants with IBD (patients) and 10 healthy individuals (controls). The bacterial components of the microbial population were identified by next-generation sequencing of partial 16S rRNA. Statistically significant dissimilarities were observed between samples for all metrics. BACKGROUND: Inflammatory bowel disease (IBD) is a chronic intestinal inflammatory condition attributed to a complex interaction between imbalances in the gut microbiome, environmental conditions, and a deregulated immune response. The aim of the study was to investigate the composition of the gut microbiome of Saudi patients with IBD.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "33970546", + "title": "Gut dysbiosis and clinical phases of pancolitis in patients with ulcerative colitis.", + "year": 2021, + "journal": "MicrobiologyOpen", + "authors": [ + "Maldonado-Arriaga B", + "Sandoval-Jim\u00e9nez S", + "Rodr\u00edguez-Silverio J", + "Lizeth Alcar\u00e1z-Estrada S", + "Cort\u00e9s-Espinosa T", + "P\u00e9rez-Cabeza de Vaca R", + "Licona-Cassani C", + "G\u00e1mez-Valdez JS", + "Shaw J", + "Mondrag\u00f3n-Ter\u00e1n P", + "Hern\u00e1ndez-Cortez C", + "Su\u00e1rez-Cuenca JA", + "Castro-Escarpulli G" + ], + "bacteria": "Roseburia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.29292576414071525, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biodiversity", + "Colitis", + "Colitis, Ulcerative", + "DNA, Bacterial", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Healthy Volunteers", + "Humans", + "Leukocyte L1 Antigen Complex", + "Male", + "RNA, Ribosomal, 16S", + "Severity of Illness Index" + ], + "raw_abstract": "Ulcerative colitis (UC) is a frequent type of inflammatory bowel disease, characterized by periods of remission and exacerbation. Gut dysbiosis may influence pathophysiology and clinical response in UC. The purpose of this study was to evaluate whether gut microbiota is related to the active and remission phases of pancolitis in patients with UC as well as in healthy participants. Fecal samples were obtained from 18 patients with UC and clinical-endoscopic evidenced pancolitis (active phase n\u00a0=\u00a09 and remission phase n\u00a0=\u00a09), as well as 15 healthy participants. After fecal DNA extraction, the 16S rRNA gene was amplified and sequenced (Illumina MiSeq), operational taxonomic units were analyzed with the QIIME software. Gut microbiota composition revealed a higher abundance of the phyla Proteobacteria and Fusobacteria in active pancolitis, as compared with remission and healthy participants. Likewise, a marked abundance of the genus Bilophila and Fusobacteria were present in active pancolitis, whereas a higher abundance of Faecalibacterium characterized both remission and healthy participants. LEfSe analysis showed that the genus\u00a0Roseburia\u00a0and Faecalibacterium were enriched in remission pancolitis, and genera\u00a0Bilophila\u00a0and\u00a0Fusobacterium\u00a0were enriched in active pancolitis. The relative abundance of Fecalibacterium and Roseburia showed a higher correlation with fecal calprotectin, while Bilophila and Fusobacterium showed AUCs (area under the curve) of 0.917 and 0.988 for active vs. remission pancolitis. The results of our study highlight the relation of gut dysbiosis with clinically relevant phases of pancolitis in patients with UC. Particularly, Fecalibacterium, Roseburia, Bilophila, and Fusobacterium were identified as genera highly related to the different clinical phases of pancolitis.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "34973740", + "title": "Polysaccharide from edible alga Gloiopeltis furcata attenuates intestinal mucosal damage by therapeutically remodeling the interactions between gut microbiota and mucin O-glycans.", + "year": 2022, + "journal": "Carbohydrate polymers", + "authors": [ + "Pan L", + "Fu T", + "Cheng H", + "Mi J", + "Shang Q", + "Yu G" + ], + "bacteria": "Roseburia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.25539830949447206, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Bacteria", + "Carbohydrate Conformation", + "Dextran Sulfate", + "Gastrointestinal Microbiome", + "Intestinal Mucosa", + "Microbial Sensitivity Tests", + "Mucins", + "Polysaccharides", + "Seaweed" + ], + "raw_abstract": "Gloiopeltis furcata is an edible alga that has long been consumed in China. However, the bioactive polysaccharides from G. furcata have been largely unexplored. Here, we show for the first time that a sulfated polysaccharide from G. furcata (SAO) could improve the integrity of the colonic epithelial layer and protect against dextran sulfate sodium-induced intestinal mucosal damage. Mechanistically, SAO attenuated colonic mucosal damage by therapeutically remodeling the interactions between gut microbiota and mucin O-glycans. Specifically, SAO increased the proportions of complex long-chain mucin O-glycans in the epithelial layer with two terminal N-acetylneuraminic acid residues and promoted the growth of probiotic bacteria including Roseburia spp. and Muribaculaceae. Altogether, our study demonstrates a novel application of SAO for the treatment of inflammatory bowel disease-associated mucosal damage and forms the basis to understand the therapeutic effects of natural polysaccharides from the perspective of symbiotic interactions between host mucin O-glycome and gut microbiome.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "30849075", + "title": "Genetic effects on the commensal microbiota in inflammatory bowel disease patients.", + "year": 2019, + "journal": "PLoS genetics", + "authors": [ + "Aschard H", + "Laville V", + "Tchetgen ET", + "Knights D", + "Imhann F", + "Seksik P", + "Zaitlen N", + "Silverberg MS", + "Cosnes J", + "Weersma RK", + "Xavier R", + "Beaugerie L", + "Skurnik D", + "Sokol H" + ], + "bacteria": "Roseburia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.22779834372993155, + "mesh_terms": [ + "Adult", + "CARD Signaling Adaptor Proteins", + "Clostridiales", + "Faecalibacterium prausnitzii", + "Female", + "Gastrointestinal Microbiome", + "Genetic Association Studies", + "Genetic Predisposition to Disease", + "Genetic Variation", + "Host Microbial Interactions", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "Models, Genetic", + "Nod2 Signaling Adaptor Protein", + "Polymorphism, Single Nucleotide" + ], + "raw_abstract": "Several bacteria in the gut microbiota have been shown to be associated with inflammatory bowel disease (IBD), and dozens of IBD genetic variants have been identified in genome-wide association studies. However, the role of the microbiota in the etiology of IBD in terms of host genetic susceptibility remains unclear. Here, we studied the association between four major genetic variants associated with an increased risk of IBD and bacterial taxa in up to 633 IBD cases. We performed systematic screening for associations, identifying and replicating associations between NOD2 variants and two taxa: the Roseburia genus and the Faecalibacterium prausnitzii species. By exploring the overall association patterns between genes and bacteria, we found that IBD risk alleles were significantly enriched for associations concordant with bacteria-IBD associations. To understand the significance of this pattern in terms of the study design and known effects from the literature, we used counterfactual principles to assess the fitness of a few parsimonious gene-bacteria-IBD causal models. Our analyses showed evidence that the disease risk of these genetic variants were likely to be partially mediated by the microbiome. We confirmed these results in extensive simulation studies and sensitivity analyses using the association between NOD2 and F. prausnitzii as a case study.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "30573380", + "title": "Gut mucosal-associated microbiota better discloses inflammatory bowel disease differential patterns than faecal microbiota.", + "year": 2019, + "journal": "Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver", + "authors": [ + "Altomare A", + "Putignani L", + "Del Chierico F", + "Cocca S", + "Angeletti S", + "Ciccozzi M", + "Tripiciano C", + "Dalla Piccola B", + "Cicala M", + "Guarino MPL" + ], + "bacteria": "Roseburia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.20908202038172038, + "mesh_terms": [ + "Bacteria", + "Case-Control Studies", + "Colon", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestinal Mucosa", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: Growing evidence supports the potential role of intestinal microbiota in the pathophysiology of inflammatory bowel diseases (IBD) even if the literature does not reveal uniform alterations. The aim of the study was to evaluate the mucosal (MM) and faecal microbiota (FM) composition in a cohort of IBD patients compared to healthy controls (CTRLs). METHODS: Faecal and mucosal samples were collected from 14 IBD patients and 11 CTRLs. The V1-V3 region of 16S rRNA locus was amplified on a 454-Junior Genome Sequencer. Reads were grouped into operational taxonomic units (OTUs) at a sequence similarity level of 97% for taxonomic assignment, and aligned for OTUs matching against Greengenes database. RESULTS: Irrespective of disease localization and activity, in the MM of IBD patients a statistically significant increase of Proteobacteria (especially Enterobacteriaceae, Acidaminococcus, Veillonella dispar) and decrease of Firmicutes (especially Roseburia and Faecalibacterium prausnitzii) and Actinobacteria was found compared to CTRLs. In the colon district some specific bacterial biomarkers were identified: Enterobacteriaceae for IBD stools, Bacteroides for IBD biopsies, Mogibacteriaceae, Ruminococcaceae and Prevotella for CTRL stools, Ruminococcaceae for CTRL biopsies. CONCLUSIONS: The profiles of FM were more similar to CTRLs, suggesting that microbiota adhering to the gut mucosa better discriminates patients from controls, with the identification of some interesting biomarkers.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "27446020", + "title": "Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut.", + "year": 2016, + "journal": "Frontiers in microbiology", + "authors": [ + "Rivi\u00e8re A", + "Selak M", + "Lantin D", + "Leroy F", + "De Vuyst L" + ], + "bacteria": "Roseburia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.2025798310614053, + "mesh_terms": [], + "raw_abstract": "With the increasing amount of evidence linking certain disorders of the human body to a disturbed gut microbiota, there is a growing interest for compounds that positively influence its composition and activity through diet. Besides the consumption of probiotics to stimulate favorable bacterial communities in the human gastrointestinal tract, prebiotics such as inulin-type fructans (ITF) and arabinoxylan-oligosaccharides (AXOS) can be consumed to increase the number of bifidobacteria in the colon. Several functions have been attributed to bifidobacteria, encompassing degradation of non-digestible carbohydrates, protection against pathogens, production of vitamin B, antioxidants, and conjugated linoleic acids, and stimulation of the immune system. During life, the numbers of bifidobacteria decrease from up to 90% of the total colon microbiota in vaginally delivered breast-fed infants to <5% in the colon of adults and they decrease even more in that of elderly as well as in patients with certain disorders such as antibiotic-associated diarrhea, inflammatory bowel disease, irritable bowel syndrome, obesity, allergies, and regressive autism. It has been suggested that the bifidogenic effects of ITF and AXOS are the result of strain-specific yet complementary carbohydrate degradation mechanisms within cooperating bifidobacterial consortia. Except for a bifidogenic effect, ITF and AXOS also have shown to cause a butyrogenic effect in the human colon, i.e., an enhancement of colon butyrate production. Butyrate is an essential metabolite in the human colon, as it is the preferred energy source for the colon epithelial cells, contributes to the maintenance of the gut barrier functions, and has immunomodulatory and anti-inflammatory properties. It has been shown that the butyrogenic effects of ITF and AXOS are the result of cross-feeding interactions between bifidobacteria and butyrate-producing colon bacteria, such as Faecalibacterium prausnitzii (clostridial cluster IV) and Anaerostipes, Eubacterium, and Roseburia species (clostridial cluster XIVa). These kinds of interactions possibly favor the co-existence of bifidobacterial strains with other bifidobacteria and with butyrate-producing colon bacteria in the human colon.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "32265456", + "title": "Seasonal changes of circulating 25-hydroxyvitamin D correlate with the lower gut microbiome composition in inflammatory bowel disease patients.", + "year": 2020, + "journal": "Scientific reports", + "authors": [ + "Soltys K", + "Stuchlikova M", + "Hlavaty T", + "Gaalova B", + "Budis J", + "Gazdarica J", + "Krajcovicova A", + "Zelinkova Z", + "Szemes T", + "Kuba D", + "Drahovska H", + "Turna J", + "Stuchlik S" + ], + "bacteria": "Collinsella", + "condition": "inflammatory bowel disease", + "relevance_score": 0.2040691444116943, + "mesh_terms": [ + "Adult", + "Aged", + "Bacteria", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Male", + "Middle Aged", + "RNA, Ribosomal, 16S", + "Seasons", + "Vitamin D", + "Young Adult" + ], + "raw_abstract": "Higher probability of the development of Crohn's disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/Shigella spp.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "28786749", + "title": "Specificities of the intestinal microbiota in patients with inflammatory bowel disease and Clostridium difficile infection.", + "year": 2018, + "journal": "Gut microbes", + "authors": [ + "Sokol H", + "Jegou S", + "McQuitty C", + "Straub M", + "Leducq V", + "Landman C", + "Kirchgesner J", + "Le Gall G", + "Bourrier A", + "Nion-Larmurier I", + "Cosnes J", + "Seksik P", + "Richard ML", + "Beaugerie L" + ], + "bacteria": "Blautia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.24285953538732621, + "mesh_terms": [ + "Adult", + "Bacteria", + "Biodiversity", + "Clostridium Infections", + "Dysbiosis", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Intestines", + "Male", + "Middle Aged", + "Species Specificity", + "Young Adult" + ], + "raw_abstract": "Clostridium difficile infection (CDI) is a common complication in inflammatory bowel disease (IBD) and has been associated with poor IBD outcome. Intestinal microbiota composition in IBD patients with CDI has not been specifically evaluated to date. The fecal microbiota of 56 IBD patients, including 8 in flare with concomitant CDI, 24 in flare without CDI, and 24 in remission, as well as 24 healthy subjects, was studied using 16S sequencing. Analysis was performed using the Qiime pipeline. Compared to IBD patients without CDI, IBD patients with CDI had more pronounced dysbiosis with higher levels of Ruminococcus gnavus and Enterococcus operational taxonomic units (OTUs) and lower levels of Blautia and Dorea OTUs. Correlation network analysis suggested a disrupted ecosystem in IBD patients in flare, particularly in those with CDI. In patients with IBD, CDI is associated with a more pronounced intestinal dysbiosis with specific alterations in intestinal microorganisms.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "31776537", + "title": "Habitual animal fat consumption in shaping gut microbiota and microbial metabolites.", + "year": 2019, + "journal": "Food & function", + "authors": [ + "Wan Y", + "Tong W", + "Zhou R", + "Li J", + "Yuan J", + "Wang F", + "Li D" + ], + "bacteria": "Blautia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.2366437434326003, + "mesh_terms": [ + "Adult", + "Animals", + "Bacteria", + "Dietary Fats", + "Fatty Acids, Volatile", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Tandem Mass Spectrometry", + "Young Adult" + ], + "raw_abstract": "Short-term intervention studies support a link between animal-based diet and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. However, whether habitual animal fat intake is associated with gut-related health remains unclear. Thus, we collected dietary information, clinical data and fecal samples from 297 healthy young subjects and characterized gut microbiota by 16S rRNA gene sequencing and microbial metabolites, including short-chain fatty acids (SCFAs) and bile acids (BAs) using a gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF/MS) system and ultra performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) platform, respectively. We found that the microbial diversity of butyric acid (rho = -0.17, p = 0.004 for the Shannon index) and the concentrations of butyric acid (rho = -0.33, p < 0.001) and valeric acid (rho = -0.28, p = 0.002) were negatively associated with animal fat consumption. In line with this, the abundance of SCFAs-producing bacteria such as Blautia, Eubacterium hallii, and Megamonas were significantly lower in the high animal fat group compared with the low animal fat group (all p < 0.05). Additionally, the high animal fat group had higher concentrations of total (p = 0.06) and unconjugated (p = 0.09) BAs relative to the lower animal fat groups. The findings of our study indicate that a diet with higher animal-based fat consumption is likely to be associated with moderately unfavorable impacts on gut microbial diversity, community, and regulation of fecal SCFAs, which may influence the host cardiometabolic health in the long term among healthy Chinese adults whose diet is in a nutrition transition.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "32469069", + "title": "Crohn's Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria.", + "year": 2020, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Shahir NM", + "Wang JR", + "Wolber EA", + "Schaner MS", + "Frank DN", + "Ir D", + "Robertson CE", + "Chaumont N", + "Sadiq TS", + "Koruda MJ", + "Rahbar R", + "Nix BD", + "Newberry RD", + "Sartor RB", + "Sheikh SZ", + "Furey TS" + ], + "bacteria": "Blautia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.23577819764946045, + "mesh_terms": [ + "Aerobiosis", + "Case-Control Studies", + "Colon", + "Crohn Disease", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Ileum", + "Intestinal Mucosa", + "Male", + "Middle Aged", + "Phenotype", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "BACKGROUND: The intestinal microbiota play a key role in the onset, progression, and recurrence of Crohn disease (CD). Most microbiome studies assay fecal material, which does not provide region-specific information on mucosally adherent bacteria that directly interact with host systems. Changes in luminal oxygen have been proposed as a contributor to CD dybiosis. METHODS: The authors generated 16S rRNA data using colonic and ileal mucosal bacteria from patients with CD and without inflammatory bowel disease. We developed profiles reflecting bacterial abundance within defined aerotolerance categories. Bacterial diversity, composition, and aerotolerance profiles were compared across intestinal regions and disease phenotypes. RESULTS: Bacterial diversity decreased in CD in both the ileum and the colon. Aerotolerance profiles significantly differed between intestinal segments in patients without inflammatory bowel disease, although both were dominated by obligate anaerobes, as expected. In CD, high relative levels of obligate anaerobes were maintained in the colon and increased in the ileum. Relative abundances of similar and distinct taxa were altered in colon and ileum. Notably, several obligate anaerobes, such as Bacteroides fragilis, dramatically increased in CD in one or both intestinal segments, although specific increasing taxa varied across patients. Increased abundance of taxa from the Proteobacteria phylum was found only in the ileum. Bacterial diversity was significantly reduced in resected tissues of patients who developed postoperative disease recurrence across 2 independent cohorts, with common lower abundance of bacteria from the Bacteroides, Streptococcus, and Blautia genera. CONCLUSIONS: Mucosally adherent bacteria in the colon and ileum show distinct alterations in CD that provide additional insights not revealed in fecal material.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "39026313", + "title": "Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease.", + "year": 2024, + "journal": "Microbiome", + "authors": [ + "Tian X", + "Li S", + "Wang C", + "Zhang Y", + "Feng X", + "Yan Q", + "Guo R", + "Wu F", + "Wu C", + "Wang Y", + "Huo X", + "Ma X" + ], + "bacteria": "Blautia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.22740080050403583, + "mesh_terms": [ + "Humans", + "Virome", + "Gastrointestinal Microbiome", + "Animals", + "Feces", + "Mice", + "Inflammatory Bowel Diseases", + "Female", + "Male", + "Adult", + "Middle Aged", + "Crohn Disease", + "Bacteriophages", + "Colitis, Ulcerative", + "Bacteria", + "China", + "Fecal Microbiota Transplantation", + "Case-Control Studies", + "Viruses" + ], + "raw_abstract": "BACKGROUND: The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS: In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella\u00a0species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS: Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "37676484", + "title": "Regulation of gut microbiota and alleviation of DSS-induced colitis by vitexin.", + "year": 2023, + "journal": "European journal of nutrition", + "authors": [ + "Li S", + "Luo L", + "Wang S", + "Sun Q", + "Zhang Y", + "Huang K", + "Guan X" + ], + "bacteria": "Blautia", + "condition": "inflammatory bowel disease", + "relevance_score": 0.207272882053482, + "mesh_terms": [ + "Humans", + "Mice", + "Animals", + "Gastrointestinal Microbiome", + "Cytokines", + "Colitis", + "Inflammation", + "Bacteria", + "Dextran Sulfate", + "Disease Models, Animal", + "Mice, Inbred C57BL", + "Colon" + ], + "raw_abstract": "PURPOSE: Vitexin is one of the flavonoids in millet and has a variety of biological activities. However, the function of vitexin on colitis is not clear. This research studied the regulation of vitexin on colitis and investigated the possible mechanisms. METHODS: An in vitro fermentation model was used to evaluate the regulation of vitexin on gut microbiota of patients with inflammatory bowel disease (IBD). At the same time, an acute colitis mice model induced by dextran sodium sulfate (DSS) was used to evaluate the effects of vitexin on intestinal inflammation, barrier and gut microbiota. RESULTS: In this study, it was found that vitexin altered the structure of gut microbiota by decreasing harmful bacteria, such as Veillonella, Terrisporobacter, Klebsiella, Paeniclostridium, and increasing beneficial bacteria, such as Parabacteroides, Flavonifractor, Blautia after in vitro fermentation with the feces of colitis patients. Further, DSS-induced colitis mice models revealed that vitexin treatment significantly improved colitis symptoms, maintained intestinal barrier and down-regulated the expression of inflammatory factors, such as IL-1\u03b2 and TNF-\u03b1. In addition, vitexin also improved the diversity of gut microbiota of colitis mice by decreasing the abundance of harmful bacteria. CONCLUSION: This research suggested that vitexin could alleviate colitis by regulating gut microbiota and attenuated gut inflammation.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "27824645", + "title": "A Single Species of Clostridium Subcluster XIVa Decreased in Ulcerative Colitis Patients.", + "year": 2016, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Takeshita K", + "Mizuno S", + "Mikami Y", + "Sujino T", + "Saigusa K", + "Matsuoka K", + "Naganuma M", + "Sato T", + "Takada T", + "Tsuji H", + "Kushiro A", + "Nomoto K", + "Kanai T" + ], + "bacteria": "Fusicatenibacter", + "condition": "inflammatory bowel disease", + "relevance_score": 0.29641496402916745, + "mesh_terms": [ + "Adult", + "Aged", + "Animals", + "Case-Control Studies", + "Clostridium", + "Colitis, Ulcerative", + "Disease Progression", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Intestinal Mucosa", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Middle Aged", + "Mucous Membrane", + "RNA, Ribosomal, 16S", + "Species Specificity", + "Young Adult" + ], + "raw_abstract": "BACKGROUND: Imbalance of the intestinal microbiota is associated with gastrointestinal disease and autoimmune disease and metabolic syndrome. Analysis of the intestinal microbiota has recently progressed, and the association with inflammatory bowel disease has been reported at the species level. Such findings suggest that the recovery of homeostasis in the intestinal microbiota could cure inflammatory bowel disease. We aimed to search new probiotic candidates for inflammatory bowel disease through translational research by analysis of ulcerative colitis (UC) patients' intestinal microbiota and clarify the effects of them on inflammation. Here, we focused on Fusicatenibacter saccharivorans, which belongs to Clostridium subcluster XIVa and was successfully isolated and cultured in 2013. We analyzed the association of F. saccharivorans to UC patients' activity and inflammation for the first time. METHODS: Feces from UC patients and healthy controls were analyzed by 16S ribosomal RNA gene sequences. F. saccharivorans was administered to murine colitis model. Colitic lamina propria mononuclear cells from UC patients and mice were stimulated with F. saccharivorans. RESULTS: The whole fecal bacteria in active UC patients were less than that in quiescent UC patients. Furthermore, F. saccharivorans was decreased in active UC patients and increased in quiescent. The administration of F. saccharivorans improved murine colitis. F. saccharivorans induced interleukin 10 production by lamina propria mononuclear cells from not only colitis model mice but also UC patients. CONCLUSIONS: F. saccharivorans decreased in correlation to UC activity and suppresses intestinal inflammation. These results suggest that F. saccharivorans could lead to a novel UC treatment.", + "condition_dir": "microbiome-uc-ibd/inflammatory_bowel_disease" + }, + { + "pmid": "39981988", + "title": "Nutraceutical Blends Promote Weight Loss, Inflammation Reduction, and Better Sleep: The Role of Faecalibacterium prausnitzii in Overweight Adults-A Double-Blind Trial.", + "year": 2025, + "journal": "Molecular nutrition & food research", + "authors": [ + "Santamarina AB", + "Filho VN", + "de Freitas JA", + "Franco LAM", + "Martins RC", + "Fonseca JV", + "Orellana Turri JA", + "Hufnagel MT", + "Demarque DP", + "da Silva BFRB", + "Gusm\u00e3o AF", + "Olivieri EHR", + "de Souza E", + "de Souza EA", + "Otoch JP", + "Pessoa AFM" + ], + "bacteria": "Adlercreutzia", + "condition": "anti-inflammatory", + "relevance_score": 0.23631852830971803, + "mesh_terms": [], + "raw_abstract": "This study explores the effects of a nutraceutical blend with prebiotics, \u03b2-glucans, essential minerals, and silymarin on gut microbiota, inflammation, and sleep quality in obesity through microbiota reshaping and metabolic improvements over 90 days. A double-blind, randomized trial was conducted on 77 participants divided into two groups receiving either a standard nutraceutical blend (NSupple) or a silymarin-enriched blend (NSupple_Silybum). Fecal and plasma samples were collected at baseline and post-supplementation for gut microbiota, metabolic, and inflammatory marker analysis. The results showed a reduction in body weight, waist-to-height ratio, total cholesterol, and fractions in the NSupple_Silybum group. There was a dysbiosis recovery shown by the increase in beneficial gut bacteria, such as Lentisphaerae phylum, Lactobacillus and Faecalibacterium genera, and Faecalibacterium prausnitzii in the NSupple group, with a concurrent reduction in Adlercreutzia and Sutterella in the NSupple_Silybum group. Both groups demonstrated improved inflammatory profiles by the reduced TNF-\u03b1/IL-10 ratio, reduced cortisol levels, and reduced Firmicutes/Bacteroides ratio. Additionally, improvements in sleep quality were associated with reductions in pro-inflammatory cytokines and improved microbiota composition. The nutraceutical blend reshaped gut microbiota, enhanced anti-inflammatory species, and improved metabolic and sleep parameters, highlighting its potential as a nutritional strategy for managing obesity and reducing inflammation.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "31941439", + "title": "Deficiency of Gankyrin in the small intestine is associated with augmented colitis accompanied by altered bacterial composition of intestinal microbiota.", + "year": 2020, + "journal": "BMC gastroenterology", + "authors": [ + "Sakurai T", + "Nishiyama H", + "Nagai T", + "Goto S", + "Ogata H", + "Kudo M" + ], + "bacteria": "Bilophila", + "condition": "anti-inflammatory", + "relevance_score": 0.4411342221395806, + "mesh_terms": [ + "Animals", + "Colitis", + "Colon", + "Crohn Disease", + "Dextran Sulfate", + "Disease Models, Animal", + "Epithelial Cells", + "Gastrointestinal Microbiome", + "Gene Deletion", + "Humans", + "Intestinal Mucosa", + "Intestine, Small", + "Intestines", + "Mice", + "RNA, Ribosomal, 16S", + "Transcription Factors" + ], + "raw_abstract": "BACKGROUND: Gankyrin (GK) is an oncoprotein which regulates inflammatory responses and its inhibition is considered as a possible anti-inflammatory therapy for inflammatory bowel disease (IBD). METHODS: In this study, we investigated the role of GK in epithelial cells using mice with intestinal epithelial cell-specific GK deletion in (i) the entire small intestine and colon (Villin-Cre;Gankyrin RESULT: Unexpectedly, GK-deficiency in the upper small bowel augmented inflammatory activity compared with control mice when colitis was induced with dextran sodium sulfate. Biochemical analyses have revealed GK-deficiency to have caused reduction in the expression of antimicrobial peptides, \u03b1-Defensin-5 and -6, in the upper small bowel. Examination of human samples have further confirmed that the reduction of GK expression in the small bowel is associated with colonic involvement in human Crohn's disease. Through the sequencing of bacterial 16S rRNA gene amplicons, bacteria potentially deleterious to intestinal homeostasis such as Helicobacter japonicum and Bilophila were found to be over-represented in colitis induced Villin-Cre;Gankyrin CONCLUSION: These results highlight the distinct site dependence of the pro- and anti-inflammatory functions of GK and provide important insights into the pathogenesis of IBD.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "32996156", + "title": "Bifidobacterium bifidum TMC3115 ameliorates milk protein allergy in by affecting gut microbiota: A randomized double-blind control trial.", + "year": 2020, + "journal": "Journal of food biochemistry", + "authors": [ + "Jing W", + "Liu Q", + "Wang W" + ], + "bacteria": "Bilophila", + "condition": "anti-inflammatory", + "relevance_score": 0.30283549943222715, + "mesh_terms": [ + "Animals", + "Bifidobacterium bifidum", + "Cattle", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Infant", + "Milk Hypersensitivity", + "Milk Proteins" + ], + "raw_abstract": "We aimed to explore the effects of Bifidobacterium bifidum TMC3115 intervention on cow's milk protein allergy (CMPA) and gut microbiota in infants. A total 256 CMPA infants were randomly and evenly assigned into an intervention group (B. bifidum) and a control group (placebo). Allergic scores, anti-inflammatory responses, and secondary outcomes were measured. Fecal specimens were collected, and the gut microbiota were analyzed by using 16S rDNA sequencing. After 6-month B. bifidum intervention, B. bifidum TMC3115 consumption reduced allergic scores, and improved anti-inflammatory responses and secondary outcomes in CMPA infants. LEfSe analysis showed Bifidobacterium, Lactobacillus, Turicibacter, Sutterella, and Parabacteroides were the most predominant phylum in the intervention group, whereas the Firmicutes (Anaerovibrio, Christensenellaceae, Oscillibacter, Bilophila, Dorea, and Roseburia) were most dominant phyla in the control group. Serum IgE or IgG2 had a strong relationship with \u03b1-diversity scores of gut microbiota. PRACTICAL APPLICATIONS: There is a high level of prevalence of milk allergy in infants, which is difficult to be treated. Bifidobacterium bifidum TMC3115 supplement reduced allergic scores, improved anti-inflammatory responses, and reduced serum level of IgE and increased the level of IgG2 in the infants. On the contrary, B. bifidum supplement increased the genus proportion of probiotics and reduced the proportion of pathogens. The improvement of gut microbiota will be beneficial in the prevention of milk allergy. B. bifidum TMC3115 reduces milk allergy in the infants by regulating gut microbiota, and should be developed a potential way in the prevention of infant milk allergy.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "38684664", + "title": "Gut microbiome composition and metabolic activity in women with diverticulitis.", + "year": 2024, + "journal": "Nature communications", + "authors": [ + "Ma W", + "Wang Y", + "Nguyen LH", + "Mehta RS", + "Ha J", + "Bhosle A", + "Mclver LJ", + "Song M", + "Clish CB", + "Strate LL", + "Huttenhower C", + "Chan AT" + ], + "bacteria": "Bilophila", + "condition": "anti-inflammatory", + "relevance_score": 0.28334220663762627, + "mesh_terms": [ + "Humans", + "Female", + "Gastrointestinal Microbiome", + "Middle Aged", + "Diverticulitis", + "Feces", + "Aged", + "Prospective Studies", + "Bilophila", + "Metabolomics", + "Case-Control Studies", + "Clostridiales", + "Bile Acids and Salts", + "Adult", + "Dietary Fiber", + "Metabolome", + "Metagenomics" + ], + "raw_abstract": "The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large prospective cohort, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 women diagnosed with diverticulitis requiring antibiotics or hospitalizations (cases), matched to 121 women without diverticulitis (controls) according to age and race. Overall microbial community structure and metabolomic profiles differed in diverticulitis cases compared to controls, including enrichment of pro-inflammatory Ruminococcus gnavus, 1,7-dimethyluric acid, and histidine-related metabolites, and depletion of butyrate-producing bacteria and anti-inflammatory ceramides. Through integrated multi-omic analysis, we detected covarying microbial and metabolic features, such as Bilophila wadsworthia and bile acids, specific to diverticulitis. Additionally, we observed that microbial composition modulated the protective association between a prudent fiber-rich diet and diverticulitis. Our findings offer insights into the perturbations in inflammation-related microbial and metabolic signatures associated with diverticulitis, supporting the potential of microbial-based diagnostics and therapeutic targets.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "33058981", + "title": "Hypoglycemic effects and mechanism of different molecular weights of konjac glucomannans in type 2 diabetic rats.", + "year": 2020, + "journal": "International journal of biological macromolecules", + "authors": [ + "Deng J", + "Zhong J", + "Long J", + "Zou X", + "Wang D", + "Song Y", + "Zhou K", + "Liang Y", + "Huang R", + "Wei X", + "Li M", + "Sun Y" + ], + "bacteria": "Romboutsia", + "condition": "anti-inflammatory", + "relevance_score": 0.31154186866238825, + "mesh_terms": [ + "Animals", + "Biomarkers", + "Blood Glucose", + "Body Weight", + "Diabetes Mellitus, Experimental", + "Diabetes Mellitus, Type 2", + "Drinking Behavior", + "Fasting", + "Feces", + "Feeding Behavior", + "Gastrointestinal Microbiome", + "Glucagon-Like Peptide 1", + "Glucose Tolerance Test", + "Hypoglycemic Agents", + "Insulin Resistance", + "Lipids", + "Magnetic Resonance Spectroscopy", + "Male", + "Mannans", + "Molecular Weight", + "Multivariate Analysis", + "Oxidative Stress", + "Phylogeny", + "Rats, Sprague-Dawley", + "Scattering, Radiation", + "Spectrophotometry, Ultraviolet", + "Spectroscopy, Fourier Transform Infrared", + "X-Ray Diffraction" + ], + "raw_abstract": "Konjac glucomannan (KGM) is a hypoglycemic polysaccharide with a wide range of molecular weights. But study on hypoglycemic effects of KGMs relate to molecular weight is limited. In this study, KGMs with high and medium molecular weights, and the degraded KGMs were analyzed with physicochemical properties, hypoglycemic effects and mechanisms. Results showed that as the molecular weight KGMs decreased, the viscosity decreased, molecular flexibility increased, while chemical groups, crystal structures and main chains showed little change. KGMs with medium molecular weights (KGM-M1, KGM-M2) showed better effects on increasing body weight, decreasing levels of fasting blood glucose, insulin resistance, total cholesterol and low density lipoprotein cholesterol, and enhancing integrity of pancreas and colon, than KGMs with high or low molecular weights (KGM-H, KGM-L) in type 2 diabetic rats. Mechanism analysis suggested that KGM-M1 and KGM-M2 had higher antioxidant and anti-inflammatory activities on elevating superoxide dismutase, decreasing malondialdehyde and tumor necrosis factor-\u03b1 levels. Moreover, KGM-M1 and KGM-M2 increased gut microbiota diversity, Bacteroidetes/Firmicutes ratio and Muribaculaceae, decreased Romboutsia and Klebsiella, and improved 6 diabetic related metabolites. Combined, KGM-M1 and KGM-M2 showed higher hypoglycemic effects, due to regulatory activities of antioxidant, anti-inflammatory, intestinal microbiota, and relieved metabolic disorders.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "38458480", + "title": "Tangshen Formula alleviates inflammatory injury against aged diabetic kidney disease through modulating gut microbiota composition and related amino acid metabolism.", + "year": 2024, + "journal": "Experimental gerontology", + "authors": [ + "Chen DQ", + "Zhang HJ", + "Zhang W", + "Feng K", + "Liu H", + "Zhao HL", + "Li P" + ], + "bacteria": "Romboutsia", + "condition": "anti-inflammatory", + "relevance_score": 0.2340580001523753, + "mesh_terms": [ + "Humans", + "Aged", + "Mice", + "Animals", + "Diabetic Nephropathies", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Tryptophan", + "Inflammation", + "Anti-Inflammatory Agents", + "Arginine", + "Diabetes Mellitus", + "Drugs, Chinese Herbal" + ], + "raw_abstract": "Diabetic kidney disease (DKD) is leading causes and one of the fastest growing causes of chronic kidney disease worldwide, and leads to high morbidity and mortality. Emerging evidences have revealed gut microbiota dysbiosis and related metabolism dysfunction play a dominant role in DKD progression and treatment through modulating inflammation. Our previous studies showed that Tangshen Formula (TSF), a Chinese herbal prescription, exhibited anti-inflammatory effect on DKD, but underlying mechanism that involved gut microbiota and related metabolism in aged model remained obscure. Here, BTBR ob/ob mice were used to establish aged DKD model, and 16S rRNA sequence and untargeted metabolomic analyses were employed to investigate the correlation between colonic microbiota and serum metabolism. The aged ob/ob mice exhibited obvious glomerular and renal tubule injury and kidney function decline in kidney, while TSF treatment significantly attenuated these abnormalities. TSF also exhibited potent anti-inflammatory effect in aged ob/ob mice indicating by reduced proinflammatory factor IL-6 and TNF-\u03b1, MCP-1 and COX-2 in serum, kidney and intestine, which suggested the involvement of gut microbiota with TSF effect. The 16S rDNA sequencing of the colonic microbiome and untargeted serum metabolomics analysis revealed significant differences in gut microbiota structure and serum metabolomic profiles between WT and ob/ob mice. Notably, TSF treatment reshaped the structure of gut microbiota and corrected the disorder of metabolism especially tryptophan metabolism and arginine biosynthesis. TSF increased Anaeroplasma and Barnesiella genera and decreased Romboutsia, Akkermansia, and Collinsella genera, and further elevated tryptophan, 5-hydroxyindoleacetate, glutamic acid, aspartate and reduced 4-hydroxy-2-quinolinecarboxylic acid, indole-3-acetic acid, xanthurenic acid, glutamine. Further correlation analysis indicated that disturbed gut microbiota was linked to tryptophan metabolism and arginine biosynthesis to regulate inflammation in aged DKD. Our data revealed that TSF attenuated renal inflammation by modulating gut microbiota and related amino acid metabolism in aged DKD model, highlighting gut microbiota and related metabolism functioned as potential therapeutic target for DKD in elderly patients.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "25644014", + "title": "Uncoupling of pro- and anti-inflammatory properties of Staphylococcus aureus.", + "year": 2015, + "journal": "Infection and immunity", + "authors": [ + "Peres AG", + "Stegen C", + "Li J", + "Xu AQ", + "Levast B", + "Surette MG", + "Cousineau B", + "Desrosiers M", + "Madrenas J" + ], + "bacteria": "Staphylococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.6842785949085587, + "mesh_terms": [ + "Cell Wall", + "Extracellular Signal-Regulated MAP Kinases", + "Humans", + "Inflammation", + "Interleukin-10", + "Phagocytosis", + "Phosphatidylinositol 3-Kinases", + "Proto-Oncogene Proteins c-akt", + "Signal Transduction", + "Staphylococcal Infections", + "Staphylococcus aureus", + "T-Lymphocytes", + "TOR Serine-Threonine Kinases", + "Toll-Like Receptor 2", + "Tumor Necrosis Factor-alpha", + "p38 Mitogen-Activated Protein Kinases" + ], + "raw_abstract": "Staphylococcus aureus is a Gram-positive bacterium that is carried by a quarter of the healthy human population and that can cause severe infections. This pathobiosis has been linked to a balance between Toll-like receptor 2 (TLR2)-dependent pro- and anti-inflammatory responses. The relationship between these two types of responses is unknown. Analysis of 16 nasal isolates of S. aureus showed heterogeneity in their capacity to induce pro- and anti-inflammatory responses, suggesting that these two responses are independent of each other. Uncoupling of these responses was corroborated by selective signaling through phosphoinositol 3-kinase (PI3K)-Akt-mTOR and extracellular signal-regulated kinase (ERK) for the anti-inflammatory response and through p38 for the proinflammatory response. Uncoupling was also observed at the level of phagocytosis and phagosomal processing of S. aureus, which were required solely for the proinflammatory response. Importantly, the anti-inflammatory properties of an S. aureus isolate correlated with its ability to modulate T cell immunity. Our results suggest the presence of anti-inflammatory TLR2 ligands in the staphylococcal cell wall, whose identification may provide templates for novel immunomodulatory drugs.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "26341395", + "title": "Evaluation of in vitro anti-inflammatory and antibacterial potential of Crescentia cujete leaves and stem bark.", + "year": 2015, + "journal": "BMC research notes", + "authors": [ + "Parvin MS", + "Das N", + "Jahan N", + "Akhter MA", + "Nahar L", + "Islam ME" + ], + "bacteria": "Staphylococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.41668831563337916, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Anti-Inflammatory Agents", + "Bignoniaceae", + "Drug Evaluation, Preclinical", + "Erythrocyte Membrane", + "Escherichia coli", + "Flavonoids", + "Hemolysis", + "Humans", + "Microbial Sensitivity Tests", + "Phenols", + "Plant Bark", + "Plant Extracts", + "Plant Leaves", + "Staphylococcus aureus" + ], + "raw_abstract": "BACKGROUND: The various parts of Cresecentia cujete have some important biological activities. In folklore medicine leaves are used to treat hematomas, tumors and hypertension. Fruit decoction is used to treat diarrhea, stomachaches, cold, bronchitis, cough, asthma, and urethritis. The present study was designed to explore the anti-inflammatory and antibacterial potential of C. cujete leaves and stem bark. Anti-inflammatory activity was evaluated by in vitro human red blood cell (HRBC) membrane stabilization method and antibacterial activity by disc diffusion method. METHODS: In vitro anti-inflammatory activity was evaluated by human red blood cell (HRBC) membrane stabilization method while in vitro antibacterial activity was evaluated using cultures of Escherichia coli and Staphylococcus aureus by disc diffusion method. Total phenolic (TPC) and total flavonoid contents (TFC) of the crude extract and fractions were also determined by Folin-Ciocalteu's phenol reagent and by aluminium chloride method, respectively. RESULTS: The crude ethanol extract (CEE) of leaves and bark (concentration of each 1.0 mg/ml) demonstrated strong membrane stabilizing activity (53.86 and 61.85% protection, respectively), whereas their chloroform fractions (CHF) revealed moderate activity (48.74 \u00b1 0.56 and 43.55 \u00b1 6.20 %, respectively) compared with standard aspirin (concentration 0.10 mg/ml) which showed 75.81% protection in this test. All the samples showed a dose dependent anti-inflammatory activity in HRBC membrane stabilization test. Total phenolic (TPC) and total flavonoid contents (TFC) of the crude extract and fractions were also determined. Again, in in vitro antibacterial study, the extractives exhibited potent antibacterial activity. CONCLUSION: Results from this study showed that the leaves and bark of C. cujete possessed anti-inflammatory as well as antibacterial activities indicating that the plant extract has therapeutic potential against the bacterial infection and also have effect on disease processes by causing destabilization of biological membranes.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "36724077", + "title": "Staphylococcus aureus stimulates neutrophil itaconate production that suppresses the oxidative burst.", + "year": 2023, + "journal": "Cell reports", + "authors": [ + "Tomlinson KL", + "Riquelme SA", + "Baskota SU", + "Drikic M", + "Monk IR", + "Stinear TP", + "Lewis IA", + "Prince AS" + ], + "bacteria": "Staphylococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.37344378311013926, + "mesh_terms": [ + "Humans", + "Animals", + "Mice", + "Staphylococcus aureus", + "Neutrophils", + "Respiratory Burst", + "Staphylococcal Infections" + ], + "raw_abstract": "Neutrophils are critical in the host defense against Staphylococcus aureus, a major human pathogen. However, even in the setting of a robust neutrophil response, S.\u00a0aureus can evade immune clearance. Here, we demonstrate that S.\u00a0aureus impairs neutrophil function by triggering the production of the anti-inflammatory metabolite itaconate. The enzyme that synthesizes itaconate, Irg1, is selectively expressed in neutrophils during S.\u00a0aureus pneumonia. Itaconate inhibits neutrophil glycolysis and oxidative burst, which impairs survival and bacterial killing. In a murine pneumonia model, neutrophil Irg1 expression protects the lung from excessive inflammation but compromises bacterial clearance. S.\u00a0aureus is thus able to evade the innate immune response by targeting neutrophil metabolism and inducing the production of the anti-inflammatory metabolite itaconate.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "33649898", + "title": "In Vitro Anti-staphylococcal and Anti-inflammatory Abilities of Lacticaseibacillus rhamnosus from Infant Gut Microbiota as Potential Probiotic Against Infectious Women Mastitis.", + "year": 2021, + "journal": "Probiotics and antimicrobial proteins", + "authors": [ + "Bousmaha-Marroki L", + "Boutillier D", + "Marroki A", + "Grangette C" + ], + "bacteria": "Staphylococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.3241711811742981, + "mesh_terms": [ + "Anti-Inflammatory Agents", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Infant", + "Lacticaseibacillus rhamnosus", + "Mastitis", + "Probiotics", + "Staphylococcus aureus", + "Staphylococcus epidermidis" + ], + "raw_abstract": "Infectious mastitis is the major cause of early weaning, depriving infants of breastfeeding benefits. It is associated with an inflammatory condition of the breast and lowered resistance to infection. Drug administration during lactation often being contra-indicated, it is therefore important to consider safe therapeutic alternatives to antibiotic and anti-inflammatory therapies, such as probiotics. In this study, we investigated in vitro the probiotic potential of thirteen Lacticaseibacillus (formerly Lactobacillus) rhamnosus strains isolated from the gut microbiota of breastfed healthy infants. Strains were assessed for their \u03b2-hemolytic activity, their resistance to antibiotics, and their antimicrobial activities against strains of Staphylococcus and Streptococcus, most often involved in women mastitis. Their immunomodulating abilities were also studied using in vitro stimulation of human immune cells. None of the strains exhibited \u03b2-hemolytic activity, and all of them were sensitive to ampicillin, penicillin, tetracycline, rifampicin, erythromycin, chloramphenicol, and imipenem but showed resistance to ceftazidime, trimethoprim/sulfamethoxazole, vancomycin, and cefotaxime, reported to be chromosomally encoded and not inducible or transferable. Four L. rhamnosus strains were selected for their large anti-staphylococcal spectrum: L. rhamnosus VR1-5 and L. rhamnosus VR3-1 inhibiting S. aureus, S. epidermis, and S. warneri and L. rhamnosus CB9-2 and L. rhamnosus CB10-5 exerting antagonistic effect against S. aureus and S. epidermis strains. Antimicrobial compounds released in cell-free supernatant showed proteinaceous nature and were thermoresistant. The immune modulatory analysis of the L. rhamnosus strains revealed two strains with significant anti-inflammatory potential, highlighted by strong induction of IL-10 and a weak pro-Th1 cytokine secretion (IL-12 and IFN-\u03b3). L. rhamnosus CB9-2 combined a large anti-staphylococcal activity spectrum and a promising anti-inflammatory profile. This strain, used individually or in a mixture, can be considered as a probiotic candidate for the management of infectious mastitis during lactation.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "28683409", + "title": "Thymus vulgaris L. extract has antimicrobial and anti-inflammatory effects in the absence of cytotoxicity and genotoxicity.", + "year": 2017, + "journal": "Archives of oral biology", + "authors": [ + "Oliveira JR", + "de Jesus Viegas D", + "Martins APR", + "Carvalho CAT", + "Soares CP", + "Camargo SEA", + "Jorge AOC", + "de Oliveira LD" + ], + "bacteria": "Staphylococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.3060558701246488, + "mesh_terms": [ + "Animals", + "Biofilms", + "Candida albicans", + "Cell Survival", + "Enterococcus faecalis", + "Enzyme-Linked Immunosorbent Assay", + "Fibroblasts", + "Gingiva", + "Humans", + "Interleukin-1beta", + "Macrophages", + "Mice", + "Plant Extracts", + "Pseudomonas aeruginosa", + "Staphylococcus aureus", + "Stem Cells", + "Streptococcus mutans", + "Thymus Plant", + "Tumor Cells, Cultured", + "Tumor Necrosis Factor-alpha" + ], + "raw_abstract": "OBJECTIVES: This study evaluated the biological effects of the T. vulgaris L. extract., such as antimicrobial activity on planktonic cultures and mono- and polymicrobial biofilms, cytotoxicity, anti-inflammatory activity and genotoxicity. METHODS: Monomicrobial biofilms of Candida albicans, Staphylococcus aureus, Enterococcus faecalis, Streptococcus mutans and Pseudomonas aeruginosa and polymicrobial biofilms composed by C. albicans with each bacterium were formed for 48h and exposed for 5min to the plant extract. Murine macrophages (RAW 264.7), human gingival fibroblasts (FMM-1), human breast carcinoma cells (MCF-7) and cervical carcinoma cells (HeLa) were also exposed to the plant extract for 5min and the cell viability were analyzed by MTT, neutral red (NR) and crystal violet (CV) assays. Interleukin-1 beta (IL-1\u03b2) and tumor necrosis factor alpha (TNF-\u03b1) produced by RAW 264.7 was quantified by ELISA, after 24h exposure to the plant extract, both in the absence and presence of lipopolysaccharide (LPS) from Escherichia coli. Genotoxicity of the plant extract was evaluated by micronucleus formation (MN) in 1000 cells. The results were analyzed by T-Test or ANOVA and Tukey's Test (P\u22640.05). RESULTS: All biofilms showed significant reductions in CFU/mL (colony-forming units per milliliter). Cell viability was above 50% for all cell lines. Anti-inflammatory effect on the synthesis of IL-1\u03b2 and TNF-\u03b1 was observed. The MN was similar or lower than the control group in all cells. CONCLUSIONS: T. vulgaris L. extract was effective against all biofilms, promoted high cell viability, anti-inflammatory effect and presented no genotoxicity.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "33495449", + "title": "Human organoid biofilm model for assessing antibiofilm activity of novel agents.", + "year": 2021, + "journal": "NPJ biofilms and microbiomes", + "authors": [ + "Wu BC", + "Haney EF", + "Akhoundsadegh N", + "Pletzer D", + "Trimble MJ", + "Adriaans AE", + "Nibbering PH", + "Hancock REW" + ], + "bacteria": "Staphylococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.27861625548034524, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Anti-Inflammatory Agents", + "Bacterial Load", + "Biofilms", + "Burns", + "Drug Evaluation, Preclinical", + "Drug Therapy, Combination", + "Humans", + "Methicillin-Resistant Staphylococcus aureus", + "Models, Biological", + "Oligopeptides", + "Organoids", + "Pseudomonas aeruginosa", + "Skin" + ], + "raw_abstract": "Bacterial biofilms cause 65% of all human infections and are highly resistant to antibiotic therapy but lack specific treatments. To provide a human organoid model for studying host-microbe interplay and enabling screening for novel antibiofilm agents, a human epidermis organoid model with robust methicillin-resistant Staphylococcus aureus (MRSA) USA300 and Pseudomonas aeruginosa PAO1 biofilm was developed. Treatment of 1-day and 3-day MRSA and PAO1 biofilms with antibiofilm peptide DJK-5 significantly and substantially reduced the bacterial burden. This model enabled the screening of synthetic host defense peptides, revealing their superior antibiofilm activity against MRSA compared to the antibiotic mupirocin. The model was extended to evaluate thermally wounded skin infected with MRSA biofilms resulting in increased bacterial load, cytotoxicity, and pro-inflammatory cytokine levels that were all reduced upon treatment with DJK-5. Combination treatment of DJK-5 with an anti-inflammatory peptide, 1002, further reduced cytotoxicity and skin inflammation.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "32533268", + "title": "The Role of New IL-1 Family Members (IL-36 and IL-38) in Atopic Dermatitis, Allergic Asthma, and Allergic Rhinitis.", + "year": 2020, + "journal": "Current allergy and asthma reports", + "authors": [ + "Tsang MS", + "Sun X", + "Wong CK" + ], + "bacteria": "Staphylococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.2782350889262604, + "mesh_terms": [ + "Animals", + "Asthma", + "Dermatitis, Atopic", + "Disease Models, Animal", + "Humans", + "Interleukin-1", + "Interleukins", + "Mice", + "Rhinitis, Allergic", + "Staphylococcus aureus" + ], + "raw_abstract": "PURPOSE OF REVIEW: Since the discovery of its very first member in 1974, the IL-1 family has expanded into a group of 11 potent molecules which are essential in both innate and acquired immunity. Pro-inflammatory cytokines IL-36\u03b1, IL-36\u03b2, and IL-36\u03b3 and their receptor antagonists IL-36Ra and IL-38, which belong to the IL-36 subfamily, are some of the most recently identified members. Recent studies show that these members possess pro-inflammatory and anti-inflammatory activities and may take part in the pathogenesis of allergy. In this review, the involvement and importance of these newly described IL-1 family members in the most common allergic diseases, i.e., atopic dermatitis (AD), allergic asthma, and allergic rhinitis, will be discussed. RECENT FINDINGS: Dysregulation of IL-36 and IL-38 was observed in the skin and respiratory tract of AD, allergic rhinitis, and allergic asthma individuals. Although the upregulation in IL-36\u03b1 and IL-36\u03b3 observed in the lesional skin of AD patients was unexpectedly small, IL-36 may play an important role in AD pathogenesis especially upon Staphylococcus aureus colonization. While IL-36\u03b3 regulates eosinophils to induce an inflammatory response in allergic rhinitis, IL-36\u03b1 was found to regulate Th17 immunity. IL-36 receptor antagonists, IL-36Ra and IL-38, however, both show promising anti-inflammatory activities against allergic asthma. Of note, IL-38 in allergic asthmatic children is significantly lower than their healthy counterparts, while the anti-inflammatory effects of IL-38 in allergic asthma exacerbation upon viral-like infection were demonstrated in in vitro, HDM-induced, and humanized mice models. Dysregulated expression of IL-36 and IL-38 observed in allergic patients and mice models revealed that they may have essential roles in the pathogenesis in AD, allergic rhinitis, and allergic asthma, especially during the host defense against pathogens at inflammatory sites. Their receptor antagonists, IL-36Ra and IL-38, could also be promising biologics in the control of allergy. Since allergic diseases are phenotypically complex, contradictory data obtained in different studies may be explained if further stratification of disease endotypes is explored. Genetically modified mice model and investigation in anti-IL-36 treatment may be useful to characterize the therapeutic potential of these cytokines in the regulation of allergy in the future.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "28392456", + "title": "Anti-inflammatory activity of Crateva adansonii DC on keratinocytes infected by Staphylococcus aureus: From traditional practice to scientific approach using HPTLC-densitometry.", + "year": 2017, + "journal": "Journal of ethnopharmacology", + "authors": [ + "Ahama-Esseh K", + "Bodet C", + "Quashie-Mensah-Attoh A", + "Garcia M", + "Th\u00e9ry-Kon\u00e9 I", + "Dorat J", + "De Souza C", + "Enguehard-Gueiffier C", + "Boudesocque-Delaye L" + ], + "bacteria": "Staphylococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.2666695686772073, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Anti-Inflammatory Agents", + "Antioxidants", + "Biphenyl Compounds", + "Capparaceae", + "Cell Survival", + "Cells, Cultured", + "Cytokines", + "Flavonoids", + "Humans", + "Keratinocytes", + "Microbial Sensitivity Tests", + "Picrates", + "Plant Extracts", + "Plant Leaves", + "RNA, Messenger", + "Staphylococcus aureus" + ], + "raw_abstract": "ETHNOPHARMACOLIGICAL RELEVANCE: Leaves of Crateva adansonii DC (Capparidaceae), a small bush found in Togo, are widely used in traditional medicine to cure infectious abscesses. Traditional healers of Lom\u00e9 harvest only budding leaves early in the morning, in specific area in order to prepare their drugs. AIM OF THE STUDY: The main goal was to validate the ancestral picking practices, and to assess the activity of C. adansonii medicine towards infectious abscesses. MATERIALS AND METHODS: A phytochemical screening of various C. adansonii leaf samples was performed using an original HPTLC-densitometry protocol and major flavonoids were identified and quantified. C. adansonii samples were collected in different neighborhoods of Lom\u00e9, at different harvesting-times and at different ages. Radical scavenging capacity, using DPPH assay, was used to quickly screen all extracts. Extracts were tested for anti-Staphylococcus aureus activity and anti-inflammatory effect on human primary keratinocytes infected by S. aureus. IL6, IL8 and TNF\u03b1 expression and production were assessed by RT-PCR and ELISA assays. RESULTS: Using antioxidant activity as selection criteria, optimal extracts were obtained with budding leaves, collected at 5:00am in Djidjol\u00e9 neighborhood. This extract showed the strongest anti-inflammatory effect on S. aureus-infected keratinocytes by reducing IL6, IL8 and TNF\u03b1 expression and production. None of the extracts inhibited the growth of S. aureus. CONCLUSIONS: Those results validate the traditional practices and the potential of C. adansonii as anti-inflammatory drug. Our findings suggest that traditional healers should add to C. adansonii leaves an antibacterial plant of Togo Pharmacopeia, in order to improve abscess healing.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "39094711", + "title": "Control of pathogenic bacterial biofilm associated with acne and the anti-inflammatory potential of an essential oil blend.", + "year": 2024, + "journal": "Microbial pathogenesis", + "authors": [ + "Ram\u00edrez N", + "Cassola F", + "Gambero A", + "Sartoratto A", + "G\u00f3mez Castellanos LM", + "Ribeiro G", + "Ferreira Rodrigues RA", + "Duarte MCT" + ], + "bacteria": "Staphylococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.24963656924838115, + "mesh_terms": [ + "Biofilms", + "Oils, Volatile", + "Humans", + "Acne Vulgaris", + "Mice", + "Anti-Inflammatory Agents", + "Anti-Bacterial Agents", + "Propionibacterium acnes", + "Staphylococcus epidermidis", + "Animals", + "Staphylococcus aureus", + "Keratinocytes", + "Microbial Sensitivity Tests", + "Macrophages", + "Tumor Necrosis Factor-alpha", + "Fibroblasts", + "Cell Survival", + "HaCaT Cells", + "Cell Line", + "Plant Oils" + ], + "raw_abstract": "Acne is one of the most common skin conditions worldwide, with multifactorial origins it affects areas of the skin with hair follicles and sebaceous glands that become clogged. Bacterial incidence aggravates treatment due to resistance to antimicrobial agents and production of virulence factors such as biofilm formation. Based on these information, this study aims to conduct in vitro evaluations of the antibacterial activity of essential oils (EOs), alone and in combination, against Propionibacterium acnes, Staphylococcus aureus, and Staphylococcus epidermidis in planktonic and biofilm forms. This study also assessed the anti-inflammatory potential (TNF-\u03b1) and the effects of EOs on the viability of human keratinocytes (HaCaT), murine fibroblasts (3T3-L1), and bone marrow-derived macrophages (BMDMs). Of all EOs tested, 13 had active action against P. acnes, 9 against S. aureus, and 9 against S. epidermidis at concentrations of 0.125-2.0\u00a0mg/mL. Among the most active plant species, a blend of essential oil (BEOs) was selected, with Cymbopogon martini (Roxb.) Will. Watson, Eugenia uniflora L., and Varronia curassavica Jacq., the latter due to its anti-inflammatory action. This BEOs showed higher inhibition rates when compared to chloramphenicol against S. aureus and S. epidermidis, and higher eradication rates when compared to chloramphenicol for the three target species. The BEOs did not affect the cell viability of cell lines evaluated, and the levels of TNF-\u03b1 decreased. According to these results, the BEOs evaluated showed potential for the development of an alternative natural formulation for the treatment of acne.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "27239229", + "title": "Analysis of cultivable microbiota and diet intake pattern of the long-lived naked mole-rat.", + "year": 2016, + "journal": "Gut pathogens", + "authors": [ + "Debebe T", + "Holtze S", + "Morhart M", + "Hildebrandt TB", + "Rodewald S", + "Huse K", + "Platzer M", + "Wyohannes D", + "Yirga S", + "Lemma A", + "Thieme R", + "K\u00f6nig B", + "Birkenmeier G" + ], + "bacteria": "Staphylococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.2281987653217769, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: A variety of microbial communities exist throughout the human and animal body. Genetics, environmental factors and long-term dietary habit contribute to shaping the composition of the gut microbiota. For this reason the study of the gut microbiota of a mammal exhibiting an extraordinary life span is of great importance. The naked mole-rat (Heterocephalus glaber) is a eusocial mammal known for its longevity and cancer resistance. METHODS: Here we analyzed its gut microbiota by cultivating the bacteria under aerobic and anaerobic conditions and identifying their species by mass spectrometry. RESULTS: Altogether, 29 species of microbes were identified, predominantly belonging to Firmicutes, and Bacteroidetes. The most frequent species were Bacillus megaterium (45.2\u00a0%), followed by Bacteroides thetaiotaomicron (19.4\u00a0%), Bacteroides ovatus, Staphylococcus sciuri and Paenibacillus spp., each with a frequency of 16.1\u00a0%. CONCLUSION: Overall, the gut of the naked mole-rat is colonized by diverse, but low numbers of cultivable microbes compared with humans and mice. The primary food plants of the rodents are rich in polyphenols and related compounds, possessing anti-microbial, anti-inflammatory, anti-oxidative as well as anti-cancer activity which may contribute to their exceptionally healthy life.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "29297666", + "title": "[Comparative Genotyping of Staphylococcus aureus Strains Isolated from Skin Lesions, Nasal Cavities, and Feces of Children with Atopic Dermatitis].", + "year": 2016, + "journal": "Vestnik Rossiiskoi akademii meditsinskikh nauk", + "authors": [ + "Pikina AP", + "Shkoporov AN", + "Kulagina EV", + "Khokhlova EV", + "Chaplin AV", + "Volodin NN", + "Kafarskaya LI", + "Korotkly NG", + "Efimov BA" + ], + "bacteria": "Staphylococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.20074970208920875, + "mesh_terms": [ + "Bacteriological Techniques", + "Child", + "Colony Count, Microbial", + "Dermatitis, Atopic", + "Feces", + "Female", + "Genotype", + "Humans", + "Male", + "Nasal Cavity", + "Skin", + "Staphylococcus aureus" + ], + "raw_abstract": "BACKGROUND: The lesion of skin of the majority atopic dermatitis patients is chronically colonized by bacteria belonging to the species Staphylococcus aureus. Topical antibacterial and anti-inflammatory therapy treatment are often ineffective due to fast recolonization by S. aureus and exacerbation of allergic process. AIMS: Our aim was to determine a frequency of S. aureus colonization in skin lesions, mucous membranes of the nasal cavity and intestine of children with atopic dermatitis, to compare the genotypes of Staphylococcus aureus strains isolated from different biotopes of atopic dermatitis patients, and to clarify whether the intestinal and nasal cavities microbiota may act as a source of S. aureus recolonization of skin lesions. MATERIALS AND METHODS: Bacteriological examination of fecal samples, skin, and nasal swabs was conducted in 38 atopic dermatitis patients. The pure bacterial cultures of S. aureus were identified using API Staph (Biomerieux, France) and Vitek 2 MS (Biomerieux, France). Isolates of S. aureus were subjected to genotyping by analysis of rRNA internal 16S-23S rRNA spacer regions and high resolution melting analysis (HMR) of polymorphic spa X-regions. RESULTS: 99% S. aureus strains were successfully identified using MALDI-TOF mass-spectrometry. S. aureus cultures were isolated from all biotopes in 31,6% of children, from skin and nasal cavities \u2014 in 42% of cases, from skin and feces \u2014 in 2,6% of cases, only from skin \u2014 in 10,5%, from nasal cavities and feces \u2014 in 2,6%, and only from nasal cavities \u2014 in 2,6% of cases. In 8% of children, S. aureus was not detected in any of the biotopes. Genotyping of the isolates enabled the detection of 17 different genotypes. A match between the genotypes of skin and nasal strains, and skin and fecal strains was observed in 88% and 61% of the cases respectively. CONCLUSIONS: The observed a high-frequency matching genotypes suggests the possibility of migration of S. aureus strains inside biotopes in humans and the absence of specialization to colonization of any of the niches.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "39395980", + "title": "Aggregatibacter is inversely associated with inflammatory mediators in sputa of patients with chronic airway diseases and reduces inflammation in vitro.", + "year": 2024, + "journal": "Respiratory research", + "authors": [ + "Goeteyn E", + "Taylor SL", + "Dicker A", + "Boll\u00e9 L", + "Wauters M", + "Joossens M", + "Van Braeckel E", + "Simpson JL", + "Burr L", + "Chalmers JD", + "Rogers GB", + "Crabb\u00e9 A" + ], + "bacteria": "Aggregatibacter", + "condition": "anti-inflammatory", + "relevance_score": 0.47416714331572546, + "mesh_terms": [ + "Humans", + "Sputum", + "Female", + "Male", + "Middle Aged", + "Inflammation Mediators", + "Aged", + "Adult", + "Cohort Studies", + "Asthma", + "Inflammation", + "Chronic Disease", + "Bronchiectasis" + ], + "raw_abstract": "BACKGROUND: Chronic airway disease (CAD) is characterized by chronic airway inflammation and colonization of the lungs by pro-inflammatory pathogens. However, while various other bacterial species are present in the lower airways, it is not fully understood how they influence inflammation. We aimed to identify novel anti-inflammatory species present in lower airway samples of patients with CAD. METHODS: Paired sputum microbiome and inflammatory marker data of adults with CAD across three separate cohorts (Australian asthma and bronchiectasis, Scottish bronchiectasis) was analyzed using Linear discriminant analysis Effect Size (LEfSE) and Spearman correlation analysis to identify species associated with a low inflammatory profile in patients. RESULTS: We identified the genus Aggregatibacter as more abundant in patients with lower levels of airway inflammatory markers in two CAD cohorts (Australian asthma and bronchiectasis). In addition, the relative abundance of Aggregatibacter was inversely correlated with sputum IL-8 (Australian bronchiectasis) and IL-1\u03b2 levels (Australian asthma and bronchiectasis). Subsequent in vitro testing, using a physiologically relevant three-dimensional lung epithelial cell model, revealed that Aggregatibacter spp. (i.e. A. actinomycetemcomitans, A. aphrophilus) and their cell-free supernatant exerted anti-inflammatory activity without influencing host cell viability. CONCLUSIONS: These findings suggest that Aggregatibacter spp. might act to reduce airway inflammation in CAD patients.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "36219470", + "title": "Immune response characterization of primary gingival fibroblasts from Grade C periodontitis patients.", + "year": 2023, + "journal": "Journal of periodontology", + "authors": [ + "Stolf CS", + "Sacramento CM", + "Alvarenga CAPG", + "Vieira JR", + "Ara\u00fajo CF", + "Monteiro MF", + "Paz HES", + "Santamaria MP", + "Ruiz KGS", + "Casarin RCV" + ], + "bacteria": "Aggregatibacter", + "condition": "anti-inflammatory", + "relevance_score": 0.2627323099573111, + "mesh_terms": [ + "Humans", + "Interleukin-10", + "Interleukin-17", + "Periodontitis", + "Cytokines", + "Gingiva", + "Tumor Necrosis Factor-alpha", + "Immunity", + "Anti-Inflammatory Agents", + "Fibroblasts" + ], + "raw_abstract": "BACKGROUND: Grade C, Stage 3-4 Periodontitis (Perio4C) is a rapidly destructive disease caused by an unequilibrated immune response that starts after the primary contact of the periodontopathogens with the gingival tissue. However, it is still unclear how this imbalanced response initiates and what is the role of the connective tissue cells in the progression of this disease. Thus, this study aims to assess the local immune response of Perio4C patients through the exposure of primary gingival fibroblast cells (GFs) with Aggregatibacter actinomycetemcomitans protein extract (AaPE) and the quantification of the inflammatory cytokines interleukin (IL)-4, IL-17, tumor necrosis factor (TNF)-\u03b1, IL-1\u03b2, interferon (IFN)-\u03b3, and IL-10 super-family members (IL-10, IL-19, and IL-24) secreted by them. METHODS: Gingival biopsies from nine periodontally health (PH) and eight Perio4C patients were harvested, and the primary culture of GFs was obtained. The cells were exposed to AaPE (5 and 20\u00a0\u03bcg/ml) and 12-myristate 13-phorbol acetate and ionomycin - calcium salt (PMA). The supernatant was collected after 1.5 and 3\u00a0h, and a cytokine panel was evaluated. RESULTS: Clustering analysis indicated dissimilar and stimuli-dependent cytokine production between Perio4C and PH subjects. Perio4C GFs presented lower production of IL-4, TNF-\u03b1, IFN-\u03b3, IL-17, IL-10, IL-24, and IL-19, while IL-1\u03b2 levels were similar to the PH group, leading to a disruption in the pro-/anti-inflammatory cytokine ratio (p\u00a0<\u00a00.05). IL-1\u03b2 and IL-10 super-family were the most discriminative representants for PH and Perio4C, respectively. CONCLUSION: GFs from individuals with Perio4C tended to hypo-respond to stimulation with AaPE, producing lower concentrations of some pro- and anti-inflammatory molecules, trending to develop a pro-inflammatory extracellular environment.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "35962564", + "title": "The serum immunoglobulin G titres against Porphyromonas gingivalis as a predictor of clinical response to 1-year treatment with biological disease-modifying antirheumatic drugs in rheumatoid arthritis patients: A retrospective cohort study.", + "year": 2023, + "journal": "Modern rheumatology", + "authors": [ + "Kobayashi T", + "Ito S", + "Murasawa A", + "Ishikawa H", + "Tabeta K" + ], + "bacteria": "Aggregatibacter", + "condition": "anti-inflammatory", + "relevance_score": 0.23373722461973526, + "mesh_terms": [ + "Humans", + "Porphyromonas gingivalis", + "Periodontitis", + "Retrospective Studies", + "Antirheumatic Agents", + "Arthritis, Rheumatoid", + "Immunoglobulin G" + ], + "raw_abstract": "OBJECTIVES: The aim is to evaluate the relevance of serum immunoglobulin G (IgG) titres against periodontopathic bacteria to predict the clinical response to 1-year treatment with biological disease-modifying antirheumatic drugs (bDMARDs) in rheumatoid arthritis (RA) patients. METHODS: Data were collected from 50 RA patients who had received conventional synthetic DMARDs, corticosteroids, or non-steroidal anti-inflammatory drugs before (baseline) and after 1-year treatment with bDMARDs in a retrospective cohort study. Changes in rheumatologic conditions were compared between the two groups for low and high baseline IgG titres against Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans according to their median measurements. RESULTS: Twenty-five patients with low anti-P. gingivalis IgG titres showed significantly greater decreases in changes in the Clinical Disease Activity Index and swollen joint count than 25 patients with high anti-P. gingivalis IgG titres (p\u2009=\u2009.04 for both). Bivariate and multivariate analyses revealed a significantly positive association of baseline anti-P. gingivalis IgG titres with Clinical Disease Activity Index changes (p\u2009=\u2009.02 and p\u2009=\u2009.002). However, post-treatment rheumatologic conditions were comparable between 25 patients each in the low and high baseline anti-A. actinomycetemcomitans IgG titre groups. CONCLUSIONS: Baseline serum anti-P. gingivalis IgG titres are predictive of the clinical response to 1-year treatment with bDMARDs in RA patients.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "26479870", + "title": "Malva sylvestris Inhibits Inflammatory Response in Oral Human Cells. An In Vitro Infection Model.", + "year": 2015, + "journal": "PloS one", + "authors": [ + "Benso B", + "Rosalen PL", + "Alencar SM", + "Murata RM" + ], + "bacteria": "Aggregatibacter", + "condition": "anti-inflammatory", + "relevance_score": 0.21768991263467555, + "mesh_terms": [ + "Aggregatibacter actinomycetemcomitans", + "Anti-Infective Agents", + "Anti-Inflammatory Agents", + "Apoptosis", + "Cell Movement", + "Cell Proliferation", + "Cells, Cultured", + "Cytokines", + "Enzyme-Linked Immunosorbent Assay", + "Epithelial Cells", + "Humans", + "Inflammation", + "Keratinocytes", + "Malva", + "Mouth", + "Plant Extracts", + "RNA, Messenger", + "Real-Time Polymerase Chain Reaction", + "Reverse Transcriptase Polymerase Chain Reaction" + ], + "raw_abstract": "The aim of this study was to investigate the in vitro anti-inflammatory activity of Malva sylvestris extract (MSE) and fractions in a co-culture model of cells infected by Aggregatibacter actinomycetemcomitans. In addition, we evaluated the phytochemical content in the extract and fractions of M. sylvestris and demonstrated that polyphenols were the most frequent group in all samples studied. An in vitro dual-chamber model to mimic the periodontal structure was developed using a monolayer of epithelial keratinocytes (OBA-9) and a subepithelial layer of fibroblasts (HGF-1). The invasive periodontopathogen A. actinomycetemcomitans (D7S-1) was applied to migrate through the cell layers and induce the synthesis of immune factors and cytokines in the host cells. In an attempt to analyze the antimicrobial properties of MSE and fractions, a susceptibility test was carried out. The extract (MIC 175 \u03bcg/mL, MBC 500\u03bcg/mL) and chloroform fraction (MIC 150 \u03bcg/mL, MBC 250 \u03bcg/mL) were found to have inhibitory activity. The extract and all fractions were assessed using a cytotoxicity test and results showed that concentrations under 100 \u03bcg/mL did not significantly reduce cell viability compared to the control group (p > 0.05, viability > 90%). In order to analyze the inflammatory response, transcriptional factors and cytokines were quantified in the supernatant released from the cells. The chloroform fraction was the most effective in reducing the bacterial colonization (p< 0.05) and controlling inflammatory mediators, and promoted the down-regulation of genes including IL-1beta, IL-6, IL-10, CD14, PTGS, MMP-1 and FOS as well as the reduction of the IL-1beta, IL-6, IL-8 and GM-CSF protein levels (p< 0.05). Malva sylvestris and its chloroform fraction minimized the A. actinomycetemcomitans infection and inflammation processes in oral human cells by a putative pathway that involves important cytokines and receptors. Therefore, this natural product may be considered as a successful dual anti-inflammatory-antimicrobial candidate.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "29761921", + "title": "Trans-cinnamic aldehyde inhibits Aggregatibacter actinomycetemcomitans-induced inflammation in THP-1-derived macrophages via autophagy activation.", + "year": 2018, + "journal": "Journal of periodontology", + "authors": [ + "Chung J", + "Kim S", + "Lee HA", + "Park MH", + "Kim S", + "Song YR", + "Na HS" + ], + "bacteria": "Aggregatibacter", + "condition": "anti-inflammatory", + "relevance_score": 0.21186315896122668, + "mesh_terms": [ + "Acrolein", + "Aggregatibacter actinomycetemcomitans", + "Animals", + "Autophagy", + "Humans", + "Inflammation", + "Lipopolysaccharides", + "Macrophages", + "Mice", + "X-Ray Microtomography" + ], + "raw_abstract": "BACKGROUND: Inflammation is an essential response against bacterial infection as a host defense mechanism, which can lead to tissue damage. Aggregatibacter actinomycetemcomitans (Aa) is major pathogen for aggressive periodontitis characterized by rapid destruction of periodontal tissue surrounding teeth. Trans-cinnamic aldehyde is a key bioactive compound of the cinnamon extracts, which has anti-inflammatory, antioxidant, antipyretic, antimicrobial, and anti-cancer properties. The objective of the present study was to investigate the anti-inflammatory effect of trans-cinnamic aldehyde against Aa infection in human THP-1 derived macrophages and on Aa-induced periodontitis in mice. METHODS: THP-1 cells were differentiated with phorbol 12-mystristate 13-acetate and were infected with live Aa. Trans-cinnamic aldehyde was pretreated 30 minutes before the bacterial infection. Cytokine production was determined by enzyme-linked immunosorbent assay (ELISA) and protein expressions were detected by Western blot analysis. Autophagosome formation was detected by Cyto-ID. Viable cell count was carried out to determine bacterial adhesion, internalization, and intracellular survival. Experimental periodontitis was induced by inoculating Aa orally to mice, and microcomputed tomography was used to evaluate bone loss. RESULTS: Pretreatment of trans-cinnamic aldehyde significantly inhibited Aa-stimulated release of tumor necrosis factor-\u03b1 and interleukin (IL)-1\u03b2. Pretreatment of trans-cinnamic aldehyde inhibited Aa-induced expression of TLR signaling pathway as well as the phosphorylation of JNK, p38, and nuclear factor (NF)-\u03baB. Also, trans-cinnamic aldehyde treatment downregulated the expression of pro-IL-1\u03b2, caspase-1, and inflammasome components. Trans-cinnamic aldehyde treatment significantly decreased intracellular survival of Aa. Moreover, the autophagosome formation and the expressions of autophagy markers including Beclin-1, ATG5, and LC3 were increased. Finally, trans-cinnamic aldehyde significantly inhibited bone loss in Aa-induced mouse periodontitis. CONCLUSIONS: Trans-cinnamic aldehyde inhibited Aa-stimulated expression of inflammatory responses and inhibited intracellular bacterial survival via autophagy activation. These results suggest that trans-cinnamic aldehyde may serve as an anti-inflammatory agent for aggressive periodontitis.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "27739345", + "title": "Rosuvastatin Inhibits Interleukin (IL)-8 and IL-6 Production in Human Coronary Artery Endothelial Cells Stimulated With Aggregatibacter actinomycetemcomitans Serotype b.", + "year": 2017, + "journal": "Journal of periodontology", + "authors": [ + "Gualtero DF", + "Viafara-Garcia SM", + "Morantes SJ", + "Buitrago DM", + "Gonzalez OA", + "Lafaurie GI" + ], + "bacteria": "Aggregatibacter", + "condition": "anti-inflammatory", + "relevance_score": 0.20489370216510286, + "mesh_terms": [ + "Aggregatibacter actinomycetemcomitans", + "Biomarkers", + "Coronary Vessels", + "Endothelial Cells", + "Enzyme-Linked Immunosorbent Assay", + "Flow Cytometry", + "Humans", + "Intercellular Adhesion Molecule-1", + "Interleukin-6", + "Interleukin-8", + "Lipopolysaccharides", + "NF-kappa B", + "Platelet Endothelial Cell Adhesion Molecule-1", + "Polymerase Chain Reaction", + "Rosuvastatin Calcium" + ], + "raw_abstract": "BACKGROUND: Rosuvastatin exhibits anti-inflammatory effects and reduces periodontal diseases and atherosclerosis; however, its role in regulating periodontopathogen-induced endothelial proinflammatory responses remains unclear. The purpose of this study is to determine whether rosuvastatin can reduce the proinflammatory response induced by Aggregatibacter actinomycetemcomitans (Aa) in human coronary artery endothelial cells (HCAECs). METHODS: HCAECs were stimulated with purified Aa serotype b lipopolysaccharide (LPS) (Aa-LPS), heat-killed (HK) bacteria (Aa-HK), or live bacteria. Expression of Toll-like receptors and cellular adhesion molecules were evaluated by fluorometric enzyme-linked immunosorbent assay. Endothelial cell activation was evaluated by quantifying nuclear factor (NF)-kappa B-p65 and cytokine expression levels by quantitative polymerase chain reaction and flow cytometry. Effect of rosuvastatin in expression of the atheroprotective factor Kr\u00fcppel-like factor 2 (KLF2) and cytokines were also studied using similar approaches. RESULTS: HCAECs showed increased interleukin (IL)-6, IL-8, intercellular adhesion molecule 1, and platelet endothelial cell adhesion molecule 1 expression when stimulated with Aa-LPS or Aa-HK. NF-\u03baB-p65 activation was induced by all antigens. Aa-induced IL-6 and IL-8 production was inhibited by rosuvastatin, particularly at higher doses. Interestingly, reduced IL-6 and IL-8 levels were observed in HCAECs stimulated with Aa in the presence of higher concentrations of rosuvastatin. This anti-inflammatory effect correlated with a significant increase of rosuvastatin-induced KLF2. CONCLUSIONS: These results suggest Aa-induced proinflammatory endothelial responses are regulated by rosuvastatin in a mechanism that appears to involve KLF2 activation. Use of rosuvastatin to prevent cardiovascular disease may reduce risk of endothelial activation by bacterial antigens.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "39122666", + "title": "Use of extracorporeal hemoperfusion therapy in an adult horse with Clostridioides difficile colitis and severe systemic inflammatory response syndrome.", + "year": 2024, + "journal": "Journal of veterinary internal medicine", + "authors": [ + "Hobbs KJ", + "Le Sueur ANV", + "Hallowell K", + "Martin E", + "Sheats MK", + "Ueda Y" + ], + "bacteria": "Clostridioides", + "condition": "anti-inflammatory", + "relevance_score": 0.29211441941888455, + "mesh_terms": [ + "Animals", + "Horses", + "Horse Diseases", + "Hemoperfusion", + "Systemic Inflammatory Response Syndrome", + "Clostridioides difficile", + "Male", + "Clostridium Infections", + "Colitis" + ], + "raw_abstract": "An 8-year-old American Quarter Horse gelding was treated with extracorporeal hemoperfusion (HP) therapy for treatment of Clostridioides difficile (C. difficile) colitis-induced systemic inflammatory response syndrome (SIRS). The gelding developed C. difficile associated peracute colitis and severe SIRS as evidenced by a positive fecal C. difficile PCR and tachypnea, tachycardia, fever, neutropenia, altered mucous membrane color, and hyperlactatemia. Concurrent acute kidney injury in the horse limited the use of routine anti-inflammatory and anti-lipopolysaccharide treatments, including flunixin meglumine and polymyxin B, because of potential for nephrosis. Extracorporeal HP therapy was performed twice within 48\u2009hours of the onset of severe SIRS during which the horse's physical examination variables stabilized. The horse was euthanized after 4\u2009days because of laminitis. These findings support further investigation of extracorporeal HP therapy as an adjunctive treatment for severe SIRS/sepsis in horses.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "39923847", + "title": "Citrulline Inhibits Clostridioides difficile Infection With Anti-inflammatory Effects.", + "year": 2025, + "journal": "Cellular and molecular gastroenterology and hepatology", + "authors": [ + "Xie Y", + "Irwin S", + "Nelson B", + "van Daelen M", + "Fontenot L", + "Jacobs JP", + "Cappelletti M", + "Feng H", + "Li Y", + "Koon HW" + ], + "bacteria": "Clostridioides", + "condition": "anti-inflammatory", + "relevance_score": 0.2677610046623462, + "mesh_terms": [], + "raw_abstract": "BACKGROUND & AIMS: Clostridioides difficile infection (CDI) causes colitis and diarrhea. C.\u00a0difficile bacterium produces toxins A and B, which cause intestinal inflammation. A metabolomics analysis discovered fecal metabolites with anti-inflammatory effects in CDI. We aimed to identify an anti-CDI metabolite that can inhibit CDI-mediated colitis and prevent recurrence. METHODS: Fresh human colonic tissues and primary human cells were used to determine metabolite effects. Humanized C.\u00a0difficile-infected HuCD34-NCG mice and antibiotics-treated human gut microbiota-treated (ABX\u00a0+ HGM) hamsters were used to simulate the human environment. RESULTS: High-throughput screening and fecal metabolomics analysis identified anti-inflammatory metabolites. Compared with other tested metabolites, citrulline preserved the mucosal integrity of toxin-exposed fresh human colonic tissues with reduced macrophage inflammatory protein 1 alpha (MIP-1a) and increased interleukin-10 (IL-10) expression. Oral citrulline treatment alleviated cecal inflammation in hamsters infected with C.\u00a0difficile ribotype 027. This was accomplished by the augmented expression of cecal IL-10 and the diminished level of cecal MIP-1a. Citrulline and vancomycin synergistically prevented recurrence in the infected ABX\u00a0+ HGM hamsters. In C57BL/6J mice infected with C.\u00a0difficile VPI10463, citrulline ameliorated colitis by reducing colonic Ccl3 mRNA expression. In immunologically humanized HuCD34-NCG mice infected with toxin B-expressing C.\u00a0difficile ribotype 017, citrulline ameliorated colitis with increased human IL-10 expression in colonic macrophages. Citrulline suppressed MIP-1a secretion and GSK3a/b dephosphorylation in the toxin A-exposed human colonic epithelial cells and promoted IL-10 expression in toxin B-exposed human macrophages and heat shock protein 27 phosphorylation. CONCLUSION: Citrulline exerts anti-inflammatory effects in the intestines against C.\u00a0difficile toxins and inhibits CDI recurrence in mice and hamsters.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "34994339", + "title": "Antibiotics with Antiviral and Anti-Inflammatory Potential Against Covid-19: A Review.", + "year": 2023, + "journal": "Current reviews in clinical and experimental pharmacology", + "authors": [ + "Abadi B", + "Ilaghi M", + "Shahsavani Y", + "Faramarzpour M", + "Oghazian MB", + "Rahimi HR" + ], + "bacteria": "Clostridioides", + "condition": "anti-inflammatory", + "relevance_score": 0.24743824261235642, + "mesh_terms": [ + "Child", + "Humans", + "Aged", + "COVID-19", + "SARS-CoV-2", + "Antiviral Agents", + "Anti-Bacterial Agents", + "Coinfection", + "Anti-Inflammatory Agents" + ], + "raw_abstract": "In Covid-19 cases, elderly patients in long-term care facilities, children younger than five years with moderate symptoms, and patients admitted to ICU or with comorbidities are at a high risk of coinfection, as suggested by the evidence. Thus, in these patients, antibiotic therapy based on empirical evidence is necessary. Finding appropriate antimicrobial agents, especially with antiviral and anti-inflammatory properties, is a promising approach to target the virus and its complications, hyper-inflammation, and microorganisms resulting in co-infection. Moreover, indiscriminate use of antibiotics can be accompanied by Clostridioides difficile colitis, the emergence of resistant microorganisms, and adverse drug reactions, particularly kidney damage and QT prolongation. Therefore, rational administration of efficient antibiotics is an important issue. The main objective of the present review is to provide a summary of antibiotics with possible antiviral activity against SARS-CoV-2 and anti-immunomodulatory effects to guide scientists for further research. Besides, the findings can help health professionals in the rational prescription of antibiotics in Covid-19 patients with a high risk of co-infection.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "36628948", + "title": "Genistein Inhibits Clostridioides difficile Infection via Estrogen Receptors and Lysine-Deficient Protein Kinase 1.", + "year": 2023, + "journal": "The Journal of infectious diseases", + "authors": [ + "Xie Y", + "Fontenot L", + "Estrada AC", + "Nelson B", + "Bullock A", + "Faull KF", + "Feng H", + "Sun M", + "Koon HW" + ], + "bacteria": "Clostridioides", + "condition": "anti-inflammatory", + "relevance_score": 0.2449036913305806, + "mesh_terms": [ + "Female", + "Humans", + "Mice", + "Animals", + "Genistein", + "Receptors, Estrogen", + "Lysine", + "Chemokine CCL3", + "Leukocytes, Mononuclear", + "Isoflavones", + "Estrogens", + "Clostridium Infections", + "Protein Kinases" + ], + "raw_abstract": "BACKGROUND: Clostridioides difficile infection (CDI) is a debilitating nosocomial disease. Postmenopausal women may have an increased risk of CDI, suggesting estrogen influence. Soybean products contain a representative estrogenic isoflavone, genistein. METHODS: The anti-inflammatory and antiapoptotic effects of genistein were determined using primary human cells and fresh colonic tissues. The effects of oral genistein therapy among mice and hamsters were evaluated. RESULTS: Within 10 days of CDI, female c57BL/6J mice in a standard environment (regular diet) had a 50% survival rate, while those with estrogen depletion and in an isoflavone-free environment (soy-free diet) had a 25% survival rate. Oral genistein improved their 10-day survival rate to 100% on a regular diet and 75% in an isoflavone-free environment. Genistein reduced macrophage inflammatory protein-1\u03b1 (MIP-1\u03b1) secretion in fresh human colonic tissues exposed to toxins. Genistein inhibited MIP-1\u03b1 secretion in primary human peripheral blood mononuclear cells, abolished apoptosis and BCL-2-associated X (BAX) expression in human colonic epithelial cells, and activated lysine-deficient protein kinase 1 (WNK1) phosphorylation in both cell types. The anti-inflammatory and antiapoptotic effects of genistein were abolished by inhibiting estrogen receptors and WNK1. CONCLUSIONS: Genistein reduces CDI disease activity by inhibiting proinflammatory cytokine expression and apoptosis via the estrogen receptor/G-protein estrogen receptor/WNK1 pathways.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "39633586", + "title": "Using nutrition to help recovery from infections.", + "year": 2025, + "journal": "Current opinion in gastroenterology", + "authors": [ + "Moura IB", + "Buckley AM" + ], + "bacteria": "Clostridioides", + "condition": "anti-inflammatory", + "relevance_score": 0.24299379885126363, + "mesh_terms": [ + "Humans", + "Gastrointestinal Microbiome", + "Dysbiosis", + "Anti-Bacterial Agents", + "Clostridium Infections", + "Dietary Fiber", + "Clostridioides difficile" + ], + "raw_abstract": "PURPOSE OF REVIEW: Antibiotics are a cornerstone of modern medicine, but antibiotic consumption can have depleting effects on the gut microbiota, potentially leading to gastrointestinal symptoms and other diseases, namely Clostridioides difficile infection. Because nutrition is a major driver of gut microbiota diversity and function, here we explore the current evidence on the potential of diets in alleviate the deleterious effects of antibiotics consumed during infections. RECENT FINDINGS: Beneficial nutrients can enhance the symbiotic effect of the gut microbiota with the host, supporting anti-inflammatory responses and maintaining tight junction integrity. Short-chain fatty acids have been shown to positively affect the immune response, reducing the severity of C. difficile infection, whereas high-fibre diets have been shown to promote faster recovery of the gut microbiota after antibiotic therapy. SUMMARY: The role of nutrition during infection is gaining momentum, with key findings exploring the effect of some nutrients in limiting the severity of infections and helping the microbiota recover from antibiotic-induced dysbiosis. Although this field is in its infancy, these findings open the possibility of personalised nutrition as a way of restoring microbiome diversity. But more work is needed to identify the most effective types and combinations of nutrients to achieve this.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "33725006", + "title": "Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis.", + "year": 2021, + "journal": "PloS one", + "authors": [ + "Vega L", + "Herrera G", + "Mu\u00f1oz M", + "Patarroyo MA", + "Maloney JG", + "Sant\u00edn M", + "Ram\u00edrez JD" + ], + "bacteria": "Clostridioides", + "condition": "anti-inflammatory", + "relevance_score": 0.21240462784595313, + "mesh_terms": [ + "Blastocystis", + "Blastocystis Infections", + "Clostridioides difficile", + "Clostridium Infections", + "Diarrhea", + "Feces", + "Gastrointestinal Microbiome", + "Humans" + ], + "raw_abstract": "Blastocystis and Clostridioides difficile co-occurrence is considered a rare event since the colonization by Blastocystis is prevented under a decrease in beneficial bacteria in the microbiota when there is C. difficile infection (CDI). This scenario has been reported once, but no information on the gut microbiota profiling is available. The present study is motivated by knowing which members of the microbiota can be found in this rare scenario and how this co-occurrence may impact the abundance of other bacteria, eukaryotes or archaea present in the gut microbiota. This study aimed to describe the bacterial and eukaryotic communities using amplicon-based sequencing of the 16S- and 18S-rRNA regions of three patient groups: (1) Blastocystis and C. difficile infection (B+/C+, n = 31), (2) C. difficile infection only (B-/C+, n = 44), and (3) without Blastocystis or C. difficile (B-/C-, n = 40). Blastocystis was subtyped using amplicon-based sequencing of the 18S-rRNA gene, revealing circulation of subtypes ST1 (43.4%), ST3 (35.85%) and ST5 (20.75%) among the study population. We found that B+/C+ patients had a higher abundance of some beneficial bacteria (such as butyrate producers or bacteria with anti-inflammatory properties) compared with non-Blastocystis-colonized patients, which may suggest a shift towards an increase in beneficial bacteria when Blastocystis colonizes patients with CDI. Regarding eukaryotic communities, statistical differences in the abundance of some eukaryotic genera between the study groups were not observed. Thus, this study provides preliminary descriptive information of a potential microbiota profiling of differential presence by Blastocystis and C. difficile.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "36746838", + "title": "Lactococcus lactis as an Interleukin Delivery System for Prophylaxis and Treatment of Inflammatory and Autoimmune Diseases.", + "year": 2024, + "journal": "Probiotics and antimicrobial proteins", + "authors": [ + "Campos GM", + "Am\u00e9rico MF", + "Dos Santos Freitas A", + "Barroso FAL", + "da Cruz Ferraz Dutra J", + "Quaresma LS", + "Cordeiro BF", + "Laguna JG", + "de Jesus LCL", + "Fontes AM", + "Birbrair A", + "Santos TM", + "Azevedo V" + ], + "bacteria": "Lactococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.43994221636694725, + "mesh_terms": [ + "Humans", + "Lactococcus lactis", + "Interleukins", + "Cytokines", + "Autoimmune Diseases", + "Anti-Inflammatory Agents" + ], + "raw_abstract": "Target delivery of therapeutic agents with anti-inflammatory properties using probiotics as delivery and recombinant protein\u00a0expression vehicles is a promising approach for the prevention and treatment of many diseases, such as cancer and intestinal immune disorders. Lactococcus lactis, a Lactic Acid Bacteria (LAB) widely used in the dairy industry, is one of the most important microorganisms with GRAS status for human consumption, for which biotechnological tools have already been developed to express and deliver recombinant biomolecules with anti-inflammatory properties. Cytokines, for \u00a0example, are immune system\u00a0communication molecules present at virtually all levels of the immune response. They are essential in cellular and humoral processes, such as hampering inflammation or adjuvating in the adaptive immune response, making them good candidates for therapeutic approaches. This review discusses the advances in\u00a0the\u00a0development of new therapies and prophylactic approaches using LAB to deliver/express cytokines for the treatment of inflammatory and autoimmune\u00a0diseases in the future.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "30768688", + "title": "The Alternate Consumption of Quercetin and Alliin in the Traditional Asian Diet Reshaped Microbiota and Altered Gene Expression of Colonic Epithelial Cells in Rats.", + "year": 2019, + "journal": "Journal of food science", + "authors": [ + "Yu J", + "Guo H", + "Xie J", + "Luo J", + "Li Y", + "Liu L", + "Ou S", + "Zhang G", + "Peng X" + ], + "bacteria": "Lactococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.2401616398451237, + "mesh_terms": [ + "Animals", + "Bacteria", + "Colon", + "Cysteine", + "Diet", + "Epithelial Cells", + "Feces", + "Gastrointestinal Microbiome", + "Gene Expression Regulation", + "Intestinal Mucosa", + "Male", + "Quercetin", + "RNA, Ribosomal, 16S", + "Rats" + ], + "raw_abstract": "The diet of traditional Asian is similar to the Mediterranean that was considered as a healthy dietary pattern. The report was scarce on whether different plant-derived components with similar anti-oxidative and anti-inflammatory function such as quercetin and alliin in traditional Asian diet consumed in an alternate style cooperatively affect health including the growth of host and the status of the gut microbiota and colonic epithelial immunity. In the present study, the effects of alternate consumption of quercetin and alliin on host health judging by the profile of gut microbiota and gene expression of colonic epithelial cells were investigated with the Illumina MiSeq sequencing (16S rRNA genes) and Illumina HiSeq (RNA-seq) technique, respectively. The results showed that the alternate consumption significantly increased the rat body weight and reshaped the gut microbiota composition. At the phylum level, it significantly increased the relative abundance of fecal Firmicutes and Cyanobacteria but decreased that of Bacteroidetes (P < 0.05) and increased the relative abundance of Candidatus Arthromitus, Lactococcus, Geobacillus, and Ruminococcus at the genus level that benefits the host's health. The alternate consumption of quercetin and alliin also altered 13 genes expression involved in the KEGG pathways of complement and coagulation cascades and hematopoietic cell lineage to improve the gut immunity. Therefore, the alternate consumption of quercetin and alliin in traditional Asian diet can contribute beneficial metabolic effects by optimizing gut microbiota and altering the immunologic function of colonic epithelial cells, resulting in its potential to improve the sub-health status.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "30305667", + "title": "Gut microbiome modulation during treatment of mucositis with the dairy bacterium Lactococcus lactis and recombinant strain secreting human antimicrobial PAP.", + "year": 2018, + "journal": "Scientific reports", + "authors": [ + "Carvalho R", + "Vaz A", + "Pereira FL", + "Dorella F", + "Aguiar E", + "Chatel JM", + "Bermudez L", + "Langella P", + "Fernandes G", + "Figueiredo H", + "Goes-Neto A", + "Azevedo V" + ], + "bacteria": "Lactococcus", + "condition": "anti-inflammatory", + "relevance_score": 0.22170041214473665, + "mesh_terms": [ + "Animals", + "Anti-Infective Agents", + "Biodiversity", + "Feces", + "Female", + "Fluorouracil", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Lactococcus lactis", + "Mice, Inbred BALB C", + "Mucositis", + "Pancreatitis-Associated Proteins", + "Phylogeny", + "Recombination, Genetic" + ], + "raw_abstract": "Mucositis is an inflammatory condition of the gut, caused by an adverse effect of chemotherapy drugs, such as 5-fluorouracil (5-FU). In an attempt to develop alternative treatments for the disease, several research groups have proposed the use of probiotics, in particular, Lactic Acid Bacteria (LAB). In this context, the use of recombinant LAB, for delivering anti-inflammatory compounds has also been explored. In previous work, we demonstrated that either Lactococcus lactis NZ9000 or a recombinant strain expressing an antimicrobial peptide involved in human gut homeostasis, the Pancreatitis-associated Protein (PAP), could ameliorate 5-FU-induced mucositis in mice. However, the impact of these strains on the gut microbiota still needs to be elucidated. Therefore, in the present study, we aimed to characterize the effects of both Lactococci strains in the gut microbiome of mice through a 16\u2009S rRNA gene sequencing metagenomic approach. Our data show 5-FU caused a significant decrease in protective bacteria and increase of several bacteria associated with pro-inflammatory traits. The Lactococci strains were shown to reduce several potential opportunistic microbes, while PAP delivery was able to suppress the growth of Enterobacteriaceae during inflammation. We conclude the strain secreting antimicrobial PAP was more effective in the control of 5-FU-dysbiosis.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "32229219", + "title": "Reductions in anti-inflammatory gut bacteria are associated with depression in a sample of young adults.", + "year": 2020, + "journal": "Brain, behavior, and immunity", + "authors": [ + "Liu RT", + "Rowan-Nash AD", + "Sheehan AE", + "Walsh RFL", + "Sanzari CM", + "Korry BJ", + "Belenky P" + ], + "bacteria": "Flavonifractor", + "condition": "anti-inflammatory", + "relevance_score": 0.2356865276278009, + "mesh_terms": [ + "Anti-Inflammatory Agents", + "Bacteria", + "Depression", + "Depressive Disorder, Major", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Young Adult" + ], + "raw_abstract": "We assessed the gut microbiota of 90 American young adults, comparing 43 participants with major depressive disorder (MDD) and 47 healthy controls, and found that the MDD subjects had significantly different gut microbiota compared to the healthy controls at multiple taxonomic levels. At the phylum level, participants with MDD had lower levels of Firmicutes and higher levels of Bacteroidetes, with similar trends in the at the class (Clostridia and Bacteroidia) and order (Clostridiales and Bacteroidales) levels. At the genus level, the MDD group had lower levels of Faecalibacterium and other related members of the family Ruminococcaceae, which was also reduced relative to healthy controls. Additionally, the class Gammaproteobacteria and genus Flavonifractor were enriched in participants with MDD. Accordingly, predicted functional differences between the two groups include a reduced abundance of short-chain fatty acid production pathways in the MDD group. We also demonstrated that the magnitude of taxonomic changes was associated with the severity of depressive symptoms in many cases, and that most changes were present regardless of whether depressed participants were taking psychotropic medications. Overall, our results support a link between MDD and lower levels of anti-inflammatory, butyrate-producing bacteria, and may support a connection between the gut microbiota and the chronic, low-grade inflammation often observed in MDD patients.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "32996156", + "title": "Bifidobacterium bifidum TMC3115 ameliorates milk protein allergy in by affecting gut microbiota: A randomized double-blind control trial.", + "year": 2020, + "journal": "Journal of food biochemistry", + "authors": [ + "Jing W", + "Liu Q", + "Wang W" + ], + "bacteria": "Oscillibacter", + "condition": "anti-inflammatory", + "relevance_score": 0.30283549943222715, + "mesh_terms": [ + "Animals", + "Bifidobacterium bifidum", + "Cattle", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Infant", + "Milk Hypersensitivity", + "Milk Proteins" + ], + "raw_abstract": "We aimed to explore the effects of Bifidobacterium bifidum TMC3115 intervention on cow's milk protein allergy (CMPA) and gut microbiota in infants. A total 256 CMPA infants were randomly and evenly assigned into an intervention group (B. bifidum) and a control group (placebo). Allergic scores, anti-inflammatory responses, and secondary outcomes were measured. Fecal specimens were collected, and the gut microbiota were analyzed by using 16S rDNA sequencing. After 6-month B. bifidum intervention, B. bifidum TMC3115 consumption reduced allergic scores, and improved anti-inflammatory responses and secondary outcomes in CMPA infants. LEfSe analysis showed Bifidobacterium, Lactobacillus, Turicibacter, Sutterella, and Parabacteroides were the most predominant phylum in the intervention group, whereas the Firmicutes (Anaerovibrio, Christensenellaceae, Oscillibacter, Bilophila, Dorea, and Roseburia) were most dominant phyla in the control group. Serum IgE or IgG2 had a strong relationship with \u03b1-diversity scores of gut microbiota. PRACTICAL APPLICATIONS: There is a high level of prevalence of milk allergy in infants, which is difficult to be treated. Bifidobacterium bifidum TMC3115 supplement reduced allergic scores, improved anti-inflammatory responses, and reduced serum level of IgE and increased the level of IgG2 in the infants. On the contrary, B. bifidum supplement increased the genus proportion of probiotics and reduced the proportion of pathogens. The improvement of gut microbiota will be beneficial in the prevention of milk allergy. B. bifidum TMC3115 reduces milk allergy in the infants by regulating gut microbiota, and should be developed a potential way in the prevention of infant milk allergy.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "34399527", + "title": "Ethanol extract of Sargarsum fusiforme alleviates HFD/STZ-induced hyperglycemia in association with modulation of gut microbiota and intestinal metabolites in type 2 diabetic mice.", + "year": 2021, + "journal": "Food research international (Ottawa, Ont.)", + "authors": [ + "Wu S", + "Zuo J", + "Cheng Y", + "Zhang Y", + "Zhang Z", + "Wu M", + "Yang Y", + "Tong H" + ], + "bacteria": "Oscillibacter", + "condition": "anti-inflammatory", + "relevance_score": 0.23948567082371303, + "mesh_terms": [ + "Animals", + "Diabetes Mellitus, Experimental", + "Diabetes Mellitus, Type 2", + "Diet, High-Fat", + "Ethanol", + "Gastrointestinal Microbiome", + "Hyperglycemia", + "Mice", + "Plant Extracts", + "Streptozocin" + ], + "raw_abstract": "Type 2 diabetes mellitus (T2DM) is considered a rapidly growing chronic disease that threatens human health worldwide. Extracts of various seaweeds have been shown to have anti-diabetic activity. Sargarsum fusiforme, an edible brown seaweed, has been shown to possess anti-inflammatory, anti-diabetic and anti-obesity activities. In this study, we investigated the beneficial effect of an ethanol extract of S. fusiforme (EE) on type 2 diabetes in mice induced with high-fat diet (HFD) and streptozotocin (STZ). Administering EE to the diabetic mice significantly reduced food intake, water intake and fasting blood glucose (FBG), while improving glucose tolerance, lipid profile and ameliorating hepatic oxidative stress. Furthermore, these animals also exhibited significantly diminished epididymal fat deposition, as well as less pathological changes in the heart and liver tissues, while displaying some highly enriched benign gut bacteria (e.g., Intestinimonas, Oscillibacter, Lachnoclostridium, unidentified_Lachnospiraceae, Roseburia and Anaerotruncus) and a lower abundance of bacteria associated with diabetes or other metabolic diseases (e.g., Enterorhabdus and Romboutsia). Metabolomic analysis revealed reduced levels of branched-chain amino acids (BCAA), such as l-valine and l-isoleucine, aromatic amino acids (AAA), such as l-tyrosine and l-phenylalanine, and increased levels of 4-hydroxyphenylacetic acid (4-HPA) in the gut content, suggesting that EE may impact T2DM through modulation of these compounds in the gut of the animals. Taken together, the results implied that S. fusiforme may contain valuable active components other than polysaccharides that have potential benefit in alleviating T2DM.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "33549142", + "title": "Could dysbiosis of inflammatory and anti-inflammatory gut bacteria have an implications in the development of type 2 diabetes? A pilot investigation.", + "year": 2021, + "journal": "BMC research notes", + "authors": [ + "Kulkarni P", + "Devkumar P", + "Chattopadhyay I" + ], + "bacteria": "Butyrivibrio", + "condition": "anti-inflammatory", + "relevance_score": 0.34138150785478155, + "mesh_terms": [ + "Actinobacteria", + "Anti-Inflammatory Agents", + "Bacteria", + "Bacteroides", + "Clostridiales", + "Diabetes Mellitus, Type 2", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Lactobacillus", + "Pilot Projects", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: Differential alterations in gut microbiota and chronic low-grade inflammation play a critical role in the development of Type 2 diabetes (T2D). Here we aimed to investigate if dysbiosis of inflammation and anti-inflammation-associated gut bacterial communities in fecal samples of individuals had any influence on T2D using a 16S rRNA gene of V3 region sequencing at Illumina MiSeq platform. RESULTS: Our findings showed that a higher abundance of inflammatory bacteria such as Lactobacillus ruminis, Ruminococcus gnavus, Bacteroides caccae, Butyricimonas, and Collinsella aerofaciens, and lower abundance of anti-inflammatory bacteria such as Faecalibacterium prausnitzii, and Butyrivibrio that likely play a role in the development of T2D. Our findings hint the potential of indigenous microbiota in developing diagnostic markers and therapeutic targets in T2D.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "37479064", + "title": "Development of a time-dependent oral colon delivery system of anaerobic Odoribacter splanchnicus for bacteriotherapy.", + "year": 2023, + "journal": "European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V", + "authors": [ + "Bosch B", + "Moutaharrik S", + "Gazzaniga A", + "Hiippala K", + "Santos HA", + "Maroni A", + "Satokari R" + ], + "bacteria": "Odoribacter", + "condition": "anti-inflammatory", + "relevance_score": 0.2795286428736188, + "mesh_terms": [ + "Inflammatory Bowel Diseases", + "Anaerobiosis", + "Drug Delivery Systems", + "Tablets", + "Anti-Inflammatory Agents", + "Humans", + "Bacteroidetes", + "Hydrogen-Ion Concentration", + "Colon" + ], + "raw_abstract": "Odoribacter (O.) splanchnicus is an anaerobic member of the human intestinal microbiota. Its decrease in abundance has been associated with inflammatory bowel disease (IBD), non-alcoholic fatty liver, and cystic fibrosis. Considering the anti-inflammatory properties of O. splanchnicus and its possible use for IBD, intestinal isolate O. splanchnicus 57 was here formulated for oral colonic release based on a time-dependent strategy. Freeze-drying protocol was determined to ensure O. splanchnicus 57 viability during the process. Disintegrating tablets, containing the freeze-dried O. splanchnicus 57, were manufactured by direct compression and coated by powder-layering technique with hydroxypropyl methylcellulose (Methocel\u2122 E50) in a tangential-spray fluid bed. Eudragit\u00ae L was then applied by spray-coating in a top-spray fluid bed. Double-coated tablets were tested for release, showing gastric resistance properties and, as desired, lag phases of reproducible duration prior to release in phosphate buffer pH 6.8. The cell viability and anti-inflammatory activity of the strain were assessed after the main manufacturing steps. While freeze-drying did not affect bacterial viability, the tableting and coating processes were more stressful. Nonetheless, O. splanchnicus 57 cells survived manufacturing and the final formulations had 10", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "33147448", + "title": "Airway Microbiota-Host Interactions Regulate Secretory Leukocyte Protease Inhibitor Levels and Influence Allergic Airway Inflammation.", + "year": 2020, + "journal": "Cell reports", + "authors": [ + "Jaeger N", + "McDonough RT", + "Rosen AL", + "Hernandez-Leyva A", + "Wilson NG", + "Lint MA", + "Russler-Germain EV", + "Chai JN", + "Bacharier LB", + "Hsieh CS", + "Kau AL" + ], + "bacteria": "Haemophilus", + "condition": "anti-inflammatory", + "relevance_score": 0.2725121402435068, + "mesh_terms": [ + "A549 Cells", + "Adolescent", + "Adult", + "Animals", + "Antigens", + "Bordetella", + "Child", + "Colony Count, Microbial", + "Disease Models, Animal", + "Host Microbial Interactions", + "Humans", + "Hypersensitivity", + "Immunity", + "Inflammation", + "Lung", + "Mice, Inbred C57BL", + "Microbiota", + "Ovalbumin", + "Secretory Leukocyte Peptidase Inhibitor", + "Th17 Cells", + "Transcriptome", + "Young Adult" + ], + "raw_abstract": "Homeostatic mucosal immune responses are fine-tuned by naturally evolved interactions with native microbes, and integrating these relationships into experimental models can provide new insights into human diseases. Here, we leverage a murine-adapted airway microbe, Bordetella pseudohinzii (Bph), to investigate how chronic colonization impacts mucosal immunity and the development of allergic airway inflammation (AAI). Colonization with Bph induces the differentiation of interleukin-17A (IL-17A)-secreting T-helper cells that aid in controlling bacterial abundance. Bph colonization protects from AAI and is associated with increased production of secretory leukocyte protease inhibitor (SLPI), an antimicrobial peptide with anti-inflammatory properties. These findings are additionally supported by clinical data showing that higher levels of upper respiratory SLPI correlate both with greater asthma control and the presence of Haemophilus, a bacterial genus associated with AAI. We propose that SLPI could be used as a biomarker of beneficial host-commensal relationships in the airway.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "37696680", + "title": "Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Del Chierico F", + "Cardile S", + "Baldelli V", + "Alterio T", + "Reddel S", + "Bramuzzo M", + "Knafelz D", + "Lega S", + "Bracci F", + "Torre G", + "Maggiore G", + "Putignani L" + ], + "bacteria": "Haemophilus", + "condition": "anti-inflammatory", + "relevance_score": 0.24816817620103612, + "mesh_terms": [ + "Humans", + "Child", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Cholangitis, Sclerosing", + "Dysbiosis", + "RNA, Ribosomal, 16S", + "Bacteria", + "Bacteroidetes", + "Italy" + ], + "raw_abstract": "BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis. METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs). RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients. CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC. In this study, we report the gut microbiota and mycobiota dysbiosis in pediatric patients affected by primary sclerosing cholangitis (PSC) associated with ulcerative colitis (UC), with an increase in pro-inflammatory pathobionts and a reduction in anti-inflammatory commensals.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "32758647", + "title": "Traditional application and modern pharmacological research of Artemisia annua L.", + "year": 2020, + "journal": "Pharmacology & therapeutics", + "authors": [ + "Feng X", + "Cao S", + "Qiu F", + "Zhang B" + ], + "bacteria": "Haemophilus", + "condition": "anti-inflammatory", + "relevance_score": 0.24597874166061215, + "mesh_terms": [ + "Animals", + "Anti-Infective Agents", + "Anti-Inflammatory Agents", + "Antineoplastic Agents, Phytogenic", + "Artemisia annua", + "Humans", + "Plant Extracts" + ], + "raw_abstract": "As a Traditional Chinese Medicine, Artemisia annua L. (A. annua) has been used for the treatment of various diseases since ancient times, including intermittent fevers due to malaria, bone steaming and heat/fever arising from exhaustion, tuberculosis, lice, wounds, scabies, dysentery et al. With the discovery of artemisinin and its excellent anti-malarial activity, A. annua has received great attention. Recently, A. annua has been revealed to show inhibitory effects against parasites (e.g. Plasmodium, Toxoplasma gondii, Leishmania, Acanthamoeba, Schistosoma), viruses (e.g. hepatitis A virus, herpes simplex viruses 1 and 2, human immunodeficiency virus), fungi (Candida, Malassezia, Saccharomyces spp.) and bacteria (Enterococcus, Streptococcus, Staphylococcus, Bacillus, Listeria, Haemophilus, Escherichia, Pseudomonas, Klebsiella, Acinetobacter, Salmonella, Yersinia spp.). A. annua has also been reported to possess anti-inflammatory and anti-cancer actions and been employed for the treatment of osteoarthritis, leukemia, colon cancer, renal cell carcinoma, breast cancer, non-small cell lung cancer, prostate cancre and hepatoma. Besides, the immunoregulation, anti-adipogenic, anti-ulcerogenic, anti-asthmatic, anti-nociceptive and anti-osteoporotic activities of A. annua were also evaluated. Along these lines, this review summarizes the traditional application and modern pharmacological research of A. annua, providing novel insights of A. annua in the treatment of various diseases.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "27104764", + "title": "Cigarette Smoke-Induced Lung Disease Predisposes to More Severe Infection with Nontypeable Haemophilus influenzae: Protective Effects of Andrographolide.", + "year": 2016, + "journal": "Journal of natural products", + "authors": [ + "Tan WS", + "Peh HY", + "Liao W", + "Pang CH", + "Chan TK", + "Lau SH", + "Chow VT", + "Wong WS" + ], + "bacteria": "Haemophilus", + "condition": "anti-inflammatory", + "relevance_score": 0.23074394176991664, + "mesh_terms": [ + "Andrographis", + "Animals", + "Diterpenes", + "Female", + "Glutamate-Cysteine Ligase", + "Haemophilus Infections", + "Haemophilus influenzae", + "Heme Oxygenase-1", + "Humans", + "Matrix Metalloproteinase 8", + "Mice", + "Mice, Inbred BALB C", + "Mice, Inbred C57BL", + "Molecular Structure", + "Neutrophil Infiltration", + "Neutrophils", + "Plants, Medicinal", + "Pneumonia", + "Pulmonary Disease, Chronic Obstructive", + "Smoking", + "Nicotiana", + "Tumor Necrosis Factor-alpha" + ], + "raw_abstract": "Cigarette smoke (CS) is associated with many maladies, one of which is chronic obstructive pulmonary disease (COPD). As the disease progresses, patients are more prone to develop COPD exacerbation episodes by bacterial infection, particularly to nontypeable Haemophilus influenza (NTHi) infection. The present study aimed to develop a CS-exposed mouse model that increases inflammation induced by NTHi challenge and investigate the protective effects of andrographolide, a bioactive molecule with anti-inflammatory and antioxidant properties isolated from the plant Andrographis paniculata. Female BALB/c mice exposed to 2 weeks of CS followed by a single intratracheal instillation of NTHi developed increased macrophage and neutrophil pulmonary infiltration, augmented cytokine levels, and heightened oxidative damage. Andrographolide effectively reduced lung cellular infiltrates and decreased lung levels of TNF-\u03b1, IL-1\u03b2, CXCL1/KC, 8-OHdG, matrix metalloproteinase-8 (MMP-8), and MMP-9. The protective actions of andrographolide on CS-predisposed NTHi inflammation might be attributable to increased nuclear factor erythroid-2-related factor 2 (Nrf2) activation and decreased Kelch-like ECH-associated protein 1 (Keap1) repressor function, resulting in enhanced gene expression of antioxidant enzymes including heme oxygenase-1 (HO-1), glutathione reductase (GR), glutathione peroxidase-2 (GPx-2), glutamate-cysteine ligase modifier (GCLM), and NAD(P)H quinone oxidoreductase 1 (NQO1). Taken together, these findings strongly support a therapeutic potential for andrographolide in preventing lung inflammation caused by NTHi in cigarette smokers.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "37029178", + "title": "Lung microbiome and cytokine profiles in different disease states of COPD: a cohort study.", + "year": 2023, + "journal": "Scientific reports", + "authors": [ + "Xue Q", + "Xie Y", + "He Y", + "Yu Y", + "Fang G", + "Yu W", + "Wu J", + "Li J", + "Zhao L", + "Deng X", + "Li R", + "Wang F", + "Zheng Y", + "Gao Z" + ], + "bacteria": "Haemophilus", + "condition": "anti-inflammatory", + "relevance_score": 0.22229792572941978, + "mesh_terms": [ + "Humans", + "Cohort Studies", + "Tumor Necrosis Factor-alpha", + "Pulmonary Disease, Chronic Obstructive", + "Lung", + "Microbiota", + "Haemophilus", + "Sputum", + "Disease Progression" + ], + "raw_abstract": "Increasing evidence indicates that respiratory tract microecological disorders may play a role in the pathogenesis of chronic obstructive pulmonary disease (COPD). Understanding the composition of the respiratory microbiome in COPD and its relevance to respiratory immunity will help develop microbiome-based diagnostic and therapeutic approaches. One hundred longitudinal sputum samples from 35 subjects with acute exacerbation of COPD (AECOPD) were analysed for respiratory bacterial microbiome using 16S ribosomal RNA amplicon sequencing technology, and the sputum supernatant was analysed for 12 cytokines using a Luminex liquid suspension chip. Unsupervised hierarchical clustering was employed to evaluate the existence of distinct microbial clusters. In AECOPD, the respiratory microbial diversity decreased, and the community composition changed significantly. The abundances of Haemophilus, Moraxella, Klebsiella, and Pseudomonas increased significantly. Significant positive correlations between the abundance of Pseudomonas and TNF-\u03b1, abundance of Klebsiella and the percentage of eosinophils were observed. Furthermore, COPD can be divided into four clusters based on the respiratory microbiome. AECOPD-related cluster was characterized by the enrichment of Pseudomonas and Haemophilus and a high level of TNF-\u03b1. Lactobacillus and Veillonella are enriched in therapy-related phenotypes and may play potential probiotic roles. There are two inflammatory endotypes in the stable state: Gemella is associated with the Th2 inflammatory endotypes, whereas Prevotella is associated with the Th17 inflammatory endotypes. Nevertheless, no differences in clinical manifestations were found between these two endotypes. The sputum microbiome is associated with the disease status of COPD, allowing us to distinguish different inflammatory endotypes. Targeted anti-inflammatory and anti-infective therapies may improve the long-term prognosis of COPD.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "30915434", + "title": "Metabolic analyses reveal common adaptations in two invasive Haemophilus influenzae strains.", + "year": 2019, + "journal": "Pathogens and disease", + "authors": [ + "Muda NM", + "Nasreen M", + "Dhouib R", + "Hosmer J", + "Hill J", + "Mahawar M", + "Schirra HJ", + "McEwan AG", + "Kappler U" + ], + "bacteria": "Haemophilus", + "condition": "anti-inflammatory", + "relevance_score": 0.20840486160981422, + "mesh_terms": [ + "Adaptation, Physiological", + "Biofilms", + "Energy Metabolism", + "Gene Expression Regulation, Bacterial", + "Genome, Bacterial", + "Genomics", + "Haemophilus Infections", + "Haemophilus influenzae", + "Host-Pathogen Interactions", + "Humans", + "Microbial Viability", + "Oxygen Consumption", + "Phenotype", + "Pulmonary Disease, Chronic Obstructive", + "Respiratory Mucosa" + ], + "raw_abstract": "Non-typeable Haemophilus influenzae (NTHi) is a major pathogen in upper and lower respiratory tract infections in humans, and is increasingly also associated with invasive disease. We have examined two unrelated NTHi invasive disease isolates, R2866 and C188, in order to identify metabolic and physiological properties that distinguish them from respiratory tract disease isolates such as Hi2019. While the general use of the Hi metabolic network was similar across all three strains, the two invasive isolates secreted increased amounts of succinate, which can have anti-inflammatory properties. In addition, they showed a common shift in their carbon source utilization patterns, with strongly enhanced metabolism of nucleoside substrates, glucose and sialic acid. The latter two are major compounds present in blood and cerebrospinal fluid (CSF). Interestingly, C188 and R2866 also shared a reduced ability to invade or survive intracellularly in 16HBE14 bronchial epithelial cells relative to Hi2019 (4-fold (4 h), 25-fold (24 h) reduction). Altered metabolic properties, such as the ones observed here, could arise from genomic adaptations that NTHi undergo during infection. Together these data indicate that shifts in substrate preferences in otherwise conserved metabolic pathways may underlie strain niche specificity and thus have the potential to alter the outcomes of host-NTHi interactions.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "26202987", + "title": "Phosphocholine-Modified Macromolecules and Canonical Nicotinic Agonists Inhibit ATP-Induced IL-1\u03b2 Release.", + "year": 2015, + "journal": "Journal of immunology (Baltimore, Md. : 1950)", + "authors": [ + "Hecker A", + "K\u00fcllmar M", + "Wilker S", + "Richter K", + "Zakrzewicz A", + "Atanasova S", + "Mathes V", + "Timm T", + "Lerner S", + "Klein J", + "Kaufmann A", + "Bauer S", + "Padberg W", + "Kummer W", + "Janciauskiene S", + "Fronius M", + "Schweda EK", + "Lochnit G", + "Grau V" + ], + "bacteria": "Haemophilus", + "condition": "anti-inflammatory", + "relevance_score": 0.20729995107797686, + "mesh_terms": [ + "Acetylcholine", + "Adenosine Triphosphate", + "Animals", + "Blotting, Western", + "Cells, Cultured", + "Choline", + "Dose-Response Relationship, Drug", + "Humans", + "Interleukin-1beta", + "Lipopolysaccharides", + "Membrane Potentials", + "Monocytes", + "Nicotine", + "Nicotinic Agonists", + "Phosphorylcholine", + "RNA Interference", + "Rats", + "Receptors, Nicotinic", + "Reverse Transcriptase Polymerase Chain Reaction", + "U937 Cells", + "alpha7 Nicotinic Acetylcholine Receptor" + ], + "raw_abstract": "IL-1\u03b2 is a potent proinflammatory cytokine of the innate immune system that is involved in host defense against infection. However, increased production of IL-1\u03b2 plays a pathogenic role in various inflammatory diseases, such as rheumatoid arthritis, gout, sepsis, stroke, and transplant rejection. To prevent detrimental collateral damage, IL-1\u03b2 release is tightly controlled and typically requires two consecutive danger signals. LPS from Gram-negative bacteria is a prototypical first signal inducing pro-IL-1\u03b2 synthesis, whereas extracellular ATP is a typical second signal sensed by the ATP receptor P2X7 that triggers activation of the NLRP3-containing inflammasome, proteolytic cleavage of pro-IL-1\u03b2 by caspase-1, and release of mature IL-1\u03b2. Mechanisms controlling IL-1\u03b2 release, even in the presence of both danger signals, are needed to protect from collateral damage and are of therapeutic interest. In this article, we show that acetylcholine, choline, phosphocholine, phosphocholine-modified LPS from Haemophilus influenzae, and phosphocholine-modified protein efficiently inhibit ATP-mediated IL-1\u03b2 release in human and rat monocytes via nicotinic acetylcholine receptors containing subunits \u03b17, \u03b19, and/or \u03b110. Of note, we identify receptors for phosphocholine-modified macromolecules that are synthesized by microbes and eukaryotic parasites and are well-known modulators of the immune system. Our data suggest that an endogenous anti-inflammatory cholinergic control mechanism effectively controls ATP-mediated release of IL-1\u03b2 and that the same mechanism is used by symbionts and misused by parasites to evade innate immune responses of the host.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "35085362", + "title": "Access to highly specialized growth substrates and production of epithelial immunomodulatory metabolites determine survival of Haemophilus influenzae in human airway epithelial cells.", + "year": 2022, + "journal": "PLoS pathogens", + "authors": [ + "Hosmer J", + "Nasreen M", + "Dhouib R", + "Essilfie AT", + "Schirra HJ", + "Henningham A", + "Fantino E", + "Sly P", + "McEwan AG", + "Kappler U" + ], + "bacteria": "Haemophilus", + "condition": "anti-inflammatory", + "relevance_score": 0.20128749648243574, + "mesh_terms": [ + "Animals", + "Haemophilus Infections", + "Haemophilus influenzae", + "Host-Pathogen Interactions", + "Humans", + "Intercellular Signaling Peptides and Proteins", + "Mice", + "Respiratory Mucosa" + ], + "raw_abstract": "Haemophilus influenzae (Hi) infections are associated with recurring acute exacerbations of chronic respiratory diseases in children and adults including otitis media, pneumonia, chronic obstructive pulmonary disease and asthma. Here, we show that persistence and recurrence of Hi infections are closely linked to Hi metabolic properties, where preferred growth substrates are aligned to the metabolome of human airway epithelial surfaces and include lactate, pentoses, and nucleosides, but not glucose that is typically used for studies of Hi growth in vitro. Enzymatic and physiological investigations revealed that utilization of lactate, the preferred Hi carbon source, required the LldD L-lactate dehydrogenase (conservation: 98.8% of strains), but not the two redox-balancing D-lactate dehydrogenases Dld and LdhA. Utilization of preferred substrates was directly linked to Hi infection and persistence. When unable to utilize L-lactate or forced to rely on salvaged guanine, Hi showed reduced extra- and intra-cellular persistence in a murine model of lung infection and in primary normal human nasal epithelia, with up to 3000-fold attenuation observed in competitive infections. In contrast, D-lactate dehydrogenase mutants only showed a very slight reduction compared to the wild-type strain. Interestingly, acetate, the major Hi metabolic end-product, had anti-inflammatory effects on cultured human tissue cells in the presence of live but not heat-killed Hi, suggesting that metabolic endproducts also influence HI-host interactions. Our work provides significant new insights into the critical role of metabolism for Hi persistence in contact with host cells and reveals for the first time the immunomodulatory potential of Hi metabolites.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "37871735", + "title": "The co-regulation of the gut microbiome and host genes might play essential roles in metformin gastrointestinal intolerance.", + "year": 2023, + "journal": "Toxicology and applied pharmacology", + "authors": [ + "Zhang H", + "Lai J", + "Zhang L", + "Zhang W", + "Liu X", + "Gong Q", + "Tian H", + "Yang M", + "Yang T", + "Zhao R", + "Li D", + "Huang H", + "Zhao Y", + "Yan S", + "Yu M", + "Xiyang Y", + "Shi L", + "Yang L", + "Wang L", + "Chen W", + "Cao X" + ], + "bacteria": "Barnesiella", + "condition": "anti-inflammatory", + "relevance_score": 0.4149977700856175, + "mesh_terms": [ + "Humans", + "Metformin", + "Gastrointestinal Microbiome", + "Diabetes Mellitus, Type 2", + "RNA, Ribosomal, 16S", + "Bile Acids and Salts", + "Anti-Inflammatory Agents" + ], + "raw_abstract": "Metformin is commonly used, but approximately 20% of patients experience gastrointestinal intolerance, leading to medication discontinuation for unclear reasons and a lack of effective management strategies. In this study, the 18 fecal and blood samples were analyzed using 16S rRNA and mRNA transcriptome, respectively. These samples included 3 fecal and 4 blood from metformin-tolerant T2D patients before and after metformin treatment (T and Ta), 3 fecal and 5 blood from metformin-intolerant T2D patients before and after treatment (TS and TSa), and 6 fecal samples from healthy controls. The results showed that certain anti-inflammatory gut bacteria and gene, such as Barnesiella (p\u00a0=\u00a00.046), Parabacteroides goldsteinii (p\u00a0=\u00a00.016), and the gene JUND (p\u00a0=\u00a00.0002), exhibited higher levels in metformin-intolerant patients, and which decreased after metformin treatment (p\u00a0<\u00a00.05). This potentially invalidates patients' anti-inflammatory effect and intestinal mucus barrier protection, which may lead to alterations in intestinal permeability, decreased gut barrier function, and gastrointestinal symptoms, including diarrhea, bloating, and nausea. After metformin treatment, primary bile acids (PBAs) production species: Weissella confusa, Weissella paramesenteroides, Lactobacillus brevis, and Lactobacillus plantarum increased (p\u00a0<\u00a00.05). The species converting PBAs to secondary bile acids (SBAs): Parabacteroides distasonis decreased (p\u00a0<\u00a00.05). This might result in accumulation of PBAs, which also may lead to anti-inflammatory gene JUND and SQSTM1 downregulated. In conclusion, this study suggests that metformin intolerance may be attributed to a decrease in anti-inflammatory-related flora and genes, and also alterations in PBAs accumulation-related flora. These findings open up possibilities for future research targeting gut flora and host genes to prevent metformin intolerance.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "38458480", + "title": "Tangshen Formula alleviates inflammatory injury against aged diabetic kidney disease through modulating gut microbiota composition and related amino acid metabolism.", + "year": 2024, + "journal": "Experimental gerontology", + "authors": [ + "Chen DQ", + "Zhang HJ", + "Zhang W", + "Feng K", + "Liu H", + "Zhao HL", + "Li P" + ], + "bacteria": "Barnesiella", + "condition": "anti-inflammatory", + "relevance_score": 0.2340580001523753, + "mesh_terms": [ + "Humans", + "Aged", + "Mice", + "Animals", + "Diabetic Nephropathies", + "Gastrointestinal Microbiome", + "RNA, Ribosomal, 16S", + "Tryptophan", + "Inflammation", + "Anti-Inflammatory Agents", + "Arginine", + "Diabetes Mellitus", + "Drugs, Chinese Herbal" + ], + "raw_abstract": "Diabetic kidney disease (DKD) is leading causes and one of the fastest growing causes of chronic kidney disease worldwide, and leads to high morbidity and mortality. Emerging evidences have revealed gut microbiota dysbiosis and related metabolism dysfunction play a dominant role in DKD progression and treatment through modulating inflammation. Our previous studies showed that Tangshen Formula (TSF), a Chinese herbal prescription, exhibited anti-inflammatory effect on DKD, but underlying mechanism that involved gut microbiota and related metabolism in aged model remained obscure. Here, BTBR ob/ob mice were used to establish aged DKD model, and 16S rRNA sequence and untargeted metabolomic analyses were employed to investigate the correlation between colonic microbiota and serum metabolism. The aged ob/ob mice exhibited obvious glomerular and renal tubule injury and kidney function decline in kidney, while TSF treatment significantly attenuated these abnormalities. TSF also exhibited potent anti-inflammatory effect in aged ob/ob mice indicating by reduced proinflammatory factor IL-6 and TNF-\u03b1, MCP-1 and COX-2 in serum, kidney and intestine, which suggested the involvement of gut microbiota with TSF effect. The 16S rDNA sequencing of the colonic microbiome and untargeted serum metabolomics analysis revealed significant differences in gut microbiota structure and serum metabolomic profiles between WT and ob/ob mice. Notably, TSF treatment reshaped the structure of gut microbiota and corrected the disorder of metabolism especially tryptophan metabolism and arginine biosynthesis. TSF increased Anaeroplasma and Barnesiella genera and decreased Romboutsia, Akkermansia, and Collinsella genera, and further elevated tryptophan, 5-hydroxyindoleacetate, glutamic acid, aspartate and reduced 4-hydroxy-2-quinolinecarboxylic acid, indole-3-acetic acid, xanthurenic acid, glutamine. Further correlation analysis indicated that disturbed gut microbiota was linked to tryptophan metabolism and arginine biosynthesis to regulate inflammation in aged DKD. Our data revealed that TSF attenuated renal inflammation by modulating gut microbiota and related amino acid metabolism in aged DKD model, highlighting gut microbiota and related metabolism functioned as potential therapeutic target for DKD in elderly patients.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "27776263", + "title": "Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly.", + "year": 2017, + "journal": "Neurobiology of aging", + "authors": [ + "Cattaneo A", + "Cattane N", + "Galluzzi S", + "Provasi S", + "Lopizzo N", + "Festari C", + "Ferrari C", + "Guerra UP", + "Paghera B", + "Muscio C", + "Bianchetti A", + "Volta GD", + "Turla M", + "Cotelli MS", + "Gennuso M", + "Prelle A", + "Zanetti O", + "Lussignoli G", + "Mirabile D", + "Bellandi D", + "Gentile S", + "Belotti G", + "Villani D", + "Harach T", + "Bolmont T", + "Padovani A", + "Boccardi M", + "Frisoni GB" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.4647562495466715, + "mesh_terms": [ + "Aged", + "Alzheimer Disease", + "Amyloid beta-Peptides", + "Brain", + "Cognition Disorders", + "Cytokines", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Inflammation Mediators", + "Intestines", + "Male", + "Middle Aged", + "Plaque, Amyloid" + ], + "raw_abstract": "The pathway leading from amyloid-\u03b2 deposition to cognitive impairment is believed to be a cornerstone of the pathogenesis of Alzheimer's disease (AD). However, what drives amyloid buildup in sporadic nongenetic cases of AD is still unknown. AD brains feature an inflammatory reaction around amyloid plaques, and a specific subset of the gut microbiota (GMB) may promote brain inflammation. We investigated the possible role of the GMB in AD pathogenesis by studying the association of brain amyloidosis with (1) GMB taxa with pro- and anti-inflammatory activity; and (2) peripheral inflammation in cognitively impaired patients. We measured the stool abundance of selected bacterial GMB taxa (Escherichia/Shigella, Pseudomonas aeruginosa, Eubacterium rectale, Eubacterium hallii, Faecalibacterium prausnitzii, and Bacteroides fragilis) and the blood expression levels of cytokines (pro-inflammatory cytokines: CXCL2, CXCL10, interleukin [IL]-1\u03b2, IL-6, IL-18, IL-8, inflammasome complex (NLRP3), tumor necrosis factor-alpha [TNF-\u03b1]; anti-inflammatory cytokines: IL-4, IL-10, IL-13) in cognitively impaired patients with (n\u00a0= 40, Amy+) and with no brain amyloidosis (n\u00a0= 33, Amy-) and also in a group of controls (n\u00a0= 10, no brain amyloidosis and no cognitive impairment). Amy+ patients showed higher levels of pro-inflammatory cytokines (IL-6, CXCL2, NLRP3, and IL-1\u03b2) compared with both controls and with Amy- patients. A reduction of the anti-inflammatory cytokine IL-10 was observed in Amy+ versus Amy-. Amy+ showed lower abundance of E.\u00a0rectale and higher abundance of Escherichia/Shigella compared with both healthy controls (fold change, FC\u00a0=\u00a0-9.6, p < 0.001 and FC\u00a0=\u00a0+12.8, p < 0.001, respectively) and to Amy- (FC\u00a0=\u00a0-7.7, p < 0.001 and FC\u00a0=\u00a0+7.4, p\u00a0= 0.003). A positive correlation was observed between pro-inflammatory cytokines IL-1\u03b2, NLRP3, and CXCL2 with abundance of the inflammatory bacteria taxon Escherichia/Shigella (rho\u00a0= 0.60, p < 0.001; rho\u00a0= 0.57, p < 0.001; and rho\u00a0= 0.30, p\u00a0= 0.007, respectively) and a negative correlation with the anti-inflammatory E.\u00a0rectale (rho\u00a0=\u00a0-0.48, p < 0.001; rho\u00a0=\u00a0-0.25, p\u00a0= 0.024; rho\u00a0=\u00a0-0.49, p < 0.001). Our data indicate that an increase in the abundance of a pro-inflammatory GMB taxon, Escherichia/Shigella, and a reduction in the abundance of an anti-inflammatory taxon, E.\u00a0rectale, are possibly associated with a peripheral inflammatory state in patients with cognitive impairment and brain amyloidosis. A possible causal relation between GMB-related inflammation and amyloidosis deserves further investigation.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "39343844", + "title": "Therapeutic Effects of Bacteroides fragilis Vesicles in a Model of Chemically Induced Colitis in Rats.", + "year": 2024, + "journal": "Bulletin of experimental biology and medicine", + "authors": [ + "Shagaleeva OY", + "Kashatnikova DA", + "Vorobyeva EA", + "Kardonsky DA", + "Silantiev AS", + "Efimov BA", + "Ivanov VA", + "Bespyatikh YA", + "Zakharzhevskaya NB" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.4105712894027188, + "mesh_terms": [ + "Animals", + "Bacteroides fragilis", + "Rats", + "Colitis", + "Disease Models, Animal", + "Dextran Sulfate", + "Colon", + "Male", + "Rats, Wistar" + ], + "raw_abstract": "The anti-inflammatory properties of Bacteroides fragilis vesicles were studied in a rat model of dextran sodium sulfate-induced colitis. According to the histology results, addition of B. fragilis vesicles to the therapy promoted colon repair. Evaluation of the disease activity index confirms the high rate of colon recovery: against the background of vesicle administration, the absence of blood in stool, normal stool consistency, and body weight normalization were observed.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "35684075", + "title": "Gut Microbiota Modulation, Anti-Diabetic and Anti-Inflammatory Properties of Polyphenol Extract from Mung Bean Seed Coat (", + "year": 2022, + "journal": "Nutrients", + "authors": [ + "Charoensiddhi S", + "Chanput WP", + "Sae-Tan S" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.3477548699316046, + "mesh_terms": [ + "Anti-Inflammatory Agents", + "Diabetes Mellitus", + "Fabaceae", + "Gastrointestinal Microbiome", + "Humans", + "Plant Extracts", + "Polyphenols", + "Seeds", + "Vigna" + ], + "raw_abstract": "The present study investigated the gut health, anti-diabetic, and anti-inflammatory activities of mung bean seed coat extract (MSE). MSE was obtained by pressurized liquid extraction (PLE) using 50% ethanol as the extracting solvent. After 24 h of in vitro human fecal fermentation, MSE exhibited higher productions of total short-chain fatty acids (SCFA) than those of the control group (CON) and other polyphenol-rich substrates, including gallic acid (GA) and vitexin (VIT) (p > 0.05), but still lower than the fructo-oligosaccharide (FOS). In 16S-rRNA next-generation sequencing, MSE regulated the composition of gut microbiota by stimulating the growth of the beneficial bacteria Enterococcus, Ruminococcus, Blautia, and Bacteroides and decreasing the growth of the potential pathogenic bacteria Escherichia-Shigella. Similarly, qPCR showed increased numbers of Bifidobacterium, Lactobacillus, Faecalibacterium prausnitzii, and Prevotella, compared with those of CON (p < 0.05). MSE also reduced reactive oxygen species and increased glucose uptake in insulin-resistant HepG2 cells dose-dependently. The anti-inflammatory activity of MSE was observed in LPS-stimulated THP-1 monocytes with the reduction of TNF\u03b1, IL-1\u03b2, IL-6, and IL-8 genes. The data demonstrated the potential applications of MSE as a dietary supplement with gut health benefits and its ability to mitigate diabetes and inflammatory-related diseases.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "35597036", + "title": "Fuzhuan brick tea polysaccharides serve as a promising candidate for remodeling the gut microbiota from colitis subjects in vitro: Fermentation characteristic and anti-inflammatory activity.", + "year": 2022, + "journal": "Food chemistry", + "authors": [ + "Chen G", + "Wang M", + "Zeng Z", + "Xie M", + "Xu W", + "Peng Y", + "Zhou W", + "Sun Y", + "Zeng X", + "Liu Z" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.34289066737109486, + "mesh_terms": [ + "Anti-Inflammatory Agents", + "Colitis", + "Fatty Acids, Volatile", + "Fermentation", + "Gastrointestinal Microbiome", + "Humans", + "Inflammatory Bowel Diseases", + "Polysaccharides", + "Tea" + ], + "raw_abstract": "The purified fraction 3 of polysaccharides from Fuzhuan brick tea (FBTPS-3) could attenuate the colitis and modulate the gut microbiota. However, the relationship between anti-inflammatory effect of FBTPS-3 and the gut microbiota is still unknown. Thus, the anaerobic fermentation in vitro was used to investigate the potential mechanism. FBTPS-3 could be utilized and degraded by gut microbiota from inflammatory bowel disease (IBD) subjects. Furthermore, FBTPS-3 could modulate the composition and structure of IBD gut microbiota toward to that of healthy group. FBTPS-3 showed a superior modulated effect on IBD gut microbiota by increasing Bacteroides and decreasing Escherichia/Shigella. Furthermore, the fermentation solution rather than FBTPS-3 itself showed anti-inflammatory effects on lipopolysaccharide-treated RAW264.7 macrophages, which might be due to the metabolites such as short-chain fatty acids (SCFAs). Thus, FBTPS-3 can be expected as novel prebiotics for treatment of IBD via modulating gut microbiota, and promoting the production of SCFAs.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "33549142", + "title": "Could dysbiosis of inflammatory and anti-inflammatory gut bacteria have an implications in the development of type 2 diabetes? A pilot investigation.", + "year": 2021, + "journal": "BMC research notes", + "authors": [ + "Kulkarni P", + "Devkumar P", + "Chattopadhyay I" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.34138150785478155, + "mesh_terms": [ + "Actinobacteria", + "Anti-Inflammatory Agents", + "Bacteria", + "Bacteroides", + "Clostridiales", + "Diabetes Mellitus, Type 2", + "Dysbiosis", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Lactobacillus", + "Pilot Projects", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: Differential alterations in gut microbiota and chronic low-grade inflammation play a critical role in the development of Type 2 diabetes (T2D). Here we aimed to investigate if dysbiosis of inflammation and anti-inflammation-associated gut bacterial communities in fecal samples of individuals had any influence on T2D using a 16S rRNA gene of V3 region sequencing at Illumina MiSeq platform. RESULTS: Our findings showed that a higher abundance of inflammatory bacteria such as Lactobacillus ruminis, Ruminococcus gnavus, Bacteroides caccae, Butyricimonas, and Collinsella aerofaciens, and lower abundance of anti-inflammatory bacteria such as Faecalibacterium prausnitzii, and Butyrivibrio that likely play a role in the development of T2D. Our findings hint the potential of indigenous microbiota in developing diagnostic markers and therapeutic targets in T2D.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "32156386", + "title": "Ethanol extract of propolis prevents high-fat diet-induced insulin resistance and obesity in association with modulation of gut microbiota in mice.", + "year": 2020, + "journal": "Food research international (Ottawa, Ont.)", + "authors": [ + "Cai W", + "Xu J", + "Li G", + "Liu T", + "Guo X", + "Wang H", + "Luo L" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.3399194987695632, + "mesh_terms": [ + "Animals", + "Bacteria", + "Cytokines", + "Diet, High-Fat", + "Endotoxemia", + "Ethanol", + "Gastrointestinal Microbiome", + "Gene Expression Regulation", + "Glucose Tolerance Test", + "Insulin Resistance", + "Male", + "Mice", + "Mice, Inbred C57BL", + "Obesity", + "Propolis" + ], + "raw_abstract": "Propolis has beneficial effects anti-inflammatory, anti-diabetes and anti-obesity in human or murine models, but its mechanism has not been fully elucidated. This study was to investigate the effects of ethanol extract of propolis (EEP) on the gut microbiota, and to analyze the associations between these alterations of gut microbiota and insulin resistance and obesity in high fat diet (HFD)-fed mice. Male C57BL/6J mice were fed with chow diet, high-fat diet, and high-fat diet supplemented with 1% EEP or 2%EEP. EEP supplementation reduced HFD-induced weight gain and liver fat accumulation, proinflammatory cytokines and insulin resistance, and improved glucose tolerance and lipid profile. Meanwhile, EEP supplementation in HFD-fed mice increased anti-obesity and anti-inflammatory bacteria such as genera Roseburia and Intestinimonas and species Parabacteroides goldsteinii and Parabacteroides distasonis, and reduced pro-inflammatory bacteria such as genera Faecalibaculum and Prevotella and species Bacteroides vulgatus. These dominant bacterial taxa altered by EEP were significantly associated with the metabolic parameters of insulin resistance and obesityin HFD-fed mice. The results in this study indicated that EEP reduced HFD-induced obesity and insulin resistant, which may be mediated by modulating the composition and function of gut microbiota.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "34348201", + "title": "Home-based exercise training influences gut bacterial levels in multiple sclerosis.", + "year": 2021, + "journal": "Complementary therapies in clinical practice", + "authors": [ + "Mokhtarzade M", + "Molanouri Shamsi M", + "Abolhasani M", + "Bakhshi B", + "Sahraian MA", + "Quinn LS", + "Negaresh R" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.3236034277308845, + "mesh_terms": [ + "Exercise", + "Faecalibacterium prausnitzii", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Multiple Sclerosis", + "Verrucomicrobia" + ], + "raw_abstract": "BACKGROUND: Multiple sclerosis is associated with gut microbiome alterations. The current study aimed to investigate the effect of home-based exercise on gut bacteria in people with multiple sclerosis (MS). We also examined the association of exercise-induced gut bacterial modulation with circulating levels of inflammatory and anti-inflammatory cytokines. MATERIALS AND METHODS: Forty-two people with MS (female/male: 31/11, expanded disability scale status <5) participated in this study and were divided into two groups: 6 months of home-based exercise (5 sessions per week) and controls. Before and after the intervention, the following parameters were assessed: gut microbiota, including faecalibacterium prausnitzii, akkermansia muciniphila, prevotella and bacteroides counts; cytokine levels including interleukin (IL)-10 and tumor necrosis factor-alpha (TNF-\u03b1); and psychosocial factors including anxiety, depression, and fatigue. RESULTS: Home-based exercise significantly increased prevotella counts, and decreased akkermansia muciniphila counts (p\u00a0<\u00a00.05); however, there were no significant effects on faecalibacterium prausnitzii and bacteroides counts (p\u00a0>\u00a00.05). There were no significant effects of home-based exercise on circulating cytokine levels (p\u00a0>\u00a00.05). Moreover, home-based exercise was associated with significant improvements in anxiety and depression (p\u00a0<\u00a00.05); however, fatigue revealed no significant change (p\u00a0>\u00a00.05). Akkermansia muciniphila, prevotella and bacteroides count changes in response to the intervention were correlated with changes in IL-10 (r\u00a0=\u00a0-0.052, r\u00a0=\u00a00.67, and r\u00a0=\u00a0-0.55, respectively). CONCLUSION: In general, our data revealed the effect of exercise on gut bacteria, especially prevotella, and akkermansia muciniphila counts, which can probably have a beneficial effect on MS disease pathology and course; however, the lack of changes in cytokines following exercise suggests the possible role of mechanisms other than modulation of circulating IL-10 and TNF- \u03b1 levels.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "34351455", + "title": "Dietary inflammatory index and its relationship with gut microbiota in individuals with intestinal constipation: a cross-sectional study.", + "year": 2022, + "journal": "European journal of nutrition", + "authors": [ + "Costa LM", + "Mendes MM", + "Oliveira AC", + "Magalh\u00e3es KG", + "Shivappa N", + "Hebert JR", + "da Costa THM", + "Botelho PB" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.319742665332215, + "mesh_terms": [ + "Adult", + "Constipation", + "Cross-Sectional Studies", + "Diet", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "OBJECTIVE: To determine whether there is an association between the inflammatory potential of the diet, measured by the dietary inflammatory index (DII\u00ae), and the composition of intestinal microbiota in adults with functional constipation (FC). METHODS: A cross-sectional study was carried out with 68 adults with FC. Energy-adjusted DII (E-DII) was calculated from data obtained from food surveys, serum inflammation markers were measured and the composition of the intestinal microbiota was evaluated using the 16S rRNA gene sequencing method. Participants were assigned into two groups: anti-inflammatory diet (AD: E-DII\u2009<\u20090) and pro-inflammatory diet (PD: E-DII\u2009\u2265\u20090). Associations of E-DII scores with microbial diversity and composition were examined using differences between the E-DII groups and linear and hierarchical regression. RESULTS: E- DII was inversely correlated with relative abundance of Hungatella spp. and Bacteroides fragilis and positively correlated with Bacteroides thetaiotaomicron and Bacteroides caccae (p\u2009<\u20090.05). B. fragilis was positively correlated with IL-10. The AD group had higher relative abundances for the genus Blautia and Hungatella, lower abundances of Bacteroides thetaiotamicron and Bacteroides spp. (p\u2009<\u20090.05), as well as higher frequency of evacuation (p\u2009=\u20090.02) and lower use of laxatives (p\u2009=\u20090.05). The AD group showed a reduction in the abundance of Desulfovibrio spp. and Butyrivibrio, Butyrivibrio crossotus, Bacteroides clarus, Bacteroides coprophilus and Bacteroides intestinalis (all p\u2009<\u20090.05). The greater abundance of Bacteroides clarus increased the individual's chance of performing a manual evacuation maneuver. CONCLUSION: Therefore, the results of this study demonstrated that the inflammatory potential of the diet is associated with the gut microbiota in individuals with FC.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "32387599", + "title": "The homogenous polysaccharide SY01-23 purified from leaf of Morus alba L. has bioactivity on human gut Bacteroides ovatus and Bacteroides cellulosilyticus.", + "year": 2020, + "journal": "International journal of biological macromolecules", + "authors": [ + "Wang Y", + "Shao S", + "Guo C", + "Zhang S", + "Li M", + "Ding K" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.31294787806434365, + "mesh_terms": [], + "raw_abstract": "Function of mulberry leaf (Morus alba L.) polysaccharide has been reported on antitumor, immunostimulatory and anti-inflammatory effects. However, the bioactivity on human gut microbiota is unclear so far. Here, three homogenous polysaccharides named SY01-21, SY01-22, SY01-23 were isolated from mulberry leaf with molecular weight 57\u00a0kDa, 25\u00a0kDa and 7.2\u00a0kDa, respectively. The monosaccharide composition of SY01-21 contained rhamnose, galactose and arabinose in a molar ratio of 7.60:43.52:48.88. SY01-22 contained rhamnose, galacturonic acid, glucose, galactose, xylose and arabinose in a molar ratio of 14.61:9.06:1.35:34.65:2.99:37.34. SY01-23 contained rhamnose, glucuronic acid, galacturonic acid, glucose, galactose, xylose and arabinose in a molar ratio of 23.00:4.12:24.60:5.74:17.28:1.12:24.13. Bioactivity test showed SY01-21 promoted the growth of Bacteroides cellulosilyticus (BC) while SY01-22 benefited the growth of Bacteroides ovatus (BO). Interestingly, SY01-23 boosted the growth of both BO and BC. However, Bacteroides thetaiotamicron (BT) only grew on 5\u00a0mg/mL SY01-21. Intriguingly, the growth of co-culture of BT with BO or BC was better than monoculture. This suggested that cross-feeding might exist between them. Besides, we found BO and BC generated acetate and propionate by utilizing SY01-23. The above results suggested that SY01-23 might modify human gut microbiota by driving colonization of Bacteroides in the gut to improve wellness.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "29382366", + "title": "Age and fecal microbial strain-specific differences in patients with spondyloarthritis.", + "year": 2018, + "journal": "Arthritis research & therapy", + "authors": [ + "Stoll ML", + "Weiss PF", + "Weiss JE", + "Nigrovic PA", + "Edelheit BS", + "Bridges SL", + "Danila MI", + "Spencer CH", + "Punaro MG", + "Schikler K", + "Reiff A", + "Kumar R", + "Cron RQ", + "Morrow CD", + "Lefkowitz EJ" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.30327063899538204, + "mesh_terms": [ + "Adolescent", + "Adult", + "Age Factors", + "Arthritis, Juvenile", + "Bacteria", + "Child", + "DNA, Bacterial", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "RNA, Ribosomal, 16S", + "Sequence Analysis, DNA", + "Species Specificity", + "Spondylarthritis" + ], + "raw_abstract": "BACKGROUND: Prior studies have demonstrated abnormalities in the composition of the gastrointestinal microbiota in pediatric and adult patients with spondyloarthritis (SpA). In particular, diminished fecal abundance of Faecalibacterium prausnitzii and abnormalities in both directions in the abundance of the Bacteroides genus have been identified. METHODS: We obtained fecal specimens from 30 children with treatment-na\u00efve enthesitis-related arthritis (ERA) and 19 healthy controls, as well as specimens from 11 adult patients with longstanding SpA and 10 adult healthy controls. All of the samples underwent sequencing of the 16S ribosomal DNA. A subset of the pediatric fecal samples was subjected to shotgun metagenomics sequencing. RESULTS: ERA patients had decreased abundance of the anti-inflammatory F. prausnitzii A2-165 strain (41\u2009\u00b1\u200928% versus 54\u2009\u00b1\u200920% of all sequences matching F. prausnitzii, p\u2009=\u20090.084) and an increased abundance of the control F. prausnitzii L2/6 strain (28\u2009\u00b1\u200928% versus 15\u2009\u00b1\u200915%, p\u2009=\u20090.038). Similar trends were observed in adults with longstanding SpA (n\u2009=\u200911) and controls (n\u2009=\u200910). In contrast, the fecal abundance of Bacteroides fragilis was increased in ERA subjects (2.0\u2009\u00b1\u20094.0% versus 0.45\u2009\u00b1\u20090.7% of all sequences, p\u2009=\u20090.045), yet was diminished in adult subjects (0.2\u2009\u00b1\u2009% versus 1.0\u2009\u00b1\u2009% of all sequences, p\u2009=\u20090.106). Shotgun metagenomics sequencing of the fecal DNA in the pediatric subjects revealed diminished coverage of the butanoate pathway (abundance normalized to controls of 1\u2009\u00b1\u20090.48 versus 0.72\u2009\u00b1\u20090.33 in ERA, p\u2009=\u20090.037). CONCLUSIONS: The anti-inflammatory F. prausnitzii A2-165 strain appears to be depleted in both pediatric and adult SpA. In contrast, B. fragilis may be depleted in adult disease yet abundant in pediatric SpA, suggesting developmental effects on the immune system.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "37696680", + "title": "Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.", + "year": 2024, + "journal": "Inflammatory bowel diseases", + "authors": [ + "Del Chierico F", + "Cardile S", + "Baldelli V", + "Alterio T", + "Reddel S", + "Bramuzzo M", + "Knafelz D", + "Lega S", + "Bracci F", + "Torre G", + "Maggiore G", + "Putignani L" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.28187735298331656, + "mesh_terms": [ + "Humans", + "Child", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Cholangitis, Sclerosing", + "Dysbiosis", + "RNA, Ribosomal, 16S", + "Bacteria", + "Bacteroidetes", + "Italy" + ], + "raw_abstract": "BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis. METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs). RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients. CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC. In this study, we report the gut microbiota and mycobiota dysbiosis in pediatric patients affected by primary sclerosing cholangitis (PSC) associated with ulcerative colitis (UC), with an increase in pro-inflammatory pathobionts and a reduction in anti-inflammatory commensals.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "26482265", + "title": "The influence of non-steroidal anti-inflammatory drugs on the gut microbiome.", + "year": 2016, + "journal": "Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases", + "authors": [ + "Rogers MAM", + "Aronoff DM" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.27524603390388563, + "mesh_terms": [ + "Adult", + "Aged", + "Aged, 80 and over", + "Anti-Inflammatory Agents, Non-Steroidal", + "Area Under Curve", + "Bacteria", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Male", + "Middle Aged" + ], + "raw_abstract": "The composition of the gut microbiome with the use of non-steroidal anti-inflammatory drugs (NSAIDs) has not been fully characterized. Drug use within the past 30 days was ascertained in 155 adults, and stool specimens were submitted for analysis. Area under the receiver operating characteristic curve (AUC) was calculated in logit models to distinguish the relative abundance of operational taxonomic units (OTUs) by medication class. The type of medication had a greater influence on the gut microbiome than the number of medications. NSAIDs were particularly associated with distinct microbial populations. Four OTUs (Prevotella species, Bacteroides species, family Ruminococcaceae, and Barnesiella species) discriminated aspirin users from those using no medication (AUC = 0.96; 95% CI 0.84-1.00). The microbiome profile of celecoxib users was similar to that of ibuprofen users, with both showing enrichment of Acidaminococcaceae and Enterobacteriaceae. Bacteria from families Propionibacteriaceae, Pseudomonadaceae, Puniceicoccaceae and Rikenellaceae were more abundant in ibuprofen users than in controls or naproxen users. Bacteroides species and Erysipelotrichaceae species discriminated individuals using NSAIDs plus proton-pump inhibitors from those using NSAIDs alone (AUC = 0.96; 95% CI 0.87-1.00). Bacteroides species and a bacterium of family Ruminococcaceae discriminated individuals using NSAIDs in combination with antidepressants and laxatives from those using NSAIDs alone (AUC = 0.98; 95% CI 0.93-1.00). In conclusion, bacteria in the gastrointestinal tract reflect the combinations of medications that people ingest. The bacterial composition of the gut varied with the type of NSAID ingested.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "25887483", + "title": "Comparative analysis of gut microbiota in elderly people of urbanized towns and longevity villages.", + "year": 2015, + "journal": "BMC microbiology", + "authors": [ + "Park SH", + "Kim KA", + "Ahn YT", + "Jeong JJ", + "Huh CS", + "Kim DH" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.26354970508393133, + "mesh_terms": [ + "Adult", + "Aged", + "Aged, 80 and over", + "Bacteria", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Longevity", + "Male", + "Metagenomics", + "Microbiota", + "Middle Aged", + "Republic of Korea", + "Rural Population", + "Sequence Analysis, DNA", + "Urban Population" + ], + "raw_abstract": "BACKGROUND: To understand differences in the gut microbiota between elderly people of urbanized town communities (UTC) and longevity village communities (LVC), we analyzed fecal microbiota collected from individuals living in 2 UTC (Seoul and Chuncheon) and 3 LVC (Gurye, Damyang, and Soonchang) selected on the basis of indices for superlongevity (the ratio of centenarians to the total population) and longevity (the ratio of those aged 85\u00a0years or greater to those aged 65\u00a0years or greater) in South Korea by 454 pyrosequencing. RESULTS: Taxonomy-based analysis showed that The relative abundance of Firmicutes, Tenericutes, and Actinobacteria was significantly lower in LVC than in UTC. Due to an increase of Firmicutes and a reduction of Bacteroidetes, the ratio of Firmicutes to Bacteroidetes in the gut microbiota was greater in UTC adults than in UTC children or LVC adults. The population levels of Bacteroides, Prevotella, and Lachnospira were significantly higher in LVC than in UTC, but the levels of Dialister, Subdoligranulum, Megamonas, EF401882_g, and AM275436_g were lower in LVC than in UTC. Although most of the species detected in LVC were detected in UTC, some Bacteroides spp. and Faecalibacterium spp. were detected only in LVC. Among Bacteroides spp., ACWH_s, EF403317_s, and EF403722_s were detected in children and LVC samples only but FJ363527_s, 4P000677_s, and 4P000015_s were detected in UTC samples. EF402172_s and EF404388_s, members of Faecalibacterium spp., which are known to have anti-inflammatory properties, were detected in LVC and children only (>3.9% of total sequence). In addition, the fecal lipopolysaccharides (LPS) content was significantly higher in UTC than in LVC. CONCLUSIONS: These findings suggest that maintaining gut microbiota, including Faecalibacterium spp. EF402172_s and EF404388_s, as well as low LPS levels may play an important role in preserving residents' health in LVC.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "30656592", + "title": "Human gut microbes are susceptible to antimicrobial food additives in vitro.", + "year": 2019, + "journal": "Folia microbiologica", + "authors": [ + "Hrncirova L", + "Hudcovic T", + "Sukova E", + "Machova V", + "Trckova E", + "Krejsek J", + "Hrncir T" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.26207037624102086, + "mesh_terms": [ + "Anti-Bacterial Agents", + "Food Additives", + "Gastrointestinal Microbiome", + "Gastrointestinal Tract", + "Humans" + ], + "raw_abstract": "The aim of this work was to test the hypothesis that antimicrobial food additives may alter the composition of human gut microbiota by selectively suppressing the growth of susceptible gut microbes. To explore the influence of antimicrobial food additives on the composition of the human gut microbiota, we examined the susceptibility of both aerobic and anaerobic gut bacteria to sodium benzoate, sodium nitrite, and potassium sorbate, and their combinations, using a broth microdilution method. The tested bacteria exhibited a wide range of susceptibilities to food additives. For example, the most susceptible strain, Bacteroides coprocola, was almost 580 times more susceptible to sodium nitrite than the most resistant strain, Enterococcus faecalis. However, most importantly, we found that gut microbes with known anti-inflammatory properties, such as Clostridium tyrobutyricum or Lactobacillus paracasei, were significantly more susceptible to additives than microbes with known proinflammatory or colitogenic properties, such as Bacteroides thetaiotaomicron or Enterococcus faecalis. Our data show that some human gut microbes are highly susceptible to antimicrobial food additives. We speculate that permanent exposure of human gut microbiota to even low levels of additives may modify the composition and function of gut microbiota and thus influence the host's immune system. Whether the effect of additive-modified gut microbiota on the human immune system could explain, at least in part, the increasing incidence of allergies and autoimmune diseases remains to be shown.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "27982124", + "title": "The human intestinal microbiota of constipated-predominant irritable bowel syndrome patients exhibits anti-inflammatory properties.", + "year": 2016, + "journal": "Scientific reports", + "authors": [ + "Gobert AP", + "Sagrestani G", + "Delmas E", + "Wilson KT", + "Verriere TG", + "Dapoigny M", + "Del'homme C", + "Bernalier-Donadille A" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.24704499986445966, + "mesh_terms": [ + "Animals", + "Anti-Inflammatory Agents", + "Colitis", + "Cytokines", + "Dextran Sulfate", + "Dysbiosis", + "Gastrointestinal Microbiome", + "Humans", + "Inflammation", + "Intestines", + "Irritable Bowel Syndrome", + "Mice", + "Mice, Inbred C57BL", + "Microbiota", + "Rats" + ], + "raw_abstract": "The intestinal microbiota of patients with constipated-predominant irritable bowel syndrome (C-IBS) displays chronic dysbiosis. Our aim was to determine whether this microbial imbalance instigates perturbation of the host intestinal mucosal immune response, using a model of human microbiota-associated rats (HMAR) and dextran sulfate sodium (DSS)-induced experimental colitis. The analysis of the microbiota composition revealed a decrease of the relative abundance of Bacteroides, Roseburia-Eubacterium rectale and Bifidobacterium and an increase of Enterobacteriaceae, Desulfovibrio sp., and mainly Akkermansia muciniphila in C-IBS patients compared to healthy individuals. The bacterial diversity of the gut microbiota of healthy individuals or C-IBS patients was maintained in corresponding HMAR. Animals harboring a C-IBS microbiota had reduced DSS colitis with a decreased expression of pro-inflammatory cytokines from innate, Th1, and Th17 responses. The pre-treatment of conventional C57BL/6 mice or HMAR with A. muciniphila, but not with Escherichia coli, prior exposure to DSS also resulted in a reduction of colitis severity, highlighting that the anti-inflammatory effect of the gut microbiota of C-IBS patients is mediated, in part, by A. muciniphila. This work highlights a novel aspect of the crosstalk between the gut microbiota of C-IBS patients and host intestinal homeostasis.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "33321137", + "title": "Interaction of sulfated polysaccharides with intestinal Bacteroidales plays an important role in its biological activities.", + "year": 2021, + "journal": "International journal of biological macromolecules", + "authors": [ + "Sun X", + "Liu Y", + "Jiang P", + "Song S", + "Ai C" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.23910486799858116, + "mesh_terms": [ + "Adult", + "Anti-Inflammatory Agents", + "Bacteria", + "Bacteroidetes", + "DNA, Bacterial", + "Feces", + "Female", + "Fermentation", + "Gastrointestinal Microbiome", + "High-Throughput Nucleotide Sequencing", + "Humans", + "Male", + "Polysaccharides", + "Sequence Analysis, DNA", + "Species Specificity", + "Sulfates", + "Young Adult" + ], + "raw_abstract": "The bioactivities of sulfated polysaccharides have shown to be associated with the gut microbiota, but the underlying mechanisms remain unclear. In this study, the effect of sulfated polysaccharides from pacific abalone (AGSP) on the human gut microbiota was analyzed via an in vitro fermentation model. The results revealed that AGSP altered the overall structure of the gut microbiota and increased relative abundances of some Bacteroidales members, implying that intestinal Bacteroidales can play important roles in the bioactivities of AGSP. To elucidate the underlying mechanisms, some species from the Bacteroides and Parabacteroides within Bacteroidales were isolated, and their characteristics on AGSP utilization were analyzed. It showed that AGSP utilization by intestinal Bacteroidales was species-dependent, and some species that liberated AGSP breakdown products promoted the growth of others unable to live in AGSP, forming an AGSP utilization network. The in vitro cell model showed that AGSP oligosaccharides had better anti-inflammatory activity and weaker cytotoxicity, implying that microbial degradation of AGSP can influence its reaction with host cells. These results indicated that the interaction between polysaccharides and gut microbes can together determine the beneficial effects of polysaccharides on the host health.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "34083551", + "title": "Bacteroides uniformis CECT 7771 alleviates inflammation within the gut-adipose tissue axis involving TLR5 signaling in obese mice.", + "year": 2021, + "journal": "Scientific reports", + "authors": [ + "Fabersani E", + "Portune K", + "Campillo I", + "L\u00f3pez-Almela I", + "la Paz SM", + "Roman\u00ed-P\u00e9rez M", + "Ben\u00edtez-P\u00e1ez A", + "Sanz Y" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.23767921139979886, + "mesh_terms": [ + "Adaptive Immunity", + "Adipose Tissue", + "Animals", + "Bacteroides", + "Bacteroides Infections", + "Cytokines", + "Disease Models, Animal", + "Energy Metabolism", + "Gastroenteritis", + "Gastrointestinal Microbiome", + "Immunity, Innate", + "Inflammation Mediators", + "Mice", + "Mice, Obese", + "Phenotype", + "Signal Transduction", + "Toll-Like Receptor 5" + ], + "raw_abstract": "This study investigated the immune mechanisms whereby administration of Bacteroides uniformis CECT 7771 reduces metabolic dysfunction in obesity. C57BL/6 adult male mice were fed a standard diet or a Western diet high in fat and fructose, supplemented or not with B. uniformis CECT 7771 for 14\u00a0weeks. B. uniformis CECT 7771 reduced body weight gain, plasma cholesterol, triglyceride, glucose, and leptin levels; and improved oral glucose tolerance in obese mice. Moreover, B. uniformis CECT 7771 modulated the gut microbiota and immune alterations associated with obesity, increasing Tregs and reducing B cells, total macrophages and the M1/M2 ratio in both the gut and epididymal adipose tissue (EAT) of obese mice. B. uniformis CECT 7771 also increased the concentration of the anti-inflammatory cytokine IL-10 in the gut, EAT and peripheral blood, and protective cytokines TSLP and IL-33, involved in Treg induction and type 2 innate lymphoid cells activation, in the EAT. It also restored the obesity-reduced TLR5 expression in the ileum and EAT. The findings indicate that the administration of a human intestinal bacterium with immunoregulatory properties on the intestinal mucosa helps reverse the immuno-metabolic dysfunction caused by a Western diet acting over the gut-adipose tissue axis.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "39981988", + "title": "Nutraceutical Blends Promote Weight Loss, Inflammation Reduction, and Better Sleep: The Role of Faecalibacterium prausnitzii in Overweight Adults-A Double-Blind Trial.", + "year": 2025, + "journal": "Molecular nutrition & food research", + "authors": [ + "Santamarina AB", + "Filho VN", + "de Freitas JA", + "Franco LAM", + "Martins RC", + "Fonseca JV", + "Orellana Turri JA", + "Hufnagel MT", + "Demarque DP", + "da Silva BFRB", + "Gusm\u00e3o AF", + "Olivieri EHR", + "de Souza E", + "de Souza EA", + "Otoch JP", + "Pessoa AFM" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.23631852830971803, + "mesh_terms": [], + "raw_abstract": "This study explores the effects of a nutraceutical blend with prebiotics, \u03b2-glucans, essential minerals, and silymarin on gut microbiota, inflammation, and sleep quality in obesity through microbiota reshaping and metabolic improvements over 90 days. A double-blind, randomized trial was conducted on 77 participants divided into two groups receiving either a standard nutraceutical blend (NSupple) or a silymarin-enriched blend (NSupple_Silybum). Fecal and plasma samples were collected at baseline and post-supplementation for gut microbiota, metabolic, and inflammatory marker analysis. The results showed a reduction in body weight, waist-to-height ratio, total cholesterol, and fractions in the NSupple_Silybum group. There was a dysbiosis recovery shown by the increase in beneficial gut bacteria, such as Lentisphaerae phylum, Lactobacillus and Faecalibacterium genera, and Faecalibacterium prausnitzii in the NSupple group, with a concurrent reduction in Adlercreutzia and Sutterella in the NSupple_Silybum group. Both groups demonstrated improved inflammatory profiles by the reduced TNF-\u03b1/IL-10 ratio, reduced cortisol levels, and reduced Firmicutes/Bacteroides ratio. Additionally, improvements in sleep quality were associated with reductions in pro-inflammatory cytokines and improved microbiota composition. The nutraceutical blend reshaped gut microbiota, enhanced anti-inflammatory species, and improved metabolic and sleep parameters, highlighting its potential as a nutritional strategy for managing obesity and reducing inflammation.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "29933394", + "title": "Alterations in the gut bacterial microbiome in fungal Keratitis patients.", + "year": 2018, + "journal": "PloS one", + "authors": [ + "Kalyana Chakravarthy S", + "Jayasudha R", + "Ranjith K", + "Dutta A", + "Pinna NK", + "Mande SS", + "Sharma S", + "Garg P", + "Murthy SI", + "Shivaji S" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.23112310014844364, + "mesh_terms": [ + "Adult", + "Aged", + "Aged, 80 and over", + "Cohort Studies", + "Feces", + "Female", + "Gastrointestinal Microbiome", + "Humans", + "Keratitis", + "Male", + "Middle Aged", + "Models, Biological", + "Mycoses", + "Young Adult" + ], + "raw_abstract": "Dysbiosis in the gut microbiome has been implicated in several diseases including auto-immune diseases, inflammatory diseases, cancers and mental disorders. Keratitis is an inflammatory disease of the eye significantly contributing to corneal blindness in the developing world. It would be worthwhile to investigate the possibility of dysbiosis in the gut microbiome being associated with Keratitis. Here, we have analyzed fungal and bacterial populations in stool samples through high-throughput sequencing of the ITS2 region for fungi and V3-V4 region of 16S rRNA gene for bacteria in healthy controls (HC, n = 31) and patients with fungal keratitis (FK, n = 32). Candida albicans (2 OTUs), Aspergillus (1 OTU) and 3 other denovo-OTUs were enriched in FK samples and an unclassified denovo-OTU was enriched in HC samples. However, the overall abundances of these 'discriminatory' OTUs were very low (< 0.001%) and not indicative of significant dysbiosis in the fungal community inhabiting the gut of FK patients. In contrast, the gut bacterial richness and diversity in FK patients was significantly decreased when compared to HC. 52 OTUs were significantly enriched in HC samples whereas only 5 OTUs in FK. The OTUs prominently enriched in HC were identified as Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Lachnospira, Mitsuokella multacida, Bacteroides plebeius, Megasphaera and Lachnospiraceae. In FK samples, 5 OTUs affiliated to Bacteroides fragilis, Dorea, Treponema, Fusobacteriaceae, and Acidimicrobiales were significantly higher in abundance. The functional implications are that Faecalibacterium prausnitzii, an anti-inflammatory bacterium and Megasphaera, Mitsuokella multacida and Lachnospira are butyrate producers, which were enriched in HC patients, whereas Treponema and Bacteroides fragilis, which are pathogenic were abundant in FK patients, playing a potential pro-inflammatory role. Heatmap, PCoA plots and functional profiles further confirm the distinct patterns of gut bacterial composition in FK and HC samples. Our study demonstrates dysbiosis in the gut bacterial microbiomes of FK patients compared to HC. Further, based on inferred functions, it appears that dysbiosis in the gut of FK subjects is strongly associated with the disease phenotype with decrease in abundance of beneficial bacteria and increase in abundance of pro-inflammatory and pathogenic bacteria.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "27239229", + "title": "Analysis of cultivable microbiota and diet intake pattern of the long-lived naked mole-rat.", + "year": 2016, + "journal": "Gut pathogens", + "authors": [ + "Debebe T", + "Holtze S", + "Morhart M", + "Hildebrandt TB", + "Rodewald S", + "Huse K", + "Platzer M", + "Wyohannes D", + "Yirga S", + "Lemma A", + "Thieme R", + "K\u00f6nig B", + "Birkenmeier G" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.23000652679751404, + "mesh_terms": [], + "raw_abstract": "BACKGROUND: A variety of microbial communities exist throughout the human and animal body. Genetics, environmental factors and long-term dietary habit contribute to shaping the composition of the gut microbiota. For this reason the study of the gut microbiota of a mammal exhibiting an extraordinary life span is of great importance. The naked mole-rat (Heterocephalus glaber) is a eusocial mammal known for its longevity and cancer resistance. METHODS: Here we analyzed its gut microbiota by cultivating the bacteria under aerobic and anaerobic conditions and identifying their species by mass spectrometry. RESULTS: Altogether, 29 species of microbes were identified, predominantly belonging to Firmicutes, and Bacteroidetes. The most frequent species were Bacillus megaterium (45.2\u00a0%), followed by Bacteroides thetaiotaomicron (19.4\u00a0%), Bacteroides ovatus, Staphylococcus sciuri and Paenibacillus spp., each with a frequency of 16.1\u00a0%. CONCLUSION: Overall, the gut of the naked mole-rat is colonized by diverse, but low numbers of cultivable microbes compared with humans and mice. The primary food plants of the rodents are rich in polyphenols and related compounds, possessing anti-microbial, anti-inflammatory, anti-oxidative as well as anti-cancer activity which may contribute to their exceptionally healthy life.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "39457054", + "title": "Novelties on Neuroinflammation in Alzheimer's Disease-Focus on Gut and Oral Microbiota Involvement.", + "year": 2024, + "journal": "International journal of molecular sciences", + "authors": [ + "Popescu C", + "Munteanu C", + "Anghelescu A", + "Ciobanu V", + "Sp\u00eenu A", + "Andone I", + "Mandu M", + "Bistriceanu R", + "B\u0103il\u0103 M", + "Postoiu RL", + "Vl\u0103dulescu-Trandafir AI", + "Giuvara S", + "Malaelea AD", + "Onose G" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.21880793785914687, + "mesh_terms": [ + "Humans", + "Alzheimer Disease", + "Gastrointestinal Microbiome", + "Mouth", + "Neuroinflammatory Diseases", + "Dysbiosis", + "Animals", + "Brain-Gut Axis" + ], + "raw_abstract": "Recent studies underscore the role of gut and oral microbiota in influencing neuroinflammation through the microbiota-gut-brain axis, including in Alzheimer's disease (AD). This review aims to provide a comprehensive synthesis of recent findings on the involvement of gut and oral microbiota in the neuroinflammatory processes associated with AD, emphasizing novel insights and therapeutic implications. This review reveals that dysbiosis in AD patients' gut and oral microbiota is linked to heightened peripheral and central inflammatory responses. Specific bacterial taxa, such as Bacteroides and Firmicutes in the gut, as well as Porphyromonas gingivalis in the oral cavity, are notably altered in AD, leading to significant changes in microglial activation and cytokine production. Gut microbiota alterations are associated with increased intestinal permeability, facilitating the translocation of endotoxins like lipopolysaccharides (LPS) into the bloodstream and exacerbating neuroinflammation by activating the brain's toll-like receptor 4 (TLR4) pathways. Furthermore, microbiota-derived metabolites, including short-chain fatty acids (SCFAs) and amyloid peptides, can cross the blood-brain barrier and modulate neuroinflammatory responses. While microbial amyloids may contribute to amyloid-beta aggregation in the brain, certain SCFAs like butyrate exhibit anti-inflammatory properties, suggesting a potential therapeutic avenue to mitigate neuroinflammation. This review not only highlights the critical role of microbiota in AD pathology but also offers a ray of hope by suggesting that modulating gut and oral microbiota could represent a novel therapeutic strategy for reducing neuroinflammation and slowing disease progression.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "29726280", + "title": "Modulatory effect of three probiotic strains on infants' gut microbial composition and immunological parameters on a placebo-controlled, double-blind, randomised study.", + "year": 2018, + "journal": "Beneficial microbes", + "authors": [ + "De Andr\u00e9s J", + "Manzano S", + "Garc\u00eda C", + "Rodr\u00edguez JM", + "Espinosa-Martos I", + "Jim\u00e9nez E" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.21529426167403862, + "mesh_terms": [ + "Bifidobacterium bifidum", + "Bifidobacterium longum subspecies infantis", + "Cytokines", + "Double-Blind Method", + "Feces", + "Gastrointestinal Microbiome", + "Humans", + "Immunity", + "Immunoglobulins", + "Infant", + "Infant Health", + "Lactobacillus helveticus", + "Probiotics", + "RNA, Ribosomal, 16S" + ], + "raw_abstract": "The gut microbiota plays a crucial role in gastrointestinal health. Current use of probiotics is aimed at modulating the bacterial gut composition to alleviate specific diseases. The safety and tolerance of three probiotic strains (Bifidobacterium longum subsp. infantis R0033, Lactobacillus helveticus R0052 and Bifidobacterium bifidum R0071) has recently been described. The objective of the present study was to analyse the microbiological composition and immunological parameters of faecal samples obtained from healthy infants from 3 to 12 months of age after receiving either one of the three probiotic strains or placebo for 8 weeks. 16S ribosomal RNA gene sequencing and multiplexing technology was used for analysis. Faecal sample analysis showed that the most abundant genus in all four groups of infants pre- and post-intervention was Bifidobacterium, representing approximately 50% of the sequences. After the intervention period the microbial composition of faecal samples in the probiotic groups did not display notable changes. In contrast, a decrease in different Bifidobacterium species, such as B. bifidum and Bifidobacterium breve and an increase in Bacteroides, Blautia, Clostridium, Coprococcus and Faecalibacterium genera was observed in the placebo group. The analysis of a wide range of immune factors in faecal samples suggests a modulatory effect by these three probiotic strains during the intervention period. The anti-inflammatory ratio interleukin (IL)-10/IL-12 increased at the end of the intervention period in the B. infantis R0033 group while the TNF-\u03b1/IL-10 ratio increased in the L. helveticus R0052 group. The decrease of the IL-10/IL-12 ratio together with the increase of the tumour necrosis factor alpha (TNF-\u03b1)/IL-10 ratio demonstrated a pro-inflammatory profile in the placebo group. In conclusion, the species profile of the microbiome observed in all three probiotic groups resembled that of a younger infant, similar to an unweaned infant, when compared to the placebo group which may also be related with an anti-inflammatory effect.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "38959643", + "title": "Berberine alleviates high-energy and low-protein diet-induced fatty liver hemorrhagic syndrome in laying hens: insights from microbiome and metabolomics.", + "year": 2024, + "journal": "Poultry science", + "authors": [ + "Cheng X", + "Hu Y", + "Kuang J", + "Guo X", + "Cao H", + "Wu H", + "Hu G", + "Zhuang Y" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.21477572109378393, + "mesh_terms": [ + "Animals", + "Chickens", + "Gastrointestinal Microbiome", + "Female", + "Poultry Diseases", + "Animal Feed", + "Berberine", + "Diet, Protein-Restricted", + "Metabolomics", + "Fatty Liver", + "Lipid Metabolism", + "Dietary Supplements" + ], + "raw_abstract": "Berberine (BBR), a well-known quaternary ammonium alkaloid, is recognized for its ability to prevent and alleviate metabolic disorders because of its anti-oxidative and anti-inflammatory properties. However, the underlying mechanisms of BBR to mitigate fatty liver hemorrhagic syndrome (FLHS) through the modulation of gut microbiota and their metabolism remained unclear. The results revealed that BBR ameliorates lipid metabolism disorder in high-energy and low-protein (HELP) diet-induced FLHS laying hens, as evidenced by improved liver function and lipid deposition of the liver, reduced blood lipids, and the expression of liver lipid synthesis-related factors. Moreover, BBR alleviated HELP diet-induced barrier dysfunction, increased microbial population, and dysregulated lipid metabolism in the ileum. BBR reshaped the HELP-perturbed gut microbiota, particularly declining the abundance of Desulfovibrio_piger and elevating the abundance of Bacteroides_salanitronis_DSM_18170. Meanwhile, metabolomic profiling analysis revealed that BBR reshaped microbial metabolism and function, particularly by reducing the levels of hydrocinnamic acid, dehydroanonaine, and leucinic acid. Furthermore, fecal microbiota transplantation (FMT) experiments revealed that BBR-enriched gut microbiota alleviated hepatic lipid deposition and intestinal inflammation compared with those chicks that received a gut microbiota by HELP. Collectively, our study provided evidence that BBR effectively alleviated FLHS induced by HELP by reshaping the microbial and metabolic homeostasis within the liver-gut axis.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "37946480", + "title": "Integrated 'omics analysis for the gut microbiota response to moxibustion in a rat model of chronic fatigue syndrome.", + "year": 2023, + "journal": "Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan", + "authors": [ + "Chaoran LI", + "Yan Y", + "Chuwen F", + "Heng LI", + "Yuanyuan QU", + "Yulin W", + "Delong W", + "Qingyong W", + "Jing G", + "Tianyu S", + "Xiaowei S", + "Xue W", + "Yunlong H", + "Zhongren S", + "Tiansong Y" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.2120813738450238, + "mesh_terms": [ + "Rats", + "Male", + "Animals", + "Gastrointestinal Microbiome", + "Rats, Sprague-Dawley", + "Moxibustion", + "Fatigue Syndrome, Chronic", + "RNA, Ribosomal, 16S", + "Metabolomics" + ], + "raw_abstract": "OBJECTIVE: To observe the efficacy of moxibustion in the treatment of chronic fatigue syndrome (CFS) and explore the effects on gut microbiota and metabolic profiles. METHODS: Forty-eight male Sprague-Dawley rats were randomly assigned to control group (Con), CFS model group (Mod, established by multiple chronic stress for 35 d), MoxA group (CFS model with moxibustion Shenque (CV8) and Guanyuan (CV4), 10 min/d, 28 d) and MoxB group (CFS model with moxibustion Zusanli (ST36), 10 min/d, 28 d). Open-field test (OFT) and Morris-water-maze test (MWMT) were determined for assessment the CFS model and the therapeutic effects of moxibustion.16S rRNA gene sequencing analysis based gut microbiota integrated untargeted liquid chromatograph-mass spectrometer (LC-MS) based fecal metabolomics were executed, as well as Spearman correlation analysis, was utilized to uncover the functional relevance between the potential metabolites and gut microbiota. RESULTS: The results of our behavioral tests showed that moxibustion improved the performance of CFS rats in the OFT and the MWMT. Microbiome profiling analysis revealed that the gut microbiomes of CFS rats were less diverse with altered composition, including increases in pro-inflammatory species (such as Proteobacteria) and decreases in anti-inflammatory species (such as Bacteroides, Lactobacillus, Ruminococcus, and Prevotella). Moxibustion partially normalized these changes in the gut microbiota. Furthermore, CFS was associated with metabolic disorders, which were effectively ameliorated by moxibustion. This was demonstrated by the normalization of 33 microbiota-related metabolites, including mannose ( CONCLUSIONS: In this study, we demonstrated that moxibustion has an antifatigue-like effect. The results from the 16S rRNA gene sequencing and metabolomics analysis suggest that the therapeutic effects of moxibustion on CFS are related to the regulation of gut microorganisms and their metabolites. The increase in Bacteroides and decrease in LCA may be key targets for the moxibustion treatment of CFS.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "38604285", + "title": "Recent alcohol intake impacts microbiota in adult burn patients.", + "year": 2024, + "journal": "Alcohol (Fayetteville, N.Y.)", + "authors": [ + "Hoisington AJ", + "Choy K", + "Khair S", + "Dyamenahalli KU", + "Najarro KM", + "Wiktor AJ", + "Frank DN", + "Burnham EL", + "McMahan RH", + "Kovacs EJ" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.20882820338682148, + "mesh_terms": [ + "Humans", + "Burns", + "Male", + "Adult", + "Female", + "Alcohol Drinking", + "Gastrointestinal Microbiome", + "Middle Aged", + "Feces", + "Glycerophospholipids", + "Fatty Acids, Volatile", + "Dysbiosis", + "Biomarkers", + "Young Adult" + ], + "raw_abstract": "Alcohol use is associated with an increased incidence of negative health outcomes in burn patients due to biological mechanisms that include a dysregulated inflammatory response and increased intestinal permeability. This study used phosphatidylethanol (PEth) in blood, a direct biomarker of recent alcohol use, to investigate associations between a recent history of alcohol use and the fecal microbiota, short chain fatty acids, and inflammatory markers in the first week after a burn injury for nineteen participants. Burn patients were grouped according to PEth levels of low or high and differences in the overall fecal microbial community were observed between these cohorts. Two genera that contributed to the differences and had higher relative abundance in the low PEth burn patient group were Akkermansia, a mucin degrading bacteria that improves intestinal barrier function, and Bacteroides, a potentially anti-inflammatory bacteria. There was no statistically significant difference between levels of short chain fatty acids or intestinal permeability across the two groups. To our knowledge, this study represents the first report to evaluate the effects of burn injury and recent alcohol use on early post burn microbiota dysbiosis, inflammatory response, and levels of short chain fatty acids. Future studies in this field are warranted to better understand the factors associated with negative health outcomes and develop interventional trials.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "38358546", + "title": "A study on the association between gut microbiota, inflammation, and type 2 diabetes.", + "year": 2024, + "journal": "Applied microbiology and biotechnology", + "authors": [ + "Liu N", + "Yan X", + "Lv B", + "Wu Y", + "Hu X", + "Zheng C", + "Tao S", + "Deng R", + "Dou J", + "Zeng B", + "Jiang G" + ], + "bacteria": "Bacteroides", + "condition": "anti-inflammatory", + "relevance_score": 0.20011591309382665, + "mesh_terms": [ + "Mice", + "Animals", + "Humans", + "Mice, Inbred C57BL", + "Gastrointestinal Microbiome", + "NF-kappa B", + "Diabetes Mellitus, Type 2", + "RNA, Ribosomal, 16S", + "Skatole", + "Tryptophan", + "Inflammation", + "Bacteroides" + ], + "raw_abstract": "Type 2 diabetes mellitus (T2DM) was reported to be associated with impaired immune response and alterations in microbial composition and function. However, the underlying mechanism remains elusive. To investigate the association among retinoic acid-inducible gene-I-like receptors (RLRs) signaling pathway, intestinal bacterial microbiome, microbial tryptophan metabolites, inflammation, and a longer course of T2DM, 14 patients with T2DM and 7 healthy controls were enrolled. 16S rRNA amplicon sequencing and untargeted metabolomics were utilized to analyze the stool samples. RNA sequencing (RNA-seq) was carried out on the peripheral blood samples. Additionally, C57BL/6J specific pathogen-free (SPF) mice were used. It was found that the longer course of T2DM could lead to a decrease in the abundance of probiotics in the intestinal microbiome. In addition, the production of microbial tryptophan derivative skatole declined as a consequence of the reduced abundance of related intestinal microbes. Furthermore, low abundances of probiotics, such as Bacteroides and Faecalibacterium, could trigger the inflammatory response by activating the RLRs signaling pathway. The increased level of the member of TNF receptor-associated factors (TRAF) family, nuclear factor kappa-B (NF-\u03baB) activator (TANK), in the animal colon activated nuclear factor kappa B subunit 2 (NF\u03baB2), resulting in inflammatory damage. In summary, it was revealed that the low abundances of probiotics could activate the RLR signaling pathway, which could in turn activate its downstream signaling pathway, NF-\u03baB, highlighting a relationship among gut microbes, inflammation, and a longer course of T2DM. KEY POINTS: Hyperglycemia may suppress tryptophanase activity. The low abundance of Bacteroides combined with the decrease of Dopa decarboxylase (DDC) activity may lead to the decrease of the production of tryptophan microbial derivative skatole, and the low abundance of Bacteroides or reduced skatole may further lead to the increase of blood glucose by downregulating the expression of glucagon-like peptide-1 (GLP1). A low abundance of anti-inflammatory bacteria may induce an inflammatory response by triggering the RLR signaling pathway and then activating its downstream NF-\u03baB signaling pathway in prolonged T2DM.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "38608475", + "title": "Turtle peptide and its derivative peptide ameliorated DSS-induced ulcerative colitis by inhibiting inflammation and modulating the composition of the gut microbiota.", + "year": 2024, + "journal": "International immunopharmacology", + "authors": [ + "Guo HX", + "Wang BB", + "Wu HY", + "Feng HY", + "Zhang HY", + "Gao W", + "Yuan B" + ], + "bacteria": "Parasutterella", + "condition": "anti-inflammatory", + "relevance_score": 0.30599448942684726, + "mesh_terms": [ + "Animals", + "Colitis, Ulcerative", + "Gastrointestinal Microbiome", + "Dextran Sulfate", + "Mice", + "Peptides", + "Anti-Inflammatory Agents", + "Turtles", + "Male", + "Mice, Inbred C57BL", + "Toll-Like Receptor 4", + "NF-kappa B", + "Disease Models, Animal", + "Intestinal Mucosa", + "Colon", + "Humans", + "Oxidative Stress", + "Signal Transduction" + ], + "raw_abstract": "Ulcerative colitis (UC) is a recurrent intestinal disease with an increasing incidence worldwide that seriously affects the life of patients. Turtle peptide (TP) is a bioactive peptide extracted from turtles that has anti-inflammatory, antioxidant and anti-aging properties. However, studies investigating the effect of TP on the progression of UC are lacking. The aim of this study was to investigate effects and underlying mechanisms of TP and its derivative peptide GPAGPIGPV (GP-9) in alleviating UC in mice. The results showed that 500\u00a0mg/kg TP treatment significantly ameliorated colitis symptoms and oxidative stress in UC mice. TP alleviated intestinal barrier damage in UC mice by promoting mucosal repair and increasing the expression of tight junction proteins (ZO1, occludin and claudin-1). TP also modulated the composition of the gut microbiota by increasing the abundance of the beneficial bacteria Anaerotignum, Prevotellaceae_UCG-001, Alistipes, and Lachno-spiraceae_NK4A136_group and decreasing the abundance of the harmful bacteria Prevotella_9 and Parasutterella. Furthermore, we characterized the peptide composition of TP and found that GP-9 ameliorated the symptoms of dextran sodium sulfate (DSS)-induced colitis in mice by inhibiting the TLR4/NF-\u03baB signaling pathway. In conclusion, TP and its derivative peptides ameliorated DSS-induced ulcerative colitis by inhibiting the expression of inflammatory factors and modulating the composition of the intestinal microbiota; this study provides a theoretical basis for the application of TP and its derivative peptides for their anti-inflammatory activity.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "36040412", + "title": "Quantitative Fecal Microbiota Profiles Relate to Therapy Response During Induction With Tumor Necrosis Factor \u03b1 Antagonist Infliximab in Pediatric Inflammatory Bowel Disease.", + "year": 2023, + "journal": "Inflammatory bowel diseases", + "authors": [ + "H\u00f6yhty\u00e4 M", + "Korpela K", + "Saqib S", + "Junkkari S", + "Nissil\u00e4 E", + "Nikkonen A", + "Dikareva E", + "Salonen A", + "de Vos WM", + "Kolho KL" + ], + "bacteria": "Parasutterella", + "condition": "anti-inflammatory", + "relevance_score": 0.20477158357576425, + "mesh_terms": [ + "Humans", + "Child", + "Infliximab", + "Tumor Necrosis Factor-alpha", + "Tumor Necrosis Factor Inhibitors", + "Inflammatory Bowel Diseases", + "Feces", + "Microbiota", + "Leukocyte L1 Antigen Complex" + ], + "raw_abstract": "BACKGROUND: The role of intestinal microbiota in inflammatory bowel diseases is intensively researched. Pediatric studies on the relation between microbiota and treatment response are sparse. We aimed to determine whether absolute abundances of gut microbes characterize the response to infliximab induction in pediatric inflammatory bowel disease. METHODS: We recruited pediatric patients with inflammatory bowel disease introduced to infliximab at Children's Hospital, University of Helsinki. Stool samples were collected at 0, 2, and 6 weeks for microbiota and calprotectin analyses. We defined treatment response as fecal calprotectin value <100 \u00b5g/g at week 6. Intestinal microbiota were analyzed by 16S ribosomal RNA gene amplicon sequencing using the Illumina MiSeq platform. We analyzed total bacterial counts using quantitative polymerase chain reaction and transformed the relative abundances into absolute abundances based on the total counts. RESULTS: At baseline, the intestinal microbiota in the treatment responsive group (n\u2005=\u200510) showed a higher absolute abundance of Bifidobacteriales and a lower absolute abundance of Actinomycetales than nonresponders (n\u2005=\u200519). The level of inflammation according to fecal calprotectin showed no statistically significant association with the absolute abundances of fecal microbiota. The results on relative abundances differed from the absolute abundances. At the genus level, the responders had an increased relative abundance of Anaerosporobacter but a reduced relative abundance of Parasutterella at baseline. CONCLUSIONS: High absolute abundance of Bifidobacteriales in the gut microbiota of pediatric patients reflects anti-inflammatory characteristics associated with rapid response to therapy. This warrants further studies on whether modification of pretreatment microbiota might improve the outcomes. We studied absolute and relative abundances of fecal microbiota in relation to response to induction therapy with infliximab in pediatric inflammatory bowel disease. We discovered that a high absolute abundance of anti-inflammatory Bifidobacteriales at baseline associated with response.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + }, + { + "pmid": "39353590", + "title": "Characterisation of potential anti-inflammatory next-generation probiotics resistant to bisphenol A.", + "year": 2024, + "journal": "Beneficial microbes", + "authors": [ + "L\u00f3pez-Moreno A", + "Carbonne C", + "Kropp C", + "Rios-Covian D", + "Pepke F", + "Langella P", + "Aguilera M", + "Martin R" + ], + "bacteria": "Paeniclostridium", + "condition": "anti-inflammatory", + "relevance_score": 0.36226161879718155, + "mesh_terms": [ + "Benzhydryl Compounds", + "Phenols", + "Probiotics", + "Humans", + "Animals", + "Bacillus", + "Mice", + "Anti-Inflammatory Agents", + "HT29 Cells", + "Colitis", + "Cytokines", + "Gastrointestinal Microbiome", + "Inflammatory Bowel Diseases", + "Disease Models, Animal", + "Mice, Inbred C57BL", + "Bisphenol A Compounds" + ], + "raw_abstract": "The world is witnessing an increasing incidence of chronic non-communicable diseases (NCDs), such as inflammatory bowel disease (IBD), a group of complex gastrointestinal disorders characterised by inflammation. It is believed that environmental factors, such as exposure to pollutants and endocrine-disrupting chemicals (i.e. bisphenol A [BPA]), are playing a role in IBD pathophysiology. New research suggests a potential treatment solution: next-generation probiotic (NGP) strains isolated from human gut microbiota that can biodegrade xenobiotics and thus possibly modulate IBD triggered by these xenobiotics. In this study, we hypothesised that specific BPA-tolerant bacteria would exhibit beneficial, anti-inflammatory properties that could counter the effects of BPA exposure and concomitantly reduce colitis severity. We observed that two such strains, Bacillus sp. AM1 and Paeniclostridium sp., exhibited potential anti-inflammatory properties in vitro and in vivo. First, these bacteria were able to decrease the secretion of interleukin (IL)-8 cytokines by HT-29 cells that had been exposed to the proinflammatory cytokine tumour necrosis factor (TNF)-\u03b1. Second, when treated with Bacillus sp. AM1 and Paeniclostridium sp. (this latter had a stronger reducing effect on inflammatory markers), mice with chemically induced colitis displayed lower levels of colon damage, monocyte chemotactic protein 1 (MCP-1), lipocalin-2 (LCN-2), and proinflammatory cytokines (IL-1\u03b2 and IL-6). Future research should clarify the underlying mechanisms at play and identify potential strategies for counteracting the systemic effects of IBD, including those exacerbated by BPA exposure. Our results suggest that one such strategy could be treatment with BPA-tolerant bacteria that possess anti-inflammatory properties.", + "condition_dir": "microbiome-uc-ibd/anti-inflammatory" + } +] \ No newline at end of file