study_id	study_name	study_abstract	lineage
MGYS00006748	Soils' metagenomes (countryside of Sao Paulo - Brazil)	We collected eight soil samples from different locations in the countryside of Sao Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing and analyzed the soil metagenomes based on shotgun sequencing to identify antibiotic resistance genes.	root:Environmental:Terrestrial:Soil
MGYS00006747	16S microbiome sequences from 101 fecal samples from zoo mammals	In this study, we examine the taxonomic composition and metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using 16S amplicon sequencing and an untargeted metabolomics platform to analyze 101 fecal samples from a range of mammalian species. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species were related to the host-microbe interface, including modified and degraded host and dietary compounds. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically-distant microbiomes are more functionally diverse than redundant.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006746	General soil fungi from 150 German grassland and 150 German forest plots from 2011, 2014 and 2017 (Illumina MiSeq)	The German Biodiversity Exploratories aim to regularly monitor general fungi in German soils. The project considers 150 grassland and 150 forest plots in total, which are distributed along a north-south transect across Germany. The three sites, each consisting of 50 grassland and 50 forest plots, are Schorfheide-Chorin in Northern Germany, Hainich-Duen in Central Germany and Swabian Alb in the South of the country. Grasslands and forests are characterized by different land-use intensities and management regimes, respectively. The arbuscular mycorrhiza fungi were assessed using Illumina MiSeq sequencing of the internal transcripted spacer2 (ITS2) region after a joint soil sampling carried out in May 2011, 2014 and 2017, each time on all 300 plots.	root:Environmental:Terrestrial:Soil
MGYS00006745	Arbuscular mycorrhizal fungi from 150 German grassland and 150 German forest plots from 2011, 2014 and 2017 (Illumina MiSeq)	The German Biodiversity Exploratories aim to regularly monitor arbuscular mycorrhizal in German soils. The project considers 150 grassland and 150 forest plots in total, which are distributed along a north-south transect across Germany. The three sites, each consisting of 50 grassland and 50 forest plots, are Schorfheide-Chorin in Northern Germany, Hainich-Duen in Central Germany and Swabian Alb in the South of the country. Grasslands and forests are characterized by different land-use intensities and management regimes, respectively.The arbuscular mycorrhiza fungi were assessed using Illumina MiSeq sequencing of the small subunit (SSU) gene after a joint soil sampling carried out in May 2011, 2014 and 2017, each time on all 300 plots.	root:Environmental:Terrestrial:Soil
MGYS00005502	Bacterial diversity and community composition in grassland and forest soils of the German Biodiversity Exploratories	Bacterial diversity and community composition should be assessed for grassland and forest soils in the three German Biodiversity Exploratories (Schorfheide-Chorin, Hainich-Dün, Schwäbische Alb). Grassland soil samples were derived from meadows, pastures or mown pastures that were either fertilized or non-fertilized. Forest soil samples were derived from age class forest, selection forest or natural forest and dominated by either beech, oak, pine or spruce trees.The study focused on the effect of land use, management, fertilization and tree species as well as edaphic parameters onto the bacterial community and diversity to identify drivers of diversity and community composition.	root:Environmental:Terrestrial:Soil
MGYS00006741	Analysis of Candidatus Udaeobacter representatives in forest and grassland soils	The aim of the project was to investigate Candidatus Udaeobacter phylotypes in forest and grassland soils derived from the German Biodiversity Exploratories	root:Environmental:Terrestrial:Soil
MGYS00006743	Soil fungi from forest and grassland ecosystems across Germany (raw sequence reads 2011)	"The provided sequences were produced in the frame of the core project ""Soil Fungi"" of the German Biodiversity Exploratories. In May 2011, soil was taken on 300 study plots across three regions in Germany (south - Schwäbische Alb, central - Hainich-Dün, north - Schorfheide-Chorin). After extracting the DNA with the MoBio PowerSoil extraction kit, the fungal ITS (primers: ITS1f and ITS4) was targeted and amplified. The provided sequences are produced with the Roche 454 pyrosequencer."	root:Environmental:Terrestrial:Soil
MGYS00006744	Changes in acidobacterial community composition from German grassland soils with land use intensity	In the frame of the German Biodiversity Exploratories (http://www.biodiversity-exploratories.de), the sampling plots were located in three regions in Germany: Schorfheide-Chorin in Brandenburg, national park Hainich-Dün Thuringia, and biosphere reserve Schwäbische Alb in Baden-Wuerttemberg. In every region, 50 grassland sites with different land use intensities were investigated, resulting in a total of 150 plots analysed in this study. The coordinated soil sampling campaign took place in May 2011. The acidobacterial community composition in soil samples was analyzed by high-throughput Illumina sequencing targeting the V3 region of the 16S rRNA.	root:Environmental:Terrestrial:Soil
MGYS00006740	Biodiversity Exploratories Rhizosphere 2015	Biodiversity Exploratories Rhizosphere 2015	root:Environmental:Terrestrial:Soil
MGYS00000692	16S rRNA gene and transcript based analysis of different methods to extract DNA and RNA from soil	Central objective of this study is to compare different nucleic acid extraction methods with respect to abundance and diversity of 16S rRNA genes and transcripts.  Grassland soil derived from the German Biodiversity Exploratories Schwäbische Alb, Schorfheide Chorin and Hainich-Dün.	root:Environmental:Terrestrial:Soil
MGYS00006742	Microbial genomic DNA was extracted from the root, rhizosphere and bulk soil compartments from grassland phytometer plant species and was then used as templates for bacterial 16S and/or fungal ITS rDNA paired-end amplicon sequencing using Illumina MiSeq	Investigation of the root and rhizosphere microbial community composition of forb and grass phytometer plants out planted in sites of different land-use intensity in the German Biodiversity Exploratories (Hainich-Dün) by means of 16S and ITS rDNA paired-end amplicon sequencing using Illumina MiSeq. The study focused on the effect of plant functional group (grasses vs. forbs) and land-use as well as edaphic parameters onto the bacterial and fungal community and diversity.	root:Environmental:Terrestrial:Soil
MGYS00006736	Shotgun metagenomics of faecal samples collected from Brent geese	A set of 29 faecal samples were collected from light-bellied brent geese (Branta bernicla) in Iceland in May 2023 and were stored dry frozen at -70 degrees Celsius. The DNA was extracted using Qiagen DNEasy PowerSoil Pro kits and shotgun metagenomic data produced using Illumina Novaseq 250bp chemistry.	root:Host-associated:Birds:Digestive system:Fecal
MGYS00001228	16S rRNA amplicon sequences for dugout DNA samples	Three methods to profile microbial community are compared. This sample is 16S rRNA amplicon sequencing of a single DNA sample.	root:Environmental:Aquatic:Freshwater
MGYS00001980	EMG produced TPA metagenomics assembly of the Human Microbiome Project (HMP) Metagenomic WGS Projects, deeper sequencing of the human microbiome samples: Production Phase (human metagenome) data set	The human metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set,(PRJNA48479).  This project includes samples from the following biomes : Fecal,Oral,Attached Keratinized gingiva,buccal mucosa,hard palate,Palatine tonsils,Saliva,Subgingival plaque,Supragingival plaque,Throat,Introitus,Midpoint vagina,posterior fornix,anterior nares,retroauricular crease.	root:Host-associated:Human
MGYS00006570	EMG produced TPA metagenomics assembly of PRJNA230567 data set (Systems Biology of Lipid Accumulating Organisms).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA230567, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Engineered:Wastewater.	root:Engineered:Wastewater
MGYS00006725	DNA meta-barcoding strategies for species identification in food of animal origin	Two projects: 1. species identification/quantification for processed fish food; 2. species identification/quantification for pure, processed and mock meat products.	root:Engineered:Food production
MGYS00006724	Annual Dynamics of Bacterial & Archaeal Communities in the West Spitsbergen Current (2018-2019)	"This dataset contains 16S rRNA amplicon sequences, derived from autonomous sampling between August 2018 to August 2019 in the West Spitsbergen Current (mooring F4-S-3). The data is part of the LTER ""FRAM"" (Fram Strait, Arctic Ocean) of the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research."	root:Environmental:Aquatic:Marine
MGYS00006722	Annual Dynamics of Microeukaryotic Communities in the West Spitsbergen Current (2018-2019)	18S rRNA amplicon sequences derived from autonomous sampling in the West Spitsbergen Current (mooring F4-S-3).	root:Environmental:Aquatic:Marine
MGYS00006723	Annual Dynamics of Microeukaryotic Communities in the West Spitsbergen Current (2019-2020)	18S rRNA amplicon sequences derived from autonomous sampling in the West Spitsbergen Current (mooring F4-S-4).	root:Environmental:Aquatic:Marine
MGYS00006721	Annual Dynamics of Bacterial & Archaeal Communities in the West Spitsbergen Current (2019-2020)	16S rRNA amplicon sequences derived from autonomous sampling in the West Spitsbergen Current (mooring F4-S-4).	root:Environmental:Aquatic:Marine
MGYS00006720	Annual Dynamics of Bacterial & Archaeal Communities in the West Spitsbergen Current (2018-2019)	16S rRNA amplicon sequences derived from autonomous sampling in the West Spitsbergen Current (mooring F4-S-3).	root:Environmental:Aquatic:Marine
MGYS00006719	Annual Dynamics of Bacterial & Archaeal Communities in the East Greenland Current (2018-2019)	16S rRNA amplicon sequences derived from autonomous sampling in the East Greenland Current (mooring EGC-5).	root:Environmental:Aquatic:Marine
MGYS00006717	Annual Dynamics of Microeukaryotic Communities in Fram Strait (2016-2017)	18S rRNA amplicon sequences derived from moored autonomous samplers. Moorings: F4-S-1, HG-IV-S-1, Fevi-34, EGC-3	root:Environmental:Aquatic:Marine
MGYS00006718	Annual Dynamics of Bacterial & Archaeal Communities in the East Greenland Current (2019-2020)	16S rRNA amplicon sequences derived from autonomous sampling in the East Greenland Current (mooring EGC-6).	root:Environmental:Aquatic:Marine
MGYS00006714	Regional and vertical patterns in microbial communities across Fram Strait (2015-2019)	This study portrays bacterial and archaeal community composition over five summers in the Arctic Fram Strait (80°N). The dataset includes 16S rRNA gene amplicons derived from annual samplings along a longitudinal transect (6°W–12°E) from the surface to the lower photic zone, covering Arctic- / Atlantic-influenced waters in western / eastern Fram Strait.	root:Environmental:Aquatic:Marine
MGYS00006716	Annual Dynamics of Microeukaryotic Communities in Fram Strait (2017-2018)	18S rRNA amplicon sequences derived from moored autonomous samplers. Moorings: F4-S-2, HG-IV-S-2, Fevi-36, EGC-4.	root:Environmental:Aquatic:Marine
MGYS00006715	Pelagic free-living and particle-associated microbial communities across Fram Strait	Water samples were collected in Fram Strait during the Polarstern cruise PS99.2 (June 24th – July 16th 2016) from Greenland shelf to west coast of Spitsbergen. For assessing bacterial and archaeal community composition 4-8 L of water were filtered with peristaltic pump through successive membrane filters of 5 μm and 0.22 μm. The extracted genomic DNA was isolated and the hypervariable V4-V5 (515F - 926R) region of the 16S rRNA was amplified and sequenced using Illumina MiSeq platform in a 2 × 300 bp paired-end run.	root:Environmental:Aquatic:Marine
MGYS00006712	Annual Dynamics of Bacterial & Archaeal Communities in Fram Strait (2016-2017)	16S rRNA amplicon sequences derived from moored autonomous samplers. Moorings: F4-S-1, HG-IV-S-1, Fevi-34, EGC-3.	root:Environmental:Aquatic:Marine
MGYS00006713	Annual Dynamics of Bacterial & Archaeal Communities in Fram Strait (2017-2018)	16S rRNA amplicon sequences derived from moored autonomous samplers. Moorings: F4-S-2, HG-IV-S-2, Fevi-36, EGC-4.	root:Environmental:Aquatic:Marine
MGYS00006709	Kongsfjorden_July_2016	In an Arctic glacial fjord, the phytoplankton bloom is controlled by light transparency together with nutrient supply and Atlantic inflow. To explore the issues of climate change and glacial melting in an Arctic fjord, the biological and physiochemical environments of Kongsfjorden, a glacial fjord in Svalbard, have been investigated. The hydrography of Kongsfjorden is controlled by the water mass balance of Atlantic inflow, Arctic waters, and glacial melt through the cross-shelf exchange, and its dominant water masses are determined according to the temperature-salinity diagram.	root:Environmental:Aquatic:Marine
MGYS00006711	Phytoplankton-derived biopolymers and seasonal bacterial diversity in Fram Strait	"Here, we investigated seasonal bacterial community composition in context of the bioavailable fraction of dissolved organic carbon (DOC) in the eastern Fram Strait. The dataset is affiliated with the project ""Plankton Ecology and Biogeochemistry in a Changing Arctic Ocean"" (PEBCAO) and the LTER ""FRAM""."	root:Environmental:Aquatic:Marine
MGYS00006710	Contrasting summer microbiome communities of the Fram Strait		root:Environmental:Aquatic:Marine
MGYS00004542	particle-attached and free-living bacteria kongsfjorden	particle attached and free-living bacteria kongsfjorden	root:Environmental:Aquatic:Marine
MGYS00006708	Particle -attached and free-living archaea from surface waters of kongsfjorden	particle-attached and free-living archaea kongsfjorden	root:Environmental:Aquatic:Marine
MGYS00006707	16S rDNA amplicon sequencing of NEREA size-fractionated samples	Analysis of the V4-V5 region of 16S rDNA through amplicon sequencing. Samples were collected monthly across different sampling sites in the Gulf of Naples (Italy). Seawater was collected at different depths and subjected to size fractionation filtering. The DNA was extracted and amplified by PCR.	root:Environmental:Aquatic:Marine
MGYS00006706	18S rDNA amplicon sequencing of NEREA size-fractionated samples	Analysis of the V9 region of 18S rDNA through amplicon sequencing. Samples were collected monthly across different sampling sites in the Gulf of Naples (Italy). Seawater was collected at different depths and subjected to size fractionation filtering. The DNA was extracted and amplified by PCR.	root:Environmental:Aquatic:Marine
MGYS00006705	Seasonality of rare and abundant bacterial taxa in Radiales E2 Gijon/Xixon time-series station	In this 3-years time-series study in coastal waters of the Bay of Biscay we have identified the largest number of bacterial taxa with significant seasonality to date (83 taxa). Among these seasonal taxa, 24 cycled between rare and abundant, but most of them were always-rare (59 taxa), with maximum abundances predominately found in winter. We demonstrate that recurrent seasonal patterns in marine bacterioplankton are largely driven by lineages that never account >1% of total community abundance. Such dynamics characterized by seasonal growth and loss opens new perspectives in the ecology of rare marine bacteria, hitherto characterized by dormancy and episodic boom and bust, as envisioned by the seed-bank hypothesis. The effect of abiotic factors and phytoplankton composition on the dynamics of abundant and rare taxa have been also explored in this study, including taxa in the attached fraction (> 3 microns) in a selection of samples over the 3 years.	root:Environmental:Aquatic:Marine
MGYS00006702	LMO 16S 2012-13 (3 um)	Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2012-13 collected directly on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00006704	LMO 2015, 2016, 2019 (0.2, 3-0.2, 3)	Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2014-15 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00002774	marine metagenome Targeted Locus (Loci)	Seasonal variation in bacterioplankton community composition in the Baltic Sea.	root:Environmental:Aquatic:Marine
MGYS00006703	LMO 2012 (3-0.2) resequencing	Resequencing of bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2012 using a single filter setup: 0.2 um after prefiltering with a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00006700	LMO 2011-16 (0.2, 3-0.2, 3) resequencing	Resequencing of bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2011-16 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00006701	LMO 16S 2013 (3 um)	Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2014-15 collected on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00006699	LMO 2018 (0.2, 3-0.2, 3)	Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2018 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00002766	Baltic Sea high-frequency temporal study 2012 at the Linnaeus Microbial Observatory Targeted Locus (Loci)	The goal of our high temporal resolution study is to elucidate intra- and interannual detailed differences in bacterial community composition between different filter size fraction, i.e. particle attached vs. free living marine bacterioplankton.	root:Environmental:Aquatic:Marine
MGYS00006697	LMO 16S 2014, 2015 (0.2, 3-0.2, 3)	Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2014-15 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00006696	LMO 16S 2011, 2012, 2013 (0.2, 3-0.2, 3)	Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2011-13 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00006698	LMO 2017 (0.2, 3-0.2, 3)	Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2017 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00006695	LMO 2011, 2012, 2013 (0.2, 3-0.2, 3)	Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2011-13 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00006694	LMO 2015, 2016 (0.2, 3-0.2, 3)	Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2015-16 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00006693	LMO 2016, 2017 (0.2, 3-0.2, 3)	Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2016-17 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00006690	L4 fungal time series	17 year molecular time series of fungal ITS at L4 station, WCO	root:Environmental:Aquatic:Marine
MGYS00006691	Baltic Sea 16S gene amplicons from Linnaeus Microbial Observatory sampled regularly since 2011	This study includes surveys of microbial communities at Linnaeus Microbial Observatory (LMO) since 2011. Samples have been collected at LMO at different time intervals, 16S amplicons have been sequenced from different filter fractions and also in different sequencing projects.	root:Environmental:Aquatic:Marine
MGYS00006692	LMO 2013 (0.2, 3-0.2, 3)	Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2013 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter.	root:Environmental:Aquatic:Marine
MGYS00002841	Transplant and re-transplant microcosms of Baltic Proper and Bothnian Sea bacterioplankton Targeted Locus (Loci)	The aim of this study was to investigate the effects of increased precipitation, meaning increased loads of terrigenous carbon and lowered salinity by transferring marine bacterioplankton between humic rich and low saline Bothnian Sea water and transparent higher saline Baltic proper water and vice versa.	root:Environmental:Aquatic:Marine
MGYS00006686	Helgoland 2019	Environmental DNA and zooplankton samples taken at Helgoland Roads in June 2019	root:Environmental:Aquatic:Marine
MGYS00003999	16s data marine community of L4 station	We collected monthly water samples at the L4 station of the Western Channel Observatory. The prokaryote community composition was determined by sequencing of the 16s rRNA gene using the illumina platform.	root:Environmental:Aquatic:Marine
MGYS00006688	Eukaryotic microbial community at the LTER site Helgoland Roads	Water samples were collected from the long-term ecological research (LTER) site at Helgoland and the eukaryotic microbial community was assessed. 18S V4 region was amplified using the primer set 528iF /964iR and amplicon sequencing was performed on an Illumina MiSeqTM sequencer in a 2 × 300 bp paired-end run.	root:Environmental:Aquatic:Marine
MGYS00006689	Marine metagenome ICM_MPI	The seasonal structure of the bacterial communities of the Helgoland Roads.	root:Environmental:Aquatic:Marine
MGYS00006687	18S community profiles at the the end of a spring bloom at LTER Helgoland Roads	This data set includes eukaryotic microbial community profiles from samples collected in May 2016, via the remote-controlled Automated Filtration System for Marine Microbes (AUTOFIM)  implemented in parallel to the Long Term Ecological Research (LTER) observatory Helgoland Roads in the German Bight.	root:Environmental:Aquatic:Marine
MGYS00006684	Distribution of chytrids infecting diatoms	Vertical and temporal distribution of chytrids infecting diatoms in the Gulf of Naples (Italy, Mediterranean Sea)	root:Environmental:Aquatic:Marine
MGYS00006685	Metabarcoding Eukaryotic plankton  time series samples from long-term ecological research site MareChiara (LTER-MC)	Metabarcoding analysis of a 48 sample time series from Jan 2011 to Dec 2013 targeting 18S V4 rRNA of Eukaryotic plankton from the Long-Term Ecological Research site MareChiara (LTER-MC) in the Gulf of Naples, Mediterranean Sea. For DNA extraction, about 3 liters of surface sea-water sample (0.5 m) was filtered under mild pressure on each of two cellulose ester filters (47 mm diameter, 1.2 μm pore-size, EMD Millipore, USA). Filters were stored at −80°C. Nextera dual index approach and 2 × 250 bp were applied for V4 region sequencing on a MiSeq platform.	root:Environmental:Aquatic:Marine
MGYS00006683	Temporal diversity and community structure of the planktonic protist assemblage at the Long Term Ecological Research (LTER) station MareChiara in the Gulf of Naples(Mediterranean Sea) assessed using V4 Illumina sequencing.	We tracked temporal changes in protist diversity at the Long Term Ecological Research (LTER) station MareChiara in the Gulf of Naples (Mediterranean Sea) on eight dates in 2011 using V4 Illumina sequencing. Samples for metabarcoding analyses were collected from surface waters at the LTER-MC station on eight dates from February to December 2011. The dates were selected based on light microscopy phytoplankton data, which were used as proxies for the seasonal phase and trophic status of the system.  For DNA extraction, about 3 litres of surface sample (0.5 m) was filtered under mild pressure on each of two cellulose ester filters (47 mm diameter, 1.2 μm pore-size, EMD Millipore, USA). Filters were immediately frozen with liquid nitrogen and stored at −80◦C. Nextera dual index approach and to 2 × 250 bp were applied for V4 region sequencing on a MiSeq platform.	root:Environmental:Aquatic:Marine
MGYS00006680	SOLA sampling point Raw sequence reads	Raw environmental eukaryotic samples from the SOLA (Service d'Observation Laboratoire Arago) sampling point, in the North Western Mediterranean sea. These samples are part of a time series, from 2015 to 2017.	root:Environmental:Aquatic:Marine
MGYS00004525	SOLA Raw sequence reads	Raw environmental eukaryotic samples from the SOLA (Service d''Observation Laboratoire Arago) sampling point, in the North Western Mediterranean sea. These samples are part of a time series, from 2007 to 2015, that is investigating the seasonal reoccurrence of rhythmic species.	root:Environmental:Aquatic:Marine
MGYS00006682	Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep-sea fishes	The deep-sea provides global vital functions such as sequestration of carbon from the atmosphere. The increased anthropogenic pressures and interest in expanding deep-sea fisheries makes this pristine ecosystem particularly vulnerable, whose conservation largely depends on rapid knowledge acquisition. In view of the limitations of traditional methods to explore the biodiversity of this vast ecosystem, the analysis of traces of macroorganismal DNA released into the water column arises as a cost-effective, non-invasive alternative. Yet, the success of this approach requires understanding of the stratification of DNA traces in the ocean. This study provides evidence that fish DNA traces can be used to establish depth-specific fish diversity and abundance throughout the water column, opening a promising avenue for gathering knowledge about the deep-sea ecosystem.	root:Environmental:Aquatic:Marine
MGYS00006681	Marine fish eDNA metabarcoding		root:Environmental:Aquatic:Marine
MGYS00006679	Time series of Synechococcus diversity at the SOMLIT-ASTAN station	The genetic diversity of Synechococcus population in the English Channel off Roscoff was assessed every two weeks by sequencing the high resolution petB gene marker at the long-term coastal observatory SOMLIT-ASTAN station from July 1st 2009 to December 19th 2011.	root:Environmental:Aquatic:Marine
MGYS00006678	Dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea	"Here we report a comprehensive dataset covering spatiotemporal variations in prokaryotic and eukaryotic microbial communities and physicochemical parameters in the Baltic Sea. Within 13-months (Jan 2019-Feb 2020), we took 346 water samples during monthly cruises at 19 stations along the salinity gradient. We performed 16S and 18S DNA metabarcoding and microscopy based counting, and saw that both salinity and season are strongly reflected in the dataset. 
It provides unique opportunities for both technical and ecological analyses, and is valuable for both environmental monitoring and as a biodiversity reference for future studies, in the context of eutrophication and the prospect of climate change."	root:Environmental:Aquatic:Marine
MGYS00006676	Blanes Bay Microbial Observatory (BBMO) time-series 18S rRNA gene pico- and nano-plankton (10 years monthly samples)	This study includes 18S rRNA-gene sequences (V4 region) of pico- and nanoplankton from Blanes Bay Microbial Observatory (BBMO) monthly sampled during 10 years. It contains 120 pico-samples and 120 nano-samples.	root:Environmental:Aquatic:Marine:Coastal
MGYS00006675	16S rRNA gene amplicon time-series in Blanes Bay Microbial Observatory (BBMO)	This study includes 16S rRNA-gene sequences (V3-V4 region) of bacterioplankton monthly sampled from the Blanes Bay Microbial Observatory (BBMO). It contains 11 years of samples from the 0.22-3 μm  size fraction and 10 years from the 3-20 μm size fraction.	root:Environmental:Aquatic:Marine:Coastal
MGYS00006677	Bacterial diversity of marine planktonic size-fractionated samples	16S rRNA sequencing of a 2-years temporal serie in Blanes Bay Microbial Observatory.	root:Environmental:Aquatic:Marine:Coastal
MGYS00000335	Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis	Vulvovaginal candidiasis (VVC) is one of the most prevalent vaginal infectious diseases with controversial reports about the vaginal microbiota diversity. We determined the vaginal microbial community in patients with VVC, bacterial vaginiasis (BV), and mixed infection of VVC and BV using the Illumina sequencing of 16S rRNA tags. Our results revealed for the first time the highly variable patterns of the vaginal microbiome from VVC patients. In general, the alpha-diversity results of species richness and evenness showed an increased order from normal control, VVC only, mixed infection of BV and VVC, to BV. The beta-diversity comparison of community structures also showed an intermediate composition of VVC between the control and BV. Detailed comparison showed that while the control and BV communities had typical patterns, the vaginal microbiota of VVC is complex. The mixed BV and VVC infection group showed a unique pattern with relatively higher abundance of Lactobacillus than the BV group but higher abundance of Prevotella, Gardnerella, and Atopobium than the normal control. The VVC-only group, however, could not be described by any single profile. They spanned from a community structure similar to the normal control (predominated with Lactobacillus) to BV-like community structures (abundant with Gardnerella and Atopobium). Treatment of VVC showed inconsistent changes of vaginal microbiota, with four BV/VVC samples recovered to a higher Lactobacillus level while many VVC-only patients did not. These results will be useful for future study about the role of vaginal microbiota in VVC and related infectious diseases.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00001412	16S metabarcoding of bacteria associated with cultured strains of the brown alga Ectocarpus sp.	We examined the bacterial flora associated with 20 cultured strains of Ectocarpus sp. from different locations, and recorded both the bacterial diversity associated directly to the alga and that found in the culture medium. Experiments were carried out to amplify an approximately 400 bp fragment of the bacterial 16S comprising the V3 and V4 regions and sequenced on the Illumina MiSeq platform using V2 reagents ( 2x250 bp reads).	root:Host-associated:Algae:Brown Algae
MGYS00005333	EMG produced TPA metagenomics assembly of the Gut microbial dysbiosis in young adults with obesity (Gut microbial dysbiosis in young adults with obesity) data set.	The Gut microbial dysbiosis in young adults with obesity Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12123.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001538	Oil spill dispersant strategies and bioremediation efficientcy	After accidental oil spills to seawater from production or transport facilities the oil will be spread on the water surface and in the water column, and a number of weathering processes will appear. Typical operational methods to remove the oil from the sea surface include physical limitation of the surface spreading with booms and collection of the oil by skimmers. An alternative method to remove surfaced oil is to use chemical dispersants. These chemicals create a more hydrophilic oil surface, resulting in the generation of small droplets by wave actions, which are spread into the water column. The generation of small droplet dispersions may increase the natural biodegradation of the oil in the seawater column. Recently, dispersant methods have also been used for sub-surface oil spills (blow-outs). The Norwegian Research Council and several oil companies have funded this research project in order to improve our knowledge and understanding about the effects of dispersant strategies on oil biodegradation and the microbial communities and processes involved. The data from this project will contribute to the optimization of dispersant strategies. The project will include experimental studies simulating both surface and subsurface oil discharges. The focus will be molecular microbiology analyses and bioinformatics, including phylogenetic characterization of microbial communities (characterization of 16S rRNA genes) and investigations of biochemical pathways associated with degradation of alkanes and aromatic oil compounds. Metagenomic and metatranscriptomic studies may be expected to be part of this work. Finally, generated experimental data should be incorporated into OSCAR model, a industry standard model for predicting the fate of the oil in the marine water column after an accidental oil spill.	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
MGYS00004561	nifH gene in KH-11-10 and KH-13-7 cruises	This study aims to describe diazotroph community structure in the euphotic zone in the western and eastern subtropical South Pacific	root:Environmental:Aquatic:Marine
MGYS00002949	Baltic Sea	This is a 16S rRNA pyrosequencing study of ferruginous surface sediment samples collected from the Skagerrak (North Sea) and Bothnian Bay (Baltic Sea area).	root:Environmental:Aquatic:Marine:Sediment
MGYS00000793	Temperate forest soil Metagenome	The overall aims of this study were (1) to explore soil bacterial communities in four typical temperate forest types from Changbai Mountain (Broad-leaved Korean pine mixed forest, Secondary poplar-birch forest, Spruce-fir forest, and Larch forest) with newly developed bar-coded 454 pyrosequencing method; (2) to elucidate the biotic and abiotic factors controlling the abundance, diversity and composition of soil bacterial communities; (3) to test if the differentiation of soil bacterial communities in these temperate forests support the copiotroph/oligotroph functional classification model and the non-random co-occurrence patterns. This study will provide the first glimpse at the potential role of above-ground vegetation in allowing niche differentiation of soil bacterial communities in natural temperate forests situated in Changbai Mountain, and tries to reveal the intrinsic mechanism of such differentiation.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00003084	Marine metagenome ICM_AWP	Variation of Microplanktonic Communities Composition with Depth in an area under a Meddy Influence.	root:Environmental:Aquatic:Marine
MGYS00003008	Marine subseafloor sediment Targeted Locus (Loci)	We propose to apply 454-based tag pyrosequencing to investigate how microbial communities change with depth, lithology, and porewater geochemistry in the sediment that underlies one of the highest productivity regions in the world ocean. To accomplish this goal, we propose to analyze extracted DNA from 16 samples taken in high resolution in conjunction with detailed porewater geochemistry. This dataset will provide an unprecedented insight into the microbial ecology of a highly productive open ocean site (35 cm/k.y) to a sediment depth of 750 m and an age of 2.1 Ma. We anticipate that through this use of next-generation sequencing technology in combination with biogeochemical and cell count data sets collected during IODP expedition 323, we will obtain significant insight into this previously uncharted ecosystem.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002670	Macroalgal Morphology affects composition and settlement of microbial communities	Macroalgae (seaweeds) have an intimate relationship with their microbial symbionts. Microbial communities associated with macroalgal surfaces (epibiota) are generally host-specific and, historically, there has been great interest in the role of biological compounds and chemical warfare in  microbial community assembly on seaweeds. However, the interaction between seaweeds and their environment may also influence community assembly of their microbiota. In this experiment, I ask whether the interaction between water flow and seaweed morphology affects the settlement and structure of microbial biofilms. I test whether three common algal morphologies select for differential biofilm communities using artificial macro algae units (AM units) made out of latex. I find that morphology does affect initial microbial settlement and community structure, but that eventual dominance of substrate specialists (in our case, a latex degrader) swamps the influence of morphology in long-term biofilms.	root:Environmental:Aquatic:Marine
MGYS00001223	Interferon-lambda and interleukin-22 cooperate for the induction of interferon-stimulated genes and control of rotavirus infection	The epithelium is the major entry point for many viruses but the processes protecting barrier surfaces against viral infections are incompletely understood. We identify interleukin (IL)-22 produced by group 3 innate lymphoid cells (ILC3s) as an amplifier of interferon (IFN)-lambda signaling, a synergism required to curtail replication of rotavirus, the leading cause of childhood gastroenteritis. Cooperation between IL-22 and IFN-lambda receptors, both of which are preferentially expressed by intestinal epithelial cells, was required for optimal STAT1 transcription factor activation and expression of interferon-stimulated genes. This data suggests that epithelial cells are protected against virus replication by co-opting two evolutionarily related cytokine networks. These data may inform the design of novel immunotherapies of virus infections that are sensitive to IFNs.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00003985	Baselines Initiative 16S rRNA gene dataset: Baselines Amplicon Release 1 (R1) Caribbean Sea near Curacao (including saline pond samples in Curacao) 2015	The overall objective of this project (Baselines Initiative) is to generate several 16S rRNA gene databases to establish robust baseline information on the biological communities in marine ecosystems. This field study was conducted in the Caribbean Sea near Curacao (and saline ponds in Curacao as well) in April 2015 to examine phytoplankton community diversity.	root:Environmental:Aquatic:Marine
MGYS00001789	Amplicon sequencing of Tara Oceans RNA samples corresponding to size fractions for protists.	Analysis of RNA tags in Tara Oceans Protists size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small and large cell sizes. The RNA was extracted, cDNA prepared then amplified by PCR.	root:Environmental:Aquatic:Marine
MGYS00004246	Successional trajectories of coastal bacterioplankton communities in response to co-exposure of cadmium and phenanthrene	Coexistence of multiple contaminants in coastal aquatic ecosystems can lead to complicated circumstances in ecotoxicological assessment for biological communities due to potential interaction between contaminants. We chose cadmium (Cd) and phenanthrene (PHE) as representatives of heavy metals and polycyclic aromatic hydrocarbons, respectively. Contamination process was mimicked using coastal water microcosms contaminated by Cd (1 mg/L), PHE (1 mg/L), and their mixture over two weeks.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002449	Nuunat- ORMS formation during oil biodegradation at low temperature	Biodegradation study of chemically dispersed oil and ORMS formation in cold local (5C) Norwegian seawater over 64 days incubation period containing natural microbial community and selected diatom population of Fragilariopsis cylindrus.	root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
MGYS00005230	Flores_fecal_EBI	Fecal samples from Flores_SMP for EBI submission	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002121	PETROMAKS E#9	Biodegradation study was conducted with two different oils (naphthenic and asphaltenic) at two different temperatures (5C and 13C). The aim of the study was to evaluate differences in biodegradation and microbial community dynamics between two oils at different temperatures.	root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
MGYS00004077	"Planktonic bacterial communities in the arctic Canada Basin and
                Kongsfjorden"	"Planktonic bacteria play key role in biogeochemical cycles and energy
                flow in marine ecosystems. However, our knowledge of the extent and character of
                bacterial diversity in polar marine environments is still limited. Here we present
                the use of high throughput DNA pyrosequencing and statistical inference to assess
                the diversity of planktonic bacteria in the arctic Canada Basin, and Kongsfjorden in
                Spitsbergen. The V3 region of the 16S rRNA gene was amplified from seawater samples
                collected from the upper water column. The number of bacterial 16S rRNA sequences
                obtained from each sites varied from 7433 to 9218. In the Canada Basin, the most
                abundant bacterial groups in two sites of water at 10m depth were the Proteobacteria
                (mainly Alphaproteobacteria), Actinobacteria, Bacteroidetes and Cyanobacteria.
                Different bacterial communities were observed in the deeper water (80 or 100m depth)
                at the two sites. The Proteobacteria and Bacteroidetes also formed the dominant
                bacterial groups in surface water of Kongsfjorden. However, Gammaproteobacteria
                accounted for more than 90% of the Proteobacteria."	root:Environmental:Aquatic:Marine
MGYS00004040	marine sediment metagenome Targeted Locus (Loci)	Site U1387 offers a chance to study the response of microbial assemblage to specific seafloor events such as contourite depositions, changes in bottom current energy, shifts in organic matter deposition rates, and geochemical changes that are representative of seafloor processes during rapid climate change.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004148	Microbial community structures of chimney in DODO and Solitaire hydrothermal fields	Difference of microbial diversity by the 16S rRNA gene in chimney structures between two hydrothermal fields on central Indian Ridge.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00006674	WGS of bacterial strains from food industry	In this study, strains were isolated from different points of the food industry and characterized by classical microbiological methods. DNA was then extracted and sequenced by shotgun technology to assess metabolic potential.	root:Engineered:Food production
MGYS00006670	EMG produced TPA metagenomics assembly of PRJEB31095 data set (The intestinal microbiome from two ecotypes of Atlantic cod and three additional Gadidae species.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB31095, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system:Intestine.	root:Host-associated:Fish:Digestive system:Intestine
MGYS00006672	EMG produced TPA metagenomics assembly of PRJNA482836 data set (Gut microbiome from Piaractus mesopotamicus Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA482836, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.	root:Host-associated:Fish:Digestive system
MGYS00006673	EMG produced TPA metagenomics assembly of PRJEB42464 data set (Gut Microbiomes of European Farm Rainbow Trout).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB42464, and was assembled with megahit v1.2.9, metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.	root:Host-associated:Fish:Digestive system
MGYS00006671	EMG produced TPA metagenomics assembly of PRJEB19833 data set (Mid- and hind-gut of rainbow trout gastrointestinal tract (GIT) fed alternative protein diet).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19833, and was assembled with metaSPAdes v3.15.3, megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.	root:Host-associated:Fish:Digestive system
MGYS00006668	EMG produced TPA metagenomics assembly of PRJNA663846 data set (Metagenomic analysis of stomach contents of Acanthopagrus latus).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA663846, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.	root:Host-associated:Fish:Digestive system
MGYS00006666	EMG produced TPA metagenomics assembly of PRJEB29346 data set (Metagenomic shotgun sequencing of the Atlantic cod intestinal microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB29346, and was assembled with unknown v0.0. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system:Intestine.	root:Host-associated:Fish:Digestive system:Intestine
MGYS00006669	EMG produced TPA metagenomics assembly of PRJEB19785 data set (Metagenomics of the mid- and hind-gut of rainbow trout gastrointestinal tract (GIT) fed alternative protein diets).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19785, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.	root:Host-associated:Fish:Digestive system
MGYS00006667	EMG produced TPA metagenomics assembly of PRJNA434147 data set (Delta Smelt gut content study).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA434147, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.	root:Host-associated:Fish:Digestive system
MGYS00006664	EMG produced TPA metagenomics assembly of PRJEB30661 data set (TO INVESTIGATE THE MICROBIAL COMMUNITY ASSOCIATED WITH FISH GUT).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB30661, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.	root:Host-associated:Fish:Digestive system
MGYS00006665	EMG produced TPA metagenomics assembly of PRJNA433811 data set (shotgun metagenome sequencing salmo salar gut microbiota).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA433811, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.	root:Host-associated:Fish:Digestive system
MGYS00006663	EMG produced TPA metagenomics assembly of PRJNA506751 data set (Puffer fish gut Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA506751, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.	root:Host-associated:Fish:Digestive system
MGYS00002675	EMG produced TPA metagenomics assembly of the Oral microbiome Metagenome (human oral metagenome) data set.	The human oral metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA255922.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00006028	Bio-GO-SHIP: Global marine 'omics studies of repeat hydrography transects	"The Global Ocean Shipboard Hydrographic Investigations Program (GO-SHIP) is a ship-based global survey of ocean hydrographic sections, which are repeatedly measured on a decadal time scale. The program covers a suite of physical (light, heat, currents, water column structure, etc.) and chemical (nutrients, oxygen, dissolved organic and inorganic carbon, pH, etc.) state variables over the full ocean water column, and in areas of the ocean inaccessible to other platforms. The principal scientific objectives for GO-SHIP are: (1) understanding and documenting the large-scale ocean water property distributions, their changes, and drivers of those changes, and (2) addressing questions of how a future ocean will increase in dissolved inorganic carbon, become more acidified and more stratified, and experience changes in circulation and ventilation processes due to global warming and altered water cycle.The vision of the biological GO-SHIP initiative, or ""Bio-GO-SHIP,"" is to develop a deep understanding of the link between the physio-chemical environment and global ocean plankton diversity, abundance, and biogeochemical roles in the context of a changing ocean. This will be achieved through systematic, high-quality, and calibrated sampling of marine 'omics products.In this BioProject, we aim to provide a singular resource for Bio-GO-SHIP 'omics datasets. We also provide appropriate metadata such that the 'omics data may be linked to the broad range of state variables measured by GO-SHIP and associated oceanographic transects."	root:Environmental:Aquatic:Marine
MGYS00005851	metabarcoding of eDNAbyss sediment samples	Sediments were collected using multicore sampler, or simple cores when a submarine or a remote operated vehicle (ROV) were present. The cores were collected and sliced according to sediment depth and using a standardized scheme. Slices were preserved and treated individually. When hard substrate was collected, the gear ELFES designed on purpose to scratch and collect the surface of substrate, or bulk samples were retained after sieving communities. Nucleic acids (DNA or RNA) were extracted and submitted to a PCR-ligation protocols using 6 sets of primers pairs targeting metazoans (2 primer pairs targeting a fragment of Cytochrome Oxydase I and one of rDNA18S V1-V2), microeukaryotes (2 primer pairs targeting rDNA 18S V4 and V9) and prokaryotes (2 sets of primer pairs targeting rDNA16S V4-V5 respectively defined for prokaryotes in general, and archaebacterial in particular).	root:Environmental:Aquatic:Marine:Sediment
MGYS00006281	Metagenomes from an Argentine salt flat	Analysis of assembled metagenomes from an Argentine salt flat	root:Environmental:Terrestrial:Soil
MGYS00006069	EMG produced TPA metagenomics assembly of PRJEB11419 data set (American Gut Project).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11419, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human.	root:Host-associated:Human
MGYS00006006	Extensive microbial novelty in the Hadza and Nepali gut microbiome reveals how lifestyle impacts composition and function	The gut microbiome has been identified as a key to immune and metabolic health, especially in industrialized populations. Non-industrialized individuals harbor more diverse microbiomes and distinct bacterial lineages, but systemic under-sampling has hindered insight into the extent and functional consequences of these differences. Here, we performed ultra-deep metagenomic sequencing and laboratory strain isolation on fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophage, and eukaryotes, and find that 43% are novel upon aggregating with existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, and high-resolution strain tracking reveal dynamics in the hunter-gatherer gut microbiome that are distinct from industrialized populations. Industrialized versus Hadza gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. We use phylogenomics to reveal that global spread of the spirochaete Treponema succinifaciens parallels historic human migration prior to its extinction in industrialized populations. When combined with a detailed definition of gut-resident strains that are vanishing in industrialized populations, our data demonstrate extensive perturbation in many facets of the gut microbiome brought on by the industrialized lifestyle.	root:Host-associated:Human:Digestive system
MGYS00002061	EMG produced TPA metagenomics assembly of the Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn''s disease (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA321058. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000633	Microbial composition of samples from infant gut	The microbial composition of the gut likely contributes to a wide-range of health and disease states including intestinal inflammation, atopic disease, and possibly diseases of adulthood, such as heart disease and obesity. The early establishment of the gut microflora is suspected to have a particularly profound impact protecting the gut from infectious disease and on long-term subsequent health by predisposing individuals to atopic or autoimmune disease later in life. In contrast to the large-scale efforts of the Human Microbiome Project to characterize the microbial flora of healthy adults, relatively little has been accomplished to characterize the early establishment of the microbiota in infants.  The administration of antibiotics to infants has the capacity to profoundly affect the early acquisition, establishment, and natural maturation of commensal microflora. Prematurity is another major factor that is thought to influence 'normal' gut microbial composition in early life. A high number of pre-term infants receive antibiotic therapy prophylactically; the immediate and long-term effects of antibiotic treatment on infant and later health outcomes are unknown. We hypothesize that gestational age influences the ability to support 'normal' gut microbiota, and that antibiotic administration in the first few weeks of life can alter or delay the development of a 'normal' microbiota and may lead to adverse health outcomes. If we hope to promote the healthy establishment of early gut colonization and thereby improve health outcomes, we need to establish what 'normal' colonization looks like across gestational ages and apply this knowledge as a benchmark to understand the impact of antibiotic treatment in early postnatal life.  In this project, we propose to examine the microbiome in four cohorts ranging from extremely preterm to term, with birth weights appropriate for gestational age: Group 1) 23 to 27 weeks and extremely low birth weight [ELBW, <1000 grams]; Group 2) 28 to 32 weeks and very low birth weight [VLBW, >1000 to <1500 grams]; Group 3) 33 to 36 weeks and low birth weight [LBW, >1500 to <2500 grams]; and Group 4) term (37 to 42 weeks) and normal [>2500 to <4000 gram] birth weight. The infant gut microbiome will be assessed longitudinally in study infants from the first postnatal week to 18 months of age, and will include untreated and antibiotic-treated infants.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00002529	Dark ocean microbial diversity	The goal of the study is to assess the diversity of bacteria and archaea in the water masses of the open ocean.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00001036	16S rRNA gene sequences from temperate soils Targeted Locus (Loci)	Both climate and pH are key in determining soil archaeal community structure and diversity	root:Environmental:Terrestrial:Soil
MGYS00004597	Peru margin subsurface	Investigation of the microbial diversity in subsurface sediments of Peru margin	root:Environmental:Aquatic:Marine:Sediment
MGYS00002238	Oral microbial changes in ASD children	This project depicts the characteristics of oral microbiome in autistic children.	root:Host-associated:Human:Digestive system:Oral
MGYS00000716	structural analysis of microbial community for feild soil and compost made from coffee lees	Our final end is to change organic agriculture to matter production system based on scientific basis by stationary measurement of soil microbial community.This year,We analyze bacteria and fungi community at feild soil fertilized by compost made from coffee lees.We also analyze compost made from coffee lees.	root:Environmental:Terrestrial:Soil
MGYS00001656	Universal metabarcoding of pico- mesoplankton reveals seasonal dynamics and a bacterial bloom	Most studies of biodiversity focus on either macroscopic or microbial communities, with little or no simultaneous study of eukaryotes and prokaryotes. We tested whether a universal metabarcoding approach could be used to study the total diversity and temporal dynamics of aquatic pico- to mesoplankton communities in a shallow temperate lake. The approach revealed significant changes in the relative abundance of eukaryotic and prokaryotic plankton communities over a period of three months. These patterns, based on sequencing reads, fit with counts using traditional methods. We also witnessed the bloom of a conditionally rare bacterial taxon belonging to Arcicella, a genus that has been largely overlooked in freshwaters. Our data demonstrate the potential of universal metabarcoding as a complement to traditional studies of plankton communities, and for long-term monitoring across a broad range of organisms.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00002810	peptide incubation in GOM C6 seawater bacteria Metagenome	Study bacteria community changes in the peptide decomposition in different seawater	root:Environmental:Aquatic:Marine
MGYS00002567	Biogeography of pelagic bacterioplankton across an antagonistic temperature-salinity gradient in the Red Sea	The Red Sea is a unique marine ecosystem with contrasting gradients of temperature and salinity along its north to south axis. It is an extremely oligotrophic environment that is characterized by perpetual year-round water column stratification, high annual solar irradiation, and negligible riverine and precipitation inputs. In this study, we investigated whether the contemporary environmental conditions shape community assemblages by pyrosequencing 16S rRNA genes of bacteria in surface water samples collected from the northeastern half of this water body. A combined total of 1,855 operational taxonomic units (OTUs) were recovered as free-living and particle-attached bacterioplankton. Here, a few major OTUs affiliated with Cyanobacteria and Proteobacteria accounted for ~93% of all sequences whereas a tail of “rare” OTUs represented most of the diversity. OTUs allied to Surface 1a/b SAR11 clades and Prochlorococcus related to the high light-adapted (HL2) ecotype were the most widespread and predominant sequence types. Interestingly, the frequency of taxa that are typically found in the upper mesopelagic zone was significantly elevated in the northern transects compared to those in the central, presumably as a direct effect of deep convective mixing in the Gulf of Aqaba and waters exchange with the northern Red. Although temperature was the best predictor of species richness across all major lineages, both spatial and environmental distances correlated strongly with genetic distances. Our results suggest that the bacterial diversity of the Red Sea is as high as in other tropical seas and provide evidence for fundamental differences in the biogeography of pelagic communities between the northern and central regions.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00000710	Alwernia Metagenome	Pyrosequencing of V3-V4 16S rRNA gene fragments amplified from metagenomic DNA isolated from heavy metals-contaminated soils collected near chromium green-producing facility in Alwernia, Poland.  Two samples of soils from Alwernia, Poland, collected at the vicinity of chromium green-producing factory.	root:Environmental:Terrestrial:Soil
MGYS00003004	Submarine Ligurian Canyons Water Prokaryotic and Protist Communities	Planktonic prokaryote communities in a submarine canyon system in the Ligurian Sea (NW Mediterranean)	root:Environmental:Aquatic:Marine
MGYS00004596	Marine sediment in Arctic Raw sequence reads	This study assessed the diversity and distribution of fungal communities associated with marine sediments in Arctic.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002552	North Pacific Subtropical Gyre Microbial Community	16S amplicon libraries were collected as a portion of the Seasonal and decadal changes in temperature drive Prochlorococcus ecotype distribution patterns, also known as Prochlorococcus of Warming Ocean Waters (POWOW) Cruise series. The samples were collected in January 2013 (KM1301) and July 2013 (KM1312) in the Eastern North Pacific Ocean. The goal of this project was to characterize ecosystem scale changes associated with shifts in temperature.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00003089	Marine metagenome ICM_JRV	Microeukaryote diversity in the Gulf of Maine: Under-explored microbial diversity in a well-studied coastal marine ecosystem.	root:Environmental:Aquatic:Marine:Coastal
MGYS00003115	Diversity and structure of benthic bacterial community from South-Eastern Pacific Ocean, Targeted Locus (Loci)	Assessing diversity and structure of sediment microbial communities under the influence of the oxygen minimum zone of an Eastern Boundary Current ecosystem: the Humboldt marine ecosystem	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00006562	EMG produced TPA metagenomics assembly of PRJEB54673 data set (Paediatric Oral Microbiome).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB54673, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00006660	Picoplankton 16S rRNA gene sequences (DNA and RNA) from Vertical Profiles (surface to 4000m depth) sampled during the Malaspina 2010 circumglobal expedition	The study here includes 182 samples (91 DNA and 91 RNA) of the 16S from the Malaspina-2010 expedition. The samples were sequenced using Illumina MiSeq 2x250bp.	root:Environmental:Aquatic:Marine
MGYS00006659	Amplicon 18S rRNA Illumina TAGs from Malaspina Bathypelagic samples	"Bathypelagic samples collected during the global
circumnavigation Expedition Malaspina 2010 were generated by
amplifying the 18S rRNA gene
using primers XXXXX and XXXX. Sequencing was performed in an Illumina
MiSeq platform (iTAGs) using 2x250 bp paired-end approach at
Genoscope. The data generated has been used mainly to describe the
eukaryotic diversity from bathypelagic samples and describe its
biogeography."	root:Environmental:Aquatic:Marine
MGYS00006658	Amplicon 16S rRNA Illumina TAGs from Malaspina Bathypelagic samples	"Bathypelagic samples collected during the global
circumnavigation Expedition Malaspina 2010 were generated by
amplifying the V4 and V5 hypervariable regions of the 16S rRNA gene
using primers 515F-Y (5’-GTGYCAGCMGCCGCGGTAA-3’) and 926R
(5′-CCGYCAATTYMTTTRAGTTT-3′). Sequencing was performed in an Illumina
MiSeq platform (iTAGs) using 2x250 bp paired-end approach at
Genoscope. The data generated has been used mainly to describe the
bacterial diversity from bathypelagic samples and describe its
biogeography."	root:Environmental:Aquatic:Marine
MGYS00002392	Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for protists.	Analysis of 18S DNA in Tara Oceans Protists size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small and large cell sizes. The DNA was extracted and amplified by PCR.	root:Environmental:Aquatic:Marine
MGYS00004011	Microbial communities of methane seeps in shallow, porous sands off Elba	The methane cold seeps near Pomonte (Elba) are unique ecosystems situated in very shallow and porous coastal sands. We investigated the influence on hydrodynamics on microbial community structure and function. Understanding these ecosystems is important to estimate their role in carbon cycling and their emission of methane to the atmosphere.	root:Environmental:Aquatic:Marine:Sediment
MGYS00000988	Global fungal diversity	This is a global dataset of unprecedented scope to disentangle the relative roles of climatic, edaphic, floristic, and spatial variables governing global-scale patterns of soil fungal diversity. We also address key macro-ecological phenomena such as latitudinal gradients of diversity and Rapoport’s rule (expansion of species’ latitudinal range with increasing latitude) as well as cross-biome and cross-continental biogeographic relationships in multiple phylogenetic and functional groups of fungi.	root:Environmental:Terrestrial:Soil
MGYS00001509	Diversity of Pico- to Mesoplankton Along the 2000 km Salinity Gradient of the Baltic Sea	Microscopic plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. Next Generation Sequencing (NGS) of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 105 sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but also novel groups to the Baltic were observed, such as relatives to the coccolithophore Emiliana huxleyi in the northern Baltic Sea. The deep sequencing also enabled accurate enumeration of highly resolved (> 99% identity) operational taxonomic units, which revealed contrasting distribution profiles among closely related populations, reflecting niche partitioning into ecotypes. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.	root:Environmental:Aquatic:Marine
MGYS00004228	marine sediment metagenome Genome sequencing and assembly	To share species we detected in the South China Sea	root:Environmental:Aquatic:Marine:Sediment
MGYS00003016	Distinctive community structure and high diversity in particle-associated prokaryotes in tropical and subtropical Pacific Ocean surface seawater	The specific aim of this project was to determine bacterial and archaeal community structures in the PA assemblage in comparison to the free-living (FL) assemblage in the tropical and subtropical Pacific Ocean.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00003989	Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the Western Antarctic Peninsula	The classic view of polar ocean foodwebs emphasizes large predators sustained by energy and materials flow through short, efficient diatom-krill-predator food chains. Bacterial activity is generally low in cold polar waters compared to lower latitudes. This view appears to be changing, with new studies of microbial foodwebs in Arctic and Antarctic oceans. We characterized bacterial, archaeal, and eukaryotic community diversity and composition from two depths (near surface and below the euphotic zone) at four sites, including the inshore and offshore, and north and south corners of a sampling grid along the western coast of the Antarctic Peninsula (WAP). We detected up to 2-fold higher richness in microbial eukaryotes at surface and deep inshore northern stations as compared to southern ones but offshore northern and southern stations revealed either no trend or higher richness at depth in the south. In contrast, bacterial and archaeal richness showed no significant differences either inshore or offshore at northern versus southern extents but did vary with depth. Archaea were virtually absent in summer surface waters but were present in summer deep and winter surface samples. Overall, winter bacterial and archaeal assemblages most closely resembled summer sub-euphotic zone assemblages, reflecting well-established seasonal patterns of water column turnover and stratification that result in an isolated layer of “winter water” below the euphotic zone. Inter-domain heterotroph-phototroph interactions were evident from network analysis. The WAP is among the most rapidly warming regions on earth. Our results provide a baseline against which future change in microbial communities may be assessed.	root:Environmental:Aquatic:Marine
MGYS00004213	Abalone seed nursing ecosystem Metagenome	In this study, using abalone seed nursing pond as a model system, we separately collected the time-series samples of three	root:Environmental:Aquatic:Marine
MGYS00001536	Habitat diversity and ecosystem multifunctionality - the importance of direct and indirect effects	Ecosystems worldwide are facing habitat homogenization due to human activities. While it is commonly proposed that such homogenization can have negative repercussions for ecosystem functioning, this remains to be explicitly studied. Here, we expand on the framework for the functional consequences of biodiversity loss, by scaling up from the level of species to the level of entire habitats. Just as species diversity generally begets ecosystem functioning through positive interactions, we hypothesize that different habitats within ecosystems can facilitate each other through structural complementarity and by the exchange of material and energy. We show that experimental ecosystems constituted by a diversity of habitats have higher levels of multiple ecosystem functions compared to ecosystems with low habitat diversity. The effect of habitat diversity on multifunctionality varied with season; it was direct in summer, indirect via changes in species diversity in autumn, whereas there was no effect in spring. We propose that jointly considering habitat and species diversity will prove valuable for both research and environmental management.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00000818	Hydrocarbon polluted soil Targeted Locus (Loci)	The aim of the study was to determine the microbial diversity in soil from a landfarming site amended with hydrocarbon contaminants. To determine the microbial diversity amplicon pyrosequencing was used of different regions of the 16S rRNA gene.	root:Environmental:Terrestrial:Soil
MGYS00004112	Marine metagenome ICM_CNE	Temporal Dynamics of Coastal Bacterioplankton	root:Environmental:Aquatic:Marine
MGYS00001476	Comparison of limnic and marine particle-associated microbial communities	Marine and limnic particles are hotspots of organic matter mineralization significantly affecting biogeochemical element cycling. Fluorescence in-situ hybridization with rRNA-targeted probes and tag pyrosequencing of 16S rRNA genes were combined to investigate bacterial diversity and community composition on limnic and coastal marine particles, defined operationally by a diameter of >5 and >10 μm, respectively. Samples were obtained from Lake Stechlin and Grosse Fuchskuhle, the Adriatic Sea and the North Sea. On average, particle abundance was higher in limnic (1×107 L-1) than in marine systems. Whereas limnic particles were smaller in size (average areas of 471 vs. 2050 μm2), they were more densely colonized compared to marine ones (average bacterial densities of 7.3 vs. 3.6 cells per 100 μm2). Therefore, particle-associated (PA) bacteria accounted on average for a larger fraction of total bacteria in limnic (15%) than in marine environments (4%). Unlike previously suggested limnic PA bacteria harbored beyond Alphaproteobacteria and Betaproteobacteria sizeable populations of Gammaproteobacteria, Actinobacteria and Bacteroidetes. Marine particles were colonized by Planctomycetes and Betaproteobacteria additionally to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. PA bacteria were in 2/3 of the cases more diverse than free-living (FL) bacteria. Accordingly, we propose a new index to characterize particle colonization based on the PA/FL Chao1 diversity index ratio. Large heterogeneities in individual particle colonization could be shown. However, high-throughput sequencing revealed significant overlap between PA and FL communities and thus highlights an underestimated connectivity between these fractions. Overall, despite seemingly similar ecological niches our study found large differences between limnic and marine PA communities.	root:Environmental:Aquatic:Marine
MGYS00002546	Pelagic Gulf of Mexico Targeted loci environmental	Methane and microbial dynamics in the Gulf of Mexico water column	root:Environmental:Aquatic:Marine:Pelagic
MGYS00002584	Marine Sediment from the Berkeley Bay Targeted Locus (Loci)	Community analysis (16S) of a marine samples enriched with perchlorate	root:Environmental:Aquatic:Marine:Sediment
MGYS00001658	Vertical organization of freshwater sediment microbial communities: implications for microbial activities and burial processes	Microbial activity in lake sediments plays a key role in the cycling of nutrients and organic matter that continuously sink from water columns. As organic matter accumulates at the sediment surface, upper sediment layers become buried, resulting in a decrease in microbial activity and cell turnover rate with increasing depth. To better understand the structure of freshwater sediment communities and how the burial processes influence it, we quantified the distribution of a broad range of environmental parameters and the community structure of microbial archaea, bacteria, and eukaryotes in the sediments of a clear, temperate lake. Our findings suggest that the two uppermost horizons of the sediment community, which cover approximately the last 70 years, are characterized by a high taxa replacement influenced by “present” environmental parameters. Richness effects became increasingly important in the lowest studied horizon (14-30 cm, age 70-150 a) and could be readily explained by conservative “past” environmental parameters. The lowest horizon is also characterized by a switch in dominance toward archaea, as has been found in marine sediments. Our pioneering study shows that the freshwater lake's community structure, taxa, and vertical arrangement share many features previously observed for marine sediments.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00002775	Amundsen Gulf Overwintering Eukaryote Community	Year-long time series of eukaryote community in Amundsen Gulf, Arctic Ocean	root:Environmental:Aquatic:Marine
MGYS00004496	Enrichment of abundant sedimentary Bathyarchaeota demonstrating organoautotrophic metabolic capabilities	metabolic capabilities of Bathyarchaeota	root:Environmental:Aquatic:Marine
MGYS00004176	Evaluation of filtration and DNA extraction methods for environmental DNA biodiversity assessments across multiple trophic levels.	Methods evaluation for sample collection and nucleic acid extraction from multiple trophic levels simultaneously (i.e. bacteria, phytoplankton, zooplankton, vertebrates). Specifically, filter types and DNA extraction kits were evaluated for producing Illumina MiSeq reads for 12S, 16S and 18S amplicons from water samples collected in Monterey Bay California.	root:Environmental:Aquatic:Marine
MGYS00003006	A study on microbial functional groups producing a climate related gas in the ocean	Dimethylsulfoniopropionate (DMSP), the precursor of dimethyl sulfide (DMS), is mainly produced by marine phytoplankton, and is one of the most important sulfur and carbon sources for marine bacteria. To reveal the abundance and distribution of bacterial DMSP-degrading genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we performed deep sequencing of environmental DNA obtained from DMS hotspot samples in the Pacific Ocean.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004160	uncultured bacterium Targeted Locus (Loci)	The bacterial community at 2,000-m depth was studied over one-year survey in 2011 at the ANTARES site (Northwestern Mediterranean Sea). The most active member were analysed in October and May through ribosomal diversity.	root:Environmental:Aquatic:Marine
MGYS00001224	TRIF signalling drives homeostatic intestinal epithelial antimicrobial peptide expression	Recent results indicate a significant contribution of innate immune signalling to maintain mucosal homeostasis but the precise underlying signal transduction pathways are ill-defined. By comparative analysis of intestinal epithelial cells isolated from conventionally raised and germ-free mice as well as animals deficient in the adaptor molecules MyD88 and TRIF, the Toll-like receptors (TLR) 3 and 4, as well as the type I and III interferon (IFN) receptors, we demonstrate significant TLR-mediated signalling under homeostatic conditions. Surprisingly, homeostatic expression of Reg3γ and Paneth cell enteric antimicrobial peptides critically relied on TRIF and in part TLR3 but was independent of IFN receptor signalling. Reduced antimicrobial peptide expression was associated with signicantly lower numbers of Paneth cells and a reduced Paneth cell maturation and differentiation factor expression in TRIF mutant compared to wildtype epithelium. This phenotype was not transferred to TRIF sufficient germ-free animals during cohousing. Low antimicrobial peptide expression in TRIF deficient mice caused reduced immediate killing of orally administered bacteria but was not associated with significant alterations in the overall composition of the enteric microbiota. The phenotype was rapidly restored in a TRIF-independent fashion after transient epithelial damage. Our results identify TRIF signalling as truly homeostatic pathway to maintain intestinal epithelial barrier function revealing fundamental differences in the innate immune signalling between mucosal homeostasis and tissue repair.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00002510	Hatteras return: Oligotrich and choreotrich ciliates diversity at small scales	Hatteras return: diversity and community composition of Oligotrich and choreotrich ciliates at small scales (1-3 km) off the New England coast	root:Environmental:Aquatic:Marine
MGYS00004565	Coral metagenome ICM_CCB	Exploring the microbial diversity and testing co-evolutionary hypotheses in Caribbean coral species using a 454-tag sequencing approach.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00005716	Metabarcoding of eDNAbyss water samples	Water from different depths was prefiltered in situ using Salsa pump or collected in CTD bottled before being filtered onboard to retain small cell sizes or nucleic acids (DNA/RNA). Nucleic acids were extracted from filters and submitted to a PCR-ligation protocols using 6 sets of primers pairs targeting metazoans (2 primer pairs targeting a fragment of Cytochrome Oxydase I and one of rDNA18S V1-V2), microeukaryotes (2 primer pairs targeting rDNA 18S V4 and V9) and prokaryotes (2 sets of primer pairs targeting rDNA16S V4-V5 respectively defined for prokaryotes in general, and archaebacterial in particular).	root:Environmental:Aquatic:Marine
MGYS00004038	Uncultured Microbial Consortia in Industrialized Sites on Egypt''s Red Sea Coast Targeted loci environmental	Egypt''s Red Sea Coast: Phylogenetic Analysis of Uncultured Microbial Consortia in Industrialized Sites	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004190	Oxic sediment - Microbial Metagenome	SSU 16S pyrosequencing project of the microbial metagenome of an oxic deep-sea sediment from the Eastern Mediterranean.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004320	Sediment bacterial 16S in Hachiro polder.	Sediment bacterial 16S ribosomal RNA gene from surface to depth 30 m at hot spots of high concentration phosphate water springs in Hachiro polder.	root:Environmental:Aquatic:Marine:Sediment
MGYS00005115	Microbes in drinking water and biofilms (18S rDNA amplicon study)	18S rDNA amplicon study of bulk water and shower hose biofilm samples. Cold water samples were collected from the water outlet of a drinking water treatment plant and from the water inlet of two neighboring buildings, warm water samples (ca 37 degrees C) were taken from showers within the two buildings: one building with a copper-silver-ionization-system to disinfect the water, the other building without such a system. Biofilms were taken from shower hoses within the two buildings. For further experimental details see: Stüken et al. 2018. Environ Sci Technol.;52(6):3354-3364. doi: 10.1021/acs.est.7b0596318S rDNA amplicons were generated with forward primer 1391F (GTA CAC ACC GCC CGTC) and reverse primer 1510R (CCT TCY GCA GGT TCA CCT AC). AdapterRemoval ver 2.3.0 and cutadapt vers. 1.18. were used to prepare samples for sequence submission (removal of remaining Illumina adapters, demultiplexing, removal of heterogeneity spacers, primers, low quality bases and sequences < 50 bp lengths).	root:Environmental:Aquatic:Freshwater
MGYS00002605	Mariana and Kermadec Trench sediment 16S rRNA gene sequencing	This project studies the microbial communities within the Mariana and Kermadec trenches as a function of trench, sediment, and water depth using 16S rRNA gene sequencing.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003015	Protists tag sequencing of 18S rRNA HV 9	First comprehensive description of protist community diversity in meso- bathypelagic regions of the Ross Sea (Antarctica)	root:Environmental:Aquatic:Marine
MGYS00003118	Diversity and abundance of Bathyarchaeota (MCG) in South China Sea sediments and the implication of its ecological roles	understand the niche separation and adaptation of different bathyarchaeotal subgroups.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002818	Seawater Targeted Locus (Loci)	We applied culture-independent, high throughput pyrosequencing to characterize the microbial communities associated with coastal seawater adjacent to populated Broward County, FL. These waters flow over adjacent coral reefs, which help compose the Florida reef tract, and also close to recreational beaches. In partnership with the NOAA FACE program to survey water quality, 38 total nearshore seawater samples were collected and characterized for bacterial populations from 6 distinct coastal locales - the Port Everglades and Hillsboro Inlets, Hollywood and Broward wastewater outfalls, and associated reef waters over the course of one year. More than 227,000 quality checked 16S rRNA V4 amplicon sequences were generated for longitudinal taxonomic profiles of marine bacteria and archaea. From these sequences, 4447 unique OTUs were found and there was a mean OTU count of 5986.816 across all site. Sequences were found to vary significantly due to seasonal effects and by site, but depth showed no significant correlation. Abundant microbial taxa across all samples included Synechococcus, Pelagibacteraceae, Bacteroidetes, and various Proteobacteria. Inlet-based communities significantly differed from outfall and reef communities, with a relative increase in Rhodobacteraceae and Cryomorphaceae, and depletion of SAR406 sequences. Unifrac analysis confirmed significant differences in the inlet populations relative to reef and outfall microbial communities. However, based on alpha diversity measurements, the outfalls sites showed the most diversity with the occurrence of Thiotrichales, Alteromonadales, and the archaean Thermoplasmata. This study also found increased levels of Firmicutes, Chloroflexi, and sludge associated bacterial OTUs such as SBR1093 at the outfall and reef sites.	root:Environmental:Aquatic:Marine:Coastal
MGYS00001560	THERMOPHILIC HYDROGEN PRODUCTION IN ACIDOGENIC PACKED BED REACTOR (APBR) FED WITH SUGARCANE VINASSE: PERFORMANCE DURING LONG-TERM OPERATION	This study aimed to evaluate the long-term operation of an up-flow anaerobic packed bed reactor (APBR) filled with low-density of polyethylene (LDP) and applied to thermophilic hydrogen production using sugarcane vinasse as substrate. The APBR was operated at organic loading rate (OLR) of 84.2 kg-COD.m-3.d-1, value determined in earlier study. The maximum values of hydrogen production and yield were 5,252.6 mL-H2.d-1 and 3.7 mol-H2.mol-1total carbohydrates, respectively. However, as the OLR applied was constant, the values of specific organic load rate (sOLR) decreased throughout operation from values from 1.38 to 0.72 g-Total carbohydrates.g-VS-1.h-1, thus, interfering negatively on hydrogen production. sOLR values around 1.22 g-Total carbohydrates.g-VS-1.h-1 indicated optimal conditions for hydrogen production. The microbial community was study by 454-pyrosequencing analysis. Organisms belonging to genera Caloramotor, Clostridium, Thermoanaerobacterium, Thermohydrogenium, Caldanaerobius and Megasphaera were detected in samples taken from reactor at days 30 and 60 of operation, suggesting a role in the hydrogen production.	root:Engineered:Bioreactor:Continuous culture
MGYS00002702	Metagenomic sequence from soil bacteria	This data contains metagenomic 16S rDNA sequence of soil bacteria. 16S rDNA sequence was amplified according to illumina protocol. The aim of this project is to analyze bacterial flora.	root:Environmental:Terrestrial:Soil
MGYS00004050	Prince Edward Island marine metgenome Raw sequence reads	Marine and terrestrial ecosystems of the Prince Edward islands (PEIs) are reciprocally connected and any changes in the community composition of one ecosystem will directly influence the other. In the present study, we investigated the pelagic marine microbial community structure (Bacteria, Phytoplankton and Archaea) and dynamics in the PEIs inshore coastline by high throughput sequencing technologies (pyrosequencing). The study revealed temporal shifts in the bacterial community composition during the period of 2012 to 2015.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00002122	PETROMAKS E#12	The aim of the study was to asses biodegradation efficiency of dispersed oil of two Norwegian seawater sources. One source of seawater used in the study was local (Trondheimsfjord), while the other source was Svalbard seawater (Van Mijenfjord). The biodegradation experiment was conducted at 0-2C over the period of 64 days.	root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
MGYS00004276	Environmental Foraminifera Raw sequence reads	Paleotsunami deposits are primary source of information on past big tsunami events and thereby are critical for earthquake and tsunami hazard assessment. They usually form sandy layers preserved in coastal sediments that may contain indicators of marine origin such as foraminifera microfossils and the geochemical signal of saltwater. Environmental DNA sequencing of marine species targets in a series of up to about 2000 years old sandy paleotsunami deposits is promising to detect ancient tsunami events even in the absence of microfossil and sedimentological evidence.The DNA content of 10 environmental coastal sediment samples was extacted from paleotsunami deposit and peat layers of a core and additional peat and beach sand surface samples taken from a wetland on eastern Hokkaido Island (Japan) facing the Kuril Trench subduction zone generating frequent large tsunamigenic earthquakes. The 37f hypervariable region of the foraminiferal SSU rDNA was PCR amplified and PCR products were pooled in one library for Illumiona MiSeq sequence and diversity analyses.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00002583	Microbial community in marine sediments	16S rRNA amplicon sequencing on the Eastern South Pacific Ocean sediments	root:Environmental:Aquatic:Marine:Sediment
MGYS00004129	Microbial diversity in shallow water hydrothermal sediments of Gueishan Island, Taiwan	To better understand the benthic ecosystem near vents off Gueishan Island, we examined the microbial communities across the three domains of life in sediments collected at different distances from the vent area using small-subunit ribosomal RNA pyrosequencing.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004594	Arctic water Metagenome	Diversity and distribution of aquatic fungal communities in the Ny-Ålesund Region, Svalbard, High Arctic	root:Environmental:Aquatic:Marine
MGYS00003086	Marine metagenome ICM_VAG	Community Structure Of Benthic Bacteria In Upwelling Ecosystem.	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00005267	characterizing the gut communitties of twins discordant for obesity in gnotobiotic mice	International efforts to characterize the human microbiome in health and disease are producing massive amounts of data about organismal and gene content in our body habitat -associated microbial communities. A challenge is to complement these efforts with a preclinical research pipeline that tests the degree to which a person's physiologic or pathological phenotype can be ascribed to their microbiome and that offers an opportunity to evaluate potential strategies for microbiome-based therapeutics. Here we illustrate such a pre-clinical pipeline by transplanting previously frozen, uncultured fecal microbiota samples from four sets of adult female mono- and dizygotic twins discordant for obesity into groups of adult germ-free C57Bl/6J mice fed a low-fat, plant polysaccharide-rich diet. Capture of a human donor's microbiota in recipient mice is highly reproducible within and between experiments. The increased adiposity phenotype of obese co-twins is transmissible not only with the intact uncultured fecal communities, but with bacterial culture collections generated from these fecal samples. Co-housing mice five days after they received transplants of culture collections from the obese or lean member of a discordant twin pair ameliorated the increased adiposity phenotype that normally develops in recipients of the obese donor's culture collection, while having no effect on the adiposity phenotype of recipients of the lean co-twin's culture collection. These results correlate with taxonomic and metabolic changes in co-housed mice harboring the obese co-twin's culture collection. Our results demonstrate a way to perform pre-clinical studies of microbiome-associated human phenotypes, including methods for identifying, producing and testing candidate probiotic species as therapeutic or preventative agents.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006651	EMG produced TPA metagenomics assembly of PRJEB52139 data set (HoloFood Chicken Caecum Metatranscriptome).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB52139, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.	root:Host-associated:Birds:Digestive system:Ceca
MGYS00005155	Bacerial and archaeal diversity in Central Park	Soil biota play key roles in the functioning of terrestrial ecosystems, however, compared to our knowledge of aboveground plant and animal diversity, the biodiversity found in soils remains largely uncharacterized. Here we present an assessment of soil biodiversity and biogeographical patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system can harbor large amounts of undescribed soil biodiversity. Despite high variability across the Park, belowground diversity patterns were predictable based on soil characteristics, with prokaryotic and eukaryotic communities exhibiting overlapping biogeographical patterns. Further, Central Park soils harbored nearly as many distinct soil microbial taxa and types of soil communities as we found in biomes across the globe (including arctic, tropical and desert soils). This integrated cross-domain investigation highlights that the amount and patterning of novel and uncharacterized diversity at a single urban location matches that observed across natural ecosystems spanning multiple biomes and continents. Our data therefore suggest that the dominant factors controlling soil biodiversity differ markedly to those controlling aboveground plant and animal diversity.	root:Environmental:Terrestrial:Soil
MGYS00005045	Exploring Fronts With Multiple Robots – Schmidt Ocean Institute Cruise to the Pacific Ocean in 2018	"Samples were obtained during the Schmidt Ocean Institute cruise ""Exploring Fronts With Mutiple Robots"" to the Pacific Ocean in 2018 (https://schmidtocean.org/cruise/exploring_fronts_with_multiple_aerial-surface-underwater-vehicles/). Water samples for microplankton analysis were collected using a multi water sampler (rosette) from the research vessel ""Falkor"" and concentrated on board in a 0.2 μm Sterivex filter. This expedition target the Subtropical Front, located approximately 1,000 nautical miles off the coast of Southern California. The study includes samples from: (i) amplicon sequencing after 18S amplification by PCR using TAReuk454FWD1/ TAReukREV3_modified primer set and (ii) amplicon sequencing after 16S amplification by PCR using 515F/926R primer set. Libraries were constructed according to Illumina Library protocol."	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005318	Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny	Scleractinian corals’ microbial symbionts influence host health, yet how these coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that corals exhibit anatomical compartmentalization of the microbiome such that the coral surface mucus layer, tissue, and skeleton microbiomes show distinct modern microbial ecology and evolutionary assembly. In corals, these compartments differ greatly in microbial community composition, richness, and response to host vs. environmental drivers. We also find evidence of coral-microbe phylosymbiosis, in which coral microbiome composition and richness reflects coral phylogeny. Surprisingly, the coral skeleton represents the most biodiverse coral microbiome, and also shows the strongest evidence of phylosymbiosis. Together these results trace microbial symbiosis across anatomy during the evolution of a basal animal lineage.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00005154	Human gut microbiome viewed across age and geography	Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005092	Characterization of bacterial communities in soil under no-tillage practices with contrasting fertilization strategies	Long term experiment in Argentina.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000889	16S rRNA gene-based analysis of soil prokaryotic communities inhabiting fields of the Mezquital Valley, Mexico	Central objective of this study is to analyze the diversity and composition of prokaryotic communities present in fields of the Mezquital Valley, Mexico.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000880	Natural saline soil, Sicily (Italy) Targeted Locus (Loci)	16S rRNA analysis to inspect distribution of different bacterial groups as a function of spatial gradients of soil salinity and pH	root:Environmental:Terrestrial:Soil
MGYS00002838	Northern Gulf of Mexico Hypoxia can Alter Sediment Communities of Nitrifying Archaea	The sediments were obtained from station Z02 located at the 20 m isobath south of Terrebonne Bay in the northern Gulf of Mexico (latitude 28.875oN; longitude 90.428oW). The cores were collected in April and September 2006.	root:Environmental:Aquatic:Marine:Sediment
MGYS00000814	Forest Soil Metagenome - Eucalyptus urograndis and Acacia mangium	Forest soil under three different compositions: 1 - Eucalyptus urograndis monoculture 2 - Acacia mangium monoculture 3 - Mixed plantation	root:Environmental:Terrestrial:Soil
MGYS00004215	22V-SMAR-TVG10 Targeted Locus (Loci)	Bacterial Diversity of Deep-sea Environment	root:Environmental:Aquatic:Marine:Sediment
MGYS00004006	Ocean Targeted Locus (Loci)	The cyanobacteria Prochlorococcus and Synechococcus are important marine primary producers. We explored their distributions and co-variance along a physico-chemical gradient from coastal to open ocean waters in the Northeastern Pacific Ocean. Based on 16S rRNA gene sequencing we identified two new clades of Synechococcus, EPC1 and EPC2, and delineated an interannual pattern in a dynamic transition zone where upwelled and eastern boundary current waters mix. In years when more oligotrophic water intrudes further inshore Prochlorococcus HLI and LLI are more abundant, while under stronger upwelling Synechococcus I and IV dominate. However, contributions of some cyanobacterial clades are proportionally relatively constant, e.g., Synechococcus EPC2. In addition to supporting observations that Prochlorococcus LLI thrive at higher irradiances than other LL taxa, the results suggest LLI tolerate lower temperatures than reported. The phylogenetic precision of our analytical approach and depth of barcoded pyrosequencing also allowed us to detect clades at low abundance in unexpected places. For example, Prochlorococcus at the coast, and sequences related to freshwater Cyanobium spp. in the open ocean, although it remains unclear whether these come from resident or advected cells. Our study enhances understanding of cyanobacterial distributions by applying state-of-the-art phylogenetic analysis tools to an ecologically important eastern boundary system.	root:Environmental:Aquatic:Marine
MGYS00006551	EMG produced TPA metagenomics assembly of PRJEB62473 data set (The INTEGRATE project).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB62473, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002649	ADDOMEx Tier 3 Experiments: Mesocosm Si with Gulf of Mexico coastal waters	Here we describe microbial community dynamics in the Mesocosm-Si experiment. Using 16S rRNA gene sequencing of filtered water samples collected every 24 hours from the mesocosm treatments, we characterized community membership and structure to determine how the mesocosm communities responded to a passively dosed (via silicone tubing) water accomdated fraction of oil.	root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
MGYS00000938	Complex Heteropolysaccharide Enriched Soils Targeted Locus (Loci)	Stable-isotope-probing of two soils using two complex heteropolysaccharides as a substrate.	root:Environmental:Terrestrial:Soil
MGYS00000879	Otumba arable soil Metagenome	Soil microbial biomass has been determined since the mid 1970’s by the chloroform fumigation incubation technique as proposed by Jenkinson and Powlson (1976). The microbial biomass C can be determined by subtracting the CO2 emitted from an unfumigated soil (mineralization of soil organic matter) from that emitted from a chloroform fumigated inoculated soil (mineralization of soil organic matter and killed soil microorganisms) and dividing the difference by a proportionality factor (kC 1⁄4 0.45). The question remained which microorganisms recolonized a fumigated soil. An arable soil was fumigated for one day with ethanol-free chloroform or left unfumigated and incubated aerobically after removal of the chloroform for 10 days. The bacterial population structures were determined in the fumigated and unfumigated soil after 0, 1, 5 and 10 days by means of 454 pyrosequencing of the 16S rRNA gene.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001010	Haerbin black soil Genome sequencing	Black soil different fertilizer	root:Environmental:Terrestrial:Soil
MGYS00003931	Plasma soil pretreatment trail	Plasma is the fourth state of matter and it can be generated by coupling sufficient quantities of energy to a gas to induce ionization. Plasma treatment is known for its antimicrobial properties by generating agents such as reactive oxygen and nitrogen species to kill and reduce proliferation of various microorganisms. Here, we examine an effect of plasma exposure on soil samples. Various exposure times and plasma properties were tested. Microbial communities of soil samples were examined by sequencing ribosomal 16S gene and comparing abundance of different microbial groups in treated and non-treated samples.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00002522	Standard filtration practices significantly distort planktonic microbial diversity estimates	Filtration is the standard method for isolating planktonic microbial biomass for analysis. It is unclear how the taxonomic composition of biomass on a filter changes as a function of filtered water volume, potentially due to filter clogging. Using seawater from a marine oxygen minimum zone, we conducted experiments to quantify the 16S rRNA gene composition of biomass on a prefilter (GF/A, 1.6 um pore size) and a downstream collection filter (Sterivex, 0.2 um) over a range of typical collection volumes, from 50 to 5000 ml. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences affiliated with Vibrionales decreased from ~40-60% of the prefilter datasets at low volumes (50-500 ml) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Taxa shown previously to be associated with marine particles, including diverse members of the Deltaproteobacteria, Planctomycetes and Bacteroidetes, were among those showing the greatest increase with filter volume (4 to 27-fold). Metrics of taxon richness (97% sequence clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise serious concerns for studies using filter fractionation to separate biomass for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.	root:Environmental:Aquatic:Marine
MGYS00000652	Bacterial diversity in agricultural soils	Barcoded amplicon sequencing targeting V4 regions of 16S gene from uncultured soil bacteria.	root:Environmental:Terrestrial:Soil
MGYS00004566	Marine metagenome ICM_BSP	Seasonal dynamics of bacterioplankton communities in the Baltic Sea Proper.	root:Environmental:Aquatic:Marine
MGYS00004567	Marine metagenome ICM_ABR	Diversity of active microbial communities in surface seawaters along a north-south transect in the South Pacific Ocean.	root:Environmental:Aquatic:Marine
MGYS00004046	Prokaryotic community structure in the deep Southwest Indian Ocean with an emphasis on actinobacteria Targeted Locus (Loci)	Knowledge about the biodiversity extent and biogeography of deep-sea microorganisms is far from adequate. Due to its remote location, the related investigations of the Southwest Indian Ocean (SWIR) remaine extremely difficult and the microbial diversity at the SWIR has rarely been studied. Only two studies got limited numbers of 16S rRNA gene sequences, and much more in-depth sequencing efforts to evaluate the abundance and diversity of prokaryotes at the SWIR are still needed. In this study, pyrosequencing was used to investigate the community structure and biogeography of prokaryotes, especially actinobacteria, in the deep SWIR. It also identified the factors in contributing to the distribution of the prokaryotes and actinobacteria, the historical contingencies, contemporary environmental factors, or both? The results would provide further insights on the prokaryotic, especially actinobacterial community structure at the SWIR and help to understand the underling mechanisms of the microbial distribution in the deep ocean. To our knowledge, this is the first report on the biodiversity and biogeography of actinobacteria at the SWIR.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00005171	Soil bacterial diversity is associated with human population density in urban greenspaces	Urban greenspaces form a vital part of the urban ecosystem and provide an extensive array of ecosystem services, including pollutant degradation, water management, carbon maintenance, and nutrient cycling. However, while the soil microbiota in these ecosystems are essential to these services they remain under-characterized. Here we aimed to determine whether turf grass soil bacterial communities were associated with human population density across a range of greenspaces in parks, streets, and residential areas across a major urban area. Results showed that bacterial diversity was significantly positively correlated with population density within the immediate vicinity of the sampled areas; and species diversity was greater in park and street soils, when compared with residential zones. Population density and greenspace type (park vs street vs residential area) also associated with the composition and structure of the bacterial community. Edaphic properties, including pH, moisture and texture, were also significantly correlated with microbial composition and structure. Co-occurrence network analysis revealed that microbial guilds in urban soils were well connected. Soil moisture and texture together with population density and greenspace type showed strong correlations with several network topological features including assortativity degree, edge density, average path, average betweenness and closeness. These results indicate that changes in urban demographics, as well as the changes in land-use may influence the diversity and structure of urban soil microbial communities. As urbanization is rapidly growing across the planet, understanding the consequences of different urban zoning on soil microbiota represents an unmet need.	root:Environmental:Terrestrial:Soil
MGYS00000770	Colonization patterns of soil microbial communities in the Atacama Desert	The Atacama Desert is one of the driest deserts in the world and its soil characterized by extremely low moisture, organic carbon content, and oxidizing conditions has been considered to be at the dry limit for life. We collected soil samples from 3 geographic locations in the hyper-arid zone of the Atacama Desert, and from 3 locations along a North-South transect of increasing rainfall, to identify what factors might shape the diversity of its soil microbiome. Analyses of non-culture based, high throughput DNA sequence data revealed that communities from the 6 geographic locations were structurally and phylogenetically distinct (ANOVA test for observed OTU0.03, p<0.001; UniFrac distances) and that communities from locations in the hyper-arid zone displayed the lowest levels of diversity. We found bacterial taxa similar to those found in other arid soil communities with an abundance of Rubrobacterales, Actinomycetales, Acidimicrobiales, and a number of families from the Thermoleophilia. The extremely low abundance of Firmicutes, the phylum that comprises most sporulating bacteria, indicated that most bacteria in the soil were in the form of vegetative cells. No archaea were found in an of the soil samples. Integrating molecular data with climate and soil geochemistry, we found that air relative humidity (RH) and soil conductivity significantly correlated with microbial communities diversity metrics (least square linear regression for observed OTU0.03 and air RH and soil conductivity, p<0.001; UniFrac PCoA spearman’s correlation for air RH and soil conductivity, p<0.0001), indicating that water availability and salt content are key factors in shaping the Atacama soil microbiome. Mineralization studies showed communities actively metabolizing in all soil samples with increased rates in soils from the southern locations. These findings suggest that over geological time, and due to rare rain events, physicochemical factors potentially played a major role in selecting microorganisms that are most adapted to extreme desiccating conditions.	root:Environmental:Terrestrial:Soil:Desert
MGYS00004116	Archaeal diversity of surface seawater (A3,A5,G3,G5) Targeted Locus (Loci)	To investigate the archaeal diversity of sea water from Greatwall cove and Ardley cove, Fildes Peninsula, four surface water samples were collected during the 29th Chinese Antarctic scientific expedition in 2013.	root:Environmental:Aquatic:Marine
MGYS00001724	16S amplicon based soil and leaf microbiome survey in Hungarian vineyards	Seven Hungarian wine regions have been sampled for leaf and 20cm deep soil samples from the same plants. All vineyards are of different soil types and grape cultivars. Total DNA has been extracted and 16S amplicon sequencing has been applied to the samples.	root:Host-associated:Plants
MGYS00002807	Southern Ocean	Southern Ocean bacterioplankton community	root:Environmental:Aquatic:Marine:Oceanic
MGYS00001813	Investigation of the suitability of Remane’s species minimum concept in a Mediterranean transitional waters ecosystem	The aim of the present study was to investigate the sediment bacterial diversity of a transect river-lagoon-open sea, i.e. from freshwater to marine, occurring at Amvrakikos Gulf (Ionian Sea, Western Greece) and to test whether it follows the Remane's concept, both in terms of species composition but also of functionality. Remane’s Artenminimum (“species minimum”) concept was developed for the Baltic Sea, the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient. It argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum, which occurs at salinity 5 to 8, because the number of brackish specialists does not compensate for the decline in marine and freshwater diversity. DNA was extracted from sediment samples collected in situ from six stations along the aforementioned transect and sequenced for the 16S rRNA gene.	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00004651	Composition and Genetic Diversity of Microbial Communities in Subtropical Coastal Wetland Sediments	This study aimed to examine the composition and genetic diversity of bacterial, archaeal and fungal communities in surface sediments of a subtropical coastal wetland.	root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
MGYS00002736	CARBOM cruise 2013 flow cytometry sorted phytoplankton		root:Environmental:Aquatic:Marine
MGYS00005232	Dorrestein_3D_metabolic_map	Skin samples from human 3D metabolic map	root:Host-associated:Human:Skin
MGYS00000813	Bacterial community composition of divergent soil habitats in a polar desert Metagenome	A 16S rDNA sequencing approach was used to examine the differences in diversity and community composition between three divergent soil habitats of the McMurdo Dry Valleys, Antarctica.	root:Environmental:Terrestrial:Soil:Desert
MGYS00004599	Microbial communities associated with Juncus roemerianus and Spartina alterniflora vegetated sediments in Louisiana saltmarshes	"""Saltmarshes are typically dominated by perennial grasses with large underground rhizome systems that can change local sediment conditions and be important in shaping the sediment microbial community. Factors that control plant zonation in saltmarshes (e.g. salinity) are also likely to influence the microbial community, but little is known as to whether microbial communities share distribution patterns with plants in these systems. To determine the extent to which microbial assemblages are influenced by saltmarsh plant communities, as well as to examine patterns in microbial community structure at local and regional scales, we sampled sediments at three saltmarshes in Louisiana, USA. All three systems exhibit a patchy distribution of Juncus roemerianus stands within a Spartina alterniflora marsh. Sediment samples were collected from the interior of several J. roemerianus stands as well as from the S. alterniflora matrix. Samples were assayed for extracellular enzyme activity and DNA extracted to determine microbial community composition. Denaturing gradient gel electrophoresis of rRNA gene fragments was used to determine regional patterns in bacterial, archaeal, and fungal assemblages, while Illumina sequencing was used to examine local, vegetation-driven, patterns in community structure at one site. Both enzyme activity and microbial community structure were primarily influenced by regional site. Within individual saltmarshes, bacterial and archaeal communities differed between J. roemerianus and S. alterniflora vegetated sediments, while fungal communities did not. These results highlight the importance of the plant community in shaping the sediment microbial community in saltmarshes, but also demonstrate that regional scale factors are at least as important."""	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00004045	Marine metagenome ICM_WBS	Pyrosequencing as a paleometagenomical tool offers a window into Holocene plankton, littoral fauna, and terrestrial vegetation in the Black Sea.	root:Environmental:Aquatic:Marine
MGYS00004052	"Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing
                in Naples Bay"	"Haptophytes are a key phylum of marine protists, including ~300
                described morphospecies and 80 morphogenera. We used 454-pyrosequencing on large
                subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size
                fractioned plankton samples collected in the Bay of Naples. One group-specific
                primer set targeting an overlapping region of the LSU rDNA D1/D2 region was used to
                amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two
                size fractions (0.8-3 or 3-20 μm) and two sampling depths (subsurface, at 1m, or
                deep-chlorophyll-maximum (DCM) at 23m)."	root:Environmental:Aquatic:Marine:Coastal
MGYS00000998	Soil microbiome CENEB Metagenome	This project investigated three agricultural practices, i.e. different raised bed planting systems (tilled raised beds vs permanent raised beds), different levels of residue retention (full, partial and no retention of crop residue) and two application rates of inorganic N fertilizer (0 or 300 kg N ha-1), at a 20-year long-term field experiment cultivated with wheat (Triticum spp. L.) and maize (Zea mays L.). This study included also the effect of residue burning	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00005501	Plant niche rather than soil or species shapes the microbiota	Plant niche rather than soil or species shapes the microbiota. Plants are colonised in 2 weeks time and this process is continuous.	root:Environmental:Terrestrial:Soil
MGYS00000833	Soil bacteria on root-knot nematodes and in bulk soil, 16S rRNA genes	Bacterial communities associated with juveniles of the plant-parasitic nematode Meloidogyne hapla in three arable soils of differing supressiveness	root:Host-associated
MGYS00001457	Bacterial community during the Austral summer in the Amundsen Sea Polynya, Antarctica	454-pyrosequencing (16S rDNA) dataset of bacterial community in the Amundsen Sea Polynya from the ASPIRE research expedition in Antarctica during the Austral summer 2010-2011.  In situ and experimental incubation samples are included in this dataset.	root:Environmental:Aquatic:Marine
MGYS00002644	Bacterial Biogeography of Coastal Water in the Northern East China Sea	The Northern East China Sea is a unique marine ecosystem with multiple environmental gradients (e.g. salinity, pH, and nutrients) along northwest to southeast, forming a horn-shaped pattern with Hangzhou Bay as the tip. This study applied 16S amplicon high-throughput sequencing with Illumina MiSeq technique and multiple statistical analyses to quantitatively reveal the relative contributions of local environmental conditions and regional spatial factors in shaping bacterial biogeographic pattern of coastal water using 95 surface water samples collected from 95 sites across 8 coastal zones, from Hangzhou Bay (northwest) to outside of Sanmen Bay (southeast), in the Northern East China Sea across a > 200 km scale.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002663	Red Sea microbial plankton Raw sequence reads	To examine the diversity of the microbial plankton in the northern and southern extremes of the Red Sea.	root:Environmental:Aquatic:Marine
MGYS00002819	Marine bacteria Targeted Locus (Loci)	This study examines the composition of bacterial communities associated with four species of crustose coralline algae.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00004067	marine sediment metagenome Metagenome	Bacteria in marine sediments (High Arctic)	root:Environmental:Aquatic:Marine:Sediment
MGYS00004197	SB Marine Metagenome	The study of bacterial diversity.  Marine metagenome from Malaysian coastal water.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004324	Temporal dynamics of bacterioplankton community in response to excessive nitrate loading in the oligotrophic coastal water	Coastal ecosystems are receiving elevated inputs of nitrogen (N), primarily as nitrate, from anthropogenic sources. Bacterioplankton play important roles in marine N-cycle. Understanding how excessive N-loading affects marine bacterioplankton communities is critical for the insight into the biodiversity of marine ecosystems under the condition of eutrophic disturbance. In this study, the oligotrophic coastal water microcosms were perturbed with a certain nitrate level of 1.0 mg L-1 in two loading modes: 1) one-off loading (OL) with the level of 1.0 mg L-1 at the beginning; 2) periodic loading (PL) with the level of 0.125 mg L-1 every two days during 16 days.	root:Environmental:Aquatic:Marine:Coastal
MGYS00000810	Characterization of Growing Bacterial Populations in McMurdo Dry Valley (Antarctica) Soils through Stable Isotope Probing with 18O-water	Stable isotope probing of soil bacterial DNA with 18O labeled water was performed to identify which bacterial populations are active by sequencing 16S rRNA gene sequences from heavy and light fractions of soil DNA.	root:Environmental:Terrestrial:Soil
MGYS00004322	Evidence  of  bacterioplankton community adaption in responses to  long-term mariculture disturbance	Mariculture activity acts as a disturbance to bacterioplankton community because it results in coastal eutrophication known to alter the bacterial composition. However, to what extent that such disturbance affects turnover of bacterioplankton community composition (BCC) and network interactions among bacterial assemblages are largely unknown. To this end, using 454  pyrosequencing of bacterial 16S rRNA gene, we evaluated the effects of mariculture disturbance on the temporal dynamics of BCC in Xiangshan Bay, the East China Sea. Clearly seasonal succession and sites (fish farm and control sites) separation of BCC were observed, which follow the time-decay for similarity  relationship.  Sampling  time  and mariculture  disturbance  respectively contributed 19.3% (P = 0.001) and 4.3% (P = 0.008) variations of the BCC. However, seasonal dynamics of bacterial alpha-diversity had no obvious trend, but were tightly associated with the relative abundances of potential bacterial predators. The temporal succession of the  BCC was significantly correlated with seawater temperature, chemical oxygen demand, N/P  ratio, dissolved inorganic nitrogen and chlorophyll a. We observed over the three seasons the  same change pattern for a few dominant bacterial families under mariculture disturbance. Additionally, mariculture disturbance considerably decelerated the temporal turnover rate, but  intensified the network interactions of bacterial community. These results demonstrate that BCC is sensitive to mariculture disturbance in this study region, while the consistency with which sensitive bacterial assemblages could characterize such disturbance. Low temporal turnover rate and complex network interactions, thus enabling bacterial communities were adaptive to long-term mariculture disturbance.	root:Environmental:Aquatic:Marine:Coastal
MGYS00001160	Bacterial communitiesl in first and subsequent rounds in Korean ginseng field soil	Investigation of bacterial diversities and communities in the soil of ginseng fields at the first round and subsequent round	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00004212	Foraminifera Metagenome	Spatial patchiness is a natural feature that strongly influences the level of species richness we perceive in surface sediments sampled in the deep-sea. Recent environmental DNA (eDNA) surveys of benthic micro- and meiofauna confirmed this exceptional richness. However, it is unknown to which extent the results of these studies, based usually on few grams of sediment, are affected by spatial patchiness of deep-sea benthos. Here, we analyse the eDNA diversity of Foraminifera in 42 deep-sea sediment samples collected across different scales in the Southern Ocean.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004177	Spatial Variation of Coastal Bacterioplankton Community along a Nitrogen and Phosphorus Co-pollution Gradient	Anthropogenic discharges of nitrogen (N) and phosphorus (P) have caused widespread threats to coastal ecosystems. Bacterioplankton are known to play crucial roles in N/P cycling in marine environments, but little is known about how bacterioplankton community responds to N-P co-pollution. Here, we collected surface seawater samples along a transect in East China Sea. We applied 16S rRNA gene amplicon pyrosequencing to investigate the spatial variation of bacterioplankton communities under a N-P co-pollution gradient. The bacterioplankton communities were dominated by Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidetes and Betaproteobacteria, which were distinct from those of sediment bacterial assemblages at the same transect. The bacterioplankton community compositions (BCCs) did not vary consistently along the pollution gradient, but clustered into nearshore and offshore groups. The combined environmental factors and spatial distances contributed 30.4% and 12.2% to the variation of the BCC, respectivelys, with a high auto-correlated effect that constrained 25.8% variation. In addition, a series of sensitive bacterial OTUs were identified, whose abundances were significantly associated with the N and/or P levels. This study demonstrates that coastal N-P co-pollution dramatically alter the BCCs, while these changes could be characterized by a few sensitive bacterioplanktonic OTUs.	root:Environmental:Aquatic:Marine
MGYS00004047	Peruvian eddy shotgun metagenomes	Shotgun metagenomes sampled from a mesoscale water eddy during strong upwelling conditions in Eastern tropical South Pacific waters off the Peruvian coast, February to March 2013.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00006649	EMG produced TPA metagenomics assembly of PRJNA748214 data set (saliva samples Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA748214, and was assembled with metaSPAdes v3.14.1, SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006644	EMG produced TPA metagenomics assembly of PRJNA408025 data set (Global studies of microbial diversity in pig gut).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA408025, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006647	EMG produced TPA metagenomics assembly of PRJNA737271 data set (Piglet gut and in-barn manure from farms on Raised Without Antibiotics program display a reduced antimicrobial resistance but an increased prevalence of pathogens).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA737271, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Mixed.	root:Mixed
MGYS00006646	EMG produced TPA metagenomics assembly of PRJNA645191 data set (Parity is associated with maternal gut microbiome composition during pregnancy and offspring microbiome composition in pigs).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA645191, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006645	EMG produced TPA metagenomics assembly of PRJNA575543 data set (Metagenomic characterization of intestinal regions in pigs with contrasting feed efficiency).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA575543, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.	root:Host-associated:Mammals:Digestive system
MGYS00006641	EMG produced TPA metagenomics assembly of PRJNA547717 data set (human oral metagenome Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA547717, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00006643	EMG produced TPA metagenomics assembly of PRJEB21574 data set (We studied the effect of different zinc sources on the intestinal microbiome in weaned pigs).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB21574, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006642	EMG produced TPA metagenomics assembly of PRJDB5315 data set (Metgenomic analysis of human saliva microbiome from healthy subjects).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJDB5315, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006364	EMG produced TPA metagenomics assembly of PRJEB36291 data set (Defining the oral microbiome by Whole Genome Sequencing and resistome analysis: the complexity of the healthy picture).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB36291, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00006640	EMG produced TPA metagenomics assembly of PRJNA678453 data set (Species-specific gene expression of the oral microbiota in health and diesease).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA678453, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00006639	EMG produced TPA metagenomics assembly of PRJNA741688 data set (saliva metagenomic analysis of Crohn`s disease-related periodontitis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA741688, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006638	Early life nasopharyngeal bacteriome in a low-income community in South Africa	Public description:Imbalances in early life nasopharyngeal (NP) bacterial profiles have been associated with lower respiratory tract infection (LRTI) but are understudied in low-income communities where risk factors for LRTI are prevalent. We intensively investigated longitudinal NP bacterial profiles, and associated exposures, among infants born in low-income households in South Africa	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00005157	Eukaryotic diversity in Central Park	Soil biota play key roles in the functioning of terrestrial ecosystems, however, compared to our knowledge of aboveground plant and animal diversity, the biodiversity found in soils remains largely uncharacterized. Here we present an assessment of soil biodiversity and biogeographical patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system can harbor large amounts of undescribed soil biodiversity. Despite high variability across the Park, belowground diversity patterns were predictable based on soil characteristics, with prokaryotic and eukaryotic communities exhibiting overlapping biogeographical patterns. Further, Central Park soils harbored nearly as many distinct soil microbial taxa and types of soil communities as we found in biomes across the globe (including arctic, tropical and desert soils). This integrated cross-domain investigation highlights that the amount and patterning of novel and uncharacterized diversity at a single urban location matches that observed across natural ecosystems spanning multiple biomes and continents. Our data therefore suggest that the dominant factors controlling soil biodiversity differ markedly to those controlling aboveground plant and animal diversity.	root:Mixed
MGYS00001368	Comprehensive amplicon-based metagenome analyses reveal long-term impacts of timber harvesting on soil microbial communities at reforested sites across North America.	Soil management is necessary to ensure the fertility of reforested land, yet the long-term impact of harvesting on the soil microbial communities which mediate fertility remains largely a matter of conjecture. In 1989, the North American-wide ‘long-term soil productivity’ (LTSP) study was initiated to assess the impacts of organic matter removal on forest soils on a decadal timeframe. We sampled comprehensively within the LTSP framework in six biogeographic zones throughout British Columbia, California, Ontario and Texas, producing ITS and 16S pyrotag libraries. We observed major expansions in populations of desiccation, radiation and heat-resistant organisms from a broad diversity of fungal and bacterial groups. By identifying specific taxa, genes and processes altered post-harvesting, we contribute to refining long-term monitoring efforts and reveal important phenomenon impacting long-term forest regeneration.	root:Host-associated:Plants:Rhizosphere:Forest soil
MGYS00002652	Marine Water Column Samples Targeted loci environmental	Surface water samples collected from locations within Mobile Bay out into the northern Gulf of Mexico shelf region off the coast of Alabama for examination of microbial eukaryotes. 20-24 L water samples were collected bi-monthly from July 2009- Dec 2011, prefiltered through a 150um mesh and eukaryotic fraction was collected on a 0.7um glass fiber filter. This data was used to explore spatial and temporal variation as well as impact of the Deepwater Horizon Oil Spill on this community.	root:Environmental:Aquatic:Marine
MGYS00001362	Ecozone dependent impact of forest harvesting on soil microbial community structure	Here we examined the microbial communities in soils from both the organic and mineral layer from 18 sites in six ecozones across North America. This is 16S rRNA gene data	root:Environmental:Terrestrial:Soil:Loam:Forest soil
MGYS00006637	Metagenomes of marine macroalgae, surrounding seawater and surrounding sediments	Here we analysed the microbial ecology of marine macroalgae, surrounding seawater, and surrounding sediment at Weihai, China (122.12 N, 37.56 E). Metagenomic sequencing of marine macroalgae, surrounding seawater, and surrounding sediment samples collected on 4 sampling dates in the year 2018-2019. For macroalgae, loosely attached microorganisms were removed by washing whole macroalgae thrice in flasks about 80% filled with sterile seawater on a shaker and collecting the washing suspensions in sterile bottles. Algae were then put in sterile seawater and remaining bacteria were removed by ultrasonication (2x 60s, 50-60 kHz). Suspensions with removed bacteria of each sample were subsequently pooled with the previously obtained washing suspensions. Then the washing suspension of each sample was filtered on 0.2 μm pore size polycarbonate membrane filters. Seawater samples were filtered on a 0.2 μm pore size polycarbonate membrane filters. For sediments, DNA was extracted from 300 mg sub-samples. Sequencing was done on the Illumina novaseq 6000 platform and 2x 150 base pair chemistry.	root:Environmental:Aquatic:Marine
MGYS00000596	American Gut Project	The American Gut project is the largest crowdsourced citizen science project to date. Fecal, oral, skin, and other body site samples collected from thousands of participants represent the largest human microbiome cohort in existence. Detailed health and lifestyle and diet data associated with each sample is enabling us to deeply examine associations between the human microbiome and factors such as diet (from vegan to near carnivore and everything in between), season, amount of sleep, and disease states such as IBD, diabetes, or autism spectrum disorder-as well as many other factors not listed here. The American Gut project also encompasses the British Gut and Australian Gut projects, widening the cohort beyond North America. As the project continues to grow, we will be able to identify significant associations that would not be possible with smaller, geographically and health/disease status-limited cohorts.	root:Host-associated:Human
MGYS00006636	EMG produced TPA metagenomics assembly of PRJNA932553 data set (Oral microbiome in periodontitis).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA932553, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00006366	EMG produced TPA metagenomics assembly of PRJNA548383 data set (Subgingival Microbiome of Tobacco Cigarette Smokers with and without Periodontal Disease).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA548383, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00006621	EMG produced TPA metagenomics assembly of PRJNA373834 data set (Metagenomic analysis of gut microbiota in sows and piglets).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA373834, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006635	EMG produced TPA metagenomics assembly of PRJNA752888 data set (Longitudinal saliva bacteriome and early childhood caries).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA752888, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00003168	Microbial indicators of anthropogenic marine pollution identified by 16S and 18S metagenomic library analysis	Microbial indicators of anthropogenic marine pollution identified by 16S and 18S metagenomic library analysis. Research supported by FP7 European Project “Winning Applications of nanoTEchnology for Resolutive hydropurification – WATER” (Grant Agreement n° 316082).	root:Environmental:Aquatic:Marine
MGYS00001502	Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease	The intestinal microbiota influence neurodevelopment, modulate behavior, and contribute to neurological disorders. However, a functional link between gut bacteria and neurodegenerative diseases remains unexplored. Synucleinopathies are characterized by aggregation of the protein α-synuclein (αSyn), often resulting in motor dysfunction as exemplified by Parkinson's disease (PD). Using mice that overexpress αSyn, we report herein that gut microbiota are required for motor deficits, microglia activation, and αSyn pathology. Antibiotic treatment ameliorates, while microbial re-colonization promotes, pathophysiology in adult animals, suggesting that postnatal signaling between the gut and the brain modulates disease. Indeed, oral administration of specific microbial metabolites to germ-free mice promotes neuroinflammation and motor symptoms. Remarkably, colonization of αSyn-overexpressing mice with microbiota from PD-affected patients enhances physical impairments compared to microbiota transplants from healthy human donors. These findings reveal that gut bacteria regulate movement disorders in mice and suggest that alterations in the human microbiome represent a risk factor for PD.	root:Host-associated
MGYS00005200	Metabarcoding surveys of the Arctic marine environment	This is a collection of samples taken for metabarcoding of environmental samples following the Earth Microbiome Project protocol.For bacteria and archaea, we used the following primer set published by Apprill et al. (doi:10.3354/ame01753)515F GTGCCAGCMGCCGCGGTAA806RB GGACTACNVGGGTWTCTAATFor Eukaryotes, we used the following primer set published by Stoeck et al. (doi:10.1111/j.1365-294X.2009.04480.x)TAReuk454FWD1 CCAGCASCYGCGGTAATTCCTAReukREV3_modified ACTTTCGTTCTTGATYRATGA	root:Mixed
MGYS00000910	Different agricultural practices amended with bean residues Metagenome	To investigate how different management practices affected the bacterial community structure in soil, ii) to investigate how the application of bean residue affected the bacterial community structure in soil with different agricultural practices and iii) compare the bacterial populations involved in the mineralization of bean residue with those when maize residue was applied to soil.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00002604	Community structure of Archaea in the western North Pacific and the Arctic Ocean	we report archaeal community structure in the western North Pacific and the Arctic Ocean based on the deep sequencing of 16S rRNA genes directly amplified from seawater filtrates.	root:Environmental:Aquatic:Marine
MGYS00004564	Marine DNA/RNA samples from Western English Channel site L4	Marine DNA/RNA samples from Western English Channel site L4.   The seasonal structure of microbial communities in the Western English Channel - 2007   Here we present a multi-omic study of the Bacterial and Archaeal diversity found at the L4 long-term marine observatory.  We have previously generated a six year time series from L4 that showed that the bacterial community shows strong seasonal structuring and diversity peaks every year on the winter solstice.  Here we further confirm this pattern by extending this study to include genes and transcripts generated for eight additional time points in 2008.  This data includes further 16S datasets as well as eight metagenomes (1.2GB) and eight metatranscriptomes (157MB).  These time points cover three seasons (Jan, April and August) and include day and night (diel) samples.  In addition, the August samples (4) include 4 consecutive samplings within 24 hours at six hour intervals.  Using these data we test whether Archaea also show the same observed seasonal patterns and whether these patterns hold true at the gene (functional) level.   Analysis of this combined data set allows five main conclusions to be drawn.  First, Archaea show evidence of following the same seasonal patterns as Bacteria, but have ~6% the richness.  Second, for both Bacteria and Archaea, we confirm that higher 16S diversity reflects higher diversity at the gene-level (including expressed genes) and this diversity also peaks at the winter solstice. Third, interestingly, detectable diversity appears to be higher at night, and this is of special potential relevance as there is more diversity in winter when nights are longer.  Fourth, despite the diversity of these communities, night and day samples taken using Lagrangian (drift) sampling were successful in isolating the same community suggesting communities are more structured than is commonly believed. Finally, this data, as expected, contains a large proportion of orphan genes without known homologues.  When compared to the housekeeping genes identified through SEED subsystem classification, these unknown genes appear to be driving the differences between samples across seasons.  This underscores the importance of determining the functions of more of these sequences in the future.   In summary, this study further confirms the strong seasonal patterns characterizing both the bacterial and archaeal communities at this important marine site.  The finding that, despite the huge diversity of these communities, there are evident signs of predictable patterns and detectable stability over time provides compelling evidence that renewed efforts should	root:Environmental:Aquatic:Marine
MGYS00001790	Elevated CO2 induces a bloom of microphytobenthos	The geological storage of carbon dioxide (CO2), captured from large industries and power plants, is expected to be an important component of future carbon emissions mitigation globally. Alongside the need to understand the impacts of a CO2 leak on the marine environment, there is an urgent need to develop monitoring protocols for leakage detection. In the present study, sediment cores were exposed to seawater acidified using CO2 to five different pH levels (8.0, 7.5, 7.0, 6.5 and 6) for a period of 10 weeks. A pink microphytobenthos mat containing Spirulina sp. and diatoms appeared on top of sediment exposed to pH 7.0 and 7.5 after five weeks, peaked at eight weeks and was still present in small patches within the pH 7.0 cores after 10 weeks. Quantitative PCR measurements of the abundance of cyanobacterial 16S rRNA also indicated an increase to the abundance of cyanobacterial or chloroplast 16S rRNA within the pH 7.0 treatments after 10 weeks incubation. Detailed comparisons of the microbial communities with the pH 7.0, 7.5 and 8 treatments revealed a shift in community composition within the pH 7.0 cores: an increase in abundance of sequence most closely related to Spirulina sp. and the diatom Navicula sp., and a corresponding decrease to the abundance of Alphaproteobacteria, specifically of the family Rhodospirillales, the Crenarchaeota Class Marine Group I and the Planctomycetes Class OM190. Monitoring for blooms of microphytobenthos may prove useful as an indicator of a CO2 leak from injection pipeline failure in coastal areas.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003072	Whale fall	Deep-sea whale falls create sulfidic habitats of which microbial structure is poorly evaluated. We sampled the sediment in the whale fall area and targeted the V9 of the 18S SSU to determine the protistan community.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004019	Baltic Expression Project	cDNA  samples were pyrosequenced using 16S rRNA primers. Samples from which cDNA was obtained were surface marine sediment samples from the Bothnian Bay (Baltic Sea) and Skagerrak (North Sea).	root:Environmental:Aquatic:Marine:Sediment
MGYS00004671	Gulf of Mexico Alkane Reactors Metagenome	Pyrosequencing of Gulf of Mexico sediments from anaerobic batch reactors with short-chain alkanes.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004389	Depth profile of ancient sediments	Recruitment of bacteria from the different depth of sediments	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004090	marine metagenome Targeted Locus (Loci)	This project investigated the production of different classes of iron-binding ligands, iron concentrations, macronutrient concentrations, and phytoplankton and bacterioplankton assemblage composition in iron amended microcosm incubations conducted in oligotrophic waters collected off the Southern California Bight.	root:Environmental:Aquatic:Marine
MGYS00003085	Marine metagenome ICM_LCR	The LACAr cooperative project: microbial diversity in coastal systems along a latitudinal gradient from South Atlantic to the Caribbean.	root:Environmental:Aquatic:Marine
MGYS00000657	Composition and structure of soil fungal community in Inner Mongolian steppe	Fungi serve important roles in terrestrial ecosystem. However, its geographic distribution and driving factors shaping fungal community structure remain elusive. In this study, we utilized Illumina Miseq sequencing technique for the nuclear ribosomal internal transcribed spacer 2 (ITS2) region to investigate soil fungal distribution along a 360-km transect in Inner Mongolian steppe.	root:Environmental:Terrestrial:Soil
MGYS00000962	Soil bacteria Targeted Locus (Loci)	The goal of this study was to assess the spatial distribution of soil bacteria in an agricultural context. We compared soil bacterial communities in corn and switchgrass cropping systems across a topographic gradient and two years. In addition, we quantified scale-specific spatial patterning of soil bacterial communities. Because of their important role in biogeochemical cycling, understanding spatial patterning of microbial communities is important for our ability to model carbon and nitrogen cycling.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00002405	Polymetallic nodule field Targeted loci environmental	Abyssal sediments, polymetallic nodules, and water-column samples were collected from the UKSRL1 claim area within the Clarion-Clipperton fracture zone in the Pacific Ocean.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002648	ADDOMEx	Here we describe microbial community dynamics in the GOMOO mesocosm experiment. Using 16S rRNA gene sequencing of filtered water samples collected every 12 hours from the mesocosm treatments, we characterized community membership and structure to determine how the mesocosm communities responded to the water accomdated fraction of oil with and without the dispersant Corexit.	root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
MGYS00001034	Changes in the bacterial communities of subtropical soils from Argentina with different land uses.	The goal of this study was to analyze the modifications in the structure of the bacterial communities from Argentinean subtropical soils caused by changes in land use. The samples included soils from undisturbed forests and from sites that were deforested between 100 and 5 years ago and used for soybean or sugar cane cultivation. The changes in community structure were evaluated by 454 GS FLX high throughput sequencing of the 16S rRNA gene.	root:Environmental:Terrestrial:Soil
MGYS00001563	Evaluation of molecular techniques in characterization of deep terrestrial biosphere	Depending to the methods used for characterization of uncultured microbial communities from environmental samples, the results may differ profoundly. Here we have employed three different molecular community screening tools (DGGE, cloning, NGS) and compared their performance for revealing the microbial community profiles in groundwater samples. DGGE is a quick method for community profiling, but may leave many of the microbial groups present undetected. Cloning libraries generally perform better than DGGE, but is labor-intensive and cost ineffective, and may also suffer from incompatibility between insert and transformation host. The NGS method performed best and gave the most complete picture of the uncultured microbial community, but the drawback of this method is the shortness of the sequence reads obtained. In this paper we discuss the pros and cons of these methosd in environmental microbiology.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00002448	Biological rejuvenation of iron oxides in bioturbated marine sediments	This project seeked to understand the distribution of iron-oxidizing Zetaproteobacteria in coastal marine sediments, which could allude to their importance to the Fe cycle in these systems.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00003172	San Diego Seagrass	For a comparative analysis of microbial community structure between sites with and without seagrass in and outside of San Diego Bay.	root:Host-associated:Plants
MGYS00004365	PCB-contaminated sediment Genome sequencing	Extracellular organic matter (EOM) from Micrococcus luteus was used to enhance biphenyl biodegradation. The effect of the EOM on the composition of bacterial community was investigated by Illumina high-throughput sequencing.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004193	L''Atalante sediment - Extracellular Metagenome	SSU 16S pyrosequencing project of the extracellular DNA metagenome of a DHAB sediment (L''Atalante) from the Eastern Mediterranean.	root:Environmental:Aquatic:Marine:Sediment
MGYS00001767	Plastisphere Targeted Locus (Loci)	Plastic marine debris is a recent introduction to marine ecosystems resulting from the widespread use of polymers in consumer goods after World War II. The current global annual production of plastic is 245 million tonnes or 35 kg of plastic for each of the 7 billion humans on the planet, rivaling the combined biomass of all humans. Drifter buoys and physical oceanographic models demonstrate that surface particles passively migrate from the coastline to the central gyres in less than 60 days, illustrating how quickly human-generated debris can impact the ‘pristine’ gyre interiors, more than 1000 km from land. Plastic debris has been implicated as a vector for transportation of harmful algal species and persistent organic pollutants, and provides a substrate for microbes that moves between environments and lasts much longer than most natural floating substrates. Despite increases in plastic production no significant trend in plastic accumulation has been observed since 1985. Physical shearing and photodegradation are known mechanisms of plastic degradation, but microbial degradation has also been implicated. Unpublished data from our laboratories employing pyrotag amplicon sequencing targeting bacterial and eukaryotic small subunit ribosomal RNA gene sequences, together with Scanning Electron Microscopy (SEM) data are consistent with the notion that plastic debris harbors a unique association of microbes including members capable of degrading plastic. The term ‘Plastisphere’ describes this unique microbial community attached to and surrounding marine plastic debris and distinct from microbes in the surrounding seawater and on natural substrates such as macroalgae. This proposal will: (1) characterize diversity through amplicon sequencing and comparative -omics combined with SEM and confocal microscopy to investigate the microbial composition of the Plastisphere; (2) describe function of the Plastisphere taking a cultivation-independent environmental DNA gene expression approach, as well as a cultivation-based approach to interrogate environmental clones and microbial isolates for the ability to degrade hydrocarbons; and (3) determine key biological factors that control the fate of plastic debris in the upper water column.	root:Environmental:Aquatic:Marine
MGYS00000592	EFFECT OF POSTNATAL LOW-DOSE EXPOSURE TO ENVIRONMENTAL CHEMICALS ON THE GUT MICROBIOME IN A RODENT MODEL	Using the Sprague-Dawley rat model, three chemicals that are widely used in personal care products, i.e. diethyl phthalate (DEP), methyl paraben (MPB), triclosan (TCS) and their mixture (MIX), were administered at doses comparable to human exposure from birth through adulthood. The fecal samples were collected at two time points, i.e. postnatal day (PND) 62 (adolescence) and PND 181 (adulthood).  The gut microbiome was profiled by 16S rRNA gene sequencing followed by taxonomic assignment and diversity analysis.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006631	EMG produced TPA metagenomics assembly of PRJEB54966 data set (Papua New Guinean oral metagenomes).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB54966, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00006629	EMG produced TPA metagenomics assembly of PRJNA779415 data set (Vaginal microbiome of reproductive age mother daughter pairs).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA779415, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00006630	EMG produced TPA metagenomics assembly of PRJEB37382 data set (Assessment of different methods for library preparation of human vaginal samples).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB37382, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00006628	EMG produced TPA metagenomics assembly of PRJEB51898 data set (Vaginal metagenome dataset of 47 healthy women).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB51898, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00006627	EMG produced TPA metagenomics assembly of PRJNA669294 data set (Effect of metronidazole on vaginal microbiota associated with asymptomatic bacterial vaginosis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA669294, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00006626	EMG produced TPA metagenomics assembly of PRJNA760651 data set (Exploring the possible link between the gut microbiome and fat deposition in pigs).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA760651, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006625	EMG produced TPA metagenomics assembly of PRJNA741980 data set (Comparison of viromes and microbiomes of 14 pig fecal samples).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA741980, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006623	EMG produced TPA metagenomics assembly of PRJNA793167 data set (Healthy and diarrhea piglets feces microbiota analysis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA793167, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006622	EMG produced TPA metagenomics assembly of PRJEB19642 data set (Metagenomic analysis of gut microbiota in sows and piglets (EBI)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19642, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006624	EMG produced TPA metagenomics assembly of PRJEB15296 data set (Structure and function of the fecal microbiota in diarrhoeic neonatal piglets).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB15296, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006620	EMG produced TPA metagenomics assembly of PRJNA389749 data set (Caecal Metagenome of Pigs).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA389749, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum.	root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
MGYS00006619	EMG produced TPA metagenomics assembly of PRJNA757683 data set (Apical Periodontitis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA757683, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006615	EMG produced TPA metagenomics assembly of PRJNA380727 data set (human saliva metagenome Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA380727, and was assembled with metaSPAdes v3.15.3, SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006614	EMG produced TPA metagenomics assembly of PRJNA470402 data set (human saliva metagenome Raw reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA470402, and was assembled with metaSPAdes v3.15.3, SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006618	EMG produced TPA metagenomics assembly of PRJNA791464 data set (Oral saliva microorganisms in 3-year-old children with different caries risk).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA791464, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006617	EMG produced TPA metagenomics assembly of PRJDB10606 data set (Shotgun metagenome sequencing of saliva microbiome of MRONJ patients using HiSeq).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJDB10606, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006616	EMG produced TPA metagenomics assembly of PRJNA762218 data set (Salivary Microbiome in Adenoid Cystic Carcinoma).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA762218, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006613	18S rRNA amplicon sequencing from the Ocean Sampling Day (OSD) campaign June 2018	Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. The OSD2018 event is a continuation of the successful OSD events of Micro B3 project (https://www.microb3.eu/osd.html).	root:Environmental:Aquatic:Marine
MGYS00006612	18S rRNA amplicon sequencing from the Ocean Sampling Day (OSD) campaign June 2019	Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. The OSD2019 event is a continuation of the successful OSD events of Micro B3 project (https://www.microb3.eu/osd.html).	root:Environmental:Aquatic:Marine
MGYS00006611	18S rRNA amplicon sequencing from the Ocean Sampling Day (OSD) campaign June 2018	Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. The OSD2018 event is a continuation of the successful OSD events of Micro B3 project (https://www.microb3.eu/osd.html).	root:Environmental:Aquatic:Marine
MGYS00006609	Amplicon sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for protists.	Analysis of 18S DNA in Tara Oceans Polar Circle Protists size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small and large cell sizes. The DNA was extracted and amplified by PCR.	root:Environmental:Aquatic:Marine
MGYS00006608	16S rRNA amplicon sequencing from the Ocean Sampling Day (OSD) campaign June 2018	Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. The OSD2018 event is a continuation of the successful OSD events of Micro B3 project (https://www.microb3.eu/osd.html).	root:Environmental:Aquatic:Marine
MGYS00006607	16S rRNA amplicon sequencing from the Ocean Sampling Day (OSD) campaign June 2019	Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. The OSD2019 event is a continuation of the successful OSD events of Micro B3 project (https://www.microb3.eu/osd.html).	root:Environmental:Aquatic:Marine
MGYS00006606	Amplicon sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for prokaryotes.	Analysis of 16S DNA in Tara Oceans Polar Circle Prokaryotes size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small cell sizes. The DNA was extracted and amplified by PCR.	root:Environmental:Aquatic:Marine
MGYS00006605	Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for prokaryotes.	Analysis of 16S DNA in Tara Oceans Prokaryotes size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small cell sizes. The DNA was extracted and amplified by PCR.	root:Environmental:Aquatic:Marine
MGYS00006601	sponge metagenome genome assembly, odCliOrie1.metagenome	This project provides the full unbinned assembly of Cliona orientalis and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006599	sponge metagenome genome assembly, odXesMuta1.metagenome	This project provides the full unbinned assembly of Xestospongia muta and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006600	annelid metagenome genome assembly, wcBraLoba9.metagenome	This project provides the full unbinned assembly of Branchellion lobata and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Annelida
MGYS00006598	sponge metagenome genome assembly, odAgeOroi1.metagenome	This project provides the full unbinned assembly of Agelas oroides and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006597	sponge metagenome genome assembly, ooOscLobu1.metagenome	This project provides the full unbinned assembly of Oscarella lobularis and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006596	mollusc metagenome genome assembly, xbBatBroo1.metagenome	This project provides the full unbinned assembly of Bathymodiolus brooksi and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Mollusca
MGYS00006595	mollusc metagenome genome assembly, xgAlvStru1.metagenome	This project provides the full unbinned assembly of Alviniconcha strummeri and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Mollusca
MGYS00006594	annelid metagenome genome assembly, wsLamColu1.metagenome	This project provides the full unbinned assembly of Lamellibrachia columna and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Annelida
MGYS00006593	sponge metagenome genome assembly, ohAphBeat7.metagenome	This project provides the full unbinned assembly of Aphrocallistes beatrix and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006592	sponge metagenome genome assembly, odPetFici3.metagenome	This project provides the full unbinned assembly of Petrosia ficiformis and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006591	sponge metagenome genome assembly, odCraCram1.metagenome	This project provides the full unbinned assembly of Crambe crambe and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006590	mollusc metagenome genome assembly, xcSepLess1.metagenome	This project provides the full unbinned assembly of Sepioteuthis lessoniana and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Mollusca
MGYS00006589	sponge metagenome genome assembly, odAplAero1.metagenome	This project provides the full unbinned assembly of Aplysina aerophoba and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006588	sponge metagenome genome assembly, odSpoLacu1.metagenome	This project provides the full unbinned assembly of Spongilla lacustris and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006587	sponge metagenome genome assembly, odChoReni1.metagenome	This project provides the full unbinned assembly of Chondrosia reniformis and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006586	Trididemnum clinides seq squirt metagenome assembly, kaTriClin1.metagenome	This project provides the sea squirt metagenome assembly of Trididemnum clinides. It contains the full unbinned assembly of Trididemnum clinides and associated organisms plus the MAGs and bins derived from this assembly. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Tunicates:Ascidians
MGYS00006585	sponge metagenome genome assembly, odSpoOffi2.metagenome	This project provides the full unbinned assembly of Spongia officinalis and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006584	sponge metagenome genome assembly, odHalPani1.metagenome	This project provides the full unbinned assembly of Halichondria panicea and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006583	lichen metagenome genome assembly, glLicPygm2.metagenome	This project provides the genome assembly of lichen metagenome. The assembly is provided by the Darwin Tree of Life Project (https: //www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Fungi
MGYS00006582	sponge metagenome genome assembly, odEunFrag1.metagenome	This project provides the full unbinned assembly of Eunapius fragilis and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006581	sponge metagenome genome assembly, odXesBerg1.metagenome	This project provides the full unbinned assembly of Xestospongia bergquistia and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006580	sponge metagenome genome assembly, ooCorCand1.metagenome	This project provides the full unbinned assembly of Corticium candelabrum and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Porifera
MGYS00006579	algae metagenome genome assembly, uoEpiScrs1.metagenome	This project provides the full unbinned assembly of Epithemia sp. CRS-2021b and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).	root:Host-associated:Algae
MGYS00006577	Malaspina Expedition 2010 Microbial Vertical Profiles Metagenomes	"Here we present a dataset of 76 microbial metagenomes of the picoplankton size fraction (0.2-3.0 μm) collected in 11 stations along the Malaspina Expedition circumnavigation (http://www.expedicionmalaspina.es; Duarte 2015) that cover  vertical profiles sampled at 7 depths, from the surface to 4,000 m deep (or the sea floor in shallower waters), plus 5 additional metagenomes. This Malaspina Microbial Vertical Profiles metagenomes (MProfile) dataset produced 1.66 Tbp of raw DNA sequences. Six L seawater samples were collected and filtered through a 200 and a 20 μm mesh to remove large plankton, the prokarotic free-living size fraction (0.2 to  3.0 μm) was recovered in each sample by pumping water serially through 47-mm polycarbonate membrane filters of 3.0 μm and 0.22 μm pore sizes with a peristaltic pump. DNA was extracted using a standard phenol-chloroform protocol and was sequenced at the National Center for Genomic Analsis (CNAG-CRG. Barcelona, Spain; www.cnag.es), funded by project MALASPINOMICS (CTM2011-15461-E, led by Carlos M Duarte) on the Illumina HiSeq2000 sequencing platform utilizing a TruSeq paired-end cluster kit, v3, following a 2x100 indexed run recipe. 

References: Duarte CM. 2015. Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition. Limnology and Oceanography Bulletin 24:11-14; Sánchez, P. et al., 2023. Marine picoplankton metagenomes from eleven vertical profiles obtained by the Malaspina Expedition in the tropical and subtropical oceans. bioRxiv 2023.02.06.526790; doi: https://doi.org/10.1101/2023.02.06.526790"	root:Environmental:Aquatic:Marine
MGYS00006578	Analisi metagenomica (16S) su suolo rizosferico di nocciolo	Piante di nocciolo di 4 anni di due varieta' diverse (Tonda di Giffoni e Mortarella) concimate con fertilizzante di sintesi (NPK), compost di sansa, zolfo e bentonite, zolfo e bentonite + compost di sansa	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00006576	EMG produced TPA metagenomics assembly of PRJNA340003 data set (Metagenomic reconstruction of bacterioplankton community metabolism in the northern Gulf of Mexico Dead Zone).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA340003, and was assembled with SPAdes v3.11.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00006574	EMG produced TPA metagenomics assembly of PRJEB42572 data set (Dental plaque microbiomes from hunter-gatherer and subsistence farmer populations in Cameroon).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB42572, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00001988	EMG produced TPA metagenomics assembly of the Gut microbial succession follows acute secretory diarrhea in humans (cholera_succession) data set	The cholera_succession Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9150. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system
MGYS00005023	EMG produced TPA metagenomics assembly of the The gut microbiome in Crohn's disease and modulation by exclusive enteral nutrition (123CD-metagenomics) data set.	The 123CD-metagenomics Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB15371.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002425	EMG produced TPA metagenomics assembly of the Metagenomic sequencing of preterm infant gut microbiota raw sequence reads () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA301903.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00006563	EMG produced TPA metagenomics assembly of PRJEB42399 data set (Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their adult caregivers).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB42399, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Skin.	root:Host-associated:Human:Skin
MGYS00002659	Bacteria exposure experiment North Sea	Bacterial sequencing (V3-V4 16S rDNA region) of plastic debris exposed for 5 or 10 months at the North Sea environment	root:Engineered:Solid waste
MGYS00002364	Parfrey_euk_testing_samples_515_806	Comparison of different sample types using different primers and platforms	root:Mixed
MGYS00000965	Soil bacteria (Pico de Aguila) Metagenome	In this study, the effect of deforestation and cultivation of maize (Zea mays L.) on the physicochemical characteristics and the bacterial community structure in soil were studied at the national park ‘Nevado de Toluca’ in Mexico. Soil was sampled from three forested areas in the national park with natural vegetation, and from three deforested areas cultivated with maize or grazed by animals and characterized while the bacterial community structure was investigated through 454 pyrosequencing of the 16S rRNA gene	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00002519	Reciprocal transplantation experiment of salt marsh sediments Targeted loci	A reciprocal transplant experiment of rhizome associated bacterial communities between five salt marshes along the US East Coast to examine the roles that dispersal and environmental selection play in driving microbial community dynamics using bacterial v4v5 16S rRNA tag sequencing.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003993	Archaea 16S 01-13 Genome sequencing and assembly	Archaea 16S rRNA gene	root:Environmental:Aquatic:Marine:Sediment
MGYS00004044	16S rRNA Analysis of Osaka Bay Microbiomes	16S rRNA gene sequencing project for a time-series nine seawater samples from the 5 m depth at the entrance of Osaka Bay, Japan every 3 hours over a period of 24 h.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004066	"Deep-sea post-eruption ""snowblower"" microbial blooms raw sequence reads"	Microbial community analysis of fluid samples and white flocculent material from active snowblower vents as well as orange flocculent material found on top of newly formed lava flows. Samples were collected following the 2011 eruption at Axial Seamount, an active volcano on the Juan de Fuca Ridge.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00006572	Metatranscriptomics analysis of bacterial comunities in two moss species	Metatranscriptomics analysis of bacterial comunities in two moss species	root:Host-associated:Plants:Phylloplane:Epiphytes
MGYS00000437	The effect of different loading rates of biochar on soil microbes	Biochar and its applications in soil is involved in many aspects related to soil health and quality, for instance, chemical and physical changes in soil. However, the major aspect, which is still far from being understood and has so far received less attention than any other aspects, is the impact of biochar applications on soil microbes and how microorganisms in soil interact and adjust with biochar-modified soil environments	root:Environmental:Terrestrial:Soil
MGYS00002492	Metagenomes of Sediments from Red Sea Atlantis II and Discovery Deep Brine Pools	The study focuses on Atlantis II and Discovery deeps brine pool sites, specifically sub-seafloor sediment.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00004347	Surface sediment of Yellow Sea, Bohai Sea and north East China Sea Metagenome	This is a microbial assemblages study targeting the surface sediments of the northern part of Chinese marginal seas	root:Environmental:Aquatic:Marine:Sediment
MGYS00003722	3Soil16S		root:Environmental:Terrestrial:Soil
MGYS00002363	Song_2012_family_study	Human-associated microbial community composition is highly variable across host individuals, but the sources of this variability remain poorly understood. Previous studies have explored some possible contributing factors such as (genetic) relatedness, diet, and developmental stage. A likely additional cause is that our microbial communities are shaped by our unique surroundings, including the individuals with whom we interact at various stages of life. To quantify potential microbial exchange, we surveyed fecal, oral, and skin microbiota from 159 humans and 36 dogs across 60 families consisting of spousal units with children, dogs, both, or neither. Members of the same family, particularly couples, shared more of their microbiota than did individuals from different households, with an especially strong effect of co-habitation on skin compared to oral or fecal microbiota. Dog ownership, but not children, had a significant effect on the extent to which cohabiting adults shared skin (forehead and palm) microbiota, and dog-owning adults shared more microbial taxa with each other than with those who did not. Furthermore, adults shared more skin microbiota with their own dogs than with other dogs. These results suggest that direct and frequent contact with our cohabitants may significantly shape the composition of our microbial communities.	root:Host-associated
MGYS00003117	uncultured marine eukaryote Targeted loci environmental	Identification of mixotrophic protists in Antarctic marine water samples based upon bromodeoxyuridine incorporation via grazing on labelled bacteria and subsequent 454 amplicon sequencing of the V9 region of the 18S ribosomal RNA gene.	root:Environmental:Aquatic:Marine
MGYS00003990	Marine subseafloor sediment Targeted Locus (Loci)	We examine the relationship between subseafloor microbial diversity and paleoceanographic conditions in samples from three sediment cores from the Eastern Mediterranean Sea and the Black Sea. All three cores record dramatic changes in oceanographic/limnic conditions resulting from oscillation between oligotrophic and euxinic condition, yet they also differ remarkably between sites. Our motivation for this study is based on the premise that paleoenvironmental conditions in the overlying water column are intimately linked to the composition of aquatic microbial communities and thus the inoculum for subseafloor communities. Our study will address the long-standing question to what degree the composition of subseafloor microbial communities is linked to paleoenvironmental conditions at time of deposition. The sample set at both Mediterranean sites is composed of carbonate-rich, organic-lean sediments and interspersed so-called sapropels, that is, organic-rich black layers that were deposited during climates that were probably warmer and more humid than today, when the Mediterranean was euxinic. The samples from the discovery basin are influenced by a highly saline brine and thus may select for halophilic sedimentary microbes. The Black Sea sample set is composed of organic-lean coccolith ooze deposited during the recent few thousand years, an organic-rich sapropel deposited during the early Holocene and below of sediment deposited during the late glacial/early Holocene when the Black Sea was still a freshwater lake. We examine both archaeal and bacterial diversity with a 454-based tag sequencing survey. We can address questions relating to the paleoenvironmental history at each site as well as to the relationship of microbial communities in sediments deposited during euxinic conditions at three sites along a salinity gradient remote to each other, in two different ocean basins. The sample set will be accompanied by an in-depth biogeochemical characterization of its sedimentary habitat. Sediment sampling and characterization are performed and mutually integrated on the same cruise (RV Meteor, M84-1, February 9-22, 2011) by the proponents of this proposal.	root:Environmental:Aquatic:Marine:Sediment
MGYS00001024	Environment Targeted Locus (Loci)	The application of fresh digestate, derived from the anaerobic treatment of animal wastes, is known to affect the short-term dynamics of microbial communities. A metagenomic study was carried out to test the effect of livestock-derived digestate amendment on an agricultural soil bacterial, yeasts and fungal community structure and dynamics.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00003091	Ocean crust Targeted Locus (Loci)	Much of the earth''s microbial biomass exists in the subsurface, and a sizable fraction of this is in oceanic igneous rocks. If microbial life in the igneous ocean crust extends to the depth of the ~120°C isotherm (the current upper temperature limit of life) then the volume of rock available for microbial colonization is about the same as the volume of the oceans. Most of this volume is difficult to sample but microorganisms have been identified from deep layers of the igneous ocean crust.  Additional understanding of the deep igneous biome comes from microorganisms extracted from subsurface fluids; although unattached microorganisms in aquifer fluids are not necessarily representative of the microorganisms attached to the host rocks. Another difficulty is that the ocean crust is mineralogically heterogeneous typically on the 0.01 mm to 10 mm scale and if the mineralogy influences or controls the microbial communities, then the ocean crust is microbially heterogeneous on the 0.01 to 10 mm scale. Community structure that is determined from bulk crustal rock samples will not be informative about how communities are associated with crustal minerals. Also, molecular and sample processing methods are not currently available to determine the community structure of minerals in igneous rocks.  In situ colonization of mono-mineralic substrates in the ocean crust is one method of determining microbial community structure of the minerals that make up the crust. We devised a method of incubating a wide variety of mono-mineral aggregates in the ocean floor simultaneously so that they all experienced the same temperature, water composition, and pressure. The mass of each incubated mineral was large enough to expect recovery of adequate amounts of DNA for analysis. The location chosen for this experiment was Integrated Ocean Drilling Program (IODP) borehole 1301A, which is located at 47° 45.210'' N, 127° 45.833'' W in 3.6 Ma old ocean crust in the northeast Pacific Ocean.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00004036	Bacterial population dynamics in a natural assemblage upon the addition of artificial alginate particles and alginolytic Alteromonas macleodii	Investigation of alginate degradation by marine bacterial communities from macroalgae-rich habitats in Southern California.	root:Environmental:Aquatic:Marine
MGYS00001008	CK1/MNPK1/NPK1 Targeted Locus (Loci)	The goal of present study is to examine what soil bacterial taxa were significantly affected by Cu amendments, and what taxa were the keystone organisms in Cu-contaminated soils using network analysis approach	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00000725	soil metagenome Metagenome	Increased exploration and exploitation of resources in the Arctic is leading to a higher risk of petroleum contamination. A number of Arctic microorganisms can use petroleum for growth-supporting carbon and energy, but traditional approaches for stimulating these microorganisms (e.g. nutrient addition) have varied in effectiveness between sites. Consistent environmental controls on microbial community response to disturbance from petroleum contaminants and nutrient amendments across Arctic soils have not been identified, nor is it known whether specific taxa are universally associated with efficient bioremediation. In this study, we contaminated 18 varied Arctic soils with diesel and treated subsamples of each with monoammonium phosphate (MAP). Bacterial community composition of uncontaminated, diesel-contaminated, and diesel + MAP soils was assessed through multiplexed 16S rRNA gene sequencing on an Ion Torrent Personal Genome Machine, while hydrocarbon degradation was measured by GC analysis. The predictability with which bacterial communities respond to these disturbances suggests that costly and time-consuming contaminated site assessments may not be necessary in the future.   Top 15 cm soils collected from across the Arctic, left untreated, or treated with diesel or diesel   nutrients.	root:Environmental:Terrestrial:Soil
MGYS00000886	Arable soil Targeted Locus (Loci)	Manure unspiked and spiked with SDZ in two different concentrations was applied three times, and the bacterial community composition in soil was monitored over a period of 193 days. To differentiate between short and longer-term effects, the soil was sampled 3 and 60 days after each manure application, respectively.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00004138	Diversity and abundance of Bathyarchaeota (MCG) in South China Sea sediments and the implication of its ecological roles	Diversity and abundance of Bathyarchaeota	root:Environmental:Aquatic:Marine:Sediment
MGYS00002660	Diet analysis of Pacific Bluefin Tuna larvae	Metagenetic analysis on gut contents of Pacific Bluefin Tuna larvae and planktons in environmental water	root:Environmental:Aquatic:Marine
MGYS00000426	Changes in microbiota composition in colitis-prone mdr1a mice	The symbiotic relationship between gut microbiota and the host is necessary for intestinal homeostasis.  Loss of tolerance to the gut microbiota results in chronic inflammatory bowel diseases (IBD), such as Crohn’s disease and Ulcerative colitis. The microbiota resides in two compartments-the gut lumen and mucus layer. Most published findings focus on luminal microbial communities in IBD pathogenesis with much less being understood about the bacteria resident in the mucus layer that abuts the epithelium. Thus, the precise interactions between microbiota and the intestinal mucosa during IBD development are still unknown. To address this, we investigated colitis progression in the mdr1a-/- spontaneous model of colitis. We examined microbiota composition in the mucus and lumen in mdr1a-/- mice and wild-type littermate controls at an early pre-colitic and a later post-colitic stage. We aim to identify if bacterial differences in specific niches  precede IBD development and progression. Our study provides valuable insight in microbiota-host interactions in normal and diseased states, revealing new approaches for the management of IBD.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00004568	Marine metagenome ICM_BSR	Examining the Free-Living and Particle-Associated Bacterial Community in the Black Sea''s Suboxic Zone.	root:Environmental:Aquatic:Marine
MGYS00002773	Microbial Processes and Biodiversity: OCEAN	Study of microbial communities (16S rRNA and 18S rRNA genes) in two coastal oceans observatories located in contrasting latitudes: (i) Equatorial Atlantic Ocean - Equatorial Atlantic Microbial Observatory (EAMO) and (ii) Mediterranean Sea - Blanes Bay Microbial Observatory (BBMO).	root:Environmental:Aquatic:Marine:Coastal
MGYS00004032	Diversity of Microbial Eukaryotes in Sea Waters From Fildes Peninsula,King George Island, Antarctica	To investigate molecular diversity of microbial eukaryotes in sea water from Greatwall cove and Ardley cove, Fildes Peninsula, ten water samples were collected during the 29th Chinese Antarctic scientific expedition in 2013. After pyrosequencing and analysis, the molecular diversity of microbial eukaryotes of sea water from Greatwall cove and Ardley cove was generally achieved.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002554	Nutrient addition mesocosm experiment Targeted Locus (Loci)	Amplicon sequencing of environmental planktonic organisms to assess the interactions during a nutrient addition experiments.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002523	South China Sea interfaces 16S amplicon sequencing	16S amplicon sequencing of microbial communities at geological interfaces in South China Sea marine sediments sampled during IODP expedition 349.	root:Environmental:Aquatic:Marine:Sediment
MGYS00000961	Arable and pasture soils spiked with anthracene Metagenome	Two soils were contaminated with 500 mg anthracene using acetone. Five different treatments were applied to the anthracene-contaminated soil. In a first treatment, soil was amended with two adult Eisenia fetida earthworms (0.35 g) and with a developed clitellum. The earthworms were fed 60 g carrot every two weeks. In a second treatment, soil was amended with 60 g organic material (carrot) every two weeks. As such, the effect of the earthworms on the removal of anthracene could be differentiated from that of the organic material applied. In a third treatment, soil was mixed for 10 min every 7 days. In a fourth treatment, soil was amended with 24.9 g kg-1 soil surfactant Surfynol® 485 and mixed. In a fifth treatment, soil was left unamended and served as control so that remediation capacity of the autochthonous microorganisms could be determined. Two more treatments were used in this study. In a first additional treatment, both soils were applied with the same amount of acetone used as carrier to contaminate the soil with anthracene and in a second additional treatment, unamended soil was used and served as control.	root:Environmental:Terrestrial:Soil
MGYS00002518	Marine planktonic ciliates: SSU rDNA	Diversity and biogeography of marine planktonic ciliates in the NW Atlanctic Ocean	root:Environmental:Aquatic:Marine:Oceanic
MGYS00001791	Benthic microbial communities associated with hypoxia on the Black Sea shelf break (NW Crimea)	The effect of varying oxygen conditions on benthic microbial communities was investigated at the North Western Crimean shelf break (Black Sea), at water depths between 105-207 m.  Sampling was performed with a TV-MUC on April-May 2010 on board of the RV Maria S. Merian (Cruise MSM 15-a) along gradient of oxygen bottom water concentrations between oxic (150 μmol L-1, station 464), variable hypoxic (3-60 μmol L-1 O2, stations 487 and 393) and anoxic, sulfidic conditions (station 448).	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00001602	Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms	The nitrogen cycling bacterial community at 100 m depth in crystalline bedrock groundwater was investigated using nitrate and ammonium as substrates in a stable isotope probing study. The bacterial community was enriched with 15N ammonium or nitrate for 28 days after which the enriched community and the nitrogen assimilating communities were compared using 454 amplicon sequencing of the 16S rRNA genes	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00004673	Study on bacterial diversity and functionality in the Adriatic Sea	Study on bacterial diversity and functionality in the Adriatic Sea.  PCR amplified 16S rRNA genes from an inoculum in the Adriatic Sea and bacterial communities incubated in continuous cultures with different treatments.	root:Environmental:Aquatic:Marine:Coastal
MGYS00003076	Red Sea marine sponges and seawater Targeted Locus (Loci)	The genes and transcripts of 16S rRNA were amplified from seawater, S. carteri, and X. testudinaria DNA (originating the following datasets: WTD1-WTD3, ASD1-ASD3, and AXD1-AXD3; respectively) and cDNA (originating the following datasets: WTR1-WTR3, ASR1-ASR3, and AXR1-AXR3; respectively). Purified amplicons were pooled equally and sequenced on a Roche 454 GS FLX Titanium platform. Sponge samples from the species Stylissa carteri and Xestospongia testudinaria were collected. Seawater samples were collected during the same dive. Sample location is: Fsar reef (22°23'N; 39°03'E) at the coast of Thuwal, Saudi Arabia. Depth was at 8.5-12 meters.	root:Mixed
MGYS00006571	EMG produced TPA metagenomics assembly of PRJEB34453 data set (Atlantic Ocean Metagenomes).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB34453, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00004465	Marine fungi Raw sequence reads	biogeography and seasonality of benthic fungi	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004064	Surfactant-associated bacteria in the near-surface layer of the ocean	Certain marine bacteria found in the near-surface layer of the ocean are expected to play important roles in the production and decay of surface active materials; however, the details of these processes are still unclear. Here we provide evidence supporting connection between the presence of surfactant-associated bacteria in the near-surface layer of the ocean, slicks on the sea surface, and a distinctive feature in the synthetic aperture radar (SAR) imagery of the sea surface. From DNA analyses of the in situ samples using pyrosequencing technology, we found the highest abundance of surfactant-associated bacterial taxa in the near surface layer below the slick. Our study suggests that production of surfactants by marine bacteria takes place in the organic-rich areas of the water column. Produced surfactants can then be transported to the sea surface and form slicks when certain physical conditions are met. This finding has potential applications in monitoring organic materials in the water column using remote sensing techniques. Identifying a connection between marine bacteria and production of natural surfactants may provide a better understanding of the global picture of biophysical processes at the boundary between the ocean and atmosphere, air-sea exchange of greenhouse gases, and production of climate-active marine aerosols.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004201	22V-SMAR-TVG01 Targeted Locus (Loci)	Analyzing the microbial diversity of the sediment	root:Environmental:Aquatic:Marine:Sediment
MGYS00004017	Aarhus Bay Station M5 sediment metagenome sequencing	ANME-1 draft genome binned from Aarhus Bay M5 sediment metagenome samples (Bioproject PRJNA305566)	root:Environmental:Aquatic:Marine:Sediment
MGYS00002591	Spirulina necromass degradartion in arctic marine sediments	Reveal the identity and population dynamics of responders to spirulina and acetate amendments to arctic marine sediments.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003468	EMG produced TPA metagenomics assembly of the A method for identifying metagenomic species and variable genetic elements by exhaustive co-abundance binning () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB1220.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002952	Microbial communities in marine surface water	To investigate the biogeographic patterns of microbial communities in surface water from Indian Ocean to Chinese marginal seas	root:Environmental:Aquatic:Marine
MGYS00001003	16s rRNA profiling of Park Grass microbial community	16s rRNA amplicon sequencing of DNA isolated from the Park Grass soil	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00005156	Flores_forehead_EBI	Forehead skin samples from Flores_SMP for submission to EBI	root:Host-associated:Human:Skin
MGYS00004102	marine sediment metagenome Raw sequence reads		root:Environmental:Aquatic:Marine:Sediment
MGYS00002896	Diversity of SE Pacific benthic Bacteria and Archaea communities Targeted Locus (Loci)	Characterization of the benthic bacteria and archaea communities their inferred functions and biotechnological potential.	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00001456	Sediment microbial diversity from samples of the lagoons of the Amvrakikos Gulf (Ionian Sea, Western Greece)	The aim of the present study was to explore the biodiversity patterns of microorganismic assemblages and to examine whether these patterns are associated with those of the contextual environmental parameters. For this purpose, sediment samples were collected from five lagoons (Rodia, Tsoukalio, Tsopeli, Mazoma, Logarou), located in Amvrakikos Gulf (Ionian Sea, Western Greece). In each lagoon, two sampling stations were chosen, with different connectivity degree with the sea. A number of abiotic parameters were measured for every station, including the sediment concentrations of heavy metals and elements. Microbial DNA was extracted from the sediment upper layer (0-2cm) and was further processed through deep sequencing of the V5-V6 region of the 16S rRNA gene by next generation sequencing.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004452	Marine sediment microbial communities in the presence of macrophytes	In this study we examined the sediment microbial communities in the absence and presence of two marine macrophytes (Zostera muelleri - Zm, and Caulerpa taxifolia - Ct), and at low (L) and high (H) densities of the macrophytes.Three independent and randomly obtained samples were taken from each of the five treatment groups (absent, Zm-L, Zm-H, Ct-L, Zm-H), genomic DNA extracted and PCR conducted targeting the V4 region of the 16S gene. PCR amplicons were sequenced using Illumina MiSeq 2x250 bp, with paired-end sequencing.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004169	Microbial eukaryotes present in a Norwegian coastal ecosystem and in the gut content of Calanus copepods from Raunefjorden	Use metabarcoding to characterize the diversity of Calanus prey relative to the total microbial eukaryote diversity in the co-occurring seawater habitat	root:Environmental:Aquatic:Marine
MGYS00004171	marine metagenome Raw sequence reads	Microbial diversity in coastal areas of Sichang island in Thailand	root:Environmental:Aquatic:Marine
MGYS00000789	Geothermal Springs Targeted Locus (Loci)	Studies to date suggest that this temperature-diversity gradient relationship is weak or nonexistent for Bacteria and Archaea. To test the impact of temperature as well as pH on prokaryotic diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5-99 °C and a pH range of 1.8-9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study.	root:Environmental:Terrestrial:Soil
MGYS00003984	marine sediment metagenome Targeted Locus (Loci)	The microbiological objectives of IODP Expedition 347 Baltic Sea Paleoenvironmentfocused on 1) how the phylogenetic diversity of the deep biosphere in this intracontinental sea differs from that of deep-ocean communities, and 2) are microorganisms that presently live in the deep sediments remnants of limnic and marine populations, or does the modern sedimentary environment select for thecommunity. The Expedition took place September 16, 2013 – November 1, 2013 on board the IODP Mission-Specific Platform Greatship Manisha. Cores were advanced for microbiological sampling at 4 locations: BSB-1, BSB-3, BSB-7, and BSB-9 (Figure 1) using Advanced Piston Coring (APC) and checked for contamination using perfluorcarbon tracers (PFTs).	root:Environmental:Aquatic:Marine:Sediment
MGYS00004164	Seawater coastal British Columbia	Examine the distribution of specific markers genes over time	root:Environmental:Aquatic:Marine
MGYS00004158	16S rRNA genes Random survey	Sequencing of 16S genes from fractions of 15N and 13C SIP experiments	root:Environmental:Aquatic:Marine
MGYS00004589	Diversity of archaeal amoA gene	Diversity of Archaeal amoA genes in sea water samples from Ardley cove, Fildes Peninsula, Antarctica	root:Environmental:Aquatic:Marine
MGYS00004581	Arabian Sea OMZ nirS Metagenome	nirS amplicon sequences from the Arabian Sea	root:Environmental:Aquatic:Marine
MGYS00004208	1)sediments; 2) coral floc Metagenome	Deep-sea sediments and coral flocculant material (floc) collected from a coral community impacted by the Deepwater Horizon (DWH) oil spill were examined to determine the diversity of microbes and the presence of oil-degrading genes	root:Environmental:Aquatic:Marine:Sediment
MGYS00004277	sediment metagenome Raw sequence reads	microbe community and funtion	root:Environmental:Aquatic:Marine:Sediment
MGYS00005234	Goodrich_TwinsUK_Miseq_2	second half of Goodrich_MiSeq for EBI submission	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001561	Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time and seeded with either acclimated or non-acclimated sludge	In this study, 16S rRNA gene pyrosequencing was applied in order to provide a better insight on the effect of solids retention time (SRT) on the diversity and dynamics of total, dominant and rare bacterial taxa in eight replicate lab-scale sequencing batch reactors (SBRs) operated for a period of 78 days and seeded with either acclimated or non-acclimated sludge. Rank-abundance curves showed strong abundance of few dominant operational taxonomic units (OTUs) and a long tail of rare OTUs in all reactors. Results revealed that there was no detectable effect of SRT (2d vs. 10d) on Shannon diversity index and OTU richness of both dominant and rate taxa. Nonmetric Multidimensional Scaling (NMDS) analysis showed that the total, dominant and rare bacterial taxa were highly dynamic during entire period of stable reactor performance. Also, the rare taxa were more dynamic than the dominant taxa despite expected low invasion rates because of the use of sterile synthetic media. Moving-window analysis, Global ANOSIM and NMDS analysis revealed that the bacterial community structure in replicate SBRs seeded with acclimated or non-acclimated sludge was reproducible. Overall 16S rRNA gene pyrosequencing could reveal the dynamics of rare bacterial taxa that are normally left out using conventional molecular biology methods.	root:Engineered:Bioreactor:Continuous culture
MGYS00003002	Marine sediment metagenome ICM_FIS	Sands as microbial biodiversity hotspots: Investigating the effect of grain size and biofilm formation.	root:Environmental:Aquatic:Marine:Coastal
MGYS00000812	Antarctic soil watering experiment across a natural salinity gradient	The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change induced disturbances including the melting of massive buried ice, cutting through permafrost by streams, and warming events. These processes are increasing moisture across the landscape altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition (16S rRNA genes) and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment.	root:Environmental:Terrestrial:Soil
MGYS00005075	NEON Surface Water Microbe Marker Gene Sequences - 2014	This study provides the sequence data for the NEON data product, Surface water microbe marker gene sequences (NEON.DP1.20282). The goal of this project is to track changes in the diversity and composition of bacteria, archaea and fungi in planktonic aquatic ecosystems through space and time. NEON collects water column microbes from various depths at numerous sites distributed across the United States. Total genomic DNA is extracted and the 16S and ITS regions of the rRNA cistron are sequenced using high-throughput methods. For additional details and data, visit the NEON Data Portal at http://data.neonscience.org.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004383	Oxygen minimal zone Targeted loci environmental	To study diversity of microbe community including bacteria, dizotrophs, and protist.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005093	Effect of long term fertilization strategies on soil bacterial communities	Effect of long term fertilization strategies on soil bacterial communities	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00004195	La Medee sediment - Extracellular Metagenome Metagenome	SSU 16S pyrosequencing project of the extracellular DNA metagenome of a DHAB sediment (La Medee) from the Eastern Mediterranean.	root:Environmental:Aquatic:Marine:Sediment
MGYS00000955	Arbuscular mycorrhizal fungi from soil samples Targeted Locus (Loci)	Sequence arbuscular mycorrhizal fungi from soil samples from the Andean region	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00002527	Diversity of archaeal and bacterial 16S rRNA gene in marine sediment in Aarhus Bay	This project is to study the diversity of Archaeal and bacterial 16S rRNA gene in marine sediments in Aarhus Bay.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002997	nifH diversity in the North Pacific Ocean	This study was performed to elucidate community structure of nitrogen fixing bacteria in the North Pacific Ocean	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002812	Equatorial Pacific Ocean Targeted loci environmental	To (i) document vertical distributions of bacterial diversity and community composition, (ii) investigate how these communities vary from one oceanographic region to another, and (iii) test the extent to which bacterial communities of deep subseafloor sediment may originate in the water column, we used 454 pyrosequencing technology and the v4-v6 hypervariable region of the bacterial 16S rRNA gene to examine bacterial community composition (presence/absence and relative abundance) in the water column, near-seafloor sediment (5 cm), and subseafloor sediment at three environmentally distinct Pacific sites: the very high-productivity eastern equatorial upwelling region (EQP1), the moderately high-productivity open-ocean central equatorial upwelling region (EQP8) and the very low-productivity northern gyre (EQP11) (Figure 1).	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002490	Baselines Initiative 16S rRNA gene dataset: Baselines Amplicon Release 1 (R1) Indian Ocean 2015	The overall objective of this project (Baselines Initiative) is to generate several 16S rRNA gene databases to establish robust baseline information on the biological communities in marine ecosystems. This field study was conducted in the Bay of Bengal in Auguest-September 2015 to examine phytoplankton community diversity.	root:Environmental:Aquatic:Marine
MGYS00002476	Comparative study in validity of three regions of 18S-rRNA for eukaryote amplicon sequence analyses	In the present study, we performed a detailed investigation of the 18S-rDNA, namely, numbers of registered sequences, frequencies of amplification success, the amplicon sequence variability among three regions containing V1-V3, V4-V5 and V7-V9 regions using in silico PCRs based on public databases, and the identification power by NGS-based environmental surveys of planktonic eukaryote community. Although the number of registered sequences in V4-V5 regions was remarkably higher than other regions, the identification power in NGS-based environmental surveys was lowest in V4-V5 regions due to the lowest sequence variability. The number of registered sequences in V1-V3 region was ca. two times smaller than V7-V9 region, and the sequence variability in V1-V3 region was significantly higher than that in V7-V9 region. Then, the identification power was not significant between these two regions, implying identification power is affected by combination of numbers of registered sequences and the sequence variability. We therefore believe V1-V3 region will be the best one for applying to NGS-based monitoring of planktonic eukaryote community in the near future as the number of sequences deposited increases in public databases.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002837	Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans	This study investigated the response of bacterioplankton communities to the polysaccharides chitin, alginate, and agarose using seawater microcosms at four distant locations in the Southern and Atlantic Oceans.	root:Environmental:Aquatic:Marine
MGYS00000957	AMF from contaminated and uncontaminated rhizosphere soils Metagenome	The aim of this study was to compare AMF communities from petroleum-contaminated and adjacent uncontaminated soils, and to determine whether willow planting influenced community composition.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00004317	Depth dependent (0-5,000 m) and seasonal variability in archaeal community structure in the subarctic and subtropical western North Pacific.	Archaeal community composition was examined throughout the water column (0-5,000 m) of the subtropical and subarctic western North Pacific Ocean using a pyrosequencing-based analysis of archaeal 16S rRNA gene. Samples were collected on four occasions between 2011 and 2012 to explore seasonal variability in the community composition.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00003116	Ocean sediment-basement interface Targeted Locus (Loci)	Previous studies of microbial abundance and geochemistry in deep marine sediments indicate a stimulation of microbial activity near the sediment-basement interface. Furthermore, the few studies thus far conducted in deep oceanic crust reveal an active microbial community in this habitat. Yet, the extent to which microbial communities in bottom sediments and underlying crustal habitats interact is unclear. Are microbial communities in sediments seeded from basement communities, or vice versa? If there is influence from one habitat type on the other, how far does this influence extend, both with vertical distance away from the interface and laterally along the flow path of fluids within basement? We propose to conduct tag pyrosequencing on samples from a spectrum of sediment-basement habitats to identify patterns in microbial community shifts across sediment-basement interfaces. Such comparisons will allow us to evaluate whether microbial groups from one habitat are found in another, and to examine whether members of the ''rare biosphere'' in one habitat come to dominate in another. Analysis of the pyrosequencing data will help us better understand how subsurface microbial communities are established and evolve, in addition to expanding our knowledge of microbial biogeography across sediment-basement interfaces in different oceanic basins.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00000925	uncultured soil ammonia oxidizing bacteria PCR amplicom	This library was made using 454 - pyrophosphate sequencing method to attest diversity and richness of soil ammonia oxidizing functional gene (amoA)	root:Environmental:Terrestrial:Soil
MGYS00001158	Chernobyl soils Targeted Locus (Loci)	High throughput pyrosequencing was used to get a comprehensive picture of the phylogenetic diversity of Bacteria and Archae in radionuclides-contaminated and control soils collected in the trench T22 area, within the Chernobyl exclusion zone.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00002763	Arctic Ocean	Characterization of bacterial communities from the Arctic Ocean	root:Environmental:Aquatic:Marine:Oceanic
MGYS00000997	Hydraulic fracturing fluid-groundwater-soil incubations Targeted Locus (Loci)	Soil-groundwater mixtures were incubated with different levels of hydraulic fracturing fluids to monitor degradation of organic constituents over time	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00004199	Uncultured marine eukaryotes Targeted Locus (Loci)	A community study of the large-fraction eukaryotes present in the Beaufort Sea as determined by pyrosequencing of 18S molecules.	root:Environmental:Aquatic:Marine
MGYS00004192	L''Atalante sediment - Microbial Metagenome	SSU 16S pyrosequencing project of the microbial metagenome of a DHAB sediment (L''Atalante) from the Eastern Mediterranean.	root:Environmental:Aquatic:Marine:Sediment
MGYS00001704	P2IRC 1.3 Soil microbiome as plant phenotype	The study goal is to support crop breeders in identifying microbial communities and characteristics that improve crop yield. The microbial community associated with the roots of canola grown over a three-year period in a Saskatchewan field will be analyzed. DNA extraction and analysis results from the roots and soils will identify specific microbes or communities of microbes connected with the high yielding varieties. In combination with other phenotypic data, unique identifiers of the microbial community will be determined and then tested under controlled experimental conditions to validate their link in improved crop performance.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000736	Soil microbial diversity patterns of a lowland spring environment.	The Po river plain lowland springs comprise unique paradigms of managed environments. Their current locations used to be swamps that were drained 6-7 centuries ago, and had constant use ever since. Our aims were to identify the land use effects on the microbial communities of these soils, seek for associated diversity drivers and assess the applicability of ecology theories with respect to identified patterns. We screened the microbial diversity across a land use transect via high throughput sequencing of partial 16S rRNA gene amplicons. Land use had a major effect on soil properties and microbial community structures. Total organic carbon (TOC) and pH were major diversity drivers for Bacteria, while pH was important for Archaea. We identified the potential contribution of soil amendments to the indigenous microbial communities, and also gained insights about potential roles of taxa in the organic carbon turnover. Verrucomicrobia, coincided with the higher values of the recalcitrant organic carbon while Actinobacteria and Acidobacteria correlated with the more labile organic carbon. Finally, the higher diversity found in the less enzymatically active and relatively poorer in nutrients soils, may be explained to an extend by niche based theories like the resource heterogeneity hypothesis and Connell''s intermediate disturbance hypothesis. Multiplexed 16S rRNA gene amplicons from soil DNA extracts of samples derived from three soils (each in biological triplicates).	root:Environmental:Terrestrial:Soil
MGYS00004678	Sequences obtained from two sponge genera (Hyrtios, Aiolochroia), one zoanthid (Palythoa), and marine sediments. Metagenome	Study of the diversity of bacteria present in sponges and marine sediment, by 16s rRNA gene sequencing	root:Environmental:Aquatic:Marine:Sediment
MGYS00000867	Mesocosm mine tailing cores Targeted Locus (Loci)	The objective of this study was to analyze the temporal dynamics of the microbial communities colonizing the rhizosphere of plants growing in compost-amended mine tailings with the goal of linking community structure to ecosystem function. Metalliferous mine tailings, which usually have high acid-generating potentials, are often subject to phytoremediation to prevent the dispersion (by eolian and hydraulic action) of these metal-bearing particles. Assisted phytostabilization is a type of phytoremediation technology in which the mine tailings are amended with compost (as a source of carbon and nutrients, and pH buffer) and then are seeded with a native plant specie that has been specifically selected based on its capacity to grow on the tailings without accumulating elevated levels of toxic metals in the shoot tissues. Therefore, the metal contaminants are immobilized in the soil to minimize the health and environmental risks associated with the dispersion of exposed mine tailings. A major knowledge gap in the understanding of phytostabilization as a viable alternative for the remediation of mine tailing piles is the ecology of the microorganisms that grow in the root-zone of the plants. Little is known of how these microbial communities respond to plant growth and compost amendment, how they may influence the stabilization of the metal contaminants, how they may affect or enhance plant colonization of the tailings, and how their structure may reflect the state of the phytoremediation treatment. To try to answer some of these questions, we conducted a yearlong greenhouse experiment with 3 treatments (in triplicate): (1) tailings only control, (2) tailings amended with 15% compost control, (3) tailings amended with 15% compost and seeded with a shrub (quail-bush; Atriplex lentiformis). During that year, core samples were collected every 3 months to extract metagenomic DNA and analyze the structure of the microbial communities (i.e. phylogenetic and functional structure).	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00002782	Marine sediment metagenome raw sequence reads	Marine sediment amplicon study from brine disposal vincinity	root:Environmental:Aquatic:Marine:Sediment
MGYS00004608	DD_cyano Targeted loci environmental	To understand the distribution of diverse picocyanobacterial clades and environmental factors regulating their distribution, abundance and genetic diversity was investigated in adjacent waters of Dokdo showing diverse physical properties not only by seasonal variation but also by diverse physical processes.	root:Environmental:Aquatic:Marine
MGYS00005228	characterizing the gut communitties of twins discordant for obesity in gnotobiotic mice	International efforts to characterize the human microbiome in health and disease are producing massive amounts of data about organismal and gene content in our body habitat -associated microbial communities. A challenge is to complement these efforts with a preclinical research pipeline that tests the degree to which a person's physiologic or pathological phenotype can be ascribed to their microbiome and that offers an opportunity to evaluate potential strategies for microbiome-based therapeutics. Here we illustrate such a pre-clinical pipeline by transplanting previously frozen, uncultured fecal microbiota samples from four sets of adult female mono- and dizygotic twins discordant for obesity into groups of adult germ-free C57Bl/6J mice fed a low-fat, plant polysaccharide-rich diet. Capture of a human donor's microbiota in recipient mice is highly reproducible within and between experiments. The increased adiposity phenotype of obese co-twins is transmissible not only with the intact uncultured fecal communities, but with bacterial culture collections generated from these fecal samples. Co-housing mice five days after they received transplants of culture collections from the obese or lean member of a discordant twin pair ameliorated the increased adiposity phenotype that normally develops in recipients of the obese donor's culture collection, while having no effect on the adiposity phenotype of recipients of the lean co-twin's culture collection. These results correlate with taxonomic and metabolic changes in co-housed mice harboring the obese co-twin's culture collection. Our results demonstrate a way to perform pre-clinical studies of microbiome-associated human phenotypes, including methods for identifying, producing and testing candidate probiotic species as therapeutic or preventative agents.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006067	EMG produced TPA metagenomics assembly of PRJEB29127 data set (A causal role of the gut microbiome in schizophrenia).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB29127, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Hindgut:Rectum.	root:Host-associated:Human:Digestive system:Hindgut:Rectum
MGYS00004366	coastal sediments Targeted Locus (Loci)	The goal of this project is to study the bacterial communities and hydrocarbon degrading bacterial populations from coastal sediments of Patagonia, as well as their response to oil input. The study has got relevance regarding the bioremediation of cold coastal environments, as hydrocarbon pollution in high latitude marine environments is expected to increase.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004235	Foraminifera 18S rDNA and rRNA diversity for fish farms biomonitoring	Both 18S ribosomal DNA and RNA taxonomic markers were sequenced to investigate the response of benthic foraminiferal communities to environmental gradients related to the presence of salmon fish farms in two Scotland fjords. For both DNA and RNA extractions performed on 45 sediment samples and cDNA synthesis for RNA, we PCR amplified the 37f hypervariable region of the foramnifera using tagged PCR primers prior to library preparation (TruSeq) and MiSeq paired-end sequencing. The combinations of tagged primers are contained in the paried reads and could be used to assign the sequences the their sample of origin.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002566	Uncultured eukaryotes Targeted Locus (Loci)	Tracking environmental selection of marine microbial eukaryotes using 18S rRNA genes and 18S rRNA in the Gulf of Maine	root:Environmental:Aquatic:Marine
MGYS00000850	A community genomics investigation of fungal adaptation to cold	We sampled soils across the Arctic and have identified the resident fungi using molecular methods in order to ascertain which fungi are able to grow in the coldest climates.	root:Environmental:Terrestrial:Soil
MGYS00000755	Semi arid steppe soil Metagenome	We extracted soil DNA and sequenced using 454 pyrosequencing to evaluated soil AM fungal responses on the future climate change.  Arbuscular mycorrhizal fungal DNA was extracted from a semi arid steppe in Inner Mongolia.	N/A
MGYS00005040	Bacterial communities in agricultural soils under contrasting agronomic managements and biomes of Argentina	The aim of this study was to compare soil bacterial communities in agricultural lands attempted to soybean production in different regions of Argentina. Intensive and conservative management practices were evaluated in contemporary long-term field experiments carried out in three different locations of the rolling pampas region.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00003717	Microbial community structure is affected by cropping sequences and bio-covers under long-term no-tillage	Changes in soil bacterial community composition were assessed in response to cropping sequences and bio-covers at long-term no-tillage sites. Main effects of 4 four different cropping sequences of corn (Zea mays L.), cotton (Gossypium hirsutum L.), and soybean (Glycine max L.) were rotated in four year phases for 12-yrs at two Tennessee Research and Education Centers in a randomized complete block design with split-block treatments of four winter bio-covers: hairy vetch (Vicia villosa L.), wheat (Triticum aestivum L.), poultry litter, and a fallow control. Using Illumina high-throughput sequencing of 16S rRNA genes, bacterial community composition was determined.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000858	Leaf litter Genome sequencing	Monitoring bacterial community changes during leaf litter degradation of Zea mays in arable soil	root:Environmental:Terrestrial:Soil
MGYS00001002	Soil bacterial community in temperate grassland	Anthropogenic disturbance and global climate change are greatly affecting ecosystems worldwide by ways such as widespread nitrogen (N) deposition and changing precipitation regimes. It is predicted that the mean annual precipitation and N deposition in North China will continue to increase in future. Although much of work has been focus on the response of above-ground plant community to presumed climate change, the effects of nitrogen and water addition on the soil microbial community has not yet been systematically surveyed. Given the important role of soil microbial communities in nutrient cycling in terrestrial ecosystem, the effects of nitrogen and water addition and their interaction on soil microbial communities increased our attention. The specific aims of this project are: (1) to analyze the response of soil microbial diversity and community structure to the increase of soil N inputs and soil moisture; (2) to reveal the relationship between the variation of microbial communities and the above-ground plant community. The study sites were located in Duolun county, Inner Mongolia (E 116°17’20”, N 42°2’29”). A field experiment with a constant increase in precipitation and three Nitrogen supply levels was established in 2005 to examine the potential effects of N deposition and changes in precipitation regime on the ecological processes. A split-plot experimental design was employed in this study. The block was divided into two main plots with water treatment (ambient precipitation and water addition). Each main plot was divided into twenty-eight 8 m × 8 m subplots with a 1-m wide buffer zone. Four levels of Nitrogen treatment (N0 (control), N5 (5 g N m-2 yr-1), N10 (10 g N m-2 yr-1), N15 (15 g N m-2 yr-1), each including seven replicates, were randomly assigned to each subplot within main plot. In the middle growing season from June to August, the water addition plots received 15 mm of precipitation weekly by sprinkling irrigation. A total of 180 mm precipitation, approximately 50% of mean annual rainfall, was added yearly during the growing season from 2005 to 2013.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00003073	Mediterranean mud volcano flow Targeted loci	Mud volcanoes (MVs) expel mobilized muds, gases, and fluids from the subsurface at convergent margins. These muds and fluids originate from numerous sources and depths that range from methanogenic sediment layers, destabilizing gas hydrate deposits, clay dehydration reactions, and thermogenic hydrocarbon sources–and thus represent a convenient window into the deep biosphere. The proposed sequencing opportunity will address bacterial and archaeal community diversity in recent mud flows of the Venere Mud Volcano and underlying mud volcano sediments to assess how mud flow deposition and subsurface fluids influence microbial community composition and dynamics. We sequenced 16S V4V5 amplicons from bacterial and archaeal communities at varying mud flow depths with contrasting deep fluid chemistries.	root:Environmental:Terrestrial:Volcanic
MGYS00003133	Mount Hope Bay bacteria Targeted Locus (Loci)	Coastal marine environments have been impacted by human activity for several centuries, including shoreline alteration, nutrient introduction, sedimentation, toxic compound release, and thermal modification. Mt. Hope Bay, Massachusetts is an ideal site to base a study of human pathogen presence and distribution because it has several important sources of human impact, including sewage disposal sites and the thermal outfall of a power plant within a mile of each other. The Bay has undergone limited monitoring for several different parameters, including fish populations, river runoff, meteorological forcing, tidal cycles and water chemistry as part of the Mt. Hope Bay Natural Laboratory (MHBNL) program, a 5-year interdisciplinary project at the University of Massachusetts Dartmouth School of Marine Science and Technology (SMAST). While phytoplankton and zooplankton communities in the water column have been fairly well monitored, although not at a molecular level, microbial communities remain relatively uncharacterized. This project presents comprehensive (eukaryal, bacterial, archaeal) data from small-subunit ribosomal RNA gene clone libraries and next-generation Illumina amplicon sequencing for samples collected near the thermal plume and underlying sediments of the Brayton Point Power Plant. Not surprising, our findings reveal a highly diverse consortium of the three domains including relatives of sludge bacteria, polyaromatic hydrocarbon-degrading bacteria, and representatives related to the genera Staphylococcus, Streptococcus, and Clostridium. It is clear that even limited knowledge about the overall microbial community composition can lead to important observations about the ecosystem as a whole. Furthermore, understanding whether free-living pathogens participate in relationships with other members of the microbial community will be important in understanding their distributions and persistence.	root:Environmental:Aquatic:Marine:Coastal
MGYS00006041	HoloFood Salmon Trial A+B Gut Metagenome	Metagenomic raw reads, assemblies, and bins derived from HoloFood salmon gut samples from trial A and B. The samples in this project contributed to the salmon MAG catalogue (project: PRJEB55376 [ERP140265]).	root:Host-associated:Fish:Digestive system:Intestine
MGYS00004560	Quantitative monitoring of environmental DNA using high-throughput sequencing	The goal of this project is to monitor the dynamics of environmental DNA (e.g., fish DNA found in a water sample) quantitatively. By adding internal standard DNA, a standard curve (i.e., the relationship between the number of DNA copy and sequence read) will be drawn. Based on the standard curve, sequence reads of unknown DNA (non-standard DNA) will be converted to the number of DNA copy. The environmental DNA metabarcoding combined with internal standard DNA will enable quantitative monitoring of multispecies environmental DNA.	root:Environmental:Aquatic:Marine
MGYS00005208	Compost microbe establishment and growth in agricultural soils	Compost application to soil has numerous agricultural benefits, but mechanistic understanding of benefits beyond fertility and organic matter gains – particularly those mediated by microbes such as disease suppression – is limited. Narrowing this uncertainty requires understanding which types of compost microbes will establish in agricultural soils, which types of soils will support compost microbes, and how soil microbial diversity may change following compost application. We tested the ability of plant invasion and diversity theories to address these questions. From a row crop experiment to which management treatments had been applied for 22 years, soil was collected from three systems representing different resource inputs: no input (low resource), conventional (moderate resource), and organic (high resource) systems. Live composted poultry manure was added to laboratory microcosms of these soils, and bacterial and archaeal communities were tracked using 16S rRNA sequencing of pre-invasion soils, pre-invasion compost, and the combined communities at 4 and 32 days post-invasion.	root:Environmental:Terrestrial:Soil
MGYS00004018	marine metagenome Raw sequence reads	Mariana Trench microbial eukaryotes	root:Environmental:Aquatic:Marine:Sediment
MGYS00002893	marine sediment metagenome Raw sequence reads	The Roseobacter group within the family Rhodobacteraceae consists of nearly 70 genera and app. 180 species. They thrive in a broad variety of marine habitats and were found free-living in seawater, associated with micro and macro algae, marine sponges and invertebrates as well as in biofilms, sea ice and sediments. n the present study, we describe the abundance, distribution and diversity of the Roseobacter group in rather oligotrophic deep-sea sediments derived from the Pacific Ocean as all other benthic studies were performed on relatively eutrophic coastal sites or high-energy systems.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004122	Nitrogen cycling microbes in the surface sediments of the South China Sea		root:Environmental:Aquatic:Marine:Sediment
MGYS00004103	marine sediment metagenome Raw sequence reads	XSD marine sediment metagenome Raw sequence reads	root:Environmental:Aquatic:Marine:Sediment
MGYS00004450	ASU barcoding in 5 regional seas	Metabarcoding of metazoan taxa collected in Artificial Substrate Units in 5 regional seas.	root:Environmental:Aquatic:Marine
MGYS00004139	Baselines Initiative 16S rRNA gene dataset: Baselines Amplicon Release 1 (R1) North Pacific Line-67 2009	The overall objective of this project (Baselines Initiative) is to generate several 16S rRNA gene databases to establish robust baseline information on the biological communities in marine ecosystems. This field study was conducted in the North Pacific Line-67 in October 2009 to examine phytoplankton community diversity.	root:Environmental:Aquatic:Marine
MGYS00004630	seawater metagenome Raw sequence reads	This project is to study the diversity of AAPB in Zhoushan sea area.AAPB belonging to the unclassified dominated the column, followed by Roseobacter ?The cluster analysis results by phylum ranked top was unclassified, then the Proteobacteria, Firmicutes followed, and finally the planctomycetes. The proportion of each class (clear classified phylum) of AAPB were clearly indicating that a-Proteobacteria remained dominant ,then ?-Proteobacteria and unclassified, ß-Proteobacteria and Bacilli possessed the same proportion,Planctomycetia and d- Proteobacteria occupied the minimum percentages. Obviously, in addition to the unclassified bacteria, Proteobacteria was absolute dominant member of AAPB?	root:Environmental:Aquatic:Marine
MGYS00004428	Camargue soil and sediment 16S community profiling	Characterize microbiome from camargue region in france	root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
MGYS00004307	Impact of offshore oil drilling operations on the diversity of marine benthic Foraminifera  - Raw sequence reads	Environmental impacts from offshore oil and gas activities are currently partly determined by measuring changes in macro-infaunal diversity determined using microscopy. In this study, we evaluated the applicability of using foraminiferal-specific metabarcoding (i.e. high-throughput sequencing of foraminiferal environmental DNA marker sequences). Sediment samples were collected along distance gradients from two oil platform wellheads (WHs) off Taranaki (New Zealand) and their physico-chemical properties, foraminiferal environmental DNA/RNA, and macro-infaunal composition analysed.Our results suggest that foraminiferal metabarcoding may provide a more accurate assessment of the conditions of environmental communities at the time of sampling than current methods based on morphological examination. These data highlight the potential of foraminiferal metabarcoding as an effective asset to existing monitoring techniques.	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00001188	Gastric microbiota of 120 samples Raw sequence reads	This study presented gastric microbiota in patients with gastritis, intestinal metaplasia,early gastric cancer and advanced gastric cancer,respectively.	root:Host-associated:Human:Digestive system
MGYS00004216	Uncultured eukaryote community Targeted loci environmental	Small size fraction (0.2-3 um) microbial community sample from northern Baffin Bay.	root:Environmental:Aquatic:Marine
MGYS00002588	Red Sea Zooplankton Raw sequence reads	To assess the diversity of zooplankton in the Red Sea. Samples were taken along a depth profile as well as being temporally and spatially differentiated.	root:Environmental:Aquatic:Marine
MGYS00001042	Microbial community of apple replant soils treated with fumigation or seed meal	Brassicaceae seed meal (SM) formulations were compared with pre-plant 1,3-dichloropropene/chloropicrin (Telone-C17®) soil fumigation for the ability to control apple replant disease and to suppress pathogen/parasite re-infestation of organic orchard soils at two sites in Washington State. The study also examined capacity of the SM treatment to minimize re-establishment of the causal pathogen populations and the potential contribution of altered rhizosphere microbiology to disease suppression.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00004674	Marine sponges and seawater Targeted Locus (Loci)	Assessment of microbial diversity of marine sponges and seawater	root:Environmental:Aquatic:Marine
MGYS00004301	Sediment sample Metagenome	Given the complexity in microbial transformation of arsenic in deep aquifer sediment, we aim to shade light of indigenous bacterial community structure in arsenic-enriched deep aquifer sediment and how the communities changes under controlled redox condition favoring reductive dissolution and release of arsenic from the sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00000959	Microbial Ecology of Thailand Tsunami and Non-Tsunami Affected Terrestrials	This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2)	root:Environmental:Terrestrial:Soil
MGYS00000944	Grassland 16S amplicons	Evaluate the relative importance of soil characteristics, climate, and plant roots on rhizosphere community assembly.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00002500	BrdU_MAB_SS Metagenome	Marine bacterial communities of the Mid-Atlantic Bight and Sargasso Sea	root:Environmental:Aquatic:Marine
MGYS00000848	Diversity of bacteria, archaea, fungi and algae in coal mine drainage remediation systems treating elevated manganese	Water discharging from abandoned coal mines can contain extremely high manganese levels, and removing this metal is an ongoing challenge. Passive Mn remediation systems promote the growth of certain bacteria and fungi that catalyze the transformation of soluble Mn(II) to insoluble Mn(III/IV) minerals, but system performance is unpredictable. Mn-oxidizing organisms likely belong to complex communities that include algae and archaea, as well as bacteria and fungi that do not oxidize Mn. Community interactions could be modulating the efficiency of Mn oxidation in the treatment beds. Using a targeted sequencing approach, we aimed to determine the diversity and composition of microbial communities inhabiting several different Mn remediation systems, compared with surrounding uncontaminated soil, and to establish the abundance of known Mn-oxidizing microorganisms relative to the entire community. Four Mn treatment beds in Pennsylvania were selected, each treating metal-contaminated discharge from abandoned coal mines. Rock or sediment samples were collected near the influent, in the middle and near the effluent of each bed, as well as from surrounding uncontaminated soil. Amplicon pyrosequencing was carried out with primers targeting bacteria (small subunit rRNA), archaea (small subunit rRNA), fungi (internal transcribed spacer) and algae (plastid large subunit rRNA).	root:Environmental:Terrestrial:Soil
MGYS00000784	Soil bacterial and fungal community changes during primary succession on lava flows in Iceland	Soil microbial communities (SMCs) play a critical role in the cycling of carbon and nutrients in terrestrial ecosystems, as well as regulating plant productivity and diversity. However, very little is known about long-term (decades-centuries) structural changes in these communities. The development of aboveground-belowground linkages during century-scale succession is also poorly understood. This study investigates SMC and plant communities undergoing primary succession on an 850-year chronosequence of lava flows in Iceland. We hypothesised that communities of microfungi and bacteria would respond to progressive changes in vegetation and that SMC diversity would increase with terrain age. This project has implications for studies of primary succession and the biogeochemical impact of vegetation change in high-latitude ecosystems.	root:Environmental:Terrestrial:Soil
MGYS00004196	BSM marine Targeted Locus	To study the bacterial diversity - coastal marine water from Malaysia.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004570	Marine metagenome ICM_ICR	The Indian Ocean Cooperative 454 Run Project	root:Environmental:Aquatic:Marine
MGYS00004110	Marine metagenome ICM_AGW	Amazon-Guianas Water bacterial communities of the Amazon-Guianas water-sediment system.	root:Environmental:Aquatic:Marine
MGYS00002473	Microbial diversity of the central Arctic Ocean	"We aimed to explore the community composition and turnover of eukaryotic and bacterial
                microorganisms associated with ice-associated and sinking algal aggregates, as well as their similarity
                to potential source communities of sea ice, water and deep-sea sediments using Illumina tag sequencing.
                We sampled algae aggregates growing in melt ponds on sea ice, deposited algae aggregates at the seafloor
                in more than 4000 m water depth, sea ice, upper water column, sediment surface and the gut content of
                holothurians feeding on the deposits."	root:Host-associated:Algae
MGYS00001577	Seasonal assemblages and short-lived blooms in coastal northwest Atlantic Ocean bacterioplankton	Temperate oceans are inhabited by diverse and temporally dynamic bacterioplankton communities. However, the role of the environment, resources and phytoplankton dynamics in shaping marine bacterioplankton communities at different time scales remains poorly constrained. Here, we combined time-series observations (time scales of weeks to years) with molecular analysis of formalin-fixed samples from a coastal inlet of the northwest Atlantic Ocean to show that a combination of temperature, nitrate, small phytoplankton and Synechococcus abundances are best predictors for annual bacterioplankton community variability, explaining 38% of the variation. Using Bayesian mixed modeling we identified assemblages of co-occurring bacteria associated with different seasonal periods, including the spring bloom (e.g. Polaribacter, Ulvibacter, Alteromonadales, and ARCTIC96B-16) and the autumn bloom (e.g. OM42, OM25, OM38 and Arctic96A-1 clades of Alpha-proteobacteria and SAR86, OM60, and SAR92 clades of Gamma-proteobacteria). Community variability over spring bloom development was best explained by silicate (32%) – an indication of rapid succession of bacterial taxa in response to diatom biomass– while nanophytoplankton as well as picophytoplankton abundance explained community variability (16-27%) over the transition into and out of the autumn bloom. Moreover, the seasonal structure was punctuated with short-lived blooms of rare bacteria including the KSA-1 clade of Sphingobacteria related to aromatic hydrocarbon-degrading bacteria.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00003511	EMG produced TPA metagenomics assembly of the Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease (CHD102-metagenomics) data set.	The CHD102-metagenomics Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB15111.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003619	EMG produced TPA metagenomics assembly of the A longitudinal analysis of the developing gut microbiome in infants from Finland, Estonia, and Russian Karelia (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA290380.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system
MGYS00006569	EMG produced TPA metagenomics assembly of PRJNA986291 data set (CForBio.metagenome).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA986291, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil:Loam:Forest soil.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00003009	Archaea Arctic Ocean Survey Targeted Locus (Loci)	Eukaryota microbial diversity in different regions of the Arctic Ocean (Hudson Bay, Baffin Bay, canadian Archipelago, Laptev Sea)	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004497	Enrichment of abundant sedimentary Bathyarchaeota demonstrating organoautotrophic metabolic capabilities	Enrichment of Bathyarchaeota	root:Environmental:Aquatic:Marine
MGYS00004614	srb of salt marshes Targeted loci environmental	To investigate on the changes in the diversity, abundance and community structure of sulfate-reducing bacteria along a plant successional gradient in coastal salt marshes of China	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00004629	marine zooplankton environmental sample Targeted Locus (Loci)	Amplicon sequencing of marine zooplankton in the Red Sea	root:Environmental:Aquatic:Marine
MGYS00004084	Loihi Seamount basalts Targeted Locus (Loci)	Extracellular enzyme activity (alkaline phosphatase and leucine aminopeptidase), qPCR for prokaryotic biomass and Ion Torrent pyrotags of the V6 hypervariable region of 16S rRNA were analyzed from basalt samples collected from Loihi Seamount, HI	root:Environmental:Aquatic:Marine:Sediment
MGYS00001189	DNA from FIT can replace stool for microbiota-based colorectal	Using DNA extracted from fecal immunochemical test cartridges rather than directly from stool for detecting colorectal cancer based on the gut microbiome.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001255	Human feces metagenome 16s rDNA sequencing	The precise effects of HIV-1 on the human microbiome are unclear. Initial cross-sectional studies provided contradictory associations between microbial richness and HIV status and suggested shifts from Bacteroides to Prevotella predominance following HIV-1 infection, which have not been found in animal models or in studies matched for HIV-1 risk groups.This was a cross-sectional study where we first tested 129 HIV-1-infected subjects and 27 HIV-negative controls in Barcelona (BCN0). Findings were internally validated in 110 subjects from BCN0 providing a second fecal sample 1 month later. External validation was obtained in 77 HIV-1-infected and 7 non-infected subjects from Stockholm. In all study participants, we produced MiSeq 16S rRNA data on fecal microbiomes and collected comprehensive metadata.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006568	EMG produced TPA metagenomics assembly of PRJEB32890 data set (The integrated mouse gut metagenome catalog (iMGMC), comprising 4.6 million unique genes and 660 high-quality metagenome-assembled genomes (MAGs)  linked to reconstructed full-length 16S rRNA gene sequences).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB32890, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006567	EMG produced TPA metagenomics assembly of PRJEB40358 data set (Dysbiotic Lesional Microbiome with Filaggrin Missense Variants Associate with Atopic Dermatitis in India).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB40358, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Skin.	root:Host-associated:Human:Skin
MGYS00003575	EMG produced TPA metagenomics assembly of the C.diff FMT (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA240307.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001075	16S sequencing of Malawian children	To gain insights into the interrelationships among childhood undernutrition, the gut microbiota, and gut mucosal immune/barrier function, we purified bacterial strains targeted by immunoglobulin A (IgA) from the fecal microbiota of two cohorts of Malawian infants and children. IgA responses to several bacterial taxa, including Enterobacteriaceae, correlated with anthropometric measurements of nutritional status in longitudinal studies. The relationship between IgA responses and growth was further explained by enteropathogen burden. Gnotobiotic mouse recipients of an IgA+ bacterial consortium purified from the gut microbiota of undernourished children exhibited a diet-dependent enteropathy characterized by rapid disruption of the small intestinal and colonic epithelial barrier, weight loss, and sepsis that could be prevented by administering two IgA-targeted bacterial species from a healthy microbiota. Dissection of a culture collection of 11 IgA-targeted strains from an undernourished donor, sufficient to transmit these phenotypes, disclosed that Enterobacteriaceae interacted with other consortium members to produce enteropathy. These findings indicate that bacterial targets of IgA responses have etiologic, diagnostic, and therapeutic implications for childhood undernutrition.	root:Host-associated:Human:Digestive system
MGYS00006566	Dewar Creek GAL08 Study Amplicons	Sediment samples from Dewar Creek hot spring in British Columbia, Canada, we processed for 16S rRNA gene sequencing. The goal of this project was to access the abundance of GAL08 (Acidobacteria) at Dewar Creek at varying temperatures over multiple sampling seasons.	root:Environmental:Aquatic:Thermal springs
MGYS00006553	EMG produced TPA metagenomics assembly of PRJEB27928 data set (Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB27928, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001278	Host lifestyle affects human microbiota on daily timescales	Background,disturbance to human microbiota has been associated with numerous pathologies. Yet, we lack a comprehensive understanding for how human health and lifestyle affect the dynamics of human-associated microbial communities. Results, we link over 10,000 longitudinal measurements of host wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time-series show overall microbial communities to be stable for months. However, rare events in each of the subjects life rapidly and broadly impacted microbiota dynamics. Travel from the developed to the developing world in one subject led to a nearly two-fold increase in the Bacteroidetes to Firmicutes ratio, which reversed upon return. Enteric infection in the other subject resulted in the permanent decline of most gut bacterial taxa, which were replaced by genetically-similar species. Still, even during periods of overall community stability, we could associate the dynamics of select microbial taxa to specific host behaviors. Most prominently, changes in host fiber intake correlated with next-day abundance changes among 15 percent of gut microbiota members.Conclusions,our findings suggest that although human-associated microbial communities are generally stable, they can be quickly and profoundly altered by common human actions and experiences.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000580	Gut microbiota of Juvenile Idiopathic arthritis	Characterization of gut microbiota in Juvenile Idiopathic arthritis and comparison with healthy subjects.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000501	Gut microbiota of stroke patients differentiates from healthy controls	Gut microbiota of stroke patients differentiates from healthy controls	root:Host-associated:Human:Digestive system
MGYS00001215	Colonic transit time relates to bacterial metabolism and mucosal turnover in the gut	Little is known about how colonic transit time relates to human colonic metabolism, and its importance for host health, although stool consistency, a proxy for colonic transit time, has recently been negatively associated with gut microbial richness. Here we show that colonic transit time in humans, assessed using radiopaque markers, is associated with overall gut microbial composition, diversity and metabolism. We find that a long colonic transit time associates with high microbial richness and is accompanied by a shift in colonic metabolism from carbohydrate fermentation to protein catabolism as reflected by microbial metabolites in urine, which results in a number of deleterious protein-derived metabolites. Additionally, longer colonic transit time correlates with metabolites reflecting reduced renewal of the colonic mucosa. Together, this suggests that high gut microbial richness does not per se imply a healthy gut microbial ecosystem, and contributes to the understanding of the aetiology of diseases where increased transit time is a risk factor.	root:Host-associated:Human:Digestive system
MGYS00001211	human gut metagenome Metagenome	The objective of this study was to investigate the general characteristics and environmental factors, such as dietary pattern and physical activities, of elderly women from Seoul and Jeju Island, and to characterize the composition of their fecal microbiota	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006565	Analisi metagenomica ( ITS2) su suolo rizosferico di nocciolo	Piante di nocciolo di 4 anni di due varieta' diverse (Tonda di Giffoni e Mortarella) concimate con fertilizzante di sintesi (NPK), compost di sansa, zolfo e bentonite, zolfo e bentonite + compost di sansa	root:Environmental:Terrestrial:Soil:Crop
MGYS00006126	Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention	16s rRNA sequences from fecal samples from obese participants enrolled in the DIETFITS randomized clinical trial. Participants were randomized to either a low-carbohydrate or low-fat dietary intervention for 1 year. Fecal samples were collected prior to diet initiation and after 10 weeks of dietary intervention.	root:Host-associated:Human:Digestive system
MGYS00006023	Observational Study on the Diagnostic Evaluation of the Intestinal Microbiota of Patients With COVID-19. (EDIFICE)	In the context of the COVID-19 pandemic, the role of the gut microbiome is yet unknown. The aim of this trial is to evaluate the clinical contribution of the gut microbiome composition and diversity on the disease severity and to estimate the viral load in stool samples.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006121	Dietary intervention of people with Parkinson's disease	[Placeholder]	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006543	BioSolWest	"""BioSolWest is a research project focused on assessing the soil biological health in the western region of Paraná, Brazil. Over a span of two years, we conducted a comprehensive study in 14 rural properties with clayey and sandy soils. Parameters such as carbon biomass, basal respiration, qCO2, microbial biomass nitrogen, and fungal and bacterial quantities were evaluated using epifluorescence microscopy. The project also involved metagenomic analysis (shotgun) to examine the microbial composition in the best and worst performing samples each year. Through this project, we aim to gain insights into the soil's biological characteristics and promote sustainable agricultural practices in the region."""	root:Environmental:Terrestrial:Soil
MGYS00006542	PfSGS	Plant Growth-Promoting Rhizobacteria (PGPR) play a pivotal role in agriculture, enhancing plant growth, controlling pathogens, and offering environmentally-friendly alternatives to agrochemicals. Among them, Pseudomonas species are well-known inhabitants of the rhizosphere due to their competitive potential and adaptability to various environments. In this study, the aim was to investigate the effect of different doses of Pseudomonas fluorescens on soybean cultivation and its impact on the soil microbial composition and the soil-plant system.	root:Environmental:Terrestrial:Soil
MGYS00006561	EMG produced TPA metagenomics assembly of PRJNA797778 data set (Vaginal Microbiome Research Consortium).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA797778, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00006560	CForBio.metagenome	This study collected 36 soil samples from 12 Chinese forests to investigate how soil microbes response to environmental changes.	root:Environmental:Terrestrial:Soil:Loam:Forest soil
MGYS00006226	Effects of Dietary Fiber Intervention on Gut Microbiota in Healthy People	Aim of this project was to investgigate the effect of fiber-rich diets in the human gut microbiome. The participants were asked to visit the study center sober and received the intervention meal or placebo meal. Additionally, a capsule with food coloring was administered. The intake of the dye stains the stool green which helps to associate collected stool samples and food intake. 16S rRNA gene was sequenced at ZIEL Core Facility Microbiome, Technical University Munich, Germany.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006225	Human intervention study: anthocyanins supplementation and the impacts on gut microbiota	Dietary polyphenols are natural compounds occurring in plants, including foods such as fruits, vegetables, cereals, tea, coffee and wine. Epidemiological studies and associated meta-analyses strongly suggest that long term consumption of diets rich in plant polyphenols offer protection against development several chronic diseases. In this study, the long term consumption of anthocyanin-rich fruit juice impacts the gut microbiota enriching specific bacteria and increase the expression of important antioxidative markers.	root:Host-associated:Human:Digestive system
MGYS00006224	The effect of nutritional intervention with lactoferrin, galactooligosacharides and vitamin D on the gut microbiota composition of healthy elderly women	in the present study, we examined the effect of bovine lactoferrin, galactoligosacharides and vitamind D on the gut microbiota composition of 25 elderly women. Participants were distributed into two groups receiving either the dietary intervention (n=12) or the placebo treatment (n=13) for a total period of 9 weeks. During the first 3 weeks of the study, the intervention group consumed 1 g/day bLF, followed by 3 weeks of 1 g/day bLF and 2.64g/day active galactooligosaccharides (GOS), and 3 weeks of 1 g/day bLF, 2.64g/day GOS and 20 μg/day of vitamin D. The placebo group received maltodextrin, in matching dosages with the supplements administrated to the intervention group. Fecal bacterial composition was profiled using partial 16S rRNA gene amplicon sequencing and short-chain fatty acids analysis (SCFA) concentrations were determined with high liquid performance chromatography. Finally, the fecal levels of calprotectin, zonulin, and alpha-1-antitrypsin were measured, as markers of gastrointestinal barrier and inflammation.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006559	Influence of gut microbiota on short-term low carbohydrate diet intervention for weight loss therapy	To date, much progress has been made in dietary therapy for obese patients. A low-carbohydrate diet (LCD) has reached a revival in its clinical use during the past decade with undefined mechanisms and debatable efficacy. Gut microbiota has been suggested to promote energy harvesting. Here, we propose that gut microbiota contributes to the inconsistent outcome under LCD. To test this hypothesis, patients with obesity or overweight were randomly assigned either to a normal diet (ND) or LCD group with ad libitum energy intake for 12 weeks. Using matched sampling, the microbiome profile at baseline and end-stage was examined. The relative abundance of butyrate-producing bacteria, Porphyromonadaceae Parabacteroides and Ruminococcaceae Oscillospira, was markedly increased after LCD intervention for 12 weeks. Moreover, within LCD group, participants with a higher relative abundance of Bacteroidaceae Bacteroides at baseline exhibited a better response to LCD intervention and achieved greater weight loss outcomes. Nevertheless, the adoption of an artificial neural network (ANN)-based prediction model greatly surpasses general linear model in predicting weight loss outcomes after LCD intervention. Therefore, gut microbiota served as a positive outcome predictor has the potential to predict weight loss outcomes after short-term LCD intervention. Gut microbiota may help to guide the clinical application of short-term LCD intervention to develop effective weight loss strategies.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006558	Systems Biology of Lipid Accumulating Organisms	Characterization of microbial communities at the genomic, transcriptomic, proteomic and metabolomic levels, with a special interest on lipid accumulating bacterial populations, which are naturally enriched in biological wastewater treatment systems and may be harnessed for the conversion of mixed lipid substrates (wastewater) into biodiesel. The project aims to elucidate the genetic blueprints and the functional relevance of specific populations within the community. It focuses on within-population genetic and functional heterogeneity, trying to understand how fine-scale variations contribute to differing lipid accumulating phenotypes. Insights from this project will contribute to the understanding the functioning of microbial ecosystems, and improve optimization and modeling strategies for current and future biological wastewater treatment processes.  This BioProject contains datasets derived from the same biological wastewater treatment plant. The date includes metagenomes, metatranscriptomes and organisms isolated in pure cultures.	root:Engineered:Wastewater
MGYS00006554	EMG produced TPA metagenomics assembly of PRJNA217052 data set (Fiji COMP).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA217052, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Mixed.	root:Mixed
MGYS00006552	EMG produced TPA metagenomics assembly of PRJEB28367 data set (Metagenomic Analysis of the Marine Sponge, Cinachyrella keukenthali: Insights into an Emerging Model Sponge).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB28367, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Porifera.	root:Host-associated:Porifera
MGYS00006549	Metatranscriptome24H1-3	Metatranscriptome, 24h of culture15NaNO3	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00002304	EMG produced TPA metagenomics assembly of the Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2013 (2013 'Omics from the diffuse hydrothermal vents of Axial Seamount) data set	The 2013 'Omics from the diffuse hydrothermal vents of Axial Seamount Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB7866. This project includes samples from the following biomes : Hydrothermal vents.	root:Environmental:Aquatic:Marine:Hydrothermal vents:Microbial mats
MGYS00006544	EMG produced TPA metagenomics assembly of PRJNA777294 data set (Tracking Genomic Characteristics across Oceanic Provinces: Contrasting Early and Mature Plastic Biofilm Communities).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA777294, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00002243	Human bronchoalveolar lavage, oral wash, nasal swab and saline/reagent control microbiota 16S rRNA gene amplicon sequencing	No studies to date have examined the relationship within an individual between bacterial communities along sites of the upper aerodigestive tract. Our objective was to perform an intra-subject and inter-site analysis to determine the contribution of two upper mucosal sites (mouth and nose) as source communities for the bacterial microbiome of the lower sites (lungs and stomach). Oral wash, bronchoalveolar lavage (BAL), nasal swab, and gastric aspirate samples were collected from 28 healthy subjects.	root:Host-associated:Human
MGYS00006539	Microbial community study upland peatland site, Northumberland	Comparative study of microbial communities between restored and degraded peatland sites from Whitelee Moor, Northumberland National Park	root:Environmental:Terrestrial:Soil
MGYS00006537	Humpback Whale Blow Metagenome Raw sequence reads	This Bioproject comprised the amplification of bacterial 16S rRNA gene derived from humpback whale blow in Hervey Bay, Queensland, Australia, with an aim to assess theinterannual difference and core microbiota.	root:Host-associated:Mammals:Respiratory system
MGYS00006536	Using drones to sample whale blow microbiota	We developed a low-cost multirotor UAV incorporating a sterile petri dish with a remotely operated ‘flip lid’ to sample whale blow with minimal disturbance to the whales. This design addressed several sampling challenges: accessibility; safety; cost, and critically, minimized the collection of atmospheric and seawater microbiota and other potential sources of sample contamination. We collected 59 samples of blow from northward migrating humpback whales off Sydney, Australia and used high throughput sequencing of bacterial ribosomal gene markers to identify putative respiratory tract microbiota. Model-based comparisons with seawater and drone-captured air demonstrated that our system minimized external sources of contamination and successfully captured sufficient material to identify whale blow-specific microbial taxa.	root:Host-associated:Mammals:Respiratory system
MGYS00006538	Whale blow 16S rRNA gene Raw sequence reads	This Bioproject comprised the amplification of the 16S rRNA gene in the blow of humpback, gray, blue and long-finned pilot whales off the coast of Eastern Australia, Mexico and in the Alboran Sea (Mediterranean). We aimed to compare the blow microbiota of two whale species with different levels of sociality, by analysing the alpha and beta diversity of the microbial communities and the core bacteria.	root:Host-associated:Mammals:Respiratory system
MGYS00003194	Marine metagenomes Metagenome	Marine amplicons from Australian marine (benthic and pelagic environments	root:Environmental:Aquatic:Marine
MGYS00006533	HoloFood Chicken Caecum Metagenome – extreme sizes batch	Metagenomic raw reads from selected HoloFood chicken caecum samples. Samples within this batch come from animals with weights at the extremes of the distribution curve. Samples selected for this batch were randomised among trials (feed), age, and breed to overcome batch effect.	root:Host-associated:Birds:Digestive system
MGYS00006535	hypersaline lake metagenome Genome sequencing and assembly	Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'. We report the first stable cultivation of an association between the ultrasmall Candidate Phyla Radiation bacterium M39-6, which we named 'Ca. Absconditicoccus praedator', and its host Halorhodospira halophila M39-5, an obligately photosynthetic and anaerobic purple sulphur bacterium; we also carry out an in-depth characterization of their biology. Both were isolated from the hypersaline alkaline Lake Hotontyn Nur (Mongolia).	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00005628	Potential of fecal microbiota for early stage detection of colorectal cancer	Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved >45% relative to the FOBT while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early and late-stage cancer and could be validated in independent patient and control populations (N=335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host-microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients accompanied by an increase of lipopolysaccharide metabolism.	root:Host-associated:Human:Digestive system
MGYS00006534	Genomics and transcriptomics of enrichment cultures of marine methanotroph	The Iheya North Knoll in the mid-Okinawa Trough is a methane-rich deep-sea hydrothermal field. To cultivate methane-oxidizing bacteria from the Iheya North field, a continuous flow-through reactor cultivation was conducted using gill tissue of Bathymodiolus japonicus as an inoculum. The enriched culture consisting mainly of methane-oxidizing bacteria was subjected to genetic analyses to investigate their metabolic characteristics.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00001935	EMOSE (2017) Inter-Comparison of Marine Plankton Metagenome Analysis Methods	This study includes experiments from the following five sequencing strategies: 1) Shotgun DNA sequencing; 2) Amplicon sequencing after 18S amplification by PCR using 1391F/EukB primer set. Library were constructed according to Illumina Library protocol without any sizing; 3) Amplicon sequencing after 16S amplification by PCR using 515F/926R primer set. Library were constructed according to Illumina Library protocol without any sizing; 4) Amplicon sequencing after 16S amplification by PCR using 515F/926R primer set. Library were constructed according to Illumina Library protocol with a sizing step selecting the 450-650 bp fragments; and 5) Amplicon sequencing after 16S amplification by PCR using 515F/926R primer set. Library were constructed according to Illumina Library protocol with a sizing step selecting the 650-850 bp fragments.	root:Environmental:Aquatic:Marine
MGYS00005360	Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus	Recent evidence from high-resolution molecular studies suggests links between microbial dysbiosis in the gastrointestinal tract and a number of complex chronic diseases including diabetes mellitus. The present study forms a pilot study for the larger Luxembourg-based Diabetes Multiplex Family Study (MUST). Within the pilot study, we investigate the interplay of the gastrointestinal microbiota, lifestyle and genetic background in an observational study of families with two or more individuals affected by type 1 diabetes mellitus. Faecal samples which have undergone comprehensive biomolecular extractions are currently analysed using a multi-omics approach. Anthropometric data, including demographics, medical history, health status, medication, and dietary habits of all study participants were collected and are integrated with molecular data.	root:Host-associated:Human:Digestive system
MGYS00006532	HoloFood Chicken Caecum+Ileum Metagenome – non-targeted metabolomics batch	Metagenomic raw reads from a subset of the HoloFood chicken caecum and ileum samples. This batch is the metagenomic counterpart of animals sampled for non-targeted metabolomics; all samples come from male animals under control treatment and aged 35 days.	root:Host-associated:Birds:Digestive system
MGYS00006531	SARS-CoV-2 genome sequencing and assembly from COVID-19 autopsy tissue specimens	Viral sequence analysis of tissue specimens from fatal COVID-19 cases collected for multiple studies.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006491	EMG produced TPA metagenomics assembly of PRJEB4352 data set (Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for protist).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB4352, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00006075	EMG produced TPA metagenomics assembly of PRJEB6608 data set (Metatranscriptome sequencing of Tara Oceans DNA samples corresponding to size fractions for  prokaryotes.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6608, and was assembled with metaSPAdes v3.14.1 and megahit v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.	root:Environmental:Aquatic:Marine
MGYS00005780	EMG produced TPA metagenomics assembly of PRJNA385854 data set (Marine metagenomes from the bioGEOTRACES project).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA385854, and was assembled with SPAdes v3.12.0 and megahit v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00001648	lungbiome: Microbiome and cytokine signatures of bacterial pneumonia and tracheobronchitis	Lung transplant recipients routinely acquire infectious diseases such as bacterial pneumonia and tracheobronchitis. These two diseases are difficult to distinguish from each other, or from non-infectious airway colonization because there is considerable overlap in their signs and symptoms and respiratory culture findings. In this project, we explored the microbiome and cytokine signatures of lung transplant recipients with bacterial pneumonia, tracheobronchitis and non-infectious airway colonization.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006449	Respiratory and intestinal dysbiosis induced by acuter LPS challenge	Systemic inflammatory response syndrome (SIRS) is a severe condition which may lead to multiple organ failure, shock and death. SIRS is often accompanied by intestinal dysbiosis. However, the mechanism, role and details of microbiome alterations during the early phase of acute SIRS are not completely understood. This project characterizes the dynamic alterations of both the respiratory and intestinal microbiome during the early phase of acute SIRS.	N/A
MGYS00006421	Respiratory mycobiome of critically ill COVID patients	To understand the role of the respiratory mycobiome in critically ill COVID-19 patients and the additional impact of a CAPA diagnosis. A multi-national study of 39 COVID-19 patients in intensive care units with and without CAPA. Respiratory mycobiome was profiled using ITS1 sequencing	N/A
MGYS00006530	CF airway microbiota within baseline clinical state	The study is focused on the variation in measures of CF airway microbiota within baseline clinical state, and factors that relate to this variation. The primary objective of this study was to quantify variation in measures of CF airway microbiota within periods of baseline clinical state. Additional objectives included identifying clinical variables associated with variation in measures of airway microbiota, determining within-subject changes in airway microbiota over time, and determining the impact of sampling interval on measures of microbiota.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00005269	16S rRNA gene sequencing data from throat swabs from participants in the Busselton Health Study	A population study of respiratory tract microbiome in a largely healthy cohort of participants in the Busselton Health Study, Perth, Western Australia.	root:Host-associated:Human:Respiratory system:Nasopharyngeal:Pharynx
MGYS00006485	Host Immune Response and Mortality Risk are  Related to Distinct Lung Microbiomes in  HIV-Pneumonia Patients	Clustering HIV-pneumonia patients based on airway bacterial community composition permits stratification of subjects into functionally and immunologically distinct groups that are differentially related to mortality risk.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006475	Lower airway microbiota in patients with clinically suspected Mycobacterium avium complex lung disease	We tried to put some light on the relationship between Non-tuberculous mycobacterial lung disease and lower airway microbiota, based on clinical characterization of the patients and 16s rRNA sequencing.   The results reported Other than the genus Pseudomonas, there was no clear difference in the composition of and no significant difference in the diversity of the bacterial flora between the Mycobacterium Avium Complex-Lung Disease (MAC-LD) and non-MAC-LD groups. We found that the genus Pseudomonas and Mycobacterium Avium Complex tended to exist exclusively.	root:Host-associated:Human:Respiratory system:Pulmonary system:Trachea
MGYS00006247	Comparison of lung microbiota between antineutrophil cytoplasmic antibody-associated vasculitis and sarcoidosis	Bacterial involvements for the pathogenesis have been suggested in both antineutrophil cytoplasmic antibody-associated vasculitis (AAV) and sarcoidosis, which have lung involvements. However, exhaustive researches to assess the bacteria in the lung in AAV and in sarcoidosis have not been performed to elucidate the differences in bacterial characteristics. We sought to elucidate the distinct lung microbiota suggesting contributions of dysbiosis in the lung to the pathogenesis of AAV and sarcoidosis.	N/A
MGYS00005253	Early development of the airway microbiota in infants with cystic fibrosis	The pathogenesis of airway infection in cystic fibrosis (CF) is poorly understood.  We aimed to identify changes in the airway microbiota in infancy that could underpin deterioration and could potentially be targeted therapeutically. Thirty infants with CF diagnosed on newborn screening were followed up for up to two years.  Throat swabs were collected as a surrogate for lower airway microbiota (median 35 days between study visits). Quantitative PCR and sequencing of the 16S rRNA bacterial gene was performed using the Illumina MiSeq. Data analyses were performed in QIIME and Phyloseq in R.	root:Host-associated:Human:Digestive system:Oral:Throat
MGYS00006529	Pathogenesis of Obstruction/Emphysema and the Microbiome MiSeq	Examine the microbiome via 16S sequences of the human lung in subjects with and without COPD and HIV	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006431	The fungal intestinal microbiota predict the development of bronchopulmonary dysplasia	Prior investigations of the airway microbiome have inconsistently shown an association between bacterial community composition and bronchopulmonary dysplasia (BPD) development. However, these prior studies have focused exclusively on the bacterial microbiome. Here, we show features of the intestinal fungal microbiome predict the development of BPD in very low birthweight preterm newborns, and that this effect is transferable into mice with fecal microbiota transplant.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006528	Pseudomonas aeruginosa population sequencing	To understand the allelic spectra in well documented genes in Pseudomonas aeruginosa and track their dynamics in longitudinal patient samples	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006472	Examination of microbes in sarcoidosis BAL and tissue. Raw sequence reads	To determine if any microbes are enriched in sarcoidosis relative to healthy controls. 16S, ITS tagged sequencing; shotgun sequencing; viral purification and sequencing.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006522	LHMP - 16S V4 Sequencing of BAL/OW/IS samples on MiSeq Platform	A re-sequencing of Lung HIV Microbiome Project (LHMP) BAL/OW/IS gDNA samples on the Illumina MiSeq platform using the V4 Caporaso primer set.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006501	Analysis of the Cystic Fibrosis Lung Microbiota via Serial Illumina Sequencing	The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways in which microbial communities affect ecosystem functioning and human health. Here we describe Serial Illumina Sequencing (SI-Seq): a method for deep sequencing of the bacterial 16S rRNA gene using next-generation sequencing technology. SI-Seq serially sequences portions of the V5, V6 and V7 hypervariable regions from barcoded 16S rRNA amplicons using an Illumina short-read genome analyzer. SI-Seq obtains taxonomic resolution similar to 454 pyrosequencing for a fraction of the cost, and can produce hundreds of thousands of reads per sample even with very high multiplexing. We validated SI-Seq using single species and mock community controls, and via a comparison to cystic fibrosis lung microbiota sequenced using 454 FLX Titanium. Our control runs show that SI-Seq has a dynamic range of at least five orders of magnitude, can classify >96% of sequences to the genus level, and performs just as well as 454 and paired-end Illumina methods in estimation of standard microbial ecology diversity measurements. We illustrate the utility of SI-Seq in a pilot sample of central airway secretion samples from cystic fibrosis patients.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006527	Augmentation of Standard Clinical Microbiological Culture with Next Generation Sequencing Improves Diagnosis in Bronchoalveolar Lavage Specimens	Immunocompromised patients are at increased risk for pneumonia. Standard microbiological culture may fail to identify unusual or unexpected organisms; culture-independent methods have improved our ability to deconvolute polymicrobial patient samples. We hypothesized that a more complete assessment of the microbial composition of bronchoalveolar lavage (BAL) samples would identify changes to routine clinical laboratory procedures that improve pathogen recovery. 20 consecutive BAL samples from oncology or transplant patients were plated to three standard and four additional media, and cultivable bacteria present were identified by next-generation 16S rRNA gene sequencing (NGS16S) analysis of DNA extracted from washed culture plates. NGS16S analysis was also performed on DNA extracted directly from patient samples. 96% of all organisms identified were cultivable, but only 21% were reported by standard culture, indicating that standard work-up can be further optimized. Direct NGS16S correlated well with standard culture results, identifying the same predominant organism in 50% of samples. When different predominant organisms were identified, NGS16S most often detected anaerobes, whose growth is unsupported by standard culture conditions. Brucella agar was the best single value-added media, supporting the growth of the largest number of organisms for the most specimens. Anaerobes are underappreciated BAL constituents. NGS16S identifies more organisms per sample and allows identification of fastidious organisms, while culture is better at capturing organisms when bacterial load is low, and allows incidental recovery of non-bacterial pathogens such as yeast or molds. Molecular and culture-based methods together detect more relevant organisms in clinical samples than either method alone.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006524	Human respiratory disease lung microbiome	Microbiome sequencing of induced sputum samples from patients with COPD, Bronchiectasis or COPD and Bronchiectasis taking during periods of disease stability and during exacerbations.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006526	Metagenomic Identification of Severe Pneumonia Pathogens in Mechanically-Ventilated Patients	Metagenomic sequencing of respiratory microbial communities for etiologic pathogen identification in pneumonia may help overcome the limitations of current culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore sequencing for severe pneumonia diagnosis. We conducted a case-control study of mechanically-ventilated patients with and without pneumonia. We collected endotracheal aspirate samples (ETAs) and applied a microbial DNA enrichment method prior to performing metagenomic sequencing with the Oxford Nanopore MinION device. We compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing. We demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive clinical cultures and insights into the composition of culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006525	Lung Microbiota of Critically Ill Patients Receiving Mechanical Ventilation	The goal of this project was to determine the relationship between lung microbiota and clinical outcomes in critically ill patients. Miniature bronchoalveolar lavage was performed within 24 hours of admission on critically ill patients receiving mechanical ventilation. Bacterial communities were characterized using 16S rRNA gene amplicon sequencing using the Illumina MiSeq platform.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00002073	The Investigation and Analysis of Microbiomic Data Relating to Diseases Surrounding the Deep Lung Tissue	Exhaled breath condensate is a promising way in identifying biomarkers of lung disease but the  current devices used have disadvantages. The EcoScreen has the disadvantage of not being portable and the R-Tube cannot efficiently keep the sample cool. A 'prototpye' was been created to alleviate these issues. With the 'prototype', EBC  samples were taken and files were concatenated together with md5 checksums allowing for data verification. Data was uploaded and results were compared to current type of collection devices.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006476	Depletion of human DNA from complex clinical samples for metagenomic sequencing	Metagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. Additionally, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. This study describes a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. This method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance, underscoring the substantial impact of DNA from sources other than live bacteria in microbiological analyses of complex, chronic infection specimens.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006496	16S sequencing from human airway sites Raw sequence reads	The rationale for the present study is that evaluation of the pathogenic character of the COPD lung microbiota has been hindered by concerns that oral taxa found in the COPD lung microbiota are the result of sample contamination rather than aspiration. Therefore, we have designed the present study to sample the mild or moderate COPD lung tissue microbiota surgically—without passing the sample through the oropharynx—and avoiding potential upper airway contamination of lung samples. Demonstrating that oral microbes are true components of the COPD lung microbiota will implicate aspiration as a potential pathogenic mechanism in COPD. We hypothesized that oral bacteria are true members of the early-stage COPD lung microbiota and exhibit ecologic drift.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006484	Lung microbiota in the acute respiratory distress syndrome	Here we assess for changes in the lung microbiome in the bronchoalveaolar lavage fluid of patients with the acute respiratory distress syndrome	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006477	COPDMAP lung microbiome	Understanding the lung microbiome dynamics and its dysbiosis in COPDMAP cohort	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006523	human oral metagenome Raw sequence reads	We are the First study results clarify and characterize the variation of equilibrium of oral microbiome in non-smoking female lung cancer. Our ultimate goal is to put different experimental and methodological views into perspective for better understand flora changes upon disease onset or between different disease stages. The role of oral microbiota composition is important to evaluate how oral microbiomes biomarker at the community level could provide improved assessment in individuals and populations at risk, especially in the context of developing non-invasive diagnostic tests.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006520	Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury, part III	The goal of this experiment was to determine the relationship between lung microbiota and lung inflammation in genetically-identical mice exposed to various durations of acute hyperoxia. 10-week old mice (C57Bl/6) were exposed to 95% FiO2 (hyperoxia) for 24 or 48 hours. Bacterial communities were characterized using 16S rRNA gene sequencing.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006521	Analysis of the fetal lung microbiome	Fetal and placental tissue samples were assessed by targeted 16s rRNA gene amplicon sequencing to characterize associated microbiota.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006519	Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury, part IV	The goal of this experiment was to determine the relationship between gut microbiota and lung inflammation in genetically-identical mice exposured to various durations of acute hyperoxia. 10-week old mice (C57Bl/6) were exposed to 95% FiO2 (hyperoxia) for 0, 24, 48, or 72 hours. Bacterial communities were characterized using 16S rRNA gene sequencing.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006518	Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury, part I	The goal of this experiment was to determine the effects of hyperoxia on the microbiota of developing lungs. Newborn mouse pups were exposed either to 21% FiO2 (room air) or 75% FiO2 (hyperoxia) for two weeks. Bacterial communities were characterized using 16S rRNA gene sequencing.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006517	Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury, part II	The goal of this experiment was to determine the effects of hyperoxia on the microbiota of lungs of adult mice. 10-week old mice (C57Bl/6) were exposed to 95% FiO2 (hyperoxia) for 0, 24, 48, or 72 hours. Bacterial communities were characterized using 16S rRNA gene sequencing.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006515	Human COPD lung microbiome	Study of the lung microbiome of humans with COPD when clinically stable using sputum as samples.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006516	Nasal sinuses and lung microbiome in cystic fibrosis patients.	Argumentation the provision that the nasal sinuses of the adult Cystic Fibrosis patients with chronic rhinosinusitis become additional reservoir of infection.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006514	Allergic inflammation impacts synergistic viral-bacterial infections in C57BL/6 mice	To investigate viral-bacterial synergy in the allergic host, we developed a 'triple-threat model' by combining our fungal asthma model with a well-established model of IAV and Spn co-infection.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006513	Mycobiome of mock communities and the human lung.	Invasive fungal infections are an increasingly important cause of human morbidity and mortality. Our goal was to use an amplicon next generation sequencing assay with demonstrated good recapitulation of mock communities to describe the fungal microbiome (mycobiome) of the lung during fungal infection.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006512	Lung microbiota contribute to pulmonary inflammation and disease progression in pulmonary fibrosis, part 2	Rationale: Idiopathic pulmonary fibrosis (IPF) causes considerable global morbidity and mortality, with poorly understood mechanisms of disease progression. Recent observational studies have reported associations between lung dysbiosis, mortality and altered host defense gene expression, supporting a role for lung microbiota in IPF. However, the causal significance of altered lung microbiota in disease progression is undetermined.Objective: To examine the effect of microbiota on local alveolar inflammation and disease progression using both animal models and human IPF subjects.Methods: For human studies, we characterized lung microbiota in bronchoalveolar lavage fluid from 68 IPF patients. For animal modeling, we used a murine model of pulmonary fibrosis in conventional and germ free mice. Lung bacteria were characterized using 16S rRNA gene sequencing with novel techniques optimized for low biomass sample load. Microbiota were correlated with alveolar inflammation, measures of pulmonary fibrosis and disease progression.Main Measurements and Results: Disruption of the lung microbiome predicts disease progression, correlates with local host inflammation, and participates in disease progression. In IPF patients, lung bacterial burden predicts fibrosis progression, and microbiota diversity and composition correlate with increased alveolar pro-fibrotic cytokines. In murine models of fibrosis, lung dysbiosis precedes peak lung injury and is persistent. In germ-free animals, the absence of a microbiome protects against mortality.Conclusion: Our results demonstrate that lung microbiota contribute in the progression of IPF. We provide biologic plausibility for the hypothesis that lung dysbiosis promotes alveolar inflammation and aberrant repair. Manipulation of lung microbiota may represent a novel target for the treatment of IPF.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006511	Lung microbiota contribute to pulmonary inflammation and disease progression in pulmonary fibrosis	Rationale: Idiopathic pulmonary fibrosis (IPF) causes considerable global morbidity and mortality, with poorly understood mechanisms of disease progression. Recent observational studies have reported associations between lung dysbiosis, mortality and altered host defense gene expression, supporting a role for lung microbiota in IPF. However, the causal significance of altered lung microbiota in disease progression is undetermined.Objective: To examine the effect of microbiota on local alveolar inflammation and disease progression using both animal models and human IPF subjects.Methods: For human studies, we characterized lung microbiota in bronchoalveolar lavage fluid from 68 IPF patients. For animal modeling, we used a murine model of pulmonary fibrosis in conventional and germ free mice. Lung bacteria were characterized using 16S rRNA gene sequencing with novel techniques optimized for low biomass sample load. Microbiota were correlated with alveolar inflammation, measures of pulmonary fibrosis and disease progression.Main Measurements and Results: Disruption of the lung microbiome predicts disease progression, correlates with local host inflammation, and participates in disease progression. In IPF patients, lung bacterial burden predicts fibrosis progression, and microbiota diversity and composition correlate with increased alveolar pro-fibrotic cytokines. In murine models of fibrosis, lung dysbiosis precedes peak lung injury and is persistent. In germ-free animals, the absence of a microbiome protects against mortality.Conclusion: Our results demonstrate that lung microbiota contribute in the progression of IPF. We provide biologic plausibility for the hypothesis that lung dysbiosis promotes alveolar inflammation and aberrant repair. Manipulation of lung microbiota may represent a novel target for the treatment of IPF.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006510	Human Lung Microbiome Raw sequence reads	Meta-genomic profiling of Human Lung microbiome	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006509	16S rRNA gene sequencing of the pulmonary microbiota in sarcoidosis	16S rRNA gene sequencing of the lung microbiota of patients with sarcoidosis and patients with other interstitial lung disease	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006506	Bronchoalveolar lavage lung microbiota in children with cystic fibrosis	The goal of this study was to determine the lung microbiota in children with cystic fibrosis, differentiating true lung microbiota from contaminants that could come from the oropharynx, mouth, collection instruments, and/or reagents used to process and sequence samples. Bronchoalveolar lavage samples were collected, as well as throat, mouth, instrument, and reagent controls. DNA was isolated from each sample type and subjected to bacterial 16S rRNA gene sequencing.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006508	Gut microbiota in lung cancer patients	Investigate phylogenetic compositions in gut microbiota between lung cancer patients and healthy volunteers	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006507	Airway bacteria and P. aeruginosa pathogens under antibiotic therapy	We aimed to explore the effects of broad-spectrum combination antibiotic therapy on Pseudomonas aeruginosa populations in the lungs of cystic fibrosis patients. Sputum samples were collected daily to provide sufficient temporal resolution to capture rapid effects.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006505	Respiratory microbiota in lung cancer, bronchiectasis and healthy populations	The respiratory microbiome is a role player in human health, therefore is significant to be addressed thoroughly. The respiratory tract is the main portal through which the microorganisms enter the human body. Lung cancer and bronchiectasis are chronic lung diseases that largely burdens the humans around the world.This study intended to identify bacteria in human respiratory tract (upper and lower) in the two diseases as well as in a healthy group.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006504	human lung metagenome targeted loci cystic fibrosis	We report an approach to detect diverse bacterial and fungal taxa incomplex samples by direct analysis of community RNA in one stepusing NanoString probe sets. We designed rRNA-targeting probe sets todetect forty two bacterial and fungal genera or species common incystic fibrosis (CF) sputum, and demonstrated taxon-specificity ofthese probes as well as a linear response over more than three logsof input RNA. Culture-based analyses correlated qualitatively withrelative abundance data on bacterial and fungal taxa obtained byNanoString and the analysis of serial samples demonstrated the useof this method simultaneously detect bacteria and fungi and todetect microbes at low abundance without an amplification step. Therelative abundances of bacterial taxa detected by analysis of RNAcorrelated strongly with the relative abundances of the same taxa asmeasured by sequencing of the 16S rRNA gene amplified from communityDNA from the same sample. This method may complement other methodsdesigned to understand dynamics microbial communities, may provideinformation on bacteria and fungi in the same sample with a singleassay, and, with further development, may provide quick andeasily-interpreted diagnostic information on diverse bacteria and fungiat the genus or species level. PI Deborah Hogan	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006503	Lower respiratory microbiota from pediatric BAL samples	This study investigates the clinical utility of 16S rRNA gene-based sequencing of pediatric bronchoalveolar lavage (BAL) samples. Samples were taken from cystic fibrosis (CF), immunocompromised (IC) and non-immunocompromised (nIC) patients, and culture-independent results were compared to routine cultures of the same samples. Based on 16S rRNA gene sequencing results, we investigated the influence of diagnosis group and recent antibiotic exposure on sample diversity.While the vast majority of cultured organisms were also identified by culture-independent methods, many additional taxa, including a number of potential pathogens, were identified by 16S rRNA gene-based sequencing that were not detected by routine culture. We found that CF samples had lower alpha diversity than those from IC and nIC patients. We also saw reduced abundances of Escherichia and Corynebacterium in the CF group, and lower Streptococcus, Veillonella and Haemophilus abundance in samples from patients exposed to antibiotics. Lastly, we identified a core group of 15 taxa present in all diagnosis groups.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006502	MEU Manchester lung microbiome	Association of sputum microbiome with exacerbations, patient subgroups and host response in chronic obstructive pulmonary disease	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00005304	NTM Human Microbiome and Inflammation Study	These are airway samples from humans which contain metagenomic (microbiome) materials. They include sputum, oral wash, and BAL.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006500	Respiratory mycobiome and microbiome in cystic fibrosis	Characterization of the respiratory mycobiome and microbiome in cystic fibrosis : first evidence for inter-kingdom cross-talk during acute pulmonary exacerbation	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006499	Lung microbiota of C57BL/6J mice (Mus Musculus) Raw sequence reads	Commensal microbiota play an important role in many physiological processes. Importantly, they pose a natural threshold to colonization with pathogenic bacteria by direct competition. Here we show that acute infection of the lung with influenza A viruses causes elimination of a substantial proportion of bacteria from the small intestine. This weakens the natural shield against pathogenic bacteria and renders the intestinal epithelium vulnerable for invading bacteria. We further show that influenza A virus infection up-regulates the activity of Paneth cells a major source of antimicrobial peptides in the small intestine. This suggests that influenza A viruses affect a host mechanism of microbiota regulation to cause bacterial depletion in the small intestine. Surprisingly, the same mechanism does not apply in the respiratory tract, where influenza A virus infection causes subtle qualitative but not quantitative changes in the commensal microbiota. Overall, our date provide the first description of microbiota dynamics in an acute infection animal model.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006497	16S bacterial profiling in bronchoalveolar lavage fluid from patients with Cystic Fibrosis	Cross-sectional study to evaluate the composition of the lung microbiota through 16S profiling in bronchoalveolar lavage fluid from patients with Cystic fibrosis from the CF-AREST study cohort.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006498	Human Lung Metagenome Raw sequence reads	Measuring stability of the lung-microibome in the COPD patients.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006495	Homo sapiens Raw sequence reads	Human Lung Cancer Metagenome/Microbiome	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006474	Clinical bronchoalveolar lavage (BAL) samples Targeted loci	lung microbiome in ventilated patients	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006461	direct sequencing of 16S rRNA V3-V4 region of lung tissue from lung cancer patients raw sequence reads	The main goal of the study is to characterize the lung tissue microbiome from non-malignant tissue of lung cancer patients, and related the microbiome features to epidemiologic and clinical data.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006483	The lung microbiota in COPD patients when clinically stable and during exacerbations.	Illumina MiSeq sequencing of the bacterial 16S rRNA amplicon in sputum samples taken longitudinally from COPD patients when clinically stable (free of antibiotic or corticosteroid therapy for 4 weeks), at start of exacerbation and at end of exacerbation (10 days post start of exacerbation after standardised treatment). Patients were followed up for up to 6 months with a second clinically stable sample obtained at end of study.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006494	Human lung metagenome of 17 adult CF patients throughout the course of clinical exacerbation, treatment and recovery Targeted Locus (Loci)	Bacterial communities for sputum genomic DNA samples from 17 patients throughout the course of clinical exacerbation, treatment and recovery examined by 16S pyrotag sequencing.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006493	IPF lung tissue and swabs Targeted Locus (Loci)	Microbial community profiling of idiopathic pulmonary fibrosis patients.  Lung tissue and nasopharyngeal, oral, and rectal swabs from two patients with idiopathic pulmonary fibrosis.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006487	EMG produced TPA metagenomics assembly of PRJNA680735 data set (Metagenome of the lower urinary tract).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA680735, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Excretory system:Urethra:Urine.	root:Host-associated:Human:Excretory system:Urethra:Urine
MGYS00006492	Variation in the microbiome on the surfaces of a physical therapy gym	Various surfaces of a physical therapy gym were sampled using swabs, which were then subject to 16S rRNA analysis in order to describe how the microbiome changes according to porosity, contact frequency, cleaning frequency, and physical location within the environment.	root:Engineered:Built environment
MGYS00001361	Habitat models of wood-inhabiting fungi along a decay gradient of Norway spruce logs	Modern molecular techniques provide a comprehensive and high-resolution window into complex systems that are difficult to study with traditional macroscopic techniques. We applied culture-free DNA extraction and 454-pyrosequencing to study the fungal microflora of decaying Norway spruce (Picea abies [L.] Karst.) logs in five unmanaged boreal forests. Fungal diversity and wood density were inversely related, i.e., OTU richness generally increased as the log became increasingly decomposed. According to generalized additive mixed models white-rot fungi (e.g., Phellinus nigrolimitatus) and members of Hyphodontia did not show a clear response to the wood-density gradient, whereas Phellinus viticola and brown-rot fungi (e.g., Fomitopsis pinicola, Antrodia serialis, Coniophora olivaceae) peaked during intermediate decay and mycorrhizal fungi (e.g., Piloderma, Tylospora, Russula) increased in the later stages. This information on fungal habitat requirements facilitates development of management practices that preserve fungal diversity in managed forests.	root:Engineered:Solid waste:Composting:Wood
MGYS00006490	EMG produced TPA metagenomics assembly of PRJNA801448 data set (Metagenomic Analysis of the Urinary Microbiome of Postmenopausal Women).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA801448, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Excretory system:Urethra:Urine.	root:Host-associated:Human:Excretory system:Urethra:Urine
MGYS00006489	EMG produced TPA metagenomics assembly of PRJNA700071 data set (Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA700071, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Excretory system:Urethra:Urine.	root:Host-associated:Human:Excretory system:Urethra:Urine
MGYS00005519	EMG produced TPA metagenomics assembly of the Dechlorinating community (Dhgm_1) data set.	The Dhgm_1 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB8993.  This project includes samples from the following biomes: Host-associated, Microbial, Bacteria.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00006488	EMG produced TPA metagenomics assembly of PRJNA679884 data set (Interstitial Cystitis Urinary Metagenomics).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA679884, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Excretory system:Urethra:Urine.	root:Host-associated:Human:Excretory system:Urethra:Urine
MGYS00005261	Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis	We sequenced the V3-V5 hypervariable region of the bacterial 16S rRNA gene in DNA derived from 631 CF sputum specimens collected from 111 subjects over 10 years. We observed fluctuations in the abundances of typical CF pathogens, as well as anaerobic species, relative to changes in patients' clinical state and lung disease stage.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006486	EMG produced TPA metagenomics assembly of PRJNA385350 data set (Microbial metagenome of urinary tract infection).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA385350, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Excretory system:Urethra:Urine.	root:Host-associated:Human:Excretory system:Urethra:Urine
MGYS00006479	Respiratory Microbiota Metagenome	Alcohol-associated respiratory microbiota	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006480	Sputum microbiome in COPD patients	Microbiome data studying which microorganisms are responsible for exacerbations are limited in sputa of COPD patients. The lung microbiome is a new approach to add additional insights about the causal pathogens and the shift in bacterial community of COPD patients.The goal of this study was to identify which microorganism(s) may have triggered the exacerbations of COPD patients. We compared the sputa microbiome of COPD patients when clinically stable and during an exacerbation.This study shows a clear shift in the microbiome of patients during exacerbation, mostly toward Proteobacteria and Firmicutes.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006478	GlaxoSmithKline - UofSouthampton - AERIS COPD Lung Microbiome	Healthy human lungs are not sterile and contain a variety of commensal microbiota. Alterations in the composition of the lung microbiome, known as dysbiosis, have been associated with lung disease and in particular may play a functional role in disease severity and exacerbations in chronic obstructive pulmonary disease (COPD). The AERIS study (Acute Exacerbation and Respiratory Infections in COPD; GSK Study 114378; NCT01360398) provides a unique opportunity to observe dynamic changes in the lung microbiome and associated biomarkers in a cohort of 127 COPD patients, who were followed monthly and within 72 h of exacerbation onset over two years. We surveyed 584 sputum samples from 104 patients to analyze the lung microbiome at both stable and exacerbation time points in the first year of the study via 16S rRNA sequencing. We obtained a mean of 5.7 samples per subject, 2.1 of which were collected during an exacerbation event. Ranking subjects by GOLD status showed a significant decrease in entropy of the microbiome (Shannon diversity index) and an increase in the relative abundance of Proteobacteria, such as Haemophilus, with an increase in disease severity. The genus with the most significant increase between stable and exacerbation events was Moraxella. Exacerbations with different phenotypes (containing bacterial pathogens detected by culture compared to eosinophils in sputum) had significantly distinct ratios of Proteobacteria to Firmicutes. Moreover, using a Markov chain analysis of exacerbation phenotypes, we found that bacterial and eosinophilic but not viral exacerbations were more likely to be repeated in subsequent exacerbations within a subject. Markov chain analysis also revealed that bacterial exacerbations containing Haemophilus influenzae (Hi, mostly nontypeable) had an increased probability of repeating relative to bacterial (e.g. Moraxella) exacerbations without Hi. Finally, we analyzed the temporal stability of the lung microbiome within each subject and found that microbiome composition in both stable and exacerbation states became more variable in patients experiencing exacerbations during the year. Patients with bronchiectasis showed notably more stability in microbiome composition, which was characterized by a high proportion of Haemophilus relative to that in patients without bronchiectasis. These findings improve our understanding of lung microbiome behavior over time in COPD, providing insight into our ability to use dysbiosis as a biomarker in COPD classification and establishing for the first time infective and inflammatory longitudinal phenotypes that may be used to guide future therapeutic strategies.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006482	microbial diversity in human respiratory tract	microbial diversity in human respiratory tract of pneumonia children	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006481	Mouse Lung Microbiome Heterogeneity Across Vendors	We studied the heterogeneity of lung microbiota in C57/BL-6 mice acquired from two vendors via four shipments. We compared variation in lung microbiota with variation in lung immune tone, as assessed by concentrations of inflammatory cytokines measured via Luminex Multiplex assay.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006471	pulmonary capillary bronchitis Targeted loci environmental	To discovery involvement of pulmonary capillary bronchitis microbiome,and distinct microbial correlation under RSA infected and healthy.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006473	Effects of silver nanoparticles on mouse lung microbiome	Here we describe dose-dependent effects of different coated silver nanoparticles on the mouse lung microbiome using 16S rRNA gene sequencing on Illumina Miseq.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006469	Longitudinal Sampling of the Lung Microbiota in Individuals with Cystic Fibrosis	1 year long study of the cystic fibrosis lung microbiome via DNA isolation from sputum. 16S rRNA gene sequencing of the variable 3 region using 250bp, paired-end Illumina sequencing.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006470	human respiratory metagenome Targeted loci environmental	Twelve adult cystic fibrosis patients were enrolled in a cross-sectional study to investigate the biodiversity in paired lung sputum and sinus mucus samples by 16S sequencing of the V4 hypervariable region. The goal of the investigation was to compare and contrast the bacterial communities in these specimens, in order to better understand the ecological landscape of the cystic fibrosis respiratory system. Sputum samples were collected by expectoration immediately prior to functional endoscopic sinus surgery to treat chronic upper respiratory infections. Genomic DNA was isolated from these samples, and the V4 hypervariable region was amplified from this DNA and sequenced at the University of Minnesota Genomics Center.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006468	Anaerobic bacteria fermentation products increase tuberculosis risk in antiretroviral treated HIV-infection Sequence	Sequence data from bronchoscopy study	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006466	Human sputum 16S rDNA profiles - children with cystic fibrosis	The lung microbiome in cystic fibrosis (CF) is home to numerous pathogens shortening the life of patients. In contrast to adults whose lung infections are mostly resilient, children are more responsive to therapy. Our aim was to assess changes in the lung microbiome in children with CF that were induced by antibiotic therapy against the most important of the pathogens, Pseudomonas aeruginosa.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006467	Lung Microbiome in Idiopathic Pulmonary Fibrosis and Interferon-?	Bronchoalveolar lavage samples Genome sequencing and assembly	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006463	Diversity and Dynamics of tracheal microbiota in patients with tracheostomy	We describe the longitudinal diversity of the tracheal microbiome in patients with tracheostomy using 16S V4 rRNA gene sequencing of tracheal aspirates.	root:Host-associated:Human:Respiratory system:Pulmonary system:Trachea
MGYS00006465	human lung metagenome Targeted Locus (Loci)	microbiota clinical bronchoalveolar lavage (BAL) samples	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006464	sequencing for human-associated microbes by 16S rRNA gene Raw sequence reads	The study goal is to examine lung tissue microbiome in lung cancer patients.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006460	The Bacterial Topography of the Healthy Human Respiratory Tract	Here we study there bacterial topography of the human respiratory tract in health and demonstrate that micro-aspiration is the method of microbial dispersion in the lungs	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006462	human lung metagenome Raw sequence reads	PBB (protracted bacterial bronchitis) is a widespread pediatric disease, and relative lung microbiota dysbiosis remains unclear.In this study,12 tracheomalacia infants samples were selected for analyzed.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006458	Human pulmonary secretions and tissue Targeted Locus (Loci)	Human pulmonary microbiome - pulmonary secretions and tissue from cystic fibrosis patients and pulmonary secretions from healthy volunteers.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006459	Dynamics of airway microbiota in CF children	Here we describe the diversity of the airway microbiome in CF children using 16S V4 rRNA gene sequencing of sputum samples.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006457	16S rRNA amplicons isolated from microbial communities from the cystic fibrosis lung	Microbial communities from cystic fibrosis lung tissue.  This project sought to spatially profile microbial and viral communities in the cystic fibrosis lung using high throughput sequencing.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006450	Gut microbial community diversity of mice with allergic lung inflammation	The gut microbiome remodeling by polygonatum odoratum polysaccharide in mice with allergic lung inflammation	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006244	short read sequencing of distinct cheese rinds	Cheese rinds are a semi-complex microbial community with bacteria, fungi, and viruses. Here, we harvested cheese rinds from 11 different cheeses, and extracted DNA from the 11 microbial communities as well as the associated virome of one cheese rind.	root:Engineered:Food production:Dairy products
MGYS00006453	ITS2 and whole metagenomics from stool of human lung cancer patients from hungary	Investigating Bacteriome and Mycobiome interactions, and their contribution to lung cancer treatment. For treatment, anti-cancer combination therapy was used.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006456	Intestinal flora sequence in a mouse model of lung cancer	The effect of intestinal flora in mouse models of lung cancer and the regulation of intestinal flora after adjuvant administration	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006454	16S-based bacterial profiling of the microbiota associated with the bronchoalveolar lavage fluid of patients with COPD, healthy smokers and healthy controls. Targeted loci	16S-based amplicon sequencing profiling of the microbiota associated with the bronchial wash of COPD patients, healthy smokers and healthy controls.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006455	Comparison of the lung microbiota in patients with respiratory infection, tuberculosis, and lung cancer: a preliminary study	Recent evidence suggested that lung microbiota can be recognized as one of the ecological determinants for many respiratory diseases. However, the different of the lung microbiota and its associated lung immunity were still unclear.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006451	Bacterial microbiome of sputum samples from patients with bronchiectasis recruited in stable state	The aim of the study was to evaluate the bacterial microbiome composition and to determine associations between the observed microbial diversity and biological and clinical characteristics in sputum samples collected from patients with bronchiectasis, recruited in stable state.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006452	The respiratory tract microbiome in children with Cystic Fibrosis	Metagenomic sequencing of respiratory tract microbiome in children with Cystic Fibrosis.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006446	Horizontal transmission of gut microbiota in lung fibrosis	We determine the impact of gut microbiota in pre-clinical models of pulmonary fibrosis in different sub-strains of C57BL/6 experimental mice derived from vendors (C57BL/6J and C57BL/6Cr). We use germ free models, fecal microbiota transplantation and cohousing approaches to transmit gut microbiota and investigate causality.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006442	Cystic fibrosis lung microbiome.	Species isolated from sputum samples collected from cystic fibrosis lungs. Raw sequence reads, assembly.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006448	Lower respiratory tract microbiome composition and community interactions in smokers	Lung microbiome study conducted on active, former, and non-smokers	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006447	Lung Microbiota in Lung Transplant Recipients at CLAD Onset	The goal of this project was to determine the relationship between lung microbiota, clinical outcomes, and treatment response among lung transplant recipients with chronic rejection. Bacterial communities in acellular bronchoalveolar lavage fluid collected near the time of chronic lung allograft dysfunction (CLAD) diagnosis were characterized using 16S rRNA gene amplicon sequencing using the Illumina MiSeq platform	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006444	Microbiome Raw sequence reads	Metagenomic Analysis of Lung Microbiome in Pulmonary Tuberculosis - a pilot study	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006445	Lung microbiome dysbiosis in  lower airway in progression of lung cancer.	The difference in lung microbiota between LC patients and patients with non-lung cancer was detected by 16S ribosomal DNA gene sequencing, with the purpose of exploring the interaction between lung microbiota and lung cancer.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006443	Influence of targeted therapy on the composition of the lung microbiome of patients with cystic fibrosis	Approved targeted drugs have different effects on the rate of recovery of the lung microbiome of patients with cystic fibrosis	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006441	Lung mycobiome Raw sequence reads	Fungal Internal Transcribed Spacer (ITS2) from Broncho-alveolar lavage samples (BAL) and environental samples were was sequenced	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006439	Taxonomic signatures of Cystic Fibrosis airway microbiota	In order to gain insight into the underlying causes of severe lung disease and identify potential determinants of ecological and clinical changes in lung function, we compared the airway microbiota composition and diversity of CF patients with a substantial decline in lung function (SD) with that of patients with stable lung function (S).	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006438	The bronchial epithelial cell bacterial microbiome and host response in patients infected with human immunodeficiency virus	Here we describe the HIV bacterial microbiome and investigate using gene expression the pathways that these bacterial communities may be interacting with.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006440	Human_sputum_16S Raw sequence reads	The microbial samples were taken from sputum of 21 hospitalized patients with pneunomia, DNA was purified and the 16S rRNA DNA was amplified and sequenced	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006434	Neutrophilic Proteolysis in the Cystic Fibrosis Lung Favors a Pathogenic Microbiome	Studies of the cystic fibrosis (CF) lung microbiome have consistently shown lung disease progression is associated with decreased microbial diversity due to the dominance of opportunistic pathogens, but it remains unknown how this phenomenon is reflected in the metabolites and chemical environment of lung secretions. We investigated the microbial and metabolomic composition of CF sputum samples to determine the molecular relationships between disease severity, lung function decline and microbial infections.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006437	Experimental sepsis and the lung microbiome at extended timepoints	Here we assess for changes in the lung microbiome at 5 days, 14 days and 8 weeks after experimental sepsis in mice	root:Mixed
MGYS00006435	Human microbiome Targeted Locus (Loci)	We examined the respiratory and intestinal microbiota development in infants with CF from birth to 21 months. Gut and lung microbiome in CF in infancy. PI Juliette Madan	root:Host-associated:Human
MGYS00006436	Experimental sepsis and the lung microbiome at 24 hours	Here we assess for changes in the lung microbiome 24 hours after experimental sepsis in mice	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006433	Murine lung microbiota	Commensal bacteria control the micro-ecology of metazoan epithelial surfaces with pivotal effect on tissue homeostasis and host defense. In contrast to the upper respiratory tract, the lower respiratory tract of healthy individuals is largely considered free of microorganisms. To understand airway micro-ecology we studied microbiota of sterilely excised lungs from mice of different origin including outbred wild mice caught in the natural environment or kept under non-specific-pathogen-free (SPF) conditions as well as inbred mice maintained in non-SPF, SPF or germ-free (GF) facilities. High-throughput pyrosequencing revealed that Betaproteobacteria and Ralstonia sp. represent the major constituents of murine lung microbiota. Non-cultivatable Betaproteobacteria were also identified by 16S rRNA gene cloning analysis in all but GF mice. Additionally, Pasteurellaceae, Enterobacteria and Firmicutes were isolated from the lungs of non-SPF, but not from SPF mouse lungs. Bacterial communities were detectable by FISH at alveolar epithelia without induction of inflammation. The overall composition across samples was similar at the phylum and family level, although significant differences with respect to the origin of the mice were observed at the community level. In addition, changing from a SPF to non-SPF environment was associated with increased species richness. Notably, higher bacterial colonization correlated with more and smaller sized alveolae in those mice. Our data indicate a common microbial composition in murine lungs, which is diversified through different environmental conditions and whose richness affects lung architecture. Identification of the microbiota of murine lungs will pave the path to study their influence on pulmonary immunity to infection and allergens using mouse models.	root:Host-associated:Mammals:Respiratory system
MGYS00006432	Gut and Lung Microbiomes in AIDS with or without PCP	This study tried to explore the pathogenesis of Pneumocystis Pneumonia(PCP) in AIDS patients from the microbiome perspectives, so as to provide better strategies for the diagnosis, treatment and prevention of PCP.	root:Host-associated:Human
MGYS00006392	features of multi-site microtiota in patients with Crohn's disease	features of microtiota in oral cavity, sputum and ileum in patients with Crohn's disease	root:Host-associated:Human
MGYS00006428	COVID-19 Cadaver Microbiome (Dr. Gulnaz Javan et al.)	Study performed by Dr. Gulnaz Javan et al. Data obtained from these studies facilitated the defining of microbiome signatures in COVID-19 decedents that could be identified as taxonomic biomarkers effective for predicting the occurrence, the co-infections involved in its dysbiosis, and the evolution of the virus.	root:Host-associated:Human
MGYS00006430	lung microbiota	lung microbiota of juvenile mouse	root:Host-associated:Mammals:Respiratory system
MGYS00006429	Mouse lung metagenome Raw sequence reads	Intervention of Mahuang Fuzi Xixin decoction on lung microbiota in AR mice	root:Host-associated:Mammals:Respiratory system
MGYS00006427	Meta-omics profiling of the gut-lung axis illuminates metabolic networks and host-microbial interactions associated with elevated lung elastance in a murine model of obese asthma	We evaluated nitro-oleic acid as a host- and microbial-targeted treatment intervention for obesity-associated asthma. Allergic airway disease was induced using house dust mite and cholera toxin adjuvant in C57BL6/J mice with diet-induced obesity to model obesity-associated asthma. Mice were treated with either glycerol trioleate vehicle (n = 11) or 9,10-nitro-oleic acid (n = 11) via gavage, followed by allergen challenge 3 hours later. Controls included a mock sensitization group (n = 12) that only received adjuvant during sensitization and a group of naive obese mice (n = 7). Lung function was measured by flexiVent following a week of nitro-oleic acid treatment and allergen challenge. 16S rRNA gene (from DNA, taxa presence) and 16S rRNA (from RNA, taxa activity) sequencing were performed on stool samples collected from mice on the day of lung function measurement. Stool RNA and DNA were isolated using ZymoBIOMICS DNA/RNA Miniprep kit, and cDNA was synthesized with the SuperScript IV VILO kit. 16S rRNA amplicons were run on Illumina MiSeq. Targeting both the host and gut microbiota, NO2-OA attenuated airway inflammation, improved lung elastance, and modified the gut microbiome	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006424	Microbial communities of neonates from allergic mothers	16S rRNA sequencing was performed on lung microbiota from mouse pups born to allergic mothers and control.	root:Host-associated:Mammals:Respiratory system
MGYS00006426	Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis	The early description of cystic fibrosis (CF) was marked by malnutrition and lung infections. The diagnosis and treatment of infection has transformed disease prognosis to a median predicted survival over 50 years. Yet, chronic infections continue to significantly impact morbidity and mortality in CF. Over time, the microbial epidemiology has changed, with a rise of filamentous fungi and yeast recovered by culture from the CF respiratory tract. The pressures of cumulative and chronic exposure to antibiotics in the course of CF likely contributes to the observed changes in fungal detection.Conventional culture-based detection methods are the primary modality to identify microorganisms in CF sputum. However, the adoption of DNA sequence-based analyses has greatly expanded our understanding of bacterial diversity in CF. Unbiased 16S rRNA gene sequencing of CF respiratory samples have yielded insight into age-specific bacterial diversity and resiliency of the bacterial community during pulmonary exacerbations. However, mycologic profiling of the CF airway has remained limited. Our study aimed to molecularly define the fungal composition and community structure in CF sputa and evaluate their associations with clinical characteristics and outcomes.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006425	The lung microbiota in nontuberculous mycobacterial pulmonary disease	To compare the bacterial microbiome of disease-invaded lesions and non-invaded lung tissue from NTM-PD patients.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006423	Clinical Trial of a Probiotic and Herbal Supplement for Lung and Gut Health	Microbiome data for clinical trial of probiotic and herbal blend in healthy and asthma patients	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006422	Homo sapiens Raw sequence reads	Lung microbiota in SARS-CoV-2 infected patients	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006419	Dynamic changes of intestinal flora and metabolic function in patients with postoperative pneumonia after lung cancer surgery	This study aims to investigate the dynamic changes and metabolic function of intestinal flora in patients with lung cancer and postoperative pneumonia (POP), and to provide new ideas and targets for the prevention and treatment of POP.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006417	Microbiome analysis of the gut-lung axis in bronchiectasis (mouse model)	This submission contains data related to targeted 16S (bacteriome) and ITS (mycobiome) data from the mouse gut microbiome assessed in a controlled P. aeruginosa intratracheal infection model are also present, including 6 samples per arm, across 4 arms, from P. aeruginosa infected and P. aeruginosa uninfect mice in the presence or absence of orally administered Imipenem consisting of (24 samples). Sequence data from relevant pre-post antibiotic treatment and background contamination controls are also present.	root:Host-associated:Mammals
MGYS00006420	Lung microbiota in mice underwent intestinal ischemia/reperfusion injury (Singly housing)	To provide the data of the lung microbiota after intestinal ischemia/reperfusion injury under singly housing condition	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006418	lung cancer manifested as radiological ground-glass opacity Raw sequence reads	Using 16S rRNA gene sequencing to identify significant differences in the lower respiratory tract and lung microbiome between GGO and the non-malignant control group through the BALF and lung tissues	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006412	Microbial Dysregulation of the Lung-Gut axis in high-risk bronchiectasis	Analysis of lung and gut microbiome profiles in bronchiectasis	root:Host-associated:Human
MGYS00006416	Intestinal microbiota-derived propionic acid protects zinc  oxide nanoparticles-induced lung injury	BACKGROUND: Inhalation zinc oxide fumes results in the development of the clinical syndrome known as metal fume fever, the severe cases of which may develop to diffuse alveolar damage. However, the link between inhaled zinc oxide at nano-size (zinc oxide nanoparticles, ZnONPs)-induced acute lung injury (ALI) and intestinal microbiota remains largely unknown.OBJECTIVE: To investigate the role and mechanism of intestinal microbiota and its metabolites short chain fatty acids (SCFAs) in the pathology of ZnONPs-induced ALI and the therapeutic potential of modulating intestinal microbiota in ZnONPs-induced ALI.METHODS: Intratracheal instillation of ZnONPs was used to establish a ALI mice model; antibiotic cocktail treatment (ABX) and fecal microbiota transplantation (FMT) were used to modulate intestinal microbiota; 16S rRNA sequencing and LC-MS/MS were applied to evaluate the change of intestinal microbiota and SCFAs.RESULTS: Intratracheal instillation of ZnONPs caused macrophage-mediated ALI in mice. ABX-mediated depletion of intestinal microbiota aggravated ZnONPs-induced ALI; in contrast, FMT-mediated restoration of intestinal microbiota exerted opposite effects; ZnONPs inhalation resulted in the perturbation of intestinal flora and consequently the decrease of SCFAs (especial acetate acid or propionate acid) in the plasma; supplementation of sodium propionate, but not sodium acetate, remarkably ameliorated ZnONPs-induced ALI; GPR43 was the major receptor of propionate acid in RAW 264.7 macrophage cell lines.CONCLUSION: We illuminates a novel gut-lung axis mechanism that intestinal microbiota and its-derived metabolite propionate acid plays protective role against ZnONPs-induced ALI through repressing macrophage-mediated inflammation and oxidative stress via GPR43 receptor. FMT and supplementation of propionate acid are potential remedy strategies.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006415	An optimized approach for processing of frozen lung and lavage samples for microbiome studies	BALB/c mice bronchoalveolar lavage fluid (BALF) and lung tissue samples were collected to test different forms of sample pre-treatment and extraction methods to improve DNA yield and optimize library preparation (V4 16S rRNA) of frozen low microbial biomass samples.	root:Host-associated:Mammals:Respiratory system:Pulmonary system
MGYS00006414	Microbial diversity in the lung and gut microbiome of Plasmodium infected mice	16S rRNA amplicon sequencing study of the lung and gut microbiome of two mouse strains (C57BL/6J and DBA2), when infected or not with different strains of Plasmodium that lead to different pathologies, particularly with and without lung pathology.	root:Host-associated:Mammals
MGYS00006413	Lung fungal microbiome of critical COVID-19 patients	The study was aimed to characterize the lower respiratory tract mycobiome of COVID-19 critically ill patients and investigate the fungal microbiome diversity in comparison to COVID-19-negative patients. We performed ITS rRNA gene profiling, with the Illumina MiSeq platform to analyse the fungal microbiome in bronchoalveolar lavage (BAL) samples collected from COVID-19 critically ill subjects and patients with non-COVID-19 pneumonia	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006408	Pathogensis of Obstruction/Emphysema and the Microbiome in HIV Targeted Locus (Loci)	Microbial flora of the respiratory tract in persons with and without HIV. The flora is expected to play a role in HIV-associated Chronic obstructive pulmonary disease (COPD). We sampled the respiratory tract including oral washes (OW), induced sputum (IS), and bronchoalveolar lavages (BAL). We examined the relationship between microbial flora and smoking, HIV infection status, and COPD.	root:Host-associated:Human:Respiratory system:Pulmonary system
MGYS00006407	Lung microbiome dynamics in chronic obstructive pulmonary disease exacerbations	Increasing evidence suggests that the lung microbiome plays an important role in chronic obstructive pulmonary disease (COPD) severity. However, the dynamics of the lung microbiome during COPD exacerbations and its potential role in disease aetiology remains poorly understood. We completed a longitudinal 16S ribosomal RNA survey of the lung microbiome on 476 sputum samples collected from 87 subjects with COPD at four visits defined as stable state, exacerbation, two weeks post therapy and six weeks recovery. Our analysis revealed a dynamic lung microbiota where changes appeared to be associated with exacerbation events and indicative of specific exacerbation phenotypes. Antibiotic and steroid treatments appear to have differential effects on the lung microbiome. We depict a microbial interaction network for the lung microbiome and suggest that perturbation of a few bacterial operational taxonomic units, in particular Haemophilus spp, could greatly impact the overall microbial community structure. Furthermore, several serum and sputum biomarkers, in particular sputum interleukin-8 (IL-8), appear to be highly correlated with the structure and diversity of the microbiome. Our study furthers our understanding of lung microbiome dynamics in COPD patients and highlights its potential as a biomarker, and possibly a target, for future respiratory therapeutics.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006411	Dendrobium nobile protects against ovalbumin-induced allergic rhinitis by regulating intestinal flora and suppressing inflammation in the lungs	This project aims to elucidate the effects of intestinal flora dysbiosis on allergic rhinitis and the mechanism by which Shihu extract restores intestinal flora balance to improve allergic rhinitis.	root:Host-associated:Birds:Digestive system:Fecal
MGYS00006410	lung microbiome of  children with pneumonia	To understand involvement of lung microbiome in pneumonia etiology, and distinct microbial correlation under pneumonia infected with different pathogens.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006409	A Multi-Center Study of the Lung Microbiome in Chronic Obstructive Pulmonary Disease	An international cohort study to determine whether respiratory micro biome differs by geography, smoke exposure type, and disease severity in COPD	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006389	Impact of long-term azithromycin treatment on the respiratory microbiome in HIV-associated chronic lung disease	Obliterative bronchiolitis is a recently diagnosed chronic lung disease (CLD) detected in 30% of older children and adolescents living with HIV in Sub-Saharan Africa. Although there are no management guidelines, long-term azithromycin has been suggested as a treatment option due to its dual antimicrobial and immunomodulatory action and effectiveness in other CLDs such as cystic fibrosis, bronchiectasis and asthma. However, its effect on the respiratory bacterial community in this disease context remains unknown. Therefore, this study aims to investigate the impact of 48 weeks of once-weekly, weight-based dosing of azithromycin on the respiratory microbiome of children and adolescents with HIV-associated CLD in an individually randomised, placebo-controlled, double-blinded clinical trial in Zimbabwe and Malawi. We also assessed the persistence of the azithromycin effect on the respiratory microbiome six months post-intervention. Finally, we evaluated the differences in the respiratory microbiome of HIV-infected children with and without CLD. This study's findings extend our understanding of the pathogenesis of this novel CLD and the mechanisms underlying the effectiveness of azithromycin.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006406	Lung microbiota in mice underwent intestinal ischemia/reperfusion injury	None	root:Host-associated:Mammals
MGYS00006405	Antibiotic-induced microbiome depletion ameliorates LPS-induced acute lung injury in mice.	In this research, treatment with ABX significantly attenuated LPS-induced lung injury of mice. Considering the key role of gut microbiota in immune system, it is likely that alternations in the gut microbiota by ABX may play a role in LPS-induced lung injury.	root:Host-associated:Mammals:Gastrointestinal tract
MGYS00006403	The microbiota of human lung of pulmonary tuberculosis	An in-depth understanding of the lung microbiota of tuberculosis (TB) could provide better strategies for the prophylaxis, diagnosis, and treatment of TB.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006404	Propionic acid protects ZnONPs-induced lung injury	Inhalation zinc oxide fumes results in the development of the clinical syndrome known as metal fume fever, the severe cases of which may develop to diffuse alveolar damage. However, the link between inhaled zinc oxide at nano-size (zinc oxide nanoparticles, ZnONPs)-induced acute lung injury (ALI) and intestinal microbiota remains largely unknown.To investigate the role and mechanism of intestinal microbiota and its metabolites short chain fatty acids (SCFAs) in the pathology of ZnONPs-induced ALI and the therapeutic potential of modulating intestinal microbiota in ZnONPs-induced ALI.Intratracheal instillation of ZnONPs was used to establish a ALI mice model; antibiotic cocktail treatment (ABX) and fecal microbiota transplantation (FMT) were used to modulate intestinal microbiota; 16S rRNA sequencing and LC-MS/MS were applied to evaluate the change of intestinal microbiota and SCFAs.Intratracheal instillation of ZnONPs caused macrophage-mediated ALI in mice. ABX-mediated depletion of intestinal microbiota aggravated ZnONPs-induced ALI; in contrast, FMT-mediated restoration of intestinal microbiota exerted opposite effects; ZnONPs inhalation resulted in the perturbation of intestinal flora and consequently the decrease of SCFAs (especial acetate acid or propionate acid) in the plasma; supplementation of sodium propionate, but not sodium acetate, remarkably ameliorated ZnONPs-induced ALI; GPR43 was the major receptor of propionate acid in RAW 264.7 macrophage cell lines. We illuminates a novel gut-lung axis mechanism that intestinal microbiota and its-derived metabolite propionate acid plays protective role against ZnONPs-induced ALI through repressing macrophage-mediated inflammation and oxidative stress via GPR43 receptor. FMT and supplementation of propionate acid are potential remedy strategies	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006399	Gut microbial signature in lung cancer patients highlights specific taxa as predictors for durable clinical benefit	Stool samples for microbial 16S amplicon sequencing and clinical data were collected from 75 lung cancer patients (50 of which were treated with checkpoint inhibitors) and 31 age-matched healthy volunteers. We compared using multivariate analyses cancer patients to healthy controls, and within lung cancer we compared patients with DCB to those without DCB.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006402	study the alteration in gut and lung microbiome of asthma mice after fecal microbiota transplant	we extract 16s rRNA form fecal and lung sample of mice. Those mice were receipted fecal microbiota from healthy donors and asthmatics.	root:Host-associated:Mammals
MGYS00006401	Colonization of Stenotrophomonas and its associated microbiome between paired primary colorectal cancers and their lung metastatic tumors	Our work highlights the great potential of S. maltophilia and its associated microbiome as biomarkers in pathogenesis and prognosis of CRC lung metastases.	root:Host-associated:Human
MGYS00006400	Whole Exome Sequencing of Non-alpha-fetoprotein Elevated Lung Hepatoid Adenocarcinoma	Hepatoid adenocarcinoma (HAC) is an exceptional rare malignant tumor with prominent Hepatic-like characteristics in organs or tissue outside the liver. Most reported HAC of the lung (HAL) cases have varying degrees of serum alpha-fetoprotein (AFP) level and exhibit a similar origin and clonal evolution process to hepatocellular carcinoma. We report a case of HAL without elevating AFP level, moreover performed whole-exome sequencing (WES) and bioinformatics analyses after surgical resection. Our results showed mutations in two driver genes, NLRP3 and PBX1, and we identified HNRNPR, TP73, CFAP57, COL11A1, RUSC1, SLC6A9, DISC1, NBPF26, OR10K1 as potential driver mutation genes in HAL. In addition, 76 genes were differentially expressed in HAL tumor tissue versus normal tissue.	root:Host-associated:Mammals:Respiratory system
MGYS00006396	Lung transplant microbiome	16S rRNA amplicon sequencing of lung transplant bronchoalveolar lavage samples	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006398	Metabolome and microbiome multi-omics integration from a murine model of bronchopulmonary dysplasia	This study uses a neonatal mouse model of bronchopulmonary dysplasia (BPD) to examine the impact on the lung metabolome and microbiome. Lipopolysaccharide and hyperoxia were used as a double-hit approach to trigger lung inflammation and model BPD within the first two weeks of life. The study examines the impact of each exposure separately as well as their interaction, ultimately identifying putative metabolomic and microbiome-based biomarkers of stressors that can cause BPD. These data were then linked to a published transcriptome. Associations identified in this study have implications for the potential use of these biomarkers in clinical application and basic science research.	root:Host-associated:Mammals:Respiratory system:Pulmonary system
MGYS00006397	BALF microbial diversity of bronchiectasis patients	This study intends to explore the correlation between the diversity of bronchoalveolar lavage fluid flora, metabolites and neutrophil inflammation in patients with bronchiectasis.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006395	Black tea alleviates particulate matter-induced lung injury via the gut-lung axis in mice	Exposure to particulate matters (PMs) induces lung injury and gut microbiota disruption in mice. While daily intake of black tea or its fractions, including ethanol-soluble fraction (ES) and ethanol precipitate fraction (EP), can provide pre-protection against the PM-induced lung injury. Furthermore, the gut microbiota differentially reshaped by tea infusion (TI) and its fractions directly alleviate the injury induced by PMs, indicating gut microbiota mediates the protective effects of black tea and its fractions. Here, we performed gut microbiota 16sRNA sequencing on mice from each treatment groups.	root:Host-associated:Mammals:Digestive system
MGYS00006394	Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in advanced non-small cell lung cancer patients.	Aside from PD-L1 expression, biomarkers of response to immune checkpoint inhibitors (ICI) in non-small cell lung cancer (NSCLC) are needed. In a previous retrospective analysis, we documented that fecal Akkermansia muciniphila (Akk) associated with clinical benefit of ICI in NSCLC and kidney cancer patients. In the current study, we performed shotgun metagenomics-based microbiome profiling in a large cohort of advanced NSCLC patients (n=338) treated with first or second line ICI, to prospectively validate the predictive value of fecal Akk. Baseline stool Akk was associated with increased objective response rates and overall survival in multivariate analyses, independent of PD-L1 expression, antibiotics and performance status. Intestinal Akk was accompanied by a richer commensalism, including Eubacterium hallii and Bifidobacterium adolescentis, and a more inflamed tumor microenvironment in a subset of patients. However, antibiotic use (20% of cases) coincided with a relative dominance of Akk above 4.8% accompanied with the genus Clostridium, both associated with resistance to ICI. Our study shows significant differences in relative abundance of Akk that may represent potential biomarkers to refine patient stratification in future studies.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006393	BreathDx - Diversity and composition of the lung microbiome in patients with suspected ventilator-associated pneumonia	We evaluated how the lung microbiome differs between patients suspected of VAP with positive and negative bronchoalveolar lavage fluid (BALF) cultures and if its composition can be used to exclude the presence of pathogens that drive the use of broad spectrum antibiotics.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006387	Oral microbes contribute to the majority of lung microbiota and indicate lung health	16S rRNA gene sequencing for 99 bronchoalveolar lavage fluid 87 oropharyngeal swabs 86 nasal swabs and 81 saliva	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00006391	Lung microbiome in non-small cell lung cancer	We measured the microbiome in lung tumor and normal lung tissue from stage II NSCLC patients, to examine associations of the lung microbiome with lung cancer recurrence.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006390	Characterization of the microbiota in the lower respiratory tract of Influenza A patients	In order to detect dysbiosis and co-infections we characterized the microbial communities in the lower respiratory tract of patients with severe Influenza A.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006386	Association of bacterial community types, functional microbial processes, and lung disease in cystic fibrosis airways	We analyzed the bacterial communities of sputum samples from persons with cystic fibrosis by sequencing bacterial 16S rRNA gene amplicons. Community types (pulmotypes) were identified using a Dirichlet multinomial mixture model, and correlations were determined between pulmotypes and patient clinical status. Pulmotype-specific metabolic activity profiles suggested that pulmotype microbiota drive distinct community functions.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006388	lung metagenome Raw sequence reads	To detect changes of lung microbiota in healthy and disease states	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006385	Gastroesophageal reflux disease is associated with differences in the allograft microbiome, microbial density and inflammation in lung transplantation.	Rationale: Gastroesophageal reflux disease (GERD) may affect lung allograft inflammation and function through its effects on allograft microbial community composition in lung transplant recipients.Objectives: Our objective was to compare the allograft microbiota in lung transplant recipients with or without clinically diagnosed GERD in the first post-transplant year, and assess associations between GERD, allograft microbiota, inflammation and acute and chronic lung allograft dysfunction (ALAD/CLAD).Methods: 268 bronchoalveolar lavage samples were collected from 75 lung transplant recipients at a single transplant centre every 3 months post-transplant for 1 year. Ten transplant recipients from a separate transplant centre provided samples pre/post-anti-reflux Nissen fundoplication surgery. Microbial community composition and density were measured using 16S rRNA gene sequencing and qPCR, respectively and inflammatory markers and bile acids were quantified.Measurements and Main Results: We observed three community composition profiles (labelled community state types, CSTs 1-3). Transplant recipients with GERD were more likely to have CST1, characterized by high bacterial density and relative abundance of the oropharyngeal colonizing genera Prevotella and Veillonella. GERD was associated with more frequent transition to CST1. CST1 was associated with lower per-bacteria inflammatory cytokine levels than the pathogen-dominated CST3. Time-dependant models revealed associations between CST3 and development of ALAD/CLAD. Nissen fundoplication decreased bacterial load and pro-inflammatory cytokines.Conclusion: GERD was associated with a high density, Prevotella/Veillonella dominated CST1. CST3, but not CST1 or GERD, was associated with inflammation and early development of ALAD/CLAD. Nissen fundoplication was associated with decreases in microbial density in BALF samples, especially the CST1-specific genus, Prevotella.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006383	bacterial community diversity	bacterial composition in pulmonary tuberculosis	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006382	The airway microbiota of non-small-cell lung cancer patients and its relationship to tumor stage and EGFR gene mutation	The airway microbiota and its association with clinical parameters of lung cancer remained largely unknown. This study identified associations between sputum microbiota and clinical stage, intrathoracic metastasis, lymph node metastasis and EGFR mutation. Our study provided potential bacterial markers linked with various important clinical parameters and called for larger and deeper studies for further investigation of the nature of airway microbiota alteration and lung cancer development and progression.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006384	lung metagenome Raw sequence reads	Vitamin D3 pretreatment changed lung microbiota composition	root:Host-associated:Mammals:Respiratory system
MGYS00006381	Airway microbiomes from Portuguese patients with chronic lung disorders	We characterized the microbiome of bronchoalveolar lavage samples from individuals with and without cancer using 16S rRNA high-throughput sequencing	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006378	The role of respiratory microbiome in early bactericidal activity of anti-tuberculosis therapy and treatment outcome	The role of respiratory microbiome in earlybactericidal activity of anti-tuberculosis therapyand treatment outcome	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006375	Magnetic activated cell-sorting identifies a unique lung microbiome community associated with disease states	Studies of lung microbiome taxonomy often reveal few differences between health and disease, but microbial host response may be different between members of similar communities in health and disease. We adapted magnetic-activated cell sorting to examine populations of immunoglobulin-bound lung bacteria, determine differences in the normal lung microbiome, and distinguish the lung microbiome in HIV as a representative disease. Using bronchoalveolar lavage from 42 people living with HIV and 22 HIV-uninfected individuals, we found that while bacteria in raw BAL samples did not differ by HIV status, the immunoglobulin G-bound lung microbiome differed by disease state and was associated with an inflammatory response.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006380	Study of gut microbial diversity in lung cancer	Exploring the relationship between gut microbial diversity and the development of lung cancer using 16s rRNA technology	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006379	Monocarboxylate transporter 2 (MCT2) in murine model of lung cancer: a multi-omic analysis	These 16S rRNA amplicon sequencing data were generated using fecal DNA from tamoxifen-induced MCT2 conditional knockout mice, in the presence or absence of tamoxifen	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006374	Modulation of the pulmonary innate immune response does not change lung microbiota in healthy mice	A study determining whether modulating of murine lung immunity via inhaled TLR agonists changes lung microbiota.	root:Host-associated:Mammals:Respiratory system
MGYS00006377	Fungi sequencing of sputum	The respiratory microbiome of lung cancer patients is different from healthy people. Finding the characteristics of microorganisms is conducive to exploring new directions for the assist in distinguishing different histological types of lung cancer.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006376	Bacterial sequencing of sputum	The respiratory microbiome of lung cancer patients is different from healthy people. Finding the characteristics of microorganisms is conducive to exploring new directions for the assist in distinguishing different histological types of lung cancer.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006371	TLR5 lung microbiome and fibrosis	Raw 16S sequencing data from TLR5 fibrosis experiments	root:Host-associated:Mammals:Respiratory system
MGYS00006370	Analysis of gut, stool and lung microbiota in CF mice	Evaluation of the response of the lung and gut microbiota in wildtype and CF mice in the naive status and after Pseudomonas aeruginosa chronicinfection	root:Host-associated:Mammals
MGYS00006373	Characterize and compare the composition of the pulmonary bacterioma in women exposed to risk factors for chronic lung diseases	The present investigation aimed to characterize and compare the composition of the pulmonary bacterioma in women exposed to risk factors for chronic lung diseases (tobacco smoking and exposure to smoke from biomass-burning) but without lung function affectation.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006372	bacterial community diversity	the bacterial community diversity in Mycobacteria tuberculosis infected lung tissues	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006368	Human airway Targeted Locus (Loci)	Human airway specimen microbiome analysis from patients with Cystic Fibrosis	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006369	Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers	Lower airway microbiota from stable chronic obstructive pulmonary disease, smokers and healthy non-smokers	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006367	Human BAL Targeted Locus (Loci)	Microbiome study of the lower airways in patients with cystic fibrosis and controls	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006365	EMG produced TPA metagenomics assembly of PRJNA552294 data set (Subgingival metagenome of aggressive periodontitis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA552294, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00006363	Gut microbiome and randomized housing of TLR deficient mice	Data on gut micorbiota from TLR deficeint and wild type mice who are housed randomly to study the impact of hosuing on the gut microbiome in these mice	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006362	Lung microbiota are altered by cage and enviroment	Study was used	root:Host-associated:Mammals:Respiratory system
MGYS00006361	lung microbiota of patients S.aureus infection and COVID-19		root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006360	Sequencing of microbial diversity in feces and lungs of diabetic mice		root:Host-associated:Mammals
MGYS00006359	Correlations between the patient microbiome with response and development of immune mediated adverse effects to immunotherapy in lung cancer	Immune checkpoint inhibitors comprise a rapidly burgeoning treatment modality in multiple cancers, but outcomes to treatment, including tumor regression/response and immune-mediated adverse events, are highly variable for as yet unclear reasons. Our project seeks to identify any associations tying fecal, oral and respiratory microbiomes to immunotherapy treatment response and toxicities in lung cancer, as well as each other.	root:Host-associated:Human
MGYS00006355	Lung microbiota associations with clinical features of COPD in the SPIROMICS cohort	In this study, one of the largest bronchoscopy-based evaluations of the lung microbiome (N=181) in a multicenter COPD cohort, significant relationships between characteristics of the lung bacterial community, profiled from bronchoalveolar lavage samples, and clinical and biological features of disease were observed. These included markers of lung function impairment, symptom burden and inflammatory/immune biomarkers. In this cohort enriched in subjects with mild to moderate COPD and ever-smokers at risk for the disease, the findings suggest lung microbiota-host interactions during earlier stages of COPD that may contribute to disease pathogenesis.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006358	Lung bacterial microbiome of critical COVID-19	The study was aimed to characterize the lower respiratory tract microbiome of COVID-19 critically ill patients and investigate the microbiome diversity in comparison to COVID-19-negative patients. We performed a microbiome analysis on bronchoalveolar lavage (BAL) samples collected between April and May 2020 from 24 COVID-19 critically ill subjects and 24 patients with non-COVID-19 pneumonia.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006357	Lung microbiome of chronic obstructive pulmonary disease patients in Tshwane, South Africa	This study compared variations in the lung microbiome (using next-generation sequencing and the IS-Pro method) and virome (using next-generation sequencing) in COPD patients during stable and exacerbated states of disease	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006356	Bronchiectasis lung microbiome	Sputum lung microbiome from patients diagnosed with bronchiectasis.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006345	EcoCF- Pediatric CF lung microbiomes	This project (EcoCF) is a longitudinal study of the microbiome of pediatric cystic fibrosis patients being cared for at Columbia University between February 2010 and June 2014. The samples, which were collected as part of routine care, are bronchoalveolar lavage, expectorated sputum, and oropharyngeal swabs.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006354	Gut microbiome is associated with exercise tolerance of resected early-stage lung cancer patients	Evaluation of the associations between gut microbiota and outcomes in lung cancer patients who underwent lung resection surgery	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006353	Gut and lung microbiota in RSV-infected mice and streptomycin-treatment mice	Investigate alteration of gut and lung microbiota by RSV infection and streptomycin treatment.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006352	CF Sputum Microbiome Profiles Associated with Lung Function	"CF Sputum Profiles (N=77). Referenced in the manuscript ""Microbiome data enhances predictive models of lung function in people with cystic fibrosis"" by CYZhao et al."	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006351	NEOSTAR Study: Non-small cell lung cancer treated with nivolumab or nivolumab plus ipilimumab	Phase 2 randomized study of neoadjuvant nivolumab or nivolumab plus ipilimumab followed by surgery in patients with resectable NSCLC using major pathologic response as primary endpoint (NCT03158129)	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006319	Three clinically distinct chronic pediatric airway infections share a common core microbiota	We used bacterial 16S rRNA gene pyrosequencing and ecological statistical tools to compare the core respiratory microbiota from three cohorts of children with clinically distinct airway diseases: Protracted bacterial bronchitis, non-CF bronchiectasis, and CF. The subject groups also differed in age, geography, antibiotic and steroid use, culture results, and lung function. We found that the core respiratory microbiota of all three cohorts were strikingly similar, arguing against airway disease-specific microbiota initiating chronic infection.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006350	Microbial alteration of lower respiratory tract from critically ill patients with community-acquired pneumonia	Pneumonia is the most common infectious disease that causes significant morbidity and mortality in intensive care unit (ICU) and its mortality rate varies from 24% to 50%. Early identification of the pathogens to administrate adequate antibiotics is the most important factor in decreasing the mortality in pneumonia. In this study, we aim to investigate the microbial alteration of bronchoalveolar lavage (BAL) samples using 16S rRNA metagenomics sequencing in respiratory failure patients due to severe pneumonia in ICU.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006348	human lung metagenome Raw sequence reads	The aim of the study was to evaluate the bacterial microbiome composition and to determine associations between the observed microbial diversity and biological and clinical characteristics in sputum samples collected from patients with bronchiectasis, recruited in stable state.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006349	lung metagenome Raw sequence reads	Under eubiotic conditions commensal microbes are known to provide a natural competitive shield against invading bacterial pathogens in the densely colonized intestinal tract, on the skin or on the vaginal mucosa. A comparable function of commensal bacteria in the respiratory tract was so far not described. Here, we evaluate the role of respiratory microbiota in Pneumococcus colonization of the lung in a mouse model.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006342	Airway host-microbiome interplay associated with chronic obstructive pulmonary disease	Airway host-microbiome interactions in chronic obstructive pulmonary disease	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006347	Microbiome of human lungs with aspergillosis infection	Microbiome samples were taken from the lungs of individuals from Portugal with and without aspergillosis infection. Samples were sequenced by 16S rRNA metabarcoding and statistical analyses were performed to determine the effects and correlations of the microbiome with aspergillosis infection and a number of other relevant variables, such as cytokine levels.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006346	Lung microbiome of non-small cell lung cancer	To investigate the relationship between lung microbiome and the phenotype of inflammatory stromal infiltrate, we studied 26 pairs of DNA samples from NSCLC (non-small cell lung cancer) and adjacent tissue. The lung microbiomes were analyzed by 16S rRNA amplicon-based sequencing. Phenotype of the tumor stroma for every sample was characterized using immunohistochemistry.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006344	Whole lung tissue is the preferred sampling method for murine lung microbiota	The goal of this experiment was to determine the optimal specimen type for amplicon-based sequencing of the lung microbial communities in mice. Healthy adult C57BL/6 mice were sacrificed and either whole lung tissue or bronchoalveolar lavage fluid was collected, along with cecum and tongue tissue samples. Following DNA isolation from tissue samples and controls, bacterial communities were characterized using 16S rRNA gene sequencing.	root:Host-associated:Human
MGYS00006340	A high-risk airway mycobiome discerns COPD exacerbators with poor survival	Evaluation of airway mycobiome in COPD using targeted ITS sequencing	root:Host-associated:Human
MGYS00006343	Study of fungal clinical isolates from different anatomical sites and metagenomic of the lung microbiome of patients with cystic fibrosis	16S and ITS processed sequences.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006341	16S amplicon sequencing of sputa from tuberculosis patients	In this work we describe the results obtained from a multicenter study of the microbiota of sputum samples from patients with tuberculosis or unrelated lung diseases and healthy donors recruited in Switzerland, Italy and Bangladesh, with the ultimate goal of discovering a microbiota-based biomarker associated with tuberculosis. Bacterial 16S rDNA amplification, high-throughput sequencing and extensive bioinformatic analyses revealed patient-specific lung flora and high variability in taxon abundance. No common signature could be identified among the individuals enrolled and microbiota composition was found to be confounded by various factors, including the geographical setting. Moreover, anti-tuberculosis therapy did not cause any important variation in microbiota diversity, thus precluding its exploitation as a biomarker for the follow up of tuberculosis patients undergoing treatment.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006294	Lung microbiota in healthy lung transplant recipients	The goal of this project was to determine the relationship between lung microbiota and clinical outcomes among asymptomatic lung transplant recipients with preserved lung function. Bacterial communities in acellular bronchoalveolar lavage fluid collected during routine one-year post-transplant surveillance bronchoscopy was characterized using 16S rRNA gene amplicon sequencing using the Illumina MiSeq platform.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006339	Microbiome in Lung Explant: an IPF Study	To characterize the regional IPF lung tissue microbiome in the Microbiome In Lung Explants Study	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006337	Acute Lung Injury Registry Microbiome	Microbiome in critical illness cohort study	root:Host-associated:Human
MGYS00006338	Start of ivacaftor/lumacaftor in adult cystic fibrosis patients with homozygous Phe508del results in temporal changes in lung microbiome and metabolome.	Rationale: Targeted cystic fibrosis therapy with ivacaftor/lumacaftor partly restores chloride channel function in the airways and increases of the epithelial fluid transport in the airways. Consequently, changes in the microbiome that is adapted to cystic fibrosis lungs can occur.Objectives: To investigate the effects of ivacaftor/lumacaftor on respiratory microbial composition and microbial metabolic activity in an observational cohort study, in which we repeatedly sampled the lower respiratory tract.Methods: This was a single-center longitudinal observational cohort study in adult cystic fibrosis patients with a homozygous Phe508del mutation. Lung function measurements and microbial cultures of sputum were performed as part of routine care. An oral and nasal wash, and an exhaled breath sample were collected before and every three months after starting therapy, up to one year.	root:Host-associated:Human
MGYS00006336	Nontuberculous mycobacteria disease in cystic fibrosis	Pulmonary infections with nontuberculous mycobacteria (NTM) are increasing in prevalence and can result in significant morbidity and mortality in people with cystic fibrosis (CF). The objective of this study is to identify features of the lower airway microbiota in patients with CF and NTM infection that differ between people with and without NTM disease.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006334	Microbiota characterization in Lung Cancer	16s rRNA gene sequencing on pulmonar, oral, and faecal samples from Spanish lung cancer patients and controls.	root:Host-associated:Human
MGYS00006290	Lung microbiota of Mus musculus (C57BL/6J), Raw sequence reads	Under eubiotic conditions commensal microbes are known to provide a natural competitive shield against invading bacterial pathogens in the densely colonized intestinal tract, on the skin or on the vaginal mucosa. A comparable function of commensal bacteria in the respiratory tract was so far not described. Here, we evaluate the role of respiratory microbiota in Pneumococcus colonization of the lung in a mouse model.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006289	Lung microbiome in adult cystic fibrosis patients	Influence of target and antibiotic therapy on microbiota composition in adult cystic fibrosis patients	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006335	Mycobiome characterization in Lung Cancer	ITS1 amplicon sequencing for mycobiome characterization of pulmonar and saliva samples from Spanish lung cancer patients and controls.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006322	Human respiratory tract mycobiome and alterations in HIV infection and lung disease Targeted Locus (Loci)	Whether there are resident fungal communities in the respiratory tract is unknown, and wide gaps exist in our understanding of occult fungal infections in chronic lung diseases or in individuals with systemic disease. In this study, we characterized fungal diversity at different levels of the respiratory tract including oral washes (OW), induced sputum (IS) and bronchoalveolar lavages (BAL) from 56 individuals. We also examined relationship of fungal communities to chronic obstructive pulmonary disease and to HIV infection.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006332	human lung microbial metagenome	detection of differences in microbial community composition harbored in lungs of patients with mild to moderate COPD compared to control individuals	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006333	Stromal modulation through gastrointestinal microbial dysbiosis	The overall use of antibiotics has increased significantly in recent years. Besides fighting infections, antibiotics also alter the gut microbiota. Commensal bacteria in the gastrointestinal tract are crucial to maintain immune homeostasis, and microbial imbalance or dysbiosis affects disease susceptibility and progression. We hypothesized that antibiotic-induced dysbiosis of the gut microbiota would suppress cytokine profiles in the host, thereby leading to changes in the tumor microenvironment. Indeed, dysbiosis resulted in alterations in bacterial abundance, composition and diversity. On the host side, antibiotic-induced dysbiosis caused elongated small intestines and ceca, and B16-F10 melanoma and Lewis Lung carcinoma progressed more quickly than in orthobiotic control mice. Mechanistic studies revealed that this progression was mediated by suppressed TNF-a levels, both locally and systemically, resulting in reduced expression of tumor endothelial adhesion molecules, particularly intercellular adhesion molecule-1 (ICAM-1) and a subsequent decrease in the number of activated CD8+ T-cells in the tumor. However, suppression of ICAM-1 or its binding site, the alpha subunit of lymphocyte function-associated antigen-1, was not seen in the spleen or thymus during dysbiosis. TNF-a supplementation in dysbiotic mice was able to increase ICAM-1 expression and leukocyte trafficking into the tumor. Overall, these results demonstrate the importance of commensal bacteria in supporting anti-cancer immune surveillance, define an important role of tumor endothelial cells within this process, and suggest adverse consequences of antibiotics on distal cancer development. Significance: Antibiotic-induced dysbiosis enhances distal tumor progression by altering host cytokine levels resulting in suppression of leukocyte trafficking via modulation of tumor endothelial adhesion molecules.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006331	Human cystic fibrosis lung	Characterization of the bacterial microbiome in cystic fibrosis subjects in various regions of the lung	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006329	Respiratory microbiome Metagenome	Bacterial community in upper respiratory tract	root:Host-associated:Mammals:Respiratory system
MGYS00006330	Endotracheal tube bilfilm Targeted Locus (Loci)	To characterize bacteria in endochatracheal tube bilfilms related to VAP	root:Host-associated:Human:Respiratory system:Pulmonary system:Trachea
MGYS00006328	Microbiome analysis in sputum of CF subjects	Characterization and quantification of the bacterial microbiome in cystic fibrosis subjects over the course of antibacterial therapy	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006327	Comparison of Bacterial Communities in Bronchoalveolar Lavage between a U.S. and Malawi Population.	We have compared the lung microbiome in a U.S. and Malawi population. We identified several significant differences between the two populations which we hypothesize are related to different environmental exposures in the two countries.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006326	Changes in the Lung Microbiome Following Lung Transplantation Include the Emergence of Two Distinct Pseudomonas Species with Distinct Clinical Associations	Comparison of lung microbiota in lung transplant recipients and non-transplant control subjects	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006320	Human airway Targeted Locus (Loci)	Molecular ecology of the cystic fibrosis airway	root:Host-associated:Human:Digestive system:Oral:Throat
MGYS00006325	Bacteria Genome sequencing	Bacteria from sputum	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006324	Human airway Targeted Locus (Loci)	Human sputum bacterial communities from cystic fibrosis patients collected during pulmonary exacerbation	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006323	The effects of freeze thaw cycles on the microbial community present in sputum samples from the CF lung		root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006285	The lung microbiome in young children with cystic fibrosis: a longitudinal cohort study	Cystic fibrosis (CF) is an autosomal recessive condition with impaired mucociliary clearance and innate airway defences 1. Chronic airway infection and inflammation culminating in bronchiectasis are the main drivers of the morbidity and mortality of CF 1. There is good evidence these processes start early in life, with asymptomatic infants and pre-school children demonstrating clear associations between the presence of lower airway infection and inflammation and impaired lung function and structural airway changes 1,2.The use of 16S ribosomal RNA sequencing provides compelling evidence that CF airways are inhabited by diverse microbial communities 3-7. Perturbations in the CF airway microbiome are well described, however it is unclear what affect these have on the “infection-inflammation-structural damage” model of CF lung disease 3-12. Limited studies in young children with CF suggest microbial diversity is initially low but increases with age 3,7,9,11,12. In contrast, in older children and adults, diversity decreases with age and declining lung function 3,7,13,14. In adults, with advancing lung disease and repeated exposure to antibiotics over an extended period of time, dominant CF pathogens emerge in a relatively fixed microbiome with limited diversity 4,6,15,16.We aimed to describe the lower airway microbiome in clinically stable pre-school aged children with CF, and, using longitudinal data, explore how age influences its composition. Further analysis focused on comparing the CF microbiome with that of the non-CF lung and on examining the effect of airway inflammation and antibiotic use.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006321	Human airway Targeted Locus (Loci)	COPD related airway microbiota	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006273	Longitudinal CF Study	A study of the longitudinal dynamics of microbiome and metabolomic data from 6 CF patients. Samples were collected daily or as frequently as possible through events of CF exacerbation and dual microbiome and metabolome data generated.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006305	Airway microbiota and inflammation under Lumacaftor-ivacaftor	"Rationale Lumacaftor-ivacaftor is a cystic fibrosis transmembrane conductance regulator (CFTR) modulator combination approved in patients with cystic fibrosis (CF) homozygous for the F508del allele. This treatment showed significant clinical improvement, however limited data have addressed the evolution of airway mycobiota-microbiota and airway inflammation under lumacaftor-ivacaftor.
Objectives To investigate the effects of lumacaftor-ivacaftor on airway mycobiota-microbiota and airway inflammation in a multicentric study."	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006288	Effects of postage on recovery of pathogens from cystic fibrosis respiratory samples	The study analysed the cultured pathogens, the abundance of pathogens using qPCR and the bacterial microbiota using targeted gene sequencing of fresh and posted samples.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006286	Gut microbiome data of never-smoking subjects with lung adenocarcinoma	Gut microbiome data of never-smoking subjects with lung adenocarcinoma	root:Host-associated:Human:Digestive system:Intestine
MGYS00006304	lung microbiota and hypercapnic AECOPD	The aim of this study is to assess the link between lung microbiota composition and death in critically ill admitted for hypercapnic acute exacerbation of chronic obstructive pulmonary disease (AECOPD). Every patient receiving non-invasive or invasive ventilation for AECOPD admitted to intensive care unit from October 2018 to May 2019 were included (ADMIRE study, NCT03641235). Induced sputum or tracheal aspirate were sampled and DNA extraction was performed by QIAamp® PowerFecal® Pro DNA kit (QIAgen®). V3-V4 regions of 16SRNA coding gene was amplified to analyse the bacterial kingdom of lung microbiota (bacteriobiota) and ITS2 to analyse the fungal kingdom (mycobiota). Sequencing (2x250bp paired-end reads) was performed on MiSeq sequencer (Illumina®) and DADA2 pipeline on R software was used for bioinformatics analyses.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006284	16S rRNA lung microbiota study in mechanically ventilated patient: a pilot study	Characterization of the respiratory tract bacterial microbiota is in its infancy when compared to the gut microbiota knowledge. As key methodological steps can directly affect the accuracy of the results, it is crucial to determine a robust methodology in order to limit bias.We compared two methods of sample processing using these two different pairs of primers for bacterial microbiota analyses of respiratory samples from Intensive Care Unit (ICU) ventilated patients.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006275	nfection and rejection are the two most common complications after lung transplantation (LTx) and are associated with increased morbidity and mortality. We aimed to examine the association between airway microbiota and infection and rejection in lung transplant recipients (LTRs).	Distinct airway microbiota was observed between clinical stable recipients (or event free), infection and rejection after LTx. Alpha and beta diversity were significantly different between event free and rejection, and between infection and rejection recipients. Ten differential genera were identified by LEfSe analyses, with Corynebacterium, unclassified Enterococcaceae and unclassified Lactobacillales enriched in infection recipients, while Rothia, Granulicatella, Neisseria, Actinomyces, Leptotrichia, Lactobacillus and unclassified Aerococcaceae more abundant in rejection LTRs. Random forest analyses indicated that the combination of the 10 microbiota and procalcitonin (PCT) and T lymphocyte showed an AUC of 0.894, 0.955 and 0.913 to differentiate between event free and infection, event free and rejection, and infection and rejection recipients, respectively.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006318	EMG produced TPA metagenomics assembly of PRJNA757176 data set (Sus scrofa Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA757176, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.	root:Host-associated:Mammals:Digestive system
MGYS00006269	Characterizing the Fungal Airway Microbiome in Cystic Fibrosis and Bronchiectasis by Next Generation Sequencing	The prevalence of fungal airways disease is increasing yet the lack of standardised diagnostic criteria make interpretation of culture results challenging. Development of effective management strategies requires a more accurate and comprehensive understanding of the fungal airway microbiome.Through the use of next generation sequencing of the ITS2 region we aimed to assess the load and diversity of fungi in patients with chronic bronchial infection. Sputum samples from 87 adults with cystic fibrosis and 24 with bronchiectasis were used to investigate patterns in fungal community composition between those with recognized fungal disease and disease controls. Only 49% of the samples were positive by fungal culture while all samples produced high quality fungal sequencing profiles. Patients with Cystic fibrosis were found to have a higher fungal biomass with lower fungal diversity than those with bronchiectasis. Candida was a common OTU is all individuals, however, Candida parapsilosis was found only in cystic fibrosis sputum while Candida albicans was most common in those with bronchiectasis. This study provides a more accurate framework to characterize the fungal airways disease-phenotypes in adult suppurative lung diseases.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006274	The lung microbiota in children with cystic fibrosis captured by induced sputum sampling	"Background: Spatial topography of the cystic fibrosis (CF) lung microbiota is poorly understood in childhood. How best to sample the respiratory tract in children for microbiota analysis, and the utility of microbiota profiling in clinical management of early infection remains unclear. By comparison with bronchoalveolar lavage (BAL), we assessed the ability of induced sputum (IS) sampling to characterise the lower airway microbiota.

Methods: Sample sets from IS and two or three matched BAL compartments were obtained for microbiota analysis as part of the CF-Sputum Induction Trial (UKCRN_14615, ISRCTNR_12473810). Microbiota profiles and pathogen detection were compared between matched samples.

Results: Twenty-eight patients, aged 1.1–17.7 years, provided 30 sample sets. Within-patient BAL comparisons revealed spatial heterogeneity in 8/30 (27%) sample sets indicating that the lower airway microbiota from BAL is frequently compartmentalised in children with CF. IS samples closely resembled one or more matched BAL compartments in 15/30 (50%) sets, and were related in composition in a further 9/30 (30%). IS detected 86.2% of the Top 5 genera found across matched BAL samples. The sensitivity of IS to detect specific CF-pathogens identified in matched BAL samples at relative abundance ≥5% varied between 43 and 100%, with negative predictive values between 73 and 100%.

Conclusions: Spatial heterogeneity of the lower airway microbiota was observed in BAL samples and presents difficulties for consistent lung sampling. IS captured a microbiota signature representative of the lower airway in 80% of cases, and is a straightforward, non-invasive intervention that can be performed frequently to aid pathogen diagnosis and understand microbiota evolution in children with CF."	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006307	EMG produced TPA metagenomics assembly of PRJNA597465 data set (Species Level Characterization of Dental Plaque Associated Microbiome of Native Indian Children using Metagenome Sequencing).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA597465, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00006297	EMG produced TPA metatranscriptomics assembly of PRJNA560313 data set (Samail Ophiolite groundwater sequencing).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA560313, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Groundwater.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00006317	Mycobiome analysis in sputum of CF subjects	Characterization and quantification of the fungal microbiome in cystic fibrosis subjects over the course of antibacterial therapy	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006315	EMG produced TPA metagenomics assembly of PRJNA508385 data set (Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA508385, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00006310	EMG produced TPA metagenomics assembly of PRJNA631294 data set (Putative amylases in the human vagina).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA631294, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00006309	EMG produced TPA metagenomics assembly of PRJNA612150 data set (Fred Hutch Vaginal Metagenomics (FHVM)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA612150, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00006316	EMG produced TPA metagenomics assembly of PRJEB10293 data set (Tongue metagenome from 9 healthy individuals.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB10293, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00006314	EMG produced TPA metagenomics assembly of PRJNA650272 data set (Microbiomes in supragingival biofilms and saliva of adolescent patients with provoked and naturally occurring gingivitis relative to gingival health).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA650272, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006313	EMG produced TPA metagenomics assembly of PRJNA528558 data set (oral metagenome Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA528558, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00006311	EMG produced TPA metagenomics assembly of PRJNA656314 data set (Environmental concentrations of antibiotics alter the zebrafish gut microbiome structure and potential functions).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA656314, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.	root:Host-associated:Fish:Digestive system
MGYS00006312	EMG produced TPA metagenomics assembly of PRJNA544171 data set (Zebrafish Gut Microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA544171, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.	root:Host-associated:Fish:Digestive system
MGYS00006306	EMG produced TPA metagenomics assembly of PRJNA419274 data set (Alteration in the Oral microbiota of Indian Antartic expedition members during ship journey and stay at Antartica).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA419274, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006308	EMG produced TPA metagenomics assembly of PRJNA576566 data set (metagenomic studies of vaginal microbiome in HPV16 infection).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA576566, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Reproductive system:Vagina.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00006287	16S rRNA gene sequences of human airway microbiota	We characterized the airway microbiota of healthy Korean adults. The study population consisted of monozygotic twins, dizygotic twins, and family members of twin pairs. All subjects had not taken antibiotics within three months prior to sampling and had no current symptoms of chronic lung diseases, such as asthma and COPD. A total of 304 sputum samples collected from each subject were analyzed for airway microbiota composition using next generation sequencing of partial 16S rRNA gene sequence.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00005766	HoloFood Chicken Caecum+Ileum Metagenome	Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken caecum and ileum samples. Samples selected for this batch were randomised among trials (feed), age, and breed to overcome batch effect. The caecum samples in this project contributed to the chicken caecum MAG catalogue (project: PRJEB55374 [ERP140263]), and the ileum samples contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).	root:Host-associated:Birds:Digestive system
MGYS00006301	EMG produced TPA metagenomics assembly of PRJNA728379 data set (Metagenome of pig fecal bacteria).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA728379, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006299	EMG produced TPA metagenomics assembly of PRJNA471937 data set (Pig gut metagenome Metagenomic assembly).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA471937, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006302	EMG produced TPA metagenomics assembly of PRJNA312048 data set (gut microbe Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA312048, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.	root:Host-associated:Mammals:Digestive system
MGYS00006300	EMG produced TPA metagenomics assembly of PRJNA677897 data set (Whole metegenome sequencing of the Sicilian Black pig fecal microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA677897, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006298	EMG produced TPA metagenomics assembly of PRJNA400119 data set (pig gut metagenome Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA400119, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.	root:Host-associated:Mammals:Digestive system
MGYS00006280	gut microbiota and ventilator-associated pneumonia	The aim of this study is to assess the link between gut microbiota composition and subsequent occurrence of ventilator-associated pneumonia in critically ill influenza patients. Every patient admitted to intensive care unit from October 2019 to March 2020 who received at least 2 days of invasive mechanical ventilation were included (ancillary study of Microbe study, NCT04131569). Rectal swabs were sampled and DNA extraction was performed by QIAamp® PowerFecal® Pro DNA kit (QIAgen®). V3-V4 regions of 16SRNA coding gene was amplified to analyse the bacterial kingdom of lung microbiota (bacteriobiota) and ITS2 to analyse the fungal kingdom (mycobiota). Sequencing (2x250bp paired-end reads) was performed on MiSeq sequencer (Illumina®) and DADA2 pipeline on R software was used for bioinformatics analyses.	root:Host-associated:Human:Digestive system:Hindgut:Rectum
MGYS00006295	Effect of storage on the microbial community present in Cystic fibrosis sputum	This study aims to invesitigate if storage at room temperature affect the microbial community present in Cystic fibrosis sputum.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006296	Microbial community analysis of sputum samples from adults and pediatric patients	The goal of the study is to understand the similarities and differences in the microbial communities in adults and pediatric patients	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006292	Gut microbiome predicts efficacy and immune-related toxicities of advanced non-small cell lung cancer patients treated with anti-PD-1/PD-L1 Ab-based immunotherapy	The gut microbiome (GM) plays an important role in shaping systemic immune responses. Preclinical and clinical data suggest that GM influences anti-PD-1/PD-L1 or -CTLA-4 Ab-mediated anti-cancer responses. Furthermore, there is strong evidence that antibiotics (ATB) worsen clinical outcomes based on multiple retrospective and one prospective studies using immune checkpoint inhibition (ICI). However, whether GM profiling, at baseline or post-ATB, could represent a biomarker of response in advanced non-small cell lung cancer (NSCLC) during ICI therapy remains unknown. Moreover, the relationship between specific gut microbiota and incidence of immune-related adverse events (irAEs) remain to be precisely elucidated. The objective of the present study was to characterize the impact of ATB on specific GM signatures using metagenomics sequencing in a cohort of 70 patients with advanced NSCLC treated with anti-PD-1/anti-PD-L-1. Primary endpoints were to define specific gut microbiota associated with response and non-response, progression-free survival (PFS), overall survival (OS), and irAEs in both patients who received ATB and those who did not receive ATB.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006291	The murine lung microbiome in relation to the intestinal and vaginal bacterial communities	The first description of the bacterial population of the lung microbiota in mice. Bacterial communities from broncho-alveolar lavage fluids and lung tissue were compared to samples taken from fecal matter (caecum) and vaginal lavage fluid from female BALB/cJ mice.	root:Host-associated:Mammals:Respiratory system
MGYS00006293	Cross sectional analysis of 16S rRNA sequences obtained from bronchiectasis patient airway samples Targeted Locus (Loci)	Non-CF bronchiectasis airway microbiota.  Cross sectional analysis of 16S rRNA sequences obtained from bronchiectasis patient airway samples.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006282	EMG produced TPA metagenomics assembly of PRJNA728374 data set (Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils.).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA728374, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system.	root:Host-associated:Human:Digestive system
MGYS00006283	EMG produced TPA metagenomics assembly of PRJNA819247 data set (Infant gut microbiome Raw sequence reads).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA819247, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system.	root:Host-associated:Human:Digestive system
MGYS00006211	ARGs study in bioelectrochemical remediation	Elimination of several antibiotics in water by bioelectrochemical cells. The main objective is study how the concentration of antibiotic resistant genes (ARG) changed depending on the voltage application.	root:Environmental:Aquatic:Freshwater:Drinking water
MGYS00004656	Potential microbial consortium involved in biodegradation of diesel in mangrove sediment explored by metagenomics analysis	This study aimed to explore microbial communities potentially involved in diesel-, hexadecane- and phenanthrene- degradation in microcosm studies, constructed using mangrove sediment from Bangkhuntein, Bangkok, Thailand	root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
MGYS00000498	This a study of how variability of the soil environment affects the soil microbial function and diversity	This study has a total of 183 samples from 4 time points and 3 paired pasture and woodland sites. We have obtained continuous measurements of soil moisture and temperature for the study period and we sequenced the soil metagenome by Illumina Hiseq.	root:Environmental:Terrestrial:Soil
MGYS00006241	Freshwater stream mat viral communities from Ille-et-Vilaine, France	The viral community from an iron rich microbial mat is analyzed	root:Environmental:Aquatic:Freshwater:Lotic:Mid stream
MGYS00006278	Analysis of the Gut Microbiota: An Emerging Source of Biomarkers for Immune Checkpoint Blockade Therapy in Non-Small Cell Lung Cancer	"Background: The human gut harbors around 1013-1014 microorganisms, collectively referred to as gut microbiota. Recent studies have found that the gut microbiota may have an impact on the interaction between immune regulation and anti-cancer immunotherapies.
Methods: In order to characterize the diversity and composition of commensal microbiota and its relationship with response to immune checkpoint blockade (ICB), 16S ribosomal DNA (rDNA) sequencing was performed on 69 stool samples from advanced non-small cell lung cancer (NSCLC) patients prior to treatment with ICB.
Results: The use of antibiotics and ICB-related skin toxicity were significantly associated with reduced gut microbiota diversity. However, antibiotics (ATB) usage was not related to low ICB efficacy. Phascolarctobacterium was enriched in patients with clinical benefit and correlated with prolonged progression-free survival, whereas Dialister was more represented in patients with progressive disease, and its higher relative abundance was associated with reduced progression-free survival and overall survival, with independent prognostic value in multivariate analysis.
Conclusions: Our results corroborate the relation between the baseline gut microbiota composition and ICB clinical outcomes in advanced NSCLC patients, and provide novel potential predictive and prognostic biomarkers for immunotherapy in NSCLC."	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006279	A multiomics study on the effects of TRIKAFTA on CF patients	Novel small molecule therapies for cystic fibrosis (CF) are showing promising efficacy and becoming more widely available since recent FDA approval. The newest of these, Trikafta (TKT), is a triple therapy utilizing Ivacaftor, a CF transmembrane conductance regulator (CFTR) potentiator, combined with Tezacaftor and Elexacaftor, CFTR correctors. However, it is not yet known how these drugs will affect polymicrobial lung infections, which are the leading cause of morbidity and mortality among people with CF (pwCF). Here, we analyzed the sputum microbiome and metabolome from pwCF (n=24) before and after TKT therapy using 16S rRNA gene amplicon sequencing and untargeted metabolomics. The lung microbiome diversity, particularly its evenness, was increased (p = 0.044) and the microbiome profiles were different between individuals before and after therapy (PERMANOVA F=1.92, p=0.044). Despite these changes, the microbiomes were more similar within an individual than across the sampled population. There were no specific microbial taxa that were different in abundance before and after therapy, but collectively, the log-ratio of anaerobes to pathogens significantly decreased. The sputum metabolome also showed changes due to TKT. Beta-diversity increased after therapy (PERMANOVA F=4.22, p=0.022) and was characterized by greater variation across subjects while on treatment. This significant difference in the metabolome was driven by a decrease in peptides, amino acids, and metabolites from the kynurenine pathway. Metabolism of the three small molecules that make up TKT was extensive, including previously uncharacterized structural modifications. This study shows that TKT therapy affects both the microbiome and metabolome of airway mucus. This effect was stronger on sputum biochemistry, which may reflect changing niche spaces for microbial residency in lung mucus as the drug’s effects take hold, which then leads to changing microbiology.Why: exploratory study, not much is known about TRIKAFTA’s impact on microbiome/metabolome of CF lung Method: acquired samples pre- and post-TRIKAFTA intervention from 2 clinics for a total of 20 (subject to change) patients; 16S metagenomics (DNA extraction, PCR amplification, sequencing, analysis); metabolomics (methanol prep, LC-MS, analysis)	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006277	Lung microbiota but not mycobiota predicts day 28 mortality in critically ill influenza patients: a feasibility study	The aim of this study is to assess the prognostic value of lung microbiota in critically ill influenza patients. Every PCR-proven influenza patient admitted to intensive care unit of two hospitals for respiratory failure during 2019-2020 pandemics were included (NCT04131296). Sputum or tracheal aspirates were sampled and DNA extraction was performed by QIAamp® PowerFecal® Pro DNA kit (QIAgen®). V3-V4 regions of 16SRNA coding gene was amplified to analyse the bacterial kingdom of lung microbiota (bacteriobiota) and ITS2 to analyse the fungal kingdom (mycobiota). Sequencing (2x250bp paired-end reads) was performed on MiSeq sequencer (Illumina®) and DADA2 pipeline on R software was used for bioinformatics analyses.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006276	Oral microbiome data of never-smoking subjects with lung adenocarcinoma	Oral microbiome data of never-smoking subjects with lung adenocarcinoma	root:Host-associated:Human:Digestive system:Oral
MGYS00006270	Large multicentred study of cystic fibrosis sputum from patients across 11 sites in Europe and the USA.	Large multicentred study of cystic fibrosis sputum from patients across 11 sites in Europe and the USA.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006272	Low IgA associated with oropharyngeal microbiota changes and lung disease in primary antibody deficiency	"Common Variable Immunodeficiency (CVID) and X-linked agammaglobulinemia (XLA) are primary antibody deficiencies characterised by hypogammaglobulinemia and recurrent infections, which can lead to structural airway disease (AD) and interstitial lung disease (ILD). We investigated associations between serum IgA, oropharyngeal microbiota composition and severity of lung disease in these patients.
In this cross-sectional multicentre study we analysed oropharyngeal microbiota composition of 86 CVID patients, 12 XLA patients and 49 healthy controls (HC) using next-generation sequencing of the 16S rRNA gene. qPCR was used to estimate bacterial load. IgA was measured in serum. High resolution CT scans were scored for severity of AD and ILD.
Oropharyngeal bacterial load was increased in CVID patients with low IgA (p=0.013) and XLA (p=0.029) compared to HC. IgA status was associated with distinct beta (between-sample) diversity (p=0.039), enrichment of (Allo)prevotella, and more severe radiographic lung disease (p=0.003), independently of recent antibiotic use. AD scores were positively associated with Prevotella, Alloprevotella, and Selenomonas, and ILD scores with Streptococcus and negatively with Rothia.
In clinically stable patients with CVID and XLA, radiographic lung disease was associated with IgA deficiency and expansion of distinct oropharyngeal bacterial taxa. Our findings highlight IgA as a potential driver of upper respiratory tract microbiota homeostasis."	root:Host-associated:Human:Respiratory system:Nasopharyngeal:Pharynx
MGYS00006271	Respiratory airway microbiomes in stage I non-small cell lung cancer	"In this study, 16S sequencing was performed to assess the bacterial microbiomes in DNA isolated from pre-operative bronchial lavage fluid samples of patients with pathologic stage I non-small cell lung cancer. Thirty-five of this study's bronchial lavage fluid samples were independently processed for DNA isolation and 16S sequencing using the same methods as this study's in a past study whose data are available in the EBI ENA repository with accession number PRJEB29934 (patient identifiers used in both studies are the same). Samples were obtained from the Lung Cancer Biospecimen Resource Network, University of Virginia, VA, USA. For the samples procured by the repository, normal saline was used for collection of 20-40 ml of bronchial lavage fluids, which were centrifuged at 1,300 g for 25 minutes, following which supernatants were collected and stored at -80 oC or in liquid nitrogen.QIAamp UCP Pathogen Mini kit and Pathogen Lysis L tubes (Qiagen) were used to extract DNA from bronchial lavage fluid (0.4 ml). The protocol ""Pretreatment of Pathogen DNA from 400 μl Whole Blood (Mechanical Pre-lysis Protocol)"" provided with the kit was used. The kit's ATL buffer with reagent Dx was added to samples to make their volume to 0.4 ml before mechanical lysis. The study included 3 negative controls for DNA extraction, an empty, sterile, nuclease-free 1.5-ml microcentrifuge tube. DNA was also isolated in duplicate from a positive control, ZymoBIOMICS Microbial Community Standard (product D6300, Zymo, Irvine, CA). Bronchial lavage fluid samples of two patients were mixed 1:1 volume for DNA extraction in duplicate from final 0.4 ml. This was done for two sets of two-patients samples. 16S sequencing of isolated DNA, involving 16S PCR, sequencing library generation, and library sequencing, was performed in one batch. The 16S sequencing method suggested in the 16S Metagenomic Library preparation guide of Illumina (San Diego, CA) was followed. An ~464 bp amplicon of bacterial 16S rRNA V3-V4 region was amplified with forward and reverse primers of sequences TCGTCGGCAGCGTC-ad-CCTACGGGNGGCWGCAG and GTCTCGTGGGCTCGG-ad-GACTACHVGGGTATCTAATCC, respectively (ad = AGATGTGTATAAGAGACAG). DNA (25 ng) was subjected to 35 cycles of PCR with annealing temperature of 55 oC and KAPA HiFi HotStart DNA polymerase. For samples for which 25 ng DNA was unavailable, the maximum volume of a sample's DNA preparation was used. Amplified DNA was purified with AMPure XP beads and was indexed with Nextera XT index kit in an 8-cycle PCR to generate sequencing libraries. Libraries were purified with AMPure XP beads and 12 pmoles of each library was sequenced on a MiSeq instrument (Illumina) with v3 sequencing reagents to obtained paired 300 bp reads. A PhiX library was spiked in at 10% molarity. Multiplexed libraries were sequenced twice using two MiSeq sequencing runs. Sequencing data uploaded to ENA has merged raw (CASAVA de-multiplexed) fastq.gz files of the two runs."	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006268	Comparison of five DNA extraction and purification methods for microbiome characterization from the lung tissue.	A total of 7 individuals (four children and three adults) selected on the basis of unexpected death were included in this study.For each autopsied subject, the right upper lobe was removed, small samples were obtained from deep lung tissue, cut into small pieces, divided in five aliquots (0.4 g) and frozen at -80oC for DNA extraction. Five DNA extraction protocols were applied on each piece o sample: protocol 1, using the QIAamp DNA Mini kit (Qiagen); adding a bead-beating step (protocol 2); a phenol-chloroform step (protocol 3); both bead-beating and phenol-chloroform steps (protocol 4); and a pre-treatment step followed by the bead-beating and phenol-chloroform steps (protocol 5).For all samples, the 16S rRNA gene analysis for the bacteria and the internal transcribed spacer (ITS) region for fungal community were carried out, respectively. PCR amplification of 469  bp of the V3-V4 regions in the case of bacteria, and  spanning about 289 bp of the small subunit and the 5.8S region of the rRNA operon in the case of fungi were performed and sequencing of the amplicons using the Illumina MiSeq with 300 bp x2 chemistry.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006267	EMG produced TPA metagenomics assembly of PRJEB35524 data set (A low-digestibility protein supplementation during an energy-restricted diet reduces visceral fat and stimulates gut microbiota aminoacid metabolism in subjects with metabolic syndrome).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB35524, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system
MGYS00006266	EMG produced TPA metagenomics assembly of PRJEB17643 data set (A randomized trial of bread consumption: Personal glycemic responses and effects on clinical parameters and gut microbiome).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB17643, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system
MGYS00006263	The effect of RSV-A M37 infection on the respiratory microbiome of adults	Human volunteer challenge studies uniquely allow investigation of factors with pre-dispose to infection and study of the pre-symptomatic phase of disease. Patients were exposed to RSV on day 0 and throat swabs were collected over the course of infection for quantitative PCR and 16S rRNA sequencing analysis.	root:Host-associated:Human:Digestive system:Oral:Throat
MGYS00006264	Viral respiratory tract infections and oropharyngeal microbiome interactions in wheezing children	Early life exposure to both environmental and infectious microorganisms have been implicated as major risk factors in future disease susceptibility. Acute viral infections resulting in respiratory wheeze are not only a major reason for hospital admission in children but also a risk factor for development of asthma. To investigate if the microbiota in the lungs of children was associated with wheeze respiratory samples from children attending a paediatric hospital in Perth were compared to healthy controls using viral PCR and 16s rRNA gene qPCR and sequencing. No significant difference in bacterial diversity was observed between samples from those with wheeze and healthy controls. Within the wheeze cohort, attendance at kindergarten or preschool was associated with increased bacterial diversity. Bacterial biomass was a significant factor in explaining the variation in beta diversity.  Human rhinovirus (HRV) infection was not found to have a significant effect on bacterial alpha or beta diversity.  A significant difference in bacterial richness was observed between HRV-A and HRV-C, however this is likely due to the differences in age group between the to patient cohorts. Random forest models were unable to successfully predict individual OTU’s associated with wheeze or viral infection in this dataset due to the variation in the bacterial community.  The bacterial community within the lungs was found to be diverse and heterogeneous. Age and contact with children at day care or kindergarten were important factors in driving bacterial diversity. However, wheeze and viral infection were not found to show significant differences in the bacterial community.	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00006265	Healthy human lung microbiome from 15 volunteers	Lung metagenomes from 15 healthy volunteers were sequenced (16S V3-V4 region)	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006260	Human lung microbiome in Cystic Fibrosis - 3D reconstruction	explant or post-mortem lung lobes from human with Cystic Fibrosis	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006261	Oral, respiratory airway, and lung tissue bacterial microbiomes in stage I non-small cell lung cancer	"In this study, 16S sequencing was performed to assess the bacterial microbiomes in DNA isolated from pre-operative saliva and bronchial lavage fluid samples, and surgically resected tumor and adjacent normal lung tissues of patients with pathologic stage I non-small cell lung cancer. Samples were obtained from the Lung Cancer Biospecimen Resource Network, University of Virginia, VA, USA. For the samples procured by the repository, normal saline was used for collection of 20-40 ml of bronchial lavage fluids, which were centrifuged at 1,300 g for 25 minutes, following which , following which supernatants were collected and stored at -80 oC or in liquid nitrogen. Salivette tubes (Sarstedt, Newton, NC) were used for collecting saliva which were similarly stored. DNA and RNA were separately extracted from the same tissue samples using TissueLyser II, 5-mm stainless steel beads, and AllPrep DNA/RNA/Protein Mini kit (Qiagen, Valencia, CA). QIAamp UCP Pathogen Mini kit and Pathogen Lysis L tubes (Qiagen) were used to extract DNA from bronchial lavage fluid (0.4 ml) and saliva (0.2 ml). The protocol ""Pretreatment of Pathogen DNA from 400 μl Whole Blood (Mechanical Pre-lysis Protocol)"" provided with the kit was used. The kit's ATL buffer with reagent Dx was added to samples to make their volume to 0.4 ml before mechanical lysis. The two types of samples were processed in separate batches, and each batch included a negative control for DNA extraction, an empty, sterile, nuclease-free 1.5-ml microcentrifuge tube. DNA was also isolated in each of the two batches from a positive control, ZymoBIOMICS Microbial Community Standard (product D6300, Zymo, Irvine, CA). 16S sequencing of isolated DNA, involving 16S PCR, sequencing library generation, and library sequencing, was performed in four batches. All samples of a patient were sequenced in the same batch, and each batch included a no-template negative control for 16S PCR. The 16S sequencing method suggested in the 16S Metagenomic Library preparation guide of Illumina (San Diego, CA) was followed. An ~464 bp amplicon of bacterial 16S rRNA V3-V4 region was amplified with forward and reverse primers of sequences TCGTCGGCAGCGTC-ad-CCTACGGGNGGCWGCAG and GTCTCGTGGGCTCGG-ad-GACTACHVGGGTATCTAATCC, respectively (ad = AGATGTGTATAAGAGACAG). DNA (25 ng) was subjected to 35 cycles of PCR with annealing temperature of 55 oC and KAPA HiFi HotStart DNA polymerase. For samples for which 25 ng DNA was unavailable, the maximum volume of a sample's DNA preparation was used. Amplified DNA was purified with AMPure XP beads and was indexed with Nextera XT index kit in an 8-cycle PCR to generate sequencing libraries. Libraries were purified with AMPure XP beads and 12 pmoles of each library was sequenced on a MiSeq instrument (Illumina) with v3 sequencing reagents to obtained paired 300 bp reads. Between 46 and 48 libraries were multiplexed in each sequencing run. A PhiX library was spiked in at 10% molarity. Separately, tumor tissue RNA isolates were subjected to RNA sequencing (ENA study PRJEB29932)."	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006262	Comparison of the upper and lower airway microbiota	TS and lower airway samples (bronchoalveolar lavage fluid (BALF), bronchial brushings or both) were prospectively collected from 49 children undergoing a clinically indicated fibreoptic bronchoscopy.  Bacterial DNA was extracted for sequencing of the V4 region of the 16S rRNA gene using the Illumina MiSeq.	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00005089	EMG produced TPA metagenomics assembly of the PRJNA397112 data set (Indian Human Gut Microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA397112.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine.	root:Host-associated:Human:Digestive system
MGYS00006258	Longitudinal changes in gut microbiome are associated with BMI: insights from a digital therapeutics-based intervention	This study aimed to identify changes in the gut microbiome associated with a reduction in BMI after a dietary and lifestyle intervention for weight loss.	root:Host-associated:Human:Digestive system
MGYS00006218	IBD and gut microbiome	Using current knowledge of dietary patterns and components and their relationships to systemic inflammation in IBD this study aimed to describe the mechanistic relationship between dietary intake and gut microbiome composition and function in patients with luminal CD in remission. The first study objective was to characterize the differences in microbiome composition and function in patients consuming a diversified dietary pattern (DD) compared to a nondiversified dietary pattern (NDD). The second study objective was to compare microbiome composition and function between patients in the DD group to patients in the NDD group who received a structured dietary intervention using whole foods over 12 weeks.	root:Host-associated:Human:Digestive system
MGYS00006257	Three dimensional cartography of microbiome and metabolome data onto radiological images of the human lung	Our understanding of spatial variation of the chemical and microbial make-up of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge we developed a workflow, including the adaptation of a software, to enable the cartography of metabolomics and microbiome data onto a three dimensional (3D) organ reconstruction built off radiological images. Our methodology enabled for the first time the visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient. We detected host-derived molecules, microbial metabolites, different medications, and regiospecific metabolism of medications. Consequently, metabolomics data can now be understood in the context of microbial distributions in the lung. Our tool, which allows visualization of omics data on an organ in 3D and the browsable maps of the first 3D microbiome/metabolome reconstruction on a radiological image of a human lung are an interactive resource for the scientific community.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006254	Tackling the human archaeome: specific archaea detection in the gastrointestinal tract, lung, nose and on skin	Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea have been found to be regular commensals of the human gut, and represent keystone species in metabolic processes.Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with other parts of the human body, besides the gastro-intestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable to characterize the full spectrum of Archaea.The goal of this study was to critically assess PCR-based methods for specific Archaea detection in human tissue samples. We tested approaches to specifically detect M. smithii, M. stadtmanae and M. luminyensis, and to assess the overall archaeal abundance and diversity using next generation sequencing based technology. To test our established protocols, we determined the archaeal diversity associated with human skin, lung (bronchoalveolar lavage), gastrointestinal tract, stool and nose.Detection of Archaea was highly dependent on primer selection and sequence processing pipeline. Our proposed protocol enabled us to retrieve a novel picture of the human archaeome, as we identified for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal GIT, (iii) a mixed skin/GIT landscape for the nose, and (iv) a woesearchaeal lung landscape.Our study highlights the importance of primer and bioinformatics pipeline choice for studying the human archaeome. We were able to establish protocols that enlightened the presence of yet undetected Archaea in all investigated tissue samples and to detect biogeographic patterns of the human archaeome in respiratory tract, the gastrointestinal tract and on skin. Our results are a solid basis for further investigation of the human archaeome, and in the long term to uncover the potential  archaeal role in human health and disease.	root:Mixed
MGYS00006255	The Impact of Persistent Bacterial Bronchitis on the Pulmonary Microbiome of Children.	Persistent bacterial bronchitis (PBB) is a leading cause of chronic wet cough in young children. This study aimed to characterise the respiratory bacterial microbiota of healthy children and to assess the impact of the changes associated with the development of PBB. Blind, protected brushings were obtained from 20 healthy controls and 24 children with PBB, with an additional directed sample obtained from PBB patients. DNA was extracted, quantified using a 16S rRNA gene quantitative PCR assay prior to microbial community analysis by 16S rRNA gene sequencing. No significant difference in bacterial diversity or community composition (R2 = 0.01, P = 0.36) was observed between paired blind and non-blind brushes, showing that blind brushings are a valid means of accessing the airway microbiota in PBB A significant decrease in bacterial diversity (P < 0.001) and change in community composition (R2 = 0.08, P = 0.004) was observed between controls and patients. Bacterial communities within patients with PBB were dominated by Proteobacteria, and indicator species analysis showed that Haemophilus and Neisseria were significantly associated with the patient group.  In 15 (52.9%) cases the dominant organism by sequencing was not identified by standard routine clinical culture.The bacteria present in the lungs of patients with PBB were less diverse in terms of richness and evenness. The results validate the clinical diagnosis, and suggest that more attention to bacterial communities in children with chronic cough may lead to more rapid recognition of this condition with earlier treatment and reduction in disease burden.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006256	The lung microbiota and bacterial abundance in patients with bronchiectasis when clinically stable and during exacerbation	Characterization of bacterial populations in infectious respiratory diseases will provide a better understanding of the relationship between the lung microbiota, disease pathogenesis and treatment outcomes. Objectives: To comprehensively define lung microbiota composition during stable disease and exacerbation in bronchiectasis patients using both strict anaerobic culture and massively parallel pyrosequencing. Methods: Sputum was collected from bronchietasis patients when clinically stable and before and after completion of antibiotic treatment of pulmonary exacerbations. Bacterial abundance and community composition were analyzed using culture and 16S rDNA pyrosequencing. Measurements and Main Results: In clinically stable patients, aerobic and anaerobic bacteria were detected in 40/40 (100%) and 33/40 (83%) sputum samples, respectively. The dominant organisms cultured were P. aeruginosa (n=10 patients), H. influenzae (n=12), S. aureus(n=6), Prevotella (n=18) and Veillonella (n=13). Pyrosequencing generated over 150,000 sequences, representing 113 distinct microbial taxa; the majority of observed community richness resulted from taxa present in low abundance with similar patterns of phyla distribution in clinically stable patients and patients at the onset of exacerbation. Following antibiotic treatment of exacerbation, there was no change in total (p=0.925), aerobic(p=0.917) or anaerobic (p=0.683) viable counts and only a limited shift in community composition. There was also no correlation between lung function and microbial community diversity (ρ=0.123, p=0.549). Conclusions: A complex microbiota is present in the lungs of patients with bronchiectasis. Bacterial density and community diversity remain stable through treatment of exacerbations which suggests that changes in lung microbiota composition do not account for pulmonary exacerbations in patients with bronchiectasis.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00006253	"Alterations of Microbiota in Urine from Interstitial Cystitis
                patients"	"Background: Interstitial Cystitis (IC) is a chronic inflammatory
                condition of the bladder with unknown etiology. The aim of this study was to
                characterize the microbial community present in the urine from IC female patients
                and compare this with the microbial profile of asymptomatic healthy female (HF)
                urine. Background: Interstitial Cystitis (IC) is a chronic inflammatory condition of
                the bladder with unknown etiology. The aim of this study was to characterize the
                microbial community present in the urine from IC female patients and compare this
                with the microbial profile of asymptomatic healthy female (HF) urine. Results: The
                composition and distribution of bacterial sequences differed between the urine
                microbiota of IC and HF. Reduced sequence richness and diversity were found for IC
                patient urine, and a significant difference in the community structure of IC urine
                in relation to HF urine was observed. More than 90% of the IC sequence reads were
                identified as belonging to the bacterial genus Lactobacillus, a marked increase
                compared to the 60% in the HF urine. Conclusion: The 16S rDNA sequence data
                demonstrates a shift in the bacterial composition of IC urine. The reduced microbial
                diversity and richness is accompanied by a higher abundance of the bacterial genus
                Lactobacillus, compared to HF urine. This study demonstrates that high throughput
                sequencing analysis of the urine microbiota in IC patients is a powerful tool
                towards a better understanding of this enigmatic disease."	root:Host-associated:Human:Excretory system:Urethra:Urine
MGYS00006248	The microbial pathology of asthma	The microbial pathology of asthma study (known as Celtic Fire) is a multi-centre cross-sectional study ofasthmatic subjects (ranging in severity from Global Initiative for Asthma [GINA] step 1 - 5) and healthy controls.Subjects were recruited via three sites in the British Isles: Connolly Hospital, Dublin; The Royal BromptonHospital, London; and Swansea University Medical School, Swansea. Data (demographic and clinical) andsamples were collected from each subject and sent to the central coordinating centre, the Asmarley Centrefor Genomic Medicine (ACGM), and its associated laboratories at the National Heart and Lung Institute (NHLI),Imperial College London (ICL). The target was to recruit 120 asthmatic subjects, 20 non-smoking controlsubjects and 20 smoking control subjects.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00005094	Soil bacterial communities under long-term organic production in Buenos Aires, Argentina	Soil bacterial communities under long-term organic production in Buenos Aires, Argentina	root:Environmental:Terrestrial:Soil
MGYS00005091	Organic management on soil bacteria, comparison of different type of soils in Buenos Aires, Argentina	Evaluation of organic management in soil bacteria, comparison of different type of soils in Buenos Aires, Argentina	root:Environmental:Terrestrial:Soil
MGYS00006215	Habitual dietary fibre intake and gut microbiota responsiveness	Presently, it is difficult to predict how the gut microbiota will respond to a particular dietary intervention. Therefore, the aim of this study was to determine what influence differing habitual dietary fibre intakes had on how the gut microbiota responded to an inulin-type fructan prebiotic	root:Host-associated:Human:Digestive system
MGYS00006220	Microbiota Brain Axis in Alzheimers Disease MIND Diet Induced Effects	Alzheimers disease is a public health concern and the current study leverages a phase III randomized, interventional clinical trial to evaluate the ability of a dietary intervention to influence age associated cognitive decline in a population at risk for Alzheimers disease. Diet influences the intestinal microbiota, thus the current study investigated diet induced changes in the intestinal microbiota as a mechanism by which dietary interventions exert beneficial effects on cognition and Alzheimers disease pathogenesis. Subjects fecal baseline samples were analyzed using 16S rRNA gene amplicon sequencing. The relationship between the microbiota and baseline clinical and experimental variables were evaluated.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006223	Modulatory Effects of Triphala and Manjistha Dietary Supplementation on Human Gut Microbiota: A Double-Blind, Randomized, Placebo-Controlled Pilot Study	We evaluated the impact of two medicinal herbs, triphala and manjistha on gut microbiota composition following a 4 week randomized, double blind placebo control intervention by profiling fecal communities by 16S rRNA profiling.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006222	Gut microbiome alterations after high-fat low-carbohydrate weight reduction diet: pros and cons	OBJECTIVE The objectives were 1) determination of microbial composition of obese and normal weight subjects, 2) calculation of fiber composition of specially assigned low-calorie weight loss diet (WLD), 3) identification of microbial changes after WLD and improvements in health characteristics and associations of microbiota to fiber consumption profiles.METHODSA total of 19 overweight/obese participants with body mass index (BMI) of 28.9-44.4 kg/m2 were assigned to 20-40 % reduced calories high-fat low-carbohydrate diet for 4 weeks. Protein and fat content in composed diet was 1.5 times higher compared to that in average diet of normal weight group, while carbohydrate content was 2 times lower. Total fiber content was comparable to normal weight group. Food consumption data were obtained from assigned meals. Database of specific fiber composition of different food categories was developed and macronutrient, total and specific fiber consumption were calculated. Microbial composition was analysed before and after the intervention from 2 sequential samples by 16S rRNA sequencing. RESULTS:During intervention BMI reduced in average 2.5 ± 0.6 kg/m2 and stool frequency was normalized. Assigned diet induced significant changes in fecal microbiota. Abundance of bile resistant bacteria (Alistipes, Odoribacter splanchnicus), Ruminococcus bicirculans and Butyricimonas but also Enterobacteriaceae increased. Alistipes has been associated with lower BMI and Butyricimonas with higher values of HDL-cholesterol in blood. Importantly, abundance of bacteria often associated with inflammation such as Collinsella and Dorea decreased in parallel with decrease of BMI. Furthermore, the abundance of bifidobacteria decreased, which can be attributed to relatively low consumption of grains.  CONCLUSIONS:In conclusion, results showed that short intervention studies can alter microbial community structure and gave relevant insights into development of different dietary concepts.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006252	The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia.	Rationale: Mechanical ventilation is assumed to cause a shift in pulmonary microbial communities. Ventilator-associated pneumonia (VAP) is a frequent complication of prolonged mechanical ventilation and has a considerable morbidity and mortality. In this study we hypothesized that microbial diversity lowers with prolonged mechanical ventilation and as antibiotics are administrated; there was an effect of dominance  of a subset of well-adapted bacterial pathogens and these selection was more profound in patients that developed VAP. Methods: This is a case–control longitudinal study of patients that were originally included in an international multi–centre prospective observational cohort study of the predictive value of biological markers for development of VAP. Repeated sampling approach was applied during mechanical ventilation. Total DNA was extracted from endotracheal aspirates and variable regions 2 and 3 of bacterial 16S rRNA gene were amplified and sequenced. Results: Antibiotic use was not associated with  bacterial biodiversity decrease. There was an increase in relative abundance of Pseudomonadales, Enterobacteriales, Bacillales, and Burkholderiales within mechanical ventilation period, however it was not correlated with VAP development. In the microbial network potential pathogens Acinetobacter, Pseudomonas, Staphylococcus, Haemophilus tend to mutually exclude other species.  Conclusion: Repeated sampling approach is a useful tool to study respiratory microbiome. Together with characterization of host immune factors it will improve our understanding of microbiome dysbiosis caused by mechanical ventilation.	root:Host-associated:Human:Respiratory system:Pulmonary system:Trachea
MGYS00000575	Dietary intervention with a probiotic Bifidobacterium modulates dominant bacterial taxa in an enterotype-dependent fashion and normalizes butyrate levels in the gut of healthy adults	The modulation of the intestinal microbial ecosystem is considered to be the first target to establish probiotic efficacy in a healthy population.  A randomized, double-blind, crossover, placebo-controlled intervention study was conducted to determine the impact of the probiotic strain Bifidobacterium bifidum BB on the intestinal microbial ecology of adult healthy volunteers of both sexes. High-throughput 16S ribosomal RNA gene sequencing was used to characterize the fecal microbiota before and after four weeks of daily probiotic cells consumption.  This work shows that the intake of one billion live B. bifidum BB cells affects the relative abundance of dominant taxa in the fecal microbiota and modulates the fecal levels of butyrate. Specifically the relative abundance of family Prevotellaceae (P=0.041) and genus Prevotella (P=0.034) was significantly decreased, whereas the relative abundance of families Ruminococcaceae (P=0.039) and Rikenellaceae (P=0.010) was significantly increased. Although the overall composition of the microbiota was not affected, the dependency of the probiotic intervention on the enterotype has been highlighted observing the major effects of BB on microbiota composition in the Prevotella-dominated enterotype rather than the Bacteroides-dominated one. In addition, we observed a normalizing effect on fecal butyrate levels during the probiotic intervention. In conclusion, our study demonstrates that a single daily administration of B. bifidum BB can modify the human intestinal microbial ecology in healthy (not diseased) adults in a significant fashion. These findings can convey the need to reassess the notion of probiotics’ inability to influence the complex and stable intestinal microbial ecosystem of a healthy individual.	root:Host-associated:Human:Digestive system
MGYS00006122	Gut microbiota after dietary intervention	We analyzed the impact of a gut microbiota-targeted dietary intervention on the chronic inflammation underlying metabolic syndrome.  Human feces from central obese volunteers after whole grains, traditional Chinese medicinal foods, and prebiotics (WTP diet) dietary intervention.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006249	Immune dysregulation associated with respiratory illness in elite athletes	ABSTRACTRationale: Elite athletes are susceptible to respiratory tract infection (RTI) leading to significant training and in-competition time loss.Objective: This prospective study aimed to understand RTI susceptibility in elite athletes through systematic clinical and immune phenotyping in a cohort of 121 elite Olympic athletes.Methods/measurements: We performed comprehensive clinical and respiratory function phenotyping to identify athletes highly susceptible and non-susceptible to RTI. Baseline T and B cell peripheral lymphotype phenotyping was performed by flow cytometry with findings validated by mass cytometry in repeat samples. Viral immune response was analysed through peripheral blood mononuclear cell (PBMC) stimulation assays. Further immune phenotyping was performed through 16s rRNA microbial sequencing of oropharyngeal swabs and global untargeted plasma metabolomic profiling. Findings were compared to non-athlete healthy controls.Main Results: Clinical phenotyping revealed 23 athletes as highly susceptible to RTI with 23 athletes non-susceptible. Immune phenotyping revealed that highly susceptible athletes had a significantly reduced peripheral memory T regulatory cell compartment compared to non-susceptible athletes and healthy controls. The PBMC immune response to viral ligands in highly susceptible athletes also revealed a pro-inflammatory skewed T helper 2 response. Analysis of the oropharyngeal microbiome revealed reduced bacterial biomass in elite athletes compared to healthy controls. Metabolomic profiling revealed significant differences in sphingolipid pathway metabolites between RTI highly susceptible, non-susceptible athletes and healthy controls.Conclusion: in this study we highlight a RTI-susceptible elite athlete endotype and show the presence of a persistent reduction in circulating memory T regulatory cells with further evidence of bacterial dysbiosis and metabolic dysregulation of the sphingolipid pathway.	root:Host-associated:Human:Respiratory system:Nasopharyngeal:Pharynx
MGYS00006251	Lung and gut microbiota profiling in intensive care unit patients: a prospective pilot study	"Gut and lung microbiome play an important role in the host defense and can be predictive of clinical outcome in critically ill patients. However, the interplay between the gut and lung microbiota over time during severe illness is not fully understood and remains to be defined. This study aims to assess the longitudinal changes of the lung and gut microbiota in critically ill patients with and without infection.
Methods: We performed a prospective, observational cohort study in the intensive care unit (ICU) at Lausanne university hospital. A total of 73 endotracheal aspirates and 93 rectal-swabs were obtained from 38 critically ill adults who required mechanical ventilation. Lung and gut microbiota were characterized using bacterial 16S ribosomal RNA sequencing. The primary outcomes were the bacterial burden, community diversity and community composition of lung and gut microbiota. Secondary outcomes were ICU length of stay and ventilator-free days determined at 28 days after admission.
Results: We found a loss of alpha diversity during ICU stay which was more pronounced in infected patients than uninfected patients. The gut microbiome, more than the lung microbiome, became more dissimilar at discharge between uninfected and infected patients. The lung microbiome of patients who developed pneumonia was progressively enriched with Enterobacteriaceae and other Proteobacteria. Alpha diversity index in the lungs and Mogibacterium gut relative abundance predicted the length of mechanical ventilation.
Conclusion: Key features of the lung microbiome predicted outcome in critically ill patients. Lung and gut microbiome dysbiosis showed similar trends in critically ill patients, the interplay of gut-lung axis remains yet to be further evaluated."	root:Mixed
MGYS00006250	Bacterial microbiomes of lungs of male C57BL/6J mice optionally treated with high-fat diet to induce obesity	Briefly, male, 2-3-month old, C57BL/6J mice were treated with high-fat diet for 16 weeks to induce obesity. Age/sex-matched control mice were fed normal diet. DNA was isolated from lungs after sacrificing mice using Qiagen® DNeasy PowerSoil Kit. 16S PCR and library preparation were as per Illumina® Metagenomics Guide, using the guide's suggested V3-V4 primers; Kapa Biosystems® KAPA HiFi ReadyMix for PCR, with 35 cycles and 25 ng DNA input (when available; otherwise entire DNA sample). Indexing was with Nextera® XT v2 combinatorial dual index kit, 8 cycles of PCR. Negative controls used were for DNA extraction (three) and 16S PCR (no template; two). One positive control was ZymoBIOMICSTM Microbial Community DNA Standard, Zymo® cat. #6305). All libraries were sequenced together, at ~8 pM each, with 10% PhiX library spike-in, on Illumina® MiSeq with v3 reagents, to obtain 300 b paired-end reads.	root:Host-associated:Mammals:Respiratory system:Pulmonary system
MGYS00006245	EMG produced TPA metagenomics assembly of PRJNA340216 data set (Gut microbiota and metagenomic diversity of omnivore, vegetarian and vegan healthy subjects).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA340216, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system
MGYS00003941	Epipelagic bacterial communities of Canadian lakes	The NSERC Canadian LakePulse Network is a scientific initiative assessing environmental issues affecting Canadian lakes. Through multidisciplinary projects, LakePulse researchers use tools in lake science, spatial modelling, analytical chemistry, public health, and remote sensing to assess the status of over 600 lakes across various ecozones in Canada. The impacts of land-use, climate change and contaminants on lake health will be assessed to develop policies for better lake management.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00006242	Dietary interventions rapidly affect gut microbiota diversity and function and the host lipid mediator response in a healthy population	This study investigates mechanisms regulating the interactions between the diet, host lipid mediators and the gut microbiome.	root:Host-associated:Human:Digestive system
MGYS00006216	Higher bacterial DNAemia can affect the impact of a polyphenol-rich dietary pattern on biomarkers of intestinal permeability and cardiovascular disease risk in older subjects	Scope. Aging is characterized by increased systemic low-grade inflammation, altered gut microbiota composition and enhanced intestinal permeability (IP). The intake of polyphenol-rich (PR) foods is proposed as a promising strategy to positively affect the gut microbiota-immune system-intestinal barrier (IB) axis. In this context, the MaPLE project was designed to test the hypothesis that a PR dietary pattern may preserve and/or improve IB function in older people. Here, we tested the hypothesis that the dietary intervention might have affected the presence of bacterial factors in the bloodstream of the older volunteers participating in the MaPLE trial. Methods and results. We quantified the presence of bacterial DNA in blood by qPCR targeting the 16S rRNA gene (16S; bacterial DNAemia). Blood DNA was  taxonomically profiled via 16S sequencing. We found that higher blood 16S levels are associated to higher BMI and markers of IP, inflammation and dyslipidemia. Subjects with higher bacterial DNAemia could benefit more from the PR-dietary intervention as demonstrated by the reduction of the markers related to IP, inflammation and dyslipidemia. Finally, we found that the bacterial DNA detected in blood mostly belong to γ-Proteobacteria, whose abundance significantly decreased after the PR-diet in subjects with higher bacterial DNAemia at baseline.Conclusion. This study shows that the efficacy of the PR diet could depend on bacterial DNAemia. Bacterial DNAemia may be a relevant marker to evaluate in order to test the efficacy of dietary interventions based on PR-foods in the older populations.	root:Host-associated:Human:Circulatory system:Blood
MGYS00006217	Gut microbiome of infants at 3, 6, and 12 months of age, with different dietary interventions. Raw sequence reads	We sought to determine how the infant gut microbiota evolve during infancy, in particular in relation to hygiene-related environmental factors, allergic and atopic disorders, and a randomized dietary intervention. Therefore, 288 healthy, exclusively breastfed infants were enrolled in a dietary intervention study from three months of age. 70 were followed up at six and twelve months to study the evolution of their gut microbiota, using 16S ribosomal RNA gene targeted amplicon sequencing.	root:Host-associated:Human:Digestive system
MGYS00006124	Gut microbiome composition after spices intervention	Short-term changes in dietary intake can induce changes in the gut microbiome. While various polyphenols and polyphenol-rich foods have been shown to modulate gut microflora to different extents, the acute influence of polyphenol-rich mixed spices, typically consumed, as curry meals worldwide has not been explored in a controlled setting. We, therefore, investigated the effects of a single serving of mixed spices Indian curry consumption, in two separate doses, on the gut microbiome in young, healthy, Singaporean Chinese males.This study has shown a single serving of mixed spices containing Indian curry can significantly modify certain commensal microbes, particularly in those people who do not regularly consume these spices.	root:Host-associated:Human:Digestive system
MGYS00006239	EMG produced TPA metagenomics assembly of PRJEB36528 data set (Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using Nextstrain.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB36528, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants.	root:Host-associated:Plants
MGYS00006237	EMG produced TPA metagenomics assembly of PRJNA726355 data set (Responsiveness of rhizosphere bacteria assembled from manipulated soil microbiome suppressed Ralstonia solanacearum invasion).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA726355, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006231	EMG produced TPA metagenomics assembly of PRJNA789467 data set (Disentangling the genetic basis of rhizosphere microbiome assembly in tomato (metagenomics part)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA789467, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006238	EMG produced TPA metagenomics assembly of PRJNA743714 data set (Survey of viruses of wild Solanum species in South Africa).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA743714, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Phylloplane.	root:Host-associated:Plants:Phylloplane
MGYS00006235	EMG produced TPA metagenomics assembly of PRJNA781422 data set (NGS study of Czech honey bee virome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA781422, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.	root:Host-associated:Insecta
MGYS00006236	EMG produced TPA metatranscriptomics assembly of PRJNA411946 data set (Illumina metagenomics RNA sequencing of the virome of wild bees in Belgium).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA411946, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.	root:Host-associated:Insecta
MGYS00006234	EMG produced TPA metagenomics assembly of PRJNA685398 data set (Honey bee gut microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA685398, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006229	EMG produced TPA metagenomics assembly of PRJEB30847 data set (Shotgun metagenome sequence library from bulk soil and rhizosphere samples of wild and domesticated barley genotypes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB30847, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006233	EMG produced TPA metagenomics assembly of PRJNA494922 data set (Characterisation of the UK honey bee metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA494922, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.	root:Host-associated:Insecta
MGYS00006232	EMG produced TPA metatranscriptomics assembly of PRJNA395704 data set (Metatranscriptome_Rhizosphere_Barley Transcriptome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA395704, and was assembled with megahit v1.2.9, metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006230	EMG produced TPA metagenomics assembly of PRJNA745270 data set (metagenomics sequence of manure and unmanured rhizosphere soil of tomato plant).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA745270, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006228	EMG produced TPA metagenomics assembly of PRJNA763981 data set (SOYBEAN RHIZOSPHERE METAGENOMICS).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA763981, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006227	EMG produced TPA metagenomics assembly of PRJNA653702 data set (Soil microbial communities from Nachusa Grasslands, Illinois, United States - SOY_050217 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA653702, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizoplane:Soil.	root:Host-associated:Plants:Rhizoplane:Soil
MGYS00006221	Impact of a moderate caloric restriction on the gut microbiota composition and diversity of Italian obese patients	Although it is known that the gut microbiota (GM) can be modulated by diet, the impact of specific dietary interventions on its composition and diversity in obese patients remain to be ascertained. The present work aimed to evaluate the impact of a moderately hypocaloric Mediterranean diet on the GM of obese and overweight patients (OB). The GM of 23 OB patients (F/M= 20/3) was compared before and after 3 months of the nutritional intervention (NI). Fecal samples were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. After 3 months of NI, patients presented a statistically significant reduction of the body weight and fat mass, along with changes in the relative abundance of many microbial patterns. We observed an increased abundance in several Bacteroidetes taxa (i.e. Sphingobacteriaceae, Sphingobacterium, Bacteroides spp, Prevotella stercorea) and depletion of many Firmicutes taxa (i.e. Lachnospiraceae members, Ruminococcaceae and Ruminococcus, Veillonellaceae, Catenibacterium, Megamonas). In addition, the phylum Proteobacteria showed an increased abundance, while the genus Sutterella, within the same phylum, decreased after the intervention. Metabolic pathways related to membrane transport and cell motility showed a decreased expression after the NI.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006219	Healthy Finnish controls	The healthy Finnish controls were previously recruited as part of a dietary intervention investigating the effects of partly replacing animal proteins with plant proteins on health; the inclusion and exclusion criteria have been described elsewhere (PMID: 34837522). The fecal samples derived from 50 Finnish controls that were age-, sex- and BMI-matched with the Pakistani controls were included in the present study.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000526	Modulation of dyslipidemic children fecal microbial ecosystem by dietary intervention with hazelnuts as source of unsaturated fatty acids.	The possibility to modulate the intestinal microbial ecosystem (IME) gains increasing interest due to its potential consequences on human health. The relative abundance of specific intestinal bacterial taxa may be potentially modulated through dietary interventions. The aim of this project is to describe the fluctuation of bacterial taxa and short chain fatty acids induced in fecal samples from 15 dyslipidemic children by hazelnuts consumption as the main source of unsaturated fatty acids.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006123	Gut microbiota with the intervention of dietary oils	Dietary fats have important influences on the human body and the intestinal bacterial. This research investigated the effects of twelve common dietary fats intervention in mice, and the gut microbiota were analyzed. The dietary oils include olive oil, soybean oil, peanut oil, rapeseed oil, sunflower oil, palm oil, sesame oil, walnut oil, linseed oil, corn oil, camellia oil, and lard	root:Host-associated:Mammals:Digestive system
MGYS00006214	Baterial 16S rRNA amplicon sequencing data from Tengger desert	Bacterial amplicon libraries were prepared by amplifying the V3-V4 variable regions of the 16S rRNA genes with the primer pair of 341F and 805R. 23 soil samples, with or without agricultural reclamation, were collected from the Tengger desert. CON, the soil collected from the open field without agricultural management, the control; PLT, the soil collected from the site 10 cm apart from the planta; FTL, the soil collected from the site on the fertilization furrow, 50 cm apart from the planta.	root:Environmental:Terrestrial:Soil:Desert
MGYS00006210	EMG produced TPA metagenomics assembly of PRJNA772045 data set (Diversity, phylogenetic relationships and infectivity of viruses from tomato and surrounding weeds agroecosystems).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA772045, and was assembled with metaSPAdes v3.15.3, megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Plants.	root:Host-associated:Plants
MGYS00006181	EMG produced TPA metagenomics assembly of PRJNA579886 data set (Apis Mellifera Virome raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA579886, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.	root:Host-associated:Insecta
MGYS00006207	EMG produced TPA metagenomics assembly of PRJNA486916 data set (plant metagenome Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA486916, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants.	root:Host-associated:Plants
MGYS00006206	EMG produced TPA metagenomics assembly of PRJNA179134 data set (Tomato phyllosphere Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA179134, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Phylloplane.	root:Host-associated:Plants:Phylloplane
MGYS00006193	EMG produced TPA metagenomics assembly of PRJNA599270 data set (Honey bee gut virome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA599270, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00002684	Effects of organic matter manipulation on archaeal, bacterial, and fungal community assembly	Community assembly is not only important for community structure, it is also a strong predictor of ecosystem functioning. Understanding how communities initially form and colonize lake sediments – where essential functions like carbon cycling occur – is therefore important for whole-ecosystem processes. Here, we tested for the deterministic processes that drive assembly order. Is this order primarily determined by the sediment or by the lake conditions ? What influences how rapidly this environmental filtering occurs? Do communities become more interconnected with time because of the sediment or lake conditions? Artificial mesocosms were created with varying levels and types of terrestrial organic matter. The mesocosms were placed at the bottom of three lakes. We sampled the sediment monthly over a two-month period to characterize microbial communities.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00006213	EMG produced TPA metagenomics assembly of PRJNA255918 data set (Fumarolic ice cave sediment Metagenome).	The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA255918, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Sediment.	root:Environmental:Aquatic:Sediment
MGYS00006212	The microbiome of rock grains weathered in the soil environment.	Using a metagenomic and metatranscriptomic approach the study aims to investigate the differences and similarities between the microbial communities of basalt grains weathered in soil and its surrounding soil substrate. This will provide the foundation to characterise and harvest the full potential of the belowground microbiome to elevate rates of enhanced rock weathering (EW) and carbon dioxide removal (CDR) in agroecosystems, helping towards efforts to achieve negative C emission.	root:Environmental:Terrestrial:Soil
MGYS00006137	EMG produced TPA metagenomics assembly of PRJEB4370 data set (A gnotobiotic mouse model of phage-bacterial host dynamics in the human gut).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB4370, and was assembled with metaSPAdes v3.15.3, SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006180	EMG produced TPA metagenomics assembly of PRJNA598094 data set (Metagenomes of bacteria colonizing the gut of Apis mellifera and Apis cerana Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA598094, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006147	EMG produced TPA metagenomics assembly of PRJNA757579 data set (Adjunctive probiotic Lactobacillus rhamnosus Probio-M9 enhances the effect of anti-PD-1 antitumor therapy via regulating the gut microbiota damaged by antibiotics).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA757579, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006156	EMG produced TPA metagenomics assembly of PRJNA747837 data set (mouse gut metagenome of different environment).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA747837, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00004546	Soil microbial communities in agricultural soils of Argentina	In this project we study soil bacterial and fungal communities under long-term agricultural management with contrasting fertilization, tillage and crop rotation practices.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00006176	Anaerobic microorganisms in rice fields	Enrichment and isolation of dehalogenating microorganisms in rice fields	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00006164	EMG produced TPA metagenomics assembly of PRJNA379709 data set (Species and functional composition of gut bacteria from TGF-Beta deficient H. hepaticus positive mice).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA379709, and was assembled with SPAdes v3.15.3, metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00006209	EMG produced TPA metagenomics assembly of PRJEB42296 data set (First expansion of the public Tomato brown rugose fruit virus (ToBRFV) Nextstrain build; inclusion of new genomic and epidemiological data).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB42296, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants.	root:Host-associated:Plants
MGYS00006205	EMG produced TPA metagenomics assembly of PRJNA755742 data set (Tomato rhizosphere microbiome in the pot experiment).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA755742, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006144	EMG produced TPA metagenomics assembly of PRJNA725899 data set (Metagenomic sequencing of wild rodent colon, cecum and faeces).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA725899, and was assembled with unknown v0.0, metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Large intestine.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00006208	EMG produced TPA metagenomics assembly of PRJNA766489 data set (Culture-independent analysis of rhizosphere microbial communities associated with tomato plants).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA766489, and was assembled with metaSPAdes v3.15.3, SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006204	EMG produced TPA metagenomics assembly of PRJNA755741 data set (Tomato rhizosphere microbiome in the belowground segregation experiment).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA755741, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006203	EMG produced TPA metagenomics assembly of PRJNA590717 data set (Genome-resolved metagenomics to study the prevalence of co-infections and intraspecific heterogeneity among pathogen metapopulations within tomato and pepper fields).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA590717, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Phylloplane.	root:Host-associated:Plants:Phylloplane
MGYS00006189	EMG produced TPA metagenomics assembly of PRJNA645015 data set (Honeybee gut microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA645015, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006202	EMG produced TPA metagenomics assembly of PRJNA603603 data set (Soil and rhizospheric whole shotgun metagenomes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA603603, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere:Soil.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00006201	EMG produced TPA metagenomics assembly of PRJNA597176 data set (global study of tomato bacterial wilt soil microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA597176, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizoplane:Soil.	root:Host-associated:Plants:Rhizoplane:Soil
MGYS00006200	EMG produced TPA metagenomics assembly of PRJNA653704 data set (Soil microbial communities from Nachusa Grasslands, Illinois, United States - SOY_101317 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA653704, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizoplane:Soil.	root:Host-associated:Plants:Rhizoplane:Soil
MGYS00006199	EMG produced TPA metagenomics assembly of PRJNA653703 data set (Soil microbial communities from Nachusa Grasslands, Illinois, United States - SOY_080817 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA653703, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizoplane:Soil.	root:Host-associated:Plants:Rhizoplane:Soil
MGYS00006198	EMG produced TPA metagenomics assembly of PRJNA539517 data set (Root nodule microbial communities collected in Santa Monica, California, United States - Edamame nodules 1 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA539517, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006197	EMG produced TPA metagenomics assembly of PRJNA655215 data set (Metagenomic analyses of soybean rhizosphere).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA655215, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006196	EMG produced TPA metagenomics assembly of PRJDB5626 data set (Microbial metagenome analysis of soybean root nodules).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJDB5626, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00006195	EMG produced TPA metagenomics assembly of PRJNA787435 data set (Geographical resistome profiling in honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA787435, and was assembled with metaSPAdes v3.15.3, megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006194	EMG produced TPA metagenomics assembly of PRJNA371719 data set (Functional diversity within the simple gut microbiota of the honey bee).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA371719, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006192	EMG produced TPA metagenomics assembly of PRJNA784737 data set (Metagenomic detection of viral pathogens in Spanish honeybees).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA784737, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.	root:Host-associated:Insecta
MGYS00006191	EMG produced TPA metatranscriptomics assembly of PRJNA318490 data set (RNA shotgun metagenomic sequencing in social and solitary wild bees Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA318490, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.	root:Host-associated:Insecta
MGYS00006190	EMG produced TPA metagenomics assembly of PRJNA642095 data set (Metagenome, bees, yeasts).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA642095, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006185	EMG produced TPA metagenomics assembly of PRJNA599288 data set (Cross-species colonization of Apis cerana and Apis mellifera gut bacteria).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA599288, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006188	EMG produced TPA metatranscriptomics assembly of PRJNA172020 data set (Honey bee (Apis mellifera) and an ectoparasitic mite of honey bee, Varroa destructor Transcriptome or Gene expression).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA172020, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.	root:Host-associated:Insecta
MGYS00006187	EMG produced TPA metagenomics assembly of PRJNA786615 data set (Characterization of gut bacteria of italian honey bee Apis mellifera (Apidae: hymenoptera)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA786615, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006186	EMG produced TPA metagenomics assembly of PRJNA253368 data set (Honey bee gut metatranscriptome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA253368, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006182	EMG produced TPA metatranscriptomics assembly of PRJNA687318 data set (Metatranscriptome analysis of sympatric bee species identifies variants of bee infecting viruses, and a novel RNA virus primarily associated with Andrena).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA687318, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.	root:Host-associated:Insecta
MGYS00006184	EMG produced TPA metagenomics assembly of PRJNA400782 data set (A scientific note on the first detection of Israeli acute paralysis virus in honey bees (Apis mellifera) in Kenya using high-throughput sequencing).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA400782, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.	root:Host-associated:Insecta
MGYS00006183	EMG produced TPA metagenomics assembly of PRJNA481316 data set (honeybee viral metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA481316, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.	root:Host-associated:Insecta
MGYS00006177	EMG produced TPA metagenomics assembly of PRJNA599289 data set (Gut microbiome of honey bees in china).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA599289, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006179	EMG produced TPA metagenomics assembly of PRJNA786261 data set (Geographical resistome profiling in honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA786261, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006178	EMG produced TPA metagenomics assembly of PRJNA473901 data set (Gut microbiota of honeybees Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA473901, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00006163	EMG produced TPA metagenomics assembly of PRJNA750880 data set (Mouse intestinal phages-Health and alcohol feeding).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA750880, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006175	EMG produced TPA metagenomics assembly of PRJNA852525 data set (gut metagenome Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA852525, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006167	EMG produced TPA metagenomics assembly of PRJNA771488 data set (Dynamic impact of Blautia producta on gut microbiota).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA771488, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006172	EMG produced TPA metagenomics assembly of PRJNA841368 data set (C-section increases cecal abundance of the archetypal bile acid and glucocorticoid modifying Lachnoclostridium [Clostridium] scindens in mice).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA841368, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006170	EMG produced TPA metagenomics assembly of PRJNA828263 data set (Impact of a phage cocktail targeting Escherichia coli and Enterococcus faecalis as members of a gut bacterial consortium in vitro and in vivo).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA828263, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006153	EMG produced TPA metagenomics assembly of PRJNA705695 data set (Gut metagenomes of patients and mice with post-infection irritable bowel syndrome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA705695, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006168	EMG produced TPA metagenomics assembly of PRJNA776120 data set (Effectiveness of Jianpi Qushi Heluo formula (JQHF) in alleviating experimental passive Heymann nephritis in rats and its modulation effect on gut microbiota).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA776120, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006165	EMG produced TPA metagenomics assembly of PRJNA741607 data set (Inhibitory Effects of Lactulose on Colitis-Associated Carcinogenesis by Restoration of the Gut Microbiota in AOM/DSS Mouse Model).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA741607, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006116	EMG produced TPA metagenomics assembly of PRJNA760892 data set (Fecal Whole Metagenomic Shotgun Sequencing on mouse).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA760892, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006173	EMG produced TPA metagenomics assembly of PRJNA844935 data set (The gut microbiome in age-related sepsis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA844935, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006166	EMG produced TPA metagenomics assembly of PRJNA753725 data set (Changes of intestinal resistance genome induced by diet).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA753725, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006159	EMG produced TPA metagenomics assembly of PRJNA755346 data set (Intestinal Virome Diversity Correlates with Intestinal Microbiome Diversity in ob and Apoe mice).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA755346, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006162	EMG produced TPA metagenomics assembly of PRJNA748686 data set (mouse gut metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA748686, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006158	EMG produced TPA metagenomics assembly of PRJNA753312 data set (Mastitis microbiomes of cow and mouse Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA753312, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006171	EMG produced TPA metagenomics assembly of PRJNA838940 data set (Metagenomic sequencing of colon contents from gnotobiotic mice harboring the altered Schaedler flora).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA838940, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006169	EMG produced TPA metagenomics assembly of PRJNA785116 data set (Metagenomic sequencing).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA785116, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006155	EMG produced TPA metagenomics assembly of PRJNA738554 data set (The influence of the low-iron diet and the protective effect of Lactobacillus casei Zhang from the perspective of gut microbiota).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA738554, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006114	EMG produced TPA metagenomics assembly of PRJNA712972 data set (PIGA gene responsible for GPI anchor biosynthesis : knockout leads to gut microbiome dysbiosis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA712972, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006161	EMG produced TPA metagenomics assembly of PRJNA802607 data set (Genesis of fecal floatation is causally linked to gut microbial colonization in mice).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA802607, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006160	EMG produced TPA metagenomics assembly of PRJNA771420 data set (28-day gavage of Blautia product on gut microbiota).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA771420, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006151	EMG produced TPA metagenomics assembly of PRJNA704567 data set (Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA704567, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006157	EMG produced TPA metagenomics assembly of PRJNA693108 data set (Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA693108, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00006146	EMG produced TPA metagenomics assembly of PRJNA734104 data set (Antibiotic-induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA734104, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006145	EMG produced TPA metagenomics assembly of PRJNA730805 data set (Integrative Analysis of the Western Diet-Induced Metabolic Phenotype and Microbiota Changes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA730805, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006143	EMG produced TPA metagenomics assembly of PRJNA732220 data set (Gut microbiota of pregnant C57BL/6J mice).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA732220, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006139	EMG produced TPA metagenomics assembly of PRJNA646095 data set (Collaborative Cross founders mouse gut metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA646095, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.	root:Host-associated:Mammals:Gastrointestinal tract
MGYS00006152	EMG produced TPA metagenomics assembly of PRJNA719224 data set (Shotgun Metagenomic Analysis of Dose-Dependent TCDD-elicited Effects on Cecal Gut Microbiota).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA719224, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum.	root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
MGYS00006138	EMG produced TPA metagenomics assembly of PRJNA815731 data set (mouse gut metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA815731, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006148	EMG produced TPA metagenomics assembly of PRJNA389470 data set (Mus musculus Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA389470, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006150	EMG produced TPA metagenomics assembly of PRJNA703330 data set (Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA703330, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006142	EMG produced TPA metagenomics assembly of PRJNA691897 data set (Generation-scale evolution of the gut resistome under selective antibiotic pressure).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA691897, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006141	EMG produced TPA metagenomics assembly of PRJNA646351 data set (Metagenomic data of mice).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA646351, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006149	EMG produced TPA metagenomics assembly of PRJNA694540 data set (Effect of amylin on intestinal microflora in mice).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA694540, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006140	EMG produced TPA metagenomics assembly of PRJNA657446 data set (Alteration of gut microbiota by dietary change in mouse).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA657446, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00005096	Impact of organic management in soil borne bacterial communities	Evaluation of compost application, winter cover crops and no-tillage in an organic system for soybean, maize and wheat crop rotation in Argentina	root:Environmental:Terrestrial:Soil:Crop:Agricultural land
MGYS00006097	Metagenomics of Washed Rind Cheese Communities	"We used short and long read metagenomics to look at the microbial diversity of cheese rind biofilms from several washed rind cheeses. Short reads were assembled with metaSPAdes 3.15.3. Oxford Nanopore reads were assembled with metaFlye 2.9.1 and polished with medaka 1.7.2. The following samples were sequenced with both Illumina and Oxford Nanopore Technologies and are samples from the same style of cheese sampled at different times throughout the aging process (early, middle, and late timepoints spanning the standard aging time for each cheese style):
EL2W, EL4W, EL12W (2, 4, 12 weeks)
OM2W, OM4W, OM8W (2, 4, 8 weeks)
WH1M, WH2M, WH4M (1, 2, 4 months)"	root:Engineered:Food production:Dairy products
MGYS00006104	EMG produced TPA metagenomics assembly of PRJEB52004 data set (Tetracyclines effect on microbiome with and without Influenza infection in mouse.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB52004, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006134	EMG produced TPA metagenomics assembly of PRJNA783624 data set (A natural polyphenol exerts antitumor activity and circumvents anti-PD-1 resistance through effects on the gut microbiota).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA783624, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006136	EMG produced TPA metagenomics assembly of PRJNA812410 data set (Quantifying the impact of gut microbiota on inflammation and hypertensive organ damage).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA812410, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006135	EMG produced TPA metagenomics assembly of PRJNA799796 data set (Mouse fecal sample Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA799796, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006128	EMG produced TPA metagenomics assembly of PRJNA851186 data set (Outer Membrane Vesicles from the gut microbiome contribute to tumor immunity by eliciting cross-reactive T cells.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA851186, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006133	EMG produced TPA metagenomics assembly of PRJNA755428 data set (Green tea polyphenols modulate gut virome diversity).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA755428, and was assembled with metaSPAdes v3.15.3, unknown v0.0. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006127	EMG produced TPA metagenomics assembly of PRJEB40312 data set (Analysis of longitudinal shotgun gut metagenomes and gut metabolites on co-housing treatment to examine link between host metabolism and gut microbes relevant to the pathology of PCOS.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB40312, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006131	EMG produced TPA metagenomics assembly of PRJNA691798 data set (Fecal samples of Listeria monocytogenes infected mice metagenomes Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA691798, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006130	EMG produced TPA metagenomics assembly of PRJNA649861 data set (mouse metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA649861, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00006129	EMG produced TPA metagenomics assembly of PRJNA843121 data set (Mouse gut metagenome in early life exposure to cyanotoxin.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA843121, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00006125	Gut microbiome of IBS patients with personalized dietary intervention	In this study the efficacy of AI-based personalized microbiome diet in patients with IBS-Mix is investigated. 25 IBS-M patients (n=25, 19 females) according to Rome IV criteria were enrolled. Fecal samples were obtained from all patients twice (pre- and post intervention) and high-througput 16S rRNA sequencing was performed.	root:Host-associated:Human:Digestive system
MGYS00006092	EMG produced TPA metagenomics assembly of PRJEB39685 data set (Gut Microbiomes of European Turkey and Veal Calf Herds).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB39685, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Animal:Digestive system:Fecal.	root:Host-associated:Animal:Digestive system:Fecal
MGYS00006056	EMG produced TPA metagenomics assembly of PRJEB49834 data set (The occurrence, prevalence and fate of antibiotic resistant genes and microbial community in Ili river).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB49834, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lotic.	root:Environmental:Aquatic:Freshwater:Lentic
MGYS00006117	Holofood Salmon 16S amplicon sequencing	Holofood Salmon 16S amplicon sequencing	root:Host-associated:Fish:Digestive system
MGYS00006120	Longitudinal Multi'omics of the Human Microbiome in Inflammatory Bowel Disease	The main Inflammatory Bowel Disease (IBD) Multi'omics Database (IBDMDB) study includes multi'omics measurements from over 100 subjects, sampled biweekly over up to a year in both adult and pediatric patients with IBD (Crohn's disease and ulcerative colitis), along with non-IBD controls. Data types include fecal metagenomes, metatranscriptomes, metabolomes, and proteomes, as well as host genetics, intestinal biopsy transcriptomes, epigenetics, and 16S amplicon profiles. Subjects' medical histories and demographics are collected at baseline and medication, diet, and disease activity profiled longitudinally.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006119	MIMS Environmental/Metagenome sample from human gut metagenome	201 Italian elderly EU FP7 NU-AGE project	root:Host-associated:Human:Digestive system
MGYS00006112	16S amplicon sequences of Crete soil meta genomes	Comparison of soil community structure and functional composition across Crete's  vegetation types and ecological zones.	root:Environmental:Terrestrial:Soil
MGYS00006118	EMG produced TPA metagenomics assembly of PRJEB30074 data set (Comparative metagenome analysis of normal and arsenic contaminated soils from ballia district, Uttar Pradesh, India).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB30074, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil.	root:Environmental:Terrestrial:Soil
MGYS00006105	EMG produced TPA metagenomics assembly of PRJNA646227 data set (Samples from fecal pellets of two strains of mouse (HLB444 and Black 6); DNA extractions and mWGS sequences.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA646227, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006101	EMG produced TPA metagenomics assembly of PRJEB9443 data set (Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9443, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006103	EMG produced TPA metagenomics assembly of PRJEB50255 data set (Mouse gut metagenomes at the early stage after weaning).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB50255, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006102	EMG produced TPA metagenomics assembly of PRJEB44042 data set (Kefir ameliorates specific microbiota-gut-brain axis impairments in a mouse model relevant to autism spectrum disorder).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB44042, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006100	EMG produced TPA metagenomics assembly of PRJNA739153 data set (Aging male C57bl/6 mouse gut microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA739153, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006004	Research of extracellular vesicle content from gut microbiome and its’ role in cancer development by applying gut on chip system	The gut microbiota and their products have a critical role in human health and are involved in all physiological processes. It is well now known that altered microflora can lead to the development of various diseases, including malignancies. One of the ways in which these processes in the body are potentially influenced by the microflora is through extracellular vesicles (EVs) and the RNA content in them, but currently research methods for these processes are limited. Classical in vitro methods cannot mimic the entry of the microbiome EV from the intestinal lumen into the circulatory system, but animal models do not fully reflect the processes in the human body and are ethically questionable models for these studies. One of the most promising methods currently in microflora research is the gut on chip (GoC) platform, however so far, the available solution has not been applied and designed for the study of the microbiome EV content. Therefore, the aim of this project is to study EV RNA content of cancer patient microbiome, that can enter from lumen to circulation by applying GoC devices already developed in a collaboration between BMC and ISSP. These results will provide answers to fundamental questions about human-microorganism interactions in the future, as well as give the opportunity to study and testing of clinical microflora samples from different patients for diagnostic and therapeutic purposes.	root:Host-associated:Human:Digestive system:Hindgut
MGYS00006096	Shotgun Metagenomics approach to Identify Biosynthetic Gene-Cluster from forest soil sample.	This study aims to identify biosynthetic Gene-Cluster and taxonomic classification of the microbiome within the sample.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00006109	EMG produced TPA metagenomics assembly of PRJEB9718 data set (Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9718, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006111	The impact of exercise and/or whey protein supplementation on the gut microbiome of sedentary adults: A prospective metagenomic and metabolomic analysis.	Many components of modern living exert influence on the resident intestinal microbiota of humans with resultant impact on host health. For example, exercise-associated changes in gut microbial diversity, composition, and functional profiles have been described in cross-sectional studies of habitual athletes. However, this relationship is compounded by changes in diet that coincide with exercise such as dietary and supplementary protein consumption. To determine whether increasing physical activity and/or increased protein intake modulates gut microbial composition and function, we prospectively challenged healthy but sedentary adults with a short-term exercise regime, with and without concurrent daily whey protein consumption. Metagenomic and metabolomic-based assessments demonstrated modest changes in gut microbial composition and function following increases in physical activity. Significant changes in the diversity of the gut virome were evident in participants receiving daily whey protein supplementation. Results indicate that improved body composition with exercise is not dependent on major changes in gut microbial diversity. The diverse microbial characteristics previously observed in long-term habitual athletes may be a later response to exercise and fitness improvement.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00006110	16S-based metagenomic study of twelve French cheese varieties		root:Engineered:Food production:Dairy products
MGYS00006094	EMG produced TPA metagenomics assembly of PRJNA851847 data set (Mouse gut microbiota macrogenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA851847, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.	root:Host-associated:Mammals:Gastrointestinal tract
MGYS00006098	EMG produced TPA metagenomics assembly of PRJNA650546 data set (Evolution of bacteria in the mouse gut through the selection of genetic variations by dietary extracellular vesicles in bovine milk).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA650546, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006108	EMG produced TPA metagenomics assembly of PRJNA694773 data set (Inhibitory effects of breast milk-derived Lactobacillus rhamnosus Probio-M9 on colitis-associated carcinogenesis by restoration of the gut microbiota in a mouse model).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA694773, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006107	EMG produced TPA metagenomics assembly of PRJNA473429 data set (Effect of Down Syndrome genotype on mouse microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA473429, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006106	EMG produced TPA metagenomics assembly of PRJNA658981 data set (Whole Genome Shotgun Sequencing of Aging GOS-Fed Mouse Microbiota).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA658981, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006095	Metagenomics approach for taxonomic classification and identification of biosynthetic gene-clusters from soil microbiome.	This study focuses on taxonomic classification and functional analysis of Natural Agricultural farmland soil microbiome.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00006062	HoloFood Chicken Caecum Metagenome – deeply sequenced batch	Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken caecum samples. Samples selected for this batch were deeply sequenced, and were randomised among trials (feed), age, and breed to overcome batch effect. The samples in this project contributed to the chicken caecum MAG catalogue (project: PRJEB55374 [ERP140263]).	root:Host-associated:Birds:Digestive system
MGYS00006082	EMG produced TPA metagenomics assembly of PRJNA543206 data set (Chicken metagenome Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA543206, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Fecal.	root:Host-associated:Birds:Digestive system
MGYS00006086	HoloFood Salmon - Trial C Metagenome	HoloFood Salmon - Trial C Metagenome	root:Host-associated:Fish:Digestive system
MGYS00006091	An examination of the intestinal microbiome of pigs divergent in feed efficiency	Alterations between microbial profiles are potentially a key factor influencing feed efficiency in pigs. The objective of this study was to identify if differences in microbial diversity, relative abundance of taxa exist within the intestinal microbiota of pigs divergent in feed efficiency selected from two different farms of origin. Two populations of pigs were used in this study with piglets selected from two different farms of origin (Group A and B). In Group A, the 8 most efficient (LRFI) and 8 least efficient (HRFI) animals were selected for further analysis, while in Group B the 12 most efficient and 12 least efficient were utilised. Colonic digesta was collected from these pigs to analyse the intestinal microbiota using 16S rRNA gene sequencing. 106 of 126 identified taxa in this study differed between groups while a small number of taxa differed based on feed efficiency. Alpha diversity differed between the two groups in this study with pigs from Group A having increased alpha diversity based on Shannon and InvSimpson measures compared to pigs from Group B (P<0.05). Between HRFI and LRFI pigs across the two groups, no differences in any measures of Alpha diversity were identified (P>0.10). In agreement with these findings, beta diversity analysis established that pigs grouped based on farm of origin rather than RFI group.   Within the Bacteroidetes phylum the LRFI pigs had increased BS11 (P<0.05) and tended to have increased Bacteroidaceae (P<0.10) at family level while at genus level the LRFI pigs tended to have increased Bacteroides and CF231 (P<0.10). The increased abundance of these taxa suggest an increased capacity of the more efficient pigs to breakdown feed potentially impacting nutrient digestibility. The changes identified in this study suggest an influence of the microbiome in influencing feed efficiency. However, the differences between groups suggest that these results need to be corroborated in larger studies across multiple environments.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00006087	European grassland soils subjected to multiple disturbances	Sequencing microbial communities from multiple European grassland soils subjected to 4 different lab perturbation regimes- control, heat, drought, or flooding.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00006088	caecal microbiota on rat fed several protein	Ceacal microbiotas in rats fed milk-casein, soy-protein or fish-meal was determined by 16S rRNA gene-DGGE and pyrosequencing with bar-coded primer targeting the bacterial 16S rRNA gene.	root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
MGYS00006037	EMG produced TPA metagenomics assembly of PRJNA435487 data set (Chicken ceacal metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA435487, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.	root:Host-associated:Birds:Digestive system:Ceca
MGYS00006068	Comparision of different commercial library preparations kits for soil metagenomics studies	"In this study, we want to compare the sequencing results using different technology in library preparation in a high diversity custom soil sample. For that, we have selected four different commercial kits including different inputs.
In addition to this, we want to test the behavior of the libraries onto the sequencer in terms of clustering and data output.
It will generate the most accurate workflow to the scientific community in their metagenomic experiments."	root:Environmental:Terrestrial:Soil
MGYS00006042	HoloFood Chicken -- Prior Chicken Illeum	HoloFood Chicken -- Prior Chicken Illeum	root:Host-associated:Birds:Digestive system
MGYS00006085	Iceland Brent Goose May 2022 test metagenomics data	Test run of metagenomics sequencing on a small subset of faecal samples collected from Light-bellied Brent geese in Iceland, May 2022. DNA was extracted from the faecal samples and the NEBNEXT microbiome enrichment kit was used prior to shotgun sequencing on the NovaSeq platform.	root:Host-associated:Birds:Digestive system:Fecal
MGYS00006083	N/A	N/A	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00006079	EMG produced TPA metagenomics assembly of PRJNA417359 data set (A catalogue of chicken gut metagenome and the microbial responses to antibiotic and plant-derived benzylisoquinoline alkaloids).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA417359, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system.	root:Host-associated:Birds:Digestive system
MGYS00006071	Bio-geochemistry of alkaline waste	This project investigates the application advanced molecular biology and bioinformatic techniques to the sustainable management of alkaline wastes. These wastes are produced globally in enormous quantities by societies’ primary industries, including iron, steel and aluminium production, and a significant proportion are dumped. “Aggressive” interventions are energy intensive and disturb a waste during treatment when the most significant risk to human health is airborne dusts. Microbes that occur naturally offer exciting potential to bring about beneficial chemical changes to prevent migration of harmful contaminants from the waste into the wider environment. However, to realise this potential requires better understanding of the occurrence and activity of the microbes in these extreme environments. Using samples from an alkaline waste site, microcosm experiments were established where the desired chemical processes were occurring. Samples from these microcosms are being interrogated using ‘omics’ techniques to understand which microbes and processes are critical to achieve the desired geochemical outcome and how these can be encouraged.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00006076	The effect of dietary bioactive on gut microbiome diversity (DIME) – a pilot study	The DIME study consists of a randomised 2x2 cross-over human intervention where healthy participants (n = 20) are subjected to a diet high in bioactive-rich food for two weeks and a diet low in bioactive-rich food. There is a four-week washout between the two interventions.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006078	EMG produced TPA metagenomics assembly of PRJEB33338 data set (Metagenomics of chicken cecal contents from fast and slower growing birds).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB33338, and was assembled with metaspades v3.13. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00006081	EMG produced TPA metagenomics assembly of PRJNA385038 data set (chicken gut metagenome Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA385038, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system.	root:Host-associated:Birds:Digestive system
MGYS00006080	Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study.	Metal corrosion in seawater has been extensively studied in surface and shallow waters. However, infrastructure is increasingly being installed in deep-sea environments, where extremes of temperature, salinity, and high hydrostatic pressure increase the costs and logistical challenges associated with monitoring corrosion. Moreover, there is currently only a rudimentary understanding of the role of microbially induced corrosion, which has rarely been studied in the deep-sea. We report here an integrative study of the biofilms growing on the surface of corroding mooring chain links that had been deployed for 10 years at ~2 km depth and developed a model of microbially induced corrosion based on flux-balance analysis.	root:Environmental:Aquatic:Marine
MGYS00006074	EMG produced TPA metagenomics assembly of PRJEB1788 data set (Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for  large DNA viruses).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB1788, and was assembled with SPAdes v3.14.1, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00006073	EMG produced TPA metagenomics assembly of PRJEB48889 data set (Multi-omic analysis in a metabolic syndrome porcine model implicates arachidonic acid metabolism disorder as a risk factor for atherosclerosis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB48889, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.	root:Host-associated:Mammals:Digestive system
MGYS00006072	EMG produced TPA metagenomics assembly of PRJNA385855 data set (Temporal sampling of marine metagenomes from Station ALOHA and BATS).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA385855, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00006034	EMG produced TPA metagenomics assembly of PRJNA656268 data set (Bio-GO-SHIP: Global marine 'omics studies of repeat hydrography transects).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA656268, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.	root:Environmental:Aquatic:Marine
MGYS00005730	Study of infant stool samples in the first year of life.	Stool samples were collected from 12 Norwegian infants in the first year of life. This study has whole-genome metagenomic information of several timepoints of these infants.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005968	EMG produced TPA metagenomics assembly of PRJEB43687 data set (Shotgun metagenomic approch to identify the bacterial, archaeaa,virus, fungi and eukaryotes in Northern Indian Ocean).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB43687, and was assembled with metaSPAdes v3.14. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00006064	We fed expanded polystyrene plastic to wharf roach (Ligia exotica), then conducted metagenome sequencing of wharf roach gut to investigate microbiota alternation.	We fed expanded polystyrene plastic to wharf roach (Ligia exotica), then genomic DNA was extracted from wharf roach gut and we conducted metagenome sequencing to investigate microbiota alternation.	root:Host-associated:Arthropoda:Digestive system:Gut
MGYS00006063	EMG produced TPA metagenomics assembly of PRJEB11585 data set (Microbial metagenome sequencing from marine sponges (Spongia sp.), seawater and sediments).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11585, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Mixed.	root:Mixed
MGYS00005757	EMG produced TPA metagenomics assembly of PRJEB34634 data set (Detailed study at the genetic level at bacteria in farm animals, human/animal sewage, sewage treatment works and rivers, to work out the complex network of transmission of important antibiotic-resistant bacteria and antibiotic resistance genes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB34634, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Mixed.	root:Mixed
MGYS00006060	EMG produced TPA metagenomics assembly of PRJEB46254 data set (Deciphering the functional potential of a hypersaline marsh microbial mat community).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB46254, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Saline:Microbial mats.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Saline:Microbial mats
MGYS00006061	EMG produced TPA metagenomics assembly of PRJEB25171 data set (Flood seasonal changes in microbiota evidenced through metagenomes of freshwater lakes from Upper Amazon river basin).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB25171, and was assembled with metaSPAdes v3.15.3, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lake.	root:Environmental:Aquatic:Marine
MGYS00006055	Microbiome Signature in Natural Lakes	The crust of lateritic (canga)  is a particular environment to be a ferruginous complex that inhabiting a high species diversity, high endemism and unique species compositions generally metal-tolerant (see Jacobi et al. 2007). Lakes are formed in the top of Canga which are maintained by local rainfall patterns. Information about  the formation and dynamics of these lakes are scarce, considering that microorganisms play crucial roles in ecosystem functioning, here we aimed to understand the relationship between microbial diversity, functions and environmental parameters that sustain this peculiar amazonian environment. In this study, we compare the taxonomic and functional structure of the microbial communities from sediment in three neighboring lakes on top of the extensive lateritic crust in the southeast Amazon Basin using shotgun metagenome sequencing	root:Environmental:Aquatic:Freshwater:Lake
MGYS00006058	EMG produced TPA metagenomics assembly of PRJEB9740 data set (Shotgun Sequencing of Tara Oceans Polar Cicle DNA samples corresponding to size fractions for  prokaryotes.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9740, and was assembled with metaSPAdes v3.15.3, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00006057	EMG produced TPA metagenomics assembly of PRJNA254927 data set (Freshwater habitats river Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA254927, and was assembled with metaSPAdes v3.15.3, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater.	root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems
MGYS00006054	Multigenerational influences of the Fut2 gene on the dynamics of the gut microbiome in mice	The FUT2 gene encodes an α-1,2-fucosyltransferase responsible for the expression of ABO histo-blood-group antigens on mucosal surfaces and bodily secretions. Individuals who carry at least one functional allele are known as “secretors”, whereas those homozygous for loss-of- function mutations are known as “nonsecretors”. Nonsecretor individuals are more susceptible to chronic inflammatory disorders such as Crohn Disease, which may be mediated by alterations in the microbiome. Here, we investigated the dynamics of microbial community assembly with respect to genotype using a Fut2-deficient mouse model, taking the genotype of the maternal lineage over two generations into account. We found strong differences in community assembly of microbial communities over time, depending on the Fut2 genotype of the host and that of their progenitors. By applying interaction network analyses, we further identified patterns of specialization and stabilization over time, which are influenced by the host and parental genotype during the process of community development. We also show genotype- and breeding-dependent patterns of community susceptibility to disturbance in a novel in silico approach integrating ecological- and network analysis. Our results indicate that it may be important to investigate the influence of Fut2 genotype in a familial context in order to fully understand its role in the etiology of chronic inflammatory disorders.	root:Host-associated:Mammals:Gastrointestinal tract
MGYS00006053	Antibiotic-free conventional mice were inoculated with dysbiotic gut microbiota from both genetic and nutritional obese mice.	We show that antibiotic-free conventional mice inoculated with dysbiotic gut microbiota from both genetic and nutritional obese mice show a beneficial impact on the liver and the adipose tissue. The transfer changes both the gut microbiota and the microbiome of recipient mice.	root:Host-associated:Mammals:Digestive system
MGYS00006049	TLR5 instructs intestinal B cell responses through regulation of flagellin in the gut	Levels of flagellin, the Toll-like receptor 5 (TLR5) ligand, are low and finely regulated in the healthy gut.  TLR5-deficient mice (Tlr5-/-) displays metabolic syndrome driven by pro-inflammatory gut microbiota along with over-production of flagellin by a diversity of intestinal microbes.  This excess flagellin production results in part from abnormally low levels of flagellin-specific antibodies.  The feedback between levels of flagellin, flagellin-specific antibodies and TLR5 signaling is not well understood.  Here, we show that TLR5 deficiency on non-hematopoietic cells is required and sufficient to result in greater levels of bioactive flagellin in gut that occurs without a perturbation to the microbial diversity.  TLR5 deficiency promotes the differentiation of B cells into IgA-secreting plasma cells and reshapes immunoglobulin (Ig) repertoire in the large intestine.  Our data show that modulating microbiota gene expression, instead of altering microbiota community, would be the target for the therapeutic design of regulating intestinal B cell responses.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00006044	EMG produced TPA metagenomics assembly of PRJEB52998 data set (Soil sample transect of Hudson Valley Farm Hub, NY, USA).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB52998, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil:Clay.	root:Environmental:Terrestrial:Soil
MGYS00006052	Spatial heterogeneity of gut microbial composition along the gastrointestinal tract in natural populations of house mice	There is a growing appreciation of the role of gut microbial communities in host biology. However, the nature of variation in microbial communities among different segments of the gastrointestinal (GI) tract is not well understood. Here, we describe microbial communities from ten different segments of the GI tract (mouth, esophagus, stomach, duodenum, ileum, proximal cecum, distal cecum, colon, rectum, and feces) in wild house mice using 16S rRNA gene amplicon sequencing.  We also measured carbon and nitrogen stable isotopic ratios from hair samples of individual mice as a proxy for diet.  We identified factors that may explain differences in microbial composition among gut segments, and we tested for differences among individual mice in the composition of the microbiota. Consistent with previous studies, the lower GI tract was characterized by a greater relative abundance of anaerobic bacteria and greater microbial diversity relative to the upper GI tract. The upper and lower GI tracts also differed in the relative abundances of predicted microbial gene functions, including those involved in metabolic pathways. However, when the upper and lower GI tracts were considered separately, gut microbial composition was associated with individual mice. Finally, microbial communities derived from fecal samples were similar to those derived from the lower GI tract of their respective hosts, supporting the utility of fecal sampling for studying the gut microbiota of mice. These results show that while there is substantial heterogeneity among segments of the GI tract, individual hosts play a significant role in structuring microbial communities within particular segments of the GI tract.	root:Host-associated:Mammals:Gastrointestinal tract
MGYS00006051	Gut microbiota regulate hepatic von Willebrand Factor synthesis and arterial thrombosis via Toll-like receptor-2	The symbiotic gut microbiota plays pivotal roles in host physiology and is associated with the development of cardiovascular diseases, but microbiota-triggered pattern recognition signaling mechanisms impacting thrombosis are poorly defined. Here, we show that germ-free and Toll-like receptor (Tlr) 2-deficient mice have reduced thrombus growth following carotid artery injury relative to conventionally raised controls. Germ-free Tlr2-/- and wild-type mice were indistinguishable, but colonization with microbiota restored a significant difference in thrombus growth between genotypes. We identify reduced plasma levels of von Willebrand Factor (VWF) and reduced VWF synthesis specifically in hepatic endothelial cells as a critical factor that is regulated by gut microbiota and determines thrombus growth in Tlr2-/- mice. Static platelet aggregate formation on the extracellular matrix protein laminin was similarly reduced in germ-free wild-type, Tlr2-/-, and heterozygous Vwf+/- mice with a modest reduction in plasma VWF level. Defective matrix interaction can be restored by exposure to wild-type plasma or to purified VWF involving the VWF integrin binding site. Moreover, administration of VWF rescues defective thrombus growth in Tlr2-/- mice in vivo. These experiments delineate an unexpected pathway, in which microbiota-triggered TLR2 signaling alters the synthesis of pro-adhesive VWF by the liver endothelium and favors platelet integrin-dependent thrombus formation.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00006050	Impact of microcins on the gut microbiota	Fecal samples were collected from mice pre-DSS administration (Day -4), post-DSS administration (Day 0), then on Day 5 post-inoculation of a mouse commensal Escherichia coli strain and either wild-type E. coli Nissle 1917 or an mchDEF mutant. DNA was extracted from each sample, cleaned of DSS, then the 16S rDNA v4 region was amplified from each sample with barcoded primers. Libraries were pooled, then sequenced on an Illumina MiSeq.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00006048	TLR5 instructs intestinal B cell responses through regulation of flagellin in the gut	Levels of flagellin, the Toll-like receptor 5 (TLR5) ligand, are low and finely regulated in the healthy gut.  TLR5-deficient mice (Tlr5-/-) displays metabolic syndrome driven by pro-inflammatory gut microbiota along with over-production of flagellin by a diversity of intestinal microbes.  This excess flagellin production results in part from abnormally low levels of flagellin-specific antibodies.  The feedback between levels of flagellin, flagellin-specific antibodies and TLR5 signaling is not well understood.  Here, we show that TLR5 deficiency on non-hematopoietic cells is required and sufficient to result in greater levels of bioactive flagellin in gut that occurs without a perturbation to the microbial diversity.  TLR5 deficiency promotes the differentiation of B cells into IgA-secreting plasma cells and reshapes immunoglobulin (Ig) repertoire in the large intestine.  Our data show that modulating microbiota gene expression, instead of altering microbiota community, would be the target for the therapeutic design of regulating intestinal B cell responses.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00006047	Gut microbiota regulate hepatic von Willebrand Factor synthesis and arterial thrombosis via Toll-like receptor-2	The symbiotic gut microbiota plays pivotal roles in host physiology. Despite expanding evidence of metabolic alterations contributing to the development of cardiovascular diseases, microbiota-triggered molecular pattern recognition signaling mechanisms which impacting thrombosis are poorly defined. Here, we show that germ-free (GF) mice and mice deficient in the Toll-like receptor 2 (Tlr2) 2 have reduced thrombus growth following carotid arteryafter injury relative to conventionally-raised (CONV-R) wild-type (WT) mice. Tlr2-/- mice raised under GF conditions were indistinguishable from GF WT mice, but colonization of GF WT and GF conventionalized Tlr2-/- mice with a microbiota restored the significant difference in platelet deposition. We identify reduced plasma levels of von Willebrand Factor plasma levels (VWF) and its reduced synthesis specifically in hepatic endothelial cells as the critical factor that determines defective Tlr2-/- platelet deposition in vivo. Platelets from Tlr2-/- mice displayed reduced integrin-mediated VWF binding and diminished adhesion to extracellular matrices in vitro, as seen with thrombosis-protected heterozygous Vwf+/- mice. Administration of VWF rescued defective platelet deposition in Tlr2-/- mice without affecting platelet deposition in WT mice. These experiments delineate an unexpected pathway in which microbiota-triggered TLR2 signaling alters synthesis of pro-adhesive VWF by the liver endothelium and favors platelet-dependent vascular thrombosis.	root:Host-associated:Mammals:Digestive system
MGYS00006046	Thioguanine effects on mice gut microbiota	Male and or female mice were intra-gastrically gavaged daily with either vehicle control or thiopurine drugs (TG or MP). Caecal content (CC), caecal mucosa (CM) and faeces (F) of WT, Hprt-/- and Winnie mice were collected at day 14 post-TG administration at doses of 0, 0.5 mg/kg or 2.5 mg/kg (Winnie only). DNA was extracted from faeces at day 0 and day 14; CM and CC at day 14. DNA extracts were used as the template for PCR-based amplification of the bacterial V1-V3 region of the 16S rRNA gene using a barcoded pyrotagging approach, and sequenced with a Roche 454 FLX+ with titanium chemistry.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00006045	The Gut Microbiota of Wild Mice	The gut microbiota profoundly affects the biology of its host. The composition of the microbiota is dynamic and is affected by both host genetic and many environmental effects. The gut microbiota of laboratory mice has been studied extensively, which has uncovered many of the effects that the microbiota can have. This work has also shown that the environments of different research institutions can affect the mouse microbiota. There has been relatively limited study of the microbiota of wild mice, but this has shown that it typically differs from that of laboratory mice (and that maintaining wild caught mice in the laboratory can quite quickly alter the microbiota). There is also inter-individual variation in the microbiota of wild mice, with this principally explained by geographical location. In this study we have characterised the gut (both the caecum and rectum) microbiota of wild caught Mus musculus domesticus at three UK sites and have investigated how the microbiota varies depending on host location and host characteristics. We find that the microbiota of these mice are generally consistent with those described from other wild mice. The rectal and caecal microbiotas of individual mice are generally more similar to each other, than they are to the microbiota of other individuals. We found significant differences in the diversity of the microbiotas among mice from different sample sites. There were significant correlations of microbiota diversity and body weight, a measure of age, body-mass index, serum concentration of leptin, and virus, nematode and mite infection.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00006043	Metagenomic study of oil sludge contaminated soil	Soil sample has been aseptically collected from Group gathering station(GGS) at Gourisagar, Sivasagar of ONGC(Oil and Natural Gas Corporation), Assam, India. The site from which the soil sample was collected was being contaminated/dumped with crude oil sludge for a very long time(Approximately more than 5 years). The collected soil sample was subjected to metagenomic sequencing and the data obtained will be used for ascertaining how chronic exposure to hydrocarbons will affect the soil microorganisms.	root:Environmental:Terrestrial:Soil:Oil-contaminated
MGYS00003961	Long-term seasonal development in selected lakes of Northeast Germany	Longterm data (up to 9 years) of 8 lakes situated in Northeastern Germany are provided. Samples were taken monthly on average dividing particle-associated (greater than 5.0um) and free-living (less than 5.0um, greater than 0.2um) microbes in the water column and in two lakes in the sediment. The lakes are all located closely to each other but differ in many physicochemical parameters such as pH and conductivity. Thus, similarities as well as dissimilarities of microbial communities are of high interest. One lake (Lake Tiefwaren) was sampled after phosphate restoration.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00006040	16S metagenomics of steppe soils in Western Transbaikalia		root:Environmental:Terrestrial:Soil:Grasslands
MGYS00006027	EMG produced TPA metagenomics assembly of PRJNA530339 data set (Shotgun Metagenomics of 361 post-menopause women reveals gut microbiome change along with the bone loss).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA530339, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system.	root:Host-associated:Human:Digestive system
MGYS00006039	Metagenomics insights into Phylogenetic and Functional Diversity of Halophilic Communities inhabiting solar saltern in North Sinai,  Egypt	"In tropical and subtropical areas around the world, Solar Salterns are artificial shallow
ponds used to manufacture halite (NaCl) from seawater. Multi-pond systems are
commonly used to make them. Saline environments ranging from intermediate to
hyper-saline water (brine) and sediment, the later are characteristic of solar saltern in
North Sinai. Metagenomics by 16S rRNA Illumina amplicon sequencing and
bioinformatical analysis was used to explore the microbial diversity of Solar Saltern
and the halophilic communities were characterized. A total of 237,899 (brine) and
59,680 (sediment) reads were collected. A microbiome featuring Archaea was
discovered using 16S rRNA sequencing (20% from brine and 0.28% from sediment)
The domain Archaea (20%) comprising phylum Euryarchaeota (19.9%) was the most
abundant, followed by Crenarchaeota (0.02%) and Thaumarchaeota (0.01%), while
domain Eubacteria (13.37%) included phylum Proteobacteria (4.5%), Bacteroidetes
(3.7%), Actinobacteria (3.4%), and Firmicutes (3.3%). Eukarya was (1.68%) and
unclassified (64.23%). In sediment Bacteria and Eukarya diversity higher than those
in brine was (47.8%) and (3.38%) respectively, domain Archaea was (0.28%) and
unclassified (48.23%). The study of halophilic microorganisms in solar saltern sheds
light on species that contribute to the ecosystem's biogeochemical cycles. This study
presents a first snapshot for halophilic communities in a hypersaline environment in
north Sinai."	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
MGYS00006038	In this project we would like to study immune responses to African swine fever virus in pigs. We have realized a large animal experiment using two different viruses and pigs with different immune status. We have collected paxgene blood RNA tubes in order to investigate transcriptional changes at different stages of the early immune response.	In this project we would like to study immune responses to African swine fever virus in pigs. We have realized a large animal experiment using two different viruses and pigs with different immune status. We have collected paxgene blood RNA tubes in order to investigate transcriptional changes at different stages of the early immune response.	root:Host-associated:Mammals:Circulatory system:Blood
MGYS00006036	Cattle manure compost metagenome as a source of industrially important enzymes	Compost is an aerobic self-heating environment that houses biological degraders capable of degrading wood, starch, cellulose, lignin, lipids, peptides and other carbohydrates. It has cycle of thermophilic heating and cooling phases due to oxidation of the organic matter into inorganic matter until the maturation where it will be used as a fertilizer. Compost attracts attention as it is readily accessible hotspot for thermophilic microorganisms and its enzymes. The enzymes such as amylases, cellulases, proteases and lipases are being sought in industries and are being replaced with its mesophilic counterparts. Metagenome of manure compost was isolated and sequenced. It revealed abundances of Actinobacteria, proteobacteria, fermicutes lineages	root:Engineered:Solid waste:Composting
MGYS00006035	Analyses of biofilms in drainage water during the construction phase of the Koralm railway tunnel	"During the construction phase of the Koralm railway tunnel several samples from different sites were analysed for the presence of microbes. 16S rDNA amplicon sequencing and subsequent microbial profiling revealed the presence of bacterial consortia typical for the deep continental subsurface dominated by autotrophs, methanotrophs and methylotrophs.
Reference: Koraimann G.; Bischof K. (2022) Characterisation of microbial biofilms from tunnel drainage water. Geomechanics and Tunnelling. 15 (2022), No. 4"	root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
MGYS00006032	COVID-19 asthma microbiome	Asthma is associated with severe outcomes of respiratory viral infections. The airway and oral microbiota play important roles in mediating immune responses to viral infections. This study evaluated differences in the nasopharyngeal and salivary microbiomes between patients with and without pre-existing asthma in response to SARS-CoV-2 infection. We collected samples from coronavirus disease 2019 (COVID-19) patients with asthma and COVID-19 patients without asthma. Using 16S ribosomal RNA sequencing, we characterized the nasopharyngeal and salivary microbiomes and analyzed differences at the community and taxa levels between asthma and non-asthma groups. Our results showed that the nasopharyngeal and salivary microbiomes harbor taxa-level, but not community-level differences between COVID-19 patients with and without asthma.	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00005202	using fecal microbiota composition as a non-invasive diagnostic tool to classify colorectal carcinoma and adenoma.	We profiled the microbiota of 1185 fecal samples of colorectal carcinoma and adenoma patients and normal controls from southeastern China using 16S rRNA Illumina PE sequencing. We built random forest tree based bi-class classifier of CRC and normal and multi-class classifier of cancer, adenomas, and normal, and then test them independently. Batch effects were studied and spike-in methods were proposed as an effective strategy to model such effects and improve the results of multi-class classification. Effects of confounding factors were also studied.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006031	Olive plants bacterial microbiota	We used 16S amplicon metagenomics to characterize the taxonomical composition of bacterial microbiota associated with leaves, fruits, and soil of two olive tree genotypes (Sinopolese and Ottobratica).	root:Host-associated:Plants
MGYS00006030	EMG produced TPA metagenomics assembly of PRJEB48301 data set (Marine aquaculture microbiomes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB48301, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00006029	Exploring the microbiomes of soils associated with contrasting agricultural systems in Colombia	"Soil is one of the most diverse ecosystems on the planet, with a community of interacting bacteria, archaea, viruses, fungi, and protozoa collectively referred to as the ""soil microbiome"". These microorganisms play a crucial role in nutrient cycling, pathogen regulation, and soil carbon sequestration, and have direct and indirect effects on the health of plants and animals in terrestrial ecosystems. Biodiversity characterization has been widely used to reliably monitor and assess the state of the environment. In the last decade, the use of high-throughput sequencing has substantially advanced our understanding of the biogeography and ecology of soil bacterial and fungal communities worldwide. However, a recent review of global publications on soil biodiversity shows that Latin America contributes only 4% of the total information, whereas 87% of soil biodiversity research comes from the Northern Hemisphere. In the present study, samples of soils used for coffee cultivation were collected from 3 geographical zones located in Colombia: Quinchia (Risaralda), El Tambo (Cauca), and Minca (Magdalena) during the year 2021. The samples were processed for DNA extraction (LIMMA Laboratory - Universidad de Los Andes, Colombia) and sequenced (INTA Argentina) to obtain the final sequences. The raw sequences were loaded into ENA/MGnify with free access and subsequently subjected to taxonomic and diversity analysis for bacteria and fungi. This research was funded by the UKRI-BBSRC ""Capacity building for bioinformatics in Latin America"" (CABANA) grant, on behalf of the Global Challenges Research Fund [BB/P027849/1]."	root:Environmental:Terrestrial:Soil
MGYS00005530	Niche partitioning of methanotrophs in stratified lakes	A detailed sampling of the water column in proximity to the oxygen-methane interface of four stratified Swiss lakes was performed. Amplicon sequencing analysis of 16S rRNA and pmoA genes and 16S rRNA and pmoA transcripts was used to investigate the active methane-oxidizing bacteria inhabiting the oxygen-methane resource gradient.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00006026	EMG produced TPA metagenomics assembly of PRJNA801070 data set (Superworm (Zophobas morio) gut microbiome metagenomics).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA801070, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.	root:Host-associated:Insecta:Digestive system
MGYS00002009	EMG produced TPA metagenomics assembly of the Making and breaking DMS by salt marsh microbes (Illumina HiSeq 100bp) (Stiffkey_Saltmarsh_Sediment_SIP_Organosulfur) data set	The Stiffkey_Saltmarsh_Sediment_SIP_Organosulfur Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB1760. This project includes samples from the following biomes : Marine.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00006025	Municipal Solid wastes Metagenome	Following increase in population size, urbanization and human activities, there is poor solid waste management in urban and peri-urban areas, mostly in Sub Sahara Africa. Varieties of solid wastes such as medical waste, domestic waste and industrial waste along with their associated microbes are dumped at the same place. We are witnessing high interaction between wild and domestic animals as well as people in municipal dumps. We hypothesized the municipal dumps to be the driver for the emergence of new pathogens of public health importance. We wanted to know the abundance, diversity and dynamics of bacteria circulating in municipal dumpsite and the associated risks. This knowledge is key towards improved solid waste management, hence mitigation of the associated risks.	root:Engineered:Solid waste
MGYS00006024	Lifestyles and gut microbiome composition	This study contributes to the characterization of the gut microbiome of healthy humans in a Mediterranean population sample.	root:Host-associated:Human:Digestive system
MGYS00006021	Do below-ground genotypes influence above-ground microbiomes of grafted tomatoes?	In this study, we evaluated how below-ground genotypes of plants determine bacterial and fungal community structures in leaves in field conditions. After growing grafted tomato individuals in a filed experiment, we analyzed the leaf microbial community compositions of the sampled tomatoes based on Illumina sequencing. The contributions of below-ground genotypes on the microbiome structures were then evaluated by comparing the community datasets of eight tomato rootstock strains.	root:Host-associated:Plants:Phylloplane
MGYS00006019	Honeybee bacterial community across gut compartments	The gut bacterial microbiome of honeybee (Apis mellifera) was investigated to evaluate the composition and spatial organization in different gut portions. Adult foragers were collected in the late summer from experimental apiaries located at DISAFA (University of Turin, Italy). Microbiological analyses were performed on the dissected guts compartments (i.e. crop, midgut, ileum and rectum) of honeybee workers. High-throughput sequencing of 16S rRNA gene was used to investigate the bacterial communities associated to the gut compartments of this insect.	root:Host-associated:Insecta:Digestive system
MGYS00006022	Honeybee fungal community across gut compartments	The gut fungal microbiome of honeybee (Apis mellifera) was investigated to evaluate the composition and spatial organization in different gut portions. Adult foragers were collected in the late summer from experimental apiaries located at DISAFA (University of Turin, Italy). Microbiological analyses were performed on the dissected guts compartments (i.e. crop, midgut, ileum and rectum) of honeybee workers. High-throughput sequencing of ITS2 region were used to investigate the fungal communities associated to the gut compartments of this insect.	root:Host-associated:Insecta:Digestive system
MGYS00006020	Upper respiratory microbiome during severe SARS-CoV-2 infection	Characterize the upper respiratory microbiome during severe SARS-CoV-2 infection	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00006009	EMG produced TPA metagenomics assembly of PRJEB25419 data set (Breast Cancer Metagenomics).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB25419, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Skin.	root:Host-associated:Human:Skin
MGYS00006018	Microbiome in rhizosphere and endosphere of tomato	Bacterial, archaeal, fungal communities associated with the rhizosphere and endosphere of tomato	root:Host-associated:Plants:Phylloplane
MGYS00006017	The salivary microbiome of COVID-19 inpatients and outpatients	The aim of the study is to analyze the salivary microbiome of COVID-19 inpatients and outpatients using 16S rRNA gene sequencing.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00006016	The gut microbiome 16s rDNA sequencing data of patients with COVID-19	The gut 16s rDNA sequencing data of patients with COVID-19	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006015	Oomycete-Plant Metagenome	The goal of the analyses was to investigate the structure of the bacterial rhizospheric microbiota able to colonize the tomato root-P. parasitica pathosystem. 16S rRNA gene sequencing was used to describe the composition of the rhizospheric sub-microbiota of Solanum lycopersicum able to colonize tomato roots either axenic or partly covered with P. parasitica biofilms. Sampling was performed the 31st of May 2014, on soil supporting tomato growth (Solanum lycopersicum cv. Marmande). The experimental site was an E-W-oriented greenhouse located at the INRA Pathologie Végétale research unit in Montfavet (43.9 N 4.8 E). Thirty rhizospheric samples were grouped by 10 into three biological replicates (R1, R2, R3) on the basis of the distribution of the three samples from each area in distinct replicates. Biosamples results from the incubation and then the adhesion of microbial suspensions from R1, R2 and R3 at the root surface of tomato seedlings. M1R1, M1R2 and M1R3 correspond to the sub-microbiota adhering to axenic roots. M2R1, M2R2 and M2R3 correspond to the sub-microbiota adhering to roots partly covered with P. parasitica biofilms. An amplicon library was constructed (V3-V5 primers) for the six biosamples and sequenced using Illumina MiSeq technology. Sequence data are cleaned according to the FastQC quality parameters.	root:Host-associated:Plants:Root
MGYS00006014	Upper respiratory microbiome during SARS-CoV-2	Characterize the upper respiratory microbiome during mild-to-moderate SARS-CoV-2 infection in adult outpatients.	root:Host-associated:Human:Respiratory system:Nasopharyngeal:Nasal cavity
MGYS00006013	Gut microbiome linked to SARS-CoV-2 infection and COVID-19 severity	The gut microbiota impacts human health and contributes to regulate immune responses. Severe COVID-19 illness is characterized by a pro-inflammatory immune response. The effect of SARS-CoV-2 on altering the gut microbiome and the relevance of the gut microbiome on COVID-19 severity is unclear. This study analyses the gut microbiome associated with SARS-CoV-2 infection and COVID-19 severity.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001349	Bacterial microbiota in roots of Arabidopsis thaliana and relative Brassicaceae species	Plants host at the contact zone with soil a distinctive root-associated bacterial microbiota believed to function in plant nutrition and health. We investigated the diversity of the root microbiota within a phylogenetic framework of hosts: three Arabidopsis thaliana ecotypes along with its sister species Arabidopsis halleri and Arabidopsis lyrata as well as Cardamine hirsuta, which diverged from the former ~35 myr ago. We surveyed their microbiota under controlled environmental conditions and of A. thaliana and C. hirsuta in two natural habitats. Deep 16S rRNA gene profiling of root and corresponding soil samples identified a total of 237 quantifiable bacterial ribotypes, of which an average of 73 community members were enriched in roots. The composition of this root microbiota depends more on interactions with the environment than with host species. Inter-host species microbiota diversity is largely quantitative and is greater between the 3 Arabidopsis species than the 3 A. thaliana ecotypes. Host species-specific microbiota were identified at the levels of individual community members, taxonomic groups and whole root communities. Most of these signatures were observed in the phylogenetically distant C. hirsuta. However, the branching order of host phylogeny is incongruent with inter-species root microbiota diversity, indicating that host phylogenetic distance alone cannot explain root microbiota diversification. Our work reveals within 35 myr of host divergence a largely conserved and taxonomically narrow root microbiota, which comprises stable community members belonging to the Actinomycetales, Burkholderiales and Flavobacteriales.	root:Host-associated:Plants:Root
MGYS00006012	microbiome analysis for patietns with COVID-19	To conduct research that contributes to the control of COVID-19 infections and to contribute to society.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006011	16S rRNA amplicons from Ambargasta salt flat soil	Characterization of the halophilic microbial communities of an argentinian Salt Flat by 16sRNA amplicons	root:Environmental:Terrestrial:Soil
MGYS00006010	Influence of the Herbicide Glyphosate on the bacterial community present in a sample from an Argentine salt flat	In this study, soil samples from an Argentine salt flat with added glyphosate were cultured to study halophilic strains capable of surviving and growing under these conditions.	root:Environmental:Terrestrial:Soil
MGYS00005260	Effect of crop rotation and straw addition on microbial communities in rhizosphere and bulk soil	In this study, we analysed soil microbial responses to different crop rotation systems (rice-rice (RR), maize-maize (MM), rice-maize (MR)) and rice straw mulching in the rhizosphere of Zea maize and the surrounding bulk soil. Soils were collected from different field locations subjected to the different crop rotation systems and Zea maize were planted in a microcosm experiment. The bacterial and fungal community composition was analysed by 16S rRNA gene and ITS based amplicon sequencing.	root:Host-associated:Plants:Rhizosphere
MGYS00005227	The rhizoplane/endosphere of wild Arabidopsis accessions	To investigate the role of plant genes in shaping root-associated microbial communities, we grew wild Arabidopsis thaliana accessions in a field site where the model is known to occur. Because Arabidopsis predominantly occurs as a winter annual, we grew the plants from October until late March (~156 days). At the end of the field experiment, we collected the plants using sterile technique and plants were separated at the root collar. Samples were then flash frozen in the field before being stored at -80C.To characterize the bacteria and fungi in the rhizoplane and endosphere of the roots, samples were washed in phosphate buffer. PCR amplification and sequencing of ITS1 and the hypervariable regions V5-7 of 16S rDNA was used to characterize the bacteria and fungi of these samples.	root:Host-associated:Plants:Rhizoplane:Endophytes
MGYS00005384	Human skin bacterial metagenome and Virome Metagenome	Viruses can impact microbiome structure and function through predation and genetic exchange, but little is known of cutaneous viral communities and their interactions with their hosts. To query virus-host interactions of the skin, we performed parallel metagenomic sequencing and an integrated analysis of DNA isolated from virus-like particles (VLPs) and total microbial communities. To assess spatial, interpersonal, and temporal variance, samples were collected from eight anatomical skin sites of 16 healthy individuals over two months. Skin viral communities were dominated by tailed bacteriophages--viruses replicating on human cells were comparatively rare. Similar to the skin whole metagenome, viral community composition and diversity was strongly associated with the microenvironment of the site sampled, and temporal variation within an individual was small compared to differences between individuals. Virome communities were enriched for genes indicative of a temperate phage replication style, indicating that many infections would be non-lethal to the host and provide an opportunity for gene transfer. CRISPR spacers identified in the bacterial DNA sequences provided a record of phage predation. Among these, some spacers targeted phage found at different body sites, suggesting that CRISPR spacer acquisition may provide a mechanism to explain spatial partitioning of skin phage communities. Our findings provide new insight into the skin virome, its interactions with the whole metagenome, and establish a foundation for understanding these dynamics in skin health and disease.	root:Host-associated:Human:Skin
MGYS00002020	EMG produced TPA metagenomics assembly of the Metagenome sequencing of the Hadza hunter-gatherer gut microbiota. (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA278393. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system
MGYS00002012	EMG produced TPA metagenomics assembly of the metagenome fecal microbiota, Ilumina seq reads of 12 individuals at 2 timepoints (EKmeta) data set	The EKmeta Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6092. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system
MGYS00005160	Contrasting diversity and host association of ectomycorrhizal basidiomycetes versus root-associated ascomycetes in a dipterocarp rainforest	Ectomycorrhizal basidiomycetes and root-associated ascomycetes, including root-endophytic ascomycetes, are one of the most diverse and important belowground plant symbionts in dipterocarp rainforests. Our study aimed to compare the biodiversity, host association pattern, and community structure of ectomycorrhizal basidiomycetes with those of root-associated ascomycetes in a lowland dipterocarp rainforest in Southeast Asia. The host-plant chloroplast large-subunit of ribulose-1,5-bisphosphate caboxylase/oxygenase (rbcL) region, and fungal internal transcribed spacer 2 (ITS2) region were sequenced using a tag-encoded, massively parallel 454 pyrosequencing analysis to identify host plant and root-associated fungal taxa in root samples. In total, 1245 ascomycetous and 127 putative ectomycorrhizal basidiomycetous taxa were detected from 442 root samples. The putative ectomycorrhizal basidiomycetes  were likely to be associated with phylogenetically closely related dipterocarp taxa to greater or lesser extents, whereas host association patterns of the root-associated ascomycetes were much less distinct. The community structure of the putative ectomycorrhizal basidiomycetes was possibly more influenced by the host genetic distances than that of the root-associated ascomycetes. This study also indicated that in dipterocarp rainforests, root-associated ascomycetes were characterized by high biodiversity and indistinct host association patterns, whereas ectomycorrhizal fungi showed less biodiversity and a strong host phylogenetic preference for dipterocarp trees. Our findings suggested that root-associated ascomycetes (e.g., root-endophytic ascomycetes, may have biodiversity hotspots in the tropics, whereas biodiversity of ectomycorrhizal basidiomycetes increased with host phylogenetic diversity.	root:Host-associated:Plants:Root
MGYS00006008	EMG produced TPA metagenomics assembly of PRJEB3227 data set (Follow-up of faecal microbiota in IBS patients).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB3227, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000983	Diversity and activity of soil bacterial communities in the rhizophere of poplars from different origins	The direct isolation of total RNA and DNA from soil samples and its analysis by sequencing with high through-put techniques (454-pyroseqencing) are useful tools for metagenomic and metatranscriptomic analyses. It provides insights into the diversity and the ecosystem function of microbial communities. Furthermore, the metatranscriptomic approach provides an opportunity to detect novel genes, which might encode key functions for important biogeochemical cycles. The aim of this study was to examine the soil structure of bacterial communities in the rhizospheres of poplars from different origins. In addition the seasonal change of the bacterial community composition was investigated. In a second experiment the influence of fertilization on total and active bacterial communities was validated.  Thsi Project was funded by the State of Lower Saxony (Ministry of Science and Culture).	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00005805	EMG produced TPA metagenomics assembly of PRJEB1690 data set (This is a metagenomic study to investigate the microbial community and metabolic functions of Korean twin pairs.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB1690, and was assembled with metaSPAdes v3.13.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005264	Contribution of endophytic fungi to leaf litter communities	Endophytic fungi colonize healthy plant tissues without causing any signs of infection or damage to the host plant. Fungal endophytes are taxonomically diverse and inhabit all plant species analysed so far. Their ecological roles and the host-microbe interactions remain unclear; in particular for endophytes of forest trees. Composition of endophytic assemblages is unstable in time and affected by host identity, organ and tissue type, geographical location and environmental factors. Many endophytic fungi are also known as saprobes occurring in decomposing litter. They are supposed to enter a latent stage in the plant tissues and participate in nutrient cycling of forest ecosystems by decomposing plant litter.The main objective of this project is to study the contribution on litter decomposition by formerly endophytic fungi in forests dominated by Fagus sylvatica. The contribution of endophytic fungi is assessed in dependence of geographic location, spatial scale and forestry measures. Their contribution is compared against to litter-indigenous communities.In order to achieve our goals, we used Next Generation Sequencing to assess composition of the present and active communities via amplification of barcoding markers from DNA and RNA extracts, respectively.	root:Host-associated:Plants:Phylloplane:Endophytes
MGYS00006005	Characterization of the faecal microbiome of osteoporotic patients in Koreans	The main objective of this study was to discover the biomarkers of osteoporosis in human stool by comparing the gut microbiota of osteoporosis patients (OP) and normal human controls (HC). We collected 76 stool samples, 60 HC and 16 OP patients, examined using 16S ribosomal ribonucleic acid (rRNA) gene-based amplicon sequencing. The microbial communities of the two groups differed at lower taxonomical ranks. The data showed a significantly higher averaged taxonomic composition of Lachnospira in OP than HC among taxa.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005240	Complex community structure of ectomycorrhizal, arbuscular-mycorrhizal and root-endophytic fungi in a mixed subtropical forest of ectomycorrhizal and arbuscular-mycorrhizal plants	Most terrestrial plants interact with diverse clades of mycorrhizal and root-endophytic fungi in their roots. Through the below-ground plant_fungal association, dominant plants can benefit by interacting with host-specific mutualistic fungi, while subordinate plant species may persist by sharing other sets (ecotypes) of fungal symbionts with each other. Therefore, the host preference of root-associated fungi is the key to understand plant community structure and dynamics. Based on 454-pyrosequencing, we revealed the root-associated fungal community on co-occurring 36 plant species in an oak-dominated forest in northern Japan, and statistically evaluated the host preference of diverse mycorrhizal and root-endophytic fungi. The analysis of 278 fungal taxa indicated that several taxa in the ectomycorrhizal family Russulaceae and the ecologically-diverse ascomycete order Helotiales had significant host preference for the dominant oak (Quercus) species. On the other hand, arbuscular-mycorrhizal fungi were shared mainly among subordinate plant species. While these fungi with host preference contributed to compartmentalize the below-ground plant_fungal associations, diverse clades of ectomycorrhizal fungi and possible root-endophytes associated not only with the dominant Quercus but also with the remaining plant species. Our findings suggest that dominant and subordinate plant species can host different subsets of root-associated fungi, while diverse clades of generalist fungi can counterbalance the compartmentalization of plant_fungal associations. Such insights into the overall structure of plant_root-associated fungal associations will enable us to understand the mechanisms that facilitate the co-existence of plant species in natural communities.	root:Host-associated:Plants
MGYS00003962	Bacterial Community Spatial and Temporal Variation in a North Temperate Bog Lake	Bog lakes such as Mary Lake in northern Wisconsin are ideal systems to investigate microbial communities due to easily identified spatial boundaries and well characterized seasonal ecosystem dynamics. Multiple factors are thought to influence the bacterial communities within the lake, and our goal in this study was to analyze the spatial and temporal factors causing the variations between these populations. Molecular techniques and statistical analyses were performed to gain insight into which differences caused the greatest variability. The bacterial communities were analyzed based on conserved 16S ribosomal RNA sequences as well as on short base pair sequence reads obtained from a time series in 2009 in order to determine whether the bacterial community was more variable in space or in time. We found that while the upper and lower thermal layers of the bog were composed of similar microbial communities, these communities had different temporal patterns throughout the time series.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00005204	Community-scale properties of arbuscular mycorrhizal, ectomycorrhizal, and endophytic associations in temperate and subtropical forests	Based on high-throughput sequencing of root-associated fungi in forest ecosystems, we performed a comparative analysis of arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic associations across a latitudinal gradient from cool-temperate to subtropical regions.	root:Host-associated:Plants:Root
MGYS00006003	This is a test on a couple of samples from a bigger metagenomics study	In order to understand MGnify functionalities, as well as check and process its results with MGnifyR, we have decided to run a trial on a couple of samples that had its sequencing content reduced. Established methods and obtained results from this trial will guide us on a better assessment of the full dataset.	root:Environmental:Terrestrial:Soil
MGYS00001070	The daily dynamics of the vaginal microbiota before and after bacterial vaginosis	Bacterial vaginosis (BV) is a condition characterized by a dysbiotic state of the vaginal microbiota that could be accompanied with symptoms such as odor and discharge, but not always. Despite years of research, the etiology of BV is unknown, certainly due to our poor understanding of the vaginal microbiota prior to a BV event. Here we report on the characterization of the vaginal microbiota from samples collected prospectively and daily over 10 weeks in women who experience symptomatic BV (15 women) or asymptomatic BV (5 women), as well as from women who did not experience BV (4 women). This resource is unique, and we hope will contribute to a better understanding of the role that the vaginal microbiota play in the etiology of BV and ultimately to improve diagnostics and treatments.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00006002	EMG produced TPA metagenomics assembly of PRJEB24129 data set (Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB24129, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Engineered:Food production:Fermented beverages.	root:Engineered:Food production:Fermented beverages
MGYS00001347	16S rRNA amplicons (V4 region) of bacteria living on and in roots and leaves of Boechera stricta from field experiments in the Rocky Mountains	Bacteria living on and in leaves and roots influence many aspects of their hosts’ health, so the extent of plant genetic control over their microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies may overestimate the influence of certain plant genes on the microbiome and fail to detect others, because they do a poor job simulating true environmental heterogeneity. We conducted a large-scale field experiment to disentangle the effects of genotype, environment, age, and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta, a wild perennial mustard.  Genetic control of the microbiome varied substantially among sites, and bacterial community composition shifted as plants aged. Furthermore, a large proportion of leaf bacteria were shared with roots, suggesting inoculation from soil. Our results highlight the complexity of microbiome formation in natural environments.	root:Host-associated:Plants
MGYS00005176	Infant Microbiota and Probiotic Intake Study (IMPRINT)	The purpose of this study is to determine if supplementing healthy term infants delivered by C-section or vaginal delivery who only consume breastmilk with a probiotic for 21 consecutive days increases levels of bacteria in infants'' stool.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005236	Human genetics shape the gut microbiome	Host genetics and the gut microbiome can both influence host metabolic phenotypes. However, whether host genetic variation shapes the gut microbiome and interacts with it to affect host phenotype is unclear. Here, we addressed this question by comparing microbiotas across more than 1,000 fecal samples obtained from members of the TwinsUK population, including 416 twin-pairs. We identified a variety of microbial taxa whose abundances were influenced by host genetics. The most heritable taxon, the family Christensenellaceae, formed a co-occurrence network with other heritable Bacteria and with methanogenic Archaea, and was enriched in individuals with low BMI. Addition of Christensenella minuta to an obese donor???s fecal microbiome resulted in reduced weight gain and an altered fecal microbiota in recipient germfree mice. Our findings indicate that host genetics influence the composition of the human gut microbiome and can do so in ways that impact host metabolism.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00006001	Impact of conservative agricultural practices on soil microbial communities in South Africa	The study compares microbial communities from soil under contrasting agronomical practices in different locations of South Africa.	root:Environmental:Terrestrial:Soil
MGYS00005999	EMG produced TPA metagenomics assembly of PRJEB34573 data set (Metagenomic analysis with long and short reads of 20 biogas reactors).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB34573, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Engineered:Biogas plant.	root:Engineered:Biogas plant
MGYS00006000	Metagenomic analysis with long and short reads of 20 biogas reactors	The spread of antimicrobial resistance has been identified as one of the greatest threats to public health. Various factors, such as antibiotic consumption and antibiotic control in human and industrial use, as well as wastewater treatment and waste management play a cruicial role in the dissemination of antibiotic resistance. Mobile genetic elements, such as plasmids, gene cassettes and / or integrons on which most of the resistance genes are located, are readily transmissible resistance gene reservoirs, which also allow gene exchange between non-pathogenic and pathogenic bacterial species and vice versa. This has been increasingly observed in sewage treatment plants. The aim of this work is to investigate whether microbial diversity and density in biogas plants promote the transmission and distribution dynamics of resistance genes or whether the e. g. occasionally extreme fermentation conditions such as increased ammonium content, thermal pre-treatment, and elevated process temperatures prevents transfer or uptake of mobile DNA elements. For this purpose, the resistome of influence and effluence of various biogas processes will be analyzed using High-throughput and Long-Read Sequencing Technology.	root:Engineered:Biogas plant
MGYS00004729	Nasopharyngeal_microbiota_in_Maela_Thailand	"A longitudinal study was undertaken for 21 infants living in the Maela refugee camp on the Thailand-Burma border between 2007 and 2010. Nasopharyngeal swabs were collected monthly, from birth to 24 months of age, with additional swabs taken if the infant was diagnosed with pneumonia according to WHO clinical criteria. At the time of collection, swabs were cultured for Streptococcus pneumoniae and multiple serotype carriage was assessed. The 16S rRNA gene profiles of these 544 swabs were analysed to see how the microbiota changes with age, respiratory infection, and pneumococcal acquisition. 

This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/about/who-we-are/policies/open-access-science"	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00005989	EMG produced TPA metagenomics assembly of PRJNA466874 data set (Freshwater microbial communities from Lake Lanier, Atlanta, Georgia, United States - LL-1505 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA466874, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lake.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00005987	EMG produced TPA metagenomics assembly of PRJNA506221 data set (Microbial diversity and function in Antarctic paleomats).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA506221, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Ice:Glacial lake.	root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
MGYS00005985	EMG produced TPA metagenomics assembly of PRJNA593593 data set (Sewage microbial communities from Oakland, California, United States - Biofuel Metagenome 10).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA593593, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Engineered:Wastewater.	root:Engineered:Wastewater
MGYS00005983	EMG produced TPA metagenomics assembly of PRJNA669352 data set (Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA669352, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Engineered:Lab enrichment:Defined media.	root:Engineered:Lab enrichment:Defined media
MGYS00005981	EMG produced TPA metagenomics assembly of PRJNA673084 data set (Metagenomic analysis of microorganisms from Movile Cave - Romania).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA673084, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs.	root:Environmental:Aquatic:Thermal springs
MGYS00005789	EMG produced TPA metagenomics assembly of PRJNA366267 data set (Hot spring thermophilic microbial communities from Obsidian Pool, Yellowstone National Park, USA - site 3 B9 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA366267, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005998	Sewage microbial communities from Oakland, California, United States - Biofuel Metagenome 11	Sewage-derived enrichment culture (anaerobic medium, 0.1% glucose), biofilm phase	N/A
MGYS00005997	EMG produced TPA metagenomics assembly of PRJNA593594 data set (Sewage microbial communities from Oakland, California, United States - Biofuel Metagenome 11).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA593594, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Engineered:Wastewater.	root:Engineered:Wastewater
MGYS00005823	EMG produced TPA metagenomics assembly of PRJNA650216 data set (PMC 728.11_cyano).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA650216, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater.	root:Environmental:Aquatic:Freshwater
MGYS00005993	EMG produced TPA metagenomics assembly of PRJNA605948 data set (Candidatus Udaeobacter sp. isolate:AEW3 Genome sequencing and assembly).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA605948, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil:Forest soil.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00003080	DDCA-metagenome	Evaluation of biodiversity and prediction of environmental changes by digital dna chip for establishment of core technology for the preservation and regeneration of marine biodiversity and ecosystems	root:Environmental:Aquatic:Marine
MGYS00005996	EMG produced TPA metagenomics assembly of PRJNA563062 data set (Gut microbiome of Capybara (Hydrochoerus hydrochaeris) Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA563062, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.	root:Host-associated:Mammals:Digestive system
MGYS00005995	Correlations between shower hoses biofilm microbiome and its functions and the presence of Legionella spp.	Building plumbing systems are engineered environments in which some opportunistic pathogenic bacteria proliferate in complex biofilms, interacting and finding niches within resident microbial communities. Among these, Legionella spp. are the most reported waterborne pathogen associated with disease in industrialized countries. In this study, Shotgun sequencing has been performed on the DNA coming from shower hoses biofilms collected in different locations in Switzerland. The primary aim  of the work is to be able to correlate the microbiome compositions and specific functional annotation to the differential abundance of Legionella in the samples collected. This will help getting more insights about the ecology of Legionella and possibly identify conditions that can favour or not the growth of the opportunistic pathogen in plumbing systems.	root:Environmental:Aquatic:Freshwater:Storm water:Drainage pipe biofilm
MGYS00005994	Candidatus Udaeobacter sp. isolate:AEW3 Genome sequencing and assembly	A metagenome assembled genome was assembled from metagenomic DNA of cells which were prior to DNA extraction exposed to antibiotic pressure and separated from the soil matrix.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00005992	Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system	Assembling microbial and phage genomes from metagenomes is a powerful and appealing method to understand structure-function relationships in complex environments that are dominated by uncultured and/or under-studied groups. This study aimed to investigate the impact of incorporating long-read data into the process of reconstructing metagenome-assembled genomes (MAGs) from a complex groundwater aquifer. We generated shotgun metagenomes with traditional Illumina sequencing accompanied by long reads derived from the Oxford Nanopore sequencing platform. This work provides quantitative data to inform a cost-benefit analysis on the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups. Groundwater was collected from the Hainich Critical Zone Exploratory, a near-surface aquifer transect that is established in NW Thuringia, Germany. This data set is part of the DFG-funded CRC AquaDiva (https://www.aquadiva.uni-jena.de/) of the Friedrich Schiller University Jena.	N/A
MGYS00005991	EMG produced TPA metagenomics assembly of PRJEB35315 data set (Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB35315, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Groundwater.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00005990	Freshwater microbial communities from Lake Lanier, Atlanta, Georgia, United States - LL-1505 metagenome	Freshwater microbial communities from Lake Lanier, Atlanta, Georgia, United States	root:Environmental:Aquatic:Freshwater:Lake
MGYS00005988	Microbial diversity and function in Antarctic paleomats	Dessicated microbial mats that are thousands of years old found in the McMurdo Dry Valleys in Antarctica provide a unique opportunity to study the effects of prolonged desiccation on microbial composition and function. The goal of this work is to understand which microbes form these mats, whether they are transcriptionally active, and what mechanisms microbial cells use for long-term survival under extremely harsh conditions, with implications for our understanding of cell biology, Antarctic microbiology and biogeography, and the limits of life in cold, arid environments.	root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
MGYS00005986	Sewage microbial communities from Oakland, California, United States - Biofuel Metagenome 10	Sewage-derived enrichment culture (anaerobic medium, 0.1% glucose), planktonic phase	root:Engineered:Wastewater
MGYS00005984	Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants	Using short- and long-read to reveal microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants	root:Engineered:Lab enrichment:Defined media
MGYS00005982	Metagenomic analysis of microorganisms from Movile Cave - Romania	Samples were collected from Movile Cave (Romania) for metagenomic analysis to study microorganisms forming benthic or floating microbial mats. Emphasis was made to assemble the full genome of a Thiovulum sp. dominating veil-like structures close to the surface of a hypoxic air bell known as Air Bell 2.	root:Environmental:Aquatic:Thermal springs
MGYS00005980	marine metagenome Genome sequencing and assembly	The genome sequence of marine Synechococcus strain MITS9220 was obtained by Illumina and Oxford Nanopore MinIon sequencing. The MITS9220 culture used was non axenic and thus contained additional heterotrophic bacteria. The complete genome of one of the heterotrophic bacteria was also assembled; it belongs to the genus Thalassospira. In addition, assembly generated the complete genome of a cyanophage that also occurred in the MITS9220 culture.	N/A
MGYS00005979	EMG produced TPA metagenomics assembly of PRJNA623799 data set (marine metagenome Genome sequencing and assembly).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA623799, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon
MGYS00002024	EMG produced TPA metagenomics assembly of the Gut microbial metabolism shifts towards a more toxic profile with supplementary iron in a kinetic model of the human large intestine (TIM2_iron_study) data set	The TIM2_iron_study Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6542. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon
MGYS00005963	Metagenomics of Diamante Hot Spring	Metagenomics of Diamante Hot Spring	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005977	EMG produced TPA metagenomics assembly of PRJNA530103 data set (Viral metagenome groundwater aquifer).	TheThird Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set SRP189971, and was assembled with metSPAdes(v3.13.0).	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00005978	Viral metagenome groundwater aquifer	Viral DNA metagenome from three pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00005962	Metagenomics of Carachipampa microbialite	Metagenomics of Carachipampa microbialite	root:Environmental:Aquatic:Non-marine Saline and Alkaline
MGYS00005976	Hot spring thermophilic microbial communities from Obsidian Pool, Yellowstone National Park, USA - site 3 bottle 8 metagenome		N/A
MGYS00003602	EMG produced TPA metagenomics assembly of the Hot spring thermophilic microbial communities from Obsidian Pool, Yellowstone National Park, USA - site 3 bottle 8 metagenome (hot springs metagenome) data set.	The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366343.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00002316	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from China - AD_SCU002_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340752.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Industrial wastewater
MGYS00005975	Hot spring and microbial mat streamer communities from Octopus Spring Streamers, Yellowstone National Park, USA - OCT_B metagenome		N/A
MGYS00002328	EMG produced TPA metagenomics assembly of the Hot spring and microbial mat streamer communities from Octopus Spring Streamers, Yellowstone National Park, USA - OCT_B metagenome (hot springs metagenome) data set.	The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366312.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005974	Hot spring sediment bacterial and archeal communities from California, USA to study Microbial Dark Matter (Phase II) - Elbow Spring sediment metaG metagenome	Sequencing as part of the Microbial Dark Matter project phase II project	N/A
MGYS00002327	EMG produced TPA metagenomics assembly of the Hot spring sediment bacterial and archeal communities from California, USA to study Microbial Dark Matter (Phase II) - Elbow Spring sediment metaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364782.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005973	Hot spring sediment microbial communities from Zodletone spring, Oklahoma to study Microbial Dark Matter (Phase II) - Zodletone Spring source 2m metaG metagenome	Microbial Dark Matter project phase II - Metagenome sequencing of Hot spring sediment microbial communities	N/A
MGYS00002325	EMG produced TPA metagenomics assembly of the Hot spring sediment microbial communities from Zodletone spring, Oklahoma to study Microbial Dark Matter (Phase II) - Zodletone Spring source 2m metaG metagenome (hot springs metagenome) data set.	The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364990.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005972	Hot spring sediment bacterial and archeal communities from California, USA to study Microbial Dark Matter (Phase II) - Blank Spring sediment metaG metagenome	Sequencing as part of the Microbial Dark Matter project phase II project	N/A
MGYS00002680	EMG produced TPA metagenomics assembly of the Hot spring sediment bacterial and archeal communities from California, USA to study Microbial Dark Matter (Phase II) - Blank Spring sediment metaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364781.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005319	EMG produced TPA metagenomics assembly of the Marine microbial communities from oxygen minimum zone in mesopelagic equatorial Pacific - METZYME_3_550m metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330041.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root
MGYS00005370	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Ebb tide non-ETM metaG S.743 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365277.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00005366	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110404 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365007.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005971	Subseafloor sediment microbial communities from Guaymas Basin, Gulf of California, Mexico - Guay16, Core 4569-2, 12-15 cm metagenome	Subseafloor sediment microbial communities from the background core at a depth of 12-15 cm, 2000m below sea level	N/A
MGYS00005362	EMG produced TPA metagenomics assembly of the Subseafloor sediment microbial communities from Guaymas Basin, Gulf of California, Mexico - Guay16, Core 4569-2, 12-15 cm metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406719.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00005970	Polyethylene film was incubated in situ marine condition	The present study determines the microbes involved in biofilm formation on polyethylene plastic which was pre-incubated for 6 months in marine conditions and to know the plastic degrading microbial communities, their function, and their role in quorum sensing.	root:Engineered:Lab enrichment:Defined media
MGYS00005969	Shotgun metagenomic approch to identify the bacterial, archaeaa,virus, fungi and eukaryotes in Northern Indian Ocean	Shotgun metagenomic approch to identify the bacterial, archaeal,virus, fungi and eukaryotes in Northern Indian Ocean. The surface and chlorophyll max depth water samples were collected during the monsoon in the Arabian Sea. The water samples were filtered in 0.2 micron filter sterivex and the DNA was extracted using qiagen blood and tissue dna extraction kit. The metagenome sequence were carried out in Illumina HiSeq platform.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005965	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_s16 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005964	EMG produced TPA metagenomics assembly of PRJNA365135 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_s16 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365135, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005961	metagenomics of Laguna Verde micribialites	metagenomics of Laguna Verde micribialites	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Saline
MGYS00000462	Ocean Sampling Day (OSD) 2014: AUTHORITY-RAW amplicon and metagenome sequencing study from the June solstice in the year 2014	Sequencing of amplicon and metagenome samples from the main OSD event, representing joint effort of marine sampling stations around the world. The OSD campaign aims to analyze marine microbial community compositions and embedded functional traits on a single day, the solstice on 2014-06-21.	root:Environmental:Aquatic:Marine
MGYS00005960	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG Antarct_66 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005959	EMG produced TPA metagenomics assembly of PRJNA365148 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG Antarct_66 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365148, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005958	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG Antarct_38 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005957	EMG produced TPA metagenomics assembly of PRJNA365146 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG Antarct_38 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365146, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005956	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_51 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005955	EMG produced TPA metagenomics assembly of PRJNA365145 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_51 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365145, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005954	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_904 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005953	EMG produced TPA metagenomics assembly of PRJNA365144 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_904 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365144, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005952	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_908 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005951	EMG produced TPA metagenomics assembly of PRJNA365143 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_908 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365143, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005950	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_906 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005949	EMG produced TPA metagenomics assembly of PRJNA365142 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_906 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365142, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005948	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_s17 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005947	EMG produced TPA metagenomics assembly of PRJNA365141 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_s17 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365141, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005946	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_M9 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005945	EMG produced TPA metagenomics assembly of PRJNA365140 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_M9 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365140, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005944	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_b05 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005943	EMG produced TPA metagenomics assembly of PRJNA365139 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_b05 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365139, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005942	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_s6 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005941	EMG produced TPA metagenomics assembly of PRJNA365138 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_s6 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365138, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005940	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_s2 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005939	EMG produced TPA metagenomics assembly of PRJNA365137 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_s2 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365137, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005938	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_s12 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005937	EMG produced TPA metagenomics assembly of PRJNA365136 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_s12 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365136, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005936	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_231 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005935	EMG produced TPA metagenomics assembly of PRJNA365134 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_231 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365134, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005934	Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_215 metagenome	Identifying viral communities during a global deep-ocean expedition	N/A
MGYS00005933	EMG produced TPA metagenomics assembly of PRJNA365133 data set (Marine viral communities from the Global Malaspina Expedition - Malaspina viral metaG DeepMed_215 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA365133, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005932	Deep ocean microbial communities from the Global Malaspina Expedition - Deep seawater metaT blank metatranscriptome	Metatranscriptomic analysis of samples from a global deep-ocean expediton	N/A
MGYS00005931	EMG produced TPA metagenomics assembly of PRJNA405604 data set (Deep ocean microbial communities from the Global Malaspina Expedition - Deep seawater metaT blank metatranscriptome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA405604, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005930	Marine microbial communities from the Deep Atlantic Ocean - MP0103 metagenome		N/A
MGYS00003263	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0103 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330076.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005929	Marine microbial communities from the Deep Atlantic Ocean - MP0104 metagenome		N/A
MGYS00003262	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0104 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330127.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005928	Marine microbial communities from the Deep Atlantic Ocean - MP0203 metagenome		N/A
MGYS00003261	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0203 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329987.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005927	Marine microbial communities from the Deep Atlantic Ocean - MP0204 metagenome		N/A
MGYS00003260	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0204 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330139.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005926	Marine microbial communities from the Deep Atlantic Ocean - MP0145 metagenome		N/A
MGYS00003259	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0145 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330017.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005925	Marine microbial communities from the Deep Atlantic Ocean - MP0261 metagenome		N/A
MGYS00005924	EMG produced TPA metagenomics assembly of PRJNA330153 data set (Marine microbial communities from the Deep Atlantic Ocean - MP0261 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA330153, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005923	Marine microbial communities from the Deep Atlantic Ocean - MP0144 metagenome		N/A
MGYS00003258	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0144 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330135.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005922	Marine microbial communities from the Deep Atlantic Ocean - MP0262 metagenome		N/A
MGYS00003257	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0262 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330005.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005921	Marine microbial communities from the Deep Atlantic Ocean - MP0326 metagenome		N/A
MGYS00003256	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0326 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330089.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005920	Marine microbial communities from the Deep Atlantic Ocean - MP0327 metagenome		N/A
MGYS00003239	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0327 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330161.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005919	Marine microbial communities from the Deep Atlantic Ocean - MP0371 metagenome		N/A
MGYS00003255	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0371 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330083.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005918	Marine microbial communities from the Deep Atlantic Ocean - MP0372 metagenome		N/A
MGYS00003567	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0372 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330007.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005917	Marine microbial communities from the Deep Atlantic Ocean - MP0440 metagenome		N/A
MGYS00003582	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0440 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330154.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005916	Marine microbial communities from the Deep Atlantic Ocean - MP0441 metagenome		N/A
MGYS00003568	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0441 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330097.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005915	Marine microbial communities from the Deep Atlantic Ocean - MP0626 metagenome		N/A
MGYS00003254	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0626 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329990.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005914	Marine microbial communities from the Deep Atlantic Ocean - MP0627 metagenome		N/A
MGYS00003238	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0627 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330150.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005913	Marine microbial communities from the Deep Atlantic Ocean - MP0759 metagenome		N/A
MGYS00003237	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0759 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330079.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005912	Marine microbial communities from the Deep Atlantic Ocean - MP0740 metagenome		N/A
MGYS00003236	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0740 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330094.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005911	Marine microbial communities from the Deep Atlantic Ocean - MP0758 metagenome		N/A
MGYS00003583	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0758 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330019.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005910	Marine microbial communities from the Deep Atlantic Ocean - MP0555 metagenome		N/A
MGYS00003615	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0555 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330095.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005909	Marine microbial communities from the Deep Atlantic Ocean - MP0739 metagenome		N/A
MGYS00003461	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0739 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330002.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005908	Marine microbial communities from the Deep Atlantic Ocean - MP0556 metagenome		N/A
MGYS00003234	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP0556 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330027.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005907	Marine microbial communities from the Deep Indian Ocean - MP0901 metagenome		N/A
MGYS00003235	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Indian Ocean - MP0901 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330006.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005906	Marine microbial communities from the Deep Indian Ocean - MP0900 metagenome		N/A
MGYS00003233	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Indian Ocean - MP0900 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330081.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005905	Marine microbial communities from the Deep Indian Ocean - MP0959 metagenome		N/A
MGYS00003584	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Indian Ocean - MP0959 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330093.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005904	Marine microbial communities from the Deep Indian Ocean - MP0960 metagenome		N/A
MGYS00003232	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Indian Ocean - MP0960 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330128.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005903	Marine microbial communities from the Deep Indian Ocean - MP1140 metagenome		N/A
MGYS00003231	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Indian Ocean - MP1140 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329993.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005902	Marine microbial communities from the Deep Indian Ocean - MP1141 metagenome		N/A
MGYS00003585	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Indian Ocean - MP1141 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329989.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005901	Marine microbial communities from the Deep Indian Ocean - MP1091 metagenome		N/A
MGYS00003230	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Indian Ocean - MP1091 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330091.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005900	Marine microbial communities from the Deep Atlantic Ocean - MP1092 metagenome		N/A
MGYS00003229	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP1092 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330020.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005899	Marine microbial communities from South of Eden, South Pacific Ocean - MP1434 metagenome		N/A
MGYS00003228	EMG produced TPA metagenomics assembly of the Marine microbial communities from South of Eden, South Pacific Ocean - MP1434 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329988.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005898	Marine microbial communities from the Deep Indian Ocean - MP1201 metagenome		N/A
MGYS00003227	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Indian Ocean - MP1201 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330138.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005897	Marine microbial communities from the Deep Indian Ocean - MP1241 metagenome		N/A
MGYS00003586	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Indian Ocean - MP1241 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330140.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005896	Marine microbial communities from the Deep Indian Ocean - MP1374 metagenome		N/A
MGYS00003226	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Indian Ocean - MP1374 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330113.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005895	Marine microbial communities from the Deep Indian Ocean - MP1202 metagenome		N/A
MGYS00003225	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Indian Ocean - MP1202 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330001.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005894	Marine microbial communities from the Deep Pacific Ocean - MP1482 metagenome		N/A
MGYS00003588	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP1482 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330008.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005893	Marine microbial communities from the Deep Pacific Ocean - MP1483 metagenome		N/A
MGYS00003587	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP1483 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329986.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005892	Marine microbial communities from the Deep Pacific Ocean - MP1493 metagenome		N/A
MGYS00003224	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP1493 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330073.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005891	Marine microbial communities from the Deep Pacific Ocean - MP1649 metagenome		N/A
MGYS00003223	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP1649 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330018.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005890	Marine microbial communities from the Deep Pacific Ocean - MP1648 metagenome		N/A
MGYS00003222	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP1648 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330080.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005889	Marine microbial communities from the Deep Pacific Ocean - MP1896 metagenome		N/A
MGYS00003589	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP1896 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330119.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005888	Marine microbial communities from the Deep Pacific Ocean - MP1494 metagenome		N/A
MGYS00003221	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP1494 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330145.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005887	Marine microbial communities from the Deep Pacific Ocean - MP2052 metagenome		N/A
MGYS00003220	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP2052 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330106.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005886	Marine microbial communities from the Deep Pacific Ocean - MP1788 metagenome		N/A
MGYS00003217	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP1788 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330126.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005885	Marine microbial communities from the Deep Pacific Ocean - MP1787 metagenome		N/A
MGYS00003216	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP1787 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330136.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005884	Marine microbial communities from the Deep Pacific Ocean - MP2016 metagenome		N/A
MGYS00003215	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP2016 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330009.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005883	Marine microbial communities from the Deep Pacific Ocean - MP2053 metagenome		N/A
MGYS00003196	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP2053 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330152.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005882	Marine microbial communities from the Deep Pacific Ocean - MP2158 metagenome		N/A
MGYS00003214	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP2158 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330112.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005881	Marine microbial communities from the Deep Pacific Ocean - MP2159 metagenome		N/A
MGYS00003213	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP2159 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330085.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005880	Marine microbial communities from the Deep Pacific Ocean - MP2252 metagenome		N/A
MGYS00003211	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP2252 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330131.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005879	Marine microbial communities from East of Antigua and Barbuda, Atlantic Ocean - MP2497 metagenome		N/A
MGYS00003212	EMG produced TPA metagenomics assembly of the Marine microbial communities from East of Antigua and Barbuda, Atlantic Ocean - MP2497 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330160.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005878	Marine microbial communities from the Deep Atlantic Ocean - MP2633 metagenome		N/A
MGYS00003253	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP2633 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330088.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005877	Marine microbial communities from the Deep Pacific Ocean - MP2253 metagenome		N/A
MGYS00003210	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP2253 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329991.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005876	Marine microbial communities from the Deep Atlantic Ocean - MP2914 metagenome		N/A
MGYS00003209	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP2914 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330129.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005875	Marine microbial communities from the Deep Atlantic Ocean - MP2969 metagenome		N/A
MGYS00003368	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP2969 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330149.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005874	Marine microbial communities from the Deep Atlantic Ocean - MP2913 metagenome		N/A
MGYS00003207	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP2913 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330096.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005873	Marine microbial communities from the Deep Atlantic Ocean - MP2634 metagenome		N/A
MGYS00003208	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP2634 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329999.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005872	Marine microbial communities from the Deep Atlantic Ocean - MP2968 metagenome		N/A
MGYS00003206	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MP2968 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330077.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005871	Rhizosphere soil Cuminum cyminum Raw sequence reads	Microbial diversity analysis of rhizosphere soil samples of healthy and infected Cumin (Cuminum cyminum L.) varieties from Gujarat, India	root:Host-associated:Plants:Rhizosphere
MGYS00005870	Rhizosphere soil Barleria prionitis Raw sequence reads	Host plant rhizo-microbiome interactions: seasonal variation and microbial community structure analysis associated with Barleria prionitis	root:Host-associated:Plants:Rhizosphere
MGYS00005580	AquaDiva: Metagenomics assemblies of 32 groundwater samples	Metagenomics assemblies of 32 groundwater samples from study: PRJEB36505. These data is part of the Collaborative Research Centre AquaDiva (www.aquadiva.uni-jena.de). Assemblies performed using metaSPAdes v3.13.0.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00005861	Dec 08 reference metagenome	Checking reference metagenome	root:Environmental:Aquatic:Marine
MGYS00002008	EMG produced TPA metagenomics assembly of the Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for  prokaryotes. (APY) data set	The APY Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB1787. This project includes samples from the following biomes : Marine.	root:Environmental:Aquatic:Marine
MGYS00005869	EMG produced TPA metagenomics assembly of PRJNA693457 data set (Multi-omics of the nitrate-reducing iron(II)-oxidizing culture BP).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA693457, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Pond:Sediment.	root:Environmental:Aquatic:Freshwater:Pond:Sediment
MGYS00005787	EMG produced TPA metagenomics assembly of PRJEB4419 data set (Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for small DNA viruses.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB4419, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic,root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005867	EMG produced TPA metagenomics assembly of PRJNA682552 data set (Multi-omics of the nitrate-reducing iron(II)-oxidizing culture KS).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA682552, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005866	Ea16/NOD microbiota	Ea16/NOD microbiota	root:Host-associated:Mammals:Digestive system:Foregut
MGYS00005865	EMG produced TPA metagenomics assembly of PRJNA247822 data set (Ecological Genomics of a Seasonally Anoxic Fjord; Saanich Inlet).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA247822, and was assembled with SPAdes v3.14.1, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00005856	EMG produced TPA metagenomics assembly of PRJEB9742 data set (Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for  small DNA viruses.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9742, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005863	EMG produced TPA metagenomics assembly of PRJNA649049 data set (Comparisons of microbial diversity over time in two different pH conditions in a geoduck hatchery.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA649049, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Marginal Sea.	root:Environmental:Aquatic:Marine:Marginal Sea
MGYS00005864	Comparisons of microbial diversity over time in two different pH conditions in a geoduck hatchery.	For years, hatcheries in Washington (USA) and elsewhere have experienced unexplained mass mortality events in which entire cohorts of larvae do not survive through setting (transition from mobile larval to sessile juvenile phase). Investigations into known diseases, genetics, and water quality, among other factors, yield no direct correlations to these mortality events. Therefore, it has been proposed that more subtle shifts in the microbiome and/or water quality may be causing larval mortality. A full characterization of the resident microbial community (microbiome) in a hatchery could provide insight into the baseline microbiome and deviations from the baseline that may contribute to mortality events.	root:Environmental:Aquatic:Marine:Marginal Sea
MGYS00005862	Microbiota of field-caught Anopheles atroparvus	The microbiome profile of a local population of Anopheles atroparvus from the Ebro Delta, a former malaria transmission area of Spain, is characterized using high-throughput sequencing of the bacterial 16S ribosomal gene V3-V4 regions.	root:Host-associated:Insecta
MGYS00005547	Metagenomic assessment of the ecological functions of the soil: analysis of the soil microbiota associated with the gigantism of the plants of the Chernevaya Taiga of Siberia	Global changes in the environment and climate, food and energy shortages, loss of biodiversity and the sustainability of ecosystems are among the most important problems of the current century. As a result, modern humanity should be engaged in the preservation and protection of soil, since soil resources are the basis of the food and ecological security of the nation. Prolonged use of soil in agricultural production has a wide range of negative consequences for soil properties, among them: degradation of organic matter, increased greenhouse gas emissions, changes in soil acidity, soil depletion, etc. Use of agricultural technologies (plowing and loosening, use of mineral and organic fertilizers, etc.) causes a significant change in the biogeochemical cycles performed by a complex of soil microorganisms. In this sense, the soils of the chernevaya taiga represent a unique model that is distinguished not only by extremely high fertility, realized from internal biotic and abiotic resources, and not by agrotechnical methods, but also by the preserved pre-agricultural microbiome, not affected by the long-term agricultural practices.The soil microbiota plays a decisive role in maintaining the homeostasis of the soil ecosystem, performing key functions in ensuring the growth and development of plants and actively participating in the carbon cycle. As a part of the existing scientific paradigm, soil organic matter is predominantly microbial in origin and consists of individual chemicals combined by non-covalent bonds to humic assemblies (Kleber, Johnson, 2010; Piccolo, 2002; Schmidt et al., 2011; Simpson et al., 2007; Von Lutzow et al., 2006; Von Lutzow et al., 2007; Von Lutzow et al., 2008). The study of the kinetics and dynamics of the processes of microbial transformation of organic substances under the different soil conditions is the basis for solving the problem of rational use of soil fertility and limiting CO2 emissions to the atmosphere during agricultural use of soil (Janzen, 2006). Understanding the transformation of organic matter in soil and managing the soil carbon balance is a priority for modern farming systems and agricultural technologies, since it is organic matter that is responsible for numerous soil properties, including agroecosystem functioning and crop productivity of agricultural plants (Gattinger et al, 2012; Powlson et al, 2011).The use of metagenomic approaches for monitoring soil ecosystems will significantly change our understanding of the diversity and functional role of the microbiome in maintaining the soil health. The change in the stocks of organic carbon (Corg) is one of the most important indicators of ecosystem activity (SemenioJanzen et al., 2011). Even small changes in organic carbon stocks can lead to disproportionately large positive or negative effects on key soil properties. In this case, the peculiarities of the soil microbiome, the main driver of the processes of transformation and mineralization of organic matter, can serve as a universal and very sensitive indicator of the state of the soil, including the optimization and biologization of farming systems (Pershina et al., 2018, Ivanova et al., 2017, Pershina et al., 2015, Chirac et al., 2013). The development of new approaches to assess the impact of agrobiotechnologies on soil health and quality, combined with the metagenomic characteristics and indication of the transformation of organic matter in the soil, is one of the most promising direction for diagnostics the state of organic carbon flux in terrestrial ecosystems, and, consequently, the state of the soil as a whole.In the past decade, several global projects have been initiated to study the soil microbiomes, the most famous of them is the Earth Microbiome project (http://www.earthmicrobiome.org/). One of the features of this project is the absence of soil samples from Russia. It is necessary to recognize that, despite the importance of microbiome research in all areas of fundamental and applied biology, Russia, admittedly, is not yet in any acceptable positions in the field of metagenomic research. Within the framework of this project, it is proposed to drastically improve the current situation by creating a modern metagenomics laboratory at St. Petersburg State University and developing newest research programs for studying microbiota that will fill gaps in understanding important processes carried out by microorganisms. Significant assistance in the implementation of this project will be provided by the use of an unprecedented diversity of Russian soils, often formed under unique natural conditions and possessing great agricultural and ecological importance.The main goal of the project is not to copy or compete with existing metagenomic projects implemented in North America or Europe, but to develop and implement original approaches to the study of soil metagenomes, which will allow obtaining qualitatively new and practically significant biological knowledge. From this point of view, the obtaining of sequencing data using modern high-performance technologies is only the starting point and the basis for further analysis. The results of this analysis should be practically significant and supported by appropriate agrochemical, geological and biochemical analyzes, as well as be accompanied by further experimental studies.As it was already noted, the backlog of domestic science in the field of metagenomics is very large, so the achievement of compliance with the world level, high scientific and social significance of the project can be achieved through the use of unique objects. Without a doubt, such an object is the soil of chernevaya taiga. The analysis of the peculiarities of the soil, the height of grasses in which, without using any fertilizers or agrotechnical measures, can reach 2 m, will certainly cause public interest. And if the fundamentals of such properties (presumably rooted in the taxonomic and functional structure of the microbiome) are thoroughly studied and understood, then in the future, you can expect to receive specific microbial preparations that can at least partially incorporate the unique properties of chernevaya taiga soils into traditional farming practice. This may be especially relevant for such agro technics as zero treatment, which is in many respects typologically similar to the conditions of vegetation in the chernevaya taiga. The potential of chernevaya -taiga microbiome may have an invaluable impact on the creation of new types of drugs that provide fast and effective decomposition of crop residues. In turn, the value of the analysis of previously unexplored unique soils for the search for new biologically active compounds is difficult to overestimate. The basis of many modern antibiotics are biologically active compounds of natural origin. Since the main producers of such molecules are plants and microorganisms, the analysis of soil samples with a wide variety of bacteria living in them has great potential for the detection of new biologically active substances. The results of this study will be relevant not only in terms of creating new drugs, but also for a fundamental scientific understanding of the process of synthesizing such compounds in bacteria.Thus, the realization of the hidden potential of unique objects is one of the most promising directions in Russian metagenomic studies.The project is supported by Russian Science Foundation (grant 19-16-00049)	root:Environmental:Terrestrial:Soil
MGYS00005810	EMG produced TPA metagenomics assembly of PRJNA237344 data set (Amazon Continuum Metagenomes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA237344, and was assembled with SPAdes v3.11.1, SPAdes v3.12.0. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00003725	Arctic microbiome along Svalbard Cross Shelf transects	Global worming and climate change has been manifested in the decrease of the Arctic Ocean see ice extent and thickness. The thinner sea-ice regime that the Arctic has been facing changed Arctics primary productivity and biogeochemistry. Understand the dynamics of the microbial communities that feed Arctic phytoplankton and biologically derived carbon export will be worthwhile in order to draw future trends. In this study we present a comprehensive analysis of the biogeographic patters of Arctic microbiome diversity and distribution along two oceanographic transects in the Marginal Ice Zone around Svalbard, within strong environmental gradients (Ripfjorden, Kongsfjorden). A total of 11 stations were sample at three depths (surface, chlorophyll maximum and bottom) during the Norwegian Polar Institute MOSJ-ICE 2016 plankton-monitoring program. Samples were concentrated on board through Sterivex 0.2 mm filtration and preserved at -80oC for later DNA extraction. Amplification of 16S rRNA and 18S rRNA genes were performed and sequenced in Illumina MiSeq with a sequence depth of about 100 thousand readpairs. The prokaryotic and eukaryotic MOSJ-ICE16 data sets collection comprises highly complex and diverse microbial communities with a marked biogeographic pattern of distribution. Strong links were identified between bacterioplanckton and phytoplankton/picophytoplankton distribution driven by environmental and biogeochemical forces, most relevant to unravel the role of microbial pathways in supporting Arctic Ocean Primary productivity and system integrity.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005860	Metagenomic sequencing of preterm infant gut microbiota raw sequence reads	Dysbiotic colonization of the preterm infant gut microbiota may have lifelong effects on host health. The normal progression of colonization of preterm infants is a patterned, yet chaotic, process, and thought to be chiefly driven by host factors. While preterm infants almost universally receive early and often repeated and/or prolonged intravenous antibiotic therapy, it remains unclear if and how specific antibiotics alter the developmental progression of the gut microbiota in this population. By analyzing 401 fecal samples from 84 longitudinally-sampled preterm infants, we demonstrate that meropenem, cefotaxime, and ticarcillin-clavulanate significantly reduce species richness during their administration, and significantly enrich or deplete specific bacterial species and antibiotic resistance (AR) genes. In contrast, vancomycin and gentamicin, the antibiotics most commonly administered to preterm infants, have non-uniform effects on species richness. We show this response is predictable with 85% accuracy based on the relative abundance of only two bacterial species and two AR genes before treatment. To more fully investigate the role of the gut-associated resistome in response to specific antibiotics, we performed functional metagenomic selections for resistance to 16 clinically relevant antibiotics from a set of 21 preterm infants' gut microbiota. Of the 794 AR genes identified, 79% had not previously been classified as providing any resistance phenotype. Combined with deep shotgun sequencing of all 401 fecal samples, we find that multidrug resistant Escherichia, Klebsiella, and Enterobacter species, which are commonly associated with nosocomial infections, dominate the preterm infant gut microbiota. We show that AR genes that are enriched following specific antibiotic treatments are generally unique to the specific treatment and highly correlated (p<0.001) with the abundance of a single species. The most notable exception includes ticarcillin-clavulanate and ampicillin, both of which enrich a large number of overlapping AR genes, and are highly correlated with Klebsiella pneumoniae species in the preterm infant gut microbiota. In addition to AR genes relevant to specific antibiotics likely providing a protective function, we show that all antibiotic treatments also result in widespread collateral microbiome impact through enrichment of AR genes with no known direct activity against the specific antibiotic treatment.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005858	EMG produced TPA metagenomics assembly of PRJNA430179 data set (glacier metagenome Genome sequencing).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA430179, and was assembled with metaSPAdes v3.14.1, SPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Ice:Glacial lake.	root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
MGYS00005859	glacier metagenome Genome sequencing	research of englacial ecosystem	root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
MGYS00005857	Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for  small DNA viruses.	"Analysis of the genes and genomes present in Tara Oceans Polar Circle virus size fractions through shotgun DNA sequencing.
Seawater from different depths was precipitaded  then filtered to retain small particle sizes (Virus particles). The DNA was extracted and submitted to high throughput sequencing."	root:Environmental:Aquatic:Marine
MGYS00005854	EMG produced TPA metagenomics assembly of PRJNA698063 data set (High throughput sequencing of Tea microbial communities).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA698063, and was assembled with metaSPAdes v3.14.1, megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere:Soil.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00005855	High throughput sequencing of Tea microbial communities	This dataset contains the microbial communities associated with organically grown tea cultivation in Assam, India	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00005852	EMG produced TPA metagenomics assembly of PRJEB37860 data set (Metagenomics and metatranscriptomics data of Blattella germanica's hindgut microbiota.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB37860, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Arthropoda:Digestive system:Hindgut.	root:Host-associated:Arthropoda:Digestive system:Hindgut
MGYS00005853	Metagenomics and metatranscriptomics data of Blattella germanica's hindgut microbiota.	Pair-end metagenomics and metatranscriptomics data of the german cockroach hindgut to validate a meta-omics data integration pipeline, called gNOMO.	root:Host-associated:Arthropoda:Digestive system:Hindgut
MGYS00005850	Ecological Genomics of a Seasonally Anoxic Fjord; Saanich Inlet	Saanich Inlet is a seasonally anoxic fjord opening to the Strait of Georgia on the southeast coast of Vancouver Island, British Columbia. It is approximately 24 kilometers long with a maximal basin depth of 234 meters and receives limited freshwater input from the surrounding watershed. A shallow glacial entrance sill 75 meters deep restricts circulation within interior and basin waters for most of the year. During spring and summer months, restricted circulation combined with high levels of primary productivity in surface waters lead to oxygen loss with concomitant water column stratification indicated by accumulation of methane (CH4), Ammonia (NH3) and Hydrogen Sulfide (H2S). In late summer and fall, oxygenated nutrient-rich ocean waters upwelling through the Strait cascade into Saanich Inlet shoaling anoxic bottom waters upward and transforming the redox chemistry of the water column. This process is stable on decadal time scales exhibiting a relatively narrow deviation in the depth distribution of the oxycline at different times of year. The recurring seasonal development of water column anoxia followed by deep-water renewal enables spatiotemporal profiling of microbial community structure and function across a wide range of water column redox states.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00005725	Shotgun metagenome sequences of Anthelia biocrust samples.	Samples of biocrust (~200 mg from uppermost 3 mm) dominated by the liverwort Anthelia jurkatzkana from various locations in Iceland. DNA extracted with DNeasy Power Soil kit. Illumina Nextera XT shotgun libraries prepared and sequenced 2x75b on MiSeq.	root:Environmental:Terrestrial:Soil
MGYS00005846	EMG produced TPA metagenomics assembly of PRJEB27054 data set (Global surveillance of antimicrobial resistance).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB27054, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Engineered:Wastewater:Water and sludge.	root:Engineered:Wastewater:Water and sludge
MGYS00005847	Global surveillance of antimicrobial resistance	Antimicrobial resistance (AMR) is one of the most serious global public health threats, however, obtaining representative data on AMR for healthy human populations is difficult. We characterized the bacterial resistome from untreated sewage from 79 sites in 60 countries. We found systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data only explained a minor part of the AMR variation and no evidence for cross-selection between antimicrobial classes nor effect of travel by flight between sites were found. However, AMR abundance was strongly correlated with socio-economic, health and environmental factors, which we used to predict AMR abundances in all countries in the world. Our findings suggest that the global AMR gene diversity and abundance varies by region and are caused by national circumstances. Improving sanitation and health could potentially limit the global burden of AMR. We propose to use sewage for an ethically acceptable and economically feasible continuous global surveillance and prediction of AMR.	root:Engineered:Wastewater:Water and sludge
MGYS00005731	Herbal rhizosphere metagenomics	Herbal rhizosphere culture mix	root:Host-associated:Plants:Rhizosphere
MGYS00005140	metatranscriptomic approaches to unravel taxonomic and functional diversities of a coastal aquatic ecosystem and their reaction to hypoxia	Two previous integrative research programs: PREDHYPO (AMIDEX Foundation 2015-2016) and PREDHYP-O2 (EC2CO 2016-2017, CNRS-INSU) have enabled the coupling between physics and biogeochemical processes of the Berre lagoon sediment during laboratory experiments under controlled oxygenation conditions. These programs have also initiated regular in situ measurements during a three-year period, leading to the first-step development of a 1D predictive benthic-pelagic biogeochemical model of the lagoon. We set up a laboratory experiment to follow the biological and chemical dynamics at the sediment-water interface on the short-term period (i.e. one month incubation of sediment core samples), while we conducted an in situ approach to characterize seasonal and yearly dynamics (i.e. from may 2015 to august 2016) of biogeochemical processes at the sediment-water interface for three sites showing contrasted oxygenation conditions. Because microorganisms are key actors of biogeochemical processes and organic matter turnover, we dedicated an important part of these research programs to the characterization of taxonomic and functional responses of the sediment microbiome to hypoxia events. Based on Next Generation Sequencing (NGS) technologies (i.e. ILLUMINA), we developed a metabarcoding approach that aims at exploring taxonomic diversity of Bacteria and Archaea living in the sediment, and we developed a metatranscriptomic approach that aims at identifying metabolic activities and pathways involved in the ecosystem functions. The laboratory experiment considered triplicate samples of sediment at various depth layers and according to oxygenation conditions of the water column ranging from 0% to 100%.	root:Environmental:Aquatic:Marine:Sediment
MGYS00005845	Multi-omics of the nitrate-reducing iron(II)-oxidizing culture KS	Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS.This dataset contains: (1) Raw sequencing data of 16S (V4 region, primers 515f and 806r) rRNA amplicon sequencing of the microbial community composition of the autotrophic NRFeOx enrichment culture KS. Illumina MiSeq sequencing (Illumina, San Diego, CA, USA) using PE 250 bp MiSeq Reagent Kit v2 (500 cycles kit) were performed at Microsynth AG (Balgach, Switzerland). (2) Raw sequencing data of shotgun metagenomics. For short reads, library was prepared with TruSeq DNA PCR-Free Kit (Illumina) and sequenced with PE 150 bp on a NovaSeq 6000 totalling 55 and 48 Gbp by CeGaT, Tuebingen, Germany. For long read sequencing, library preparation with ONT Native Ligation Kit was followed by sequencing with PromethION (Oxford Nanopore Technologies) flow cell (version 9.4.1) for 72h with standard settings (basecalling with HAC mode, bias voltage -180 mV) yielding 53 Gbp in 5 million reads by the NGS Competence Center Tuebingen (NCCT) of the University of Tuebingen, Germany. (3) Short and long reads were assembled with metaSPAdes v3.13.1 using https://github.com/nf-core/mag v1.0.0. (4) Raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates). Library preparation including bacterial ribodepletion (NuGen Universal Prokaryotic RNA-Seq kit incl. bacterial ribodepletion) and Illumina NextSeq v2.5 sequencing with PE 75 bp and 21 to 62 Mio clusters per sample were performed by Microsynth AG (Balgach, Switzerland).	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005843	Reeindeer lichens as potential natural products source	Lichens have been widely used in traditional medicine, especially by indigenous communities worldwide. However, their slow growth and difficulties in the isolation of lichen symbionts and associated microbes have hindered the pharmaceutical utilisation of lichen-produced compounds. Advances in high-throughput sequencing techniques now permit detailed investigations of the complex microbial communities formed by fungi, green algae, cyanobacteria, and other bacteria within the lichen thalli. Here, we used amplicon sequencing, shotgun metagenomics, and in silico metabolomics together with compound extractions to study reindeer lichens collected from Southern Finland. Our aim was to evaluate the potential of Cladonia species as sources of novel natural products. We compared the predicted biosynthetic pathways of lichen compounds from isolated genome-sequenced lichen fungi and our environmental samples. Potential biosynthetic genes could then be further used to produce secondary metabolites in more tractable hosts. Furthermore, we detected multiple compounds by metabolite analyses, which revealed connections between the identified biosynthetic gene clusters and their products. Taken together, our results contribute to metagenomic data studies from complex lichen-symbiotic communities and provide valuable new information for use in further biochemical and pharmacological studies.	root:Host-associated:Fungi
MGYS00005844	Gut microbiome of Capybara (Hydrochoerus hydrochaeris) Metagenome	The aim of this project is to investigate the gut microbiome of Capybara (Hydrochoerus hydrochaeris), a monogastric herbivore, also known as master of the grasses, which feeds on a recalcitrant diet that has digestive efficiency comparable to that of ruminants to recover enzymatic strategies of lignocelulose degradation.	root:Host-associated:Mammals:Digestive system
MGYS00005379	EMG produced TPA metagenomics assembly of the PRJNA46333 data set (Gene-Environment Interactions at the Skin Surface).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA46333.  This project includes samples from the following biomes: root:Host-associated:Human:Skin.	root:Host-associated:Human:Skin
MGYS00002040	EMG produced TPA metagenomics assembly of the Arctic Ocean metagenomes from HLY1502 (Arctic Ocean metagenomes) data set	The Arctic Ocean metagenomes Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB14154. This project includes samples from the following biomes : Marine.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005841	The microbiome associated with the carrageenophyte Chondracanthus chamissoi from the Central Coast of Peru	Chondracanthus chamissoi belongs to the family Gigartinaceae and is considered an endemic carrageenophyte alga of the temperate coast of the South Pacific. Microbes are ubiquitously distributed, and they are also present in algae natural systems. Additionally, the algal microbiome is a pivotal part of the algae holobiont and has a key role in modulating its polysaccharide quality. Recently, unique microbiote has been isolated from polysaccharide-producers algae conferring specific  chemical properties to these compounds (e.g. agar, carrageenan). This study aims to identify specific microbiote associated to the carrageenophyte Chondracanthus chamissoi from the Central Coast of Peru including its biological, cellular, and molecular metabolism.	root:Environmental:Aquatic:Marine:Intertidal zone
MGYS00005842	sediment metagenome Metagenome	River sediment polluted with fluoroquinolones and other drugs discharged from bulk drug production in India constitute an environment with unprecedented, long-term antibiotic selection pressures. It is therefore plausible that previously unknown resistance genes have evolved and/or are promoted here. In order to search for novel resistance genes, we, therefore, analyzed such river sediments by a functional metagenomics approach	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00005839	EMG produced TPA metagenomics assembly of PRJNA655119 data set (Metatranscriptome sequencing of the extended simplified human intestinal microbiota (SIHUMIx)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA655119, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Intestine.	root:Host-associated:Human:Digestive system:Intestine
MGYS00005840	Metatranscriptome sequencing of the extended simplified human intestinal microbiota (SIHUMIx)	Metatranscriptome sequencing of the extended simplified human intestinal microbiota (SIHUMIx), consisting of eight bacterial species, namely Anaerostipes caccae (DSMZ 14662), Bacteroides thetaiotaomicron (DSMZ 2079), Bifidobacterium longum (NCC 2705), Blautia producta (DSMZ 2950), Clostridium butyricum (DSMZ 10702), Clostridium ramosum (DSMZ 1402), Escherichia coli K-12 (MG1655) and Lactobacillus plantarum (DSMZ 20174) cultivated in bioreactors under anaerobic conditions. The metatranscriptome provides information on the functional interaction of the bacterial community and also supports the identification of novel small proteins.	root:Host-associated:Human:Digestive system:Intestine
MGYS00001757	Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics	"In this study we compared methods for quantifying taxonomic composition of microbial communities. The compared methods included metagenomics, 16S rRNA amplicon sequencing and metaproteomics. This ENA study contains the metagenomic and the 16S rRNA amplicon data. The metaproteomic data is available from ProteomeXchange via the PRIDE repository(PXD006118). For the comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing. Three replicates of each community type were analyzed with metagenomics. The ""C"" type communities have same cell/phage particle number for all community members (C1 to C4). The ""P"" type communities have the same protein content for all community members (P1 to P4). The ""U"" (uneven) type communities cover a large range of protein amounts and cell numbers (U1 to U4). The 16S rRNA libraries were sequenced twice in independent runs. The prefixes ""rep1_"" and ""rep2_"" indicate the two individual runs. The 16S rRNA read files without prefix are rep1 and rep2 merged."	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00005838	Lenisia limosa and epibiotic Arcobacter	Identifying potential metabolic interactions between Lenisia limosa and it's epibiotic Arcobacter	N/A
MGYS00005837	EMG produced TPA metagenomics assembly of PRJNA277740 data set (Lenisia limosa and epibiotic Arcobacter).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA277740, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Engineered:Bioreactor:Continuous culture:Marine intertidal flat sediment inoculum:Wadden Sea-Germany.	root:Engineered:Bioreactor:Continuous culture:Marine intertidal flat sediment inoculum:Wadden Sea-Germany
MGYS00005833	EMG produced TPA metagenomics assembly of PRJNA301235 data set (Moose metagenomic assembly).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA301235, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Midgut.	root:Host-associated:Mammals:Digestive system:Midgut
MGYS00005836	EMG produced TPA metagenomics assembly of PRJNA244670 data set (Microbial consortium enriched at the cathode of a solar microbial fuel cell).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA244670, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm.	root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
MGYS00005834	EMG produced TPA metagenomics assembly of PRJEB25540 data set (Metatranscriptomics of Kentrophoros ciliate-bacteria symbiosis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB25540, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00005835	Metatranscriptomics of Kentrophoros ciliate-bacteria symbiosis	Metatranscriptomics of Kentrophoros spp., a ciliate from marine sediments with symbiotic bacteria, to complement metagenomic study of the symbiosis (PRJEB25374).	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00001759	Large variability of bathypelagic microbial eukaryotic communities across the world's oceans	In this work we study the diversity of bathypelagic microbial eukaryotes (0.8-20 m) in the global ocean. Seawater samples from 3000-4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S rDNA. The relative abundance of the most abundant Operational Taxonomic Units (OTUs) agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag-approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.	root:Environmental:Aquatic:Marine
MGYS00005832	Multi-omics of the nitrate-reducing iron(II)-oxidizing culture BP	Nitrate-reducing iron(II)-oxidizing (NDFO) bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. A second NDFO culture, culture BP, was obtained with a sample taken in 2015 at the same pond and cultured in a similar way. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture BP.This dataset contains: (1) Raw sequencing data of 16S (V4 region, primers 515f and 806r) rRNA amplicon sequencing of the microbial community composition of the autotrophic NRFeOx enrichment culture BP and of environmental samples from the pond where culture BP originates from. Illumina MiSeq sequencing (Illumina, San Diego, CA, USA) using PE 250 bp MiSeq Reagent Kit v2 (500 cycles kit) were performed at Microsynth AG (Balgach, Switzerland). (2) Raw sequencing data of near full-length 16S (primers 27F and 1492R) sequenced with PacBio Sequel SMRT at the Helmholtz research institute, Munich, Germany. (3) Raw sequencing data of shotgun metagenomics. Library was prepared with TruSeq DNA PCR-Free Kit (Illumina) and sequenced with PE 150 bp on a NovaSeq 6000 totalling 91 Gbp by CeGaT, Tuebingen, Germany. (4) Short reads were assembled with MEGAHIT v1.2.7 using https://github.com/nf-core/mag v1.0.0. (5) Raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates). Library preparation including bacterial ribodepletion (Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit) and Illumina NextSeq v2.5 sequencing with PE 75 bp and 6 to 53 Mio clusters per sample were performed by Microsynth AG (Balgach, Switzerland).	root:Environmental:Aquatic:Freshwater:Pond:Sediment
MGYS00005831	Microbial consortium enriched at the cathode of a solar microbial fuel cell	The objective of this project is to study a microbial biocathode consortium enriched at the U.S. Naval Research Laboratory's Center for Bio/Molecular Science & Engineering.  The initial inoculum for the solar microbial fuel cell was seawater collected near Rutgers, NJ, and the community has subsequently been maintained electroautotrophically via serial transfers on cathodes poised at 310 mV vs. SHE. This microbial consortium contains autotrophic organisms which can use a cathode as an electron donor and O2 as an electron acceptor, and has electrochemical properties potentially useful in bioenergy applications including microbial electrosynthesis and microbial fuel cell technology. System biology approaches will be used to identify functional genes that are relevant for bioenergy production, such as fixing CO2 as sole carbon source, electrosynthesis, O2 tolerance, etc.   Several heterotrophic constituents have been isolated in pure culture, and have been sequenced by either Illumina or PacBio technologies.  Furthermore, closed genomes and methylation data were obtained from PacBio sequencing of metagenomic DNA.    Metagenomic libraries generated from eight biological replicates of an enriched biocathode microbial community were sequenced at 2x100 base pairs (bp) (paired-end reads) using an Illumina HiSeq 2000. The reads were assembled using either IDBAUD or Ray.  The ideal k-mer length and node coverage were selected based on which gave results most similar to de novo sequencing of isolated bacterial cultures from the enriched community (Marinobacter sp. strain CP1 and Labrenzia sp. strain CP4).  Metatranscriptomic libraries were generated from four reactors inoculated with the same inoculum were grown at a set potential of 310 mV SHE until current density stabilized, cyclic voltammetry was recorded, and then two of them were set at a more positive potential (470 mV) and two remained at 310 mV for 48 hours before samples were harvested for RNA extraction.  This experiment was repeated with four more reactors inoculated with a new cell suspension from the same source electrode for a total of four biological replicates at each potential.	root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
MGYS00005830	Moose metagenomic assembly	Moose Ohio State 2015	root:Host-associated:Mammals:Digestive system:Midgut
MGYS00005829	Impact of sulfamethoxazole on the microbial community of a riverine environment	Antimicrobial resistance (AMR) is a global health issue. The impact of sub-lethal concentrations of antibiotics on antimicrobial resistance gene (ARG) spread in the environment is still unclear. In this study we used semi-realistic flume systems to mimic the riverine environment and we monitored the effect of low concentration of sulfamethoxazole on the microbial community composition and function (i.e. ARG).	root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems
MGYS00005827	Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles	The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The alpha-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, beta-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.	root:Engineered:Lab enrichment:Defined media:Anaerobic media
MGYS00005826	A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function	Swine are regarded as promising biomedical models, but the dynamics of their gastrointestinal microbiome have been much less investigated than that of humans or mice. The aim of this study was to establish an integrated multi-omics protocol to investigate the fecal microbiome of healthy swine. To this end, a preparation and analysis protocol including integrated sample preparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integration linked microbiome composition with function, and metabolic activity with protein inventories, i.e., 16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites. 16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae and Clostridiaceae. Similar microbiome compositions in feces and colon, but not ileum samples, were observed, showing that feces can serve as minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition, e.g., temporal decreased abundance of Lactobacillaceae and Streptococcaceae during the experiment, were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed a rather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associated metaproteome functions, pointing towards functional redundancy among microbiome constituents. In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomy and functionality of the intestinal microbiome of swine.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00005825	Bifidobacterium or fiber protect against diet-induced microbiota-mediated colonic mucus deterioration	Diet strongly affects gut microbiota composition and gut bacteria can influence the colonic mucus layer, a physical barrier that separates trillions of gut bacteria from the host.  However, the interplay between a Western style diet (WSD), gut microbiota composition and the intestinal mucus layer is less clear.  Here we show that mice fed a WSD have an altered colonic microbiota composition that causes increased penetrability and a reduced growth rate of the inner mucus layer. Both barrier defects can be prevented by transplanting microbiota from chow-fed mice. In addition, we found that administration of Bifidobacterium longum was sufficient to restore mucus growth whereas administration of the fiber inulin prevented increased mucus penetrability in WSD-fed mice. We hypothesize that the presence of distinct bacteria is crucial for proper mucus function.  If confirmed in humans, these findings may help to better understand diseases with an affected mucus layer, such as ulcerative colitis.	root:Host-associated:Mammals:Digestive system:Midgut
MGYS00002045	EMG produced TPA metagenomics assembly of the Microbial composition of samples from infant gut (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA63661. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005736	EMG produced TPA metagenomics assembly of PRJNA274897 data set (Oil droplet biodegradation Trondheimsfjord Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA274897, and was assembled with metaSPAdes v3.13.0. This project includes samples from the following biomes: root:Engineered:Lab enrichment:Defined media:Marine media.	root:Engineered:Lab enrichment:Defined media:Marine media
MGYS00005824	PMC 728.11_cyano	Microcystis aeruginosa PMC 728.11_cyano metagenome sequencing	root:Environmental:Aquatic:Freshwater
MGYS00005822	The unexplored social language of bacteria in human oral health and disease	Systematic analysis of small-molecule encoding biosynthetic gene clusters from shotgun metagenomic sequencing data reveals differentially abundant biosynthetic pathways in health and disease associated salivary microbiota	N/A
MGYS00005821	EMG produced TPA metagenomics assembly of PRJNA478018 data set (The unexplored social language of bacteria in human oral health and disease).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA478018, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva,root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Arthropoda:Digestive system:Oral
MGYS00001984	EMG produced TPA metagenomics assembly of the Canadian MetaMicrobiome Library Projects (Canadian MetaMicrobiome) data set	The Canadian MetaMicrobiome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA202388. This project includes samples from the following biomes : Terrestrial, Fecal.	root
MGYS00001981	EMG produced TPA metagenomics assembly of the Library preparation methodology can influence genomic and functional predictions in human microbiome research (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA298489. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system
MGYS00005820	Library preparation methodology can influence genomic and functional predictions in human microbiome research	This project investigates how library preparation and sequencing protocol influence the taxonomy and function analysis of microbial species in human microbiome research.	root:Host-associated:Human:Digestive system
MGYS00005816	EMG produced TPA metagenomics assembly of PRJEB8347 data set (Temporal and technical variability of human gut metagenomes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8347, and was assembled with SPAdes v3.14.1, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005819	EMG produced TPA metagenomics assembly of the Metagenomic analysis of soil samples from an oil contaminated military base (Enviro_05_10_2015) data set	The Enviro_05_10_2015 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB15034. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil:Sand:Oil-contaminated
MGYS00005818	EMG produced TPA metagenomics assembly of the Microbial diversity and isolation of novel hydrolases from the Kudu Rumen (Kudu Metagenome) data set	The Kudu Metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB7843. This project includes samples from the following biomes : Mammal (non-human).	root:Host-associated:Mammals
MGYS00001985	EMG produced TPA metagenomics assembly of the Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA289586. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system
MGYS00005817	Temporal and technical variability of human gut metagenomes	"Background: Metagenomics has become a prominent approach for exploring the role of the gut microbiota in human health. However, the temporal variability of the healthy gut microbiome has not yet been studied in depth using metagenomics and little is known about the effects of different sampling and preservation approaches. We performed metagenomic analysis on fecal samples from seven subjects collected over a period of up to two years to investigate temporal variability and assess preservation-induced variation, specifically, fresh frozen compared to RNALater. We also monitored short-term disturbances caused by antibiotic treatment and bowel cleansing in one subject.

Results: We find that the human gut microbiome is temporally stable and highly personalized at both taxonomic and functional levels. Over multiple time-points, samples from the same subject clustered together, even in the context of a large dataset of 888 European and American fecal metagenomes. One exception was observed in an antibiotic intervention case where, more than one year after the treatment, samples did not resemble the pre-treatment state. Clustering was not affected by preservation method. No species differed significantly in abundance, and only 0.36% of gene families were differentially abundant between preservation methods.

Conclusions: Technical variability is small compared to the temporal variability of an unperturbed gut microbiome, which in turn is much smaller than the observed between-subject variability. Thus, short-term preservation of fecal samples in RNALater is an appropriate and cost-effective alternative to freezing of fecal samples for metagenomic studies."	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005815	EMG produced TPA metagenomics assembly of PRJEB6070 data set (Potential of fecal microbiota for early stage detection of colorectal cancer).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6070, and was assembled with SPAdes v3.14.1, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system
MGYS00005813	EMG produced TPA metagenomics assembly of PRJNA407905 data set (Human saliva Metagenomes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA407905, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00005814	Human saliva Metagenomes	Our research focused on the uncultured human microbial community present in saliva of IgA immunodeficiency people and healthy people	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00005812	EMG produced TPA metagenomics assembly of PRJNA216965 data set (Dental Calculus Metagenome (archaeological)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA216965, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00005811	EMG produced TPA metagenomics assembly of PRJEB19901 data set (Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19901, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Engineered:Modeled:Simulated communities (microbial mixture).	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00005808	EMG produced TPA metagenomics assembly of PRJNA309322 data set (Pediatric MLI metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA309322, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005809	Pediatric MLI metagenome	Metagenome sequencing and gene prediction for pediatric mucosal-luminal interface aspirates	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005752	EMG produced TPA metagenomics assembly of PRJNA683594 data set (Manure metagenome from Ceftiofur-treated dairy cow).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA683594, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005807	The relationship of evergreen shrub Empetrum nigrum and soil microbial communities and functional diversity in degraded rangeland of the subarctic highland of Iceland.	Empetrum nigrum is a common species in the degraded highland rangelands of Iceland. Empetrum nigrum is well known for its ability to produce secondary metabolites (allelochemicals) that influence the germination, growth, survival, and reproduction of other plants in the community. The aim is to determine if the presence of Empetrum has an effect on soil microbial community composition and the community's main functional genes with special emphasis on genes related to carbon cycles. 4 shotgun libraries were constructed representing two soil samples from Empetrum nigrum shrub and two soil samples from vegetation cover of grasses/moss and, depths of 0-5.	root:Host-associated:Plants
MGYS00005806	This is a metagenomic study to investigate the microbial community and metabolic functions of Korean twin pairs.	This is a metagenomic study to investigate the microbial community and metabolic functions of Korean twin pairs. Fecal samples from 10 twin pairs were collected once and those of 8 pairs were collected twice with an average interval between sampling of about 2 years. Whole genome shotgun (WGS) sequencing was performed in a total of 36 fecal samples.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005803	EMG produced TPA metagenomics assembly of PRJEB4391 data set (Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the faecal microbiome of growing kittens).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB4391, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005804	Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the faecal microbiome of growing kittens	Despite being obligate carnivores, cats are fed a wide range of dietary macronutrients within commercial diets. Little is known regarding the feline gastrointestinal microbiome and how it is impacted by diet. Using 16S RNA analysis, changes in diet (protein:carbohydrate ratio) do affect fecal microbiota of growing kittens. However, to investigate potential functional differences deep Illumina shotgun sequencing is required and a study of microbial structure and function in these animals is reported here.  This is the largest and most comprehensive analysis of the feline gastrointestinal microbiome to date. It provides an overview of the taxa and gene functions present and how they are impacted by the dietary protein: carbohydrate ratio. The more diverse structure of the high-protein diet might reflect a more specialized microbiome. As anticipated, our permutation approach reduced the number of pathways to a more manageable set. The reduced data set identified six pathways readily interpretable to the study design.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005802	EMG produced TPA metagenomics assembly of PRJEB8087 data set (Metagenomes of Danish EBPR WWTPs).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8087, and was assembled with SPAdes v3.11.1, metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Engineered:Wastewater:Nutrient removal:Biological phosphorus removal:Activated sludge.	root:Engineered:Wastewater:Nutrient removal:Biological phosphorus removal:Activated sludge
MGYS00005800	EMG produced TPA metagenomics assembly of PRJNA275232 data set (Streptococcus thermophilus infected with lytic phage 2972).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA275232, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Engineered:Food production:Dairy products.	root:Engineered:Food production:Dairy products
MGYS00005801	Streptococcus thermophilus infected with lytic phage 2972	Many bacteria rely on CRISPR-Cas systems to provide adaptive immunity against phage, predation by which can shape the ecology and functioning of microbial communities. To characterize the impact of CRISPR immunization on phage genome evolution we performed long-term bacteria-phage (Streptococcus thermophilus  phage 2972) co-evolution experiments. We show that in this species CRISPR immunity drives fixation of single nucleotide polymorphisms that accumulate exclusively in phage genome regions targeted by CRISPR. Mutation rates in phage genomes highly exceed those of the host. The presence of multiple phage increased phage persistence by enabling recombination-based formation of chimeric phage genomes in which sequences heavily targeted by CRISPR are replaced. Collectively, results establish CRISPR-Cas adaptive immunity as a key driver of phage genome evolution under the conditions studied and highlight the importance of multiple co-existing phage for persistence in natural systems.	root:Engineered:Food production:Dairy products
MGYS00005798	EMG produced TPA metagenomics assembly of PRJNA60251 data set (Metagenome isolated from cow gut).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA60251, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Foregut:Rumen.	root:Host-associated:Mammals:Digestive system:Foregut:Rumen
MGYS00005799	Metagenome isolated from cow gut	The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation.  To characterize biomass-degrading genes and genomes, we sequenced and analyzed metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, we identified putative carbohydrate-active genes and expressed candidate proteins, of which 57% were enzymatically active against cellulosic substrates. We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass.	root:Host-associated:Mammals:Digestive system:Foregut:Rumen
MGYS00005796	EMG produced TPA metagenomics assembly of PRJNA427653 data set (Comprehensive Metagenomic).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA427653, and was assembled with SPAdes v3.12.0, SPAdes v3.11.1. This project includes samples from the following biomes: root:Mixed.	root:Mixed
MGYS00005797	Comprehensive Metagenomic	Microbiota as a functional assemblage of microbes plays an important role in environment and in lives of multicellular organisms. Animal gut microbiota is strongly influenced by dietary factors while soil microbial flora can be shaped by various physical, chemical, and biological conditions.	root:Mixed
MGYS00005795	EMG produced TPA metagenomics assembly of PRJEB23524 data set (WGS data from FMT trial for the treatment of recurrent Clostridium difficile infection).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB23524, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005793	EMG produced TPA metagenomics assembly of PRJNA510036 data set (Fecal transplant influence on healthy volunteers).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA510036, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005794	Fecal transplant influence on healthy volunteers	WGS metagenomics sequencing data describing fecal transplant influence on healthy voluntaries.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005791	EMG produced TPA metagenomics assembly of PRJNA385949 data set (Longitudinal Stool Study of patients with IBD and controls).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA385949, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005792	Longitudinal Stool Study of patients with IBD and controls	Longitudinal Stool Study of patients with IBD and controls. This project combines data from PRISM and STINKI cohorts to characterize the gut microbiome of individuals with IBD and controls over time.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005790	Hot spring thermophilic microbial communities from Obsidian Pool, Yellowstone National Park, USA - site 3 B9 metagenome		root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005785	EMG produced TPA metagenomics assembly of PRJEB35321 data set (Cotter Lab FF study).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB35321, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Engineered:Food production:Dairy products.	root:Engineered:Food production:Dairy products
MGYS00005786	Cotter Lab FF study	Cotter Lab FF study	root:Engineered:Food production:Dairy products
MGYS00005767	EMG produced TPA metagenomics assembly of PRJNA648297 data set (Remarkably low relative abundance of several Bifidobacterium species in the altered intestinal microbiota of Helicobacter pylori infected patients with gastric ulcer and gastric cancer).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA648297, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005779	Land use change effects on the soil microbiome of the rainforest of the northwest Colombian Amazon region.	This study aimed to characterize the microbiome present in both litter and the soil of rainforest in the northwest Colombian Amazon region, and the response of the microbiome to land use change. The study was conducted specifically in Belen de los Andaquies and Solano counties, in Caqueta state, the second most important hotspot of deforestation in the entire Amazon basin. Experimental study design included 4 study sites for comparing native forest to livestock pasture systems, within the main landscapes of the region, mountain and hill landscapes separately.	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00005784	EMG produced TPA metagenomics assembly of PRJEB43502 data set (Nitrogen fixation rates and cyanobacteria cover in a subarctic biological soil crust are enhanced by warming, wetting and light).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB43502, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil.	root:Environmental:Terrestrial:Soil
MGYS00005782	Transcriptome analysis of Antimicrobial peptide (AMP) treatments	We investigated the differential expression of genes in rumen-derived antimicrobial peptide treatments against two strains of Staphylococcus aureus.	root:Host-associated:Mammals:Digestive system:Foregut:Rumen
MGYS00005777	EMG produced TPA metagenomics assembly of PRJNA337758 data set (Marine microbial community from Cabo Rojo, Puerto Rico - PR CR 10% Liquid 3 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA337758, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005775	EMG produced TPA metagenomics assembly of PRJNA214436 data set (Pink berry consortia Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA214436, and was assembled with SPAdes v3.14.1, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00005776	Pink berry consortia Metagenome	Microbial consortia modulate biogeochemical cycles over short spatiotemporal scales that often elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the 'pink berry' consortia through an integrative, multidisciplinary study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PSB) of the family Chromatiaceae and sulfate reducing bacteria (SRB) from the Desulfobulbacaea. Metagenomic sequencing and the reconstruction of near-complete genomes for the PSB and SRB species reveals the genetic potential for sulfur cycling within the berries.    Macroscopic microbial aggregates from the Sippewissett salt marsh, dominated by anoxygenic phototrophs (purple sulfur bacteria) and sulfate reducing bacteria.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00005773	EMG produced TPA metagenomics assembly of PRJNA337836 data set (Marine sediment microbial community from La Parguera, Puerto Rico - PR Tt Sediment 1 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA337836, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Coastal:Sediment.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00005771	EMG produced TPA metagenomics assembly of PRJNA559386 data set (Sequencing of mouse gut microbiome with Nanopore Sequencing for whole genome analysis of DNA methylation.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA559386, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00005772	Sequencing of mouse gut microbiome with Nanopore Sequencing for whole genome analysis of DNA methylation.	Fecal pellets from a male 12-week-old NOD/shiltj mouse were collected before and after antibiotic treatment with Tylosin. DNA samples were extracted and sequenced with Nanopore sequencing. For each microbiome sample, nanopore sequencing raw signal is compared between the native and the WGA datasets to bin metagenomic contigs by genome of origin. Those information are also leverage to detect, classify, and fine-mapped DNA methylation across the genomes.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00005769	EMG produced TPA metagenomics assembly of PRJNA479723 data set (Nanopore metagenomics).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA479723, and was assembled with Flye v2.8.1. This project includes samples from the following biomes: root:Engineered:Wastewater:Water and sludge.	root:Engineered:Wastewater:Water and sludge
MGYS00005770	Nanopore metagenomics	WWTPs nanopore metagenomics	root:Engineered:Wastewater:Water and sludge
MGYS00005768	Remarkably low relative abundance of several Bifidobacterium species in the altered intestinal microbiota of Helicobacter pylori infected patients with gastric ulcer and gastric cancer	Stool sample	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005764	EMG produced TPA metagenomics assembly of PRJNA588037 data set (Strain-level identification of bacterial tomato pathogens directly from metagenomic sequences).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA588037, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Host-associated:Plants.	root:Host-associated:Plants
MGYS00005765	Strain-level identification of bacterial tomato pathogens directly from metagenomic sequences	Strain-level identification of bacterial tomato pathogens from Metagenomic samples sequenced with the Oxford Nanopore Technologies (ONT) MinION using ONT's WIMP software and the third party tools Sourmash, MetaMaps, and LINbase.	root:Host-associated:Plants
MGYS00005762	EMG produced TPA metagenomics assembly of PRJNA508395 data set (Nanopore long read assembly of the human gut metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA508395, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005763	Nanopore long read assembly of the human gut metagenome	Long read sequencing assembly of three healthy human gut microbiome samples, with multiple closed bacterial genomes including Prevotella copri.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005760	EMG produced TPA metagenomics assembly of PRJNA343503 data set (fruitshake sequence reads using Oxford Nanopore MinION).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA343503, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Host-associated:Plants.	root:Host-associated:Plants
MGYS00005761	fruitshake sequence reads using Oxford Nanopore MinION		root:Host-associated:Plants
MGYS00005758	EMG produced TPA metagenomics assembly of PRJNA676218 data set (Bioreactor co-culture microbial communities from Richmond, British Columbia, Canada - Phormidium sp. AB48 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA676218, and was assembled with Flye v2.8.3. This project includes samples from the following biomes: root:Engineered:Bioreactor:Continuous culture.	root:Engineered:Bioreactor:Continuous culture
MGYS00005759	Bioreactor co-culture microbial communities from Richmond, British Columbia, Canada - Phormidium sp. AB48 metagenome	Bioreactor co-culture microbial communities from Richmond, British Columbia, Canada	root:Engineered:Bioreactor:Continuous culture
MGYS00000570	Explore the effect of grass sickness on the equine faecal microbiome.	This study aims to explore the effect of grass sickness on the equine faecal microbiome by sequencing the faecal bacterial DNA of horses diagnosed with grass sickness and matched controls. Faeces was collected on rectal examination from ill horses and collected free falling from control horses. All samples were frozen at -80 until defrosted for bacterial DNA extraction.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005734	This study deals with 6 metagenomes of modified Winogradsky columns, enriched at 24 C and 28C. Furthermore three enrichment cultures are analysed, which are a mixed consortia of algae and bacteria.	This study deals with the consequences of global change scenarious on stratified microbial communities of lake ecosystems	root:Environmental:Aquatic
MGYS00003269	EMG produced TPA metagenomics assembly of the Marine microbial community from Cabo Rojo, Puerto Rico - PR CR 10% Liquid 1 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336694.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00005403	EMG produced TPA metagenomics assembly of the PRJNA336640 data set (Marine sediment microbial community from La Parguera, Puerto Rico - PR Tt Sediment 2 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336640.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00005275	EMG produced TPA metagenomics assembly of the Marine subseafloor sediment microbial communities, sample from White Oak River Estuary, NC, USA 14E metagenome (marine sediment metagenome) data set.	The marine sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA337846.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary, Sediment.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00005755	Microbiota composition of Parkinson's disease patients in southern Italy	In recent years, the hypothesis that gut microbiota associates with Parkinson's disease is growing, although a specific composition cannotbe taken as a predictive biomarker of this disease. Our main objective was to investigate dysbiosis of gut microbiota in a selected population of Parkinson's disease patients from center-south of Italy.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005747	Diversity and composition of rumen microbiome  in Sika deers (Cervus nippon yakushimae) from Yakushima Island, Japan	We characterized the rumen microbiota of wild Yaku sika population by high throughput sequencing of bacterial 16S rRNA genes. Rumen microbiota play a crucial role in digesting cellulolytic biomass for ruminant diet. Deer in Yakushima Island Japan, known as Yaku sika, graze a wide range of forage types, and have caused serious reduction of forest understory vegetation in the island while increasing their population. Dietary shifts in the host, observed especially with Yaku sika at highly populated areas, are expected to influence community composition in RM. Significantly higher diversity and distinct community structure were observed in Yaku sika from high-density areas compared to those from decreasing population density areas. These features may contribute to the flexibility of Yaku sika dietary shift and to maintain nutritional status under high density conditions.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00005746	Study on the dynamics of gastrointestinal bacteria in subadult shrimp (Litopenaeus vannamei) with acute hepatic pancreatic necrosis syndrome (AHPND)	?In order to study the response mechanism of shrimp gastrointestinal microbes to diseases, we collected the subadult shrimp with acute hepatopancreatic necrosis syndrome (AHPND). This study preliminarily discussed the gastrointestinal bacterial community structure variation and functional differentiation of subadults when AHPND outbreak, and provided a basis reference for the microbial ecological control of AHPND.	root:Host-associated:Arthropoda:Digestive system:Gut
MGYS00005745	Oral, vaginal, and intestinal microbiota analysis in pregnancy	Threatened preterm labor (TPL) and preterm birth (PTB) are significant obstetric complications during pregnancy. However, their triggers have not been fully elucidated. To identify the predisposing factors of TPL and PTB, this project analyzed the oral, vaginal, and rectal microbial profiles to identify potential inter-organ bacterial communication.	root:Host-associated:Human
MGYS00005744	Soil fungal diversity along elevation gradients	The goal of this study was to understand the diversity of soil fungi across elevational gradients and to disentangle the direct and indirect effects of climate conditions, plant communities and soil properties on soil fungal richness. This study was conducted in cool-temperate and sub-alpine forests in the University of Tokyo Chichibu Forest in central Japan. We used amplicon-based sequencing of ITS2 region (fITS7/ITS4) to characterize the soil fungal community.	root:Environmental:Terrestrial:Soil
MGYS00005754	Data of mycorrhizal fungi	Study of mycorrhizal fungi community. DNA was extracted from root tips of mycoheterotrophic plants and references.	root:Host-associated:Plants:Root
MGYS00005743	Subseafloor microbiome  project	A massive amount of microbial cells are present in the global subseafloor environment down to several kilometers below the seafloor. However, their diversity, quantity and biogeography have been largely unknown. In this project, we extracted, amplified DNA from the subseafloor microbiome by a consistent method for comparing microbial communities in different depths and sampling locations. Subsequently, we sequenced a partial sequence of 16S rRNA gene. The analyses of microbial compositions as well as correlation analysis with various environmental meta data will provide the information about the environmental factor controlling or constraining microbial composition.	root:Environmental:Aquatic:Marine:Sediment
MGYS00005753	Manure metagenome from Ceftiofur-treated dairy cow	We collected manure from a Ceftiofur treated dairy cow to investigate the abundance, mobility and host range of its antibiotic resistome using Nanopore and Pacbio technologies.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005751	Associated bacterial profiles in Porites lutea tissues affected by pink pigmentation response (PPR)	This study describes the changes in associated bacteria in the coral Porites lutea showing pink pigmentation response (PPR) using Metagenomic approach. Bacterial communities were isolated from healthy tissues of P. lutea, affected by PPR and recovered from PPR. Also samples isolated from surrounding waters and sediment were analyzed. Sediment samples showed higher diversity, followed by coral tissues showing PPR signs. Unclassified bacteria, particularly the bacteria CAB-I, BB2H16SI and Alphaproteobacteria, especially Methylobacterium predominated in PPR tissues. In contrast, Gammaproteobacteria, especially Endozoicomonas predominated in healthy tissues. We propose to use Endozoicomonas, CAB-I, BB2H16S and Methylobacterium as biomarkers to explore the progress and occurrence of PPR in P. lutea.	root:Host-associated:Invertebrates:Cnidaria:Coral
MGYS00005750	16S ribosomal RNA gene sequences from fermented foods	16S ribosomal RNA gene was amplified by PCR from traditional fermented foods and was analyzed by high-throughput sequencing.	root:Engineered:Food production:Fermented beverages
MGYS00005742	Asian Microbiome Project	Asia differs substantially among and within its regions populated by diverse ethnic groups, which maintain their own respective cultures and dietary habits. On the other hand, Oriental and Western cultures are now merging at many sites in Asia and affecting our life style, especially daily diets. To inquire into diversity in gut microbiota of Asian people, which must respond to daily diets and link to host health, Asian Microbiome Project (AMP) was established in 2009. AMP aims to build a basal microbiome database of Asians covering entire region and age group and gain an insight into the link between life style and gut microbiota. By sharing information and gained knowledge obtained in this project, we hope to promote health of Asian people.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005741	WL Reactor published in ME	"The data is the whole sequence data for the ""Bacterial population dynamics in a laboratory activated sludge reactor monitored by pyrosequencing of 16S rRNA"", Satoh et al. (2013), Microbes and Environments, 28(1), 65-70.  Bacterial community change in a laboratory activated sludge reactor was analyzed by NGS for around 8 months.  A sudden disappearance of a major population was observed around day 50th, and periodical increase and recessions were observed for many of the observed OTUs."	root:Engineered:Wastewater:Activated Sludge
MGYS00005740	Microbial communities associated with natural and commercially grown rooibos (Aspalathus linearis) plants	The Cape Floristic Region has an exceptionally high floral diversity and is recognized as one of the world''s biodiversity hotspots.  However, this region has a poor record of conservation and may endemic plant species are now classified as endangered.  One of the main threats to the region''s ecosystem is the overexploitation of economically valuable plant species such as rooibos (Aspalathus linearis).  The aim of this study was to determine the microbial rhizosphere community structures of rooibos plants in natural and commercial areas.  Rhizosphere soil, root samples and bulk soil were collected from natural and commercial rooibs sites located on two different farms situated in the Cederberg area, the north-western region of the fynbos biome.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00004323	Bacterial community of river sediment enriched with polycyclic aromatic hydrocarbons	16S rRNA gene amplicons (454-pyrosequencing) raw sequence reads of Chao Phraya River sediment enriched with polycyclic aromatic hydrocarbons. This study aimed to assess the biodegradation of mixed PAHs by indigenous bacteria in river sediment.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00005749	Effect of Bifidobacterium on the intestinal microbiota in rotavirus infected mice	Human rotavirus (RV) infection is a leading cause of dehydrating diarrhea in infants and young children worldwide. We evaluated the role of microbiota in RV infected mice, and the effect of probiotics. For DNA sequencing, DNA extraction from mixture of cecum and colonic contents from suckling mice on 2-5 days old was performed by bead beating and lysozyme digestion. 16S rDNA analysis of the microbial community structure in intestinal contents was performed using a MiSeq platform. The amplicon of V3-V4 region in 16S rDNA was purified using AMPure XP magnetic beads. The Illumina Nextera XT Index kit with dual 8-base indices was used to allow for multiplexing. PCR reactions were performed to incorporate two unique indices to the 16S amplicons. After purification with AMPure XP beads, the purified barcoded library was fluorometrically quantified using a QuantIT PicoGreen ds DNA Assay Kit. Libraries were then diluted to 4 nM using 10 mM Tris-HCl (pH 8.0), followed by pooling the same volume for multiplex sequencing. The multiplexed library pool (10 pM) was spiked with 35% PhiX control DNA (10 pM) to improve base calling during sequencing. Sequencing was conducted using a 2 x? 250-bp paired-end run with MiSeq Reagent Kit v2.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00005748	Microbial diversity on cafeteria kitchen	we conducted a biogeographical assessment of bacteria in a cafeteria kitchen to determine the diversity of microflora on each surface and to evaluate the spatial and temporal variations of the potential cross-contamination routes. High-throughput amplicon sequencing of the 16S rRNA gene from 13 surfaces in a cafeteria kitchen was performed every quarter for one year.	root:Engineered:Built environment
MGYS00005739	Metagenome sequencing of a mock fungal community consisting of 26 fungal species	We evaluated the efficacy of mycobiome analysis strategies using three NGS techniques, Illumina MiSeq, Life Technologies IonPGM, and Pacific Biosciences PacBio RS II sequencing to characterize a mock fungal community consisting of 26 species representing 15 genera.	root:Engineered:Lab enrichment
MGYS00005738	Fermentation microbiota in kusaya gravy	Kusaya is a traditional dried fish product manufactured in the Izu Islands in Japan.  Kusaya is produced by soaking fish in a unique brine called kusaya gravy, followed by drying of the fish. This kusaya gravy is a unique fermented gravy which is used repeatedly over several hundred years. In this project, the compositions of microbiota in kusaya gravy was analysed using pyrosequencing.	root:Engineered:Food production:Fermented seafood
MGYS00005650	Metagenomic and metatranscriptomic analysis of the microbial community in drinking water distribution systems of ground and surface waterworks in Finland	The water microbiome in the drinking water distribution systems (DWDSs) of five waterworks in Finland with different raw water sources and treatment processes was explored. The sampled DWDSs were from two waterworks AB with non-disinfected, recharged groundwater as source water and from three waterworks utilizing chlorinated water (two DWDSs of surface waterworks CD and one of ground waterworks E). The water microbiome was characterized by Illumina high-throughput sequencing technology.	root:Environmental:Aquatic:Freshwater:Drinking water:Delivery networks
MGYS00005737	Oil droplet biodegradation Trondheimsfjord Metagenome	We established a novel laboratory system to investigate biodegradation of Macondo oil dispersions (10 m or 30 m median droplet sizes) at low oil concentrations (2 mg L-1) in coastal Norwegian seawater at a temperature of 4-5C. Metagenomic analyses were performed on 0.5 - 1 g whole extracted DNA using Illumina HiSeq 100 bp paired end reads.	root:Engineered:Lab enrichment:Defined media:Marine media
MGYS00005735	Gut-microbiome of Tuberculosis patients	Gut-microbiome of Tuberculosis patients	root:Host-associated:Human:Digestive system:Intestine
MGYS00005590	The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology	Weaning has been described as one of the most stressful events in the life of horses. Given the importance of the interaction between the gut-brain axis and gut microbiota under stress, we evaluated (i) the effect of two different weaning methods on the composition of gut microbiota across time and (ii) how the shifts of gut microbiota composition after weaning affect the host. A total of 34 foals were randomly subjected to a progressive (P) or an abrupt (A) weaning method. In the P method, mares were separated from foals at progressively increasing intervals every day, starting from five min during the fourth week prior to weaning and ending with 6 h during the last week before weaning. In the A method, mares and foals were never separated prior to weaning (0 d). Different host phenotypes and gut microbiota composition were studied across 6 age strata (days 30, 0, 3, 5, 7, and 30 after weaning) by 16S rRNA gene sequencing. Results revealed that the beneficial species belonging to Prevotella, Paraprevotella, and Ruminococcus were more abundant in the A group prior to weaning compared to the P group, suggesting that the gut microbiota in the A cohort was better adapted to weaning. Streptococcus, on the other hand, showed the opposite pattern after weaning. Fungal loads, which are thought to increase the capacity for fermenting the complex polysaccharides from diet, were higher in P relative to A. Beyond the effects of weaning methods, maternal separation at weaning markedly shifted the composition of the gut microbiota in all foals, which fell into three distinct community types at 3 days post-weaning. Most genera in community type 2 (i.e., Eubacterium, Coprococcus, Clostridium XI, and Blautia spp.) were negatively correlated with salivary cortisol levels, but positively correlated with telomere length and N-butyrate production. Average daily gain was also greater in the foals harboring a community type 2 microbiota. Therefore, community type 2 is likely to confer better stress response adaptation following weaning. This study identified potential microbial biomarkers that could predict the likelihood for physiological adaptations to weaning in horses, although causality remains to be addressed.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00005733	Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 Pyrosequencing	Faecal samples were collected from seventeen animals fed three different diets (high fibre, high fibre supplemented with starch and high fibre supplemented with oil). DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced to investigate the faecal microbiome of the horse. The effect of age was also considered by comparing mature (8 horses aged 5-12) versus elderly horses (9 horses aged 19-28).A reduction in diversity was found in the elderly horse group and four OTUs were identified as significantly different from the adult group (P<0.001).These OTUs were predominantly in the order Clostridiales and were decreased in the elderly group. Significant differences between diets were also found at an OTU level (36 OTUs at P<0.001). The majority of differences found for both diet and age were related to the Firmucutes phylum (28) with some Bacteroidetes (4), Proteobacteria (2), Spirochaetes (1) and Actinobacteria (1).  With a high fibre diet ,with no added starch or oil, we found 30/2934 OTUs (accounting for 15.9% of sequences) present in all horses. However the core (i.e. present in all horses)  associated with a high oil supplemented diet was somewhat smaller (25/3029 OTUs, 10.3% ) and the core associated with a high oil supplemented diet was even smaller (15/2884 OTUs, 5.4% ). The core associated with samples across all three diets was extremely small (6/5689 OTUs accounting for only 2.3% of sequences) and dominated by the order Clostridiales, with the most abundant family being Lachnospiraceae. In conclusion, addition of starch or fat to the diet produced changes in the faecal bacterial community. Further, as observed in people, ageing is associated with a reduction in bacterial diversity and a change in the bacterial community structure.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005732	16S rRNA gene amplicon sequencing project of gut microbiota of deep-sea fish	We report 16S rRNA gene amplicon sequence analysis of gut microbiota of deep-sea fishes (Chlorophthalmus albatrossis, Glossanodon semifasciatus, and Helicolenus hilgendorfi) collected from Suruga Bay, Japan. The analysis revealed a low taxonomic diversity of gut microbiota in these deep-sea fishes.	root:Host-associated:Fish:Digestive system
MGYS00005729	Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows	Metaproteomics has substantially matured over the past years as a powerful tool to assess functional interactions in microbial communities. A wide variety of metaproteomic workflows is available, yet their impact on the results remains to be established.Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated the influence of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, lab-assembled human intestinal model and a human fecal sample.Although bioinformatic pipelines contributed to variability in peptide identification, wet-lab stages were the most important source of differences between analyses. Moreover, protein groups were less sensitive to those differences than peptides. Comparing taxonomic and functional profiles revealed differences between peptide- and protein-centric approaches at the taxonomic level but very similar functional profiles.These CAMPI findings present the current opportunities and challenges in metaproteomics research and provide a perspective for future benchmarking studies.	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00005726	Role of young olive trees in soil microbial communities after organic and mineral fertilization		root:Host-associated:Plants:Rhizoplane:Soil
MGYS00005724	EMG produced TPA metagenomics assembly of PRJNA330603 data set (Geotraces Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA330603, and was assembled with metaSPAdes v3.14.1 and MEGAHIT v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005723	Marine phages from the Arctic Ocean	"A combined set of 56 samples was isolated by the Suttle Laboratory from 16 different sites in the Arctic Ocean between September 1, 2002 and October 31, 2002.  The phage fraction was purified and sequenced using pyrophosphate sequencing (454 Life Sciences).    This is part of a global ocean survey of phage and virus sequences.   454 sequence data is available from the Short Read Archive (SRA): <a href=""ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000410 "">SRA000410</a>.   Metagenomics SEED ID: 4440306.3  Nature paper ID: 34  The WGS project can be found using the Project data link."	N/A
MGYS00005722	EMG produced TPA metagenomics assembly of PRJNA17769 data set (Marine phages from the Arctic Ocean).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA17769, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005721	Nitrogen fixation rates and cyanobacteria cover in a subarctic biological soil crust are enhanced by warming, wetting and light	biocrust, N-fixation, metagenomes, warming, microbAbstract textIntroduction. Areas of high latitude with volcanic andosol and winter snow cover commonly have a 3-5 mm thick biological soil crust (biocrust) characterized by the leafy liverwort Anthelia juratzkana. This biocrust can be long term or transient, especially as snow cover decreases. Although Antheliais the primary producer, the biocrust is a complex microbial community with substantial biomass and biological activities associated with bacteria and fungi. Available nitrogen is thought to bethe limiting nutrient.Methods. Acetylene reduction assays (ARA) were used as a proxy in assessing biocrust responses to temperature, moisture and light. Soil carbon and nitrogen isotopes were measured and shotgun metagenomic DNA and RNA libraries were sequenced. Decomposition rates were assessed using the tea bags index. Respiration was measured with a LI-6400 system.Results. ARA measurements yielded estimates of nitrogen fixation of 1-4 kg ha-1 yr-1. Nitrogen fixation increases with temperature up to 25 oC, with light up to ~150 moles photons m-2 s-1 as well as with moisture. In situ summer daylight is 300-3000 moles photons m-2 s-1, moisture is from 4% to saturation, and temperatures show strong diurnal cycles from 5 oC to 30 oC on sunny days. Warming effects on decomposition varied with depth and type of tea. Respiration measurements gave an estimate of ~100 kg C ha-1yr-1.There is a highly negative isotope discrimination of 15N vs. 14N in the biocrust, possibly due to fractionation between multiple compartments, from bacteria to fungi and liverworts. The microbial community is diverse, with small differences between locations and habitats. Ascomycete fungi are abundant in the surface layer, particularly the orders Heliotales and Chaetothyriales.Conclusions. Integration of in situ measurements, meteorological information and data from laboratory experiments allows us to estimate nitrogen fixation from year to year, and what effects predicted climate changes are likely to have.	root:Environmental:Terrestrial:Soil
MGYS00005608	Equine Intestinal Microbiome in Hypersensitivity Disorders	Background: Recent evidence suggests that an altered intestinal microbiome, namely a reduction of bacterial diversity or a shift in microbial composition, is associated with the development of hypersensitivity diseases in humans but this is unknown for horses.Hypothesis: We hypothesized that horses affected by either Culicoides hypersensitivity (CH) or severe equine asthma (SEA) or both show a decreased diversity of their intestinal microbiome in comparison to healthy peers.Methods: Rectal swab samples of a total of 140 horses were collected. Horses were divided into three groups. CH comprised 30 horses affected by Culicoides hypersensitivity, group SEA consisted of 30 horses suffering from severe equine asthma and group CH-SEA comprised 10 horses affected by both aforementioned diseases. For each allergic horse a healthy peer from the same stable was similarly sampled as a matched control. Microbiota in the swabs were determined by assessing the V4 region of the bacterial 16S rRNA gene by means of Illumina MiSeq. Structures of bacterial communities were investigated by means of alpha and beta diversity indices.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00001977	EMG produced TPA metagenomics assembly of the Ocean Sampling Day (OSD) 2014: AUTHORITY-RAW amplicon and metagenome sequencing study from the June solstice in the year 2014 (osd-2014) data set	The osd-2014 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set, PRJEB8682. This project includes samples from the following biomes : Marine	root:Environmental:Aquatic:Marine
MGYS00005720	Picoplankton 16S rRNA genes from the tropical and sub-tropical global-ocean sampled during the Malaspina-2010 expedition	"Surface global ocean prokaryotic picoplankton from the Malaspina-2010 expedition: Surface waters (3m depth) from a total of 122 globally-distributed stations located in the tropical and sub-tropical global ocean were sampled from December 2010 to July 2011 as part of the Malaspina-2010 expedition (Duarte 2015). Water samples were obtained with Niskin bottles attached to a CTD profiler that included sensors for conductivity, temperature, oxygen, fluorescence and turbidity. About 12L of seawater were sequentially filtered through a 20m nylon mesh, followed by a 3m and 0.2m polycarbonate filters of 47mm diameter. Only the picoplankton size-fraction (0.2-3 m) was used for sequencing. DNA was extracted using a standard phenol-chloroform protocol (Massana, et al. 1997). The V4-V5 region of the 16S rRNA gene was amplified with the primers 515F-Y (5'-GTGYCAGCMGCCGCGGTAA) and 926R (5'-CCGYCAATTYMTTTRAGTTT)  (Parada et al. 2016) and sequenced in an Illumina MiSeq platform (2x250bp) at the Research and Testing Laboratory  (Lubbock, Texas, USA; http://www.researchandtesting.com).

Duarte CM. 2015. Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition. Limnology and Oceanography Bulletin 24:11-14.

Massana R, Murray AE, Preston CM, DeLong EF. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Applied and environmental microbiology 63:50-56.

Parada AE, Needham DM, Fuhrman JA. 2016 Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 18: 1403-14."	root:Environmental:Aquatic:Marine
MGYS00005719	Picoplankton 18S rRNA genes from the tropical and sub-tropical global-ocean sampled during the Malaspina-2010 expedition	Surface global ocean eukaryotic picoplankton from the Malaspina-2010 expedition: Surface waters (3m depth) from a total of 122 globally-distributed stations located in the tropical and sub-tropical global ocean were sampled from December 2010 to July 2011 as a part of the Malaspina-2010 expedition (Duarte 2015; Estrada, et al. 2016). Water samples were obtained with Niskin bottles attached to a CTD profiler that included sensors for conductivity, temperature, oxygen, fluorescence and turbidity. About 12L of seawater were sequentially filtered through a 20m nylon mesh, followed by a 3m and 0.2m polycarbonate filters of 142mm diameter (Isopore, Millipore). Only the picoplankton size-fraction (0.2-3 m) was used for sequencing. DNA was extracted using a standard phenol-chloroform protocol (Massana, et al. 1997). The V4 region of the 18S (~380 bp) was amplified with the primers TAReuk454FWD1 and TAReukREV3 (Stoeck, et al. 2010). Duarte CM. 2015. Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition. Limnology and Oceanography Bulletin 24:11-14.Estrada M, Delgado M, Blasco D, Latasa M, Cabello AM, Benitez-Barrios V, Fraile-Nuez E, Mozetic P, Vidal M. 2016. Phytoplankton across Tropical and Subtropical Regions of the Atlantic, Indian and Pacific Oceans. PLoS One 11:e0151699.Massana R, Murray AE, Preston CM, DeLong EF. 1997. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Applied and environmental microbiology 63:50-56.Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW, Richards TA. 2010. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular ecology 19 Suppl 1:21-31.	root:Environmental:Aquatic:Marine
MGYS00005718	Picoplankton 18S rRNA gene sequences (V4 region, DNA and RNA) from Vertical Profiles (surface to 4000m depth) sampled during the Malaspina 2010 circumglobal expedition	The study here includes 182 samples (91 DNA and 91 RNA) of the 18S (V4 region) from the Malaspina-2010 expedition. The samples were sequenced using Illumina MiSeq 2x250bp.	root:Environmental:Aquatic:Marine
MGYS00005717	Picoplankton 18S rRNA gene sequences (V9 region) from Vertical Profiles (surface to 4000m depth) sampled during the Malaspina 2010 circumglobal expedition	The study here includes 40 samples (DNA) of the 18S (V9 region, DNA) from the Malaspina-2010 expedition. The samples were sequenced using Illumina MiSeq 2x250bp.	root:Environmental:Aquatic:Marine
MGYS00005715	Biogeography of Arctic picoeukaryotes during summer of 2012	Information on recent photosynthetic biomass distribution and biogeography of Arctic marine pico-eukaryotes (0.2  3 m) are needed to better understand consequences of environmental change for Arctic marine ecosystems. We analysed pico-eukaryote biomass and community composition in Fram Strait and larger parts of the central Arctic Ocean (Nansen Basin, Amundsen Basin) by chlorophyll a (Chl a) measurements, Automated Ribosomal Intergenic Spacer Analysis (ARISA), and 454-pyrosequencing. Samples were collected during summer 2012, the year with the latest record sea ice minimum. Chl a values were highest in eastern Fram Strait and pico-plankton accounted for 60-90% of Chl a biomass during the observation period. ARISA-patterns and 454-pyrosequencing revealed, that pico-eukaryote distribution is closely related to water mass distribution in the euphotic zone of the Arctic Ocean. Phaeocystaceae, Micromonas sp., Dinophyceae and Syndinales constitute a high proportion of sequence reads, while sequence abundance of autotrophic Phaeocystaceae and mixotrophic Micromonas sp. was inversely correlated. Highest sequence abundances of Phaeocystaceae were observed in the warm Atlantic waters in Fram Strait, while Micromonas sp. dominated the abundant biosphere in the arctic halocline. Our results are from particular interest, because there are hypotheses that environmental conditions in Nansen Basin might become more similar to the current conditions in Fram Strait. In regard to this we propose that in response biodiversity and biomass of pico-eukaryotes in Nansen Basin could resemble those currently observed in the Fram Strait in the future. This would significantly alter biogeochemical cycles in that area, that constitutes a large part of the central Arctic Ocean.	root:Environmental:Aquatic:Marine
MGYS00004076	"Pyrosequencing reveals effect of increased pCO2 on bacterial assemblage
                shifts in response to glucose addition in Fram Strait seawater
                mesocosms"	"Ocean acidification (OA) may stimulate primary production through
                increased availability of inorganic carbon in the photic zone, which may in turn
                change the biogenic flux of dissolved organic carbon (DOC) and the growth potential
                of heterotrophic bacteria. In order to investigate the effects of OA on marine
                bacterial assemblages, a two-by-three factorial mescosom experiment was conducted
                using surface seawater from the East Greenland Current in Fram Strait.
                Pyrosequencing of the V1-V2 region of bacterial 16S ribosomal RNA genes was used to
                investigate differences in the endpoint (Day 9) composition of bacterial assemblages
                in mineral nutrient-replete mesocosms amended with glucose (0 M, 5.3 M and 15.9
                M) under ambient (250 atm) or acidified (400 atm) partial pressure of CO2 (pCO2).
                All mesocosms showed low richness and evenness by Chao1-estimator and Shannon-Wiener
                diversity index, respectively, with general dominance by Gammaproteobacteria and
                Flavobacteria. Non-metric multidimensional scaling analysis and two-way analysis of
                variance of the Jaccard dissimilarity matrix (97% similarity cut-off) demonstrated
                that the significant community shift between 0 M to 15.9 M glucose addition at 250
                atm pCO2 was eliminated at 400 atm pCO2. These results suggest that the response
                potential of marine bacteria to DOC input may be altered under acidified
                conditions."	root:Environmental:Aquatic:Marine
MGYS00005714	Protist communities in moored long-term sediment traps (Fram Strait, Arctic)  Preservation with mercury chloride allows for PCR-based molecular genetic analyses	Protist communities in moored long-term sediment traps (Fram Strait, Arctic)  Preservation with mercury chloride allows for PCR-based molecular genetic analyses	root:Environmental:Aquatic:Marine
MGYS00005713	Microbial community 16S rRNA from Fram Strait water samples PS85 2014	Several depths of the full water column of two stations (HGIV and N4) were sequenced in order to correlate the communities of the Fram Strait water column at HAUSGARTEN with benthic communities. DNA from CTD samples was extracted and the v3v4 region of the 16S rRNA was sequenced with Illumina MiSeq.	root:Environmental:Aquatic:Marine
MGYS00005712	Pelagic eukaryotic communities across Fram Strait	"Water samples were collected in Fram Strait during the Polarstern cruise PS85 (June 6th 2014
                until July 3rd 2014) from eastern Greenland shelf to west coast of Spitsbergen. For assessing eukaryotic
                community composition 2 L of water were filtered using vacuum filtration (at 200 mbar) through
                successive membrane filters of 10 m , 3 m and 0.4 m. The extracted genomic eukaryotic DNA was pulled
                together from the different fractions and the hypervariable V4 (528iF - 964iR) region of the 18S rRNA
                was amplified and sequenced using Illumina MiSeq platform in a 2  300 bp paired-end run."	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005711	Pelagic bacterial communities across Fram Strait	"Water samples were collected in Fram Strait during the Polarstern cruise PS85 (June 6th 2014
                until July 3rd 2014) from eastern Greenland shelf to west coast of Spitsbergen. For assessing bacterial
                community composition 2 L of water were filtered with peristaltic pump through successive membrane
                filters of 3 m and 0.22 m. The extracted genomic bacterial DNA was isolated and the hypervariable
                V3-V4 (341F - 785R) region of the bacterial 16S rRNA was amplified and sequenced using Illumina MiSeq
                platform in a 2  300 bp paired-end run."	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005710	Universal Amplicon Sequences (mixed 16S/18S) from GEOTRACES Cruises GA03 and GP13	Dedicated sampling campaigns such as JGOFS, CLIVAR, and GEOTRACES have quantified critical oceanic biogeochemical processes on a global scale. Integrating these measurements with microbial community composition data is highly desirable because it would allow hypotheses about biogeographic distributions to be tested or perhaps lead to the discovery of organisms responsible for a particular biogeochemical process. A promising strategy to generate this microbial community composition data comes from high-throughput sequencing of PCR amplicons generated with the 515Y/926R universal 16S/18S primer set. The two key advantages of the 515Y/926R primers are 1) their comprehensiveness - recovering amplicons from the entire cellular microbial community - and 2) their quantitative nature - recovering gene copy abundances as shown previously with microbial community standards. Compared to metagenomes, amplicons additionally have the advantage of more easily detecting rare community members that may be biogeochemically significant (e.g. diazotrophs). In this study, we applied the 515Y/926R primers to DNA from the recently published bioGEOTRACES metagenomic dataset, and use these results to describe microbial community composition across a longitudinal transect of the southern Pacific Ocean from Australia to Tahiti (GEOTRACES section GP13) and a longitudinal transect of the northern Atlantic from Massachusetts to the Canary Islands (GEOTRACES section GA03). In addition, we conducted intercomparisons with metagenomic taxa abundances and show the two techniques correspond strongly to one another for most samples (average R^2=0.97).	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005709	Moorea Reef Archaea and Eukaryota gene survey	The Moorea Coral Reef (MCR) LTER (17.50 S, 149.83 W) is comprised of the coastal fringe of coral reefs and lagoons that surround the volcanic island of Moorea in the society islands of French Polynesia. The MCR LTER project is co-managed by the University of California Santa Barbara and California State University, Northridge, and field operations are conducted from the University of California Berkeley''s Gump Research Station situated on Cooks Bay. Primary research interests include studies of population dynamics of local corals, nutrient dynamics and diversity studies. For the MCR portion of the MIRADA project we have incorporated investigators from the Marine Biological Laboratory, UCSB faculty, faculty at Moorea''s Gump research station, the Sea Education Association''s semester at sea cruise, and have incorporated an NSF REU undergraduate in 2009 for water sampling and sample analyses. The fringing reefs off the MCR LTER lie at the interface between populated terrestrial coastlines and unproductive, oligotrophic oceanic waters. Our goal within the MIRADA project is to study the changes in microbial population patters along a transect from the island, through Cooks Bay, into the lagoon and across the fringing reef into the open ocean. In 2008 and 2009 the Marine Biological Laboratory MIRADA project partnered with the Sea Education Association to undertake offshore water sampling and geochemical analyses, incorporating an REU student in the 2009 cruise and subsequent laboratory sample analyses. We are primarily interested in the effects of the island and the fringing reef on the microbial population in terms of diversity, species richness, and correlations of specific microbial groups with local geochemical conditions. We are also interested in seasonal comparisons from samples taken in January, 2008 (summer, rainy season) and samples from the same stations collected in June, 2009 (winter, dry season) to assess the impacts of anthropogenic inputs on near- and off-shore communities. We will look for the presence of landscape-scale patterns of diversity and richness from near shore, lagoon and offshore microbial communities within all three domains, signature communities representative of specific geographic and geochemical milieu, and the co-occurrence of specific groups within the ecosystem. Preliminary sequence data analyses suggest that there is a significant correlation between the geographical region (bay, lagoon, offshore open water) and bacterial sequence diversity. We found that significant differences in community diversity can be identified from samples taken from inside and outside the fringing reef, as well as those taken from the bay and the adjacent lagoon. In further analyses we hope to identify seasonal profiles and include environmental variables to assess the breadth of this pattern. We are also in the process of completing a seasonal comparison of the MCR LTER cyanobacterial community using v6 rRNA and ntcA gene sequence data, as well as gene sequences culled from the Global Ocean Survey metagenomic dataset samples that were collected in close proximity to our offshore sites. This data can then be compared to other coastal ocean MIRADA LTER sites (e.g. Palmer Station, Santa Barbara Coastal and Virginia Coast Reserve) to identify patterns in nearshore and coastal ocean microbial populations.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004123	The Indigo Project: a global citizen science Ocean survey	Sequencing the microbiome of the world''s Oceans with data collected by citizen sailing oceanographers	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005495	Detailed study at the genetic level at bacteria in farm animals, human/animal sewage, sewage treatment works and rivers, to work out the complex network of transmission of important antibiotic-resistant bacteria and antibiotic resistance genes	"OVERALL STUDY AIM
We do not fully understand how important types (species) of bacteria and packages of genetic material (genes) coding for antibiotic resistance move between humans, animals and the environment, or where, how and why antibiotic resistance emerges. This study aims to look in detail at the genetic level at bacteria in farm animals, human/animal sewage, sewage treatment works and rivers, to work out the complex network of transmission of important antibiotic-resistant bacteria and antibiotic resistance genes. We will use this information to work out how best to slow down the spread of antibiotic resistance between humans, livestock and the environment.

STUDY BACKGROUND AND AIMS IN MORE DETAIL
Infections are one of the most common causes of ill-health in human and animal medicine, and are caused by a range of different micro-organisms, including viruses and bacteria. Amongst bacteria, there are some species, or types, of bacteria, which can live harmlessly in human and animal intestines, sewage, and rivers, but can also cause disease in humans and animals if they get into the wrong body space, such as the bloodstream or urine. Examples of these bacteria include E. coli, and other similar organisms, which belong to a family of bacteria called ""Enterobacteriaceae"".It has generally been possible to treat infections caused by bacteria using several classes of medicines, known as antibiotics. Different antibiotics kill bacteria in different ways: for example, they can switch off critical chemical processes that the bacteria need to survive, or they can break down the outer shell of the bacteria. In response to the use of antibiotics, bacteria have changed over time, finding ways to alter their structure so that antibiotics no longer have a target to act on, or by producing substances that break down the antibiotic before it has a chance to kill the bacteria. These changes to the bacteria's genetic code, so that they are no longer killed by an antibiotic, create antibiotic resistance. Bacteria can also acquire packages of genes that cause antibiotic resistance from other surrounding bacteria. This is known as horizontal gene transfer. Through these mechanisms, members of the Enterobacteriaceae family of bacteria have developed antibiotic resistance to a number of different antibiotics over a short period of time. In some cases we are no longer able to treat these infections with the antibiotics we have available.Studying antibiotic resistance and horizontal gene transfer in bacteria found in humans, animals and the environment is difficult because we cannot directly see how bacteria and their genetic material move between them. However, new ""Next Generation Sequencing"" (NGS) technologies allow scientists to look in great detail at the genetic code of large numbers of bacteria. Comparing this information across bacteria which have been living in the different parts of the environment (e.g. sewage treatment works, rivers) and in human and animal sewage allows us to see how bacteria have evolved to become resistant to antibiotics, and how resistance genes have been shared between them.This study will use NGS technologies to look at the genetic code of large numbers of Enterobacteriaceae bacteria found in humans, animals (pigs, sheep and poultry), sewage (pre-, during and post-treatment), and rivers. These different groups/areas will be sampled in different seasons of one calendar year to determine how antibiotic resistance genes move around between these locations and over time, and what factors might influence this movement. We will also be investigating whether various chemicals and nutrients in the water may be affecting how quickly horizontal gene transfer occurs. Understanding this is essential to work out how we might intervene more effectively to slow the spread of antibiotic resistance genes and bacteria, and keep our antibiotic medicines useful."	root:Mixed
MGYS00005707	EMG produced TPA metagenomics assembly of PRJNA419970 data set (Metagenomic analysis exploring soil microbial communities associated with Antarctic vascular plants).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA419970, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00005708	Metagenomic analysis exploring soil microbial communities associated with Antarctic vascular plants	The Antarctic ecosystem is one of the most stressful natural habitats, especially for terrestrial plants. Likewise, only two vascular plants have colonized the Antarctic environment, Colobanthus quitensis (Caryophyllaceae) and Deschampsia antaractica (Poaceae). Although both plants colonize Antarctica, C. quitensis is mainly found growing in association with D. antarctica in more stressful areas, while D. antarctica is capable to grow alone in areas with higher abiotic stress. Positive inter-specific interactions play a pivotal role in the structure and functioning of several ecosystems in harsh environments, and possibly they play a role in Antarctic terrestrial ecosystems.In this study, we compare the rhizosphere microbiomes associated with Colobanthus quitensis, either growing alone or associated with Deschampsia antarctica, using shotgun metagenomic DNA sequencing technology for comparative metagenomics. This approach allows us to gain insight into the rhizospheric microbial community structure associated with C. quitensis and C. quitensis  D. antarctica, through the study of soil's microbial taxonomic diversity, including non-culturable organisms. Such analysis could also provide valuable information regarding microbial functional diversity. This functional diversity might be playing important roles in conferring different degrees of tolerance to Antarctica's harsh environmental conditions such as low temperatures, desiccation, and low water and nutrient availability, which could help to explain the enigma of the success of these plant species in such harsh environments.	root:Host-associated:Plants:Rhizosphere
MGYS00005706	cvxcv	xvxvxcvx	root:Host-associated:Amphibia
MGYS00005704	EMG produced TPA metagenomics assembly of PRJNA318384 data set (marine metagenome Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA318384, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005705	marine metagenome Metagenome	Marine plastic debris has become a significant concern in ocean ecosystems worldwide. Little is known however, about its influence on microbial community structure and function. In 2008, we surveyed microbial communities and metabolic activities in seawater and on plastic on an oceanographic expedition through the 'Great Pacific garbage patch'. The concentration of plastic particles in surface seawater within different size classes (2-5 mm and > 5 mm) ranged from 0.35-3.7 particles m-3 across sampling stations. These densities and the particle size distribution were consistent with previous values reported in the North Pacific Ocean. Net community oxygen production (NCP = gross primary production  community respiration) on plastic debris was positive and so net autotrophic, whereas NCP in bulk seawater was close to zero. Scanning electron microscopy and metagenomic sequencing of plastic-attached communities revealed the dominance of a few metazoan taxa, and a diverse assemblage of photoautotrophic and heterotrophic protists and bacteria. Bryozoa, Cyanobacteria, Alphaproteobacteria and Bacteroidetes dominated all plastic particles, regardless of particle size. Bacteria inhabiting plastic were taxonomically distinct from surrounding picoplankton, and appeared well adapted to a surface-associated lifestyle. Genes with significantly higher abundances among plastic-attached bacteria included che genes, secretion system genes and nifH genes, suggesting enrichment for chemotaxis, frequent cell-to-cell interactions and nitrogen fixation. In aggregate, our findings suggest that plastic debris forms a habitat for complex microbial assemblages that have lifestyles, metabolic pathways and biogeochemical activities that are distinct from free-living planktonic microbial communities.	root:Environmental:Aquatic:Marine
MGYS00005703	Natural product discovery via metatranscriptomic analysis of three Caribbean octocoral species.	Octocorals are an important source of bioactive natural products such as the pseudopterosin family of diterpene glycosides which exhibit potent anti-inflammatory activity. Despite the promising activity of these molecules their clinical development has been hampered by a lack of sustainable supply. Identification of the genes that direct natural product biosynthesis in octocorals would set the stage for further development of octocoral-derived natural products. Identification of these genes is complicated by the complex symbiotic assemblage hosted by octocorals, which is composed of both eukaryotic and prokaryotic symbionts. As a first step in elucidating natural product biosynthesis in octocorals we acquired metatranscriptomic datasets from two Caribbean octocorals. This data will be analyzed to identify transcripts related to natural product biosynthesis.	root:Host-associated:Cnidaria
MGYS00002035	EMG produced TPA metagenomics assembly of the Light-dependent microbial metabolisms drive carbon fluxes on glacier surfaces (Ecosystem functions in cryoconites) data set	The Ecosystem functions in cryoconites Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB12327. This project includes samples from the following biomes : Freshwater.	root:Environmental:Aquatic:Freshwater:Ice:Glacier
MGYS00005702	EMG produced TPA metagenomics assembly of PRJNA389280 data set (Human gut metagenome and metatranscriptome in the inflammatory bowel disease (iHMP/HMP2)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA389280, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005701	Prokaryotic Community Profiling of the Mt. Makiling Mudspring	This study aims to determine the prokaryotic community thriving in the Mt. Makiling Solfaratic Mudspring in Los Banos, Laguna, Philippines using 16S rRNA gene amplicon Next Generation Sequencing Technology.	root:Environmental:Terrestrial:Volcanic
MGYS00005700	Effect of zinc and alternative compound on pigs' microbiota	Samples have been taken to look at changes in the gut microbiome when weaning piglets are supplemented with zinc or with an alternative compound.	root:Host-associated:Mammals:Digestive system
MGYS00005699	MF_PPS5_Study_1	Study inside facility	root:Mixed
MGYS00005697	EMG produced TPA metagenomics assembly of PRJDB4115 data set (Metgenomic analysis of human saliva microbiome from healthy subjects).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJDB4115, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00005698	Metgenomic analysis of human saliva microbiome from healthy subjects	Metgenomic analysis of human saliva microbiome from healthy subjects. Saliva microbiome from 6 healthy individual.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00005695	EMG produced TPA metagenomics assembly of PRJEB37199 data set (Microbial community dynamics of a polyester film-degrading marine enrichment culture).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB37199, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005696	Microbial community dynamics of a polyester film-degrading marine enrichment culture	"In this study, we present a multiomics approach to elucidate the biodegradation mechanism of a commercial aromatic-aliphatic copolyester film by a marine microbial enrichment culture. Marine seawater and eulittoral sediment samples were collected from three different sources: Helgoland, Germany (5411 17.0"" N 752 50.1"" E), near Athens, Greece (3753 33"" N, 2324 30"" E) and Elba, Italy (4244 00.8"" N 1009 14.4"" E). The enrichment cultures were made by inoculating the seawater/sediment slurry in marine minimal medium containing the polyester film as sole C source. Community composition and function was examined by metagenome/transcriptome analysis a)of the plastic biofilm/free-living fractions separately, b) after a starvation period (t0) and addition of new plastic substrate after one hour (t1), 24 hours (t2) and seven days (t3). In addition to the plastic film, the culture was grown on each monomer separately and metagenomes were analysed for each different growth condition."	root:Environmental:Aquatic:Marine
MGYS00005321	EMG produced TPA metagenomics assembly of the Gut and Oral Microbiome Dysbiosis in Rheumatoid Arthritis (RA) data set.	The RA Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6997.  This project includes samples from the following biomes: Host-associated, Human, Digestive system.	root:Host-associated:Human:Digestive system
MGYS00005693	EMG produced TPA metagenomics assembly of PRJEB28422 data set (The Salivary Microbiome in Health and Disease).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB28422, and was assembled with SPAdes v3.14.1, metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00005694	The Salivary Microbiome in Health and Disease	Several diseases have been associated with with shifts in the salivary microbiome. Here we explore such links in a case control cohort for colorectal cancer (see PMID:25432777, BioProject ERP005534 for matched fecal samples), amended by an independent time series of healthy controls (see PMID:25888008, BioProject ERP009422 for matched fecal samples).	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00005692	Samples of a study the Venice lagoon from a functional perspective via metagenomics.	The samples belong to a project aiming to study the Venice lagoon from a functional perspective via metagenomics.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00005679	EMG produced TPA metagenomics assembly of PRJNA649273 data set (Kidney stone patient microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA649273, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system.	root:Host-associated:Human:Digestive system
MGYS00005690	EMG produced TPA metagenomics assembly of PRJDB7293 data set (Metagenomic analysis of Kirishima hot springs).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJDB7293, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005691	Metagenomic analysis of Kirishima hot springs	Metagenomic sequencing analysis of the 9 hot springs in the Kirishima region in Kyushu's Kagoshima prefecture.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005688	EMG produced TPA metagenomics assembly of PRJNA335670 data set (Metagenomic Sequencing of Hot Springs from Central India).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA335670, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005689	Metagenomic Sequencing of Hot Springs from Central India	The Sequencing of metagenomic samples from Hot Springs of Central India	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005686	EMG produced TPA metagenomics assembly of PRJEB39386 data set (Estuarine microbiome exposed to copper oxide nanoparticles).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB39386, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Estuary:Sediment.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00005687	Estuarine microbiome exposed to copper oxide nanoparticles	"Nanomaterials usages are increasing in multiple fields. With a large spectrum of applications, the impact of nanomaterials on natural ecosystems is a growing concern in environmental science and management. Methods for nanomaterials removal from wastewaters are yet developing and currently a significant fraction of nanomaterials escapes treatment plants. As a result estuaries are becoming the final repository for nanomaterials. The implications of this towards biota have been assessed, but usually at higher concentrations than the environmentally-predicted. Moreover, the impact of nanoparticles towards ecosystem services has seldom been reported.
The aim of this project was to ascertain whether deposition of copper oxide nanoparticles (Cu NPs) in estuarine sediments will change metal speciation and bioavailability, which will in turn impact the composition and functionality of the estuarine microbial communities. For this project we selected the Douro River estuary (North Atlantic), which is of major importance in its geographical area as its watershed drains 17 % of the Iberian Peninsula.
We performed a series of microcosms enrichment experiments exposing estuarine sediments to Cu NPs, of size <50 nm, at a concentration of 10 ng/g, tested for 4 h, 7h and 24 h. The microcosms pH and dissolved oxygen was monitored, as well as concentrations of nitrate, nitrite and ammonium. DNA was extracted from the sediment and sequencing was performed using Illumina Hiseq Xten to acquire 150 bp paired-end sequences. This generated 18 Gbp per sample, after filtering adaptor sequences, contamination and low-quality reads. Links were identified between the microbial community and ecosystems services they might provide, namely the service of removing fixed nitrogen, which is critical in eutrophic ecosystems."	root:Environmental:Aquatic:Estuary:Sediment
MGYS00005684	EMG produced TPA metagenomics assembly of PRJNA628604 data set (Oral capsulized Fecal microbiota transplantation for eradication of carbapenemase-producing Enterobacteriaceae colonization with a metagenomic perspective).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA628604, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005685	Oral capsulized Fecal microbiota transplantation for eradication of carbapenemase-producing Enterobacteriaceae colonization with a metagenomic perspective	Carbapenemase-producing Enterobacteriaceae (CPE) infections lead to considerable morbidity and mortality. We assessed the potential of fecal microbiota transplantation (FMT) to eradicate CPE carriage and to explain failure or success through microbiome analyses.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005683	EMG produced TPA metagenomics assembly of PRJEB22062 data set (As part of the EFFORT project, we sampled feces from pig and poultry livestock in nine European countries (BE, BG, DK, FR, ES, GE, NL, PL, SP). More than 9000 animals were sampled, across 181 pig and 178 poultry herds to generate herd-level composite fecal samples. Using shotgun metagenomics, we have quantified and characterized the antimicrobial resistance gene pools (resistomes) in Europes two most intensively raised livestock species.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB22062, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system.	root:Host-associated:Birds:Digestive system
MGYS00005682	EMG produced TPA metagenomics assembly of PRJNA193217 data set (Chicken cecal contents Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA193217, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00005680	EMG produced TPA metagenomics assembly of PRJNA291299 data set (Caecal microbiome metagenome of laying hens).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA291299, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00005681	Caecal microbiome metagenome of laying hens	To evaluate the effects of feeding prebiotic, probiotic and synbiotic on the functional potential of caecal microbiome	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00002264	Gene expression anlayses of saliva-derived in vitro biofilms during carbohydrate fermentation and pH stress	Dental caries, one of the most globally widespread infectious diseases is intimately linked to pH dynamics. In supragingival plaque, after the addition of a carbohydrate source, bacteria rapidly decrease the pH which then subsequently recovers. In this project we studied gene transcription in naturally diverse saliva-derived in vitro grown biofilms as they were amended with sugar (corresponding to a dietary intake of carbohydrates). We applied an in vitro biofilm model system that was previously determined to be functionally and taxonomically robust and representative of health-associated dental plaque. The major goal was to characterize critical gene expression mechanisms supporting the understudied pH-recovery stage associated with health. This study provides a solid baseline for defining healthy and disease-like states and highlights the power of moving beyond single and dual species applications to capture key players and their orchestrated metabolic activities within a human oral microbiome model.	root:Host-associated:Arthropoda:Digestive system:Oral:Saliva
MGYS00005677	EMG produced TPA metagenomics assembly of PRJNA427880 data set (Baikal Rift Zone hot springs metagenome sequencing).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA427880, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005678	Baikal Rift Zone hot springs metagenome sequencing	The study aims to discover novel extremophilic taxa and extremozymes that could be used in biotechnological applications	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005676	Kermadec arc raw sequence reads	16S amplicon libraries and metagenomes from the Microbial Diversity in the Kermadec Arc project, looking at microbial diversity in subaerial hot springs and enrichments from deep-sea hydrothermal vents along the Kermadec volcanic arc. Related sequences can also be found in BioProject PRJNA412936 , which archives data from hot springs on Raoul Island/Rangitahua.	N/A
MGYS00005675	EMG produced TPA metagenomics assembly of PRJNA563459 data set (Kermadec arc raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA563459, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005674	Iron reduction in an alkali-chloride hot spring community	The study examines the potential contribution of hyperthermophilic iron-reducing organisms to maintaining reduced iron minerals in near-boiling hot spring clay sediment.	N/A
MGYS00005673	EMG produced TPA metagenomics assembly of PRJNA432589 data set (Iron reduction in an alkali-chloride hot spring community).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA432589, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005671	EMG produced TPA metagenomics assembly of PRJNA339844 data set (subsurface metagenome Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA339844, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Terrestrial:Deep subsurface.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005672	subsurface metagenome Metagenome	The shale gas basins in the Ohio-Pennsylvania-New York region contain the largest natural gasreserves in the U.S. In 2012, over 7,000 Marcellus shale gas wells were active in Pennsylvania, and Ohio isexpecting a similar level of development in its deeper, Utica-Point Pleasant shale over the next 5 years.These shale have insufficient permeability to produce natural gas at economical rates, thus their developmentrequires horizontal drilling coupled to hydraulic fracturing, or fracking. The hydraulic fracturing processinvolves wellbore detonation and high-pressure injection of large volumes (up to 20 million L) of freshwaterand sand mixed with chemical additives to propagate fissures in the shale matrix, maximizing the surfacearea for natural gas release to the wellbore. As a result of fracturing, larger flow paths and newly exposedshale surfaces offer greater biogeochemical gradients for microbial colonization with greater opportunitiesfor nutrient and genetic exchange. We know little about the indigenous microbial membership of Marcellusshale, but given current physicochemical conditions of this formation (depths > 1000m, pressures > than 50MPa, temperatures > 60oC, 20% salt content, and pore sizes < 1 m) we anticipate that organisms enrichedduring energy development will encode adaptations to these physical and geochemical conditions. Ourmotivation is to understand the biotic and engineered factors responsible for alter	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005669	EMG produced TPA metagenomics assembly of PRJNA311332 data set (Bacteria isolated from carboxylate platform fermentations inoculated with microbial communities from extreme environments.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA311332, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005670	Bacteria isolated from carboxylate platform fermentations inoculated with microbial communities from extreme environments.	In an effort to identify microbial communities with superior performances in the carboxylate platform for biofuel and high value chemical production, we screened 501 microbial communities from 77 sites across the continental U.S., Hawaii and Puerto Rico as inocula. From the best performing communities, we collected >1800 individual isolates by culturing with a variety of media and oxygen conditions. We generated draft genome sequence for 64 of the isolates, selected based on phylogenetic, ecological, and phenotypic variation. These sequences will be used to advance a system to study 1) the role of diversity in functional types within carboxylate platform fermentation communities, 2) the genetic basis for superior performance in these fermentations and 3) the basis of adaptation to extreme conditions.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005667	EMG produced TPA metagenomics assembly of PRJNA431961 data set (Geothermal fumarole subsurface microbial communities from Mt. Erebus, Antarctica).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA431961, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005668	Geothermal fumarole subsurface microbial communities from Mt. Erebus, Antarctica	Using metagenomic sequencing and binning techniques, we identified and enumerated members of the subsurface-associated microbial community in the high-elevation fumarolic sediments of Tramway Ridge	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005665	EMG produced TPA metagenomics assembly of PRJNA528468 data set (CH09 Metavirome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA528468, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005666	CH09 Metavirome	Generation of a metavirome from the CH09 hotspring in Yellowstone National Park for the identification of a virus infecting a Nanoarchaea.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005664	Coral microbial communities from various places in Mexico - Orbicella C B metatranscriptome metatranscriptome	Metatranscriptomic analysis of microbial communities associated with coral hosts	root:Host-associated:Invertebrates:Cnidaria:Coral
MGYS00005663	coral metagenome Genome sequencing	The goal of this project is to produce microbial metagenomes from corals to better understand how coral-associated microbes interact with their host.	root:Host-associated:Invertebrates:Cnidaria:Coral
MGYS00003447	Broiler Caecal Metagenome	Broiler caecal samples were analysed using metagenomics	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00005662	Coral microbial communities from various places in Mexico - Orbicella T R B metatranscriptome metatranscriptome	Metatranscriptomic analysis of microbial communities associated with coral hosts	root:Host-associated:Invertebrates:Cnidaria:Coral
MGYS00005661	Coral microbial communities from various places in Mexico - Orbicella T R C metatranscriptome metatranscriptome	Metatranscriptomic analysis of microbial communities associated with coral hosts	root:Host-associated:Invertebrates:Cnidaria:Coral
MGYS00005660	Coral microbial communities from various places in Mexico - Orbicella T R A metatranscriptome metatranscriptome	Metatranscriptomic analysis of microbial communities associated with coral hosts	root:Host-associated:Invertebrates:Cnidaria:Coral
MGYS00005659	Coral microbial communities from various places in Mexico - Orbicella C C metatranscriptome metatranscriptome	Metatranscriptomic analysis of microbial communities associated with coral hosts	root:Host-associated:Invertebrates:Cnidaria:Coral
MGYS00005658	Coral microbial communities from various places in Mexico - Orbicella C A metatranscriptome metatranscriptome	Metatranscriptomic analysis of microbial communities associated with coral hosts	root:Host-associated:Invertebrates:Cnidaria:Coral
MGYS00005657	EMG produced TPA metagenomics assembly of PRJEB19090 data set (Potential and active functions in the gut microbiota of a healthy human cohort).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19090, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005435	EMG produced TPA metagenomics assembly of the PRJNA472060 data set (Reclaimed water Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA472060.  This project includes samples from the following biomes: root:Engineered:Wastewater:Water and sludge.	root:Engineered:Wastewater:Water and sludge
MGYS00005652	EMG produced TPA metagenomics assembly of PRJNA542280 data set (Oral Microbiome in Fanconi Anemia).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA542280, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00005656	Oral Microbiome in Fanconi Anemia	Characterization of the oral microbiota in patients with Fanconi anemia and healthy controls.	root:Host-associated:Human:Digestive system:Oral
MGYS00005651	EMG produced TPA metagenomics assembly of PRJNA78025 data set (Human Oral Subgingival Plaque Microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA78025, and was assembled with metaSPAdes v3.14.1, SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00005655	Human Oral Subgingival Plaque Microbiome	The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease.  While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease.   After the removal of supragingival plaque with sterile gauze, individual subgingival plaque samples were taken from the meio-buccal aspect of four molar teeth in four quadrants per subject using sterile periodontal curettes. Bacterial DNA extraction was performed using commercially available DNA purification kit. For 16S rRNA sequencing, DNA samples were amplified using specific primers and sequenced by 454 machines. Metagenomic shotgun sequences were obtained from the Illumina instruments.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00005653	EMG produced TPA metagenomics assembly of PRJNA419239 data set (Microbial communities in two hot springs sediments derived from the Kamchatka peninsula).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA419239, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005654	Microbial communities in two hot springs sediments derived from the Kamchatka peninsula		root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00001922	SSU rRNA amplicon of the Arctic Ocean during Winter-Spring Transition	One of the main concerns about the Arctic Ocean has been the changing sea ice regime with a reduction in the summer sea ice extent and a shift in dominance from thicker, perennial multiyear ice towards thinner, first-year ice. As the dietary basis of marine food webs and central players of biogeochemical cycles, microbial communities play an irreplaceable role when evaluating the ecological impact of the Arctics thinner ice regime. During the Norwegian young sea Ice cruise 2015 (N-ICE2015), that took place in drifting pack ice north of Svalbard between January-June 2015, seawater was collected, at 5, 20 or 50, 250 m depth in 9th March, 27th April and 16th June, together with physical and biogeochemical data. Through the massively parallel sequencing of SSU rRNA amplicon we expect to get a snapshot of the Arctics microbiota diversity and structure through the dark-light transition.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00001869	Shotgun Metagenomic Sequencing of the Arctic Ocean during Winter-Spring Transition	One of the main concerns about the Arctic Ocean has been the changing sea ice regime with a reduction in the summer sea ice extent and a shift in dominance from thicker, perennial multiyear ice towards thinner, first-year ice. As the dietary basis of marine food webs and central players of biogeochemical cycles, microbial communities play an irreplaceable role when evaluating the ecological impact of the Arctics thinner ice regime. During the Norwegian young sea Ice cruise 2015 (N-ICE2015), that took place in drifting pack ice north of Svalbard between January-June 2015, seawater was collected, at 5, 20 or 50, 250 m depth in 9th March, 27th April and 16th June, together with physical and biogeochemical data. Through the massively parallel sequencing of environmental DNA (metagenomics) we expect to get a snapshot of the Arctics microbiome structure, key functions and dynamic through the dark-light transition.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00000727	1) Fungi, 2) Perscribed Burning, 3) Soil Targeted Locus (Loci)	We Ion Torrent sequenced Internal Transcribed Spacer Region 1 (ITS1) amplicons to interrogate soil fungal community responses to long-term prescribed fire treatments in a loblolly pine forest on the Piedmont of Georgia. Our deep sequence data are largely congruent with previous studies and indicate that frequent fire recurrence (3 year fire interval) leads to shifts in soil fungus communities whereas infrequent fires (6 year fire interval) permit system resetting to a state similar to that without prescribed fire. Our results suggest that shifts in the vegetation community, which are the management goal of frequent prescribed fire, accompany changes in the soil fungal community. However, these changes do not occur when the interval between fires is longer.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00005169	Switchgrass rhizosphere	Characterization of bacterial and fungal communities in switchgrass rhizosphere	root:Host-associated:Plants:Rhizosphere
MGYS00005241	Soil marker gene sequences across the Nutrient Network	Raw microbial marker gene sequences (16S rRNA and ITS) from soil samples across the Nutrient Network	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000785	Varennes Communities in Contaminated Soils	In this study, 16S and ITS primers were used to amplify the bacterial and fungal populations, respectively, in both contaminated and uncontaminated soils that had been planted with willows. The goal was to see how willows and contaminants combined to shape microbial community structure.  Uncontaminated or petroleum contaminated soils from the site of a former oil refinery in Quebec.	root:Environmental:Terrestrial:Soil
MGYS00000737	The Island Project - Fungal communities in boreal forest soils	This project investigates fungal communities in fine-scaled organic soil profiles in a long-term chronosequence of boreal forests. The forests are situated on 30 islands in the two lakes Hornavan and Uddjaure, in northern Sweden. The islands have burned with different frequency due to their different area to intercept lightning, and the forests represent a successional gradient ranging from 50 to 5000 years in age. The current project seeks to unravel the mechanisms for the observed long-term build-up of carbon in the organic soil profiles in the islands. It is highly relevant to increase understanding of these mechanisms to be able to adequately predict effects of climate change, forest management practices and other environmental changes on the large carbon stocks currently stored in boreal forest soils.  Fungal ITS2 amplicons from organic soil profiles from boreal forest chronosequence.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00005242	Sharing of diverse mycorrhizal and root-endophytic fungi between dominant and subordinate plant species in an oak-dominated forest	Most terrestrial plants interact with diverse clades of mycorrhizal and root-endophytic fungi in their roots. Through the below-ground plant_fungal association, dominant plants can benefit by interacting with host-specific mutualistic fungi, while subordinate plant species may persist by sharing other sets (ecotypes) of fungal symbionts with each other. Therefore, the host preference of root-associated fungi is the key to understand plant community structure and dynamics. Based on 454-pyrosequencing, we revealed the root-associated fungal community on co-occurring 36 plant species in an oak-dominated forest in northern Japan, and statistically evaluated the host preference of diverse mycorrhizal and root-endophytic fungi. The analysis of 278 fungal taxa indicated that several taxa in the ectomycorrhizal family Russulaceae and the ecologically-diverse ascomycete order Helotiales had significant host preference for the dominant oak (Quercus) species. On the other hand, arbuscular-mycorrhizal fungi were shared mainly among subordinate plant species. While these fungi with host preference contributed to compartmentalize the below-ground plant_fungal associations, diverse clades of ectomycorrhizal fungi and possible root-endophytes associated not only with the dominant Quercus but also with the remaining plant species. Our findings suggest that dominant and subordinate plant species can host different subsets of root-associated fungi, while diverse clades of generalist fungi can counterbalance the compartmentalization of plant_fungal associations. Such insights into the overall structure of plant_root-associated fungal associations will enable us to understand the mechanisms that facilitate the co-existence of plant species in natural communities.	root:Host-associated:Plants
MGYS00005151	Microbial assemblages associated to crop residues	Crop residues are a crucial ecological niche having significant impact on agricultural ecosystems. Here, we investigated  the dynamics of these communities in three plots during a two-year wheat-oilseed rape rotation experiment. We demonstrated that crop residues are a pivotal, shifting platform that should be took into account as a whole microbial ecosystem to manage residues-borne disease.	root:Host-associated:Plants
MGYS00005619	EMG produced TPA metagenomics assembly of PRJEB8094 data set (The initial state of the human gut microbiome determines its reshaping by antibiotics).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8094, and was assembled with metaSPAdes v3.13.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal,root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002401	Diversity of microbial community (bacteria, micro-eukaryotes and fungi) in the Passage of Lascaux Cave.	In the Passage of Lascaux Cave (France), the potential effect of season, mineral substrate and presence of stains was tested on present (DNA) and active (RNA) microbial community with high-throughput sequencing.Three genes markers of microbial diversity were analyzed, the 16S rRNA genes specific for bacteria, the 18S rRNA genes specific for micro-eukaryotes and the second internal transcribed spacer (ITS2) specific for fungi. Sequences corresponding to active microbial community were named with c.	root:Environmental:Terrestrial:Deep subsurface
MGYS00005251	Fungal and bacterial decomposer taxa on Arabidopsis thaliana litter	Niche differentiation among species is a key mechanism by which biodiversity may be linked to ecosystem function. We tested a set of widely invoked hypotheses about the extent of niche differentiation in one of the most diverse communities on Earth  decomposer microorganisms  by measuring their response to changes in three abundant litter resources: lignin, cellulose, and nitrogen (N). To do this, we used the model system Arabidopsis thaliana to manipulate lignin, cellulose, and N availability and then used high-throughput DNA sequencing to measure the response of microbial communities during decay. Re-sequencing the decomposer communities after incubation of decomposed litter with pure substrates showed that groups of species had unique substrate use profiles, such that species organized into functional guilds of decomposers that were associated with individual litter chemicals.	root:Host-associated:Plants
MGYS00005145	CW_brewery_waste	Horizontal subsurface flow constructed wetland (HSSF-CW) enhaced wtih brewery waste amendment to treat nitrogen-rich leachates of a plant nursery crop.	root:Engineered:Food production:Fermented beverages
MGYS00000688	Piloderma and Ramaria Ectomycorrhizal Mat Soils Targeted Locus	Microbial communities associated with ectomycorrhizal mat soils were investigated as part of the HJ Andrews LTER Microbial Observatory II project.  Amplicon pyrosequencing of Fungal ITS and Bacterial 16S was used to quantify the microbial communities from two ectomycorrhizal mat forming genera (Piloderma and Ramaria) as well as non-mat soils.  Samples were split into organic and mineral soil horizons prior to sequencing.   The project was designed to explore the chemical and biological properties of mat-forming ectomycorrhizal fungi in the HJ Andrews forest.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00001371	The impact of long-term N addition on temperature sensitivity to decomposition in a spruce forest	TBD	N/A
MGYS00002478	"Accuracy of protist diversity assessments: morphology compared to cloning
                and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous
                tintinnid ciliates as a case study"	"Deep-sequencing technologies are becoming nearly routine to describe
                microbial community composition in environmental samples. 18S rDNA pyrosequencing
                has revealed a vast diversity of infrequent sequences, leading to the proposition of
                the existence of an extremely diverse microbial ""rare biosphere"". While rare
                microbes no doubt exist, critical views suggest that many rare sequences may
                actually be artifacts. However, information about how diversity revealed by
                molecular methods relates to that revealed by classical morphology approaches is
                practically non-existent. To address this issue, we used different approaches to
                assess the diversity of tintinnid ciliates, a species-rich group in which species
                can be easily distinguished morphologically. We studied two Mediterranean marine
                samples with different patterns of tintinnid diversity. We estimated tintinnid
                diversity in these samples employing morphological observations as well as both
                classical cloning and sequencing and pyrosequencing of two different markers, the
                18S rDNA and the ITS regions, applying a variety of computational approaches
                currently used to analyze pyrosequence reads. We found that both molecular
                approaches were efficient in detecting the tintinnid species observed by microscopy
                and revealed similar phylogenetic structures of the tintinnid community at the
                species level. However, depending on the method used to analyze the pyrosequencing
                results, we observed discrepancies with the morphology-based assessments up to
                several orders of magnitude. In several cases, the inferred number of operational
                taxonomic units (OTUs) largely exceeded the total number of tintinnid cells in the
                samples. Such inflation of the OTU numbers corresponded to ""rare biosphere"" taxa,
                composed largely of artefacts. Our results suggest that a careful and rigorous
                analysis of pyrosequencing datasets, including data denoising and sequence
                clustering with well-adjusted parameters, is necessary to accurately describe
                microbial biodiversity using this molecular approach."	root:Environmental:Aquatic:Marine
MGYS00001376	Deciphering the pathobiome: intra-and inter-kingdom interactions involving the pathogen Erysiphe alphitoides.	Plant-inhabiting microorganisms interact directly with each other, forming complex microbial interaction networks. These networks may be disrupted by the arrival of a new species, such as a pathogen infecting the plant. Here we decipher intra-kingdom and cross-kingdom interactions involving a pathogen species, by using a Bayesian method of network inference.  We use this method to highlight the most likely interactions between Erysiphe alphitoides, the causal agent of oak powdery mildew, and other foliar microorganisms of pedunculate oak (Quercus robur L.). Our results showed that infection by E. alphitoides is accompanied by drastic changes in the foliar fungal community composition but no significant change in the bacterial community composition. Our analyses highlighted 13 fungal Operational Taxonomic Units (OTUs) and 13 bacterial OTUs that are likely to interact directly with E. alphitoides. Four of the fungal OTUs were phyllosphere yeasts. The fungal endophytes Mycosphaerella punctiformis and Monochaetia kansensis were highlighted as potential antagonists of E. alphitoides. These potential interactions will have to be validated experimentally. The study of the temporal dynamics of microbial networks during the course of infection also appears to be a promising research avenue, that will undoubtedly give deeper insights into the ecology of this disease. Overall, we showed that combining metagenomics and network ecology may improve biological control of plant diseases, by highlighting potential antagonists of pathogen species.	root:Host-associated:Plants:Phylloplane
MGYS00000987	Soil samples Targeted Locus (Loci)	We hypothesize that a certain subset of soil microorganisms, of both bacteria and fungi, is distributed across the soil-plant continuum. Such evidence would lend credibility to a hypothesis that environmentally recruited microorganisms may establish endophytically in plant tissues, including seeds, and that at least some environmentally recruited endophytes might be then available for vertical transfer via seeds.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00005649	Sediment Metagenome of River Yamuna (Faizupur Khadar  , New Delhi s3)	To understand the microbial communities found in the contaminated sediments of the river Yamuna.	N/A
MGYS00005648	EMG produced TPA metagenomics assembly of PRJNA531097 data set (Sediment Metagenome of River Yamuna (Faizupur Khadar , New Delhi s3)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531097, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005647	Sediment Metagenome of River Yamuna (Okhla Barrage, New Delhi s2)	To understand the microbial communities found in the contaminated sediments of the river Yamuna.	N/A
MGYS00005646	EMG produced TPA metagenomics assembly of PRJNA531090 data set (Sediment Metagenome of River Yamuna (Okhla Barrage, New Delhi s2)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531090, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005645	Sediment Metagenome of River Yamuna (Wazaribad , New Delhi s1)	To understand the microbial Profile, in the contaminated sediments of the river Yamuna.	N/A
MGYS00005644	EMG produced TPA metagenomics assembly of PRJNA531081 data set (Sediment Metagenome of River Yamuna (Wazaribad , New Delhi s1)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531081, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005643	Sediment Microbiome  of  River Ganga  (Jana village , Kanpur s3)	To understand the microbial communities found in the contaminated sediments of the river Ganga.	N/A
MGYS00005642	EMG produced TPA metagenomics assembly of PRJNA529797 data set (Sediment Microbiome of River Ganga (Jana village , Kanpur s3)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA529797, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005641	Sediment Microbiome  of  River Ganga  (Jajmau, Kanpur s2)	To understand the microbial communities found in the contaminated sediments of the river Ganga.	N/A
MGYS00005640	EMG produced TPA metagenomics assembly of PRJNA529770 data set (Sediment Microbiome of River Ganga (Jajmau, Kanpur s2)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA529770, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005639	Sediment Microbiome  of  River Ganga  (Nawabganj, Kanpur s1)	To understand the microbial communities found in the contaminated sediments of the river Ganga.	N/A
MGYS00005638	EMG produced TPA metagenomics assembly of PRJNA529749 data set (Sediment Microbiome of River Ganga (Nawabganj, Kanpur s1)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA529749, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005637	Sediment Microbiome  of  River Ganga  (Lalbag,Murshidabad, west Bangal F3)	To understand the microbial communities found in the sediments of the river Ganga.	N/A
MGYS00005636	EMG produced TPA metagenomics assembly of PRJNA531144 data set (Sediment Microbiome of River Ganga (Lalbag,Murshidabad, west Bangal F3)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531144, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005635	Sediment Microbiome  of  River Ganga  (Paharghati Dhulian, west Bengal F2)	To understand the microbial communities found in the sediments of the river Ganga.	N/A
MGYS00005634	EMG produced TPA metagenomics assembly of PRJNA531106 data set (Sediment Microbiome of River Ganga (Paharghati Dhulian, west Bengal F2)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531106, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005633	Sediment Microbiome  of  River Ganga  (Below Farakka bridge, west Bengal F1)	To understand the microbial communities, found in the sediments of the river Ganga	N/A
MGYS00005632	EMG produced TPA metagenomics assembly of PRJNA531084 data set (Sediment Microbiome of River Ganga (Below Farakka bridge, west Bengal F1)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA531084, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005631	EMG produced TPA metagenomics assembly of PRJEB14491 data set (metagenomic Shotgun analysis of cecum microbiome of poultry).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB14491, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00005294	Marine metagenomes from the bioGEOTRACES project	Marine metagenomes from the bioGEOTRACES project Metagenome	root:Environmental:Aquatic:Marine
MGYS00005630	Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem	The current study employed a temporal shotgun metagenomic analysis of a prolonged (64 h) coffee fermentation process (six time points) to facilitate an in-depth dissection of the structure and functions of the coffee microbiome.	root:Engineered:Food production:Fermented beverages
MGYS00005629	a take on the impact of pollution on coastal bacterial communities	Coral reefs face increased environmental threats from anthropomorphic climate change and pollution, from agriculture, industries and tourism. They are economically vital for many people worldwide, and harbour a fantastically diverse ecosystem, being the home for many species of fish and algae. Surprisingly little is known about the microbial communities living in and in the surrounding of coral reefs. The objectives of this project is to characterise the community composition and function of bacteria living in the water and the upper sediment layer in close proximity of coral reefs. In this project we sequenced 3 water samples and 3 sediment samples out of the coast of Kenya, at 3 distinct location: Mombasa, Malindi and Kisite.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00005175	marine metagenome Metagenome	To study the effect of diesel oil spills on microbial communities in the monitored basin experiment	root:Environmental:Aquatic:Marine
MGYS00005605	The impact of helminth infection on the mucosal and luminal GI microbiota of the horse	It is well established that the gastrointestinal (GI) microbiota regulate immune responses to GI pathogens. In particular, data from our group and others demonstrate that immune-modulatory GI microbes promote both immunopathology from, and facilitate chronic infection with, GI helminths. A deeper understanding of the mechanisms which govern these interactions will pave the way to designing novel approaches to helminth control, aimed at promoting an optimal immune response to infection whilst limiting pathology. Here we systematically described the impact of helminth infection on the GI microbiota in a herbivore-helminth system by comparing GI microbiota between acutely and chronically infected equine livestock and uninfected controls; and furthermore, we triangulated this data by profiling luminal and mucosal microbiota taken from throughout the GI tract at post-mortem in infected versus uninfected horses. The results revealed similarities between acute helminth infection models in mice and equines, suggesting that helminths may employ ubiquitous mechanisms in regulating host gut microbiota. Furthermore, the microbial signature of helminth infection was distinctly different between acutely and chronically infected animals, indicating that host adaptive immunity plays an important role in helminth-microbiota interactions. At post-mortem, data supported that from chronically infected animals, and also showed that the most profound impact of infection upon the GI microbiota was a significant down-regulation of methanogen populations. The implications of this finding for helminth control in the context of climate change will be discussed.Authors: Peachey L, Bull K, Jenkins T, Cantacessi C	root:Host-associated:Mammals:Digestive system
MGYS00003669	Short-term variability in the microbial, nano- and picoplankton dynamics during post-upwelling season at a fixed sampling point in St Helena Bay	The diversity and functionality of the organisms in the 10-0.2 m size range was studied at a fixed-point sampling site in St Helena Bay during the end of upwelling season.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005627	Assessing secoisolariciresinol diglucoside metabolism in the rumen	Secoisolariciresinol diglucoside, a lignan found in many plants, predominantly in flaxseed. The plant lignan can play active role enhancing antioxidant capacity, however, it need to be  metabolized into enterolignans, process which the gut microbiota is responsible. The rumen is a known efficient environment for lignan metabolism, which comprises the breakdown of  SDG into secoisolariciresinol, then to enterodiol and enterolactone. The product  enterolactone increases concentration in the rumen as flax is added in the diet of ruminants  and the compound can be transferred to milk, benefiting human health by the functional food  intake, preventing many oxidative-related disorders such as cardiovascular diseases,  atherosclerosis, Alzheimers disease, breast-cancer and others. Although the knowledge on lignans metabolism in the rumen, little information is available regarding the microorganisms  linked to secoisolariciresinol diglucoside breakdown. The main bottleneck is that just few species of the rumen microbiome can be cultured in laboratory conditions, and thus, metagenomic approaches are needed to access the rumen ecology by-passing the in vitro culture. Therefore, a fosmid library was constructed using rumen microbes DNA inserts from the rumen of cows fed up to 15g/100g (dry matter basis) of flax meal, resulting on an 11,520 fosmid clones library, using Escherichia coli strain EPI300 as host bacteria. The library was screened for secoisolariciresinol diglucoside breakdown capacity using high-performance liquid chromatography and positive clones followed to plasmid DNA purification, deep sequencing and bioinformatic data analysis. Two out of 30 library plates showed effective secoisolariciresinol diglucoside breakdown, however, no metabolism products were identified and no putative gene linked to direct secoisolariciresinol diglucoside breakdown was identified from clones genome. To our knowledge this is the first fosmid library constructed to prospect rumen microorganisms with active role in plant lignans metabolism, thus, more studies regarding the subject must be carried out to broaden genes and enzymes involved in the process.	root:Host-associated:Mammals:Digestive system:Foregut:Rumen
MGYS00005626	We investigated the presence of electroactive bacteria associated with the ennoblement, an increase of the open circuit potential of stainless steel in seawater. Metagenomic result confirmed the presence of electroactive bacteria, and an associated metatranscriptomic analysis was carried out to study the gene expression and activity of the bacteria associated with ennoblement.	Stainless steel immersed in seawater have an increased risk of localized corrosion due an increase of the Open Circuit Potential (OCP), also referred as ennoblement. That increase of potential occurs during the first days of exposure and correlates to the presence and development of microorganisms naturally found in the seawater. In a previous study about the effect of temperature on ennoblement and stainless steel microbial communities, we identified an electroactive bacteria based on 16S rRNA gene sequencing and proposed a new model to explain how microorganisms could be able to change the OCP of stainless steel. In order to investigate the role of electroactive bacteria, we used normal and applied potential conditions with a metagenomic and metatranscriptomic approach. We confirmed the presence of electroactive bacteria associated with the ennoblement and investigated the gene expression associated with the different conditions.	root:Engineered
MGYS00001864	Assembly and activity of microbial communities in the Pacific temperate rainforest	Dataset includes 16S rRNA sequences from soil RNA and DNA extractions, metatranscriptomes and geochemical data related to ecological gradients and climactic variability in the Pacific temperate rainforest.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00005601	Identification of Intestinal Bacterial Taxa with a Potential Role in Parkinsons Disease using Illumina MiSeq and Ion Torrent Next Generation Sequencing	Parkinsons disease (PD) is one of the most common neurodegenerative disorders. It has been repeatedly reported that most patients with PD suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system in the gut wall called the enteric nervous system (ENS). Such alterations and functional gastrointestinal deficits might occur years before the classical clinical symptoms of PD appear. Until now, only little is known about PD-associated changes in gut microbiota composition and their implication in PD development. Due to variance in previously published reports about the differences between community composition in PD and non-PD patients, our intention is to increase knowledge in this field with the use of two next generation sequencing (NGS) methods (Illumina MiSeq and Ion Torrent PGM) on the same set of samples. The V4 and V5 hypervariable region of bacterial 16S rRNA genes was PCR-amplified from stool samples of 39 PD patients and 25 healthy, age-matched control persons, respectively. Illumina- and Ion Torrent- based sequencing yielded divergent as well as congruent results regarding the bacterial microbiota composition of PD and control samples.Bacterial taxa with differences in relative abundance between PD and control samples that were traceable with both sequencing techniques might play a role for supporting PD diagnosis and therapy.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005584	We investigated the presence of electroactive bacteria associated with the ennoblement, an increase of the open circuit potential of stainless steel in seawater. Metagenomic result confirmed the presence of electroactive bacteria.	Stainless steel immersed in seawater have an increased risk of localized corrosion due an increase of the Open Circuit Potential (OCP), also referred as ennoblement. That increase of potential occurs during the first days of exposure and correlates to the presence and development of microorganisms naturally found in the seawater. In a previous study about the effect of temperature on ennoblement and stainless steel microbial communities, we identified an electroactive bacteria based on 16S rRNA gene sequencing and proposed a new model to explain how microorganisms could be able to change the OCP of stainless steel. In order to investigate the role of electroactive bacteria, we used normal and applied potential conditions with a metagenomic approach.	root:Engineered
MGYS00005625	EMG produced TPA metagenomics assembly of PRJEB15404 data set (Plastic Metagenome Study).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB15404, and was assembled with unknown v0.0. This project includes samples from the following biomes: root:Engineered.	root:Engineered
MGYS00005624	16s rDNA amplicon of rock samples Raw sequence reads	16s rDNA amplicon of rock samples	root:Environmental:Terrestrial:Geologic
MGYS00005623	16S rRNA amplicon sequencing of broiler caecal contents	16S rRNA amplicon sequencing of broiler caecal contents. Linked to this study: https://doi.org/10.1186/s42523-019-0015-1	root:Host-associated:Birds:Digestive system:Ceca
MGYS00005622	The environmental soil 16S rRNA amplicon	The environmental soil 16S rRNA amplicon data	root:Environmental:Terrestrial:Soil
MGYS00005621	Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession	The fine-scale temporal dynamics of the chicken gut microbiome are unexplored, but thought to be critical for chicken health and productivity. Here, we monitored the fecal microbiome of healthy chickens on days 1-7, 10, 14, 21, 28, and 35 after hatching, and performed 16S rRNA amplicon sequencing in order to obtain a high-resolution census of the fecal microbiome over time. In the period studied, the fecal microbiomes of the developing chickens showed a linear-log increase in community richness and consistent shifts in community composition. Three successional stages were detected: the first stage was dominated by vertically-transmitted or rapidly-colonizing taxa including Streptococcus and Escherichia/Shigella; in the second stage beginning on day 4, these taxa were displaced by rapid-growing taxa including Lachnospiraceae and Ruminococcus-like SVs; and in the third stage, starting on day 10, slow-growing, specialist taxa including Candidatus Arthrobacter and Romboutsia were detected. The patterns of displacement and the previously reported ecological characteristics of many of the dominant taxa observed suggest that resource competition plays an important role in regulating successional dynamics in the developing chicken gut. We propose that the boundaries between successional stages (3-4 and 14-21 days after hatching) may be optimal times for microbiome interventions.	root:Host-associated:Birds:Digestive system:Fecal
MGYS00005581	EGB sediment data (raw sequence reads)	DNA and RNA from sediment samples collected in the Eastern Gotland Basin	root:Environmental:Aquatic:Marine:Sediment
MGYS00005620	The Core Equine Faecal Microbiome: A Broader Perspective	Background: Equine gut microbiology studies to date have primarily focused on horses and ponies which represent only one of the 8 extant equine species. This is despite asses and mules comprising almost half of the worlds domesticated equines, and donkeys being superior to horses/ponies in their ability to degrade dietary fibre. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fibre degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden current bacterial, anaerobic fungal and archaeal knowledge of the equine hindgut to multiple species of equines. Taxa core to all the equine faecal samples (n=70) were determined and observations of the effect of equine type (horse, donkey, horse  donkey and zebras) on the hindgut microbiota conducted. Results: Equine type influenced both microbial concentrations and community composition. Donkeys generally were most distinct from the other equine types, with horses and zebra not differing. Despite this, a common bacterial core of 8 OTU and 16 genus level groupings of OTU was found in all the equines studied. This bacterial core represented a much larger proportion of the equine faecal microbiota than previously reported, primarily due to the detection of dominant core taxa belonging to the Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaete phyla. The majority of the core bacterial taxa lacked cultured representation. Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either despite several taxa being prevalent and dominant.Conclusions: Whilst differences were observed between equine types, a core faecal microbiome existed across all the equines. This core was composed primarily of a few dominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the dominant bacterial as well as anaerobic fungal taxa in the equine hindgut is of concern, and highlights an urgent need to isolate these taxa. Only then can fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem be elucidated.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005616	EMG produced TPA metagenomics assembly of PRJEB15448 data set (The influence of chitin addition on the lettuce rhizosphere microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB15448, and was assembled with unknown v0.0. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil.	root:Host-associated:Plants:Rhizosphere
MGYS00005614	EMG produced TPA metagenomics assembly of PRJEB34410 data set (Secrets of the hospital underbelly: abundance of antimicrobial resistance genes in hospital wastewater reflects hospital antimicrobial use and inpatient length of stay).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB34410, and was assembled with metaSPAdes v3.13.1. This project includes samples from the following biomes: root:Engineered:Wastewater.	root:Engineered:Wastewater
MGYS00005116	International Space Station vacuum cleaner bag Targeted Locus (Loci)	International Space Station (ISS) environmental microbiome- Microbial inventories of ISS filter debris.  ISS vacuum cleaner bag contents (ISS-debris) and visible accumulations of fibers and other materials associated with the vacuum bag (ISS-debris).	root:Engineered:Built environment
MGYS00005618	Fecal Microbiota in Horses with Asthma	The goal was to analyze the bacterial fecal microbiota of horses with and without asthma under different diet and housing conditions, in remission and exacerbation.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005617	16S sequencing from full scale WWTP - UAE	16S sequencing from samples collected from the aeration tank of a full scale wastewater treatment plant in the UAE over a 10 month period	root:Engineered:Wastewater
MGYS00005615	Secrets of the hospital underbelly: abundance of antimicrobial resistance genes in hospital wastewater reflects hospital antimicrobial use and inpatient length of stay	Hospitals are nodal points for antimicrobial consumption and identification of resistant pathogens and therefore hospital wastewater is a potential major source of AMR. This study uses metagenomics to study how the abundances of resistance genes in hospital wastewater are related to clinical activity within different buildings of the hospital. Sewage was collected over a 24-hour period from multiple wastewater collection points representing different specialties within a tertiary hospital site and simultaneously from community sewage works. High throughput shotgun sequencing was performed using Illumina HiSeq4000. Sequence reads were assigned taxonomically and to the AMR genes in the ResFinder database. The measured AMR gene abundances were then correlated to hospital antimicrobial usage (AMU), other data on clinical activity such as patient/ward characteristics and resistance prevalence in clinical isolates.	root:Engineered:Wastewater
MGYS00005613	Metagenomic sequencing of microbial communities present in spontaneous fermentation of coffees in northern Peru	The quality of commercial coffee berry, the principal raw material for coffee production, depends on several factors including type of plantations, the agricultural practices and the post-harvest processing. Among these, fermentation are generally considered the most relevant step, since during these phases coffee flavors precursors are formed and fixed. Fermentation is characterized by a well-defined succession of yeasts, lactic acid bacteria and acetic acid bacteria, therefore the aim of this study is to explore total bacterial and fungal communities involved in coffee fermentation. To achieve these results, shotgun metagenomics was used on fermentations from good and bad quality coffees to assess the total bacterial and fungal community, indicating that this approach has the ability to provide a comprehensive view of the coffee fermentation microbiota at the species level.	root:Host-associated:Plants
MGYS00005612	Home chemical and microbial transitions across urbanization	Westernization has propelled changes in urbanization and architecture, altering our exposure to the outdoor environment from that experienced during most of human evolution. These changes might affect the developmental exposure of infants to bacteria, immune development, and human microbiome diversity. Contemporary urban humans spend most of their time indoors, and little is known about the microbes associated with different designs of the built environment and their interaction with the human immune system. This study addresses the associations between factors associated with westernization including architectural design and the microbial biogeography of households across a gradient of urbanization in South America.	root:Mixed
MGYS00005611	Galmide	Microbiota characterization of caecal, ileum, and jejunal contents of two lines of broiler chickens divergently selected on their digestive efficiency	root:Host-associated:Birds:Digestive system
MGYS00005610	Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter	Chickens are a key food source for humans yet their microbiome contains bacteria that can be pathogenic to humans, and indeed potentially to chickens themselves. Campylobacter is present within the chicken gut and is the leading cause of bacterial foodborne gastroenteritis within humans worldwide. Infection can lead to secondary sequelae such as Guillain-Barre syndrome and stunted growth in children from low-resource areas. Despite the global health impact and economic burden of Campylobacter, how and when Campylobacter appears within chickens remains unclear. The lack of day to day microbiome data with replicates, relevant metadata, and a lack of natural infection studies have delayed our understanding of the chicken gut microbiome and Campylobacter. Here, we performed a comprehensive day to day microbiome analysis of the chicken cecum from day 3 to 35 (12 replicates each day; final n = 379). We combined metadata such as chicken weight and feed conversion rates to investigate what the driving forces are for the microbial changes within the chicken gut over time, and how this relates to Campylobacter appearance within a natural habitat setting. We found a rapidly increasing microbial diversity up to day 12 with variation observed both in terms of genera and abundance, before a stabilization of the microbial diversity after day 20. In particular, we identified a shift from competitive to environmental drivers of microbial community from days 12 to 20 creating a window of opportunity whereby Campylobacter can appear. Campylobacter was identified at day 16 which was 1 day after the most substantial changes in metabolic profiles observed. In addition, microbial variation over time is most likely influenced by the diet of the chickens whereby significant shifts in OTU abundances and beta dispersion of samples often corresponded with changes in feed. This study is unique in comparison to the most recent studies as neither sampling was sporadic nor Campylobacter was artificially introduced, thus the experiments were performed in a natural setting. We believe that our findings can be useful for future intervention strategies and help reduce the burden of Campylobacter within the food chain.	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00005609	Commensal Enterobacteriaceae protect against Salmonella colonization by competing for oxygen	Neonatal chicks are highly susceptible to colonization with Salmonella enterica serovar (S.) Enteritidis, but the underlying mechanism is not fully resolved. We show that neonatal colonization with S. Enteritidis required a virulence factor-dependent increase in epithelial oxygenation, which drove expansion of the pathogen in the lumen of the chick intestine by aerobic respiration. Co-infection experiments with an Escherichia coli strain carrying an oxygen-sensitive reporter suggested that S. Enteritidis competes with commensal Enterobacteriaceae for oxygen. Association with either spore-forming bacteria or commensal Enterobacteriaceae from adult chicken microbiota did not protect germ-free mice from S. Enteritidis colonization. However, a combination of Enterobacteriaceae and spore-forming bacteria conferred colonization resistance against S. Enteritidis at levels similar to those observed in germ-free mice associated with adult chicken microbiota. Combining spore-forming bacteria with a single avian E. coli isolate protected germ-free mice from pathogen colonization, but protection was lost when the ability to respire oxygen under microaerophilic conditions was genetically ablated in E. coli. These results show that commensal Enterobacteriaceae contribute to colonization resistance by competing with S. Enteritidis for oxygen, a resource critical for pathogen expansion.	root:Host-associated:Birds:Digestive system
MGYS00005607	New strategies for the protection of PUFA from ruminal microbiome - Nannochloropsis oceanica as a source of rumen-protected EPA	Dietary n-3 PUFA fed to ruminants are extensively hydrogenated through ruminal biohydrogenation resulting in a very low efficiency of its transfer to tissues. The development or identification of novel strategies to protect PUFA from biohydrogenation, to increase the amount of PUFA bypassing the rumen could circumvent the problem. Using naturally PUFA-protected sources such as microalgae like Nannochloropsis sp. can be an alternative but there is a need to evaluate the impact on rumen an intestinal microbiome composition.	root:Host-associated:Mammals
MGYS00005606	Omega 3 sources impacts on lambs' microbiota	Different sources of Omega 3 were studied in vitro and in vivo on lambs' microbiota fed different diets	root:Host-associated:Mammals
MGYS00005296	Metagenomic analysis of lake sediment.	Shotgun sequencing of lake sediments.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005603	Equine intestinal microbiota after feeding a prebiotic	The objective of this study was to investigate the impact of natural prebiotic active compounds on the microbial composition in different regions of the equine gastrointestinal tract. Twelve adult horses (body weight [bwt] 534  64.5 kg; age 14  7.5 years) were randomly divided into two feeding groups. Six horses received a basal diet consisting of 1.5 kg hay/100 kg bwt x d-1 and oat grains equal to 1.19 g starch/kg bwt x d-1, supplemented with Jerusalem artichoke meal providing prebiotic fructooligosaccharides + inulin in a quantity of 0.15 g/kg bwt x d-1. The remaining horses received a placebo added to the basal diet. The horses were fed for 21 d and euthanized at the end of the feeding period. Digesta samples from different parts of the gastrointestinal tract were taken, DNA extracted and the V1-V2 region of the 16S rRNA gene amplified. Supplementation with the prebiotic increased the relative abundance of Lactobacillus (P < 0.50), with a concurrent reduction of the relative abundance of Streptococcus mainly in the stomach (P < 0.05). In the hindgut, the supplemental prebiotic also increased the relative abundance of Lactobacillus but further reduced the relative abundance of fibrolytic bacteria, specifically the unclassified members of the families Lachnospiraceae (P < 0.05) and Ruminococcaceae. The relative abundance of the genus Ruminococcus increased solely in the caecum and colon transversum. Overall, the addition of the prebiotic significantly increased the diversity in nearly all parts of the gastrointestinal tract (P < 0.05). The feeding of this natural prebiotic compound to horses had an impact on the microbial community in the entire gastrointestinal tract. Furthermore, the effect on the bacterial community in the foregut (especially the stomach) was more pronounced in comparison to the effect in the hindgut. Therefore, the impact on stomach health should be carefully considered.	root:Host-associated:Mammals:Gastrointestinal tract
MGYS00005604	The microbiome of healthy fecal donor horses and recipients undergoing microbial transplantation for the treatment of diarrhea	Fecal microbial transplantation (FMT), a treatment for certain gastrointestinal conditions associated with dysbiosis in people, is also empirically employed in horses with colitis. We used high-throughput sequencing to compare the fecal microbial profile of healthy horses to that of microbial transplant recipients experiencing diarrhea, and to test whether FMT restores microbiome diversity. The fecal microbiome of horses with diarrhea was significantly more variable (higher -diversity) than that of healthy horses. An inverse correlation between diarrhea score and relative abundance of Verrucomicrobia was identified in FMT recipients. At study completion, the fecal microbiome of horses which responded to FMT was more diverse (higher -diversity) and phylogenetically more similar to that of the donor.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005594	Kidney stone patient microbiome	Metagenomic sequencing of the gut from kidney stone patients and healthy controls	root:Host-associated:Human:Digestive system
MGYS00005600	Contribution of the broiler breeders' fecal microbiota to the establishment of the eggshell microbiota	In broiler chicken production, microbial populations on the eggshell surface following oviposition are still poorly characterized, though they may significantly impact both poultry and public health. The aim of this study was to describe the microbiota of both broiler breeder hens feces and the surface of their eggs to assess the contribution of the parental fecal microbiota to the eggshell microbiota. This work is innovative and will be important to all stakeholders, including producers, breeders, veterinarians, inspectors and researchers, in the broiler breeder production chain in order to better manage the risks of bacterial contamination for poultry and public health.	root:Host-associated:Birds:Digestive system:Fecal
MGYS00005602	Tibetan chicken feces Targeted Locus (Loci)	To reveal the bacteria related TCC	root:Host-associated:Birds:Digestive system:Fecal
MGYS00005587	Air metagenomics	-	root:Environmental:Air
MGYS00005599	Daheng broilers Chicken(DH) caecum feces Targeted Locus (Loci)	To reveal the bacterial cummunity of Daheng broilers Chicken(DH) caecum feces	root:Host-associated:Birds:Digestive system:Fecal
MGYS00005598	Lohmann laying hen(LM)caecum feces Targeted Locus (Loci)	To reveal the bacterial cummunity of Lohmann laying hen(LM)caecum	root:Host-associated:Birds:Digestive system:Fecal
MGYS00005597	Tibetan Chicken(DQ) caecum feces targeted loci targeted loci	To reveal the bacterial cummunity of Tibetan Chicken(DQ)caecum	root:Host-associated:Birds:Digestive system:Fecal
MGYS00005596	Tibetan Chicken(QH) caecum feces targeted loci	To reveal the bacteria community of TCC-QH caecum	root:Host-associated:Birds:Digestive system:Fecal
MGYS00005595	Metagenomic analysis of Lake Slone sediment.	Metagenomic analysis of Lake Slone sediment.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00005593	16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan	"Gut microbiota affects health, metabolism and immunity of the host, and in the case of livestock,
also food-safety. Here, 16S rRNA gene high-throughput Illumina sequencing was used to describe the
microbiome of chicken caeca in two different breeds and management systems throughout their whole
productive lifespan. Broilers (Ross-308), as a fast-growing breed reared in an intensive system for 42-
days, and a slow-growing breed of chicken (Sasso-T451A) reared in an extensive farming system with
outdoor access for 86-days, were compared. The core microbiome and differentially abundant taxa,
as well as taxa associated with age were identified. Age was identified as the strongest influencing
factor in caecal microbiota composition, and, in general, each age-group showed an age-associated
community profile, with a transition period at the middle of their lifespan. However, substantial
differences were observed in the composition of caecal microbiota of both chicken breeds, microbiota
being richer and more complex in free-range chicken than in broilers. Several taxa positively/negatively
correlated with Campylobacter relative abundance were also identified. Especially noteworthy was
the identification by microbial community comparison of microbiota profiles suggestive of dysbiosis in
several free-range chickens, probably associated to the typhlitis observed in the lumen of their caeca."	root:Host-associated:Birds:Digestive system:Ceca
MGYS00001031	Trace element-contaminated soil Metagenome	We aimed to compare the community structure of fungi and bacteria in the rhizosphere of introduced willows to willow growth and metal uptake.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00002429	Microbial populations of Lascauxs Apse in relation to collembola and black stains on cave walls.	In the Apse of Lascaux Cave (France), the microorganisms of black stains and unstained parts of wall cave were identified with Illumina technology using three genes markers of microbial diversity were analyzed, the 16S rRNA genes specific for bacteria, the 18S rRNA genes specific for micro-eukaryotes and the second internal transcribed spacer (ITS2) specific for fungi.	root:Environmental:Terrestrial:Deep subsurface
MGYS00001742	Microbial contaminants of civil aviation jet fuel supply chains.	Contaminated water and fuel samples were obtained from ground tanks and aircraft wing tanks from airports in Europe and the Middle East. 16S rRNA and ITS genes were amplified and used to identify prokaryotic and eukaryotic taxa. Contaminated water samples were sequenced directly or placed in microcosms. Contaminated fuel samples were placed in microcosms then sequenced.	root:Engineered
MGYS00001993	Origin based predominance of Dothideomycetes and Saccharomycetes in the intestinal mycobiota of zebrafish	Fish intestinal mycobiota are hitherto poorly characterized. Using next generation sequencing, we have profiled the intestinal mycobiota of wild caught, laboratory-reared and wild-caught-laboratory-kept zebrafish, which contained more than 15 fungal classes. In wild zebrafish, mycobiota comprised mainly Dothideomycetes, whereas saprotrophic Saccharomycetes were predominant in their laboratory-reared counterparts. This pioneer study shed light into differences in intestinal fungal communities of wild-caught and laboratory-reared zebrafish, thus enriching our knowledge on fish mycobiota.	root:Host-associated:Fish:Digestive system:Intestine
MGYS00001720	Metagenomic barcode approach of the ExStream Project 2014 for eukaryotes	Freshwater fungi have a crucial role in decomposition of organic material in aquatic ecosystems. Nevertheless they remain poorly investigated compared to fungi in other habitats like soil. Especially the community response to anthropogenic stressors is addressed in a very limited number of publications only.Therefore, we created a mesocosm experiment along an artificial sidearm of a freshwater stream in Germany, to test the effects of three stressors on the community composition. 64 mesocosms were equipped with litterbags (filled with leaf litter from riparian vegetation) and former sterilized ceramic tiles, which serve as a standardized sampling area for biofilm communities. An initial period of two weeks for colonization of respective compartments was followed by two weeks with stressor exposure. As stressors we chose fine sediment, salt (NaCl) and a reduction of flow velocity and all possible combinations. Each stressor and combination was applied in eight replicates. In contrast to the majority of hitherto published fungal freshwater studies we did not use morphological criteria to assess fungal communities but used a metagenomic barcode approach of the ITS nrDNA marker.Clustering of raw reads into Operational Taxonomic Units (OTUs) with CD-HIT-OTU and usearch revealed highly identical results between the two different algorithms. However, the detected 570 OTUs exceed the number of species detected with bait- and cultivation-based methods of former studies by factor three to ten. The unique study design with two different compartments enabled the identification of three different ecological gilds according to their compartment preferences. The first gild represents aquatic fungi, the second comprises amphibious fungi, while the third contains terrestrial fungi. Each gild is characterized by a unique stressor response supporting the idea to divide the total community of freshwater fungi into specific sub-communities. While aquatic and terrestrial fungi show no significant effect caused by the applied stressors, the amphibious fungi respond significantly towards the enriched salt concentrations. However we assume this signal to be a secondary effect since the amphibious fungi are highly correlated to algal communities, which are more prone to applied stressors than the fungal communities.	root:Environmental:Aquatic:Freshwater
MGYS00002428	Microbial populations of Lascauxs Apse in relation to collembola and black stains on cave walls.	In the Apse of Lascaux Cave (France), microorganisms present on and in arthropods were identified using the 16S rRNA genes specific for bacteria and the second internal transcribed spacer (ITS2) specific for fungi.	root:Environmental:Terrestrial:Deep subsurface
MGYS00004559	Fungal diversity associated with deep-sea asphalt seep mounds	Fungal diversity in deep-sea sediments associated with asphalt seep mounds was investigated by Ion torrent ITS amplicon sequencing.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00001499	The San Pedro Ocean time-series is a marine time-series started circa 1997. This project aims to study ecological and biogeochemical implications of global marine microbial biodiversity.	The USC Microbial Observatory (Jed Fuhrman and David Caron, PIs) focuses on exploratory investigation of prokaryotic and unicellular eukaryotic diversity in the San Pedro Channel , California, with an initial focus on time-dependent changes in community composition in relation to environmental parameters. It also includes focused studies of particular microbial groups. We are currently in 12th year of this project.  Our primary sampling site is located midway between Los Angeles and the USC Wrigley Marine Laboratory on Santa Catalina approximately 900 m of water.  This site is visited monthly by ship for sampling to 500 m depth. Additional sampling is conducted on an ad hoc basis in coastal water near the lab on Catalina Island.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00001955	Amplicon Based Metagenomic Analysis of Microbial Composition of Kombucha	The aim of this study is to gain a more accurate and detailed insight about the microbial community of Kombucha during fermentation process employing 16S rRNA and ITS sequencing. Metagenomic DNA  was isolated from pellicule and liquid phase of two Kombucha samples obtained from Turkey at the days 3, 10 and 15 of the fermentation process. Isolated DNA samples were sequenced using amplicon based next generation sequencing.	root:Engineered:Food production:Fermented beverages
MGYS00000856	Pristine and TNT contaminated (tilled and untilled) soils		root:Environmental:Terrestrial:Soil
MGYS00001811	Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for  large DNA viruses.	Seawater was filtered from different depths to retain small cell sizes (Girus Organisms). The DNA was extracted and amplified by PCR.	root:Environmental:Aquatic:Marine
MGYS00000654	Rhizosphere microbial community manipulated by 2-year consecutive bio-fertilizer application exhibited excellent disease suppression to banana Fusarium wilt disease	2-year consecutive application of bio-fertilizer to a banana orchard with serious Fusarium wilt disease effectively controlled this soil-borne disease reported in our previous work. Deep pyrosequencing of 16S rRNA and ITS genes were performed to investigate how rhizosphere microbial community responded to application of bio-fertilizer (BIO), common pig manure compost (PM) and only chemical fertilizer (CF) and to explore the potential correlation between microbial community and Fusarium wilt disease suppression. In total 104,201 bacterial 16S and 154,953 fungal ITS sequence reads were obtained after basal quality control. Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Ascomycota were the most abundant bacterial and fungal phyla. The alpha diversity of bacteria was significantly increased while that of fungi significantly reduced after 2-year consecutive bio-fertilizer application. Acidobacteria and Firmucutes were significantly elevated while Proteobacteria and Ascomycota significantly depleted in the rhizosphere after bio-fertilizer application. Moreover, genera of Gp1, Gp3, Leptosphaeria and Phaeosphaeriopsis were also significantly enriched in BIO treatment compared to PM and CF treatments. Interestingly, Fusarium was also significantly reduced in BIO treatment compared to CF treatment and a slightly reduce without significance compared to PM treatment. Furthermore, the disease incidence was negatively correlated to the enrichment of Gp1, Gp3, Leptosphaeria and Phaeosphaeriopsis while positively correlated to depletion of Fusarium. In conclusion, the reduction of the Fusarium wilt disease incidence after a 2-year application of bio-fertilizer might be attributed to the fact that application of bio-fertilizer containing Bacillus sp. induced general suppression by modulating rhizosphere the microbial community.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00005592	Defining the oral microbiome by Whole Genome Sequencing and resistome analysis: the complexity of the healthy picture	The microbiome of the oral cavity is the second largest and diverse microbiota after the gut, harboring over 700 species of bacteria and including also fungi, viruses and protozoa. A detailed site-specific map of oral microorganisms (including also eukaryotes and viruses) and their relative abundance is still missing. The data of this study provide for the first time a comprehensive view of the healthy oral microbiome  and its resistome, contributing to a deeper understanding of the composition of oral microbiome in the healthy subject, and providing an important reference for future studies exploring functional and metabolic alterations associated with diseases, which might be useful in identifying microbial signatures for targeted therapies and precision medicine.	root:Host-associated:Human:Digestive system:Oral
MGYS00005591	Strongyle Infection and Gut Microbiota: Profiling of Resistant and Susceptible Horses Over a Grazing Season	"Gastrointestinal strongyles are a major threat to horses health and welfare. Given that strongyles inhabit the same niche as the gut microbiota, they may interact with each other. These beneficial or detrimental interactions are unknown in horses and could partly explain contrasted susceptibility to infection between individuals. To address these questions, an experimental pasture trial with 20 worm-free female Welsh ponies (10 susceptible (S) and 10 resistant (R) to parasite infection) was implemented for 5 months. Fecal egg counts (FEC), hematological and biochemical data, body weight and gut microbiological composition were studied in each individual after 0, 24, 43, 92 and 132 grazing days. R and S ponies displayed divergent immunological profiles and slight differences in microbiological composition under worm-free conditions. After exposure to natural infection, the predicted R ponies exhibited lower FEC after 92 and 132 grazing days, and maintained higher levels of circulating monocytes and eosinophils, while lymphocytosis persisted in S ponies. Although the overall gut microbiota diversity and structure remained similar during the parasite infection between the two groups, S ponies exhibited a reduction of bacteria such as Ruminococcus, Clostridium XIVa and members of the Lachnospiraceae family, which may have promoted a disruption of mucosal homeostasis at day 92. In line with this hypothesis, an increase in pathobionts such as Pseudomonas and Campylobacter together with changes in several predicted immunological pathways, including pathogen sensing, lipid metabolism, and activation of signal transduction that are critical for the regulation of immune system and energy homeostasis were observed in S relative to R ponies. Moreover, S ponies displayed an increase in protozoan concentrations at day 92, suggesting that strongyles and protozoa may contribute to each others success in the equine intestines. It could also be that S individuals favor the increase of these carbohydrate-degrading microorganisms to enhance the supply of nutrients needed to fight strongyle infection. Overall, this study provides a foundation to better understand the mechanisms that underpin the relationship between equines and natural strongyle infection. The profiling of horse immune response and gut microbiota should contribute to the development of novel biomarkers for strongyle infection.

Authors: Allison Clark, Guillaume Salle, Valentine Ballan, Fabrice Reigner, Annabelle Meynadier, Jacques Cortet, Christine Koch, Mickael Riou, Alexandra Blanchard, Nuria Mach"	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005589	The microbiome of healthy horses compared to those with antimicrobial associated diarrhea or primary Salmonellosis	This project compares the fecal microbiome of healthy horses to those who have developed colitis either from antimicrobial use or Salmonella without prior antimicrobial administration.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001559	Metagenomic analysis of gut microbiota in sows and piglets (EBI)	We studied the intestinal microbiome in feces from sows, five days after farrowing, their piglets during suckling and two weeks after weaning, 5-day old artificially reared and formula-fed siblings, and FP infected with Clostridium difficile.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005588	POULTRY METAGENOMICS: DIFFERENT FEEDING PRACTICES	BROILERS MAINTAINED UNDER DIFFERENT FEEDING CONDITIONS WERE ANALYSED FOR TAXONOMIC AND FUNCTIONAL ASPECTS	root:Host-associated:Birds
MGYS00005585	EMG produced TPA metagenomics assembly of PRJEB11511 data set (Assembly of a 5300-year-old Helicobacter pylori genome from the intestine content of the tyrollean glacier mummy).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11511, and was assembled with metaSPAdes v3.13.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system.	root:Host-associated:Human:Digestive system
MGYS00005586	Assembly of a 5300-year-old Helicobacter pylori genome from the intestine content of the tyrollean glacier mummy	The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its host for the past 100,000 years leading in a distinct phylogeographic pattern in modern H. pylori populations. This phylogeography is used to deduce both recent and ancient human migrations (1, 2). Owing to the complex demographic history of Europe, different hypotheses about the origin of the extant European H. pylori population (hpEurope) exist (3, 4). Here, we present a 5,300-year-old high-coverage H. pylori genome from a European Copper Age glacier mummy. Comparative sequence analysis with contemporary H. pylori classifies the Iceman Helicobacter as a cagA positive vacA s1a/i1/m1 type strain, most closely resembling a strain that today is commonly found in Central and South Asia and that substantially shaped the genomes of modern European H. pylori strains.	root:Host-associated:Human:Digestive system
MGYS00005583	equine gut metagenome Targeted Locus	Microflora of the Equine Hindgut.  This project is pyrosequencing bacterial 16S rRNA amplicons from horse fecal and cecal samples to examine the microflora in the equine hindgut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005582	Investigation of the bacterial microbiome of drinking water for poultry	Samples of drinking water were collected from poultry houses to examine the drinking water bacterial microbiome and how this changes during the production cycle.  Samples were collected for two consecutive production cycles from each six farms during the early, middle and late parts of the cycle.  Water samples (1 litre) were transported to the laboratory on ice and filtered through a 0.22m cellulose acetate filters. These filters were then frozen until DNA was extracted from them using Qiagen Powersoil Pro kit (according to manufacturers instructions).  The v4 region of the 16s rRNA gene was sequenced using an Illumina Miseq (250bp paired end reads).	root:Environmental:Aquatic:Freshwater:Drinking water
MGYS00005566	An investigation of the microbial population in different regions of the large intestine of the horse by 454 pyrosequencing	The aim of the study was to investigate the microbial population within different regions of the large intestine of the horse for healthy animals on a fibre based diet. A further question investigated was if there is a core microbial population found in all animals. Samples of luminal gut contents were collected from the terminal ileum and seven regions of the large intestine (caecum, right ventral colon (RVC), left ventral colon (LVC), left dorsal colon (LDC), right dorsal colon (RDC), small colon (SC) and the rectum) from five thoroughbred horses) and five British native breed ponies) euthanized for non-research purposes. Samples were taken in triplicate (240 samples in total).Genomic DNA was extracted, the V1-V2 region of the 16SrRNA was amplified before being sequenced using the Roche 454 GS FLX Titanium series sequencer.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00005579	Effect of Road Transport on the Equine Cecal Microbiota	"The effects of travel stress on the equine cecal microbiota are poorly understood. We hypothesized that travel would affect the equine cecal microbiota. Cecally-cannulated horses (n 14 6) were randomly assigned to one of two groups, travel (n 14 3) and control (n 14 3). Horses received a basal diet (Strategy, Purina Animal Nutrition) with 1.2% body weight mixed grass/alfalfa. Travel horses were transported to an unfamiliar location, stalled to simulate weekend horse show conditions, and then returned to the Southern Illinois University Equine Center. Control horses remained at the equine center for the entire study. Cecal fluid was collected on a 6-hour rotating schedule, four times daily throughout the 6-day study. Data were analyzed using mixed models in SAS with P < .05. Cecal bacterial DNA was extracted, followed by 16S RNA sequencing and then analyzed using QIIME 1.8.0. Averages of sequence data were reported by phase (baseline, transportation, post-travel). Although there were no effects of travel associated with b-diversity (P > .05), analysis of a-diversity measures indicated an effect within the travel group during the transportation phase as compared with baseline (P < .05). Interestingly, a-diversity was also affected for control horses in the return phase when compared to baseline. This may be due to the disruption of the return of the travel group. In addition, we identified multiple taxa affected by travel at both the genus and phylum level. Continued profiling of equine gastrointestinal microbiota is necessary to improve our understanding of equine microbial dysbiosis.

Authors: Erin Perry, Tzu-Wen L Cross, Jesse M Francis, Hannah D Holscher, Stephanie D Clark, Kelly S Swanson"	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00005578	The composition of the equine microbiota undergoes a stepwise change in response to increasing levels of domestication	"Changes to the gut microbiota have been associated with an increased incidence of disease in many species. This is particularly important during the process of domestication, where captive animals commonly suffer from gastrointestinal (GI) pathophysiology. Horses are a prime example of a domesticated species which suffers from a high incidence of (often life-threatening) GI disease. Some of the most significant factors affecting the gut microbiota in horses are diet, stress and drug administration, all of which are associated with the process of domestication. There are no studies, to date, which describe the effect of increasing levels of domestication on the equine microbiota whilst controlling effectively for confounding variables. Here we aimed to do this by measuring the GI microbiota of adult female Exmoor ponies under 3 management conditions, representing different levels of domestication. Faecal samples were collected from 29 ponies in the South West of the UK; ponies were categorised as Feral (n=10), Semi-Feral (n=10) and Domesticated (n=9), based on their management conditions. Diet was recorded and faecal counts were egg taken from all animals to assess parasite infection status. DNA was extracted and microbial composition identified via high-throughput sequencing of bacterial 16S rRNA gene. Bacterial communities were dominated by Firmicutes (36.71%) and Bacteroidetes (30.99%). Profound stepwise changes in global microbial community structure were seen in the transition from Feral -Semi-Feral- Domesticated groups  these changes were significant in a large number of bacterial phyla and at multiple taxonomic levels. In particular increases in members of the phylum Proteobacteria and Tenericutes were associated with the domesticated group; and increases in Methanobacteria were seen in the Feral group. Faecal egg counts were significantly different between groups, and regression between FEC and individual components of the microbiome revealed that a number of taxa associated with domestication level were also associated with parasite burden. Functional predictions based on microbiome data revealed increased amino acid and lipid metabolism in domesticated group, versus increased energy metabolism in feral group. Interestingly the semi-feral group had a wide variation in FEC and microbial alpha diversity and functional predictions were associated with disease pathways. In this study we have shown significant stepwise changes to GI microbiota due to domestication standardised in one breed of equine. A number of these changes were linked to parasite burden and, based on previous studies, the remainder are likely associated with diet. If we assume that the feral population has a more natural phenotype, akin to that with which horses have evolved, the data can potentially be used to provide bacterial markers of balanced gut homeostasis in domestic Exmoor ponies, and provide candidate markers in other equine breeds.

Authors: Bull K, Davies G, Meier S, Peachey L"	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005577	The effect of diet change and insulin dysregulation on the faecal microbiome of ponies	"The equine microbiome can change in response to dietary alteration and may play a role in insulin dysregulation. The aim of this study was to determine the effect of adding pasture to a hay diet on the faecal bacterial microbiome of both healthy and insulin-dysregulated ponies. Faecal samples were collected from 16 ponies before and after dietary change to enable bacterial 16S rRNA sequencing of the V3V4 region. The dominant phyla in all samples were the Firmicutes and Bacteroidetes. The evenness of the bacterial populations decreased after grazing pasture, and when a pony was moderately insulin dysregulated (P=0.001). Evenness scores negatively correlated with post-prandial glucagon-like peptide-1 concentration after a hay-only diet (r2=0.7, P=0.001). A change in diet explained 3% of faecal microbiome variability. We conclude that metabolically healthy ponies have greater microbial stability when challenged with a subtle dietary change, compared with moderately insulin-dysregulated ponies.

Authors: Danielle M Fitzgerald, Robert J Spence, Zachary K Stewart, Peter J Prentis, Martin N Sillence, Melody A de Laat"	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005576	Investigation of the bacterial microbiome of poultry litter	Samples of litter were collected from poultry houses to examine the litter bacterial microbiome and how this changes during the production cycle.  Samples were collected from six farms which used a variety of bedding types.  Samples were collected for two consecutive production cycles from each farm during the early, middle and late parts of the cycle.  Litter samples were transported to the laboratory on ice and thoroughly mixed with sterile phosphate buffered saline (PBS) at a 1:1 ratio (vol:vol). Aliquots of the PBS were frozen until DNA was extracted using Qiagen Powersoil Pro kit (according to manufacturers instructions).  The v4 region of the 16s rRNA gene was sequenced using an Illumina Miseq (250bp paired end reads).	root:Host-associated:Birds:Digestive system:Fecal
MGYS00005575	trial samples of a study in the Venice Lagoon	The samples belong to a project aiming to study the Venice lagoon from funcional prespective via metagenomics	root:Environmental:Aquatic:Marine
MGYS00005297	Mapping and Predictive Variations of Soil Bacterial Richness across French National Territory	Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and the determinism of such diversity on a wide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across French national territory, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) and environmental filters most influencing this distribution, and iii) to develop a statistical predictive model of soil bacterial richness. We used the French Soil Quality Monitoring Network (RMQS), which covers all of France with 2,173 sites. The soil bacterial richness (i.e. OTU number) was determined by pyrosequencing 16S rDNA genes directly amplified from DNA of all soil samples and related to the soil characteristics, climatic conditions, geomorphology, land use and space. Mapping of bacterial richness revealed a heterogeneous spatial distribution, structured into patches of about 111 km, where the main drivers were the soil physico-chemical properties, the spatial descriptors and the land use. Based on these drivers, a predictive model was developed, which allows a good prediction of the bacterial richness (R2adj of 0.56) and provides a reference value for a given pedoclimatic condition.	root:Environmental:Terrestrial:Soil
MGYS00005573	EMG produced TPA metagenomics assembly of PRJNA415710 data set (Elucidating the dandruff and non-dandruff scalp microbiome in Indian women and assessing the effect of coconut oil on it).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA415710, and was assembled with metaSPAdes v3.13.0. This project includes samples from the following biomes: root:Host-associated:Human:Skin.	root:Host-associated:Human:Skin
MGYS00005574	Elucidating the dandruff and non-dandruff scalp microbiome in Indian women and assessing the effect of coconut oil on it	The study aimed at exploring the scalp microbiome in Indian individuals with dandruff and non-dandruff scalp. Since, coconut oil is used in many parts of the country, the effect of coconut oil was also assessed on the microbiome in a time-course of 16 weeks.	root:Host-associated:Human:Skin
MGYS00005572	Effects of organic amendments in soil affected by fire in central Chile	This study tested the effects of fire and organic amendments on the microbial communities (16S and 18S) on Mediterranean areas of Chile	root:Environmental:Terrestrial:Soil
MGYS00005571	A metagenomic approach to understanding the microbial consequences of permafrost thaw in boreal Western Canada	This study sampled 20 lakes along a north-south permafrost gradient (continuous, discontinuous, sporadic, no permafrost) in boreal western Canada (Northwest Territories and Alberta). Samples were taken from the sediments at the edges of small boreal ponds, extracted using DNeasy Powersoil and then prepared for shotgun sequencing using an NEBNext Ultra II FS kit. Controls included: negative water only, Zymo Microbial community standard.	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00005570	Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene.	Bacterial communities present in feces of six healthy horses and 10 horses affected by colitis were analyzed by 454 high throughput sequencing of the V3-V5 region of the 16S rRNA gene.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005569	human oral microbiome, metagenomic assembly	We investigated phylogenetic and functional markers of niche partitioning of enigmatic members of the oral cavity, with a focus on members of the candidate phylum TM7. We used a metagenomic assembly and binning approach to recover metagenome-assembled genomes (MAGs) from the supragingival plaque and tongue dorsum of healthy individuals, and used long-read sequencing to associate TM7 MAGs with previously identified phylotypes through 16S rRNA sequence comparison. Our genomes represent prevalent and abundant lineages that lack genomic representation in the HOMD and National Center for Biotechnology Information (NCBI) genomic databases, including members of the Candidate Phyla Radiation. Using a multi-omics approach we show that oral TM7 species are split into plaque and tongue specialists, and that plaque TM7 phylogenetically and functionally associate with environmental TM7, while tongue TM7 associate with TM7 from animal guts. To assess the generality of our results we carried out read recruitment from approximately 200 tongue and 200 plaque Human Microbiome Project (HMP) samples; which confirm that the genomes we identified are prevalent, abundant, and site-specific. Our findings suggest that at least for TM7, dental plaque resembles non-host habitats, while tongue- and gut-associated TM7s are more strongly shaped by the host. In addition, our results shed light on other understudied members of the oral cavity, and allow for better genomic insight into prevalent, yet poorly understood members of the oral microbiome.	root:Host-associated:Human:Digestive system:Oral
MGYS00005568	Characterizing the gut microbiome of the last population of undomesticated horses living in the wild, the Przewalski horse	The domestication of animals is often viewed as one of the most important developments in modern human history. Although much attention has been paid to the effects of domestication on host phenotypes, the effects of domestication on the host gut microbiome is relatively understudied. Given the important role of the mammalian gut microbiome in host health, nutrition, and the immune system (McFall-Ngai et al. 2013), filling this knowledge gap has important potential health implications for livestock, pets, and for improving current management strategies. The diet of domesticated animals is often highly different and less varied than their ancestral diet (e.g. dogs eating Iams or Purina processed food vs. wolves eating caribou or bison). We propose to study equids as a model for investigating the effects of domestication in mammals. We collected fecal samples from 45 individuals in the last wild population of the highly endangered Przewalski horse (Equus przewalskii) in Mongolia. The horse population was monitered with binoculars and fecal material was collected within an hour (usually within minutes) of defecation, allowing each fecal sample to be associated with a particular horse. Extremely detailed metadata is available for the population investigated, including pedigree, age, social structure, health, reintroduction dates, whole-genome data and years of daily behavioral observations in the field. We will compare the gut microbiota of these samples to fecal samples collected from 36 wild, domesticated horses living in the same region of Mongolia, which will allow us to isolate the effects of domestication/species differences from effects of current diet. We hypothesize that the gut microbiome of domesticated horses will have lower microbial diversity than the microbiome of their undomesticated relatives.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005565	Temporal stability of equine microbiome	Twelve mature (aged 5-16 years) horses and ponies of mixed breed and type were fed restricted quantities of one of two fibre based diets formulated to be iso-caloric. Diet 1 comprised of 0.8% body mass (BM) of chaff based complete feed plus 0.45% BM low energy grass hay (the same hay used for both diets). Diet 2 comprised 0.1% BM of a nutrient balancer plus 1.15% BM grass hay. Faecal samples were collected at week 10 and week 16.  DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced to investigate the bacterial microbiome of the horse. The two most abundant phyla found in both diets and sampling periods were the Firmicutes and Bacteroidetes. There was a limited degree of stability within the bacterial community of the hindgut of horses over a 6 week period with between 50 -65% of the bacteria in any horse common over the period.  What is of greater interest is that the core community in the horse does not appear to be markedly more stable than the total bacterial community.  This could clearly be a factor which contributes to the horse being more susceptible to gastrointestinal challenge and warrants significant further investigation.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005567	The impact of fructooligosaccharide supplementation on the gastrointestinal microbiome of Thoroughbred youngstock during nutritional stress	Background: Feeding of domesticated horses with carbohydrate-rich diets is associated with a high risk of gastrointestinal (GI) diseases. Prebiotic supplements, such as fructooligosaccharides (FOS), are promoted as gut stabilizers by reducing potentially pathogenic bacteria in the GI tract in response to carbohydrate overload. However, studies supporting FOS use have had mixed results and use outdated culture-based techniques.Objectives: To evaluate the impact of FOS prebiotics on the GI microbiome of Thoroughbred yearlings by genetic profiling of the microbiome. Study Design: Randomized case-control study.Methods: 12 male Thoroughbred yearlings were recruited by random selection into 2 groups: a prebiotic group (receiving 30g/day FOS dietary supplement for 8 weeks) and a control group (no FOS supplement). Samples were taken prior to supplementation and subsequently bi-weekly and were analyzed through microbial 16S rRNA sequencing. Qiime 2 and Calypso were used for bioinformatics and statistical analysis.Results: The prebiotic and control group had statistically significant differences in microbiome composition and diversity in the baseline sample prior to prebiotic administration. There were no significant global GI microbiome changes over time following FOS supplementation compared to the control group. Some saccharolytic bacterial species showed diverging (increasing in FOS and decreasing in control) patterns of abundance over time between groups.Main Limitations: The small sample number may reduce the relevance of the results. Also, additional factors, such as social interactions and individual wellbeing, could influence the GI microbiome.Conclusions: Contrary to previous culture-based studies, this preliminary study shows limited effects of FOS administration on the GI microbiome, however, the alterations in abundance of some saccharolytic bacterial species show potential for further investigation. Furthermore, the difference in baseline microbiomes between our study groups prior to FOS supplementation highlight the importance of baseline samples in interventional microbiome research.	root:Host-associated:Mammals:Digestive system
MGYS00005564	The effect of host phenotype on faecal microbiome in the horse	Gastrointestinal microbial communities are implicated in host susceptibilities to  utritional/metabolic diseases; which are more prevalent in obese and/or older horses. This controlled study offered a platform to evaluate associations between host-phenotype and the fecal microbiome / metabolome. Thirty-five, Welsh Mountain pony mares were studied across 2 years (Controls, n = 6/year, 5-15 years, body condition score (BCS) 4.5-6/9; Obese, n = 6/year, 5-15 years, BCS >7/9; Aged, n = 6 Year 1; n = 5 Year 2, 19 years old). Animals were individually fed the same hay to maintenance (2% body mass as daily dry matter intake) for 2 (aged / obese) or 4 (control), 4-week periods in a randomized study. Outset phenotype was determined (body fat%, markers of insulin sensitivity). Feces were sampled on the final 3 days of feeding-periods and communities determined using Next Generation Sequencing of amplified V1-V2 hypervariable regions of bacterial 16S rRNA. Copy numbers for fecal bacteria, protozoa and fungi were similar across groups, whilst diversity was increased in the obese group. Dominant bacterial phyla in all groups were Bacteroidetes>Firmicutes> Fibrobacter. Significant differences in the bacterial communities of feces were detected between host-phenotype groups. Relative to controls, abundances of Proteobacteria were increased for aged animals and Bacteroidetes, Firmicutes and Actinobacteria were increased for obese animals. Over 500 bacterial operational taxonomic units (OTUs) differed significantly between host-phenotype groups. No consistent pattern changes in discriminant OTUs between groups were maintained across groups and between years. The core bacterial populations contained 21 OTUs, 6.7% of recovered sequences.Distance-based Redundancy Analyses separated fecal bacterial communities with respect to markers of obesity and insulin dysregulation, as opposed to age. Host-phenotype had no impact on the apparent digestibility of dietary GE or DM, fecal volatile fatty acid concentrations or the fecal metabolome (FT-IR).The current study demonstrates that host-phenotype has major effects on equine fecal microbial population structure. Changes were predominantly associated with the obese state, confirming an obesity-associated impact in the absence of nutritional differences. Clear biomarkers of animal-phenotype were not identified within either the fecal microbiome or metabolome, suggesting functional redundancy within the gut microbiome and/or metabolome.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005563	Removal of adult cyathostomins alters faecal microbiota and promotes an inflammatory phenotype in horses	The interactions between parasitic helminths and gut microbiota are considered to be an important, although as yet incompletely understood, factor in the regulation of immunity, inflammation and a range of diseases. Infection with intestinal helminths is ubiquitous in grazing horses, with cyathostomins (about 50 species of which are recorded) predominating. Consequences of infection include both chronic effects, and an acute inflammatory syndrome, acute larval cyathostominosis, which sometimes follows removal of adult helminths by administration of anthelmintic drugs. The presence of cyathostomins as a resident helminth population of the equine gut (the helminthome) provides an opportunity to investigate the effect helminth infection, and its perturbation, has on both the immune system and bacterial microbiome of the gut, as well as to determine the specific mechanisms of pathophysiology involved in equine acute larval cyathostominosis. We studied changes in the faecal microbiota of two groups of horses following treatment with anthelmintics (fenbendazole or moxidectin). We found decreases in both alpha diversity and beta diversity of the faecal microbiota at Day 7 post-treatment, which were reversed by Day 14. These changes were accompanied by increases in inflammatory biomarkers. The general pattern of faecal microbiota detected was similar to that seen in the relatively few equine gut microbiome studies reported to date. We conclude that interplay between resident cyathostomin populations and the bacterial microbiota of the equine large intestine is important in maintaining homeostasis and that disturbance of this ecology can lead to gut dysbiosis and play a role in the aetiology of inflammatory conditions in the horse, including acute larval cyathostominosis.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005560	The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins	A growing body of evidence, particularly in humans and rodents, supports the existence of a complex net- work of interactions occurring between gastrointestinal (GI) helminth parasites and the gut commensal bacteria, with substantial effects on both host immunity and metabolic potential. However, little is known of the fundamental biology of such interactions in other animal species; nonetheless, given the considerable economic losses associated with GI parasites, particularly in livestock and equines, as well as the global threat of emerging anthelmintic resistance, further explorations of the complexities of host- helminth-microbiota interactions in these species are needed. This study characterises the composition of the equine gut commensal flora associated with the presence, in faecal samples, of low (Clow) and high (Chigh) numbers of eggs of an important group of GI parasites (i.e. the cyathostomins), prior to and fol- lowing anthelmintic treatment. High-throughput sequencing of bacterial 16S rRNA amplicons and asso- ciated bioinformatics and statistical analyses of sequence data revealed strong clustering according to faecal egg counts (P = 0.003). A trend towards increased populations of Methanomicrobia (class) and Dehalobacterium (genus) was observed in Clow in comparison with Chigh. Anthelmintic treatment in Chigh was associated with a significant reduction of the bacterial Phylum TM7 14 days post-ivermectin administration, as well as a transient expansion of Adlercreutzia spp. at 2 days post-treatment. This study provides a first known insight into the discovery of the intimate mechanisms governing host-parasite- microbiota interactions in equines, and sets a basis for the development of novel, biology-based interven- tion strategies against equine GI helminths based on the manipulation of the commensal gut flora.	root:Host-associated:Mammals:Digestive system
MGYS00005562	Hospitalized Horse Fecal samples Targeted Locus (Loci)	This study is a rather limited survey on 30 hospitalized horses with or without diarrhea. The fecal samples were investigated for the presence of pathogenic Clostridium difficile and for a 16S metagenetic survey of the fecal microbiota.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005561	Broodmare faecal microbiota	Changes in faecal microbiota in broodmares around the time of foaling	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005559	Dysbiosis associated with acute helminth infections in herbivorous youngstock  observations and implications	A plethora of data points towards a role of the gastrointestinal (GI) microbiota of neonatal and young vertebrates in supporting the development and regulation of the host immune system. However, knowledge of the impact that infections by GI helminths exert on the developing microbiota of juvenile hosts is, thus far, limited. This study investigates, for the first time, the associations between acute infections by GI helminths and the faecal microbial and metabolic profiles of a cohort of equine youngstock, prior to and following treatment with parasiticides (ivermectin). We observed that high versus low parasite burdens (measured via parasite egg counts in faecal samples) were associated with specific compositional alterations of the developing microbiome; in particular, the faecal microbiota of animals with heavy worm infection burdens was characterised by lower microbial richness, and alterations to the relative abundances of bacterial taxa with immune-modulatory functions. Amino acids and glucose were increased in faecal samples from the same cohort, which indicated the likely occurrence of intestinal malabsorption. These data support the hypothesis that GI helminth infections in young livestock are associated with significant alterations to the GI microbiota, which may impact on both metabolism and development of acquired immunity. This knowledge will direct future studies aimed to identify the long-term impact of infection-induced alterations of the GI microbiota in young livestock.	root:Host-associated:Mammals:Digestive system
MGYS00005558	Intestinal microbiota present in the equine GI tract	The objective of this study was to compare the microbiota present in several compartments of the gastro-intestinal tract of horses. This data should reveal impact of different environmental conditions like low pH, low Oxygen tension and the presence of digestive enzymes on the bacterial communities present in each compartment.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00005552	Equine fecal microbiota Raw sequence reads	A healthy gastrointestinal (GI) tract with a properly established microbiota is necessary for a foal to develop into a healthy weanling. In this study, we hypothesized that gut establishment in the foal transitioning from a diet of milk to a diet of grain, forage, and pasture would be detectable through analyses of the fecal microbiotas. Fecal samples from 42 sets of foals and mares were collected at multiple time points ranging from birth to weaning. Bacterial DNA was isolated from the samples, and the V4 domains of bacterial 16S rRNA genes were amplified via polymerase chain reaction. Analyses were performed to characterize the microbiome as well as the relative abundance of microbiota present.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005557	The equine gastrointestinal microbiome: Impacts of weight-loss	Obesity is an important equine welfare issue. Dietary restriction is the most effective weight-loss tool, although individual animals range in their weight-loss propensity. Gastrointestinal-derived bacteria play a fundamental role in host-health and have been associated with obesity and weight-loss in other species. This study evaluated the faecal microbiome (next-generation sequencing of 16S rRNA genes) of 15 obese Welsh Mountain pony mares, across 2 years (n = 8 Year 1; n = 7 Year 2) before and after a 7-week period of dietary restriction (1% body mass hay as daily dry matter intake).  Losses in body mass ranged from 7.11% to 11.59%. Changes in the faecal microbiome composition following weight-loss included a reduction in the relative abundance of Firmicutes and Tenericutes and a reduction in indices of bacterial diversity. Pre-diet diversity was negatively associated with weight-loss. Pre-diet faecal acetate concentration was a strong predictor of subsequent weight-loss and negatively associated with Sphaerochaeta (Spirochaetes phyla) abundance. These data support a role for the faecal microbiome in weight-loss propensity in ponies and provide a baseline for research evaluating elements of the faecal microbiome in predicting weight-loss success in larger cohorts	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005555	Characterization of the microbiota present in different compartments of the equine gastrointestinal tract	This study was designed to provide a detailed microbiological profile of the healthy equine gastrointestinal tract, including samples collected from both the lumen and mucosa of the dorsal and antral stomach, jejunum, ileum, cecum, ventral and dorsal colon. This study will provide the most detailed microbiological map of the healthy equine GI tract to date using culture-independent sequencing methods, and will serve as a baseline against which samples from horses with various health conditions can be compared.	root:Host-associated:Mammals:Gastrointestinal tract
MGYS00005553	Investigating the impact of anthelmintic treatment on the equine microbiome	This pilot study evaluates the hypothesis that anthelmintic drug administration will alter the equine fecal microbiome. To address this hypothesis, twelve horses were administered a single dose of a combination anthelmintic drug [active ingredients: Moxidectin and Praziquantel] on day 0; fecal samples were collected on day -3 (pre-treatment), day 2 (post-treatment 1), day 9 (post-treatment 2).	root:Host-associated:Mammals:Digestive system
MGYS00005551	Early development of the intestinal microbiota in horses, and associations with mare microbiotas	Equine rectal microbiota was sampled at birth, 24 hours later and 7 days later. The microbial DNA was analyzed by 16S rDNA amplicon sequencing using Illumina MiSeq. The foal microbiotas were compared to mare fecal, vaginal and oral microbiotas. Extensive negative controls are included.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00005550	Horse feces Raw sequence reads	In equids, susceptibility to disease caused by Rhodococcus equi occurs almost exclusively in foals. This distribution might be attributable to the age-dependent maturation of immunity following birth undergone by mammalian neonates that renders them especially susceptible to infectious diseases. Expansion and diversification of the neonatal microbiome contribute to development of immunity in the gut. Moreover, diminished diversity of the gastrointestinal microbiome has been associated with risk of infections and immune dysregulation. We thus hypothesized that varying composition or reduced diversity of the intestinal microbiome of neonatal foals would contribute to increased susceptibility of their developing R. equi pneumonia. The composition and diversity indices of the fecal microbiota at 3 and 5 weeks of age were compared among 3 groups of foals: 1) foals that subsequently developed R. equi pneumonia after sampling; 2) foals that subsequently developed ultrasonographic evidence of pulmonary abscess formation or consolidation but not clinical signs (subclinical group); and, 3) foals that developed neither clinical signs nor ultrasonographic evidence of pulmonary abscess formation or consolidation. No significant differences were found among groups at either sampling time, indicating absence of evidence of an influence of composition or diversity of the fecal microbiome, or predicted fecal metagenome, on susceptibility to subsequent R. equi pneumonia. A marked and significant difference identified between a relatively short interval of time appeared to reflect ongoing adaptation to transition from a milk diet to a diet including available forage (including hay) and access to concentrate fed to the mare.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005554	The faecal microbiome of forage-fed horses in New Zealand	The faecal microbiome of forage-fed horses in New Zealand is described and the dynamics is compared pre- and post-dietary change, using pyrosequencing of the 16S and 18S rRNA genes	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005556	Changes in the Equine Fecal Microbiota Associated with the Use of Systemic Antimicrobial Drugs.	The intestinal tract is a rich and complex environment and its microbiota has been shown to have an important role in health and disease in the host. Several factors can cause disruption of the normal intestinal microbiota, including antimicrobial therapy, which is an important cause of diarrhea in horses. This study aimed to characterize changes in the fecal bacterial populations of healthy horses associated with the administration of frequently used antimicrobial drugs.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005549	effect of metronidazole on horse microbiota		root:Host-associated:Mammals
MGYS00005548	Human Oral, nasal microbiota and smoking	This project has two goals:1. To evaluate the effect of smoking on oral and nasal microbiota2. To compare the collection of different oral samples in microbiota profiling.	root:Host-associated:Human
MGYS00005546	Expression of immune regulatory genes correlate with the abundance of specific Clostridiales and Verrucomicrobia species in the equine ileum and cecum	Billions of bacteria inhabit the gastrointestinal tract. Immune-microbial cross talk is responsible for immunological homeostasis, and symbiotic microbial species induce regulatory immunity, which helps to control the inflammation levels. In this study we aimed to identify species within the equine intestinal microbiota with the potential to induce regulatory immunity. These could be future targets for preventing or treating low-grade chronic inflammation occurring as a result of intestinal microbial changes and disruption of the homeostasis. 16S rRNA gene amplicon sequencing was performed on samples of intestinal microbial content from ileum, cecum, and colon of 24 healthy horses obtained from an abattoir. Expression of genes coding for IL-6, IL-10, IL-12, IL-17, 18s, TNF, TGF, and Foxp3 in the ileum and mesenteric lymph nodes was measured by qPCR. Intestinal microbiota composition was significantly different in the cecum and colon compared to the ileum, which contains large abundances of Proteobacteria. Especially members of the Clostridiales order correlated positively with the regulatory T-cell transcription factor Foxp3 and so did the phylum Verrucomicrobia. We conclude that Clostridiales and Verrucomicrobia have the potential to induce regulatory immunity and are possible targets for intestinal microbial interventions aiming at regulatory immunity improvement.	root:Host-associated:Mammals:Digestive system
MGYS00005545	The bacterial microbiota in  different gastrointestinal tract compartments in Mongolian horses Raw sequence reads	This study was designed to provide a detailed microbiological profile of the Mongolian horses gastrointestinal tract, including samples collected from the lumen of the stomach, jejunum, ileum, cecum, ventral colon and dorsal colon.We characterized the microbial composition of the different parts of the Mongolian horse GIT using high throughput sequencing for the first time.	root:Host-associated:Mammals:Gastrointestinal tract
MGYS00005543	Temporal variation of the horse faecal microbiota	The study aimed at investigating temporal stability of faecal microbiota in horses managed on pasture. A group of 7 horses were sampled every 14 days for a year.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005544	Horse faecal material Metagenome	Characterisation of the faecal microbiome of Thoroughbred racehorses.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005541	Investigating gut microbiome in horses that had laparotomy for treatment of primary large colon disease	Horses treated surgically for colic signs associated with large colon disease are more likely to develop postoperative recurrent colic episodes. Delayed recovery of gut bacteria following surgery is one potential mechanism of this observation. The study aimed at investigating gut microbiota before and overtime following laparotomy in horses diagnosed with a primary large colon disease and to compare findings to a control group of horses undergoing emergency orthopedic treatment.	root:Host-associated:Mammals:Digestive system
MGYS00005542	Tibetan Chicken caecum feces Targeted Locus (Loci)	To reveal the bacteria community related to Tibetan Chicken caecum	root:Host-associated:Birds:Digestive system:Ceca
MGYS00005080	Molecular and Functional diversity of bacteria associated with earthworm gut		root:Host-associated:Annelida:Digestive system
MGYS00005529	Human sigmoid colon mucosal biopsy metagenomes in cohort with and without diverticula	The study''s goals were to look for associations between the microbial community and diverticulosis using a large cohort (535 patients) with and without diverticula of the sigmoid colon.	root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon
MGYS00005536	Soil microbial diversity in the Maintenance of Exotic vs. Native Diversity experiment (depth study)	Grasslands dominated by non-native species have replaced purely native-dominated areas in many parts of the world. This replacement has led to altered plant-plant interactions aboveground, but it is poorly understood how soil microbial communities differ between native and exotic plant communities. We tested how exotic vs. native plant species and summer irrigation affect bacterial and fungal community composition and diversity in a common garden experiment, Maintenance of Exotic vs. Native Diversity. In this study, the samples were taken at various soil depth: 0-10 cm, 10-30 cm, 30-60 cm, and 60-100 cm to assess if these changes are maintained in deeper soil layers.	root:Environmental:Terrestrial:Soil
MGYS00005301	Bacterial and archaeal diversity on mammalian skin	Characterization of the microorganisms on skin is essential for understanding how a host evolves in association with its microbial symbionts, modeling immune system development, diagnosing illnesses, and exploring the origins and etiology of disease. Although many studies have characterized the human microbiome, far less is known about the skin microbiome of non-human mammals. The objective of this research was to create a baseline skin microbiome dataset for the Mammalia class, testing the effects of species, location, hygiene, body region, and biological sex. The back, torso, and inner thigh regions of 187 non-human mammals and 20 human participants were collected to include representatives from 38 species and 10 mammalian orders. Animals were collected from local farms, zoos, households, and the wild. All samples were amplified using the V3-V4 16S rRNA gene region and sequenced using a MiSeq (Illumina). Human skin was significantly less diverse than all other mammalian orders according to Shannon indices (6.54 versus 3.96, p < 0.001). The factor most strongly associated with community variation for all samples was whether the host was a human (PERMANOVA, F = 37.8, p < 0.001; Figure 2). By analyzing all samples together, random forest modelling identified that human and animal samples could be distinguished correctly 98.51.2% of the time. This study represents the largest mammalian skin microbiome project to date and is the first study to elucidate the skin microbiota for 32 distinct species. Additionally, these findings are the first to demonstrate that human skin is distinct, not only distinct from other Primates, but from all 10 mammalian orders sampled. Baseline data on the mammalian skin microbiome is crucial to make informed decisions for veterinarian research and conservation strategies, as well as providing implications for mammalian evolutionary history.	root:Host-associated:Mammals:Skin
MGYS00005255	Emergent simplicity in microbial community assembly	We established laboratory-adapted and self-assembled microbial communities to study the microbial community assembly.	root:Engineered:Lab Synthesis
MGYS00005528	Population-based study on tongue microbiota composition of Japanese elderly adults	Tongue coating samples were collected from Japanese community-dwelling elderly adults aged 70-80 years in a health examination performed as a part of the follow-up survey of the Hisayama cohort study on 2016. The V1-V2 regions of 16S rRNA gene amplicons were analyzed using Ion PGM. The project goal is to understand the variation among normal tongue microbiota observed the community-dwelling elderly adults.	root:Host-associated:Human:Digestive system:Oral:tongue dorsum
MGYS00005254	Development of outbred CD1 mouse colonies with distinct standardized gut microbiota profiles.	Outbred CD1 mouse colonies were generated to be colonized with four distinct complexgut microbiota (GM) profiles representing contemporary rodent producer profiles. Mice were maintained atthe University of Missouri for nine generations and fecal samples were analyzed using 16S rRNA gene sequencing.Additionally, ninth generation mice were shipped to collaborating institutions and fecal samples were collectedand sequenced for detection of post-shipping associated shifts in GM profile.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00005183	16S rRNA amplicon V4 Rag1KO and WT mice infected with Clostridium difficile	16S rRNA amplicon sequencing of V4 region from mus musculus (C57B6 WT and RAG1KO) intestinal communities collected over the course of a study which sought to determine the role of adaptive immunity in clearance of Clostridium difficile colonization.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005182	Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysis	Microbial community analysis can be biased by multiple technical factors, such as storage conditions, DNA extraction, or amplification conditions. In a high-throughput laboratory that relies on samples obtained from thousands of different subjects, knowledge of the extent of subject-introduced sampling and storage variation on the outcome of the inferred microbiome, as well as the effect of laboratory-introduced variation caused by reagent batches, equipment, or operator on the consistency of these processes within the laboratory is paramount. Here, we analyzed the effect of sampling from different parts of the same stool specimen or on different consecutive days, as well as short-term storage of samples at different temperatures on microbiome profiles obtained by 16S rRNA gene amplification. Each of these factors had relatively little effect on the microbial composition. In addition, replicate amplification of 44 stool samples showed reproducible results. Finally, 363 independent replicate extractions and amplifications of a single human homogenized stool (HS) specimen showed reproducible results (average Lins correlation = 0.95), with little variation introduced by HS batch, operator, extraction equipment, or DNA sequencer. In all cases, variations between replicates were significantly smaller than those between individual samples; subject identity always was the largest determinant. We propose that homogenized stool specimens could be used as quality control to routinely monitor the laboratory process and to validate new methods.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00005252	Deciphering microbial interactions in synthetic human gut microbiome communities	The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.	root:Host-associated:Human:Digestive system
MGYS00005263	Microbial communities associated with Eurasian watermilfoil, water and sediment	Characterize microbial communities associated with Eurasian watermilfoil, water and sediment in freshwater lakes in Minnesota USA	root:Environmental:Aquatic:Freshwater:Lake
MGYS00005180	Antibiotic induced changes in the microbiota disrupt redox dynamics in the gut	Mouse and ex vivo gut microbial responses to broad spectrum antibiotic treatment.	root:Host-associated:Mammals:Gastrointestinal tract
MGYS00005179	EPICON Sorghum Drought Microbiome	##### Experimental design# The following sequence data was used as part of a DOE funded project to explore the relationship between drought and microbial recruitment in Sorghum bicolor. For detailed descriptions of experimental design, please see the associated publication. In brief, we planted two different sorghum cultivars (RTx430 and BTx642) within a randomized block design that accounted for treatments, genotypes and replication, with three replicate blocks in total. From this field experiment, we collected a variety of plant phenotypes, soil measurements, and rhizosphere, root and soil samples for microbial community analysis and metatranscriptomics. All samples were collected weekly at the same time of day (between 10am and 1pm) and the same day of the week for seventeen weeks following seedling emergence (TP1 to TP17).	root:Host-associated:Plants:Rhizosphere
MGYS00005177	Quantitative genetic analysis of the maize phyllosphere	Sequencing of bacterial populations on maize leaves to identify the community structure and how the genetics of the maize plant impact its microbial communities.	root:Host-associated:Plants:Phylloplane
MGYS00005178	Gut microbiome in German Shepherd dogs	The aim of this study was to explore the development of the gut microbiota in 168 German Shepherd dogs (30 litters) from 7 weeks to 18 months of age and furthermore, to study the effect of relatedness , maternal microbiota composition and living environment in a large and well-defined population of dogs.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005250	Temporal variation in pesticide biodegradation	Bacterial and phototrophic sequence reads for seasonal pesticide degradation project.	root:Environmental:Aquatic:Freshwater
MGYS00005262	The impact of tampon use on the vaginal microbiota	We conducted a cohort study with crossover design to assess the impact of tampon use on the composition and dynamics of the vaginal microbiota. Women self-collected vaginal swabs twice weekly for four menstrual cycles and used tampons as assigned during each menstrual cycle. We used 16S rRNA gene amplicon sequencing to characterize vaginal microbiota composition at each time point and observed a significant trend of decreased vaginal microbiota stability during menses compared to elsewhere during the menstrual cycle.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00005539	Non-target effects of Metarhizium brunneum on soil microbial communities	The aim of this project was the assessment of potential non-target effects of the entomopathogenic fungus and biological control agent Metarhizium brunneum on soil fungal and prokaryotic community structures. To our knowledge, this research question was assessed for the first time using next generation sequencing technology of ribosomal markers. Non-target effect studies are required for product registration and expand knowledge on the impact of agricultural applications to the environment. M. brunneum was applied against Agriotes spp. in potato in a pot. The presence of the applied strain and the microbial community structures were monitored in soil over 4 months (1 pre-treatment sampling and 2 post-treatment samplings). M. brunneum was applied in different formulations and as unformulated spores. Controls included an insecticide, non-fungal components of the formulations and untreated pots.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00005259	Dynamics of human gut microbiota and metabolites in response to prebiotic interventions	Human gut microbiota composition and SCFA concentrations in response to prebiotic fiber supplementation in young adults.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005170	Root bacterial and archaeal microbiota dynamics over the life cycle of rice plants. Targeted loci environmental	We monitored how the rice root microbiota changes over the course of the plant''s life cycle. We inspected how rhizocompartment, field geography, seasonal variation, and plant development rates affect this process.Using these data we formed a model to predict plant age and tested how abiotic factors affect microbiota development.	root:Host-associated:Plants:Root
MGYS00005150	Dietary fiber-deprived gut microbiota degrades the protective mucus barrier and promotes pathogen susceptibility	Little is known about how chronic or periodic dietary fiber deprivation impacts metabolism of the human gut microbiota and potentially leads to deterioration of colonic health. Here, we elucidated the mechanistic interactions among dietary fiber, the gut microbiota and the protective colonic mucus barrier that is one of the hosts first lines of defence. We employed a tractable approach consisting of a synthetic community of fully sequenced human gut bacteria assembled in gnotobiotic mice. The members of this community were selected to represent the phylogenetic diversity in a complete microbiota, but also based on empirical knowledge of their abilities to degrade various fiber polysaccharides and mucin glycans in vitro. The responses of this synthetic microbiota, and the corresponding impact on the host colonic mucus layer, to variation of dietary fiber were monitored by multiple readouts in conditions where mice were fed constant high- or low-fiber diets or daily alternations of the two. We show that starvation of dietary fiber diminishes the colonic mucus barrier by enhancing the activities of mucin-degrading bacteria. One-day alternations of the fiber-rich and fiber-free diets or feeding of a prebiotic diet still displayed thinner mucus barriers reflecting a residual increase in mucus-degrading bacteria and their mucin glycan-degrading enzymes. The microbiota starved of dietary fiber led to low-grade intestinal inflammation and heightened susceptibility to infection by a mucosal pathogen, Citrobacter rodentium, illustrating adverse effects of diet lacking complex natural fiber.	root:Host-associated:Mammals:Digestive system
MGYS00005174	Soil bacterial communities (Hainich National Park)	This study focuses on the influence of tree species composition, soil properties and seasonality on the structure of soil bacterial communities by employing high-throughput sequencing of the 16SrRNA gene. Soil cores were collected from bulk soil (0 - 5 cm depth) within eight tree clusters containing mono-species (beech, horn, lime and oak) and mixed-species (BOH, BOL, BHL and OHL) stands during Spring, Summer and Autumn 2012.	root:Environmental:Terrestrial:Soil
MGYS00005173	Infant (COPSAC) feces microbiome Raw sequence reads	16s rRNA gene sequencing of fecal samples of infants in the COPSAC2010 cohort	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005537	Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition	Plant roots select non-random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonised by different fungi and analysed differences in microbiome structure related to soils from distinct podzol horizons and effects of short term additions of N, a growth-limiting nutrient commonly applied as a fertiliser, but known to influence patterns of carbon allocation to roots. Ectomycorrhizal roots growing in soil from different horizons harboured distinct bacterial communities. The fungi colonising individual roots had a strong effect on the associated bacterial communities. Even closely related species within the same ectomycorrhizal genus had distinct bacterial microbiomes in unfertilised soil, but fertilisation removed this specificity. Effects of N were rapid and context dependent, being influenced by both soil type and the particular ectomycorrhizal fungi involved. Fungal community composition changed in soil from all horizons, but bacteria only responded strongly to N in soil from the B horizon where community structure was different and bacterial diversity was significantly reduced, possibly reflecting changed carbon allocation patterns.	root:Host-associated:Plants:Root
MGYS00005172	Topical treatment interventions elicit personalized and site-specific shifts in human skin bacterial communities	The skin microbiome represents a significant contributor to cutaneous health and disease. This includes its roles in immune tolerance and defense against pathogenic microorganisms. Despite these critical functions, the impact of topical interventions meant to disrupt these communities remains poorly understood. In this study, we present the effects of three clinically-relevant antiseptics, alcohol, povidone-iodine (Betadine), and chlorhexidine, on cutaneous bacterial populations. We illustrate a proficiency of these treatments in altering skin bacterial communities, a result which was highly dependent on interpersonal and body site-specific signatures. We also show that the magnitude of this response can be influenced by both the identity and relative abundances of bacterial inhabitants. By comparing the effects of antiseptic regimens, we highlight the importance of antibacterial activity and mechanical clearance to treatment disruption. We also demonstrate the potential for pre-treatment communities to inform post-treatment response. In all, these results further our understanding of treatment-derived perturbations to the skin microbiota, and establish the ability of topical interventions to influence skin bacterial dynamics.	root:Host-associated:Human:Skin
MGYS00005249	Fungal internal transcribed spacer 2 amplicons of sugarcane plant compartments and soils Targeted loci environmental	Unravelling the sugarcane microbiome	root:Host-associated:Plants:Rhizoplane:Endophytes
MGYS00005164	Topical antimicrobial treatments elicit shifts to resident skin bacterial communities and reduce colonization by Staphylococcus aureus competitors	The skin microbiome is a complex ecosystem with important implications for cutaneous health and disease. This includes its ability to educate the immune system and promote key epidermal barrier functions during infection. Despite their widespread use, the effects of topical antibiotics and antiseptics on these communities have been largely understudied. Instead the majority of work has focused on their effect in pathogenic bacteria, with little regard for their influence on broader communities. Here, we report the longitudinal impact of topical antibiotics and antiseptics on skin bacterial communities. In response to antibiotics, cutaneous populations exhibited an immediate and long-term shift in bacterial residents. By contrast, antiseptics elicited only minor changes to underlying communities. Upon deeper analysis, we detected a conserved decrease in Staphylococcus residents, a group which varied greatly in response to both antimicrobial and environmental pressures. These particular inhabitants were also shown to compete with Staphylococcus aureus for colonization at the skin surface, a stable effect which extended to multiple resident Staphylococcus species. This study demonstrates that antimicrobial drugs have distinct and durable effects on skin bacterial residents, and that these alterations have important ramifications for infection by pathogenic bacteria such as S. aureus.	root:Host-associated:Mammals:Skin
MGYS00005168	The influence of caging, bedding, and diet on the composition of the microbiota in different regions of the mouse gut	16S rRNA gene amplicon libraries generated from jejunal contents, ileal contents, ileal contents, and feces ofmice housed in static or ventilated housing, with aspen or paperchip bedding, and with one of three commercially available rodentchows, for thirteen weeks, in a fully crossed study design	root:Host-associated:Mammals:Digestive system
MGYS00005165	16S amplicons New Zealand agricultural soils	This study consists of soil samples collected from pastures under a range of land uses and across three time points (May 2014, Nov 2014, May 2015	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00005167	Perth Otitis Media Microbiome (biOMe) Study (16S rRNA amplicon data)	Recurrent acute otitis media (rAOM; recurrent ear infections) is a common disease in childhood. We characterised the microbiome of rAOM-prone and rAOM-resistant children to identify novel pathogens and potentially protective commensal bacteria, which may guide the development of more effective therapies.	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00005166	manure metagenome Targeted loci environmental	Spontaneous foaming in deep-pit swine manure storage accumulates methane and is a threat to the welfare of both human and animal in pork production industry. To understand the microbial drivers behind the foaming manure methane accumulation, we collected pit manure samples from barns across Iowa for 13 months. We integrated swine feed information, manure characteristics, bacterial community (16S rRNA gene amplicon sequencing), and methanogen communities (mcrA gene amplicon sequencing to identify the key characteristics and microbial organisms that were unique in foaming and non-foaming pit-manure. By using correlation analysis, we identified the potential microbial organisms that could influence the pit-manure community structures and potentially be used in foaming manure mitigation.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005258	METSIM gut microbiome	The gut microbiome is complex and metabolically active community that directly influences host phenotype. In this study, we profiled gut microbiota using 16S rRNA gene sequencing in 531 well-phenotyped Finnish men collected from the population-based Metabolic Syndrome In Men (METSIM) study.	root:Host-associated:Human:Digestive system
MGYS00005533	Patterns in the skin microbiota differ in children and teenagers between rural and urban environments	The skin protects from outer threats and this function is supported by commensal microbes. Alterations in skin microbiota are linked with common dermatological diseases. Thus, it is central to understand what drives these alterations. We show that the age and the living environment are associated with the composition of individual skin microbiota. The effect of living environment seems to be strongest in young children, which is notable as the first years of life are most chritical for immune system development in cross-talk with microbiota. Age-related skin physiology and lifestyle also importantly shape microbiota. In conclusion, children growing-up in contrasting environments are exposed to different microbial environment, which may influence their future health through the altered development of microbiota.	root:Host-associated:Human:Skin
MGYS00005244	Unraveling the faecal microbiota and functional capacity associated with feed efficiency in pigs	The data is used for unraveling the faecal microbiota and functional capacity associated with feed efficiency in pigs	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005246	Response of soil bacteria to anthropogenic soil variables at large spatial scales	We sought to determine the relative influences of spatial and environmental factors on entire bacterial communities and individual taxa, in both natural and human-impacted soils in the upper North Island of New Zealand. We conducted 16S rRNA (v3-v4 region) amplicon sequencing on soil samples from 110 native forests, plantation forest, horticultural or pastoral sites, which constitute the dominant land uses within temperate climate zones. These sites were located between 5 m and 300 km apart. This bacterial data was paired with extensive site metadata to determine which environmental variables were correlated with changes in bacterial community composition as a whole, as well as with changes in the abundance of specific taxa.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00005535	Microbiome of high and low methane-emitting sheep (3633 progeny)	Bacterial 16S rRNA genes were amplified from sheep rumen contents to study heritability of the rumen microbiome in regards to host genotype and methane phenotype.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00005531	Genetic associaiton with vaginal microbiome in Korean twins	We characterized the vaginal microbiome from 542 females including 222 monozygotic and 56 dizygotic twins aged 29-58 years and investigated the genetic contribution on the vaginal microbiome.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00005532	Rumen contents Targeted Locus (Loci)	Rumen microbial communities of sheep fed different diets	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00005239	DIPP Stool Metagenome	16S rRNA and metagenomes DIPP microbiome study	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005534	Drinking water distribution system biofilm samples Metagenome	This project reveals the community structure and composition of biofilms from an urban drinking water distribution system across two years.	root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
MGYS00005538	Metcalf_Mouse_Decomp_Forensics_2011_18S	Establishing the time since death or postmortem interval (PMI) is critical in the initial stages of death investigations, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess PMI, but errors can range on the scale of days, weeks or season depending on the scenario1. Limitations of forensic entomology include uncertainty in the interval between death and initial egg deposition2, lack of insects during particular weather events or seasons3, and regionally specific blowfly larval growth curves and insect communities4. Microbes may provide a novel method for estimating PMI that might avoid many of these limitations, because microbes are ubiquitous in the environment, located on humans before death, and can be reliably quantified using high-throughput DNA sequencing. However, the feasibility of using microbes forensically has yet to be rigorously tested, and we must determine whether microbial community change is sufficiently measurable and directional during decomposition to allow accurate predictions. Here, we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing estimates of PMI to within ~3 days over 48 days, and provide insight into the ecological factors underlying succession of bacteria and microbial eukaryotes within the decomposing corpse system. Our results suggest that microbial community data can be developed into a forensic tool for estimating PMI.	root:Host-associated:Mammals
MGYS00005540	Global patterns of microbial diversity associated with eelgrass, Zostera marina	Plant-associated microorganisms are essential for their hosts'' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. We focus on the microbial communities associated with Zostera marina, a marine foundation species found throughout the Northern Hemisphere, by sampling microbial communities present on the leaf and root surfaces of 129 eelgrass individuals and sequencing amplified fragments of the V4 region of the 16S rRNA gene on an Illumina MiSeq. Additionally, we sampled microbial communities from adjacent water and sediments to highlight important differences in the communities compared to those associated with plants. This study will allow us to compare global differences and detect assembly mechanisms of the microbial communities associated with roots.	root:Host-associated:Plants:Root
MGYS00000524	Gut microbiota community and functions of mouse exposed to single As, single Fe, and combined As and Fe	Mice were fed with pure water, 3mg/L As, 5mg/L Fe, and  3mg/L As + 5mg/L Fe for 90 days. Then, the fecal samples were collected, and genomic DNA was extracted  by FastDNA SPIN Kit for Soil (Qiagen, CA). Genomic DNA was amplified with a set of primers targeting the hypervairable V3 and V4 regions of 16S rRNA gene. The PCR products were quantified using Nanodrop and was sent out for pyrosequencing on the Roche 454 FLX Titanium platform. High-throughput sequencing for mouse fecal genomic DNA using Illumina Hiseq 2000 was performed to identify the function genes of gut microbiota.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005216	bovine gut metagenome Metagenome	In this study, we hypothesized that specific bacterial features influence feed efficiency phenotype of beef cattle. Rumen bacterial community composition from two cohorts of animals (heifers and steers) was determined through 16S rRNA gene sequencing to identify differentially abundant bacterial groups across varying feed efficiency phenotypes. Based on the differential abundant bacterial groups, models were built and tested to explain the variation in feed efficiency traits (average daily gain, average daily dry matter intake, and gain-to-feed efficiency).	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00001288	Saliva microbiome of pig in Japan	Metagenomic sequences of microbiome obtained from pig saliva in Japan	root:Host-associated:Mammals:Digestive system:Oral cavity:Buccal mucosa
MGYS00005289	Preparing for the manned Mars journey: Microbiome dynamics in the confined MARS 500 habitat during simulated Mars flight and landing	The MARS 500 project was the first full duration simulation of a manned flight to Mars. For 520 days, a six-man crew lived like astronauts in a specifically designed and hermetically sealed spacecraft-like environment. The MICHAm (MIcrobial ecology of Confined Habitats and humAn health, modified) study aimed to survey the microbial distribution and its community structure within the facility from the start to the end of the simulation study, and to investigate the impact of confinement. Therefore, the microbial load and biodiversity in the air and on surfaces as well as their changes over time were monitored.The cultivation approach showed that the overall microbial inventory in the air and on different surfaces was moderate compared to other non-confined rooms (air: 0 to 716 CFU/m3; average=86 CFU/m3; surface: 0 to 29,760 CFU/10 m2; average=675 CFU/10 m2). Despite the detection of fluctuations in microbial load over time and places, microbial hotspots were identified. Phylogenetic investigations revealed a higher diversity on surfaces than in air indicating the dominance of human-associated microorganisms (e.g. staphylococci). Besides cultivation-based analyses, the microbial community was also studied on the molecular level via PhyloChip analysis and next generation sequencing. The whole microbiome structure exhibited a significant change in structure and decrease in diversity over time, but potentially pathogenic microorganisms containing mobile elements increased during the confinement. Additionally, significantly different microbiome structures were identified for investigated modules.Since the majority of microorganisms were not harmful there was no alert and health concern due to potential danger caused by microorganisms. The scientific information obtained by our study is essential to evaluate biosafety risks, predict and mitigate the possible occurrence of biocorrosion, and improve the sanitary and hygienic quality of life for the crew inside closed habitats.	root:Engineered:Built environment
MGYS00005034	EMG produced TPA metagenomics assembly of the Skin metagenomes (human skin metagenome) data set.	The human skin metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA281366.  This project includes samples from the following biomes: Host-associated, Human, Skin.	root:Host-associated:Human:Skin
MGYS00005503	Characterization and Analysis of Skin- and Intestine-associated Microbiomes of Fish in the Lower Northwest Passage of Nunavut, Canada (2019)	The Towards a Sustainable Fishery for Nunavummiut (TSFN) Project seeks to increase our understanding of the fisheries resources in the lower Northwest Passage in partnership with Nunavummiut communities. Our goal is to use genomic, demographic, physiological and microbial analysis to inform strategies to retain genetically-diverse and healthy stocks for the sustainable supply of high quality fish to Inuit communities. Genetic analysis will allow the identification of fish populations, but it is also important to assess the health of this resource. We are therefore characterizing fish with respect to their microbial consortia.	root:Host-associated:Fish
MGYS00005499	Microbiota associated with Daphnia exhibiting genetic variation in behavior	In many organisms, host-associated microbial communities are acquired horizontally after birth. This process is believed to be shaped by a combination of environmental and host genetic factors. We examined whether genetic variation in animal behavior could affect the composition of the animals microbiota in different environments. The freshwater crustacean Daphnia magna is primarily planktonic, but exhibits variation in the degree to which it browses in benthic sediments. We performed an experiment with clonal lines of D. magna showing different levels of sediment-browsing intensity exposed to either bacteria-rich or bacteria-poor sediment or whose access to sediments was prevented. We find that the bacterial composition of the environment and genotype-specific browsing intensity together influence the composition of the Daphnia-associated bacterial community. Exposure to more diverse bacteria did not lead to a more diverse microbiome, but greater abundances of environment-specific bacteria were found associated with host genotypes that exhibited greater browsing behavior. Our results indicate that, although there is a great deal of variation between individuals, behavior can mediate genotype-by-environment interaction effects on microbiome composition.	root:Host-associated:Animal
MGYS00005523	Selective maternal seeding and rearing environment shape the colonization and development of the piglet gut microbiome from birth to weaning	The early-life gut microbiome establishment has long-term implications for neonate health and immune system development. However, the acquisition patterns of the early-life microbiome in piglet gut is largely unknown. Here, microbiota of 1119 samples were characterized to longitudinally assess the transmission contribution of the maternal and environmental microbiota on the colonization and development from birth through weaning. Source tracking analysis revealed that the contribution of various microbial sources on the microbiome of was gradually changed over time. The neonatal microbiota was sparsely populated and predominantly comprised of maternal vaginal microbiota that increased gradually from day 0 to day 3, and decreased till day 28. However, with the increasing piglet age, the microbiome were more associated with the floor and sows feces. Additionally, the intestinal microbial diversity, composition and function significantly changed with the age of piglets. 30 age-discriminatory bacterial taxa were identified with distinctive time-dependent changes in their relative abundance, which reflected probable selection within or adaptations of piglet gut microbiota to maternal and environmental sources. Our results demonstrated that the sow vagina, feces and floor are the primary bacterial sources for the early gut microbiota colonization in piglets, which highlights the importance of the health of sows rearing environment especially the floor to the development of the piglet gut microbiome.	root:Host-associated:Mammals:Digestive system
MGYS00005526	Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa	Linear growth delay (stunting) affects roughly 155 million children under the age of five worldwide. Treatment has been limited by a lack of understanding of the underlying pathophysiological mechanisms. Stunting is most likely associated with changes in the microbial community of the small intestine, a compartment vital for digestion and nutrient absorption. Efforts to better understand the pathophysiology have been hampered by difficulty of access to small intestinal fluids. Here, we describe for the first time the microbial community found in the upper gastrointestinal tract of stunted children. We studied 46 duodenal and 57 gastric samples from stunted children as well as 404 fecal samples from stunted and non-stunted children aged 2-5 years living in Bangui, Central African Republic and in Antananarivo, Madagascar, using 16S Illumina Amplicon sequencing and semi-quantitative culture methods. The vast majority of the stunted children showed small intestinal bacterial overgrowth dominated by bacteria that normally reside in the oropharyngeal cavity. There was an overrepresentation of oral bacteria in fecal samples of stunted children opening the way for developing non-invasive diagnostic markers. In addition, E. coli/Shigella sp. and Campylobacter sp. were found to be more prevalent in stunted children, while Clostridia, well-known butyrate producers, were reduced. Our data suggest that stunting is associated with a microbiome decompartmentalization of the gastrointestinal tract characterized by an increased presence of oropharyngeal bacteria from the stomach to the colon, hence challenging the current view of stunting arising solely as a consequence of small intestine overstimulation through recurrent infections by enteric pathogens.	root:Host-associated:Human:Digestive system
MGYS00005514	Sheep feces, epithelial and maternal samples Raw sequence reads	Development of micro biome of lambs	root:Host-associated:Mammals
MGYS00005513	Cell phone and shoe swabs across the USA Raw sequence reads	These are raw sequence reads from Illumina 16S sequencing of swabs collected from cell phones and shoes across the USA.	root:Mixed
MGYS00005524	Seasonal changes of the nasal microbial diversity of pig farmers	Background: Prior studies have demonstrated an influence of the environment on the human nasal microbiota, particularly in the case of pig farming. However, very little is known about the impact of season on the dynamics of the microbiota in a pig farm setting. Methods: We performed a longitudinal study, investigating the changes in the nasal microbiota of different samples collected in the four seasons (winter, spring, summer and fall). We collected samples from 30 pig farms in Switzerland in each season from 2014-2015. This included nasal swabs from pigs (n=225), air samples taken in the pig confinement building (n=105), and nasal swabs from pig farmers working in these pig farms (n=154 from 48 pig farmers). As controls, nasal swabs from cow farmers (n=56 from 18 cow farmers) and individuals with no contact with farm animals (n=69 from 24 non-exposed individuals) were collected. Analysis of the microbiota was performed based on 16S rRNA high-throughput sequencing utilizing the Illumina MiSeq platform and the recently developed DADA2 pipeline. Results: Alpha-diversity values were generally higher in samples received in winter with the exception of samples from the non-exposed controls which displayed low alpha-diversity values throughout the seasons with no significant differences. The microbial structure of pig farmers, cow farmers and non-exposed individuals was significantly influenced by season. Also, the farm where the samples were taken from influenced the nasal microbiota of pig and cow farmers. There was a stronger similarity for samples that originated from the same farm as compared to samples from different farms in winter and this farm-specificity was partially or completely lost in spring, summer and fall.Conclusions: Nasal microbiota of pig farmers is affected by the regular exposure to pigs throughout the year. However, season has a very strong effect on the nasal microbiota of pig farmers, pigs, and cow farmers, as well as the airborne bacterial composition. This seasonal effect is much weaker in individuals without any contact with farm animals.	root:Mixed
MGYS00005498	Linking microbiomes of soils and foliar feeding insects	We studied the legacy effects of plants on fungal and bacterial communities in soils, roots, leaves and caterpillars.	root:Mixed
MGYS00005525	Antibiotic treatment in feedlot cattle: a longitudinal study of the effect of oxytetracycline and tulathromycin on the fecal and nasopharyngeal microbiota	The effect of injectable antimicrobials on the NP and gut microbiota of beef cattle after feedlot placement was determined.	root:Host-associated:Mammals
MGYS00005505	Longitudinal microbiome analyses of acute myelogenous leukemia patients during induction chemotherapy		root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005506	Chemotherapy Induced Oral Mucositis and Microbiome		root:Host-associated:Human:Digestive system:Oral
MGYS00000646	Microbiome Quality Control Project - 16S	The MBQC is a collaborative effort to comprehensively evaluate methods for measuring the human microbiome. This pilot phase includes 16S rDNA amplicon based surveys of the human microbiome.	root:Host-associated:Human:Digestive system
MGYS00005504	Hong Kong Residences Raw sequence reads	16S rRNA sequencing reads from samples of household surfaces, residents'' skin and household air in Hong Kong residences.	root:Mixed
MGYS00005500	Microbial analysis is challenged by immigration	High throughput characterisation of microbial communities is widely used as a source of information to develop strategies for improved biological processes in humans, animals and engineered systems. However, the introduction of organisms that do not contribute or grow in the system can ruin conclusions derived from the composition. In this study we sequenced samples from digesters and their influent streams to evaluate which organisms were truly growing and which were probably just continuously fed into the system.	root:Mixed
MGYS00005527	Integrated Analysis of mtDNA Single Nucleotide Polymorphisms with the Vaginal and Placental Membrane Microbiome and Rendered Risk Estimation for Preterm Birth	Background: Although we and our microbial community and genomes (the human microbiome) have co-evolved over millions of years, to what extent the human host maternally inherited ancestral genome (mitochondrial genome) informs both microbial community composition and risk of human disease is unclear. We have previously demonstrated a significant association between the placental microbiome and risk of preterm birth, as well as (in non-pregnant subjects) association of mitochondrial DNA (mtDNA) variants (mtSNPs) with the vaginal and gut microbiome. In this study, we aimed to explore complex interactions between human host mtSNPs and the vaginal and placental membrane microbiome with associated risk of preterm birth.Methods: Maternal blood and placental tissue samples from 93 gravidae (n=54 with preterm deliveries between 23 and 0/7 and <37 and 0/7 weeks; n=39 term =37 and 0/7 weeks) were deep sequenced, and mtSNPs were called with high confidence. The microbial taxonomic abundance of the vagina (introitus and posterior fornix) and placental membranes (maternal and fetal side swabs) from the same subjects were obtained via 16S ribosomal RNA sequencing, and inferred metagenomics was employed for metabolic pathway analysis. Interactions among both microbial taxa and their inferred metagenomics pathways were examined for association with mtSNPs employing multiple linear regressions modeling for both genotype and clinical covariates with PLINK quantitative trait associations. Analyses were adjusted for multiple comparisons, with a q value <0.05 denoting significance.Results: Consistent with ours and others recent published observations, we observed an association between preterm birth and the composition of the placental membrane microbiome community (PERMANOVA p=0.042). In our cohort, no significant association between any mtSNP with the occurrence of preterm birth was observed. However, overall associations between mitochondrial genome variations and both the vaginal and placental membrane preterm microbial community were observed. Of note, several functional mtSNPs (within coding regions for electron transport genes) demonstrated significant and robust associations (q value <0.05) with both occurrence and abundance of certain taxa and their metagenomics pathways among preterm births.Conclusions: We have demonstrated for the first time that maternally inherited human mtSNPs are associated with variations in both placental membrane and vaginal microbial taxa membership and their inferred metabolic function during pregnancy, and consequentially linked to the occurrence of preterm birth.	root:Host-associated:Human
MGYS00005509	Paired mucosal j-pouch and afferent limb samples from postoperative ulcerative colitis and familial ademonatous polyposis patients from Mount Sinai Hospital, Toronto. Samples were collected during pouch endoscopy and 16S sequenced.		root:Host-associated:Human:Digestive system
MGYS00001356	Green alder encroachment shapes microbial diversity in subalpine soils.	Green alder encroachment shapes microbial diversity in subalpine soils.	root:Environmental:Terrestrial:Soil
MGYS00004237	Bacterial 16S rRNA and fungal ITS Metagenome	The flooding crisis in Thailand in 2011 is one of the biggest recorded floods which caused enormous scale of damages to ecological and human habitats and public health concerns. In this study, bacterial and fungal diversity in sediments and waters collected from flooded areas in Bangkok and suburban covering residential, agricultural, and industrial areas were analyzed using high-throughput 454 pyrosequencing of 16S rRNA/ internal transcribed spacer sequences (ITS). Proximate phylogeny analysis showed differences in microbial distribution in water and sediment samples with variation in diversity profiles according to sampling locations.	root:Environmental:Aquatic:Sediment
MGYS00002115	The study includes fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS) analyses. The main the main experimental objects are soils of different classes, quality groups and also subjected to various agrotechnical treatments	The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS) analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates) in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, thThis study has shown that: (1) fungal diversity was changed under the influence different cultivation techniques; (2) techniques of maize cultivation and season were an important factors that can influence the biochemical activity of soil. Maize cultivated in direct sowing did not cause negative changes in the fungal structure, even making it more stable  during seasonal changes; (3) full tillage and crop rotation may change fungal community and soil function. e season had a great influence on the fungal genetic structure in the soil.	root:Environmental:Terrestrial:Soil
MGYS00004713	Diamante Lake Red Biofilm Metatranscriptome	Diamante Lake Red Biofilm Metatranscriptome	root:Environmental:Aquatic:Freshwater:Lake
MGYS00005511	Raw sequence reads from soil relic DNA study	Study to assess the impact of relic (i.e. extracellular) DNA in soil on assessment of bacterial and fungal community structure.	root:Environmental:Terrestrial:Soil
MGYS00005508	Rumen and gastrointestinal tract contents Targeted Locus (Loci)	The aim of the Global Rumen Census project is to survey the diversity of microbes present in rumen samples obtained from a range of locations and farming situations.	root:Host-associated:Mammals:Digestive system
MGYS00005507	A collection of 16S reads for samples relating to pre-term infants	The NeoM (Neonatal Microbiota) Study is an ecological study investigating the microbiota of pre-term infants. Samples collected include faecal samples, skin swabs and swabs of infant incubators. Bacterial DNA was extracted from the samples using either MPBio FastDNA Spin kits or MPBio FastDNA Spin Kits for Soil and V3-V5 amplicons were generated using Bifidobacterium-optomised primers (Sim et al, 2012, PLOS ONE) and tagged with 12bp barcodes. These were then sequenced using a 454 Life Sciences GS FLX (Roche) following the Roche Amplicon Lib-L protocol. Both raw data (.sff files) and data denoised via ampliconnoise.py (as part of the Qiime pipeline) will be submitted here.	root:Mixed
MGYS00005512	Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia.	BACKGROUND:Atopic allergy has been more common among schoolchildren in Finland, as compared to Russian Karelia. These adjacent regions show one of the most contrasting socio-economical differences in the world.OBJECTIVE:We explored changes in allergy from school age to young adulthood from 2003 to 2010/2012 in these two areas. The skin and nasal microbiota were also compared.METHODS:Randomly selected children from Finnish (n = 98) and Russian Karelia (n = 82) were examined in 2003, when the children were 7-11 years of age, and again in 2010 (Finnish Karelia) and 2012 (Russian Karelia). We analysed self-reported allergy symptoms and sensitization to common allergens by serum sIgE values. The skin (volar forearm) and nasal mucosa microbiota, collected in 2012 (aged 15-20 years), identified from DNA samples, were compared with multivariate methods.RESULTS:Asthma, hay fever, atopic eczema, self-reported rhinitis, as well as atopic sensitization, were threefold to 10-fold more common in Finland, as compared to Russian Karelia. Hay fever and peanut sensitization were almost non-existent in Russia. These patterns remained throughout the 10-year follow-up. Skin microbiota, as well as bacterial and fungal communities in nasal mucosa, was contrastingly different between the populations, best characterized by the diversity and abundance of genus Acinetobacter; more abundant and diverse in Russia. Overall, diversity was significantly higher among Russian subjects (Pskin < 0.0001, Pnasal-bacteria < 0.0001 and Pnasal-fungi < 0.01). Allergic diseases were not associated with microbial diversity in Finnish subjects.CONCLUSIONS AND CLINICAL RELEVANCE:Differences in allergic phenotype, developed in early life, remain between populations. A parallel difference in the composition of skin and nasal microbiota suggests a potential underlying mechanism. Our results also suggest that high abundance and diversity of Acinetobacter might contribute to the low allergy prevalence in Russia. Implications of early-life exposure to Acinetobacter should be further investigated.	root:Host-associated:Human
MGYS00005510	anchialine metagenome Raw sequence reads	Microbial ecology is an important and growing field that has revealed the importance of microbes in many ecosystems; however, some ecosystems have yet to receive much attention including the anchialine ecosystem (nearshore bodies of water with subsurface freshwater and seawater connections). Hawaiian anchialine habitats in the Cape Kinau region of Maui and the Kona region of Hawaii exhibit distinctive, laminated orange cyanobacterial-bacterial crusts, but little is known about their composition, the composition of microbial communities in non-crust containing sites lacking the cyanobacterial-bacterial crusts, or the degree to which environmental factors structure them. During the summer of 2010, we surveyed benthic and water column microbial communities from ten anchialine habitats on Oahu, Maui, and Hawaii using high-throughput amplicon sequencing of the V6 (prokaryotic-biased) and V9 (eukaryotic-biased) hypervariable regions of the SSU rRNA gene. A subset of six anchialine habitats were also sampled in the spring, summer, and winter of 2011 to allow elucidation of seasonal effects on the Hawaiian anchialine microbial community.	root:Environmental:Aquatic
MGYS00005322	EMG produced TPA metagenomics assembly of the FVB F Partial Co2 (FVB F Partial Co2) data set.	The FVB F Partial Co2 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB13629.  This project includes samples from the following biomes: Host-associated, Mammals.	N/A
MGYS00005326	EMG produced TPA metagenomics assembly of the FVB Partial Co1 (FVB Partial Co1) data set.	The FVB Partial Co1 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB13645.  This project includes samples from the following biomes: Host-associated, Mammals.	N/A
MGYS00005521	EMG produced TPA metagenomics assembly of the Comparison or twelve metagenomes from peat matrix, fen and bog, at two different depths in troplicates (PeatMetagenome) data set.	The PeatMetagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB11421.  This project includes samples from the following biomes: Soil.	root:Environmental:Terrestrial:Soil
MGYS00005522	Comparison or twelve metagenomes from peat matrix, fen and bog, at two different depths in troplicates	Peat matrix samples were recovered from one fen and one bog at two different depths (5-10cm and 10-15cm) in triplicates (Les Pradeaux, Massif Centrale, France). Sequences were obtained by pyrosequences.	root:Environmental:Terrestrial:Soil
MGYS00005520	Dechlorinating community	Try to identify the microorganisms responsible for dechlorination and their functional genes.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00005517	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P5a_32mM metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441893.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00005144	EMG produced TPA metagenomics assembly of PRJEB20800 data set (Gut resistome modulates resilience and recovery of gut microbiota after broad-spectrum antibiotic treatment).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set ERP022986, and was assembled with SPAdes (v3.13.0).	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005516	Gut resistome modulates resilience and recovery of gut microbiota after broad-spectrum antibiotic treatment	Antibiotics have profound impacts on the microbial communities living in the human gut, where bacterial species harbor and exchange antibiotic resistance genes collectively called resistome. Human population surveys have demonstrated that gut microbial resistomes reflect local antibiotics usage patterns, while previous small cohort studies based on single antibiotic exposures have shown varying degrees of antibiotic impact on the gut microbiota and their associated resistome. However, the role of resistomes of particular gut species in their ability to persist in the face of antibiotic treatment has not been systematically studied.Applying shotgun sequencing and quantitative metagenomics, we analyzed the partial eradication and subsequent regrowth of gut microbiota in 12 healthy young men over a 6 month period following a 4-day intervention with three broad-spectrum antibiotics. The gut microbial communities of the study subjects underwent profound compositional changes due to the treatment but slowly recovered to near-baseline compositions. Immediately after the treatment, the gut microbiota featured an increased relative abundance of opportunistic and proinflammatory bacterial species, and a decreased relative abundance of short chain fatty acid producers, while exhibiting an increased functional potential for multidrug efflux pumps and virulence factors. These enrichment trends were weaker after 8 days and mostly cleared out after 42 days. However, 9 common intestinal commensal species found at baseline and associated with short chain fatty production or efficient digestion of polysaccharides remained undetectable in most of the subjects even after 180 days.Carrying genes that confer resistance to the antibiotics used in this multidrug study had specific consequences for the survival and de novo colonization potential of microbial species. While species harboring beta-lactam resistance genes were positively selected during and after the intervention, those harboring glycopeptide or aminoglycoside resistance exhibited increased odds of de novo colonization but decreased odds of survival. Despite a mild long-lasting imprint following exposure to three antibiotics, the gut microbiota of healthy young adults are resilient to a broad-spectrum antibiotic intervention, and their recovery process is modulated by antibiotic resistance gene carriage.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003598	EMG produced TPA metagenomics assembly of the Human Skin Microbiome Metagenome (human skin metagenome) data set.	The human skin metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA277905.  This project includes samples from the following biomes: Host-associated, Human, Skin.	root:Host-associated:Human:Skin
MGYS00005515	Bacterial community and resistome of lettuce plants	Characterization of bacterial communities of lettuce plants and their production environment including irrigation water, soil, an manure.Additional analysis of the bacterial resistome of the same systems.	root:Host-associated:Plants
MGYS00005298	Manure microbiome of dairy cows fed grass or grass silage diets	Manure samples were taken from 18 dairy cows on one farm.  Cows were Holstein-Friesian or Holstein-Friesian cross and all from the same herd but kept under two different systems.  Nine animals were from a group kept at pasture with a diet of grazed grass plus 5.5-7kg of concentrated per day.  The other nine were from a group kept in a cubicle house with a diet of ad libitum grass silage plus 10kg concentrates per day.  Samples were taken directly after defecation and transported to the laboratory on ice.  They were frozen at -20C until DNA extraction using Qiagen Powersoil Pro kit (according to manufacturer's instructions).  The v4 region of the 16s rRNA gene was sequenced on an Illumina Miseq (250bp paired end reads).	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00005496	Bermuda Atlantic Time-series Study metagenomes	Metagenome-assembled genome bins to assess the diversity and evolution of globally abundant deep-ocean bacteria.	root:Environmental:Aquatic:Marine
MGYS00005497	Geotraces Raw sequence reads	This study is aimed to explore the microbial lifestyle in ocean and interpret metabolic potentials using metagenome/metaproteome dataset. Furthermore, it is important to learn about various mode of energy consumption that may support marine microbes i.e. photoautotrophy, chemoautotrophy and heterotrophy.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00001769	Ligning valorization strategies based on the development of a specialized microbial community	There is an increasing interest in the development of biological routes for lignin depolymerization and valorization. Studies have been performed to elucidate the enzymatic routes and microorganism involved in lignin conversion. Considering that the vast majority of microorganisms are not likely to be cultivated in an isolated form, metagenomic approaches display great potential to gain further access to microorganisms, genes and metabolic pathways linked to lignin breakdown and upgrading into high value chemicals. The present work focused on the development of a lignin-degrading specialized community (CLig) and the application of a combination of metagenomics approaches, including comprehensive taxonomic characterization and binning-assembly for reconstruction of microbial genomes. All these efforts provide basis to portray the major bacterial pathways involved in lignin degradation and aromatic compounds conversion. From the analysis of massive DNA sequencing data, several microorganisms and enzymes linked to the metabolic pathways of interest were identified, thus constituting a promising resource of biological information for lignin valorization. Along with isolation and genome sequencing of lignolytic bacterial strain of potential biotechnological interest, pathways for lignin valorization was validated based on vanillin production from ferulic acid using feruloyl-CoA synthetase (fcs) and enoyl-CoA hydratase/aldolase (ech).	root:Engineered:Biotransformation
MGYS00005187	Eimeria population derived from 18s amplicon sequencing of chicken ceacal content	18s amplicon sequencing of Eimeria species in ceacum of Poultry (Gallus gallus).	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00005189	Anaerobic microbial community enriched with amino acids	Amino acids are important monomers that are ubiquitously present in anaerobic environments after protein hydrolysis. Anaerobic digester sludge from two sources was used to inoculate batch cultures, which were fed with twenty individual amino acids. Five successive enrichments were performed with 10% v/v transfer. 16S rRNA and rRNA gene were extracted and amplified from enrichment cultures. Amplicons were sequenced using Illumina Miseq platform. Distinct community structures were observed between the first enrichment and later enrichments. Such trajectory of community evolution indicated enrichment of specific amino acids degraders that were not abundant in the early enrichments. Based on known knowledge of fermenters, syntrophs, and methanogens, four types of communities were observed.	root:Host-associated:Human:Digestive system:Oral:tongue dorsum
MGYS00005494	Microbial community structure of sediment microbiome in the pelagic zone of Gulf of Kutch, Gujarat, India.	The pelagic sediment microbiota was assessed in the three sections of the sampled core (1m) from four locations of the Gulf of Kutch.	root:Environmental:Aquatic:Marine:Sediment
MGYS00005493	Microbial community structure of sediment microbiome in the pelagic zone of Gulf of Khambhat, Gujarat, India.	The pelagic sediment microbiota was assessed in the three sections of the sampled core (1m) from four locations of the Gulf of Khambhat and one location from the open sea (Arabian Sea).	root:Environmental:Aquatic:Marine:Sediment
MGYS00005454	EMG produced TPA metagenomics assembly of the PRJNA344863 data set (Viral Metagenomics of fecal samples of fruit bats).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA344863.  This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005463	EMG produced TPA metagenomics assembly of the PRJNA407112 data set (Investigating the viral ecology of global bee communities with high-throughput metagenomics).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA407112.  This project includes samples from the following biomes: root:Host-associated:Insecta.	root:Host-associated:Insecta
MGYS00005461	EMG produced TPA metagenomics assembly of the PRJEB6941 data set (Evaluation of methods to purify virus-like particles for the sequencing of intestinal viromes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6941.  This project includes samples from the following biomes: root:Engineered:Modeled:Simulated communities (microbial mixture).	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00005447	EMG produced TPA metagenomics assembly of the PRJNA288501 data set (Freshwater Viruses Metagenomic assembly).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA288501.  This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lentic.	root:Environmental:Aquatic:Freshwater:Lentic
MGYS00005445	EMG produced TPA metagenomics assembly of the PRJNA385126 data set (viral metagenome Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA385126.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005443	EMG produced TPA metagenomics assembly of the PRJEB22882 data set (Taxonomic and gene content analysis of the bacterial viral metagenomes from the oral cavity from healthy youngsters in Valencia).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB22882.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00005456	EMG produced TPA metagenomics assembly of the PRJEB12797 data set (Shotgun metagenomics of moose rumen).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12797.  This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Foregut:Rumen.	root:Host-associated:Mammals:Digestive system:Foregut:Rumen
MGYS00005449	EMG produced TPA metagenomics assembly of the PRJNA336829 data set (Thermophilic microbial communities from the Joint Bioenergy Institute, California, USA of rice/straw/compost enrichment - eDNA_2 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336829.  This project includes samples from the following biomes: root:Engineered:Bioreactor.	root:Engineered:Bioreactor
MGYS00005433	EMG produced TPA metagenomics assembly of the PRJNA480846 data set (Metagenome of biofouled reverse osmosis membranes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA480846.  This project includes samples from the following biomes: root:Engineered:Bioreactor.	root:Engineered:Bioreactor
MGYS00005425	EMG produced TPA metagenomics assembly of the PRJNA392180 data set (Seasonal Cycling in the Gut Microbiome of the Hadza Hunter-Gatherers of Tanzania).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA392180.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005395	EMG produced TPA metagenomics assembly of the PRJEB22997 data set (Baltic Sea reference metagenome assembly and s; transect and redoxcline.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB22997.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005423	EMG produced TPA metagenomics assembly of the PRJNA413474 data set (MTR skin microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA413474.  This project includes samples from the following biomes: root:Host-associated:Human:Skin.	root:Host-associated:Human:Skin
MGYS00005453	EMG produced TPA metagenomics assembly of the PRJNA255783 data set (Home Microbiome Metagenomes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA255783.  This project includes samples from the following biomes: root:Engineered:Built environment, root:Host-associated:Mammals.	root:Engineered:Built environment
MGYS00005441	EMG produced TPA metagenomics assembly of the PRJNA271618 data set (Baboon feces Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA271618.  This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.	root:Host-associated:Mammals:Digestive system
MGYS00005451	EMG produced TPA metagenomics assembly of the PRJEB8939 data set (Metagenomic analyses of Rumen microbiomes reveals the functional isoforms driving microbial niche differentiation for nutrient acquisition and use).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB8939.  This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Stomach:Rumen.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00005439	EMG produced TPA metagenomics assembly of the PRJDB5777 data set (Metagenome analysis of the trench microbiome project on Northwest Pacific Ocean).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB5777.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic:Aphotic zone.	root:Environmental:Aquatic:Marine:Oceanic:Aphotic zone
MGYS00005487	EMG produced TPA metagenomics assembly of the PRJNA266679 data set (Pelagic Microbial community sample from North Sea - COGITO 998_met_07 Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA266679.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Pelagic.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00005485	EMG produced TPA metagenomics assembly of the PRJNA406172 data set (Arabidopsis rhizosphere microbial communities from North Carolina - M.Oy.5.yng.040610 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406172.  This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00005421	EMG produced TPA metagenomics assembly of the PRJNA479434 data set (NRC/UOttawa - Peace Athabasca Delta Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA479434.  This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lake.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00005418	EMG produced TPA metagenomics assembly of the PRJEB13832 data set (Local surveillance of infectious diseases and antimicrobial resistance from sewage).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB13832.  This project includes samples from the following biomes: root:Engineered:Wastewater:Water and sludge.	root:Engineered:Wastewater:Water and sludge
MGYS00005475	EMG produced TPA metagenomics assembly of the PRJNA406152 data set (Arabidopsis rhizosphere microbial communities from North Carolina - M.Oy.2.old.250510 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406152.  This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00005465	EMG produced TPA metagenomics assembly of the PRJNA321634 data set (mouse gut metagenome Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA321634.  This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Large intestine.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00005473	EMG produced TPA metagenomics assembly of the PRJNA406788 data set (Rhizosphere microbial communities from Sorghum bicolor, Mead, Nebraska, USA - 072115-113_1 MetaG metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406788.  This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00005471	EMG produced TPA metagenomics assembly of the PRJNA266672 data set (Pelagic Microbial community sample from North Sea - COGITO 998_met_01 Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA266672.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005437	EMG produced TPA metagenomics assembly of the PRJEB25754 data set (Using salinity to select for progressive onset denitrifiers).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB25754.  This project includes samples from the following biomes: root:Engineered:Bioreactor.	root:Engineered:Bioreactor
MGYS00005469	EMG produced TPA metagenomics assembly of the PRJNA405734 data set (Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F01 metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405734.  This project includes samples from the following biomes: root:Engineered:Bioreactor.	root:Engineered:Bioreactor
MGYS00005467	EMG produced TPA metagenomics assembly of the PRJNA405200 data set (Marine microbial communities from the Central Pacific Ocean - Fk160115 155m metaG metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405200.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005466	mouse gut metagenome Raw sequence reads	Mice intestine metagenome	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00005464	Investigating the viral ecology of global bee communities with high-throughput metagenomics	The ecology of bee viruses is complex, as viruses are readily shared among bee species and plants. However, our understanding of bee viral communities is primarily derived from studies of North America and European Apis mellifera honey bee populations. Here, we develop a novel pipeline to rapidly, inexpensively, and robustly screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and screening through a series of filters to identify contigs specifically corresponding to viral sequences. We evaluated samples of honey bees and co-foraging non-Apis bee species (12 bee species in total) from 9 countries and 5 continents. We identified sequences corresponding to (+)ssRNA, (-)ssRNA, dsRNA, and ssDNA viruses. Overall, 127 contigs corresponding to novel viruses (previously not observed in bees), with 29 represented by >0.1% of the reads in a given sample. These 29 contigs corresponded to 9 viral families, including 6 viral families that have not been previously observed in bees. These viruses and viral families were distributed across multiple regions and species. This study provides a robust pipeline for analysis of insect viruses, and greatly expands our understanding of the diversity of viruses found in bee communities.	root:Host-associated:Insecta
MGYS00005462	Evaluation of methods to purify virus-like particles for the sequencing of intestinal viromes	In this study we used an in vitro assembled microbiota sample to evaluate the efficiency and biases of purification methods used to purify virus-like particles from gut content for metagenome sequencing. The artificial microbiome sample contained six bacteriophages (P22, phiVPE25, phi6, T3, T7 and M13)two bacterial strains (gr+: Listeria monocytogenes EGD-e and gr-: Bacteroides thetaiotaomicron VPI5482), which were mixed into feces from germ-free mice.  Three purification methods were tested: (1) Filtration + DNase (FD), (2) DTT treatment + filtration + DNase (DTT), (3) filtration + DNase + CsCl density gradient (CsCl). Additionally, metagenomes of the complete microbiome sample were sequenced (MG). Each treatment was done in duplicate.	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00005455	Viral Metagenomics of fecal samples of fruit bats	The characterisation of virome of Cameroonian fruit bats to identify novel viruses of zoonotic potential	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005452	Metagenomic analyses of Rumen microbiomes reveals the functional isoforms driving microbial niche differentiation for nutrient acquisition and use	Metagenomics has provided insights into the species composition and function of microbial communities and revealed that many species even in highly competitive environments seem to share the same sets of genes for acquiring and utilising nutrients. This questions whether niche differentiation between microbes under competitive stress exists and if so, how it is maintained. Rumen microbes exist in a highly competitive, anaerobic environment, and compete for access to the limited nutrients available in the biomass consumed by the host. The rumen microbiome affects the efficiency and health of the host, and has been mined for novel enzymes and anti microbial peptides and is known as a potent contributor to greenhouse gas emissions. A better understanding of the structure and function of this community has large potential benefits. We generated separate metagenomic libraries from 14 Limousin cows. Following assembly, gene prediction and taxonomic assignment, SNPs were identified and functional isoform diversity (pN/pS) was calculated for each gene. The independent calculations from each sample were used to calculate confidence intervals for testing for diversity of function between microbes, a signature of niche differentiation. We identified significant differences in functional diversity between competing organisms in genes involved in carbon, amino-sugar and nucleotide sugar metabolism, suggesting adaptation to utilizing different routes for nutrient acquisition in the rumen. This suggests that a greater understanding of the rumen microbiome and considering macro-ecological concepts, such as successional change and adaptation, are likely to improve strategies for increasing the efficiency and health of the host and reducing greenhouse gas emissions.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00005450	Thermophilic microbial communities from the Joint Bioenergy Institute, California, USA of rice/straw/compost enrichment - eDNA_2 metagenome		root:Engineered:Bioreactor
MGYS00005448	Freshwater Viruses Metagenomic assembly	To identify viruses, freshwater samples were collected from six different locations of Lake Ontario and Lake Erie	root:Environmental:Aquatic:Freshwater:Lentic
MGYS00005446	viral metagenome Metagenome	Viral metagenomes	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005444	Taxonomic and gene content analysis of the bacterial viral metagenomes from the oral cavity from healthy youngsters in Valencia	Samples were collected from 72 healthy young Spanish people from Valencia (Spain) in November 2012. Samples consisted of mouthwash using sterile saline serum (NaCl 0.9%) from 72 volunteers (38 females and 34 males).Sampling was anonymized and only sex was recorded.For all samples, the metagenomic analysis of the bacterial DNA viral communities was carried out, using the Illumina MiSeq with 300 bp x2 chemistry.	root:Host-associated:Human:Digestive system:Oral
MGYS00005442	Baboon feces Metagenome	Raw metagenomic sequencing reads collected from samples from 48 adult baboons in two social groups during July - August 2012.	root:Host-associated:Mammals:Digestive system
MGYS00005440	Metagenome analysis of the trench microbiome project on Northwest Pacific Ocean	The trench microbiome project analyzed planktonic microbiomes associated with sea surface to hadal waters along the water columns on Mariana, Ogasawara (Izu-Bonin), Japan and Chishima (Kuril) Trenches.	root:Environmental:Aquatic:Marine:Oceanic:Aphotic zone
MGYS00005438	Using salinity to select for progressive onset denitrifiers	To gain an understanding of the bacteria capable of performing nitrite accumulation from nitrate (denitratation) in such system a study of a nitrite accumulation bioreactor has been undertaken. Our goal was to assess how the salinity parameter affected the nitrogen removal performance of this bioreactor, and which microorganisms were responsible for the nitrite accumulation needed to sustain the denitration process in this bioreactor. The reactor used in this study was a mixed, unsealed, electron donor-limited continuous reactor with acetate and nitrate as substrates operated under diverse salinity regimes.	root:Engineered:Bioreactor
MGYS00005436	Reclaimed water Metagenome	Zero valent iron filtered and unfiltered reclaimed water collected from a tertiary wastewater treatment plant in the Mid-Atlantic United States.	root:Engineered:Wastewater:Water and sludge
MGYS00005431	EMG produced TPA metagenomics assembly of the PRJEB22104 data set (Unusual ecophysiology of Candidate phylum Acetothermia bacteria associated with anaerobic digesters revealed by complete genome sequencing and advanced in situ microscopy).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB22104.  This project includes samples from the following biomes: root:Engineered:Wastewater.	root:Engineered:Wastewater
MGYS00005429	EMG produced TPA metagenomics assembly of the PRJNA319556 data set (A mock community containing 9 viruses and four bacterial species Raw sequence reads).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA319556.  This project includes samples from the following biomes: root:Engineered.	root:Engineered
MGYS00005416	EMG produced TPA metagenomics assembly of the PRJDB4437 data set (Osaka Bay Virome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB4437.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Coastal.	root:Environmental:Aquatic:Marine:Coastal
MGYS00005434	Metagenome of biofouled reverse osmosis membranes	This project aims to understand the microbial community and its functional potential of biofouled reverse osmosis membranes used in water purification.	root:Engineered:Bioreactor
MGYS00005432	Unusual ecophysiology of Candidate phylum Acetothermia bacteria associated with anaerobic digesters revealed by complete genome sequencing and advanced in situ microscopy	Members of the candidate phylum Acetothermia are globally distributed and have been detected in diverse natural habitats as well as engineered systems. However, little is known about their physiology and ecological importance. In this study, an OTU belonging to Acetothermia was identified as one of the most abundant genus-level bacterial taxa in full-scale mesophilic anaerobic digesters at two Danish wastewater treatment plants. A closed genome was obtained by differential coverage binning of metagenomes and long Nanopore reads. Genome annotation and metabolic reconstruction revealed an anaerobic chemoheterotrophic lifestyle in which the bacterium obtain energy and carbon from the fermentation of peptides, amino acids, and simple sugars to acetate, formate and hydrogen. In contrast to previously studied Acetothermia, the genome did not encode a functional acetyl-CoA pathway required for acetogenesis. Fluorescent in situ hybridization probes targeting Acetothermia were designed and used in combination with confocal laser scanning microscopy and atomic force microscopy. This revealed an unusual morphology composed of a central rod cell with bipolar prosthecae similar to those observed in Caulobacter and Asticcacaulis. These prosthecae greatly expand the cell surface to volume ratio and allow for increased nutrient uptake, providing the bacteria with a competitive advantage under nutrient limited conditions.	root:Engineered:Wastewater
MGYS00005430	A mock community containing 9 viruses and four bacterial species Raw sequence reads	We optimised and validated a method that allows for high throughput virome analysis. For that we evaluated the quantitative effect of homogenisation, centrifugation, filtration, chloroform treatment and random amplification on a mock-virome and a bacterial mock-community using quantitative PCR and next-generation sequencing.	root:Engineered
MGYS00005419	EMG produced TPA metagenomics assembly of the PRJDB5708 data set (Metagenomic sequences of the Ofunato Bay 2015).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB5708.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Coastal.	root:Environmental:Aquatic:Marine:Coastal
MGYS00005415	EMG produced TPA metagenomics assembly of the PRJEB14899 data set (Oil spill dispersant strategies and bioremediation efficientcy).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14899.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated.	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
MGYS00005428	Denitrification-dependent anaerobic methane oxidizers in a marine oxygen minimum zone	To show presence and activity of bacteria associated with denitrification-dependent anaerobic oxidation of methane in the a permanent marine oxygen minimum zone	N/A
MGYS00005427	EMG produced TPA metagenomics assembly of the PRJNA277357 data set (Denitrification-dependent anaerobic methane oxidizers in a marine oxygen minimum zone).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA277357.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005426	Seasonal Cycling in the Gut Microbiome of the Hadza Hunter-Gatherers of Tanzania		root:Host-associated:Human:Digestive system:Large intestine
MGYS00005424	MTR skin microbiome	A metagenomic study on the skin microbiome after contact with MTR trains	root:Host-associated:Human:Skin
MGYS00005422	NRC/UOttawa - Peace Athabasca Delta Raw sequence reads	Metagenomic analysis of the hydrocarbon degradation potential of microbial communities in lakes of the Peace-Athabasca Delta, AB, Canada in relation to petroleum hydrocarbons	root:Environmental:Aquatic:Freshwater:Lake
MGYS00005420	Metagenomic sequences of the Ofunato Bay 2015	The Ofunato Bay in Iwate Prefecture, Japan, is a deep coastal bay located at the center of the Sanriku Rias coast and considered an economically and environmentally important asset. Here we present the first whole genome sequencing (WGS) study on the microbial communities of the Bay where surface water samples were collected in 2015 from three stations along its length to cover the entire bay. We sequenced 0.2-??m filter fraction, targeting the free-living fraction only, among the sequentially size-fractionated samples of 20.0-, 5.0-, 0.8- and 0.2-??m filters,. As expected, Proteobacteria (Alpha, Beta and Gamma) were the most abundant phyla in the Ofunato Bay followed by Bacteroidetes, Firmicutes, Actinobacteria, Cyanobacteria and Tenericutes. We detected a wide range of heterotrophic bacteria, Archaea and eukaryotic algae. The majority of these bacteria are considered significant in oceans and marine ecology.	root:Environmental:Aquatic:Marine:Coastal
MGYS00005417	Osaka Bay Virome	Metagenome sequencing project for Osaka Bay sea water samples by 0.22 micrometer filtrate containing viruses.	root:Environmental:Aquatic:Marine:Coastal
MGYS00005414	Metagenome and viral metagenome fraction isolated from Blanes (Mediterranean Sea)	Surface seawater samples were collected form the Blanes Bay Microbial Observatory (BBMO) in the north-western Mediterranean Sea, and they was used for metaviromics and metagenomics analyses.	N/A
MGYS00005413	EMG produced TPA metagenomics assembly of the PRJEB12379 data set (Metagenome and viral metagenome fraction isolated from Blanes (Mediterranean Sea)).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12379.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005392	EMG produced TPA metagenomics assembly of the PRJEB7772 data set (An analysis of the composition of viruses and bacteria in stool samples from IBD patients and healthy controls.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB7772.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005390	EMG produced TPA metagenomics assembly of the PRJEB8249 data set (Bariatric surgery induces long-term changes on the gut metagenome contributing to fat mass regulation).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB8249.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005388	EMG produced TPA metagenomics assembly of the PRJEB8245 data set (Metagenomic sequencing revealed altered microbiota in microscopic colitis).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB8245.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005411	EMG produced TPA metagenomics assembly of the PRJEB9524 data set (Expanded Enteric Virome and Altered Bacterial Microbiome in Acquired Immunodeficiency Syndrome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB9524.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005412	Expanded Enteric Virome and Altered Bacterial Microbiome in Acquired Immunodeficiency Syndrome	The effect of HIV on the enteric DNA virome and bacterial microbiome is incompletely characterized. Here we sequenced virus-like particles and bacterial 16S ribosomal RNA genes in stool from 40 HIV-negative subjects, 42 HIV-infected subjects and 40 HIV-infected subjects on anti-retroviral therapy (ART) living in Uganda. CD4 T cell counts inversely correlated with plasma soluble CD14 (sCD14) levels, suggesting increased translocation of pro-inflammatory microbial products across the enteric mucosa with worsening immunodeficiency. Low CD4 T cell counts were associated with expansion of the eukaryotic DNA virome including adenoviruses and Anelloviruses and changes in the bacterial microbiome including increases in Enterobacteriaceae members and decreases in Ruminococci. Thus immunodeficiency in progressive HIV infection is associated with significant alterations in the human enteric virome and bacterial microbiome. These changes may contribute to acquired immunodeficiency syndrome (AIDS) enteropathy, translocation of pro-inflammatory materials across the intestinal mucosa and systemic inflammation associated with progression to AIDS.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005409	EMG produced TPA metagenomics assembly of the PRJNA397990 data set (Georgia Aquarium Sulfur Denitrification Reactor).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA397990.  This project includes samples from the following biomes: root:Engineered:Bioreactor.	root:Engineered:Bioreactor
MGYS00005410	Georgia Aquarium Sulfur Denitrification Reactor		root:Engineered:Bioreactor
MGYS00005408	Strain-level typing, community shifts and evidence of co-infection derived from metagenomic investigation of two Salmonella outbreaks	We applied shotgun metagenomics to stool samples collected from two geographically isolated (Alabama and Colorado) outbreaks, where the etiologic agents were identified as distinct strains of Salmonella enterica serovar Heidelberg by culture-dependent methods.	N/A
MGYS00003576	EMG produced TPA metagenomics assembly of the Strain-level typing, community shifts and evidence of co-infection derived from metagenomic investigation of two Salmonella outbreaks () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA321753.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005407	EMG produced TPA metagenomics assembly of the ISS Metagenomes (PRJNA438545) data set.	The PRJNA438545 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA438545.  This project includes samples from the following biomes: root:Engineered:Built environment.	root:Engineered:Built environment
MGYS00005406	408169 Genome sequencing and assembly	Genome of Marine Group A-SAR406.	N/A
MGYS00005405	EMG produced TPA metagenomics assembly of the PRJNA374409 data set (408169 Genome sequencing and assembly).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA374409.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.	root:Environmental:Aquatic:Marine
MGYS00005399	EMG produced TPA metagenomics assembly of the PRJNA485056 data set (Metagenomic sequencing of stool samples from rural communities from north-eastern Madagascar).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA485056.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005401	EMG produced TPA metagenomics assembly of the PRJEB27445 data set (Deterministic microbial communities dynamics in salterns exposed to different light intensities).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB27445.  This project includes samples from the following biomes: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
MGYS00005397	EMG produced TPA metagenomics assembly of the PRJEB19522 data set (Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB19522.  This project includes samples from the following biomes: root:Host-associated:Plants:Phylloplane.	root:Host-associated:Plants:Phylloplane
MGYS00005402	Deterministic microbial communities dynamics in salterns exposed to different light intensities	Microbial communities thriving in salterns are influenced by high salinity and high light irradiation. Here, short read metagenomes (Illumina) were sequenced from 3 different ponds. One was applied as control with no environmental stress applied. The other pond was covered with a plastic mess decreasing the environmental light intensity.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
MGYS00005400	Metagenomic sequencing of stool samples from rural communities from north-eastern Madagascar	Stool samples from 112 individuals (two villages) in two rural communities of north-eastern Madagascar. Samples were collected by the Madagascar Health and Environmental Research (MAHERY) initiative between 2013 and 2014, and sequenced with Illumina HiSeq 2500.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005398	Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify.	Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by nitrogen isotope determinations of fern biomass and detection of N2O released. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct near full-length Rhizobiales genomes were identified from leaf-pocket enriched samples from ditch grown A. filiculoides. Annotation revealed genes for denitrification but not N2-fixation. 15N2 incorporation was active in ferns with N. azollae but not in ferns without. N2O was not detectably released from surface sterilized ferns with the Rhizobiales. N2-fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2O.	root:Host-associated:Plants:Phylloplane
MGYS00005393	EMG produced TPA metagenomics assembly of the PRJEB9818 data set (The gut DNA viromes of Malawian twins discordant for severe acute undernutrition).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB9818.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005396	Baltic Sea reference metagenome assembly and data sets; transect and redoxcline.	Two out of three datasets (the first one already published with Hugerth et al 2015) included in the Baltic Sea reference metagenome assembly. The assembly include herein is a coassembly of all three datasets, complete with annotated genes to facilitate further studies of the Baltic Sea with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00005394	The gut DNA viromes of Malawian twins discordant for severe acute undernutrition	The bacterial component of the human gut microbiota undergoes a definable program of postnatal development. Evidence is accumulating that this program is disrupted in children with severe acute malnutrition (SAM) and that their persistent gut microbiota immaturity, which is not durably repaired with current ready-to-use therapeutic food (RUTF) interventions, is causally related to disease pathogenesis. To further characterize gut microbial community development in healthy versus malnourished infants/children, we performed a time-series metagenomic study of DNA isolated from virus-like particles (VLPs) recovered from fecal samples collected during the first 30 months of postnatal life from eight pairs of mono- and dizygotic Malawian twins concordant for healthy growth, and 12 twin pairs discordant for SAM (either marasmus or kwashiorkor). Both members of discordant pairs were sampled just prior to, during and after treatment with a peanut-based RUTF. Using Random Forests and a dataset of 17,676 viral contigs assembled from shotgun sequencing reads of VLP DNAs, we identified viruses that distinguish different assembly stages of the gut microbiota in the concordant healthy twin pairs. This normal developmental program was impaired in both members of SAM discordant pairs and not repaired with RUTF. Phage plus viruses belonging to the Anelloviridae and Circoviridae families of single-stranded eukaryotic viruses discriminate  discordant pairs from concordant healthy pairs. These results disclose that apparently healthy co-twins in discordant pairs have viromes indicative of familial risk for SAM and provide a human model for delineating normal versus perturbed postnatal acquisition and retention of the gut microbiotas viral component in populations at risk for malnutrition.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005391	Bariatric surgery induces long-term changes on the gut metagenome contributing to fat mass regulation	Bariatric surgery is the most effective procedure for the treatment of obesity. Given the role of the gut microbiota in regulating host metabolism and adiposity, we investigated the long-term effects of bariatric surgery on the human gut metagenome in patients randomized to Roux-en-Y gastric bypass and vertical banded gastroplasty. Genera of the Proteobacteria were specifically enriched after bypass, and the abundance of genes for fatty acid metabolism, nitrogen metabolism and two-component systems was increased after both procedures nine years after surgery. Through colonization of germ-free mice with stools from the patients we demonstrated that the altered gut microbiota promoted reduced fat deposition in recipient mice. Recipients of bypass microbiota also had a lower respiratory quotient, indicating decreased utilization of carbohydrates as fuel. Our results suggest that the gut microbiota may play a direct role in the reduction of adiposity observed after bariatric surgery.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005389	Metagenomic sequencing revealed altered microbiota in microscopic colitis	Microscopic colitis (MC) is a disorder characterized by chronic non-bloody diarrhea predominantly affecting elderly smoking women. Since an altered microbiota is reported in several immune mediated diseases and since MC affects the gut, our hypothesis was that the microbiota would be altered in patients with MC. The bacterial microbiomes was analysed by DNA sequencing (Illumina Hiseq2000). Patients with MC had a marked reduction of Veruccomicrobia (Akkermansia spp) compared to healthy individuals. Specific Akkermansia spp PCR performed on the 10 patients and 7 controls and on an additional 5 female MC-patients confirmed the decreased levels of Akkermansia in MC patients.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005377	EMG produced TPA metagenomics assembly of the PRJNA231909 data set (A prospective, longitudinal analysis of the developing gut microbiome in infants en route to type 1 diabetes).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA231909.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003477	EMG produced TPA metagenomics assembly of the human gut metagenome Metagenome (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA356225.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.	root:Host-associated:Human:Digestive system
MGYS00005387	human gut metagenome Metagenome	This study presented the bacterial diversity of human stool sample from the Vogt-Koyanagi-Harada disease patients in Chinese population	root:Host-associated:Human:Digestive system
MGYS00005373	EMG produced TPA metagenomics assembly of the PRJEB12124 data set (Gut microbiome-dependent stratification of patients for anti-diabetic treatment).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12124.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005375	EMG produced TPA metagenomics assembly of the PRJEB9576 data set (Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB9576.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003481	EMG produced TPA metagenomics assembly of the Human gut metagenome and metatranscriptome raw sequence reads. (256318) data set.	The 256318 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA354235.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005386	EMG produced TPA metagenomics assembly of the PRJEB26427 data set (Understanding the microbial basis of body odor in teenagers and kids).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB26427.  This project includes samples from the following biomes: root:Host-associated:Human:Skin.	root:Host-associated:Human:Skin
MGYS00005383	EMG produced TPA metagenomics assembly of the PRJNA266117 data set (Human skin bacterial metagenome and Virome Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA266117.  This project includes samples from the following biomes: root:Host-associated:Human:Skin.	root:Host-associated:Human:Skin
MGYS00005381	EMG produced TPA metagenomics assembly of the PRJNA300541 data set (Antibiotic resistance exchange between microbiota in resource-poor settings in Latin America).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA300541.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005380	EMG produced TPA metagenomics assembly of the PRJNA275349 data set (Human Microbiome Environment Metagenome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA275349.  This project includes samples from the following biomes: root:Host-associated:Human.	root:Host-associated:Human
MGYS00001730	Culture-independent assessment of oral microbiota composition in pet reptiles	Culture-dependent surveys of the oral cavity of snakes have found a wide array of potential human pathogens, hence bacterial infections secondary to snakebites and cases of salmonellosis have been linked to the oral microbiota of reptiles. Further, another set of literature records demonstrate that reptile oral bacteria are attributable to prey feces. Here, we used culture-independent16S rDNA amplicon sequencing to characterize the oral microbiota of snakes and other common pet reptiles and to test for the proportion of bacteria reported in literature. In our oral samples the vast majority of reported bacteria were either absent or present in very low proportions. We found strong differences between the taxonomic groups of reptiles, suggesting a highly specific and unique microbiota structure. Moreover, the oral microbiome of snakes was very different from the fecal microbiota reported for mice. Our study provides a first comprehensive survey with next-generation sequencing investigating the oral microbiota of snakes and reptiles in general and points out that it is important to readdress the current knowledge with culture independent techniques.	root:Host-associated:Reptile:Oral cavity
MGYS00005385	Soil fungal communities of Chilean temperate rainforests	Soil fungal communities of Chilean temperate rainforests were elucidated by Illumina MiSeq sequencing of the ITS2 region.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00005382	Antibiotic resistance exchange between microbiota in resource-poor settings in Latin America	Microbiome and resistome of human fecal and environmental microbiota from rural El Salvador and peri-urban Lima, Peru	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005378	A prospective, longitudinal analysis of the developing gut microbiome in infants en route to type 1 diabetes	This is a prospective, longitudinal collection of stool samples from infants at risk for disease. Infants from Finland and Estonia were recruited at birth based on HLA risk genotyping. Parents collected their infants' stool at approximately monthly intervals and promptly stored the sample in the freezer prior to shipment for sample processing and sequencing. The cohort comprised of 33 infants, 11 of which seroconverted to serum autoantibody positivity and of those, four developed T1D within the three year time-frame of this study.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005376	Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome	The gut microbiota has been typically viewed as an environmental factor for human health. Twins are well suited for investigating the concordance of their gut microbiomes and decomposing genetic and environmental influences. However, existing twin studies utilizing metagenomic shotgun sequencing have included only a few samples. Here, we sequenced fecal samples from 250 adult twins in the TwinsUK registry and constructed a comprehensive gut microbial reference gene catalog. We demonstrate heritability of many microbial taxa and functional modules in the gut microbiome, including those associated with diseases. Moreover, we identified 8 million SNPs in the gut microbiome and observe a high similarity in microbiome SNPs between twins that slowly decreases after decades of living apart. The results shed new light on the genetic and environmental influences on the composition and function of the gut microbiome that could relate to risk of complex diseases.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005374	Gut microbiome-dependent stratification of patients for anti-diabetic treatment	Dysbosis of intestinal microbiota could contribute to the pathogenesis of Type 2 Diabetes. It is yet to be known whether intestinal flora could be related to differential responds to antidiabetic therapies. This study, herein for the first time, metagenomic sequenced fecal samples from a randomized clinical trial on new onset untreated Type 2 Diabetes patients applied two treatment arms, Acarbose and Glipizide (Sulfonylurea) and analyzed the differential responses of intestinal flora in different groups. Results showed substantial impact of Acarbose on gut microbiota community but minor of Glipizide. Enterotypes with similar baseline clinical characteristics, had significant different pharmacologic respond to Acarbose on insulin resistance, gut hormones, bile acids and cardiovascular risks, indicating that different pattern of intestinal microbiota component could determine different responses of Type 2 Diabetes to antidiabetic pharmacological therapies.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005181	A meta-analysis of the effect of high fat diet on the murine gut microbiome	This project contains sequencing data (primarily 16S rRNA amplicon) from multiple published studies which are not already publicly available in a demultiplexed standard format. Note: Samples from Turnbaugh 2008 and 2009 were given pseudo quality scores of 30 (?) and are not suitable for denoising approaches.	root:Host-associated:Mammals:Digestive system
MGYS00005300	Microbial biogeography of 925 geothermal springs in New Zealand	Geothermal springs are model ecosystems to investigate microbial biogeography as they represent discrete, relatively homogenous habitats, are distributed across multiple geographical scales, span broad geochemical gradients, and have reduced metazoan interactions. Here, we report the largest known consolidated study of geothermal ecosystems to determine factors that influence biogeographical patterns. We measured bacterial and archaeal community composition, 46 physicochemical parameters, and metadata from 925 geothermal springs across New Zealand (13.9100.6 C and pH <19.7). We determined that diversity is primarily influenced by pH at temperatures <70 C; with temperature only having a significant effect for values >70 C. Further, community dissimilarity increases with geographic distance, with niche selection driving assembly at a localised scale. Surprisingly, two genera (Venenivibrio and Acidithiobacillus) dominated in both average relative abundance (11.2% and 11.1%, respectively) and prevalence (74.2% and 62.9%, respectively). These findings provide an unprecedented insight into ecological behaviour in geothermal springs, and a foundation to improve the characterisation of microbial biogeographical processes.	root:Environmental:Aquatic:Thermal springs
MGYS00005221	Nasal Microbiome Samples from NYU-Rutgers Cohort	The nasal lavage samples	root:Host-associated:Human:Respiratory system:Nasopharyngeal:Nasal cavity
MGYS00002686	EMG produced TPA metagenomics assembly of the Hospital Metagenomics (Colonization and Succession of Hospital-Associated Microbiota) data set.	The Colonization and Succession of Hospital-Associated Microbiota Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB13117.  This project includes samples from the following biomes: Engineered,Built environment.	root:Engineered:Built environment
MGYS00003510	EMG produced TPA metagenomics assembly of the Gut microbiota of 10 pairs of Chinese infant twins (Gut microbiota of 10 pairs of Chinese infant twins) data set.	The Gut microbiota of 10 pairs of Chinese infant twins Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12669.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005335	EMG produced TPA metagenomics assembly of the Metagenomics of BMS sulfide deposits (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB5792.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Hydrothermal vents, Sediment.	N/A
MGYS00005332	EMG produced TPA metagenomics assembly of the Metal availability predicts community metallogenomes in marine oxygen minimum zones (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA254808.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	N/A
MGYS00005365	EMG produced TPA metagenomics assembly of the Marine microbial communities from Deepwater Horizon Oil Spill, sample DHOS BM58 plume metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336904.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic, Oil-contaminated.	N/A
MGYS00005331	EMG produced TPA metagenomics assembly of the metagenomic data for ekhotsk sea () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA398459.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	N/A
MGYS00005330	EMG produced TPA metagenomics assembly of the Red Sea metagenomes (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA289734.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	N/A
MGYS00005369	EMG produced TPA metagenomics assembly of the Marine sediment microbial communities from Kolumbo Volcano mats, Greece - white/grey mat metagenome (marine sediment metagenome) data set.	The marine sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA337731.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Hydrothermal vents, Microbial mats.	N/A
MGYS00005368	Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - fosmids plate 2 metagenome		N/A
MGYS00003603	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - fosmids plate 2 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330364.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003487	EMG produced TPA metagenomics assembly of the Oral microbiome samples from the Philippines (Phillipines oral microbiome) data set.	The Phillipines oral microbiome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14383.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Oral, Saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00005329	EMG produced TPA metagenomics assembly of the Marine microbial communities from Deepwater Horizon Oil Spill, sample DHOS OV011 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336903.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic, Oil-contaminated.	N/A
MGYS00005364	Estuarine microbial communities from the Columbia River estuary - Flood tide non-ETM metaG S.733 metagenome	Sequencing of microbial communities from the Columbia River estuary to analyze effect of nutrient fluxes	N/A
MGYS00005363	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Flood tide non-ETM metaG S.733 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365284.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00001983	EMG produced TPA metagenomics assembly of the Pediatric Fecal Metagenome (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA215106. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001982	EMG produced TPA metagenomics assembly of the stool samples Raw sequence reads (stool) data set	The stool Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA363080. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system
MGYS00005285	EMG produced TPA metagenomics assembly of the A metagenome-wide association study of gut microbiota in type 2 diabetes. (gut metagenome) data set.	The gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA422434.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005359	Pediatric Fecal Metagenome	Functional metagenomic selections were performed from various pediatric fecal metagenomes, enriched for children in the first two years of life. A major goal was to understand how antibiotic resistance genes establish and propagate among developing intestinal microbiomes.  Fecal metagenomic DNA was cloned into an E. coli library and subjected to selections for antibiotic resistance. After selection, resistance-conferring fragments (the only fragments conferring survival to E. coli in the presence of the drugs) were PCR-amplified, sequenced, and assembled.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005358	stool samples Raw sequence reads	stool and meconium 16s RNA samples Raw sequence reads	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002038	EMG produced TPA metagenomics assembly of the Roux-en-Y gastric bypass surgery of morbidly obese patients shows swift and persistent changes of the individual gut microbiota (GBP) data set	The GBP Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB12947. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005357	Human Gut Microbiome Metagenome	Gut microbiome diversity	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002050	EMG produced TPA metagenomics assembly of the Rapid evolution of the human gut virome (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA196801. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system
MGYS00001987	EMG produced TPA metagenomics assembly of the Human gastric microbiome metagenome (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA297869. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Intestine
MGYS00005356	Human gastric microbiome metagenome	Human gastric microbiome	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005355	Rapid evolution of the human gut virome	Longitudinal characterization of intestinal viral particles from WGS sequence.	root:Host-associated:Human:Digestive system
MGYS00005354	Metagenome sequencing of the Hadza hunter-gatherer gut microbiota.	By human microbiome sequencing we can better understand how host evolutionary and ontogenetic history is reflected in the microbial function. However, there has been no information on the gut metagenome configuration in hunter-gatherer populations, posing a gap in our knowledge of gut microbiota (GM)-host mutualism arising from a lifestyle that describes over 90% of human evolutionary history. Here, we present the first metagenomic analysis of GM from Hadza hunter-gatherers of Tanzania, showing a unique enrichment in metabolic pathways that align with the dietary and environmental factors characteristic of their foraging lifestyle. We found that the Hadza GM is adapted for broad spectrum carbohydrate metabolism, reflecting the complex polysaccharides in their diet. Furthermore, the Hadza GM is equipped for branched-chain amino acid degradation and aromatic amino acid biosynthesis. Resistome functionality demonstrates the existence of antibiotic resistance genes in a population with little to no antibiotic exposure, indicating the ubiquitous presence of environmentally derived resistances. Our results demonstrate how the functional specificity of the GM correlates with environment and lifestyle, and how complexity from the exogenous environment is matched by endogenous homeostasis. The Hadza gut metagenome structure allows to appreciate the co-adaptive functional role of the GM in complementing the human physiology, providing a better understanding of the versatility of human life and subsistence.	root:Host-associated:Human:Digestive system
MGYS00002334	EMG produced TPA metagenomics assembly of the Metagenomes from human infant fecal samples with and without necrotizing enterocolitis (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA273761.  This project includes samples from the following biomes: Host-associated, Animal, Digestive system, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005353	human gut and groundwater harbor non-photosynthetic bacteria	S. C. Di Rienzi, I. Sharon, K. C. Wrighton, O. Koren, L. A. Hug, B. C. Thomas, J. K. Goodrich, J. T. Bell, T. D. Spector, J. F. Banfield, and R. E. Ley, The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria., Elife, vol. 2, pp. e01102e01102, Jan. 2013.	N/A
MGYS00003536	EMG produced TPA metagenomics assembly of the human gut and groundwater harbor non-photosynthetic bacteria (metagenome) data set.	The metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA321218.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00002420	EMG produced TPA metagenomics assembly of the seawater metagenome Genome sequencing and assembly (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329908.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003653	EMG produced TPA metagenomics assembly of the human gut metagenome in RA (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA356102.  This project includes samples from the following biomes: Host-associated, Human, Digestive system.	root:Host-associated:Human:Digestive system
MGYS00005352	seawater metagenome Metagenomic assembly	ESRF shotgun metagenomics project	root:Environmental:Aquatic:Lentic:Brackish
MGYS00005351	human gut metagenome in RA	Gut microbiome make contributions to human host, and intestinal dysbiosis is associated with rheumatoid arthritis. Here we firstly demonstrated that the human gut microbiome related to rheumatoid arthritis could be divided into subtyping groups under different human enterotypes, which indicate the associations between rheumatoid arthritis and gut microbiome were diverse. In rheumatoid arthritis-related microbiota, Prevotella could be an indicator of early rheumatoid arthritis patients but insufficient to differentiate RA patients from healthy controls, and Bacteroides coprocola enriched in group 3 and Bacteroides dorei enriched in group 4 were considered to be as indicators of serious rheumatoid arthritis patients. Our findings provide additional evidences supporting that rheumatoid arthritis is a heterogeneous disease. Thus, the study of association between disease and gut microbiome should be conducted under different human gut enterotypes.	root:Host-associated:Human:Digestive system
MGYS00002319	EMG produced TPA metagenomics assembly of the sludge metagenome Metagenomic assembly (sludge metagenome) data set.	The sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA427366.  This project includes samples from the following biomes: Engineered, Wastewater, Water and sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00002062	EMG produced TPA metagenomics assembly of the Identification of fungi and ameba from human wound genomic sequencing (human wound) data set	The human wound Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA344941. This project includes samples from the following biomes : Human skin.	root:Host-associated:Human:Circulatory system
MGYS00005350	Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn''s disease	This is an uncontrolled, prospective open-label study of FMT from healthy donors to subjects with active CD. A single FMT was performed via colonoscopy. Stool samples were collected prior to FMT and at two time points, four and eight weeks after FMT. Recipients microbial diversity, mucosal T-cell phenotypes and clinical and inflammatory parameters were measured over 12 weeks, and safety over 26 weeks.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005349	sludge metagenome Metagenomic assembly	Sludge from the petroleum refinery having phenol-degrading bacteria for the study of genetic evolution in bacteria	root:Engineered:Wastewater:Activated Sludge
MGYS00005348	Identification of fungi and ameba from human wound genomic sequencing	Hypothesis-free detection of pathogens directly in sample material from patients with infectious diseases of unknown origin using next generation sequencing (NGS) is an important goal of diagnostic research. However, NGS is highly susceptible to contamination, which complicates the interpretation of diagnostic results from samples with (poly-)microbial contamination. The potential of NGS for hypothesis-free diagnostic approaches of such difficult sample material is examined in the study presented here, using the example of formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and invasive amebiasis.	root:Host-associated:Human:Circulatory system
MGYS00005347	Metagenomes from human infant fecal samples with and without necrotizing enterocolitis	Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. This study compares microbial communities of 10 co-hospitalized infants, five of which had a diagnosis of necrotizing enterocolitis.  Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, a genome-resolved analysis revealed that strains colonizing each baby were typically distinct. In particular, no strain was common to all infants that developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to spread of bacteria among infants. Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically-relevant time scales.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005323	EMG produced TPA metagenomics assembly of the A DSS colitis mouse model was used to assess the microbial metabolic landscape during inflammation. (Metagenomic sequencing of cecal microbiota from DSS colitis mouse model) data set.	The Metagenomic sequencing of cecal microbiota from DSS colitis mouse model Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB15095.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Large intestine.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00005324	EMG produced TPA metagenomics assembly of the WGS of Acinetobacter baumannii ATCC 17978 passaged in presence of antibiotics in mouse model () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA485355.  This project includes samples from the following biomes: Host-associated, Mammals, Respiratory system.	root:Host-associated:Mammals:Respiratory system
MGYS00005325	EMG produced TPA metagenomics assembly of the Sheep faecal microbiota (Sheep faecal microbiota) data set.	The Sheep faecal microbiota Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14312.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Large intestine, Fecal.	root:Host-associated:Mammals:Digestive system:Midgut
MGYS00005327	EMG produced TPA metagenomics assembly of the PRJNA477326 data set (Identification of bloodstream pathogens in the gut microbiome).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA477326.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005346	Identification of bloodstream pathogens in the gut microbiome	Identify enteric strains matching patient bloodstream isolates.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005345	Sheep faecal microbiota	In this study, faecal 16S rDNA (V4) profile, metagenome and metaproteome were analyzed from five lactating Sarda sheep coming from the same flock, free-grazing and with no evidence of clinical symptoms. DNA sequences were obtained using an Illumina HiScan instrumentation.	root:Host-associated:Mammals:Digestive system:Midgut
MGYS00005344	Sus scrofa domesticus Metagenome	We describe here the metagenomics-derived viral sequences found in fecal samples collected from adult pigs with diarrhea in China. Feces can be the source of numerous viral infections in humans and animals. A library was then constructed using Nextera XT DNA Sample Preparation Kit (Illumina) and then sequenced using the Miseq Illumina platform with 250 bases paired ends with a distinct molecular tag .	N/A
MGYS00005328	EMG produced TPA metagenomics assembly of the Sus scrofa domesticus Metagenome (Sus scrofa domesticus) data set.	The Sus scrofa domesticus Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA475617.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005343	A DSS colitis mouse model was used to assess the microbial metabolic landscape during inflammation.	A total of 24 C57BL6 mice were used for this analysis. Six mice received dextran sodium sulfate (DSS) (3%) in their drinking water ab libitum. In addition to DSS treatment 6 mice were given sodium tungstate (0.2%) or sodium tungstate plus DSS in their drinking water ab libitum. A control group was included where 6 mice were given untreated water. All animals received their treatments for a total of 9 days.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00005342	WGS of Acinetobacter baumannii ATCC 17978 passaged in presence of antibiotics in mouse model	Acinetobacter baumannii ATCC17978 was infected oropharyngeally into Balb/c mice or in Balb/c mice depleted of neutrophils by cyclophosphamide treatment. Mice were treated with various antibiotics, and infection was allowed to proceed for 24 hours before lungs were removed and bacteria were pooled. The pooled bacteria were either sequenced en masse, or used to reinfect mice to enrich for bacteria resistant to the antibiotic. At least three parallel lines of bacteria were maintained during the sequential passaging in either the neutrophil replete or depleted mice. Data deposited are the total sequencing reads of the pool to identify mutants that arose after each passage, the relative abundance of each of the mutants. Passage number refers to the number of sequential passages. Cyclophosphamide refers to neutrophil depleted mice.	root:Host-associated:Mammals:Respiratory system
MGYS00005341	Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease	Coronary heart disease (CHD) is top risk factor for health in modern society, causing high mortality rate each year. However, there is no reliable way for early diagnosis and prevention of CHD so far. So study the mechanism of CHD and development of novel biomarkers is urgently needed. In this study, metabolomics and metagenomics technology are applied to discover new biomarkers from plasma and urine of 59 CHD patients and 43 healthy controls and trace their origin. We identify GlcNAc-6-P which has good diagnostic capability and can be used as potential biomarkers for CHD, together with mannitol and 15 plasma cholines. These identified metabolites show significant correlations with clinical biochemical indexes. Meanwhile, GlcNAc-6-P and mannitol are potential metabolites originated from intestinal microbiota. Association analysis on species and function levels between intestinal microbes and metabolites suggest a close correlation between Clostridium sp. HGF2 and GlcNAc-6-P, Clostridium sp. HGF2, Streptococcus sp. M143, Streptococcus sp. M334 and mannitol. These suggest the metabolic abnormality is significant and gut microbiota dysbiosis happens in CHD patients.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005340	A longitudinal analysis of the developing gut microbiome in infants from Finland, Estonia, and Russian Karelia	This is a longitudinal collection of stool samples from infants at risk for disease. Approximately 1,000 newborns were recruited to the birth cohort as part of the international DIABIMMUNE Study (http://www.diabimmune.org/) for which the consent rate was 80% in Tartu, Estonia, 59% in Espoo, Finland, and 24% in Petrozavodsk, Russia. Recruitment took place between September 2008 and May 2010 in Estonia and Finland, and between September 2008 and July 2011 in Russia. Follow-up was completed in April 2013 in Estonia and Finland, and in October 2013 in Russia. The final number of children included in the present study was 74 from each country. Inclusion criteria included positive cord blood testing for HLA DR-DQ alleles conferring increased risk for autoimmunity. The participating children were monitored prospectively for infections, use of drugs including antibiotics, and other life events.	root:Host-associated:Human:Digestive system
MGYS00005339	Gut microbiota of 10 pairs of Chinese infant twins	Early colonization of intestinal microflora in the human gut is a complex process. It remains unclear when intestinal microflora colonization occurs and how it proceeds. we recruited 10 healthy pairs of twins, including five monozygotic(MZ) and five dizygotic(DZ) twin pairs,who ranged in age from 0 to 6 years old.We performed shotgun metagenomic sequencing on 20 samples and generated averaged data output of 2G per sample.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005338	Gut microbial dysbiosis in young adults with obesity	Obesity has become a global epidemic as a high risk factor for type 2 diabetes, cardiovascular diseases and cancer. Besides human genetics, our gut microbiome is another contributor to human obesity. Here we perform metagenome-wide association studies (MGWAS) on fecal samples from a case-control cohort including 95 Chinese young adults with obesity and 105 normal-weight controls, and 23 obese patients after weight-loss treatment. We discover and validate microbial species deregulated in obesity, and show the changes of gut microbial composition after weight-loss treatment.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005334	EMG produced TPA metagenomics assembly of the Marine microbial community from La Parguera, Puerto Rico - BB Mangrove A Liquid metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336672.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Mangrove swamp.	root:Environmental:Aquatic:Marine
MGYS00005336	C.diff FMT		root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002053	EMG produced TPA metagenomics assembly of the Uncultured Antibiotic Resistance Genes from Grassland and Agricultural Soil (soil metagenome) data set	The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA244044. This project includes samples from the following biomes : Grassland, Soil.	root:Environmental:Terrestrial:Soil
MGYS00002688	EMG produced TPA metagenomics assembly of the Acid sulfate soil microbial profile - pre-investigation (Acid sulfate soil microbial profile - pre-investigation) data set.	The Acid sulfate soil microbial profile - pre-investigation Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6384.  This project includes samples from the following biomes: Environmental, Terrestrial, Soil.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00002309	EMG produced TPA metagenomics assembly of the The antibiotic resistance potential of the preterm infant gut microbiome measured using shotgun metagenomics. (Antibiotic resistance within the preterm infant gut.) data set.	The Antibiotic resistance within the preterm infant gut. Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB15257.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005283	EMG produced TPA metagenomics assembly of the Lab-scale EBPR reactor Metagenome (bioreactor sludge metagenome) data set.	The bioreactor sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA254356.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00005281	EMG produced TPA metagenomics assembly of the Richness of human gut microbiome correlates with metabolic markers (MetaHIT-Richness) data set.	The MetaHIT-Richness Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB4336.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005277	EMG produced TPA metagenomics assembly of the Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel (Gut microbiota and motility) data set.	The Gut microbiota and motility Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB9169.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005273	EMG produced TPA metagenomics assembly of the Comparison of meta-barcoding and shotgun metagenomic analysis of fungi associated with spontaneous wine fermentation (food metagenome) data set.	The food metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA305659.  This project includes samples from the following biomes: Engineered, Food production, Fermented beverages.	root:Engineered:Food production:Fermented beverages
MGYS00005271	EMG produced TPA metagenomics assembly of the Bioreactor inoculated with sediment Metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA158439.  This project includes samples from the following biomes: Engineered, Bioreactor, Continuous culture, Marine sediment inoculum, Wadden Sea-Germany.	root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum:Wadden Sea-Germany
MGYS00005279	EMG produced TPA metagenomics assembly of the Wastewater bioreactor microbial communities from Cape Town, South Africa - Thiocy_expt_500_biof metagenome (wastewater metagenome) data set.	The wastewater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA377111.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00002005	EMG produced TPA metagenomics assembly of the Core genomes of cosmopolitan surface ocean plankton (jcvi_gos_circumnavigation) data set	The jcvi_gos_circumnavigation Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8968. This project includes samples from the following biomes : Marine.	root:Environmental:Aquatic:Marine:Oceanic:Photic zone
MGYS00002034	EMG produced TPA metagenomics assembly of the Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2014 (2014 'Omics from the diffuse hydrothermal vents of Axial Seamount) data set	The 2014 'Omics from the diffuse hydrothermal vents of Axial Seamount Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB12000. This project includes samples from the following biomes : Hydrothermal vents.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00002039	EMG produced TPA metagenomics assembly of the Metagenomic characterization of three Swedish sewage treatment plants (Swedish STPs) data set	The Swedish STPs Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB14051. This project includes samples from the following biomes : Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00002019	EMG produced TPA metagenomics assembly of the Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life (InfantGut) data set	The InfantGut Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6456. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon
MGYS00005286	EMG produced TPA metagenomics assembly of the mouse gut metagenome Raw sequence reads (mouse gut metagenome) data set.	The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA386849.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005320	EMG produced TPA metagenomics assembly of the PRJEB2280 data set (Viral metagenomic study of two freshwater Lakes.).	The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB2280.  This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lake.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00002058	EMG produced TPA metagenomics assembly of the Shotgun sequencing on multiple activated sludge samples (activated sludge metagenome) data set	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA288131. This project includes samples from the following biomes : Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00005226	Rabbit INRA sire line 1001 cecal microbiota	Experiment based on a cross fostering between a rabbit line selected for lower residual feed intake and a non-selected control line to study direct and maternal effects of feed efficiency	root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
MGYS00005316	Turkey intestinal contents Raw sequence read	Turkeys were fed an antibiotic (bacitracin methylene disalicylate (BMD)) at sub-therapeutic (50g/ton of feed) or therapeutic (200g/ton) concentrations for 14 weeks, and its effect on turkey intestinal microbial communities were evaluated by 16S rRNA gene analysis.	root:Host-associated:Birds:Digestive system
MGYS00005218	16S rRNA Marker-gene survey Two-sample titration dataset	16S rRNA marker-gene survey assessment dataset generated using mixtures of human stool DNA extracts. We used samples collected from participants in an Enterotoxigenic Escherichia coli (ETEC) vaccine trial. A two-sample titration mixture design was used where DNA from stool samples collected prior to ETEC exposure were titrated into stools samples collected after exposure, in effect diluting the amount of ETEC in the mixed sample. Independent titration series were produced using samples from five trial participants. The titration series consisted of 9 samples including the unmixed samples. Four 16S PCR replicates were generated for each titration. The PCR products were sent to two independent laboratories for library preparation and sequencing. The libraries were sequenced twice at each laboratory resulting in four sequencing datasets.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005317	High temporal resolution study of coastal marine microbial communities Raw sequence reads	Weekly microbial time-series sampling was conducted at two coastal sites in Sydney, Australia based on their exposure to high (Foreshore Beach) and low (Maroubra Beach) stormwater and sewage pollution. Foreshore Beach, within Botany Bay is frequently exposed to stormwater input, as well as periodic sewage overflows released from upstream overflow outlets and discharged into Botany Bay. Maroubra Beach is east facing, exposed to the Tasman Sea, where water quality is less impacted by stormwater input.	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00005206	Microbial drivers of the human pharyngeal microbiome are associated with age-related macular degeneration	While the etiology of age-related macular degeneration (AMD), a major blinding disease, remains unknown, the disease is strongly associated with variants in the complement factor H (CFH) gene. CFH variants also confer susceptibility to invasive infection with Neisseria meningitidis, a bacterial colonizer of the nasopharyngeal mucosa. This shared susceptibility locus implicates complement deregulation as a common disease mechanism, and suggests the possibility that microbial interactions with host complement may trigger AMD. In this study, we address this possibility by testing the hypothesis that AMD is associated with specific microbial colonization of the human nasopharynx. Shotgun sequencing of the V3-V6 region of the microbial 16S ribosomal RNA gene was used to comprehensively and accurately describe the human pharyngeal microbiome, at genus level, in 260 AMD patients and 386 controls.	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00005219	A Multi-Omic Association Study of Trimethylamine N-Oxide	Trimethylamine N-Oxide (TMAO) is a circulating metabolite that has been implicated in the development of atherosclerosis and cardiovascular disease. Manor et al. identify blood markers, metabolites, proteins, gut microbiota patterns, and diets that are significantly associated with levels of plasma TMAO.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005213	human gut metagenome Raw sequence reads	Raw sequence reads of human gut metagenome	root:Host-associated:Human:Digestive system
MGYS00005315	Who eats the tough stuff  DNA stable isotope probing (SIP) of bacteria and fungi degrading 13C-labelled lignin and cellulose in forest soils	Decomposition and storage of plant-derived carbon has become a hot topic in environmental research. Since carbon dioxide has been detected as one of the most relevant drivers of global climate change, its potential storage and fate in soils has become key for predicting climate scenarios. Unfortunately, studies with a focus on the decomposition and driving factors are still lacking for precise modelling of the fluxes in a changing world. The main actors of carbon degradation in soils have not been fully identified, especially in regard to bacteria very little is known about their contribution to degradation of persistent carbon components. In the present study, the active microbial community involved in degrading 13C-labelled cellulose and lignin in forest soils was identified using a DNA stable isotopic probing (SIP) approach. Microbial activity assessed by measurements of 13CO2 increased with labelled substrate addition, during a 28 days incubation period. Within the vast microbial communities, bacterial and fungal members specialized in degrading cellulose (e.g. Devosia (Rhizobiales), Sebacinales), lignin (e.g. Sphingopyxis (Sphingomonadales), Paucibacter (Burkholderiales), Xylariales, Auriculariales, Helotiales), and both substrates (e.g. Caulobacter (Caulobacterales), Schizoporaceae, Orbiliales) have been identified. Over the course of the experiment, a successional shift from early degrading colonizers (e.g. Brevundimonas (Caulobacterales), Trichosporonales, Hymenochaetales, Gomphales) to late stage beneficiary microorganisms (e.g. Sphingopyxis (Sphingomonadales), Devosia (Rhizobiales), Orbiliales) became evident. These results provide novel insights into the degradation processes of woody plant debris in soil, disentangling the active microbial degraders from the beneficiaries, within the vast complexity of the soil microbiome.	root:Environmental:Terrestrial:Soil:Loam:Forest soil
MGYS00005220	16s rRNA sequencing of mice fecal microbiota	Mouse gut microbiota diversity under conditions of different feed was sequenced using a HiSeq 2500 platform.	root:Host-associated:Mammals:Digestive system
MGYS00005210	Influence of maternal microbiology on the microbiological and immunological health of the developing bovine intestinal tract.	Digesta and epithelial scrapings from domestic cattle between birth and 21 days of age.	root:Host-associated:Mammals:Digestive system
MGYS00005214	Rhizosphere	Characterization of the bacterial communities associated with the rhizosphere and soils surrounding Arabidopsis and Brachypodium	root:Host-associated:Plants:Rhizosphere
MGYS00005314	Fecal microbiota of patients over time at one long-term acute care hospital	Multidrug-resistant organisms (MDROs) pose an increasing public health threat, particulary in healthcare-associated environments. One such organism of increasing concern are the carbapenemase-producing Enterobacteriaceae (CPE), for which few effective antibiotics exist. Because gastrointestinal tract colonization precedes infection in many patients, preventing initial acquisition in the GI tract is one potential strategy to limit this serious disease. This longitudinal study aimed to identify risk factors associated with acquisition of CPE, including patient clinical variables and the resident gut microbiota throughout patient stay, at one longterm acute care hospital.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005198	Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development.	It has been previously reported that ursodeoxycholic acid (UDCA), a therapeutic bile acid, reduced risk for advanced colorectal adenoma in men but not women. Interactions between the gut microbiome and fecal bile acid composition as a factor in colorectal cancer neoplasia have been postulated but evidence is limited to small cohorts and animal studies. Using banked stool samples collected as part of a phase III randomized clinical trial of UDCA for the prevention of colorectal adenomatous polyps, we compared change in the microbiome composition after a 3-year intervention in a subset of participants randomized to oral UDCA at 8-10 mg/kg of body weight per day (n = 198) or placebo (n = 203). Study participants randomized to UDCA experienced compositional changes in their microbiome that were statistically more similar to other individuals in the UDCA arm than to those in the placebo arm. This reflected a UDCA-associated shift in microbial community composition (P < 0.001), independent of sex, with no evidence of a UDCA effect on microbial richness (P > 0.05). These UDCA-associated shifts in microbial community distance metrics from baseline to end-of-study were not associated with risk of any or advanced adenoma (all P > 0.05) in men or women. Separate analyses of microbial networks revealed an overrepresentation of Faecalibacterium prausnitzii in the post-UDCA arm and an inverse relationship between F prausnitzii and Ruminococcus gnavus. In men who received UDCA, the overrepresentation of F prausnitzii and underrepresentation of R gnavus were more prominent in those with no adenoma recurrence at follow-up compared to men with recurrence. This relationship was not observed in women. Daily UDCA use modestly influences the relative abundance of microbial species in stool and affects the microbial network composition with suggestive evidence for sex-specific effects of UDCA on stool microbial community composition as a modifier of colorectal adenoma risk.[This text is derived from our Open Access publication of the same title as this project.]	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005194	the upper respiratory tract microbiome of chronic rhinosinusitis patients	Swab samples were taken from the anterior nares (nose), nasopharynx, maxillary sinus and ethmoid sinus of 200 patients with chronic rhinosinusitis. Bacterial DNA was extracted, the V4 region of the 16S rRNA gene was amplified by PCR and the libraries were sequenced on an Illumina MiSeq machine. Samples were sequenced on five different runs.	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00005223	Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data	We developed an open-source R package, decontam, to identify and remove contaminating DNA sequences from marker-gene and metagenomics datasets. We validated decontam on a 16S rRNA gene oral mucosa microbiome dataset generated in our laboratory, and on additional datasets derived from previous studies.	root:Host-associated:Human:Digestive system:Oral
MGYS00005313	Arable land and chronosequenced forest land soil from different depth Raw sequence reads	Our study's aim was to investigate the vertical assembly of soil microbiomes at a fine scale during the successional development of restored ecosystems, and their contribution to soil ecosystem multi-nutrients cycling at subsurface profiles.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00005207	Raw sequence reads	CA Study	root:Host-associated:Human:Digestive system
MGYS00005212	Body site is a more determinant factor than human population diversity in healthy skin microbiome	To characterize the diversity of cutaneous microbiomes in different ethnic groups.	root:Host-associated:Human:Skin
MGYS00005215	Corbiculate bee gut amplicons Raw sequence reads	16S rRNA amplicons from corbiculate bee gut community	root:Host-associated:Insecta:Digestive system
MGYS00005205	Soil microbial distribution	Soil microbial distribution in agricultural lands	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00005217	Microbial diversity of consumption milk during processing and storage	Bovine milk contains a complex microbial community that affects the quality and safety of the product. Detailed knowledge of this microbiota is, therefore, of importance for the dairy industry. In this study, the bacterial composition of consumption milk was assessed during different stages in the production line and throughout the storage in cartons by using culturing techniques and 16S rRNA marker gene sequencing. Monthly samples from two dairies were analyzed to capture the seasonal variations in the milk microbiota. Although there was a core microbiota present in milk samples from both dairies, the composition of the bacterial communities were significantly influenced by sampling month, processing stage and storage temperature. Overall, a higher abundance of operational taxonomic units (OTUs) within the order Bacillales was detected in samples of raw and pasteurized milk from the spring and summer months, while Pseudomonadales and Lactobacillales OTUs were predominant in the winter months. OTUs belonging to the order Lactobacillales, Pseudomonadales, Clostridiales and Bacillales were significantly more abundant in milk samples taken immediately after pasteurization compared to raw milk samples. During storage of milk in cartons at 4 C, the bacterial composition remained stable throughout the product shelf life, while storage at 8 C significantly increased the abundance of OTUs belonging to the genus Bacillus and the plate count levels of presumptive Bacillus cereus. The knowledge obtained in this work will be useful to the dairy industry during their quality assurance work and risk assessment practices.	root:Engineered:Food production:Dairy products
MGYS00005203	16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome	Changes in the relative abundances of many intestinal microorganisms, both those that naturally occur in the human gut microbiome and those that are considered pathogens, have been associated with a range of diseases. To more accurately diagnose health conditions, medical practitioners could benefit from a molecular, culture-independent assay for the quantification of these microorganisms in the context of a healthy reference range. Here we present the targeted sequencing of the microbial 16S rRNA gene of clinically relevant gut microorganisms as a method to provide a gut screening test that could assist in the clinical diagnosis of certain health conditions. We evaluated the possibility of detecting 46 clinical prokaryotic targets in the human gut, 28 of which could be identified with high precision and sensitivity by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. These targets included 20 commensal, 3 beneficial (probiotic), and 5 pathogenic intestinal microbial taxa. Using stool microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay quantifies 28 targets in the context of a healthy reference range and correctly reflected 38/38 verification samples of real and synthetic stool material containing known gut pathogens. Thus, we have established a method to determine microbiome composition with a focus on clinically relevant taxa, which has the potential to contribute to patient diagnosis, treatment, and monitoring.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005201	Succession of dairy cow microbiota from birth to lactation	Our objective was to measure the succession of gut-associated archaeal, bacterial, and fungal communities in dairy cows from birth to lactation and to correlate these communities to calf diet as well as growth and health.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00005211	Composition and temporal stability of the gut microbiota in older persons	Goals of this study are to refine our understanding of diet-microbiota associations and differential taxon abundance, to identify microbiota configurations associated with ageing in both community and long-stay residential care elderly subjects, to determine associations of these configurations with health, to determine if particular microbiota profiles are more variable over time than others, and to assess the role of antibiotics in temporal instability, using 16S rDNA sequences from faecal gut microbiota. These data will provide improved gut microbiota profile definitions, and inform on design of dietary or antibiotic interventions that target gut microbiota.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005209	Fecal microbiota Targeted Locus (Loci)	Quantitative Trait Locus mapping of microbiota and expressed immunoglobulin A from G10 progeny of an advanced intercross of C57Bl6 X HR	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00005193	Composition and variation of respiratory microbiota in healthy military personnel Metagenome	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 microbiome 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 and subjected to pyrosequencing of 16S rDNA V3 to V1 region. The study produced a large set of pyrosequencing data of bacterial 16S rDNA V3-V1 region for respiratory microbiome of healthy active duty service members. Pre-processing of sequencing reads shows good data quality. The derived microbiome profiles are consistent both internally and with previous reports, suggesting utility for further analyses and association studies using sequence and demographic data.	root:Host-associated:Human:Respiratory system:Nasopharyngeal:Nasal cavity
MGYS00005224	human nose/throat Targeted loci	The aim of this study was to investigate the relationship between the nose/throat microbiome and influenza virus infection.	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00005197	Human oral microbiome of Spanish adolescents	We provide a snapshot of the adolescent oral microbiome throughout Spain and how it varies with life-style and other factors.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00005192	Human faecal 16S Raw sequence reads	16S raw reads of IBD patients and controls. The aim was to examine differences between patients in relapse and remission	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005225	Gut microbial factors implicated in disease progression and treatment response in pediatric ulcerative colitis	This project collected and profiled stool samples and rectal biopsies from pediatric patients with new-onset ulcerative colitis (UC) to evaluate the role of the gut microbiome in the efficacy of two conventional treatments.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005186	Impact of rainforest transformation on phylogenetic and functional diversity of soil prokaryotic communities in Sumatra (Indonesia)	This project investigates the impact of lowland rainforest transformation on diversity and ecosystem function of soil prokaryotic communities. To identify changes in indigenous prokaryotic community composition accompanying rainforest transformation, comparative phylogenetic analyses of soil samples from lowland rainforest, jungle rubber, rubber plantations, and oil palm plantations were performed.	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00005312	16S rRNA amplicon analysis of Pozo Bravo Lake, Catamarca, Argentina.	16S rRNA amplicon analysis of Pozo Bravo Lake, Catamarca, Argentina.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00005222	Ultra-high throughput multiplexing and sequencing of long amplicon regions on the Illumina HiSeq 2500 platform	Amplification, sequencing and analysis of the 16S rRNA gene affords characterization of microbial community composition. As this tool has become more popular and projects have grown in size and scope, greater sample multiplexing is becoming necessary while maintaining high quality sequencing. Here, modifications to the Illumina HiSeq 2500 platform are described that afford 300 bp paired-end reads of higher quality than those produced by the current Illumina MiSeq platform. To make this method feasible and flexible to different amplicon regions, a 2-Step PCR amplification protocol is also described that allows for amplification and sequencing of different amplicon regions, and that improves amplification success from low bacterial bioburden samples.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00005195	GEMS diarrheal case/control study Targeted Locus (Loci)	16S rRNA gene survey of diarrheal stool from children under 5 and matched controls.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005188	A simplified framework for dissecting complex host-microbiota interactions	Charachterization of the microbiome in the roots of Arabidopsis plants growing in agar plates. Plants were germinated in plates with one of two phosphate conditions (+Pi or -Pi), and then transfered to a new plate with one of two Pi concentrations (100uM or 30uM). The plate of the second phosphate treatment was also inoculated with one of 25 synthetic bacterial communities, or kept under axenic conditions. The bacterial synthetic communities were made from pairs of bacterial blocks, were each block is made of 8-9 individual bacterial strains.	root:Host-associated:Plants:Root
MGYS00005191	Microbiota of Ustekinumab-treated Crohn's subjects.	The fecal microbiota is a rich source of biomarkers that have previously been shown to be predictive of numerous disease states. Less well studied is the effect of immunomodulatory therapy on the microbiota and its role in response to therapy. This study explored associations between the fecal microbiota and therapeutic response of ustekinumab (UST; STELARA) treated Crohn's disease (CD) patients in the phase 2 CERTIFI study. Using stool samples collected over the course of 22 weeks, the composition of these subjects'' fecal bacterial communities was characterized by sequencing the 16S rRNA gene.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005199	16S rRNA gene amplicon sequencing of endometrial cancer-associated bacteria	16S rRNA gene amplicon sequence of tissue, stool, urine, peritoneal fluid, tumor specimens and controls from the reproductive tract from a cohort of women with endometrial cancer	root:Host-associated:Human:Reproductive system:Female
MGYS00005309	A study of the metagenome of broiler chickens	An investigation into the metagenome of broiler chickens	root:Host-associated:Birds
MGYS00005311	Biological activates of fermented Aloe arborescence juice	The efficacy of plant-based drugs have received growing attention due to minimal or no side effects. Several plant-based extracts have been shown to be effective in cancer therapy and prevention including and among these plants, Aloe arborescens. Given the several health promoting attributes to A. arborescens, the main objectives of the present study were to evaluate the anticancer efficacy, immunomodulatory and antimicrobial effect of the fermented juice as well as the safety pattern on normal human PMNCs.  Furthermore, determining the causative bacteria participating in the fermentation process.	root:Engineered:Food production:Fermented vegetables
MGYS00002380	Pelagic sediment metagenome of Gulf of Khambhat	Community structure and pollutant degradation ability of deep sediment microflora of Gulf of Khambhat using culture independent approach	root:Environmental:Aquatic:Marine:Sediment
MGYS00002379	Pelagic sediment metagenome of Gulf of Kutch	Study of microflora associated with the Pelagic Sediments of the Gulf of Kutch using metagenomics	root:Environmental:Aquatic:Marine:Sediment
MGYS00005196	Replication and Refinement of a Vaginal Microbial Signature of Preterm Birth	We conducted a longitudinal study based on weekly sampling of the vaginal microbiota during pregnancy. Analysis was based on 16S rDNA amplicon sequencing, and was performed on two study cohorts. One cohort consisted of 39 women (30 term, 9 preterm deliveries) at low risk for preterm birth enrolled at Stanford University; the other cohort consisted of 96 women (55 term, 41 preterm) at high-risk for preterm birth enrolled at the University of Alabama, Birmingham. A case-control study design was used to compare features of the microbiota in women who delivered preterm (cases) with those of women who delivered at term (controls).	root:Host-associated:Human:Reproductive system:Vagina
MGYS00005152	16S rRNA sequence of rumen microbes in dairy cattle	"The 16S rRNA sequence data was generated in the project entitled ""Reduction of methane emissions from dairy cows and concurrent improvement of feed efficiency obtained through host genetics and next generation sequencing of rumen microbiome"" using Illumina sequencing technology."	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00005184	Association of host genome with intestinal microbial composition in a large healthy cohort	"Intestinal microbiota is known to be important in health and disease. Its composition is influenced by both environmental and host factors. However, few large-scale studies have evaluated the association between host genetic variation and the composition of microbiota. We recruited a cohort of 1,561 healthy individuals, of whom 270 belong in
123 families, and found that almost one-third of fecal bacterial taxa were heritable. In addition, we identified 58 SNPs associated with the relative abundance of 33 taxa in 1 ,098 discovery subjects. Among these, four loci were replicated in a second cohort of 463 subjects: rs621711 78 (nearest gene UBR3) associated with Rikenellaceae, rs1394174 (CNTN6) associated
with Faecalibacterium, rs59846192 (DMRTB1) associated with Lachnospira, and rs28473221 (SALL3) associated with Eubacterium. After correction for multiple testing, six associations of 58 remained significant, one of which replicated. These results identify associations between specific genetic variants and the gut microbiome."	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005310	A catalog of microbial genes from the bovine rumen reveals the determinants of herbivory	The rumen microbiome is responsible for the unique nature of ruminants. A thorough knowledge of the genetic potential of rumen symbiotic microbes is therefore crucial for the sustainability of ruminant production systems. Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen and constructed 324 high quality metagenomic species. These metagenomic species were prevalent in the rumen of 77 cattle fed various diets whereas known rumen microbial genomes were less abundant. Compared to human, pig and mouse gut metagenome catalogs, the rumen is richer in functions and microbial species associated to the degradation of lignocellulosic material and production of methane. Genes coding for enzymes that deconstruct lignocellulosic substrates showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. These data bring new insights on functions, enzymes and microbes of the rumen, critical to understand phenotypes and biological processes.	root:Host-associated:Mammals:Digestive system:Foregut:Rumen
MGYS00005109	EMG produced TPA metagenomics assembly of the Isolation and Identification of the Follicular Microbiome: Implications for Acne Research (PRJNA435265) data set.	The PRJNA435265 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA435265.  This project includes samples from the following biomes: root:Host-associated:Human:Skin.	root:Host-associated:Human:Skin
MGYS00005307	Microbial metagenomes of Spongia agaricina	This study approaches the diversity, composition and function of microbial communities associated with the marine sponge Spongia agaricina, sampled in the northeast Atlantic. Shotgun metagenome sequencing (Illumina) was employed to decipher the functional features of the S. agaricina microbiome under different methods of metagenomic DNA extraction.	root:Host-associated:Porifera
MGYS00005308	Analysis of plasmidome of high-altitude lakes from the Andean Puna	The high-altitude lakes of the Andean Puna are exposed to multiple extreme conditions including high UV radiation, high concentration of arsenic, heavy metals and dissolved salts, high thermal amplitude and low oxygen pressure. Despite inhospitable conditions, various microbial ecosystems can develop successfully through adaptation mechanisms, which can be encoded in plasmids and can thus be transmitted in the microbial community. The aim of this study was the characterization of plasmidome (overall plasmid population) of cultivable and non-cultivable organisms of lakes from the Andean Puna, analyzing their functions and ecological significance. Genetic determinants of plasmid nature essentials to survive in these environments were sought.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00005299	16S rRNA gene profiling of atopic dermatitis and psoriasis patients compared to healthy volunteers	Characterization of host-microbe interactions in patients with allergic (model: atopic dermatitis) and autoimmune (model: psoriasis) disorders by 16S rRNA gene sequencing and microarray transcriptional profiling. Skin swabs were collected from the lesional skin of a large cohort of atopic dermatitis and psoriasis patients and subjected to 16S rRNA sequencing on the Roche 454 platform.	root:Host-associated:Human:Skin
MGYS00001295	Human skin bacterial and fungal microbiotas analyses	Using high-throughput 16S rDNA and ITS1 sequencing, we characterized skin bacterial and fungal microbiotas from healthy and dandruff subjects, comparing scalp and forehead (lesional and non-lesional skin sites).	root:Host-associated:Human:Skin
MGYS00005303	Tick-symbiont interactions	Obligatory hematophagous arthropods such as lice, bugs, flies and ticks harbor bacterial endosymbionts which are expected to complete missing dietary needs, and numerous genomics and some experimental evidences currently support this expectation. In hard ticks (Acari: Ixodidae) serval linages of bacterial symbionts has been documented, and very few were experimentally shown to be essential to some aspects of ticks fitness, mostly showing reduction in reproductive fitness. In order to pinpoint the nature of hard ticks-nutritional symbionts interactions, we tested the effect of antibiotic treatment and massive elimination of Coxiella-like endosymbionts (CLE) on the development and fitness of the brown dog tick (Rhipicephalus sanguineus). Administration of ofloxacin to repleted nymphs resulted in significant and acute reduction of the tick microbial community load and in CLE numbers in subsequent life stages (aposymbiotic ticks). As a result, aposymbiotic female, but not male nymphs, suffered a delayed post-feeding development. Additionally, aposymbiotic adult females needed a significantly prolonged feeding period in order to replete, and had reduced engorgement weight. Weight conversion into eggs was lower in aposymbiotic females, which resulted in reduced fecundity, as well as excessive reduced fertility. Eggs produced by aposymbiotic females were also free of CLE and resulting aposymbiotic larvae were unable to feed successfully. These results first demonstrate that the observed effects are due to CLE reduction and not due to antibiotic administration; and second, suggest that the contribution of CLE to its Rh. sanguineus host is not mandatory for oocyte development and embryogenesis, but is required under high physiological demands such as blood meal processing and tissue build up, which are more prominent in females, presumably via supplementing the host with essential micro and macronutrients. Further nutrient complementary studies are required to support this hypothesis.	N/A
MGYS00000492	Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for  prokaryotes or protist.	Seawater was filtered from different depths to retain small and large cell sizes (Protists and bacteria Organisms). The DNA was extracted and amplified by PCR.	root:Environmental:Aquatic:Marine
MGYS00005305	Swabs from the International Space Station Raw sequence reads	16S sequencing of 15 swabs from the International Space Station	root:Engineered:Built environment
MGYS00005190	An optimized model for screening colorectal cancer established using large-scale experimental sequence-based faecal microbial community data	Objective To establish methods and effective microbial biomarkers for early colorectal cancer (CRC)-specific-screening via gut microbiota detection in the clinic.Design 5,588 stool samples 16S ribosomal RNA (rRNA) gene were sequenced, and used the relative abundance of taxonomic and functional features to develop a model resembling the populations that consisted of 3 cohorts and 3 classification models (RF, XGBoost, and GBM) that distinguished the CRC group from the control group and identified potential microbial biomarkers.Results Microbiome-based classification distinguished patients with CRC from normal participants and excluded other CRC-relevant diseases. The area under the receiver operator characteristic (AUROC) curve was 92.2%. Known associations with oral pathogenic features, benefits-generated features, and functional features of CRC were confirmed by the model.Conclusions Our optimized prediction model was established using large-scale experimental population-based data and other sequence-based faecal microbial community data. This model can be used to identify high-risk groups and has the potential to become a novel screening method for CRC biomarkers due to its low 1-specificity (i.e. false-positive rate) and good stability.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005302	Effects of forest-management practices on below-ground fungal diversity and community composition in Idaho	We studied the fungal community composition in response to forest management practices which included: biomass harvesting, fertilization, and biochar amendments. The study site was located in the inter-mountain region of Idaho.	root:Engineered:Solid waste:Composting:Wood
MGYS00005153	Contrasting the roles of mycorrhizal compatibility in community development between arbuscular- versus ecto-mycorhizal systems	Feedback between plant species and the soil mycorrhizal fungi (biotic agents) shapes interspecific plant interactions, but it remains uncertain whether its effects are an essential component of plant community development. Two most dominant mycorrhizal types in temperate forests, arbuscular mycorrhizal and ectomycorrhizal plant species, can drive distinct dynamics in which the composition of the fungal community changes due to associations with plant community composition, and these changes differentially feed back on plant growth through the effects of (i) plant-fungus compatibility and (ii) common fungal networks. Here we investigate how plant community development is linked with mycorrhizal types, contrasting the effects of arbuscular mycorrhizal (AM) versus ectomycorrhizal (EcM) associations on seedling establishment. By simulating the scenario where established tree community modifies the soil fungal component (i.e., AM versus EcM inocula) and alters the competitive environment for new seedlings, we found that competition for soil nutrients influenced seedling establishment. The results showed that compatible seedlings had significantly greater leaf and root biomasses than incompatible seedlings, a benefit from the presence of established competitors through enhancing positive nutrient feedbacks. While plant-soil feedback mediated tree-seedling interactions for both AM and EcM associations, the estimated compatibility effects were more positive for EcM relative to AM associations. Notably, this coincided with the more pronounced sharing of fungal species and more structured formation of common fungal network in EcM systems compared to AM systems. Together these results suggest the link between seedling establishment and mycorrhizal functional differentiation.	root:Host-associated:Plants:Root
MGYS00005233	CHILD gut microbiome and asthma	Asthma is a multifactorial disease with an alarming increase in prevalence. Like several other immune-mediated diseases, asthma pathogenesis is being studied in the context of the hygiene hypothesis. Antibiotic-driven gut microbial shifts exclusively in the neonatal period increase airway inflammation in mice. We hypothesized that similar microbial changes in infant humans have a causal role in disease. To test this, 319 children enrolled in the Canadian Healthy Infant Longitudinal Development (CHILD) study were grouped into four phenotypes: atopic + wheeze (AW), atopic only, wheeze only, and controls, based on clinical data at 1 year. The fecal microbiome of 3-month and 1-year samples was evaluated by 16S rRNA gene sequencing (Illumina). A subset of samples in the AW and control groups was selected for qPCR, short chain fatty acid (SCFA) and urine metabolomic analyses. Finally, germ-free mice were inoculated with feces from one AW patient or with the same inoculum plus 4 bacterial strains found more commonly in controls. These mice were bred and the F1 generation was evaluated for OVA-induced airway inflammation. Results: At 3 months of age, 4 OTUs were identified by sequencing and qPCR as decreased in AW children, who also had a significantly increased risk of asthma diagnosis, based on their asthma predictive index at 3 years of age. These children exhibited decreased fecal acetate and propionate, and alterations in bacterial and host-derived metabolites mostly at 3 months of age. Finally, oral inoculation of mice with these 4 bacterial strains ameliorated airway inflammation. These results reveal taxonomic and functional gut microbial changes in infants associated with an increased risk of asthma. Decreased production of SCFA at this young age may lead to changes in energy harvest, bile acid and urobilinogen metabolism. This study suggests an associative and possibly causal role of early infancy shifts in gut microbiota with risk of asthma in human infants.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00005231	xenomicrobiota_transplanted_into_germfree_mice	Xenomicrobiota from a variety of different environments were transplanted into germfree mice. Assembly and composition of the gut-selected communities were analyzed by amplicon-sequencing. In a follow-up experiment, mice that harbored gut-selected communities were cohoused with each other.	root:Host-associated:Mammals:Digestive system
MGYS00005229	Bacterial variation in human body habitats across space and time	We applied multiplexed barcoded 16S ribosomal RNA gene pyrosequencing to survey the diversity and distribution of bacteria in and on healthy adults	root:Host-associated:Human
MGYS00005248	Cervical Microbiota Associated with Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses	It is increasingly recognized that microbes that reside in and on human body sites play major roles in modifying the pathogenesis of several diseases, including cancer. However, specific microbes or microbial communities that can be mechanistically linked to cervical carcinogenesis remain largely unexplored. The purpose of the study was to examine the association between cervical microbiota and high-grade cervical intraepithelial neoplasia (CIN 2+) in women infected with high-risk (HR) human papillomaviruses (HPV) and to assess whether the cervical microbiota are associated with oxidative DNA damage as indicated by the presence of cervical cells positive for 8-hydroxy-2'-deoxyguanosine. The study included 340 women diagnosed with CIN 2+ (cases) and 90 diagnosed with CIN 1 (non-cases). Microbiota composition was determined by Illumina sequencing of the 16S rRNA gene amplified from DNA extracted from cervical mucus samples. Measures of alpha/beta-diversity were not associated with either CIN severity or oxidative DNA damage. However, a cervical mucosal community type (CT) dominated by L. iners and unclassified Lactobacillus spp. was associated with CIN 2+ (OR = 3.48; 95% CI, 1.279.55). Sequence reads mapping to Lactobacillaceae, Lactobacillus, L. reuteri, and several subgenus level Lactobacillus operational taxonomic units were also associated with CIN 2+ when examined independently (effect size >2.0; P < 0.05). Our 16S rRNA sequencing results need confirmation in independent studies using whole-genome shotgun sequencing and that would allow sharpening the suggested associations at finer taxonomic levels. Our results provide little evidence that DNA oxidative damage mediates the effect of the microbiome on the natural history of HPV infection and CIN severity. Cancer Prev Res; 9(5); 35766. 2016 AACR.	root:Host-associated:Human:Reproductive system:Vagina:posterior fornix
MGYS00005266	human vaginal metagenome Genome sequencing and assembly	"The Multi-Omic Microbiome Study-Pregnancy Initiative (MOMS-PI) is a collaborative project with the Global Alliance to Prevent Prematurity and Stillbirth (GAPPS) based at Seattle Children's and is funded by the NIH Roadmap Human Microbiome Project. Together, we are committed to understanding the impact of the vaginal microbiome on pregnancy, pregnancy-related complications and the impact on the fetal microbiome. Preterm birth is the leading cause of death in neonates, thus our efforts are largely focused on assessing the role of the microbiome on preterm birth and maternal-infant health.MOMS-PI is a multifaceted initiative to generate large and comprehensive datasets using six ""omics"" technologies: 1) metagenomic rRNA gene sequencing, 2) whole metagenomic shotgun sequencing, 3) metatranscriptomics, 4) metabolomics/lipidomics, 5) immunoproteomics and 6) interactomics. Samples will be collected throughout the course of pregnancy from a cohort of ~2000 women. We believe this large-scale, innovative effort will lead to insights into how the microbiome impacts risk for preterm birth and the temporal dynamics of the pregnancy microbiome."	root:Host-associated:Human:Reproductive system:Vagina
MGYS00005161	Organic agricultural field soil Raw sequence reads	Study investigated effects of cover crops and organic fertilizers on bacterial community structure in organically managed agricultural field soils in Minnesota	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00005163	Metagenomic analysis of nematode beetle association	Insects and nematodes represent the most species-rich animal taxa and they occur together in a variety of associations. Necromenic nematodes of the genus Pristionchus are found on scarab beetles with more than 30 species known from worldwide samplings. However, little is known about the dynamics and succession of nematodes and bacteria during the decomposition of beetle carcasses. Here, we study nematode and bacterial succession of the decomposing rhinoceros beetle Oryctes borbonicus on La Reunion Island. We show that Pristionchus pacificus exits the arrested dauer stage seven days after the beetles  death. Surprisingly, new dauers are seen after 11 days suggesting that some worms return to the dauer stage already after one reproductive cycle. We used high-throughput sequencing of the 16S rRNA genes of decaying beetles, beetle guts and nematodes to study bacterial communities in comparison to soil. We find that soil environments have the most diverse bacterial communities. The bacterial community of living and decaying beetles are more stable but one single bacterial family dominates the microbiome of decaying beetles. In contrast, the microbiome of nematodes is relatively similar even across different families. This study represents the first characterization of the dynamics of nematode-bacterial interactions during the decomposition of insects.	root:Host-associated:Insecta
MGYS00005162	Infant airway microbiome Raw sequence reads	16s rRNA gene sequencing of aspirates from the hypopharynx of infants	root:Host-associated:Human:Respiratory system:Nasopharyngeal:Pharynx
MGYS00005245	uncultured prokaryote Targeted loci environmental	Survey of biofilm bacterial community diversity (16S rRNA) in New Zealand streams	root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
MGYS00005243	Soil Microbial communities from weed germination bioassay targeted loci environmental	characterize soil bacterial and fungal communities that were associated with weed seed and seedling	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001186	Capsule Patients	Illumina 16S rRNA gene sequence data from fecal samples of patients treated with capsules for recurrent Clostridium difficile infection.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005159	Microbiome analysis complements fecal occult blood test for improved detection	Using microbiome-based models to differentiate healthy patients from those with colonic lesions.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005158	vaginal microbiota of pregnant women	vaginal microbiota of pregnant women	root:Host-associated:Human:Reproductive system:Vagina
MGYS00005237	Altering the intestinal microbiota during a critical developmental window	Disruption of the microbiota by low-dose antibiotic exposure can alter host metabolism and adiposity. We now show that low-dose penicillin (LDP) delivered from birth enhanced metabolic alterations, and that there were additive effects in combination with high fat diet. LDP that was limited to early life was sufficient for sustained effects on body composition. After the cessation of penicillin, the microbial communities recovered, yet metabolic phenotypes persisted, indicating that microbiota interactions in infancy may be critical determinants of long-term host effects. Early-life LDP was associated with alterations in ileal expression of genes involved in immunity. The growth promotion phenotype was transferrable to germ-free hosts by LDP-selected microbiota, not antibiotics per se. These studies characterize important variables in early-life microbe-host metabolic interaction, and identify several taxa consistently linked with metabolic alterations.	root:Host-associated:Mammals:Digestive system
MGYS00005238	Human skin microbiota Metagenome	The variability in skin microbial communities within a human population can be the cause of many factors, including occupation, diet, age, gender, surroundings and so on. In this study, we explored the differences in the bacterial community structure associated with seven skin sites in 71 healthy Chinese over six days and its correlations with age, gender, physical skin parameters, and whether participants lived in an urban versus suburban location of the same city.	root:Host-associated:Human:Skin
MGYS00005235	16S rRNA gene sequences of human gut microbiota	We characterized the gut microbiota of Korean twin and their families. The study population consisted of 155 monozygotic twin pairs (n=310), 37 dizygotic twin pairs (n=74), and their parents and siblings (n=288). Among them, fecal samples from 84 individuals were provided twice at two time points. Therefore, a total of 756 fecal samples were analyzed. The V4 region of the 16S rRNA gene was sequenced using an Illumina MiSeq platform.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005247	Fecal microbiota of Japanese healthy adults	Fecal microbiota of Japanese healthy adults. 16s rRNA gene library of V1-V2 hyper variable regions derived from the fecal samples of 516 subjects.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005265	Symbiodinium ITS2 Arabian Seas	Next-generation sequencing of the ITS2 marker gene was used to assess Symbiodinium community composition and diversity comprising 892 samples from 46 hard and soft coral genera.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00005257	Root fungi in temperate forests Metagenome	In this study, we want to elucidate the influence of forest management on root associated fungal richness.	root:Host-associated:Plants:Root
MGYS00005101	Skin metagenomes	Skin shotgun metagenomes from psoriasis patients	root:Host-associated:Human:Skin
MGYS00005102	Understanding the microbial basis of body odor in teenagers and kids	Metagenomics samples of multiple skin sites (underarm, neck & head scalp) from teenagers and kids	root:Host-associated:Human:Skin
MGYS00005268	Rhizotypes of plant-root fungal biome	Here we show that diverse root-associated fungi form highly-compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities is partitioned into semi-discrete types even within a single host plant population. Intensive DNA-barcoding of root-associated fungi in a monodominant beech forest reveals that the network representing symbiont-symbiont co-occurrence pattern is compartmentalized into clear modules, which consist of diverse functional groups of mycorrhizal and endophytic fungi. As a result, each terminal root of the host plant is colonized by either of the two largest fugal species sets, forming rhizotypes. Thus, species-rich root microbiome can have alternative stable states as recently shown in relationship between gut microbiome type and human health.	root:Host-associated:Plants
MGYS00005295	EMG produced TPA metagenomics assembly of PRJEB34384 data set (Two metagenomes from outflow channels of Lost Hammer ultrasaline, perennial spring from Canadian High Arctic.).	TheThird Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set ERP117276, and was assembled with metSPAdes(v3.13.0).	root:Environmental:Aquatic:Sediment
MGYS00005128	Predicting antibiotic resistance in clinical infections caused by Enterobacterales from aggregated population-level taxonomy-adjusted AMR estimates derived from quantitative metagenomic analysis of pooled human faecal samples	Antimicrobial resistance (AMR) is a global health threat, especially in low-/middle-income countries (LMICs), where there is limited surveillance to inform empiric antibiotic treatment guidelines. Enterobacterales are a particular AMR problem, and a common cause of disease. We developed a novel approach for AMR surveillance in Enterobacterales by profiling metagenomes of pooled human faecal material from three sites (n=563 individuals; Cambodia, Kenya, UK) to derive a taxonomy-adjusted AMR metric which could be used to predict the aggregate burden of resistant Enterobacterales infections within each setting. Samples were sequenced (Illumina); taxonomic and resistance gene profiling was performed using ResPipe (https://gitlab.com/hsgweon/ResPipe). Data on organisms causing bacteraemia and meningitis and susceptibility results from 2010-2017 were collated for each site. Bayesian generalised linear models with a binomial likelihood were fitted to determine the capacity of the metric to predict AMR in Enterobacterales infections in each setting. The most informative model predicted the proportion of resistant infections in the target populations for 14/14 of antibiotics in the UK, 12/12 in Kenya, and 8/12 in Cambodia. Intermittent metagenomics of pooled human samples could be a powerful tool in determining and monitoring the burden of AMR in clinical infections, especially in resource-limited settings.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002700	Soil metagenome from healthy and unhealthy agricultural soil	Soil samples were collected from healthy and unhealthy agricultural soil. Soil health was determined based on plant productivity and farmer's perception. DNA was extracted and subjected to metagenome sequencing.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00005149	aquifer metagenome raw sequence reads	Microbial communities from subsurface basaltic aquifers in C sequestration operations	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00005256	20150129pengxin.mouse	20150129pengxin.mouse	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005292	International Space Station Microbial Observatory - Microbial Diversity	The environmental microbiome study was designed to decipher microbial diversity of the International Space Station surfaces in terms of spatial and temporal distributions by the next-generation sequencing of 16S rRNA and ITS.	root:Engineered:Built environment
MGYS00005141	Temporal sampling of marine metagenomes from Station ALOHA and BATS		root:Environmental:Aquatic:Marine:Oceanic
MGYS00005293	International Space Station flight project EXTREMOPHILES.	16S rRNA sequences obtained of Wipe samples taken from ISS indoor surfaces	N/A
MGYS00005291	Inflated Lunar/Mars Analog Habitat Microbiome	The raw sequence data come from the microbial succession study of the Inflated Lunar/Mars Analog Habitat (ILMAH). Bacterial monitoring for several surfaces was conducted before and during a 30-day occupation by three student astronauts.	root:Engineered:Built environment
MGYS00005290	Microbial diversity on kitchen sinks and bathroom tiles	This study examined the microbial and chemical signatures of indoor surfaces that are periodically wet: kitchen sinks and bathroom shower tiles. Removable surfaces were installed in a home and subject to typical household conditions for one month. Both DNA and RNA from the surfaces were isolated, and 16S and ITS amplicons were generated to target the bacterial and fungal communities, respectively.	root:Engineered:Built environment
MGYS00005288	Networks depicting the fine-scale co-occurrences of fungi in soil horizons	Fungi in soil play pivotal roles in nutrient cycling, pest controls, and plant community succession in terrestrial ecosystems. Despite the ecosystem functions provided by soil fungi, our knowledge of the assembly processes of belowground fungi has been limited. Based on the high-throughput sequencing data of fungi in a cool temperate forest in northern Japan, we analyze how taxonomically and functionally diverse fungi show correlated fine-scale distributions in soil. By uncovering pairs of fungi that co-occurred in the same soil samples more/less frequently than expected by chance, networks depicting fine-scale distributions of fungi are inferred at the O and A horizons. The results then leads to the working hypothesis that mycorrhizal, endophytic, saprotrophic, and pathogenic fungi as well as fungi with unknown functions form compartmentalized networks of potential facilitative, antagonistic, and/or competitive interactions in belowground ecosystems. Overall, this study provides a research basis for further understanding how interspecific interactions, along with sharing of niches among fungi, drive the dynamics of poorly explored biospheres in soil.	root:Environmental:Terrestrial:Soil
MGYS00005287	mouse gut metagenome Raw sequence reads	This study presented the bacteria of feces sample from the C57BL/6 mice.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005284	Lab-scale EBPR reactor Metagenome	Two lab-scale EBPR bioreactors were operated for approximately one year with samples taken at multiple time points to assess the dynamics of the microbial and viral communities.	root:Engineered:Bioreactor
MGYS00005282	Richness of human gut microbiome correlates with metabolic markers	We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They harbour known and previously unknown bacterial species at different proportions; individuals with a low bacterial richness (23% of the population) are characterized by more marked overall adiposity, insulin resistance and dyslipidaemia and a more pronounced inflammatory phenotype when compared with high bacterial richness individuals. The obese individuals among the former also gain more weight over time. Only a few bacterial species are sufficient to distinguish between individuals with high and low bacterial richness, and even between lean and obese. Our classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00005280	Wastewater bioreactor microbial communities from Cape Town, South Africa - Thiocy_expt_500_biof metagenome		root:Engineered:Wastewater
MGYS00005278	Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel	To understand how different diets, the consumers gut microbiota, and the enteric nervous system (ENS) interact to regulate gut motility, we developed a gnotobiotic mouse model that mimics short-term dietary changes that happen when humans are traveling to places with different culinary traditions. Studying animals transplanted with the microbiota from humans representing each cuisine and fed a sequence of diets representing those of all donors, we find that correlations between bacterial species abundances and transit times are diet dependent. However, the levels of unconjugated bile acids  reflecting microbial bile salt hydrolase activity  correlate with faster transit across diets, including a Bangladeshi diet. Mice harboring a consortium of sequenced bacterial strains from the Bangladeshi donors microbiota and fed a Bangladeshi diet revealed that the commonly used spice, turmeric, slows transit times. Turmeric affects gut motility via bacterial bile acid deconjugation and modulation of Ret signaling in the ENS. These results demonstrate how a single food ingredient interacts with a functional microbiota trait to regulate host physiology.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005274	Comparison of meta-barcoding and shotgun metagenomic analysis of fungi associated with spontaneous wine fermentation	Wine is a complex beverage, comprised of thousands of metabolites that are produced through the action of yeasts and bacteria in fermenting grape must. To ensure a robust and reliable fermentation, most commercial wines are produced via inoculation with large amounts of the major wine yeast, Saccharomyces cerevisiae. However, there is a growing trend towards the use of uninoculated or wild fermentations, in which the yeasts and bacteria that are naturally associated with the vineyard or winery perform the fermentation. The varied metabolic contributions of the numerous non-Saccharomyces species in this microbial community are thought to impart complexity and desirable taste and aroma attributes to wild ferments when compared to their inoculated counterparts.In order the map the microflora of spontaneous fermentation, metagenomic techniques were used to characterise and monitor the progression of fungal species in several wild fermentations. Both amplicon-based ITS phylotyping and shotgun metagenomics were used to assess community structure, in addition to the isolation, sequencing and de novo assembly of the first reference genomes for several dominant wine-associated species.	root:Engineered:Food production:Fermented beverages
MGYS00005272	Bioreactor inoculated with sediment Metagenome	Metagenomic contigs were binned following isolation from a continuous culture bioreactor inoculated with sediment from the German Wadden Sea.  Eight samples were taken from the bioreactor at different time points (between day 48 and day 185 of cultivation).	root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum:Wadden Sea-Germany
MGYS00005270	Canadian MetaMicrobiome Library Projects	Our studies aim to probe various environments, including the soil and gut environments, for interesting or novel microbial functions of industrial, environmental, or medical relevance. We apply sequence- and function-based metagenomic techniques to explore these environments.	root
MGYS00005185	Fungal community across a tropical forest disturbance gradient	Woody debris is an important component of forest ecosystems, forming a substantial carbon pool and habitat for a diversity of organisms, including specialist species. The decomposition of woody debris is controlled by both abiotic and biotic factors. However, much less is known about the biotic factors, such as the contribution of fungi to nutrient cycling in tropical biomes. Moreover, given the high rates of tropical deforestation and forest degradation, it is vital to better understand anthropogenic impacts on essential biotic processes, such as decomposition. Hence, we set out to link the impacts of forest degradation and the role of biotic characteristics, especially fungal diversity and composition, in determining woody debris decomposition rates in a tropical biomeSpecifically, we examined the following questions; (i) what is the effect of wood species identity on the diversity and community structure of fungi; (ii) how does fungal diversity and composition in woody debris change through time and with state of decay; (iii) how does the degree of forest disturbance affect fungal diversity and community structure and (iv) how do these factors determine the rate of wood decomposition?	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00005143	Distinct spatial patterns of bacterial diversity shaped by salivary flow on tooth surfaces in humans	Bacteria that inhabit the oral cavity of humans Raw sequence reads	root:Host-associated:Human:Digestive system:Oral
MGYS00005146	We sequenced the bacterial compositions of 2,882 samples from the foxtail millet rhizoplane, rhizosphere and corresponding bulk soil from two well-separated geographic locations.	The root microbes play pivotal roles in plant productivity, nutrient uptakes and disease resistance. The microbial communities were widely investigated by the 16S amplicons sequencing in crops and model plants. We sequenced the bacterial compositions of 2,882 samples from the foxtail millet rhizoplane, rhizosphere and corresponding bulk soil from two well-separated geographic locations.We revealed the root microbial composition of the foxtail millet and defined the core rhizoplane bacteria.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00005148	Two metagenomes from outflow channels of Lost Hammer ultrasaline, perennial spring from Canadian High Arctic.	Characterization of microorganisms that thrive in extreme habitats, often called extremophiles, enable us to understand how biology functions at the frontiers of life. This knowledge allows us to model the potential habitability of environments in Solar System bodies such as Mars and Jupiter's icy moon Europa, as well as understand the long-term evolution and fate of microbial life on Earth. The samples for this study were collected from immediate surroundings of a cold, hypersaline spring in the Canadian Arctic as planetary analogue for Europa.	root:Environmental:Aquatic:Sediment
MGYS00005147	Persistent gut microbiota immaturity in malnourished Bangladeshi children	Therapeutic food interventions have reduced mortality in children with severe acute malnutrition (SAM) but incomplete restoration of healthy growth remains a major problem. The relationships between the type of nutritional intervention, the gut microbiota, and therapeutic responses are unclear. In the current study, bacterial species whose proportional representation define a healthy gut microbiota as it assembles during the first two postnatal years were identified by applying a machine-learning-based approach to 16S rRNA datasets generated from monthly fecal samples obtained from a birth-cohort of children, living in an urban slum of Dhaka, Bangladesh, who exhibited consistently healthy growth. These age-discriminatory bacterial species were incorporated into a model that computes a relative microbiota maturity index and microbiota-for-age Z-score that compare development (defined here as maturation) of a childs fecal microbiota relative to healthy children of similar chronologic age. The model was applied to twins and triplets (to test for associations of these indices with genetic and environmental factors including diarrhea), children with SAM enrolled in a randomized trial of two food interventions, and children with moderate acute malnutrition. Our results indicate that SAM is associated with significant relative microbiota immaturity that is only partially ameliorated following two widely used nutritional interventions. Immaturity is also evident in less severe forms of malnutrition and correlates with anthropometric measurements. Microbiota maturity indices provide a microbial measure of human postnatal development, a way of classifying malnourished states, and a parameter for judging therapeutic efficacy. More prolonged interventions with existing or new therapeutic foods and/or addition of gut microbes may be needed to achieve enduring repair of gut microbiota immaturity in childhood malnutrition and improve clinical outcomes. (Subramanian et al., doi:10.1038/nature13421)	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005142	Characterizing postnatal co-development of the gut microbiota and mucosal IgA responses in healthy twin pairs and a gnotobiotic mouse model	Abstract: Immunoglobulin A (IgA) is the major class of antibody secreted by the gut mucosa, where it contributes to barrier function by preventing microbial and food antigens from interacting with host tissues1,2. The lack of metrics for quantifying development of the gut microbiota and mucosal immune system has hindered the ability to dissect the effects of microbial, host and environmental factors on their co-development. Therefore, we subjected fecal samples, collected monthly during the first 3 postnatal years from 40 healthy USA twin pairs, to bacterial 16S rRNA gene sequencing and to fluorescence-activated cell sorting to distinguish IgA-targeted from non-targeted taxa. Applying a machine-learning algorithm (Random Forests), we identified a set of 25 age-discriminatory bacterial taxa whose patterns of representation define a program of microbiota assembly/maturation shared across twin pairs. Remarkably, IgA responses to 30 taxa, including a subset of the age-discriminatory organisms, converge on a pattern shared across twin pairs by the second postnatal year; the observed targeting patterns were not simple reflections of relative abundance or taxonomy. Zygosity, delivery mode, and breast versus formula feeding had small albeit statistically significant effects on targeting. In follow-up studies, young germ-free mice were colonized with fecal microbiota obtained from two twin pairs at 6 and 18 months of age, and fed a sequence of human diets designed to simulate the transition from milk feeding to complementary foods. Distinct age-associated differences in mucosal IgA responses to the transplanted human microbiota were recapitulated in both diet contexts for both twin pairs, suggesting that intrinsic properties of their community members play a dominant role in dictating IgA responses.  This approach can be used to define gut mucosal immune development in health and disease states, and help identify ways to repair or prevent perturbations in this facet of host immunity.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005136	Metatranscriptome of an algal bloom from St Helena Bay on the west coast of South Africa	The aim of this project is to investigate changes in gene expression specifically genes linked to PCD the duration of an algal bloom event. The study was motivated by the paucity of knowledge in changes in microbial complexity in algal blooms and by the lack of empirical evidence of PCD from field and natural environments such as algal blooms. Despite the progress made, algal blooms remain poorly understood, specifically why a particular taxa proliferates to dominate the bloom remains a challenge and a call for species specific information has been made. Concomitant to documenting the changes in microbial diversity and environment conditions during an algal bloom, changes in gene expression in relation to PCD will also be assessed to provide a contextual understanding of PCD during a bloom event.	root:Environmental:Aquatic:Marine
MGYS00005139	Prunus Root and soil microbial community Targeted loci	Amplicon-based sequencing was used to examine the bacteria, fungi, and oomycetes associated with soils collected from almond orchards throughout the central valley of California. Later, peach seedlings were grown in these soils in a greenhouse, and amplicon sequencing was used to examine the root-associated microbial community.	root:Host-associated:Plants:Root
MGYS00005138	Infant nasopharyngeal bacteria microbiome	"Bacterial community profiling of nasopharyngeal (NP) aspirates across a birth cohort of 234 infants. Multiple samples per child, including ""healthy"" NP samples collected in the absence of respiratory symptoms and ""infection"" NP samples collected during episodes of acute respiratory illness."	root:Host-associated:Human:Respiratory system:Nasopharyngeal
MGYS00005118	Mouse fecal microbiome after exposure to high LET radiation	Space travel is associated with continuous low-dose-rate exposure to high Linear Energy Transfer (LET) radiation. Pathophysiological manifestations after low-dose radiation exposure are strongly influenced by non-cytocidal radiation effects including microbiome and cellular gene expression. Using a mouse model for exposure to high LET radiation, we observed substantial changes in the composition and functional potential of the microbiome. These were paralleled by changes in the abundance of multiple metabolites, which were related to the enzymatic activity of the altered metagenome by means of metabolic network modeling. There was a complex dynamic in microbial and metabolic composition at different radiation doses, suggestive of transient, dose-dependent interactions between microbial ecology and signals from the hosts cellular damage repair processes. Functional shifts included features associated with dysbiosis at the onset of chronic inflammatory responses, which could pre-dispose space travelers to systemic, long-term health risks.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00005117	Analysis of dust samples from the Russian part of the ISS	Our study focuses on the hardiest microorganisms inhabiting the ISS, in order to assess their diversity, and capabilities to resist certain stresses. We specifically selected dust samples from the Russian modules that were obtained 8-10 years ago, and stored since then under sealed conditions on Earth. Targeting long-time survivors and spore-forming microorganisms, we assessed consequently the cultivable microbial community of these samples, in order to obtain model microbial strains that could help to analyze specific adaptation towards environmental stresses, such as desiccation and lack of nutrients. In this study, we analyzed these microorganisms with respect to their resistance towards thermal stress and exposure to clinically relevant antibiotics. In addition, we assessed the bacterial and archaeal community via molecular methods (NGS sequencing) and compared our new data with the previously derived information from the ISS microbiome.	root:Engineered:Built environment
MGYS00005137	Bacterial endophytes of tree species belonging to the family Pinaceae Targeted loci environmental	Bacterial endophytes of tree species belonging to the family Pinaceae. Tree species were collected along the native range of Pinus flexilis	root:Host-associated:Plants:Phylloplane:Endophytes
MGYS00005133	16S rRNA gene amplicon sequencing of patients with colorectal cancer	A collection of 16S rRNA gene amplicon sequences from patients with colorectal cancer, and technical controls. Samples come from stool, mucosa, tissue biopsies and tumor biopsies.	root:Host-associated:Human:Digestive system
MGYS00005134	Ice Wedge Polygon	Frozen soil samples were collected that represent topographically high and low areas from basins of various ages around Barrow, Alaska. All of the sites are coordinated with portable or permanent Eddy covariance towers that have been used to study gas exchange. The samples were collected from several transects that include polygon rims and centers. At each site two cores were taken from rims and three from centers. The cores were approximately 25 cm deep, and so only include the active layer. Specifically samples were obtained from matching sets of polygon rims and centers from 3 different basins. This produced 24 samples: 3 basins x 2 types (rim/center) x 4 depths (6-10, 16-20, 26-30, 36-40cm). These were supplemented with smaller cores from additional basins: 3 basins x 2 types x 2 depths (6-10, 16-20cm). For the samples high refers to polygon rims, low to polygon centers. Additional abundant biological and chemical metadata have been collected for these samples.	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00005135	Flores_palm_EBI	palm samples from Flores_SMP for submission to EBI	root:Host-associated:Human:Skin
MGYS00005132	Gut and nasal microbiome in Parkinson''s disease	Amplicon sequencing and metagenomic data of nasal and stool samples of PD patients, RBD patients and healthy controls.	root:Host-associated:Human
MGYS00005131	Metagenomics of gut microbiome from diarrheal samples	Stool samples from diarrheal patients were used to study the structural and functional diversity of the gut microflora.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005130	Gut Microbiome Alterations Drive Distinct Metabolic Expression Patterns in a Cohort of Italian Patients with Parkinson's Disease	Parkinson's disease is a neurodegenerative disorder characterized by the accumulation of intracellular aggregates of misfolded alpha-synuclein along the cerebral axis. Several studies report the association between intestinal dysbiosis and Parkinson, although a cause-effect relationship yet remains to be established. Herein, the composition of the microbiota in fecal extracts of 64 patients with Parkinson's disease and 51 controls was determined using a next generation sequencing approach. A hypothetical functional profile based on the 16S rRNA profile using a predictive metagenomic tool was also performed. A significant decrease in the abundance of taxa belonging to the phylum Firmicutes, particularly in the Lachnospiraceae family was detected in the patient group. Key members of the Lachnospiraceae family, such as the genus Blautia and some related species, were significantly reduced in patients compared to controls. Moreover, consistent with depletion of short chain fatty acids-producing bacteria, genera and species within the Lachnospiraceae family (Butyrivibrio, Pseudobutyrivibrio, Coprococcus, Roseburia and Roseburia faecis) were also decreased. Interestingly, the relative abundance of Brevibacteriaceae and Lachnospiraceae was positively associated with tremor-dominant phenotype, whereas abundance of Enterobacteriaceae and Escherichia was positively associated with non-TD phenotypes. Finally, the functional prediction of gut metagenome composition in patients, in comparison with those of healthy controls, showed the presence of 81 significantly altered metabolic pathways. In particular, there was a significant increase of most pathways of the amino acids and lipids metabolisms, of other secondary metabolites, and in the metabolism and biodegradation of xenobiotics.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005129	Gut microbiota in Parkinson's disease: temporal stability and disease progression	Aiming to explore the temporal stability of gut microbiota in Parkinson's disease and the potential relationship of microbiota and disease progression, we characterized the gut bacterial communities of 64 Parkinson's patients and 64 control subjects from two stool samples per subject, collected on average 2.25 years apart. Microbial communities were analyzed with amplicon sequencing of the V3-V4 variable regions of the 16S rRNA gene, performed on the Illumina MiSeq platform.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005085	Home Microbiome Metagenomes	The project identifies patterns in microbial communities associated with different home and home occupant (human and pet) surfaces.	root:Engineered:Built environment
MGYS00003071	uncultured prokaryote Metagenome	In the present study, microbial communities ofsponges, Sediments and Seawater inhabitingcoral reef ecosystems were investigated usingbarcoded pyrosequencing of 16S rRNA geneamplicons. Our main goals were to compare thebacterial and archaeal richness and composition ofsponge species, sediment and seawaterinhabiting coral reef systems. FLX 454 titanium pyrosequencingstudy.	root:Mixed
MGYS00003014	Temperate invertebrates associated prokaryotic diversity	This study compares gorgonian microbiomes to those from other surrounding fauna and seawater using partial 16S rRNA gene amplicons.	root:Mixed
MGYS00002942	Biogeography of cyanobacterial consortia from the culture collection of microorganisms from extreme environments	Very little is known about how members of the phylum cyanobacteria affect and respond to changes in complex biological systems. To fill this knowledge-gap we selected 26 photosynthetic consortia, based on their collection site and growth condition, from a total of over 1,200 environmental samples available in the Culture Collection of Microorganisms from Extreme Environments (CCMEE) for 16S rRNA sequencing to identify common community members and potential keystone species. Results from this work will help to determine the nutritional and environmental requirements of microorganisms that can currently only be grown in co-culture and to define the molecular processes that facilitate carbon and nitrogen sequestration by these phototrophic consortia and the individual organisms that contribute to them.	root:Mixed
MGYS00002844	Marine Lakes Jellyfish and water Metagenome	In the present study, microbial communities of jellyfish and water inhabiting Marine Lakes ecosystems were investigated using barcoded pyrosequencing of 16S rRNA gene amplicons. FLX 454 titanium pyrosequencing study.	root:Mixed
MGYS00002839	Coral Reef Biotopes Metagenome	In the present study, microbial communities of sponges, Sediments and Seawater inhabiting coral reef ecosystems were investigated using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial and archaeal richness and composition of two sponge species, sediment and seawater inhabiting coral reef systems. FLX 454 titanium pyrosequencing study. Note that the sequences submitted are raw sequences prior to any analysis and thus contain short sequences, poor quality sequences and chimera. These will need to be filtered out using, e.g., using qiime scripts such as split_libraries and pick_otus with the usearch_ref argument, which will provide a chimera check and filter out poor quality sequences.	root:Mixed
MGYS00002776	16S rRNA gene Sequencing of Ircinia felix tissue	16S rRNA gene sequencing of tissue from the Caribbean sponge, Ircinia felix, and surrounding sediment and ambient water. The goals of this study were to assess the overall bacterial community changes between the three sample types as a correlation to nutrient processing by the sponges.	root:Mixed
MGYS00002446	Design and Evaluation of Illumina MiSeq compatible 18S rRNA Primers for Improved Characterization of Mixed Phototrophic Communities.	A systematic analysis of the most commonly amplified 18S rRNA hypervariable regions and the effect that PCR/sequencing bias has on community representation. The V4 and V8-V9 hypervariable regions were amplified for seven mock communities and for freshwater, marine, and wastewater samples to compare the sequenced community structure to theoretical communities and validate these results with environmental samples.	root:Mixed
MGYS00004633	16S rRNA gene metabarcoding reveals a potential metabolic role for intracellular bacteria in a major marine planktonic calcifier (Foraminifera).	We have investigated the possibility of bacterial symbiosis in Globigerina bulloides, a palaeoceanographically important planktonic foraminifera commonly used in investigations of climatically sensitive sub-polar and temperate water masses and wind driven upwelling regions of the worlds oceans. G. bulloides is unusual, since it lacks the protist algal symbionts often found in other spinose species and has an atypical geochemical shell signature. This is suggestive of a divergent ecology, making it a good candidate for investigating potential bacterial symbiosis as a contributory factor in shell calcification. Such ecological information is essential to fully evaluate the potential response of G. bulloides to ocean acidification and climate change.	root:Host-associated:Protists
MGYS00004695	Effect of sediment smothering on the sponge holobiont	Dredging can cause increased sedimentation in marine communities and smothering of sessile benthic organisms. In order to provide pressure:response values for sponges to sedimentation and tease apart the cause:effect pathways of dredging pressures, five heterotrophic and phototrophic species were repeatedly smothered by sediments every 4 days, and cleaned after 4, 16 and 30 days. This study shows that non-continuous sediment smothering for up to 30 days does not alter the health and composition of adult sponge holobionts as most species possess either active or passive self-cleaning strategies which allow them to continue with their feeding activity. However, although those smothering conditions seem tolerable by most species, it is expected that the combined effect of all three dredging-related pressures will increase the negative effects on sponges under realistic field conditions. These experimental results will assist regulators and environmental managers in reducing risks from dredging development although experimental research combining sedimentation, SSC and light attenuation is required before final thresholds can be derived for dredging impacts on sponges.	root:Host-associated:Porifera
MGYS00004694	Effect of suspended sediments on the sponge holobiont	Dredging can cause high suspended sediment concentrations (SSC) in the water column, posing risks to filter feeding organisms like sponges as sediment may clog their aquiferous systems and reduce feeding. In order to provide pressure:response values for sponges to SSC and tease apart the cause:effect pathways of dredging pressures, five heterotrophic and phototrophic species were experimentally exposed to a range of dredging-relevant SSC of up to 100 mg L-1, with light compensation across treatments to ensure that SSC was the primary physical parameter. This study shows that some sponge species exposed to high SSC (=23 mg L-1) for extended periods (28 d) have lower survival, increased necrosis, and reduced feeding ability with an associated depletion of energy reserves. In contrast, SSC of =10 mg L-1 causes few if any negative effects for most species and is thus suggested as a reasonable sub-lethal threshold for sponges. Microbial communities did not change significantly among SSC treatments, although nutritional shift from mixotrophy towards increased phototrophy was detected for some sponge species exposed to high SSC. However, it is expected that the combined effect of SSC with low light availability and sediment smothering will increase the negative effects on sponges.	root:Host-associated:Porifera
MGYS00004677	Deep Sea Sponge and Seawater Targeted Locus (Loci)	The microbiota of four individual deep water sponges, Lissodendoryx diversichela, Poecillastra compressa, Inflatella pellicula, and Stelletta normani, together with surrounding seawater were analysed by pyrosequencing of a region of the 16S rRNA gene common to Bacteria and Archaea. The microbial communities of L. diversichela, P. compressa and I. pellicula were typical of low microbial abundance (LMA) sponges while S. normani was found to have a community more typical of high microbial abundance (HMA) sponges. Analysis of the deep sea sponge microbiota revealed that the three LMA-like sponges shared a set of abundant OTUs that were distinct from those associated with sponges from shallow waters.	root:Environmental:Aquatic:Marine
MGYS00004048	Sponge Raw sequence reads	Describe the microbiome of Mediterranean sponges	root:Host-associated:Porifera
MGYS00003986	16S Miseq Illumina sequences from sponge associated with sponges in Vietnam	Analysis of microbial communities associated with sponges in Vietnam	root:Host-associated:Porifera
MGYS00003123	Microbial diversity associated with South African marine Latrunculid sponges	This study investigates the microbial communities associated with indigenous Latrunculid sponges found in South African coastal waters. The study aims to identify dominant bacteria associated with the Latrunculid sponges in order to assess the possible interactions between sponge hosts and their harboured symbionts. Latrunculid sponges are well known producers of secondary metabolites including discorhabdins, makaluvamines and tsitsikammamines which have anti-cancer, anti-microbial and anti-malarial activity. Associated microbial symbionts may aid in, or be responsible for the production of these secondary metabolites.	root:Host-associated:Porifera
MGYS00002938	Microbial Diversity in Antarctic Shelf Sponges	Investigation of the microbial diversity in Antarctic shelf sponges	root:Host-associated:Porifera
MGYS00002780	Microbiota composition and metabolomic profiles of the deep sea sponges Weberella bursa, Stryphnus fortis and Geodia barretti along a depth gradient	In this study we assessed prokaryotic community and metabolite profiles of the three deep sea sponges: W. bursa, S. fortis and G. barretti collected at the Davis Strait at depth range of 200 - 1400 m. Microbial composition was investigated using 16S rRNA gene amplicon sequencing by applying the Illumina MiSeq technology and metabolomic profiles were screened using UPLC-QTOF mass spectrometry. The overall aim of this study is to investigate to what extend depth influences microbial composition and metabolite profiles of the deep sea sponges.	root:Host-associated:Porifera
MGYS00002762	Xestospongia muta Raw sequence reads	The giant barrel sponge, Xestospongia muta represents a foundation and ecologically important species of Caribbean coral reefs. In April 2012 an outbreak of Sponge Orange Band (SOB) Disease occurred in Southeast Florida, USA. This study provides one of the most extensive profiles of healthy and SOB-associated microbial communities within Xestospongia muta to date with implications of a possible polymicrobial origin for SOB.	root:Host-associated:Porifera
MGYS00002651	Prokaryotic community analysis of the marine sponges Xestospongia muta and Agelas sventres along a depth gradient	In this study we investigated prokaryotic community of marine sponges Xestospongia muta and Agelas sventres along a depth gradient. We employed 16S rRNA gene amplicon sequencing from sponge''s tissue and their cultivable microbial fractions by using the Illumina MiSeq technology.	root:Host-associated:Porifera
MGYS00002547	Coral Reef Biotopes Metagenome_M	In the present study, microbial communities of sponges, Sediments and Seawater inhabiting coral reef ecosystems were investigated using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial and archaeal richness and composition of two sponge species, sediment and seawater inhabiting coral reef systems. FLX 454 titanium pyrosequencing study. Note that the sequences submitted are raw sequences prior to any analysis and thus contain short sequences, poor quality sequences and chimera. These will need to be filtered out using, e.g., using qiime scripts such as split_libraries and pick_otus with the usearch_ref argument, which will provide a chimera check and filter out poor quality sequences..	root:Host-associated:Porifera
MGYS00001398	Bacterial community diversity associated with apple replant diseases	To investigate the effects of soil disinfection treatments on the bacterial community composition and diversity adhering to the apple roots	root:Host-associated:Plants:Root
MGYS00003734	Potato rhizosphere Metagenome	The goal is to study the diversity of potato-associated bacteria in the Central Andean Highlands	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00001063	Root microbiome Targeted Locus (Loci)	Procaryotes are known to have a role in the establishment of ectomycorrhizal symbiosis. Our goal was to decribe the structure of fungal and bacterial communities associated to ectomycorrhizosphere/rhizosphere and the surrounding bulk soil of truffle-inoculated seedlings.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00001040	Mulberry surface soil Targeted Locus (Loci)	A survey of bacterial community in mulberry surface soil	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00001016	Soil sample	A field study was conducted to compare bacterial communities of rhizosheaths of wheat grown under wheat-cotton and wheat-rice rotation and to study the effects of PGPB inoculation.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00001015	Apple rhizosphere soil Metagenome	Pyrosequencing was used to charicterize the bacteria community change of apple rhizosphere under replant and new plant condition to reveal the mechanism of apple replant disease in Beijing.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00001012	Rhizosphere soil Metagenome	Healthy and bacterial wilted tomato plants rhizosphere soil	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00001000	Sugar beet rhizosphere microbiome Targeted Locus (Loci)	Study to reveal the diversity of bacteria in the rhizosphere of wild sugar beets in their natural habitat and of commercial sugar beet cultivars in natural and standard soil	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000999	Bamboo soil bacterial community with different elevation Metagenome	To understand what trend of bacterial structure and diversity in bamboo soils across elevations	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000996	Rhizosphere soil sample Targeted Locus (Loci)	Comparing microbial Communities in the Soil Rhizosphere of Six Plant Species in an Alpine Meadow on the Qinghai-Tibet Plateau	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000979	Water melon soil Targeted Locus (Loci)	Microbial community in water melon rhizosphere after grafting	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000976	Soils planted Panax notoginseng	To study on the role of microorganisms in soils to the replant disease of Panax notoginseng.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000949	Plant root microbiome	Due to the long durations spent inside by many humans, indoor air quality has become a growing concern. Biofiltration has emerged as a potential mechanism to clean the indoor air of harmful volatile organic compounds (VOCs), which are usually at higher concentrations indoors than outdoors. Root-associated microbes are thought to drive the functioning of plant-based biofilters, or biowalls, converting VOCs into biomass, energy, and carbon dioxide. But little is known about the root communities of such artificially grown plants, how or whether they differ from those grown in soil, and whether any changes in composition are driven by VOCs. In this study, we investigate how bacterial communities on biofilter plant roots change over time and in response to VOC exposure. Through analyses of 16S rRNA amplicon sequence libraries, we compare root communities from soil-grown plants versus those from two biowalls, while also comparing communities from roots exposed to clean- versus VOC-laden- air in a laboratory biofiltration system. Results show differences in bacterial communities between soil- versus biowall-grown plants, and between those from between clean air versus VOC exposed plant roots. Biowall-grown and VOC-exposed roots both harbored enriched levels of bacteria from the genus Hyphomicrobium. Given their known capacities to break down aromatic and halogenated compounds, we hypothesize these bacteria to be important VOC-degraders. While different strains of Hyphomicrobium proliferated in the two studied biowalls and our lab experiment, strains were shared across plant species suggesting that a wide range of ornamental houseplants harbor similar microbes of potential use in living biofilters.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000891	SEPTANTE Targeted Locus (Loci)	The consequences of a variable carbon bias on soil bacterial populations were investigated in artificial exudation system. An artificial exudation system was set up in which octopine was brought along with other carbon compounds at four different ratios. rrs-amplicon pyrosequencing analyses were performed to reveal the impact on the structure and diversity of bacterial community.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000883	Banana rhizosphere soil Targeted Locus (Loci)	16S rRNA amplicons of diseased and disease suppressive soil and soil after biological remediation.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000878	paddy soil Genome sequencing	Paddy soil Genome sequencing	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00002779	Rhizobiome of Northeastern Atlantic seagrasses	This project aimed at revealing the microbial diversity associated with the rhizosphere of the seagrasses Zostera marina, Z. noltii and Cymodocea nodosa, through the sequencing of 16S rRNA amplicons using Illumina Miseq-platform. The rhizobiomes of these seagrasses were compared within one sampling site, and between two different geographical locations  Portugal and France. Besides, we evaluated differences between the rhizobiomes and their surrounding environment (i.e., bulk sediments and seawater). This study improves the understanding of microbial processes in the rhizosphere of seagrasses, highlighting the importance of bacteria involved in the sulfur cycle for the fitness of the plants.	root:Host-associated:Plants:Rhizosphere
MGYS00001264	Soil Metagenome	A high-protein soybean cultivar was grown in three different fields that were continuously cropped for 1, 2, and 3 years. By analyzing the diversity of fungi in rhizosphere soil during the branching period of soybeans planted in these three fields, and comparing the diversity of fungi in rhizosphere soil during periods of high incidence of root rot disease, the dominant fungi responsible for soybean root rot disease could be identified.	root:Host-associated:Plants:Rhizosphere
MGYS00000967	willow rhizosphere Metagenome	Plants interact closely with microbes, which are partly responsible for plant growth, health and adaptation to stressful environments. Engineering the plant-associated microbiome could improve plants survival and performance in stressful environments such as contaminated soils. Here, willow cuttings were planted into highly petroleum-contaminated soils that had been gamma-irradiated and subjected to one of four treatments: inoculation with rhizosphere soil from a willow that grew well (LA) or sub-optimally (SM) in highly contaminated soils or with bulk soil in which the planted willow had died (DE) or no inoculation (CO). Samples were taken from the starting inoculum, at the beginning of the experiment (T0) and after 100 days of growth (TF). Short hypervariable regions of archaeal/bacterial 16S rRNA genes and the fungal ITS region were amplified from soil DNA extracts and sequenced on the Illumina MiSeq. Willow growth was monitored throughout the experiment, and plant biomass was measured at TF. CO willows were significantly smaller throughout the experiment, while DE willows were the largest at TF. Microbiomes of different treatments was divergent at T0, but for most samples, had converged on highly similar communities by TF. Willow biomass was more strongly linked to overall microbial community structure at T0 than to microbial community structure at TF, and the relative abundance of many genera at T0 was significantly correlated to final willow root and shoot biomass. Although microbial communities had mostly converged at TF, lasting differences in willow growth were observed, probably linked to differences in T0 microbial communities.	root:Host-associated:Plants:Rhizosphere
MGYS00000845	rhizosphere soil named MPt17+Pt2, MPt17, Pt2 and CK Metagenome	A 454 pyrosequencing analysis on the bacterial communities from four selected soils was presented. The results showed that the dominant bacterial communities of the soil samples were similar. A total of 11,911 OTUs with 80,772 valid reads were identified, which could be assigned into 29 different phyla, 147 families and 279 genera.	root:Host-associated:Plants:Rhizosphere
MGYS00000842	Monsoon bacterial diversity of pneumatophore-rhizosphere of Avicennia Marina in vellar estuarine Metagenome	Pneumatophore-rhizosphere soil of Avicennia Marina in vellar estuarine	root:Host-associated:Plants:Rhizosphere
MGYS00000841	Monsoon bacterial diversity of pneumatophore-rhizosphere of Avicennia Marina in vellar estuarine Metagenome	Pneumatophore-rhizosphere soil of Avicennia Marina in vellar estuarine	root:Host-associated:Plants:Rhizosphere
MGYS00000829	Wetland peat Targeted Locus (Loci)	Restoration of wetlands has a great potential to reverse land subsidence on peat islands previously drained for agriculture, thereby reducing risk of levee failure. In addition, the high primary production and slow decomposition rates found in restored wetlands may result in a net atmospheric CO2 sequestration. However, one major concern is the emission of CH4 that could potentially offset the carbon captured due to primary production. In wetland ecosystems, microorganisms play key roles in governing greenhouse gas flux. In this study, we collected belowground samples from a restored wetland largely vegetated with cattails and tules from a pilot-scale restoration project. We selected sites that exhibited gradients in physicochemical conditions, peat accretion rates and CH4 emission. From each site, we collected samples from the bulk peat, cattail rhizomes and tule rhizomes. Pyrosequencing of amplified V8 regions of 16S rRNA genes was used to generate microbial community profiles in order to to identify community patterns and indicator species that are associated with biogeochemistry and CH4 emission along the gradients.	root:Host-associated:Plants:Rhizosphere
MGYS00000826	Soil Metagenome	Mechanisms of microbes-mediated carbon and nitrogen cycles in the rhizosphere soil under long-term fertilization practices	root:Host-associated:Plants:Rhizosphere
MGYS00000817	Microbial diversity in rhizosphere soil	Thanks to next generation sequencing techniques such as amplicon pyrosequencing, microbial diversity can be studied to an unprecedented degree. Given the importance of soil and especially of the rhizosphere for plant growth and biogeochemical cycles, the aim of the study is to determine the microbial diversity present in rhizosphere soil.  Rhizosphere soil associated with Thymus zygis plants from the Sierra Nevada National Park in Southern Spain.	root:Host-associated:Plants:Rhizosphere
MGYS00000798	Apple rhizosphere soil Metagenome	Application of compost at different rates on apple rhizosphere soil was studied, and pyrosequencing was employed to characterize the bacterial community structure.	root:Host-associated:Plants:Rhizosphere
MGYS00000794	Bacterial community of rhizosphere soil in Longgang Longterm Fertilization Metagenome	Bacterial community of rhizosphere soil in 9 different fertilization treatments for 5 years was measured with 454-sequencing.	root:Host-associated:Plants:Rhizosphere
MGYS00000781	Rhizosphere bacterial community 16S sequencing from field grown wheat	We sequenced bacterial communities both loosely and tightly bound to wheat roots growing in the field. We studied changes in community compostition over different plant stages, soil types, genotypes and rotations. Plasticity in the rhizosphere microbiome offers promise for beneficially manipulating the soil ecology of intense cereal systems.	root:Host-associated:Plants:Rhizosphere
MGYS00000757	Sansui tobacco rhizosphere Metagenome	Bacterial community from tobacco rhizosphere soil in Sansui.  Tobacco rhizosphere soil were collected in 2011 at Sansui county.	root:Host-associated:Plants:Rhizosphere
MGYS00000696	Laguna Brava Targeted Locus (Loci)	To study the diversity of AM fungal associated to vegetation adapted to extreme environmental conditions in high Andean wetlands.  AMF from rhizospheric soil and alophyte plants.	root:Host-associated:Plants:Rhizosphere
MGYS00000695	Pampa ondulada Targeted Locus (Loci)	Impact of agronomic management of soil on arbuscular mycorrhizal fungal diversity.  Pampa ondulada soybean rhzosphere AMF.	root:Host-associated:Plants:Rhizosphere
MGYS00001794	wheat associated microbiome Raw sequence reads	This study is about testing an artificially elevated JA signalling on the wheat associated microbial community structure	root:Host-associated:Plants
MGYS00001676	Tomato phyllosphere Metagenome	Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato).  Targeted and whole metagenomes from different organs of the tomato plant.	root:Host-associated:Plants:Phylloplane
MGYS00000832	Phyllosphere bacterial community of Wolffia australiana Targeted Locus (Loci)	We aimed at analyzing the composition and structure of the phyllosphere bacterial communities of W. australiana and addressed two major questions: (1) what is the specialty of the bacterial community in the phyllosphere of floating macrophytes; (2) what controls the bacterial communities of the macrophyte phyllosphere in paddy soils.  16S rDNA V3 section of bacteria associated with phyllosphere of Wolffia australiana, water, and soil in paddy-soil ecosystem.	root:Host-associated:Plants
MGYS00002954	oyster metagenome Targeted loci environmental	We studied microbial communities related to Pacific oysters in Puget Sound estuarine of Washington State, USA.	root:Host-associated:Mollusca
MGYS00002074	Identification of bovine respiratory disease complex associated bacteria using a 16S rRNA gene amplicon sequencing assay	Bacteria, many of which are normal flora of the bovine upper respiratory tract, can cause and exacerbate virus or stess induced bovine respiratory disease complex (BRDC). The objective of this study was to develop a single universal assay, based on high throughput phylogenetic (16S ribosomal RNA (rRNA) gene) PCR amplicon sequencing, with potential to accurately identify and differentiate bacteria in post-mortem tissue samples harvested from fatal BRDC cases.	root:Host-associated:Mammals:Respiratory system:Pulmonary system
MGYS00002079	Bos taurus breed:Angus Hereford Targeted Locus (Loci)	Nasopharyngeal microbiota of feedlot cattle exposed to commingling and auction market stress.	root:Host-associated:Mammals:Respiratory system:Nasopharyngeal
MGYS00002078	Bos taurus Targeted Locus (Loci)	Monitoring the nasopharyngeal microbiota in feedlot cattle from entry to exit	root:Host-associated:Mammals:Respiratory system:Nasopharyngeal
MGYS00002077	Characterization of the nasopharyngeal microbiota in naturally occurring respiratory disease in feedlot cattle	Bovine respiratory disease (BRD) is a major cause of morbidity, mortality and economic loss in the US cattle industry. In view of the importance of this disease complex, and the need to reduce antimicrobial use in food producing animals, there is growing interest in developing novel strategies to enhance host immune defenses against respiratory pathogens. The cooperative interactions between microbes and their hosts have been recognized for years, and there is increasing evidence that mucosal bacterial populations act, not only as a reservoir of potential pathogens, but also in regulating local and systemic immune homeostasis through a complex cross talk with the epithelium, local immune system and mucosal neuronal pathways. In this study we used culture-independent techniques to characterize the nasopharyngeal microbiome of cattle during the initial processing phase in the commercial feedlot. In addition, we compared the dynamics of change in these microbial communities, between clinically healthy calves and those that develop BRD within the first month of entry in to the feedlot.	root:Host-associated:Mammals:Respiratory system:Nasopharyngeal
MGYS00002076	Characterization of nasopharyngeal microbiotas as the source of lung microbiotas in clinically healthy feedlot cattle	Efficient characterization of airway microbiota is expected to provide insights into the pathophysiology of respiratory diseases. No studies have examined the relationships between bacterial communities along the upper and lower respiratory tract in clinically healthy feedlot cattle using next generation sequencing. Therefore, our objective was to characterize the composition and structure of the nasopharyngeal microbiota as the source of lung microbiotas in clinically healthy feedlot cattle.	root:Host-associated:Mammals:Respiratory system:Nasopharyngeal
MGYS00002075	Respiratory microbiome in feedlot cattle Raw sequence reads	The primary objective of this study was to apply next generation techniques to characterize the composition and structure of the respiratory tract microbial communities in clinically healthy feedlot cattle.	root:Host-associated:Mammals:Respiratory system
MGYS00003431	Mesocricetus auratus Metagenome	Intestinal and biliary microbiome of the hamster (Syrian Golden Hamster) infected with the liver fluke, Opisthorchis viverrini.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00000562	Sheep rumen microbiome	Rumen metagenome and metatranscriptome sequencing from low and high methane producing sheep.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00003893	Metagonimus yokogawai infected mouse cecal microbiome	We performed a 16S rRNA amplicon analysis to investigate changes in the gut microbiome due to M. yokogawai infection in ICR mice using high-throughput sequencing technology.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00004556	The Caprine Abomasal Microbiome	Haemonchus contortus is one of the most injurious helminth parasite for small ruminants. In this study, we characterized the impact of H. contortus infection on the caprine abomasal microbiome.	root:Host-associated:Mammals:Digestive system
MGYS00003440	Gut microbiome in rats treated with [saline or helminths], [PBS or E. coli], and [PBS or LPS]	We need a description here.	root:Host-associated:Mammals:Digestive system
MGYS00004438	invertebrate gut metagenome Raw sequence reads	comparison of intestinal microbiota composition of sea cucumber in two habitats	root:Host-associated:Invertebrates:Echinodermata
MGYS00002767	Microbiome variation in mesophotic corals	Here, we provide the first detailed assessment of the prokaryotic community associated withmultiple scleractinian corals over a depth gradient to the lower mesophotic realm (15-85 m).	root:Host-associated:Invertebrates:Cnidaria:Coral
MGYS00002761	marine metagenome Raw sequence reads	Adaptation to reef habitats through selection on the coral animal and its associated microbiome	root:Host-associated:Invertebrates:Cnidaria:Coral
MGYS00001047	Microbiota of Dipteran gut, plant litter and cow dung	Soil dwelling Dipteran larvae of Dilophus febrilis were fed with either one of the food sources cow dung (Bos primigenius taurus), dwarf shrub litter (Vaccinium gaultheroides) and grass litter (Dactylis glomerata). Afterwards the whole gut content of each specimen as well as its feeding source were extracted and analysed using massive parallel sequencing . The aim was to evaluate whether the microbial community in the Dipteran gut is species-specific or diet-related.	root:Host-associated:Insecta:Digestive system
MGYS00005098	Isolation and Identification of the Follicular Microbiome: Implications for Acne Research	In this study, we compare the both sequencing methods (16S vs. WGS) and collection methods (pore strip, glue strip, swab) to develop recommendations for collecting microbiome information for studies of acne vulgaris.	root:Host-associated:Human:Skin
MGYS00005037	Human Skin Microbiome Metagenome	Human Skin Microbiome	root:Host-associated:Human:Skin
MGYS00000605	Skin microbiome in human volunteers inoculated with H. ducreyi Raw sequence reads	The aim of this project was to investigate the interaction of the skin microbiome and Haemophilus ducreyi during experimental infection of human volunteers. We hypothesized that the skin microbiome influences susceptibility to H. ducreyi infection and that infection with H. ducreyi causes changes in the skin microbiome. To address these hypotheses, we collected skin swab samples prior to inoculation with H. ducreyi, at Days 1, 2 and 5 post-inoculation, at clinical endpoint, and at the test of cure visit. Samples from four dose-matched pairs of volunteers that either resolved the infection or formed pustules were subjected to barcoded amplification and pyrosequencing of the V1-V3 region of bacterial 16S rRNA genes. We compared alpha and beta diversity measurements of the microbiomes of resolvers and pustule formers, and determined signature bacteria that were associated with infection resolution or pustule formation.	root:Host-associated:Human:Skin
MGYS00001299	Oral tongue plaque Metagenome	To probe the microbial basis of halitosis in natural human populations, we em-ployed a longitudinal study design to compare the tongue microbiota associated with halitosis in 29 Chinese adults who underwent a consecutive three-day evaluation for the amount of volatile sulfur compounds (VSC) excreted orally. Three levels of the disease state (healthy, halitosis and severe halitosis) were defined based on the Halimeter value. Community structure of the tongue plaques was more sensitive to changes of disease state than to inter-personal variations or difference in sampling time. Within each subject, the structure of microbiota was relatively stable, while their variations were correlated with the change in Halimeter value. Severe halitosis micro-biota were the most conserved in community structure, whereas the healthy ones were relatively varied. Halitosis-associated bacteria were identified, among which the rela-tive abundance of Leptotrichia and Prevotella was positively correlated with halitosis severity whereas Haemophilus demonstrated a negative relationship with disease. Our study provided one of the first organismal profiles of disease-associated tongue mi-crobiota and revealed microbes that can potentially be used to evaluate halitosis state and progress.	root:Host-associated:Human:Digestive system:Oral:tongue dorsum
MGYS00002262	Human oral microbiome associated with OC regiment	Quantitative assessment of anti-gingivitis methods based on the microbiota holds great potential yet remains challenging. Although anti-gingivitis efficacy of different oral care products has been studied from clinical outcomes, we know little about their impacts on oral microbiota and its metabolic capabilities. Here, ninety one adults underwent controlled transitions from naturally occurring gingivitis, to healthy gingivae using different anti-gingivitis products. Oral care product regimen, which contains stannous chloride in toothpaste and cetylpyridinium chloride in mouthwash, showed significant better anti-plaque and anti-gingivitis efficacy than placebo toothpaste in twenty seven days parallel study. Microbial diversity for regimen group was significantly decreased from Baseline Day 0 to Day 27. Meanwhile, plaque microbiota structure exhibited a continuous transition along the first principal component, which correlated with changes of Mazza Gingival Index and Plaque Index. Thirteen oral bacteria tend to be affected by two antibacterial activess. Metabonomic analysis of saliva indicates reduced anaerobic fermentation and tissue degradation of oral microbiota. Interestingly, microbial parameters demonstrate the ability to predict treatment effects of different product and regression of gingivitis symptom. Thus, our study provided novel insight into impacts of oral care products on microbial clades and metabolic pathways of gingivitis.	root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
MGYS00002159	Subgingival microbiome of from patients suffering from periodontitis and liver cirrhosis		root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
MGYS00003719	microbial community diversities of subgingival plaque of 9 subjects	The microbial community diversities of subgingival plaque from 3 health subjects, 3 CP patients, 3 AgP patients.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00002395	Hemoparo	Chronic periodontitis subgingival samples in patients with HFE C282Y hemochromatosis.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00002394	Subgingival plaque and peri-implant biofilm	First permanent molars frequently present severe conditions in periodontitis cases. Implant restoration is an accepted means of replacing teeth lost due to periodontitis. The present investigation focused on the microbiome analysis of 10 healthy dental implants and 10 chronic periodontitis patients using 454-prosequencing of 16S rDNA. Subgingival plaque and peri-implant biofilm were sampled at the first permanent molar site before and after implant restoration.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00002274	human oral metagenome Metagenome	In five ten-year-old children, biofilm was collected from the upper first premolars and first molars using sterilized, UV-treated paper points inserted into the subgingival sulcus at eight sites.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00002272	healthy and stomatitis denture microbiome		root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00002269	Subgingival microbiome Metagenome	Subgingival microbiome in relation to clinical outcomes after the use of antibiotics in the treatment of periodontitis.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00002257	Dental Plaque 16s rRNA v6 amplicons	Characterization of the Dental Plaques of axial spondyloarthiritis patients	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00002229	Human oral subgingival communities	16S sequencing of subgingival microbiota from subjects with chronic periodontitis and healthy subjects.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00002224	human oral metagenome Raw sequence reads	The present study aims to evaluate the composition of the subgingival plaque community associated with periodontal health and disease using high throughput sequencing approaches	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00002173	Subgingival samples from Healthy / Periodontitis subjects Targeted Locus (Loci)	Subgingival samples from Healthy / Periodontitis subjects	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00001300	Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing- Supragingival plaque	Background and Objective: The advent of next-generation sequencing has significantly facilitated characterization of the oral microbiome. Despite great efforts in streamlining the processes of sequencing and data curation, upstream steps required for amplicon library generation could still influence 16S rRNA gene-based microbial profiles. Among upstream processes, DNA extraction is a critical step that could represent a great source of bias. Accounting for bias introduced by extraction procedures is important when comparing studies that use different methods. Identifying the method that best portrays communities is also desirable. Accordingly, the aim of this study was to evaluate bias introduced by different DNA extraction procedures on oral microbiome profiles.  Design: Four DNA extraction methods were tested on mock communities consisting of seven representative oral bacteria. Additionally, supragingival plaque samples were collected from 7 individuals and divided equally to test two commonly used DNA extraction procedures. Amplicon libraries of the 16S rRNA gene were generated and sequenced via 454-pyrosequencing.  Results: Evaluation of mock communities revealed that DNA yield and bacterial species representation varied with DNA extraction method. Despite producing the lowest yield of DNA, a method that included bead beating was the only protocol able to detect all seven species in the mock community. Comparison of the performance of two commonly used methods (crude lysis and a chemical/enzymatic lysis + column-based DNA isolation) on plaque samples showed no effect of extraction protocols on taxa prevalence but global community structure and relative abundance of individual taxa were affected. At the phylum level, the latter method improved the recovery of Actinobacteria, Bacteroidetes and Spirochaetes over crude lysis.  Conclusion: DNA extraction distorts microbial profiles in simulated and clinical oral samples, reinforcing the importance of careful selection of a DNA extraction protocol to improve species recovery and facilitate data comparison across oral microbiology studies.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00002362	Combined analysis of the salivary microbiome and host defence peptides predicts dental disease	Understanding the triad of host response, microbiome and disease status is potentially informative for disease prediction, prevention, early intervention and treatment. Using longitudinal assessment of saliva and disease status, we demonstrated that partial least squares modelling of microbial, immunological and clinical measures, grouped children according to future dental disease status. Saliva was collected and dental health assessed in 33 children aged 4 years, and again 1-year later. The composition of the salivary microbiome was assessed and host defense peptides in saliva were quantified. Principle component analysis of the salivary microbiome indicated that children clustered by age and not disease status. Similarly, changes in salivary host defense peptides occurred with age and not in response to, or preceding dental caries. Partial least squares modelling of microbial, immunological and clinical baseline measures clustered children according to future dental disease status. These data demonstrate that isolated evaluation of the salivary microbiome or host response failed to predict dental disease. In contrast, combined assessment of both host response together with the microbiome revealed clusters of health and disease. This type of approach is potentially relevant to myriad diseases that are modified by hostmicrobiome interactions.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002361	Exercise frequency is associated with the oral microbiota of student athletes and non-athletes	We investigated the oral microbiota from human saliva samples of undergraduate student athletes and non-athletes, by sequencing 16S rDNA using high-throughput next-generation Illumina sequencing.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002277	Oral microbiome of young adults	Oral microbiota associated with recurrent aphthous stomatitis in young adults	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002260	Human saliva Targeted Locus (Loci)	This study aimed at investigating the salivary microbiota of fourteen non progressor (NP) and fourteen progressor (P) patients with immunoglobulin A nephropathy (IgAN).	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002259	Human saliva microbiota Targeted Locus (Loci)	African celiac children''s saliva as affected by gluten-free diet	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002256	Omnivorous, vegetarian and vegan saliva Targeted Locus (Loci)	Omnivorous, vegetarian and vegan saliva microbiota	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002246	Transplantation-associated long-term immunosuppression promotes oral colonization by potentially opportunistic pathogens without impacting other members of the salivary bacteriome	Solid-organ transplant recipients rely on pharmacological immunosuppression to prevent allograft rejection. The effect of such chronic immunosuppression on the microflora at mucosal surfaces is not known. We evaluated the salivary bacterial microbiome of 20 transplant recipients and 19 non-immunosuppressed controls via 454-pyrosequencing of 16S rRNA gene amplicons. Alpha-diversity and global community structure did not differ between transplant and control subjects. However, principal coordinate analysis showed differences in community membership. Taxa more prevalent in transplant subjects included operational taxonomic units (OTUs) of potentially opportunistic Gammaproteobacteria such as Klebsiella pneumoniae, Pseudomonas fluorescens, Acinetobacter sp., Vibrio spp., Enterobacteriaceae sp. and the genera Acinetobacter and Klebsiella. Transplant subjects had increased proportions of Pseudomonas aeruginosa, Acinetobacter sp., Enterobacteriaceae sp. and Enterococcus faecalis, among other OTUs, while increased genera included Klebsiella, Acinetobacter, Staphylococcus and Enterococcus. Furthermore, in transplant subjects, the dose of the immunosuppressant prednisone positively correlated with bacterial richness, while prednisone and mycophenolate mofetil doses positively correlated with the prevalence and proportions of transplant-associated taxa. Correlation network analysis of OTU relative abundance revealed a cluster containing potentially opportunistic pathogens as transplant-associated. This cluster positively correlated with serum levels of C-reactive protein, suggesting a link between the resident flora at mucosal compartments and systemic inflammation. Network connectivity analysis revealed opportunistic pathogens as highly connected to each other and to common oral commensals, pointing to bacterial interactions that may influence colonization. This work demonstrates that immunosuppression aimed at limiting T-cell-mediated responses creates a more permissive oral environment for potentially opportunistic pathogens without affecting other members of the salivary bacteriome.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002231	Saliva in oral cavity Targeted Locus (Loci)	to study the microbe in oral cavity of patients with dental decay	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002230	Human oral saliva Metagenome	Microbial community survey of human saliva samples with and without oral lichen plauns	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002221	microbial diversity on human oral cavity	To study the microbial diversity in saliva of oral cavity of human	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002209	Identification of salivary microbiota associated with oral malodor using 16S pyrosequencing	Both hydrogen sulfide (H2S) and methyl mercaptan (CH3SH) are frequently detected in large amounts in malodorous mouth air. We investigated the bacterial composition of saliva of 30 subjects with severe oral malodor exhibiting extreme CH3SH/H2S ratios (high H2S but low CH3SH concentrations, n = 14; high CH3SH but low H2S concentrations, n = 16) and 13 subjects without malodor, using barcoded pyrosequencing analysis of the 16S rRNA gene. Phylogenetic community analysis with the UniFrac distance metric revealed a distinct bacterial community structure in each malodor group. The H2S group showed higher proportions of the genera Neisseria, Fusobacterium, Porphyromonas and SR1 than the other two groups, whereas the CH3SH group had higher proportions of the genera Prevotella, Veillonella, Atopobium, Megasphaera, and Selenomonas. Our results suggested that distinct bacterial populations in the oral microbiota are involved in production of high levels of H2S and CH3SH in the oral cavity.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002186	Human Saliva Microbiome	16S rRNA sequencing of the saliva microbiome of healthy human adult individuals	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002261	Teeth bacterium Metagenome	To examine using 16S rDNA sequencing normal and pathogenic periodontal microflora.	root:Host-associated:Human:Digestive system:Oral:Periodontal pockets
MGYS00002234	UW - Children''s Health Cohort, Adult Participant''s Buccal Oral Microbiomes, 16S rDNA V5V6 PCR Sequences	Thinning ((T) Summer June 2005) and Nonspray ((N) Winter January 2006) Farmworker Buccal Oral 16S rDNA V5V6 PCR Microbiome raw sequence reads from the University of Washington''s Children''s Health Farmworker Cohort. Study goals were to characterize the oral microbiome of Washington State''s Yakima Valley Hispanic Farmworkers to assess human oral bacterial census diversity within a cohort with agricultural environmental bacterial exposures including farming, plant, animal and rural bacterial sources.	root:Host-associated:Human:Digestive system:Oral:buccal mucosa
MGYS00002219	human oral  metagenome Raw sequence reads	human oral surface mucosa metagenome Raw sequence reads	root:Host-associated:Human:Digestive system:Oral:buccal mucosa
MGYS00002276	molecular charactarization of endodontic infection in humans	Illumina Miseq platform sequencing can be used to explore person to person and temporal variation in oral microbiome composition of endodontic infection.	root:Host-associated:Human:Digestive system:Oral
MGYS00002273	human oral metagenome Raw sequence reads	create a new oral biofilm model where native oral biofilm is grown in vivo and then transferred to a biofilm reactor system.	root:Host-associated:Human:Digestive system:Oral
MGYS00002270	plaque, saliva, tongue coating metagenome	To exploring the oral microflora of preschool children	root:Host-associated:Human:Digestive system:Oral
MGYS00002268	Human-associated samples Metagenome	Using saliva (PK) and plaque (TK) samples of normal subjects as controls, we undertook a large-scale molecular analyses of 16S rDNA sequences to better characterize four crucial features of disease-associated oral microbiota in primary dentition: 1) the structure and composition of microbial communities from both saliva (PQ) and plaque (TQ) in patients with caries; 2) the structure and composition of microbial communities from both saliva (PS) and plaque (PQ) in patients with pigment; 3) the structure and composition of microbial communities from both saliva (PSQ) and plaque (TSQ) in patients with the mixture of caries and pigment; and 4) bacterial co-infection patterns linked with those three disease types.	root:Host-associated:Human:Digestive system:Oral
MGYS00002267	Human Oral Swabs Raw sequence reads	Human Oral Microbiome Samples	root:Host-associated:Human:Digestive system:Oral
MGYS00002266	Development and pyrosequencing analysis of an in-vitro oral biofilm model	The aim of this study was to develop an in vitro oral biofilm model using the Calgary Biofilm Device. The composition of the biofilms was determined by pyrosequencing of 16S rRNA genes.	root:Host-associated:Human:Digestive system:Oral
MGYS00002265	Microcosm Targeted Locus (Loci)	Microbial diversity based on 16S rDNA	root:Host-associated:Human:Digestive system:Oral
MGYS00002263	Saliva of human Targeted Locus (Loci)	Oral microbiology study	root:Host-associated:Human:Digestive system:Oral
MGYS00002258	Human current and never smokers	The goals of the study were to examine the role played by smoking in creating at-risk-for-harm oral microbial communities	root:Host-associated:Human:Digestive system:Oral
MGYS00002249	Human oral metagenome	Microbial diversity in dental caries and plaque	root:Host-associated:Human:Digestive system:Oral
MGYS00002248	Oral microbiome of leukemia patients	Oral microbial diversity of acute lymphoblastic leukemia patients was investigated and compared with that of healthy control subjects.  Supragingival plaque samples from acute lymphoblastic leukemia patients and healthy control subjects.	root:Host-associated:Human:Digestive system:Oral
MGYS00002237	Species within oral squamous cell carcinoma and control tissues -  Metagenome	Species within oral squamous cell carcinoma and control tissues - Metagenome	root:Host-associated:Human:Digestive system:Oral
MGYS00002236	Oral Bacterial Metagenome - Young Healthy Arabs	Bacterial community of oral cavity in young healthy Arabs	root:Host-associated:Human:Digestive system:Oral
MGYS00002233	Microbiome of Oral Leukoplakia	16s profiling of Oral Leukoplakia using V1V2 amplification and sequencing on MiSeq	root:Host-associated:Human:Digestive system:Oral
MGYS00002232	human oral metagenome	We use metagenomic analyses to investigate the complex relationship between the oral microbiome and caries in preschool children. A total of 41 preschoolers, aged 3-5 years were recruited. Saliva samples were collected, followed by DNA extraction, Illumina high-throughput sequencing and metagenomics analyses of the oral microbial communities.	root:Host-associated:Human:Digestive system:Oral
MGYS00002228	oral metagenome Metagenome	Our purposes were to utilize culture-independent molecular techniques to extend our knowledge on the breadth of bacterial diversity in the healthy human oral cavity in Egyptian individuals.	root:Host-associated:Human:Digestive system:Oral
MGYS00002227	Oral cancer bacteriome - preliminary study Metagenome	Bacterial species present within oral cancer tissue	root:Host-associated:Human:Digestive system:Oral
MGYS00002226	The human oral microbiota and interleukin 8 levels	The present study describes a 16S rRNA gene-targeted sequencing analysis in a cohort of healthy human partecipants. Nutritional habits and dental hygiene are compared with the oral microbial communities and with interleukin 8 levels in the oral cavity.	root:Host-associated:Human:Digestive system:Oral
MGYS00002225	Oral microbiome Raw sequence reads	Comparison of bacterial community diversity in human plaque and saliva samples using four different DNA extraction methods.	root:Host-associated:Human:Digestive system:Oral
MGYS00002222	human oral metagenome Metagenome	The study aims to characterize oral microbiome in HIV infection and periodontal disease. Sequencing data includes 16s v3-4 amplicon for dental plaque, cheek, and saliva samples.	root:Host-associated:Human:Digestive system:Oral
MGYS00002220	Alcohol and tobacco consumption affects bacterial richness in oral cavity biofilms	V1 16S rDNA sequences derived from human oral swab samples.	root:Host-associated:Human:Digestive system:Oral
MGYS00002218	Human oral microbiome	Human oral microbiome of non diabetic and diabetic subjects	root:Host-associated:Human:Digestive system:Oral
MGYS00002217	Oral Microbiome Metagenome	Oral Microbiome Characterization	root:Host-associated:Human:Digestive system:Oral
MGYS00002187	Metagenomics of the Microbiome in Oral Health and Disease	The development of dental caries in children provides a disease model that is well suited to a metagenomic investigation since the timeframe of caries development can be monitored within a defined study period during which longitudinal studies can be conducted. Dental caries has a well-established link to discrete, but only partially characterized changes in the dental plaque microbiome. Our study endeavors to define the relative abundance of many species comprising the dental plaque microbiome in twin pairs discordant for dental caries in association and longitudinal studies. The study power afforded by the use of discordant twin pairs for dental caries is substantially greater than similar studies using unrelated individuals. Next, we will compare the caries-free and caries-active microbiomes by deep metagenomic sequencing to identify differentially abundant genes and metabolic pathways. Lastly, we will determine the functional relevance of differentially abundant species, strains and genes by conducting targeted meta-transcriptomic studies. The statistical significance of all of the datasets will be determined which will allow for the widespread identification of species, strains, genes and transcripts associated with dental caries and dental health. These approaches are likely to enhance our understanding of dental caries onset and development and may enable in the future the development of novel treatment strategies.	root:Host-associated:Human:Digestive system:Oral
MGYS00002176	Microbiota between subgingival plaque and gingival tissue in periodontitis	Comparison of microbiota between subgingival plaque and tissue in periodontitis patients	root:Host-associated:Human:Digestive system:Oral
MGYS00002174	Human oral microbiota in periodontitis and health	We investigated the oral microbiota in saliva, supragingival and subgingival plaque of Chinese adults with and without periodontits to obtain a comprehensive view of the oral bacterial communities and identify periodontitis associated bacteria	root:Host-associated:Human:Digestive system:Oral
MGYS00002172	Oral active microbiota of dental caries	Identifying the microbial species in caries lesions is instrumental to determine the etiology of dental caries. However, a significant proportion of bacteria in carious lesions have not been cultured, and the use of molecular methods has been limited to DNA-based approaches, which detect both active and inactive or dead microorganisms. To identify the RNA-based, metabolically active bacterial composition of caries lesions at different stages of disease progression in order to provide a list of potential etiological agents of tooth decay. Non-cavitated enamel caries lesions (n=15) and dentin caries lesions samples (n=12) were collected from 13 individuals. RNA was extracted and cDNA constructed, which was used to amplify the 16S rRNA gene. The resulting 780 bp PCR products were pyrosequenced using Titanium-plus chemistry and the sequences obtained were used to determine the bacterial composition.	root:Host-associated:Human:Digestive system:Oral
MGYS00002171	Predictive modeling of early childhood caries via spatial-temporal variations of oral microbiota (Validataion study)	The strong correlation between bacterial communities and main factors (e.g., time and disease state) both between subjects and within subjects within a given niche thus suggested that oral microbiota could potentially model ECC onset. To test this hypothesis, the 34-children study cohort sampled two times during one year (T1, T3) were used as a train set for model construction, and an additional 24 child subjects were recruited and then each sampled at two time points (T3 and T4) for model validation: 14 patients including 7 experiencing caries-onset (HC group) and 7 experiencing caries- exacerbation (CC group) and ten healthy-steady controls (HH group).	root:Host-associated:Human:Digestive system:Oral
MGYS00002170	Predictive modeling of early childhood caries via spatial-temporal variations of oral microbiota	Principles for exploiting the spatial and temporal variations of microbiota for modeling chronic infections are not well established. Early Childhood Caries (ECC) is the most common disease in children and is irreversible once started; thus, its preventive intervention is crucial but usually difficult. Here we simultaneously tracked the development of microbiota at two distinct oral niches (plaque and saliva) for 34 four-year-old preschoolers over one year. During the tracked period, 10 children stayed free of caries (HHH group), 14 entered from health into cariogenesis (HCC group and HHC group), while the remaining 10 experienced caries exacerbation (CCC group).	root:Host-associated:Human:Digestive system:Oral
MGYS00002165	Liyan_caries_2011	37 samples of human oral metagenome related to Caries	root:Host-associated:Human:Digestive system:Oral
MGYS00002154	Casey periodontitis 2016	This studyexamined the saliva and subgingival microbiota of subjects with chronic periodontitis before andafter scaling and root planing and subjects without disease	root:Host-associated:Human:Digestive system:Oral
MGYS00002149	Carious dentine Genome sequencing	16S rRNA gene sequences from carious dentine	root:Host-associated:Human:Digestive system:Oral
MGYS00002148	Bacterial community development in experimental gingivitis	Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp) to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort.	root:Host-associated:Human:Digestive system:Oral
MGYS00002147	P&G gingivitis Targeted Locus	Gingivitis is the most common gum infection, yet its etiology remains elusive. We designed a retrogression-progression model (RPM) to simulate the development and reoccurrence of gingivitis. Fifty adults underwent a controlled transition from naturally occurring gingivitis (NG) to healthy gingivae (Baseline), then back to experimental gingivitis (EG). Within-subject temporal dynamics in taxonomic structure (for the 150 plaque microbiota samples) and functional profiles (for 18 of them) were observed via 16S rRNA gene and shotgun metagenomic sequencing respectively.  16S barcoded pyrosequencing for 273 oral plaque samples.	root:Host-associated:Human:Digestive system:Oral
MGYS00001302	Dental Calculus Metagenome (archaeological)	The purpose of this study was to investigate oral microbiome, dietary, and host DNA in archaeological human dental calculus (mineralized dental plaque), dentine, and bone using shotgun metagenomics and targeted 16S rRNA deep sequencing approaches. The samples in this study were obtained from four skeletons (G12, B17, B61, and B78) from the medieval site of Dalheim, Germany (ca. AD 950-1200). The skeletons exhibited osteological evidence of periodontal disease. A total of nine indexed Illumina shotgun metagenomic libraries were prepared from B61 and G12 dental calculus using different extraction and decontamination protocols. The nine indexed libraries were pooled and sequenced on a single Illumina HiSeq 2000 lane. A total of 32 indexed 454 targeted 16S rRNA libraries (V3, V5, and V6 regions) were prepared from paired dental calculus and dentine samples from G12, B17, B61, and B78, as well as from carious dentine and abscessed bone from B17. The 32 indexed libraries were pooled and sequenced on a 454 GS Junior. The genetic data associated with this project (including contig assemblies) are also available at MG-RAST in Project 365: http://metagenomics.anl.gov/linkin.cgi?project=365. Shotgun proteomic data associated with this project have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org/) via the PRIDE partner repository with the dataset identifier PXD000412 and DOI 10.6019/PXD000412.	root:Host-associated:Human:Digestive system:Oral
MGYS00001301	Supragingival plaque Raw sequence reads	Oral Microbiota	root:Host-associated:Human:Digestive system:Oral
MGYS00001174	Oral Microbiome	Microbiome associated with periodontal health and disease	root:Host-associated:Human:Digestive system:Oral
MGYS00005107	NGS approaches to metagenomics of gut microbiome	We compare the performance of 16S rRNA amplicon sequencing and shotgun metagenomics to perform taxonomic analysis of gut microbiome	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003894	feces metagenome	The 89 fresh feces samples (including 47 modified Kato-Katz thick smear-positive volunteers and 42 healthy controls from five rural communities) were collected in duplicate, with one for microscopic examination, and another one immediately stored at -80? until DNA extraction. All of the subjects were found no other parasite eggs (such as horkworms, roundworm, whipworm, pinworm, Taenia) by microscope.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003733	Human gut metagenome and metatranscriptome raw sequence reads.	We conducted metagenomic and metatranscriptomic sequencing of the human gut microbiome among 308 participants enrolled in a subcohort of men nested within the Health Professionals Follow-up Study. Using a previously validated self-sampling stool collection method (PMID24843156), participants provided up to four stool samples  one set of samples collected approximately 48 hours apart followed by a second set approximately 6 months later. DNA extracted from 929 stool samples and RNA extracted from 378 stool samples was reverse-transcribed to cDNA and sequenced using the Illumina HiSeq platform. Raw data were filtered to remove low quality and human reads. Metagenomic and metatranscriptomic read data were then profiled for functional and taxonomic composition using the HUMAnN2 and MetaPhlAn2 platforms respectively.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003475	Microbiome and Worm Infection	A study of the bacterial community of worm infected human stool via MetaGenomic Shotgun (MGS) data and 16s assembly data analysis	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003441	human stool bacteria 16s rDNA v4 region sequencing	bacterial alterions in C.difficile infection and alerations after fecal microbiota transplantation	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003191	Impact of experimental Necator americanus infection on human gut microbiota		root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002177	Association between oral and gut microbiota in Periodontal Disease	Is it possible that the relationship between periodontitis and these diseases are indirectly linked to disturbances on the intestinal microbiome?	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001647	The prebiotic fructooligosaccharide modulates metabolic dynamics and IgA production in the human gut ecosystem	Fructooligosaccharide (FOS), a prebiotic well known for its health-promoting properties, can improve the human gut ecosystem most likely through changes in its microbial composition. However, the detailed mechanism(s) of action of FOS in the modulation of the gut ecosystem remains obscure. Traditional methods of profiling microbes and metabolites could barely show any significant features due to the existence of large interindividual differences, but our novel microbe-metabolite correlation approach, combined with fecal IgA measurements, has revealed that the induction of mucosal IgA by FOS supplementation correlated with the presence of specific bacteria. Furthermore, the metabolic dynamics of butyrate, L-phenylalanine, L-lysine and tyramine were positively correlated with the dynamics of these bacteria and IgA production, whereas p-cresol was negatively correlated. Taken together, our focused intraindividual analysis with omics approaches is a powerful strategy for uncovering the gut molecular network and could provide a new vista for understanding the human gut ecosystem.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001541	Fecal microbiota of toddlers Metagenome	Fecal samples attained from 18-27 month old toddlers were pyrosequenced to ascertain the effect of maternal obesity, temperament, and other variables upon the fecal microbiota.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001258	Targeted Gene amplicons raw sequence reads	Sequencing of targeted genes like frc, but and buk genes from the microbial origin. Amplicons generated from gDNA from stool samples.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001257	Homo sapiens fecal microbiome transplant	The objective of the study was to investigate the efficacy of fresh, frozen or lyophilized fecal microbiota transplantation (FMT) via colonoscopy in patients with recurrent C. difficile associated diarrhea (RCDAD). After a course of oral vancomycin we performed FMT in 36 patients with =3 bouts of RCDAD. FMT products from thoroughly screened healthy donors after filtering stools twice were given as single (non-pooled) product either as fresh, frozen (-80C) or lyophilized. Patients submitted fresh stools pre- and on 7, 14 and 30 days post-FMT. Bacterial DNA was extracted and the V4 region of the 16S rRNA gene was amplified by PCR and amplicons were sequenced on the MiSeq (Illumina) platform. The unique aspects of this study are the comparative efficacy in different patients with recurrent CDI of FMT using the same donor providing either fresh or frozen product, or the successful use of lyophilized FMT products.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001250	Metagenome from fecal samples collect from healty human subject during probiotic intervention trial		root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001249	16s-based microbiome metagenome	Microbiome Analysis of IBS Patients	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001220	Human gut microbiota from the ALADDIN study	Characterization of mothers and infants microbiota	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001213	Human Feces Samples Metagenome	This study investigates the transfer of viral populations during human fecal microbiota transplants.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001212	A Longitudinal Study of Pediatric Subjects with Newly Diagnosed Inflammatory Bowel Disease		root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001210	Raw sequence reads of human sleep apnea patients gut microbiome	Gut microbiome of patients with sleep apnea	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001194	Alterations of the human gut microbiome in multiple sclerosis	The gut microbiome plays an important role in normal immune function and has been implicated in several autoimmune disorders. Here we use high-throughput 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=61) and healthy controls (n=43). Alterations in the gut microbiome in MS include increases in the genera Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signaling and NF-kB signaling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of the genera Prevotella and Sutterella, and decreased Sarcina, compared to untreated patients. MS patients of a second cohort show elevated breath methane compared to controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001190	Comparison of the fecal microbiota during variable collection and storage methods	Sample collection from in-patients can be challenging and potentially impacted by collection method variability. We used 16S rRNA-based sequencing to compare the microbiota profiles of variably stored and collected samples. Stool from three different patients were evaluated at different freezing and handling conditions. Additionally, rectal swabs were compared to a stool sample, collected from eight different patients over the course of 24 hours. Storage conditions did not significantly impact the microbial community, and only minor differences were observed between rectal swabs and stool. We conclude that fecal microbial communities did not change substantially after various transport and storage conditions. Rectal swabs are a suitable alternative for assessing the microbiota when fresh stool is not easily obtained.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001071	"16S rRNA profiling of ""Allergy"" and ""Healthy"" human faecal samples"		root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00004399	Shallow coastal lagoon Metagenome	In the present study, Sediment bacterial communities in monospecific stands of four habitats (mudflats and mono-specific plots of the seagrass Zostera noltei and the saltmarsh plants Juncus maritimus and Spartina maritima) were investigated.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00001248	Human gut environment Targeted loci environmental	Here we associate microbial community membership with distinct phenotypes of colorectal lesion. By performing 16S rRNA gene sequencing on mucosal biopies obtained from colorectal cancer-free patients, patients with adenomatous polyps, and patients with adenocarcinomas, we characterized the taxonomic configurations of microbial community to examine how disease progression is associated with changes in microbial community types.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00002301	Human gut metagenome and metatranscriptome in the inflammatory bowel disease (iHMP/HMP2)	We examined the dynamics of microbiome functionality in Inflammatory bowel disease (IBD) by profiling metagenomic and metatranscriptomic sequencing of the human gut microbiome among 100 individuals sampled over a one year period. Here, we present the first results based on the functional analysis of 78 paired metagenomes/metatranscriptomes and 222 additional metagenomes.	root:Host-associated:Human:Digestive system:Intestine
MGYS00003908	Children Gut Microbiota 16S	Study aimed to assess the effects of helminths and protozoa parasites in the bacterial gut microbiota of children.	root:Host-associated:Human:Digestive system
MGYS00003180	Changes in duodenal tissue-associated microbiota following hookworm infection and consecutive gluten challenges in humans with coeliac disease	A reduced diversity of the commensal microbiota is associated with the development of several inflammatory diseases. Recent reports in humans and animal models have demonstrated the beneficial therapeutic effects of infections by parasitic worms (helminths) in some inflammatory disorders, such as inflammatory bowel disease (IBD) and coeliac disease (CeD). Interestingly, these studies have described how helminths may alter the intestinal microbiota, potentially representing a mechanism by which they regulate inflammation. However, for practical reasons, these reports have primarily analysed the fecal microbiota. In the present investigation, we have assessed, for the first time, the changes in the microbiota at the site of infection by a parasitic helminth (hookworm) and gluten-dependent inflammation in humans with CeD using biopsy tissue from the duodenum. Our results demonstrate that hookworm infection and gluten exposure were associated with increases in the richness and diversity of the tissue-resident microbiota within the intestine. This may represent one mechanism by which these parasites may restore intestinal immune homeostasis and exert a therapeutic benefit in CeD, and potentially other inflammatory disorders.	root:Host-associated:Human:Digestive system
MGYS00002240	16S rDNA sequences of human oral and gut microbiome Raw sequence reads	The goals of this study is to expose the relevance between environmental microbiome and microbiome from human oral and gut	root:Host-associated:Human:Digestive system
MGYS00001270	Intestinal microbiota of the patients with Hirschsprungs disease Raw sequence reads	Hirschsprung-associated enterocolitis (HAEC) is a life-threatening complication of Hirschsprungs disease (HD). Despite the pathological mechanisms are still unclear, studies have shown that HAEC has close relationship with intestinal microbiota disturbance. This study aimed to investigate the characterization of the intestinal microbiome of HD with or without enterocolitis. During routine or emergency surgery we collected 35 intestinal content samples from five patients with HAEC and eight HD patients, including three HD patients with a history of enterocolitis (HAEC remission, HAEC-R). Using Illumina-MiSeq high-throughput sequencing, we sequenced the V4 region of bacterial 16S rRNA, and operational taxonomic units (OTUs) were defined by 97% sequence similarity. Principal coordinate analysis (PCoA) of weighted UniFrac distances was performed to compare the diversity of each intestinal microbiome sample. The microbiota differed significantly between the HD patients (characterized by Bacteroidetes) and HAEC patients (characterized by Proteobacteria), and the microbiota of HAEC-R patients was more similar to that of HAEC patients. We also observed that specimens from different intestinal sites in each HD patient differed significantly, whilst specimens from different intestinal sites in each HAEC and HAEC-R patients were more similar. In conclusion, the microbiome pattern of HAEC-R patients was more similar to that of HAEC patients than HD patients. HD patients have a relatively distinct, more stable community than HAEC and HAEC-R patients, suggesting that enterocolitis may either be caused by or result in a disruption of the patients uniquely adapted intestinal flora. The intestinal microbiota associated with enterocolitis may persist following resolution of symptoms, and could be implicated in the symptom recurrence.	root:Host-associated:Human:Digestive system
MGYS00001072	Human oral or faecal metagenome Raw sequence reads	Faecal or oral microbiomes of persons administered different antibiotics.	root:Host-associated:Human:Digestive system
MGYS00002235	Human nasal and oral cavities microbiota 16S rRNA gene amplicon sequencing	The purpose of this study was to document and compare the bacterial communities found in the nasal and oral cavities of healthy humans.	root:Host-associated:Human
MGYS00001056	Human Microbiome Environment Metagenome	The samples within this Bioproject represent the third phase (Phase III) of metagenomic sequencing (whole genome shotgun (WGS) sequencing) of microbial communities from specimens collected as a part of the NIH-supported Human Microbiome Project (HMP Consortium A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209). The sample collection represents a unique reference resource of microbiome samples from healthy adults largely residing in the USA at the time of sample collection. In the HMP Phase III component the goal has been to supplement previous WGS sequencing by generating additional sequence from as many of the specimens in the HMP collection as possible that had not been sequenced in the previous HMP Phase I and Phase II sequencing. In Phase III, a focus was placed on six of the 18 body sites: Stool (gut), Buccal mucosa (oral), Supragingival plaque (oral), Tongue dorsum (oral), Anterior nares (nasal), Posterior fornix (vaginal) and the goal was to further capture as many of the longitudinal samples (second and third visits by the same individual) as possible. From genomic DNA extracted from the collected specimens, WGS sequence was produced from libraries constructed from using a NexteraXT library construction protocol. All libraries were sequenced using a 100bp paired end approach using the Illumina HiSeq 2000 platform.	root:Host-associated:Human
MGYS00000868	Uncultured fungus Targeted Locus (Loci)	Continental scale survey of soil fungi across North America using 454 pyrosequencing and extracellular enzyme assays to assess taxonomic and functional diversity.	root:Host-associated:Fungi
MGYS00003166	Fish gut metagenome Targeted loci environmental	Globally, marine species distributions are being modified as a result of rising sea surface temperature. On the west coast of Australia, the southern distributional limits of several tropical herbivorous fish species, including the rabbitfish Siganus fuscescens, have recently expanded into temperate regions. Microbes are fundamentally important to animal health, demanding an understanding of their variation in studies of animal adaption. Range-shifting S. fuscescens thus provide a unique opportunity to assess the stability of gastrointestinal microbes under varying environmental conditions. Here, the gastrointestinal microbial communities of S. fuscescens were characterised over 2000km of Western Australia's coastline, including in the species' historical and current southern range limit. MiSeq Illumina sequencing of the 16S rRNA gene demonstrated that the microbial community differed among populations, and there was a general decrease in hindgut microbial community similarity with distance. However, the population in the newly expanded range had similar hindgut microbial communities to one population in the historical range and levels of short chain fatty acids, an indicator of microbial fermentation activity, were similar among tropical and temperate locations. These data suggest that flexibility in the hindgut microbiome may play a role in enabling range-shifting herbivores to colonise new habitats.	root:Host-associated:Fish:Digestive system
MGYS00002606	Microbial communities of white band disease-infected Acropora cervicornis	Microbial communities of white band disease-infected Acropora cervicornis (WBD pools)	root:Host-associated:Cnidaria
MGYS00003723	Chicken cecal contents Metagenome	Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, particularly the ceca. Therefore a studly goal was to use in-depth metagenomics of the ceca to examine the microbial community from the ceca of a Broiler Chicken.	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00004225	Uca urvillei Raw sequence reads	Uca urvillei gill microbiome	root:Host-associated:Arthropoda:Respiratory system:Gills
MGYS00002534	crustacean metagenome Targeted loci environmental	Bacterial assemblages from individual copepods (C. finmarchicus)	root:Host-associated:Arthropoda
MGYS00001841	Litopenaeus vannamei Metagenome	Pacific White Shrimps (Litopenaeus vannamei) are usually cultivated in large scale fisheries under less optimum conditions. Our study was aimed at finding any contaminants present inside the flesh of these commercially cultivated organisms that were imported to the USA.	root:Host-associated:Arthropoda
MGYS00003433	Helminth infections and gut microbiota  a feline perspective	The aim of this study was to investigate the qualitative and quantitative impact that infections by a widespread parasite of cats (i.e. Toxocara cati) exerts on the gut microbiota of feline hosts.	root:Host-associated:Animal:Digestive system:Fecal
MGYS00003432	Fecal bacteria of dogs and cats	The aim was to discover if the complex relationship between the host and Giardia are reflected in the faecal bacterial microbiome. Our hypothesis was that Giardia positive dogs and cats have a different microbiome structure and composition to Giardia uninfected animals. For this purpose, we used naturally infected cohorts of dogs and cats infected not only with Giardia, but also with hookworms and coccidia.	root:Host-associated:Animal:Digestive system
MGYS00002897	Marine invertebrates-associated Bacteria Raw sequence reads	An 8 week experiment was conducted to assess the changes in microbial communities from corals (Acropora millepora and Seriatopora hystrix), crustose coralline alga (Hydrolithon onkodes), foraminifera (Marginopora vertebralis and Heterostegina depressa) and sea urchin (Echinometra sp.) exposed to near-future climate change conditions, using next-generation amplicon sequencing.	root:Host-associated
MGYS00004541	"BACTERIAL COMMUNITIES IN THE ACID AND THERMOPHILIC CRATER-LAKE OF THE VOLCANO ""EL CHICHON"", MEXICO"		root:Environmental:Terrestrial:Volcanic
MGYS00004650	sediment metagenome Metagenome	To investigate the influence of birnessite-coated sand on sediment microbial communities.	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00004610	soil metagenome	The objectives of this investigation was to assess archaeal community and diversity in sediments from natural wetlands.	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00001037	Boreal peatland bacterial 16S rRNA sequences Targeted Locus (Loci)	Defining bacterial community structure in the surface layers of three boreal peatland sites	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00001028	Moorland peat bacteria and fungi (16S and ITS)	We characterised the microbial communities in degraded moorland peat, and a variety of successful natural and managed restorations at a single site. Our hypothesis was that there is a dynamic interaction between soil microbes, edaphic factors, and vegetation in degraded peatlands which will be evidenced by changes in the soil microbial community associated with degradation and restoration. The results support our hypothesis and provide a basis to inform further studies which are needed to understand the roles of microbes in peatlands, and the impact of environmental change and management strategy upon their activities. We suggest that restoration success depends partly upon the readiness and response of below-ground microbial communities to the restoration activity, and that microbial community structure in peatlands may be diagnostic of future degradation risk or the progression of restoration.	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00001017	Tibetan wetland soils Metagenome	The study is to investigate the methanogenic archaeal community by targeting the mcrA gene fragment, and to examine their link to environmental parameters	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00000972	Wetland soil Metagenome	The diversity of archaea in wetland in different seasons	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00000953	Chinampa wetland soil Metagenome	To know the bacterial diversity and variations of microbial communities in chinampa soil.	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00000920	Fungi diversity in mangrove soils Targeted Locus (Loci)	This study goal is to investigate the diversity of fungi in mangrove soils in Bamen Bay, by 454 high through-put sequencing method.	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00000919	Archaeal diversity in mangrove soils Targeted Locus (Loci)	To study the archaeal diversity in different sampling sites of mangrove soils in Bamen Bay by 454 high through-put sequencing	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00000900	Poyang Lake wetland soils Targeted Locus (Loci)	Reveal the relationships between bacterial community structure, composition and the geochemical factors.	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00000846	T-W-B	Qinghai-Tibet wetland bacterial community	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00000815	Soils Random survey	To investigate the methanotrophs diversity in two wetlands in China	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00000809	Wetland samples Metagenome	To explore the microbial community composition and function in wetlands	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00000626	Wetland soil Metagenome	Study of microbial diversity under elevated CO2 and Nitrogen	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00000873	Natural uranium-rich soils Targeted Locus (Loci)	High throughput pyrosequencing was used to assess the impact of uranium on bacterial communities by a comparative analysis of uranium-rich and control soil samples.  Soil samples with high and low uranium content were collected in the region of Bessines (Limousin, France), one of the most important natural uranium deposits in France.	root:Environmental:Terrestrial:Soil:Uranium contaminated
MGYS00000902	Soil microorganisms Targeted Locus (Loci)	Bacterial 16S sequences and fungal 18S sequences isolated from a wet tropical forest soil in Costa Rica	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00000768	Soil bacterial diversity beneath Atlantic Rainforest saprotrophic mushrooms	Sanger sequencing of isolated saprotrophic mushrooms and pyrosequencing of bacterial strains present in the mycospheres of each (mycospheric soil) and bulk soil samples.	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00000625	Tropical soils Targeted Locus (Loci)	Tropical soil archaeal diversity and community structure.  Equatorial tropical biome at central and southern Malay Peninsula and Northern Borneo.	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00000620	Malaysian Rainforest Soil Targeted Locus (Loci)	Spatial-scale independence of soil bacterial communities in Malaysian tropical forests	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00004491	permafrost metagenome Targeted loci environmental	Analysis of microbial communities in thawing permafrost taliks of a thermokarst lake.	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00000924	Arctic soil Metagenome	Sequencing of arctic soil samples on 454 platform for preliminary screening of most dominant bacteria and fungi before and after silver nanoparticles treatment	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00000904	Glacier forefield soils Targeted Locus (Loci)	Study of the diversity of soil microorganisms (bacteria, fungi, algae) along the chronosequences settled at two different glacier forefields of Southern Hemisphere, with different and contrasting environmental conditions	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00000870	Environmental Soil Sample	Increasing permafrost thaw, driven by climate change, has the potential to result in organic carbon stores being mineralized into carbon dioxide (CO2) and methane (CH4) through microbial activity. This study examines the effect of increasing temperature on community structure and metabolic activity of methanogens from the Canadian High Arctic, in an attempt to predict how warming will affect microbially controlled CH4 soil flux. Permafrost and active layer soil samples were collected at the same sites and incubated under anaerobic conditions at warmer temperatures, with and without substrate amendment. Pyrosequencing was used to examine the effects of an extended thaw cycle on methanogen diversity and the results indicate that in situ methanogen diversity, based on the relative abundance of the 16S ribosomal ribonucleic acid (rRNA) gene associated with known methanogens, is higher in the permafrost than in the active layer. Methanogen diversity was also shown to increase in both the active layer and permafrost soil after an extended thaw.	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00000827	Study of microbial community structure of permafrost soil	The goal of this study is to uncover the inter-reflections between microbes and environment in continuous permafrost near bitumen in Qiangtang basin.  Organisms were grown in pure culture after isolation from permafrost soil.	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00000807	Permafrost soil Metagenome	Sequencing of ITS hypervariable region to unravel fungal diversity in Siberian Arctic soil	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00000773	Arctic soils Metagenome	Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. We hypothesize that warmer and therefore wetter conditions in polygonal tundra will lead to important changes in microbial processes, resulting in exacerbated carbon degradation under increasing anoxic conditions. To test this hypothesis, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth.	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00000762	Permafrost Metagenome Targeted Locus	DNA sequencing of ancient permafrost samples can be used to reconstruct past plant, animal, and bacterial communities. In this study, we assess the small-scale reproducibility of taxonomic composition obtained from sequencing four molecular markers (mitochondrial 12S ribosomal DNA (rDNA), prokaryote 16S rDNA, mitochondrial cox1, and chloroplast trnL intron) from two soil cores sampled 10 cm apart. In addition, we sequenced control reactions to produce a contaminant library that was used to filter similar sequences from sample libraries. Contaminant filtering resulted in the removal of 1% of reads or 0.3% of operational taxonomic units. We found similar richness, overlap, abundance, and taxonomic diversity from the 12S, 16S, and trnL markers from each soil core. Jaccard dissimilarity across the two soil cores was highest for metazoan taxa detected by the 12S and cox1 markers. Taxonomic community distances were similar for each marker across the two soil cores when the Chi squared metric was used, however, the 12S and cox1 markers did not cluster well when the Goodall similarity metric was used. A comparison of plant macrofossil versus read abundance corroborates previous work that suggests eastern Beringia was dominated by grasses and forbs during cold stages of the Pleistocene, a habitat that is restricted to isolated sites in the present day Yukon.	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00000670	High Arctic active layer and permafrost Targeted Locus (Loci)	Samples of active layer and permafrost were collected at the McGill Arctic Research Station, Axel Heiberg Island, Nunavut, Canada. The total community genomic DNA was extracted using PowerSoil DNA Isolation Kit. The V4 region of the bacterial 16S rRNA gene and the D1/D2 region of the fungal LSU rRNA were amplified and sequenced on a 454 Life Sciences Genome Sequencer FLX using Titanium chemistry.   Samples were collected at the McGill Arctic Research Station, Axel Heiberg Island, Nunavut, Canada. Active layer freezes and thaws every year. Active layer is underlain by permanently frozen soil (permafrost).	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00001061	Oil contaminated soils Targeted Locus (Loci)	Surveying microbial communities in desert soils polluted by oil	root:Environmental:Terrestrial:Soil:Oil-contaminated
MGYS00001060	Soil Targeted Locus (Loci)	The study has surveyed microbial communities in oil contaminated soils	N/A
MGYS00001006	Microbial Community in Petroleum Contaminated Soil Metagenome	Characterization of soil microbial community in a weathered petroleum hydrocarbon contaminated soil	root:Environmental:Terrestrial:Soil:Oil-contaminated
MGYS00000960	Oil contaminated soils Targeted Locus (Loci)	Diversity of microbial communities in oil contaminated soils from six oilfields in China	N/A
MGYS00000930	Soil sample Targeted Locus (Loci)	Oil contamination	root:Environmental:Terrestrial:Soil
MGYS00000915	Bacterial community of arable soil contaminated with diesel	Bacterial community was analyzed from arable soil contaminated with diesel. Red clay was added as a biostimulating agent. The results were compared between samples.	root:Environmental:Terrestrial:Soil:Oil-contaminated
MGYS00000913	Changshu soil samples Metagenome	Organic-inorganic compound fertilizer is a novel fertilizer type in China. A field study was performed to evaluate the effect of organic-inorganic compound fertilizer to soil properties, microbial biomass, soil enzyme activity, functional genes and the bacterial community structure.	root:Environmental:Terrestrial:Soil:Oil-contaminated
MGYS00000994	Soil and tailings Genome sequencing	Bacterial community research in metalliferous mine tailings, which was supported by National Natural Science Foundation of China	root:Environmental:Terrestrial:Soil:Mine drainage
MGYS00004440	soil metagenome Raw sequence reads	Profiling of Contaminated Soils in a Typical Antimony Mining Site	root:Environmental:Aquatic:Marine:Coastal
MGYS00000952	Stordalen mire environmental genomics 2 Targeted Locus (Loci)	Further to a previous submission SRP030775, more community composition analyses of Stordalen Mire''s thaw gradient.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000906	Soil Random survey	Microbial response to climate warming	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000888	Effects of N fertilization on arbuscular mycorrhizal fungal community in an alpine meadow on the Qinghai-Tibetan Plateau	Different forms and rates of nitrogen addition indirectly effect the arbuscular mycorrhizal fungal community primarily by altering soil characteristics	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000831	RaMPs 2006 tallgrass prairie soil fungi ITS1 locus sequencing	Responses of soil-borne fungi to environmental manipulations (elevated temperature and increased intervals between precipitation events) were evaluated through ITS1 locus sequencing.  The project explores fungal community shifts in response to manipulation of environmental conditions on an ecosystem level. 23 soil samples were collected, total DNA isolated and ITS1 targets sequenced.; Project type: Targeted Locus (Loci); Target description: A total of 23 soil samples were collected in June 2006 from the established rainfall manipulation (RaMPs) experiment. Total environmental DNA was extracted and fungal ITS1 regions PCR-amplified with target specific primers. The amplicons were sequenced on GS20 platform.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000786	Prairie soil fungi, preindustrial-to-future CO2 gradient, Targeted Locus (Loci)	Soils sequester and release substantial atmospheric carbon, but the biological responses of soils to rising CO2 are not well understood. Studying fungal community responses to past and future CO2 concentrations should provide insights into how soils affect the path of rising atmospheric CO2. We studied fungal communities in a grassland ecosystem exposed to a preindustrial-to-future CO2 gradient (250-500 ppm) on two soil types, a black clay and a sandy loam. The data uploaded are from 454 pyrosequencing of ITS-1 region rDNA, obtained from soil samples. The project is a collaboration between Duke University and the USDA-ARS Grassland, Soil and Water Research Laboratory in Temple, TX.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000734	Kessler Farm Soil AOA communities Targeted Locus (Loci)	Ammonia oxidizing archaeal communities from a semi-arid tall grass prairies in Oklahoma were sequenced to gauge the diversity and response to climate warming.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000699	soil metagenome Targeted Locus (Loci)	In three California annual grassland soils, the present (DNA-based) and potentially active (RNA-based) soil bacterial and fungal communities were tracked over a summer field season and in response to a controlled rewetting of intact soil cores. Phylogenetic marker genes for bacterial (16S) and fungal (28S) RNA and DNA were sequenced and the abundance of these genes and transcripts were measured.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00001065	Soil Targeted Locus (Loci)	The goals of this study was to determine if there is a difference in bacterial community structure beneath beetle-killed trees as compared to healthy trees.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00001051	Hauturu temperate rainforest soil environmental sequencing using targeted loci (16S, 18S, ITS, COI and trnL)	From 20 soil samples we amplified DNA from five molecular markers (16S, 18S, ITS, COI and trnL) using targeted-locus next generation sequencing. Our aim was to evaluate a suite of DNA markers coupled with next generation sequencing (NGS) that span the tree of life and compare these data to traditional biodiversity monitoring tools, including mist-netting and call counts for birds, vegetation surveys, and invertebrate collection with DNA barcoding. Our sampling regime consisted of ten 20x20 metre plots, each comprising sixteen 5x5 metre sub-plots along a 700 metre elevational gradient on a temperate island forest ecosystem (Hauturu, New Zealand).	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00001041	Effects of forest managements on soil fungi	Central objective of this study was to analyze forest management effects on soil fungal community structure	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000963	Clearcut and forest ectomycorrhizal root tip communities Metagenome	Different ectomycorrhizal fungi (EMF) colonize seedlings in clearcuts versus intact forests. We were curious whether the shift in EMF community was associated with a change in the ability to access nutrients from soil organic matter, as measured by extracellular enzyme (EE) activities. Previous work in our lab had demonstrated that EMF identity can be more important than soil nutrient status and site in determining EE activities of ectomycorrhizal roots. Hence, we hypothesized that EE profiles associated with seedlings regenerating naturally in clearcuts would differ from those in adjacent forests. To test this hypothesis, naturally-regenerated subalpine fir (Abies lasiocarpa) seedlings were reciprocally transplanted between three pairs of clearcut and forest plots. One growing season after transplantation, EMF communities on seedlings originating from clearcuts and forests still differed from each other, regardless of whether they had been transplanted into clearcuts or forests. Activities of eight EE were measured on randomly-selected, individual mycorrhizal tips of transplanted seedlings. Contrary to our hypothesis, enzyme profiles were most similar among seedlings planted in the same destination, regardless of origin. Given that the EMF community depended on the site of origin, our results suggest that ectomycorrhizas exhibit a range of physiological attributes with respect to EE activities.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000951	Ground-level meiofauna 18S rDNA Targeted Locus (Loci)	Metabarcoding allows eukaryote biodiversity to be measured rapidly, cheaply, comprehensively, repeatedly, and verifiably. Metabarcoding helps to remove the taxonomic impediment, which refers to the great logistical difficulties of describing and identifying species, and thus promises to improve our ability to detect and respond to changes in the natural environment. Now, sampling has become a rate-limiting step in biodiversity measurement, and in an effort to reduce turnaround time, we use arthropod samples from southern China and Vietnam to ask whether soil, leaf litter, and aboveground samples provide similar ecological information. A soil or leaf-litter sample can be collected in minutes, whereas an aboveground sample, such as from Malaise traps or canopy fogging, can require days to set up and run, during which time they are subject to theft, damage, and deliberate contamination. Here we show that while the taxonomic compositions of soil and leaf-litter samples are very different from aboveground samples, both types of samples provide similar ecological information, in terms of ranking sites by species richness and differentiating sites by beta diversity. In fact, leaf-litter samples appear to be as or more powerful than Malaise-trap and canopy-fogging samples at detecting habitat differences. We propose that metabarcoded leaf-litter and soil samples be widely tested as a candidate method for rapid environmental monitoring in terrestrial ecosystems.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000948	Pooled Ectomycorrhizal Root Tips Targeted Locus (Loci)	Soil cores were collected from 72 forest plots (20x40 m) evenly divided into four treatments (elevated pH, elevated P, elevated pH+P, and untreated control) across 2 physiographic regions of Ohio. Each region contained 36 plots within 3 forests. Within each plot, ten cores were sampled 1-m from the base of an adult tree. Cores were sieved to separate roots and soil and root tips that were visually confirmed to be colonized by ectomycorrhizal fungi were pooled into single composite samples for each plot. Genomic DNA was extracted from the pooled root tips from each plot and the primer set ITS1-F/ITS2 was used to amplify the ITS1 region of the rRNA gene. A set of 24 Multiplex Identifiers were used to separate sequence reads into treatment x forest x region combinations and sequencing was completed on the GS-FLX 454 System.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000907	Amplicon pyrosequencing and development of new Real-time specific assays reveal Phytophthora species diversity in Holm Oak in eastern Spain	Oak decline in non calcareus soils in south-western Spain has been associated with Phytophthora cinnamomi for decades. However, other Phytophthora species such as P. quercina and P. psychrophila have been associated with Quercus decline in the eastern part of Spain where calcareous soils are predominant. With the aim of investigating the involvement of Phytophthora spp. in oak decline in eastern Spain, two forests in different geographical areas were selected as sampling sites: the Natural Park Carrascar de la Font Roja (Alicante) and the Natural Park Tinenca de Benifassa (Castellon). Soil samples were analyzed in parallel by isolation using baiting methods and by amplicon massive sequencing.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000894	Fungal ITS2 amlicons Targeted Locus (Loci)	In this project we have used high throughput 454-pyrosequencing of ITS2 amplicons to analyse fungal communities in humus and litter from 26 old-growth boreal forests in central Sweden. The sites represent a gradient in nitrogen availability and pH, as well as different vegetation types with respect to dominant tree (Pinus sylvestris, Picea abies) and understory species.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000893	DOB_RepEx Targeted Locus (Loci)	Raw sequence data from fungal amplicons sequenced from soil samples collected in major Pinus biomes across North America.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000884	Degrading lignocellulose Metagenome	Metataxonomic profiling and prediction of functional behaviour of novel lignocellulolytic microbial consortia	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000882	Forest soil sample Targeted Locus (Loci)	Evaluate the effect of short rotation of woody biomass on soil microbial community	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000876	Bacterial community composition on leaf litter of F. sylvatica Targeted Locus (Loci)	Identification of bacterial community composition on leaf litter of F. sylvatica by 454 amplicon sequecing of 16S rRNA gene fragments	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000790	Forest soil Metagenome AOA amoA gene library	Compare AOA amoA community composition in forest soils of different pH	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000751	Forest soil Metagenome	Assess the relation ship between forest age class, tree species composition and soil related biotic and abiotic parameters on the fungal community composition.  Forest soils collected from three age class forests in a subtropical forest in China.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000738	Soil microcosm Metagenome	Analysis of the microbial diversity influenced by ambient and exceeded N supply in an incubated forest soil.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000730	Bamboo invaded forest soil Metagenome	To better understand the impacts of moso bamboo invasion on the phylogenetic structure and diversity of the soil bacterial communities in moso bamboo forest, adjacent Japanese cedar plantation and bamboo-invaded transition zone.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000668	Soil Mesocosm Synthetic Targeted Locus	Soil metagenome analysis from a artificial tree experiment analyzing tree species identity and diversity, as well leaf littereffects on soil bacterial communities.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000667	Bankhead National Forest 2012 Metagenome	Bankhead National Forest 2012 Metagenome - Bacterial and Fungal Sequences	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000635	Soil microbe Metagenome	Metagenomic analysis on 16S rDNA	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000622	Leaf litter and underneath soil Targeted Locus (Loci)	Understanding the difference in bacterial community composition between leaf litter and underneath soil, and between tropical and temperate forests.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00001032	Sonoran Desert soil Targeted Locus (Loci)	Understand response of ammonia-oxidizing microorganisms to nitrogen fertilization in arid land soils	root:Environmental:Terrestrial:Soil:Desert
MGYS00001022	Cold desert Metagenome	Targetted geno-diversity Of lipase genes in cold desert Of Drass (Ladakh, Jammu and Kashmir)	root:Environmental:Terrestrial:Soil:Desert
MGYS00000981	Desert soil Targeted Locus (Loci)	Bacterial community data (cDNA; 16S rRNA gene) from desert soil samples (Namib) taken over the course of a 5 day period in April 2013 and representative of the diurnal cycle (morning, midday, night).	root:Environmental:Terrestrial:Soil:Desert
MGYS00000917	Metagenomes of Saline Desert,Kutch,Gujarat, India, Project-151, Gujarat Genomics Initiative, GSBTM, DST, Gandhinagar, Gujarat, India	Kutch Desert Metagenome is initiated as part of Project-151 of Gujarat Genomics Initiative, GSBTM, DST, Government of Gujarat, India	root:Environmental:Terrestrial:Soil:Desert
MGYS00000819	Bacteria and eukaryote in biological soil crusts Metagenome	Microbial communities in BSCs.  The sample was in the topmost 2-3 mm layers of the desert soil.	root:Environmental:Terrestrial:Soil:Desert
MGYS00000796	Saline Desert soil of Kutch, Gujarat Targeted Locus (Loci)	The microbial diversity of Kutch desert was analysed to get insight on role of CO2 on survival of microbial community in desert.	root:Environmental:Terrestrial:Soil:Desert
MGYS00000772	Saline Desert S1 Metagenome	Kutch Desert Metagenome is initiated as part of Project-151 of Gujarat Genomics Initiative, GSBTM, DST, Government of Gujarat, India.  Saline desert soil sample was collected from Desert of Kutch, India.	root:Environmental:Terrestrial:Soil:Desert
MGYS00000771	Saline Desert S2 Metagenome	Kutch Desert Metagenome is initiated as part of Project-151 of Gujarat Genomics Initiative, GSBTM, DST, Government of Gujarat, India.  Saline desert soil sample was collected from Desert of Kutch, India.	root:Environmental:Terrestrial:Soil:Desert
MGYS00000706	Sonoran Desert Targeted Locus (Loci)	Soil and Rhizosphere samples taken from the Sonoran Desert in and around Tucson, Arizona,	root:Environmental:Terrestrial:Soil:Desert
MGYS00000697	Antarctic Soil Hypolithic Samples Metagenome	The surface of hyperarid deserts is often paved with quartz rocks. These rocks are colonized by assemblages of photosynthetic microbial communities. Members of these communities, called hypoliths, are expected to represent a significant input source of Carbon and Nitrogen within this desert and other depauperate environs. The development and assembly mechanisms for these communities is yet to be fully understood. Here we aim to investigate hypolith assembly and development patterns.	root:Environmental:Terrestrial:Soil:Desert
MGYS00001057	Bacteria Targeted Locus (Loci)	The goal of present study is to examine what soil bacterial taxa were significantly affected by Cu amendments, and what taxa were the keystone organisms in Cu-contaminated soils using network analysis approach	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00001054	Bacteria_NM_soil_plots	The aim of our study was to (1) investigate the diversity of bacterial and fungal communities in a historically contaminated soil from a former coking plant site (Neuves-Maisons, France), (2) assess the impact of plant-assisted attenuation on microbial diversity, (3) characterize the temporal modifications of microbial diversity linked to edaphic parameters.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00001050	Fungi_NM_soil_plots	The aim of our study was to (1) investigate the diversity of bacterial and fungal communities in a historically contaminated soil from a former coking plant site (Neuves-Maisons, France), (2) assess the impact of plant-assisted attenuation on microbial diversity, (3) characterize the temporal modifications of microbial diversity linked to edaphic parameters.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00001007	Microorganisms responsible for carbon uptake from ethylbenzene and its degradation products	This study aimed at identifying microorganisms that are involved in the carbon uptake from ethylbenzene and its degradation products in soil microcosms. These microcosms were determined by combing stable isotope probing and high throughput sequencing techniques. Briefly total genomic DNA was extracted from microcosms that degraded approximately 80% of the added labeled or unlabeled ethylbenzene and was subject to gradient ultracentrifugation and were divided into fractions for further analysis. Heavy fractions and total genomic DNA samples from all microcosms were sampled. This BioProject contains the illumina sequences generated from the total genomic DNA samples from all microcosms.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00000995	Landfill leachate Metagenome	Microbial community structure and function of landfill	root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
MGYS00000977	Silver-induced disturbance increases diversity in soil microbial communities and selects for persistent/resistant phenotypes.	Silver-induced microbial selective pressure is becoming increasingly relevant due to the concurrent increase in biomedical uses of silver and its mass commercialisation in antibacterial consumer products. With demonstrated links between environmental resistomes and clinical pathogens it is important to identify microorganisms with the propensity for silver tolerance/resistance. This study investigated the effects of ionic Ag stress on total soil bacterial communities (a potential source of resistant phenotypes) and identified resistant/persistant populations to the near species level. Silver treatments of 50 - 400 mg Ag kg-1 soil were established in five soils. Chemical profiling using Diffusive Gradients in Thin-film devices confirmed that effective Ag selective pressure was operating throughout the 9 month incubation period, albeit with decreasing intensity. X-ray Absorption Near Edge Spectroscopy showed this was due to changes in Ag speciation to less soluble forms such as Ag0 and Ag2S. Real-time quantitative PCR and Illumina MiSeq partial sequencing of the 16S rRNA bacterial gene were used to determine the effects on bacterial diversity and population dynamics, and to identify persistent/resistant populations using both taxonomy-based and operational taxonomic unit approaches. Structural bacterial community changes occurred in all soils. 16S rRNA gene counts and a-diversity were inversely related, with the former showing immediate significant reductions following Ag application which persisted in some soils but recovered in others. These effects were influenced more by exposure time than applied Ag dose. Dominant taxa in Ag-exposed samples included a range of known persister species (mostly gram positive), including metal tolerant bacteria and slow growing Mycobacteria.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00000975	Soil Metagenome	Changes in soil bacterial populations following incubation with mixtures of hydrocarbons	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00000958	Microbial community analysis of aerobic enrichment cultures sustaining nitrification from coal biotransformation	Screening of microbial populations driving the metabolism of carbon from coal and feeding into the nitrification process.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00000898	Fungi Targeted Locus (Loci)	Culture-dependent and -independent methods capture different microbial community fractions in hydrocarbon-contaminated soils	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00000895	Uncultured soil bacteria Targeted Locus (Loci)	Describe bacterial communities inhabiting hydrocarbon-contaminated soils	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00000881	Metagenome on soil background with high concentration of arsenic and antimon Genome sequencing	Metagenome sequencing on soil background with high concentration of arsenic and antimony	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00000871	Microbial community structure and composition of raw landfill leachate of different ages	Microorganisms play a key role in the degradation of raw leachate generated in sanitary landfills, leading to the breakdown of organic matter and toxic compounds into less hazardous intermediate and end products.  To expand on the knowledge about these contaminated ecosystems, the microbial communities in leachate produced by three landfill cells of a sanitary landfill in Northeast Brazil were analyzed using a high-throughput sequencing approach of the 16S rRNA gene with universal primers.  In the related paper we describe the structure and composition as well as the metabolic function of leachate communities at different stages in the adaptation process to their environment.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00001046	Czech Republic Norway Spruce soil fungal hyphae Metagenome	We investigated fungal hyphal ingrowth and community composition in buried meshbags (3, 5, 15, 25 cm depths), amended with apatite, biotite or hornblende (1%), in a series of Norway spruce forests with different nutrient status (varying in K, P, and Mg). We assayed the fungal colonization of mineral amended mesh bags by measuring the ergosterol and performed fungal community analysis with 454 sequencing of the ITS region (ITS1f-ITS4). Bioinformatic analysis was conducted on extracted sequences from the ITS2 region.	root:Environmental:Terrestrial:Soil:Boreal forest
MGYS00001001	Sod-podzolic soil Metagenome	Our goal is to analyze seasonal dynamics of prokaryotic microorganisms of non-arable sod-podzolic soils by means of NGS sequencing technologies. The study incorporates metagenomic and metatranscriptomic data.	root:Environmental:Terrestrial:Soil:Boreal forest
MGYS00000808	Boreal forest soils Targeted Locus (Loci)	Response of soil fungi to boreal forest fires	root:Environmental:Terrestrial:Soil:Boreal forest
MGYS00004640	USS-2	environmental research	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00004296	DOW-2	environmental research	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00004294	DOS-1	environmental research	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001083	Soil Targeted Locus (Loci)	Investigate changes to soil communities with plant secondary succession	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001062	RDX degrading microbial communities	RDX degrading enrichments were obtained using four different agricultural soils as innocula. The total genomic DNA samples extracted from the communities after two amendments of 20 mg/L of RDX was degraded, was subjected to high throughput amplicon sequencing. Time zero total genomic DNA samples of the agricultural soils were also sequenced.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001053	Becker field soil DNA Metagenome	Five Streptomyces isolates and their combination plus a non-inoculated control was inoculated into field for the biocontrol of potato scab disease. Soil samples from each pot were collected pre-planting and in mid-season. the DNA sequences from each soil samples were extracted and amplified in order to understand the construction of soil microbial community during biocontrol and the influences of indigenous microbial community on biocontrol results.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001039	Ancient paddy soils Targeted Locus (Loci)	Comparing the bacterial community between ancient and modern paddy soil	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001033	Soil microbes Targeted Locus (Loci)	Mid-term abandoned agricultural land (grassland) in Veluwe, the NETHERLANDS	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001030	Metatranscriptomic analyses of plant polymer breakdown in paddy soil	Paddy soil slurries were amended with rice straw and incubated for four weeks at 30C to mimick the early stage of rice straw breakdown. The anaerobic breakdown of rice straw was studied by metatranscriptomics to gain insights into changes in microbial community structure and gene expression. The focus was on methanogen dynamics and analysing glycosyl hydrolase expression.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001029	Soil bacteria Metagenome	The study focused on determining bacterial diversity in soil that has been under (1) continuous no-tillage and (2) continuous plow-tillage for five decades. Soil bacterial diversity under a long-term soil management practice is relevant since it provides clues about the effect of long-term agricultural management practices on soil microbial environment.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001014	Iron plaque of paddy rice root Targeted Locus (Loci)	To explore the divergence of microbial community structure among iron plaque, bulk soil and rihzosphere soil of paddy field	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000982	Total soil fungi Genome sequencing	The aim of the present survey was to relate soil physicochemical parameters and patterns of fungal community composition to different soil management practices: conventional tillage or reduced tillage, retention or removal of crop residues, in an experimental design combining each tillage practice with each crop residue management practice.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000978	Agricultural soil Targeted Locus (Loci)	Bacterial community structures	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000971	a paddy soil chronosequence genome sequencing	In this study, we investigated how bacterial communities might change with respect to soil physicochemical development during 2000-year rice cultivation after reclamation from tidal wetlands, using the soil chronosequence in the Yangtze River Delta, China. This knowledge would provide useful suggestions for sustainable development of paddy ecosystem.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000970	Rice field soils bacterial 16S rRNA genes raw sequence reads	Detect the response of bacterial and archaeal community in rice field soils to rice straw addition under methanogenic conditions	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000966	Genome for paddy soils Genome sequencing	To gain a comprehensive understanding of the impacts of different fertilization regimes on the soil microbial communities, 454 pyrosequencing was used to examine differences in microbial community structures among experimental sites managed for 22 years with different chemical fertilizer treatments.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000964	Bacteria Metagenome	The aim of our survey is to detect patterns in bacterial community composition related to different soil management, consisting in a combination of tillage practice (conventional tillage and reduced tillage) and crop residue management (residue retaining and residue removal.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000946	Arable soil bacteria Metagenome	Manure application well contributes to the disturbance of bacterial communites in arable soil.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000916	Soil and cattle excrements Metagenome	Diversity of bacteria and archaea in cattle impacted soils and cattle excrements	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000912	Microbial community enriched from paddy soil	Depiction of microbial community structure	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000903	soil metagenome Targeted Locus (Loci)	Nitrous oxide reductase sequences obtained by targeted amplification of the nosZ gene from arable soils in field sites throughout Europe.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000892	Scheyern-soil Metagenome	Agricultural soil metagenome	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000890	Agriculture soils Metagenome	A central goal in ecology is to understand the factors that control microbial biodiversity and patterns in spatial distribution. In this project, the effect of limited tillage versus traditional tillage, residue retention versus removal and crop rotation (maize-wheat) versus monoculture (maize) on the bacterial community structure is being investigated.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000885	Arbuscular Mycorrhizal Fungi Metagenome	The goal of this study was to know the communities of arbuscular mycorrhizal fungi in productive fields under different soil agricultural practices	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000877	Soil Metagenome after long-term green manure	To study effect of long-term green manure	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000874	Improved cultivation Targeted Locus (Loci)	Improved cultivation	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000627	Soil Carbon Content and Relative Abundance of High Affinity H2-Oxidizing Bacteria Predict Atmospheric H2 Soil Uptake Activity Better than Soil Microbial Community Composition	We examined the microbial community structure based on ribotyping analysis as predictors for atmospheric H2 uptake rate in soil samples collected from different land-use types.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000623	Soil Targeted Locus (Loci)	The effect of biochar on soil bacterial diversity in Greater Khingan Mountains,Inner Mongolia Autonomous Region, China	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000922	Extremely alkaline saline soil Texcoco Metagenome	It is most likely that the soil of the former lake Texcoco harbors much more novel microbial species with unique characteristics. However, the extent to which new microbial species can be found in this environment has not been determined. In this project, archaeal-specific primers were used combined with 454 pyrosequencing to investigate the archaeal diversity in soils from the former lake Texcoco	root:Environmental:Terrestrial:Soil:Silt
MGYS00001055	Dune soil fungi Metagenome	This study aimed to wholly describe fungal diversity and community composition in a semi-closed coastal sand dune ecosystem, and to relate changes in fungi with variations in soil physiochemistry and shifts in ecosystem function at 8 different stages of succession.	root:Environmental:Terrestrial:Soil:Sand
MGYS00000989	Municipal Pensacola Beach Sand Metagenome	This study investigated the successional patterns of functional and taxonomic diversity for over one year after the Deepwater Horizon oil was deposited on Pensacola Beach sands (FL, USA), using metagenomic and 16S rRNA gene amplicon techniques.	root:Environmental:Terrestrial:Soil:Sand
MGYS00000899	Upper-line Targeted Locus (Loci)	Sample taken 1 m before the dune zone and the vegetation	root:Environmental:Terrestrial:Soil:Sand
MGYS00001020	Forest Soil Targeted Locus (Loci)	The purpose of this study was to explore the diversity of ammonia-oxidizing microbes (bacteria and archaea) in the soils at Coweeta LTER, a research site in western North Carolina.	root:Environmental:Terrestrial:Soil:Loam:Forest soil
MGYS00001018	Soil microflora Targeted Locus (Loci)	Tracking the soil microflora components associated with fast- and slow-growing mycelium of summer truffle (Tuber aestivum)	root:Environmental:Terrestrial:Soil:Loam:Forest soil
MGYS00001013	Soil Samples Targeted Locus (Loci)	The flow of energy within an ecosystem can be considered either top-down, where predators influence consumers, or bottom-up, where producers influence consumers. Plethodon cinereus (Red-backed Salamander) is a terrestrial keystone predator who feeds on invertebrates within the ecosystem. We investigated the impact of the removal of P. cinereus on the detritivore food web in an upland deciduous forest in northwest Ohio, USA. A total of eight aluminum enclosures, each containing a single P. cinereus under a small log, were constructed in the deciduous forest. On Day 1 of the experiment, four salamanders were evicted from four of the eight enclosures. Organic matter and soil were collected from the center of each enclosure at Day 1 and Day 21. From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU). Changes in overall fungal community composition or species diversity were not statistically significant between treatments. Statistically significant shifts in the most abundant taxonomic groups of fungi were documented in presence but not absence enclosures. We concluded that P. cinereus does not affect the overall composition or diversity of fungal communities, but does have an impact on specific groups of fungi. This study used a metagenomics-based approach to investigate a missing link among a keystone predator, P. cinereus, invertebrates, and fungal communities, all of which are critical in the detritivore food web.	root:Environmental:Terrestrial:Soil:Loam:Forest soil
MGYS00001005	Fungi Metagenome	Biodiversity and climate change in european forests	root:Environmental:Terrestrial:Soil:Loam:Forest soil
MGYS00000993	Rolainville truffle orchards Metagenome	Soil samples have been collected in a truffle orchard located in the Vosges (France). DNA was extracted and used to decipher the structure of the bacterial communities along truffle maturation.	root:Environmental:Terrestrial:Soil:Loam:Forest soil
MGYS00001169	Agricultural Soil Targeted Locus (Loci)	Study of change in soil microbial diversity due to different experimental climatic conditions	root:Environmental:Terrestrial:Soil:Crop:Agricultural land
MGYS00000935	HN	Promoting methanogenesis	root:Environmental:Terrestrial:Soil:Crop:Agricultural land
MGYS00000637	Paddy soils Metagenome	Ammonia oxidizing archaea and bacteria in Chinese paddy soils from three provinces.	root:Environmental:Terrestrial:Soil:Crop:Agricultural land
MGYS00000636	Effect of biochar on bacterial community in rice paddy soils	Impacts of biochar soil amendment (BSA) on soil bacterial community have not been well documented. In this study, we present a cross site field experiment on bacterial community changes of rice paddy in three sites (JX in Jiangxi, HN in Hunan and SC in Sichuan provinces) from South China with wheat straw biochar amended in May 2010. Using quantitative real-time PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) combined with tag-encoded amplicon pyrosequencing, changes in bacterial abundance and diversity under BSA at 0, 20 and 40 t ha-1 (C0, C1 and C2, respectively) were assessed with topsoils sampled at rice harvest.	root:Environmental:Terrestrial:Soil:Crop:Agricultural land
MGYS00000908	Rice paddy soil Metagenome		root:Environmental:Terrestrial:Soil:Crop
MGYS00004602	soil bacteria and fungi Targeted loci environmental	This study evaluated differences in community composition of all bacteria and fungi present in woody plant encroached streams and soils versus restored (woody plants removed) streams and soils	root:Environmental:Terrestrial:Soil
MGYS00004499	Amplicon-based sequencing of soil fungi from wood preservative test sites	Soil samples were collected from field sites in two AWPA (American Wood Protection Association) wood decay hazard zones in North America. Two field plots at each site were exposed to differing preservative chemistries via in-ground installations of treated wood stakes for approximately 50 years. Soil fungal communities were compared using amplicon-based DNA sequencing of the internal transcribed spacer 1 (ITS1) region of the rDNA array.	root:Environmental:Terrestrial:Soil
MGYS00004316	BES pyrosequencing	Pyrosequencing analysis of BES sample	root:Environmental:Terrestrial:Soil
MGYS00003716	Bacterial 16S rRNA gene sequencing of Antarctic soil	We analysed soil-borne microbial (bacterial, archaeal, and fungal) communities around the Fildes Region of King George Island, maritime Antarctica, which were divided into two groups according to soil elemental compositions and environmental attributes located in Holocene raised beach and Tertiary volcanic stratigraphy. This is the first study to provide evidence for the crucial influence of landforms on small-scale structures and spatial heterogeneity of soil microbial communities.	root:Environmental:Terrestrial:Soil
MGYS00002679	Soil DNA extracted from Robinson Ridge, East Antarctica Raw sequence reads	To investigate the functional potentials of microbial community	root:Environmental:Terrestrial:Soil
MGYS00001157	Oklahoma soil 10 year warming Metagenome		root:Environmental:Terrestrial:Soil
MGYS00001100	Soil Microbiomes Metagenome	To probe environmental DNA for the presence of biosynthetic gene clusters.	root:Environmental:Terrestrial:Soil
MGYS00001098	Evaluation of PGM for gene-targeted studies using nifH	To evaluate PGM as substitution of 454 for microbial ecology study	root:Environmental:Terrestrial:Soil
MGYS00001082	Acidic northern peatland Transcriptome or Gene expression	Northern peatlands play an extraordinary role in the global carbon balance. The most extensive type of these ecosystems is represented by Sphagnum-dominated acidic peatlands, which are inhabited by microorganisms whose degradation capabilities remain poorly understood. We attempted to identify microorganisms involved in degradation of cellulose, xylan, and pectin, which are the major components of Sphagnum-derived litter, and chitin, which is derived from exoskeletons of peat-inhabiting arthropods.	root:Environmental:Terrestrial:Soil
MGYS00001080	RDX degrading microbial communities from a navy installation site in Virginia	RDX degrading communities were obtained from surface soil samples from a navy installation site in Virginia. Sequences from total genomic DNA extracted from the initial soil, samples treated with glucose, without glucose, with RDX and without RDX were sequenced using amplicon sequencing procedures.	root:Environmental:Terrestrial:Soil
MGYS00001059	The Metagenome of acidic soil sample before and after the remediation of bioelectrochemistry	The Metagenome of acidic soil sample before and after the remediation of bioelectrochemistry. Besides the raw soil and control sample, other 4 acidic soil sample were operated in microbial fuel cells under different external resistance (1000, 1000, 100 and 10).	root:Environmental:Terrestrial:Soil
MGYS00001058	The samples are: (1) soil - RCM based inoculum, used for fermenting glycerol to 1,3 propanediol and (2) the final fermentation samples from select batches Genome sequencing	Soil based inoculum for glycerol to 13-PD fermentation	root:Environmental:Terrestrial:Soil
MGYS00001052	Soil enriched in organic materials Targeted Locus (Loci)	Study of the effects of organic amendments to arbuscular mycorrhizal fungi	root:Environmental:Terrestrial:Soil
MGYS00001049	Insights into soil''s environmental quality indicators for amendments made from organic residues	In order to obtain the status of microbial communities and their organization in a soil that had been fertilized with composted organic residues, DNA was extracted from soil samples fifteen days after fertilization	root:Environmental:Terrestrial:Soil
MGYS00001048	Soil Metagenome	Microbial community survey in Heilongjiang China	root:Environmental:Terrestrial:Soil
MGYS00001045	Jizan project	Soil microbiology	root:Environmental:Terrestrial:Soil
MGYS00001044	Soil Metagenome	Analyze the soil bacterial communities along elevation gradients of southwestern highlands	root:Environmental:Terrestrial:Soil
MGYS00001038	Bacteria Metagenome	To investigate how soil bacteria responsed to warming and precipitation.	root:Environmental:Terrestrial:Soil
MGYS00001035	amoA gene sequences from soil Targeted Locus (Loci)	Both climate and pH are key in determining soil archaeal community structure and diversity	root:Environmental:Terrestrial:Soil
MGYS00001027	Alpine soil eukaryote Metagenome	Investigate the eukaryote community under different water gradient in alpine ecosystem.	root:Environmental:Terrestrial:Soil
MGYS00001026	Alpine soil archaea Metagenome	Investigate the archaea community under different water gradient in alpine ecosystem.	root:Environmental:Terrestrial:Soil
MGYS00001025	The Greater Khingan Mountains Metagenome	To investigate post-fire changes in soil AMF community structure and diversity. Our work was aimed at studying the short- and long-term response of the AMF communities, so sampling was performed at sites were fires had burned 1 or 11 years prior and compared to nearby unburned control sites. To achieve the purpose, we want to evaluate (i) how soil AMF communities respond to short- and long-term effect of wildfire, and (ii) which factors affect AMF communities and whether there are thresholds for factors driving AMF communities.	root:Environmental:Terrestrial:Soil
MGYS00001023	soil metagenome Targeted Locus (Loci)	Communities of soil bacteria in relation to nutrient concentration and successional stage, in a laboratory culture experiment.	root:Environmental:Terrestrial:Soil
MGYS00001021	Tundra soil Metagenome	Investigation distribution of soil microbial community	root:Environmental:Terrestrial:Soil
MGYS00001011	Soil Metagenome	Fine-scale spatial structure of belowground communities	root:Environmental:Terrestrial:Soil
MGYS00001009	Farmers soil	Amplicon sequence originating from grassland or agricultural soil, incubated in lab for 120 days under constant humidity and temperature.	root:Environmental:Terrestrial:Soil
MGYS00001004	Yangzhou University Soil Samples Targeted Locus (Loci)	Yangzhou University Soil Samples	root:Environmental:Terrestrial:Soil
MGYS00000992	ECOFINDER LTO soil samples Metagenome	The EU FP7 EcoFINDERS project, represents a large consortium of European partners, which brings together a range of expertise and knowledge of soil biodiversity and functioning. The main aims of the project are to characterise the biodiversity of European soils according to soil types, threats, climatic zones and land uses, and to decipher the links between soil biodiversity, functioning and ecosystem services.	root:Environmental:Terrestrial:Soil
MGYS00000986	1) Fungi; 2) Soil; 3) Community Targeted Locus (Loci)	To investigate the affects of prescribed fire intervals on the soil fungal communities.	root:Environmental:Terrestrial:Soil
MGYS00000980	Uncultured Antibiotic Resistance Genes from Grassland and Agricultural Soil	Shotgun-cloned metagenomic libraries from 18 soils (9 grassland, 9 agricultural) were each expressed in E. coli and those DNA fragments conferring antibiotic resistance were isolated, sequenced, assembled, and analyzed. Each soil library was selected against a panel of 18 antibiotics.	root:Environmental:Terrestrial:Soil
MGYS00000954	Bacteria from soil, sediment and water samples Metagenome	We analyzed the bacterial community composition in the soil, sediment and water environment adjacent to pig feedlots, and determined the potential pathogenic bacteria.	root:Environmental:Terrestrial:Soil
MGYS00000947	Qiyang soil Metagenome	16S rRNA Metagenome in soil	root:Environmental:Terrestrial:Soil
MGYS00000945	Terranova Bay soil Metagenome	Achievement of a background research through the preliminary study on the terrestrial biodiversity in Victoria Land for the long-term monitoring by climate change and human activity	root:Environmental:Terrestrial:Soil
MGYS00000937	Soil bacterial 16S rRNA genes	Patterns in species persistence in soil microcosms recovering from a disturbance reject a neutral hypothesis for bacterial community assembly.	root:Environmental:Terrestrial:Soil
MGYS00000936	1-1-start Metagenome	First genome sequencing targeting archaea and bacteria in soil treatment system.  Sample collected from the first sampling layer of Column 1 of Soil Aquifer Treatment system at Day 0.	root:Environmental:Terrestrial:Soil
MGYS00000934	Fertilizer management Metagenome	Microbial 16S rRNA gene-based composition of a sorghum cropped rhizosphere soil under different fertilization managements	root:Environmental:Terrestrial:Soil
MGYS00000933	Bacterial composition of tropical earthworm casts	Tropical soils are often nutrients-depleted in their mineral form, constraining crop growth. Therefore any process leading to the mineralization of N and P trapped into the soil organic matter need to be studied with the hope to constitute a durable agricultural tool in the future. Priming effect (PE) is defined as a stimulation of the soil organic matter mineralization (SOM) by a fresh organic matter amendment (FOM). But this microbially-mediated process is not completely understood. Endogeic earthworms are ecosystem engineers known to influence the dynamic of SOM, by the wakening of soil microbial activities. During a laboratory study we followed the capacity of 3 different worm specimens (Pontoscolex corethrurus, Kynotus parvus and Dichogaster saliens) to stimulate or inhibit a Priming effect generated by a wheat straw amendment.	root:Environmental:Terrestrial:Soil
MGYS00000932	A study of microflora of plant growth substrate	The study focuses possibilities of manipulations of microflora of artificial plant growth substrates in order to optimalize and unify their microbiological properties	root:Environmental:Terrestrial:Soil
MGYS00000929	Uncultured soil denitrification bacteria Targeted Locus (Loci)	This library was made using 454 - pyrophosphate sequencing method to attest diversity and richness of soil denitrification functional gene (nosZ)	root:Environmental:Terrestrial:Soil
MGYS00000928	uncultured soil nitrogen-fixing bacteria Targeted Locus (Loci)	This library was made using 454 - pyrophosphate sequencing method to attest diversity and richness of soil nitrogen-fixing functional gene (nifH)	root:Environmental:Terrestrial:Soil
MGYS00000927	cbbL-red like:uncultured soil carbon-fixing bacteria Targeted Locus (Loci)	cbbL-red like:This library was made using 454 - pyrophosphate sequencing method to attest diversity and richness of soil carbon-fixing bacteria functional gene (cbbL-red like).	root:Environmental:Terrestrial:Soil
MGYS00000926	Uncultured bacteria soil carbon-fixing Targeted Locus (Loci)	This library was made using 454 - pyrophosphate sequencing method to attest diversity and richness of soil carbon-fixing functional gene (cbbL-green like).	root:Environmental:Terrestrial:Soil
MGYS00000923	Soil Metagenome	To investigate the effects of biochar and compost on extracellular electron transfer	root:Environmental:Terrestrial:Soil
MGYS00000921	The samples about fungi Targeted Locus (Loci)	The objectives of this study were 1) to reveal the bacterial community compositions in Black soils; 2) to determine which environmental factors are dominating predict the distribution of bacterial community structures; and 3) to compare the difference/similarity of bacterial communities among 26 black soils.	root:Environmental:Terrestrial:Soil
MGYS00000918	16S rRNA soil metagenom	Analysis of 16S rRNA soil metagenome in different parts of Russia	root:Environmental:Terrestrial:Soil
MGYS00000914	Bacteria Metagenome	Bacterial communities within soils in the Fildes Region	root:Environmental:Terrestrial:Soil
MGYS00000911	Bacterial and archaeal communities in mangrove sediments under oil contamination and nitrate stimulation	We want to reveal bacterial shift in mangrove soils under oil contamination and nitrate stimulation	root:Environmental:Terrestrial:Soil
MGYS00000909	Depth-resolved soil samples collected across an LNAPL body Metagenome	Advancements in understanding of the microbial ecology in soils containing light non-aqueous phase liquids (LNAPLs) are needed to drive development of optimized bioremediation technologies. In this study, depth-resolved characterization of geochemical parameters and microbial communities was conducted for a shallow hydrocarbon-impacted aquifer. Four distinct biogeochemical zones were identified: (I) an aerobic, low-contaminant mass zone at the top of the vadose zone, (II) a moderate to high-contaminant mass, low-oxygen to anaerobic transition zone in the middle of the vadose zone, (III) an anaerobic, high-contaminant mass zone spanning the bottom of the vadose zone and saturated zone, and (IV) a sulfate-reducing, low-contaminant mass zone below the LNAPL body. Evidence suggested hydrocarbon degradation is mediated by syntrophic fermenters and methanogens in zones II and III. Upward flux of methane likely contributes to promoting anaerobic conditions in zone II by limiting downward flux of oxygen as methane and oxygen fronts converge at the top of this zone. Observed sulfate gradients and microbial communities suggested that sulfate reduction and methanogenesis both contribute to hydrocarbon degradation in zone IV. Pyrosequencing revealed that Syntrophus- and Methanosaeta-related species dominate bacterial and archaeal communities, respectively, thus linking these genera with in situ hydrocarbon degradation in the LNAPL body.	root:Environmental:Terrestrial:Soil
MGYS00000905	Rhizobacterial soil sample	Microbial community diversity of rhizobacterial soil sample	root:Environmental:Terrestrial:Soil
MGYS00000901	Soil Genome sequencing	The analysis of bacterial community structure	root:Environmental:Terrestrial:Soil
MGYS00000896	Metagenome study of rice samples under various conditions	Microbial diversity of flooded rice soil under various situations	root:Environmental:Terrestrial:Soil
MGYS00000887	Soil mesocosm Targeted Locus (Loci)	Evaluation of the dynamics of total, core and accessory taxa in bacterial communities of a soil mesocosms in relation to the treatment of soil with Cd, employing a metagenetic approach on 16S rRNA gene based on Illumina sequencing technology.	root:Environmental:Terrestrial:Soil
MGYS00000875	Soil microbial community of soil aggregates of different size in conditions of extreme land use practicies	Investigation of microbial community composition in aggregates of different size is to some extend correlated with the task of studying of microbial population in soil microhabitats (microniches). The unique taxa found only in one of the certain size fractions of structural units may be used in in the further research as indicators of the presence of this faction in soil samples investigated. The unique taxa discovered in samples isolated from such extreme land uses as the permanent fallow (50 years), continuous wheat cropping (50 years) and wild land (15 years of soil remediation under natural vegetation after permanent fallowing) could be used as indicators of proceses of soil disturbance (soil structure loss), soil exhaustion and soil recovering processes	root:Environmental:Terrestrial:Soil
MGYS00000872	Soil microbial community Metagenome	Microbial communities structure was studied in 3 soils under different conditions: organic land use, conventional land use and forest as a control. The differencies in microbial community composition will show the biological indicators of transition between forest and agricultural lands.	root:Environmental:Terrestrial:Soil
MGYS00000869	Mushroom Farm Soil, AMD, and Iron Mound material Random survey	Evaluation of microbial community response to AMD intrusion	root:Environmental:Terrestrial:Soil
MGYS00000860	Drosera intermedia Metagenome	Bacterial communities from bulk soil and rhizosphere of Drosera intermedia plants that were either fed with flies or maintained without flies	root:Environmental:Terrestrial:Soil
MGYS00000859	Soil samples from Canadian High Arctic Targeted Locus (Loci)	16s rRNA gene sequences from bacterial communities inhabiting polar soils of the High Arctic	root:Environmental:Terrestrial:Soil
MGYS00000857	Soil eukaryotes Genome sequencing	Evaluate soil eukaryotic diversity	root:Environmental:Terrestrial:Soil
MGYS00000855	Paddy and uncultivated soil Genome sequencing	Microorganisms involved in the anaerobic oxidation of ammonium coupled to iron(III) reduction	root:Environmental:Terrestrial:Soil
MGYS00000854	Soil Random survey	Soil fusarium community	root:Environmental:Terrestrial:Soil
MGYS00000853	Shennongjia Mountain Metagenome	To understand the soil microbail community structure and diversity in Shennongjia Mountain.	root:Environmental:Terrestrial:Soil
MGYS00000852	Soil environment Metagenome	This project aims to determine the diversity of fungi surrounding individual pine trees in Point Reyes National Seashore, California	root:Environmental:Terrestrial:Soil
MGYS00000849	Agricultural soils Targeted Locus (Loci)	The variation of microbial communities following the land-use change	root:Environmental:Terrestrial:Soil
MGYS00000847	Chinese soil Metagenome	Microbial ecology of Chinese soils	root:Environmental:Terrestrial:Soil
MGYS00000844	Metagenome sequencing of Prokaryotic Microbiota from Saline Desert Soil of Little Rann of Kutch, Gujarat, India	Sample was collected from different area of kutch Runn like Farasi, Near Salt Agar, Zinzewaea, Vacheradad. Physical properties: Sample was salty, moist with fine silt, brown in color.	root:Environmental:Terrestrial:Soil
MGYS00000843	Cixi.454Reads Targeted Locus (Loci)	Soil samples from a chronosequence of 0-700 years of rice cropping in the Bay of Hangzhou, China by 454 pyrosequencing	root:Environmental:Terrestrial:Soil
MGYS00000840	Eukaryotic organisms involved in carbon fluxes in soil food webs depending on carbon from glucose, cellulose, maize leaf and root litter. Targeted Locus (Loci)	Eukaryotic organisms involved in carbon fluxes in soil food webs depending on carbon from glucose, cellulose, maize leaf and root litter.	root:Environmental:Terrestrial:Soil
MGYS00000839	Bacterial diversity in arable soil	Bacterial diversity in different depths of arable soil in Germany.	root:Environmental:Terrestrial:Soil
MGYS00000838	Food web relevant soil bacterial utilizers of different detritus substrates	Glucose, Cellulose, Maize leaf and root litter are mainly degraded by temporal dynamic specific bacterial populations.	root:Environmental:Terrestrial:Soil
MGYS00000837	Soil and water from an agricultural field Targeted Locus (Loci)	Natural soil bacteria selectively transported by seepage water are revealed to resemble root-associated microbiota. Mechanisms of mobilisation and transport appear related to preferential flow. Mobilised bacterial biomass carbon represents only a minor contribution to overall organic carbon flux.  Bacterial 16S rRNA gene pyrotags from depth resolved soil and seepage water samples from a maize field near Gottingen, Germany. Sampled in January 2010.	root:Environmental:Terrestrial:Soil
MGYS00000835	Soil 454 sequencing data	To analyze the soil bacterial and eukaryotic community structure and diversity	root:Environmental:Terrestrial:Soil
MGYS00000834	CN1E1 Metagenome	From a naphthalene-enriched community (CN1) derived from a polyaromatic hydrocarbon contaminated soil. The soil samples were obtained from a parcel on the northern Iberian Peninsula contiguous to a chemical plant (Lugones, Oviedo, 401833N, 33931W, at an altitude of 300 m).	root:Environmental:Terrestrial:Soil
MGYS00000828	Saline desert soil sample Targeted Locus (Loci)	Study of bacterial diversity of rhizospheric and non-rhizospheric soil samples from saline desert of Kutch, Gujarat	root:Environmental:Terrestrial:Soil
MGYS00000825	Bacterial diversity in an agricultural soil Metagenome	In soils, bacteria are very abundant and diverse. They are involved in various agro-ecosystem processes such as the nitrogen cycle, organic matter degradation, and soil formation. Yet little is known about the distribution and composition of bacterial communities through the soil profile, particularly in agricultural soils, as most studies have focused only on topsoils or forest and grassland soils. In the present work we used barcoded pyrosequencing analysis of the V3 region of the 16S rRNA gene to analyse bacterial diversity in a profile (depths: 10 cm, 25 cm, and 45 cm) of a well-characterized field of winter wheat. To ensure that the results obtained closely reflect real-life conditions, taxonomic assignment with the RDP classifier program was carried out with three bootstrap scores: 0, 0.80, and 0.99. We found biomass and bacterial quantity and diversity to decrease greatly with depth. Depth also had an impact, in terms of relative sequence abundance, on 81% of the most represented OTUs (relative abundance =1%), notably the OTUs Proteobacteria, Bacteroidetes, Actinobacteridae, and Acidobacteria. Bacterial community composition differed more strongly between the topsoil (10 cm and 25 cm) and subsoil (45 cm) than between levels in the topsoil. The subsoil also contained more unknown bacteria, 53.96% on the average, than did the topsoil, with 42.06% at 10 cm and 45.59% at 25 cm. Most of these unknown bacteria seem to belong to the taxa Deltaproteobacteria, Actinobacteria, Rhizobiales, and Acidobacteria.	root:Environmental:Terrestrial:Soil
MGYS00000824	16S sequences from B. vivipara roots and bulk soil		root:Environmental:Terrestrial:Soil
MGYS00000822	Cellar mud Targeted Locus (Loci)	Cellar mud	root:Environmental:Terrestrial:Soil
MGYS00000821	Soil microcosms 16S Illumina Paired end reads		root:Environmental:Terrestrial:Soil
MGYS00000820	AM fungal DNA from soils in a semiarid steppe Metagenome	To investigate the effects of warming, precipitation and N fertilization on arbuscular mycorrhizal fungal community in a semiarid steppe.   We collected samples from experimental plots (full factorial design of warming, precipitation and N fertilization) and extracted AM fungal DNA. Fungal DNA were sequenced using 454 pyrosequencing. In August 2011, soil samples from a semiarid steppe in Inner Mongolia were collected.	N/A
MGYS00000816	Black soil Targeted Locus (Loci)	The objectives of this study were 1) to reveal the bacterial community compositions in Black soils; 2) to determine environmental factors.  Soil samples were collected from 26 farmlands across a wide range of Black soil zone of Northeast China in September 2012. Soil pH varied from 4.56 to 6.57. Soil total C and total N varied from 11.77 to 53.53 gkg-1 and from 0.99 to 4.25 gkg-1, respectively. Soil MBC ranged from 64 to 595 mgkg-1.	root:Environmental:Terrestrial:Soil
MGYS00000811	Paddy soil Genome sequencing	Microorganisms involved in the iron biogeochemical cycling.  Soil samples were collected from the long-term fertilization experiment site (established in 1990) located in the Taoyuan Agro-ecosystem Research Station (2855N, 11127E), central Hunan Province of China. The paddy soil in this station was developed from quaternary red clay and classified as a waterloggogenic paddy soil.	root:Environmental:Terrestrial:Soil
MGYS00000806	Soil bacterial diversity Metagenome	Assess the influence of fire burning on the community structure of soil bacteria community	root:Environmental:Terrestrial:Soil
MGYS00000804	UNDSUB Targeted Locus (Loci)	Survey of 16S rRNA genes from undisturbed subsoil adjacent to a surface mined site	root:Environmental:Terrestrial:Soil
MGYS00000803	Agricultural soil samples pyrosequencing of nifH gene from soil samples	The aim of this study was to examine the abundance, diversity and structure of diazotroph communities in a gradient of Argentinean agricultural soils, under different agricultural practices, using deep pyrosequencing-based analysis of the nifH gene.	root:Environmental:Terrestrial:Soil
MGYS00000801	Soil from rural backyards Targeted Locus (Loci)	In the State of Yucatan, Mexico, there are a number of rural houses where the sewage daily produced by laundry and general washing has for decades been disposed directly on the soil of the backyards. This wastewater contains not only a mixture of several detergents, mainly in powder, but occasionally also bleach, soap, hot water, and even food scraps. It is to be expected that this exert a selective pressure when present in soils, bringing about modifications in the structure of the edaphic bacterial communities. In the present work, bacterial community structures of three samples from detergent-contaminated soils and three from non-contaminated soils were assessed by 16S rRNA pyrosequencing. The results may contribute to better understand how selective pressure imposed by this anthropogenic contamination can modify soil bacterial communities, to plan possible remediation procedures, and to find out how to use the metagenomes of contaminated environments in the search for biotechnological products.	root:Environmental:Terrestrial:Soil
MGYS00000800	Contaminated Beach - Tabasco State, Mexico Targeted Locus (Loci)	To introduce options for oil spills remediation by obtaining diesel degrading consortia.  Environmental samples taken from oil contaminated soil located on the coast of Tabasco State in Mexico.	root:Environmental:Terrestrial:Soil
MGYS00000799	Agricultural field soil Metagenome	To identify soil bacteria and fungal community assemblages associated with biodegradable mulch films.  Samples collected from Knoxville, TN, Lubbock, TX, and Mount Vernon, WA.	root:Environmental:Terrestrial:Soil
MGYS00000797	Whole genome amplification influence on microbial community profiles	This study comprised a systematic evaluation of bias in microbial community profiles induced by whole genome amplification.  Environmental soil sample from Wildekamp near Bennekom (The Netherlands).	root:Environmental:Terrestrial:Soil
MGYS00000792	Maritime Antarctic soils Targeted Locus (Loci)	This project characterised the diversity of bacterial communities associated with 42 vegetation-free soils along a maritime Antarctic latitudinal gradient (60-72oS) using 16S rRNA gene amplicon pyrosequencing. The dataset provides a base-line for future monitoring of maritime Antarctic soil bacterial communities.	root:Environmental:Terrestrial:Soil
MGYS00000791	Pig farm & soil Targeted Locus (Loci)	16S amplicon sequencing of pig and farm soil from Wenzhou, China.  GBPM (A1) swine manure 2013-01-04 Wenzhou, China pig farm (adult pig) GSPM (A2) swine manure 2013-01-04 Wenzhou, China pig farm (juvenile pig) ABPM (A3) swine manure 2013-01-04 Wenzhou, China pig farm (adult pig) ASPM (A4) swine manure 2013-01-04 Wenzhou, China pig farm (juvenile pig) GPMS (A7) soil 2013-01-09 Wenzhou, China test field APMS (A8) soil 2013-01-09 Wenzhou, China test field	root:Environmental:Terrestrial:Soil
MGYS00000788	Black soil Targeted Locus (Loci)	We investigated the soil bacterial community compositions among 26 soil samples collected from black soil zone in NE China by using a high resolution bar-coded pyrosequencing technique. The objectives of this study were 1) to reveal the bacterial community compositions in Black soils; 2) to determine which environmental factors are dominating predict the distribution of bacterial community structures; and 3) to compare the difference/similarity of bacterial communities among 26 black soils.  Soil samples were collected from 26 farmlands across a wide range of Black soil zone of Northeast China in September 2012. Soil pH varied from 4.56 to 6.57. Soil total C and total N varied from 11.77 to 53.53 gkg-1 and from 0.99 to 4.25 gkg-1, respectively. Soil MBC ranged from 64 to 595 mgkg-1.	root:Environmental:Terrestrial:Soil
MGYS00000787	Paddy field soil Targeted Locus (Loci)	"Phosphorus fertilization is an important agricultural practice for improving plant nutrition and achieving high crop yield, due to their effects on soil cycling of organic compounds, soil nutrient dynamics. As the underling mechanisms, soil microorganisms play critical roles in regulating the cycling of carbon, nutrient availability and soil fertility since these organisms regulate many fundamental processes. Thus microbial indicators such as microbial diversity and composition are believed to be more dynamic than based on physical and chemical properties, and may have the potential to serve as early indicators of change in the quality of the soil ecosystem. This study determined the effects of phosphorus fertilization on soil bacterial community structures and corresponding changes in soil quality.  A plot experiment on P management for paddy field was established in April 2005 at the demonstration park of YuHang County Agricultural Research Station (3018''51.84""N, 11954''13.37""E) in ZheJiang, China. The soil samples from a field experiment after 7-year of chemical P fertilization with superphosphate along a gradient of 0 (P-0), 30 (P-30), 60 (P-60), 90 (P-90) kg P ha-1.y-1 , using superphosphate since 2005, in order to evaluate the role of P on the bacterial community structure."	root:Environmental:Terrestrial:Soil
MGYS00000783	Rice fields Targeted Locus (Loci)	Genetically modified (GM) crops soil	root:Environmental:Terrestrial:Soil
MGYS00000782	Big Brown Mine Targeted Locus (Loci)	16S rRNA short reads from soil DNA sampled in 2009 at Texas, USA	root:Environmental:Terrestrial:Soil
MGYS00000780	Wuliangsuhai wetland soil ,Wuliangsuhai sediment ,Wuliangsuhai farmland soil Targeted Locus (Loci)	Bacteria are important drivers for biogeochemical cycles in freshwater aquatic environments, particularly nutrient-rich eutrophic lakes. Sediments from Lake Wuliangsuhai and soils from Wuliangsuhai wetland were surveyed to characterize the structure and diversity of its microbial communities using barcoded pyrosequencing based on the 16s rDNA. Investigations of sediment and soil bacterial communities were believed to be able to obtain a better understanding of aquatic and wetland ecosystems. The results of this research identified the relationships they share with their environment; and provide new insights into and add valuable reference for the bacterial communities in eutrophic lakes and wetlands	root:Environmental:Terrestrial:Soil
MGYS00000779	Arctic tundra soils Targeted Locus (Loci)	To understanding the relationships between bacterial community structure and environmental variables in Arctic tundra soil.	root:Environmental:Terrestrial:Soil
MGYS00000778	1996OB Targeted Locus (Loci)	Survey of 16S rRNA genes associated with surface mining-disturbed overburden (1996)	root:Environmental:Terrestrial:Soil
MGYS00000775	Bacterial community structures of soils and anodes of microbial fuel cells	Study the responses of bacterial community structures to bioelectrochemically enhanced remediation of petroleum hydrocarbons contaminated soil	root:Environmental:Terrestrial:Soil
MGYS00000769	Improved Yield of High Molecular Weight DNA Coincides with Increased Microbial Diversity Access from Iron Oxide Cemented Sub-Surface Clay Environments	Despite more than three decades of progress, extraction of high molecular weight (HMW) DNA from soils with high clay or iron oxide cemented clay content has remained challenging. HMW DNA is desirable for next generation sequencing as it yields the most comprehensive coverage in DNA libraries. Several nucleic acid extraction procedures that included liquid N2 grinding and bead milling were compared for preparation of HMW DNA from samples that exhibit strong nucleic acid adsorption. pH manipulation or use of alternative ion solutions (eg. Na2SO4 and NH4H2PO4) offered no improvement in nucleic acid recovery. Lysis by liquid N2 grinding in concentrated guanidine followed by concentrated sodium phosphate extraction supported HMW DNA recovery from clays high in iron oxides and low in humus. DNA recovered using 1 M sodium phosphate buffer (PB) as a competitive desorptive wash was 15.22  2.33 g DNA/g clay, with most DNA consisting of >20 Kb fragments, compared to 2.46  0.25 g DNA/g clay with the PowerlyzerTM soil DNA system (MoBio). Increasing PB concentration in the lysis reagent coincided with increasing DNA fragment length during initial extraction. Rarefaction plots based on 16S rRNA (V1/V3 region) pyrosequencing libraries from A-horizon and clay soils showed an ~80% and ~400% larger accessed diversity compared to a previous grinding protocol or the PowerlyzerTM soil DNA system, respectively. The observed diversity from the Firmicutes showed the strongest increase with >3-fold more operational taxonomic units (OTU) recovered. Additionally, some OTUs having more than 100 sequences in libraries prepared from DNA acquired using the PB desorption method were absent in samples extracted using the PowerLyzerTM reagents or prior lysis methods.	root:Environmental:Terrestrial:Soil
MGYS00000767	DG Metagenome	Swamp soil diversity.	root:Environmental:Terrestrial:Soil
MGYS00000766	RA Metagenome	Swamp soil diversity.	root:Environmental:Terrestrial:Soil
MGYS00000765	Bulk soil Metagenome	Characterization of bacterial community structure from paddy field bulk soil with alfalfa-rice crop rotation.	root:Environmental:Terrestrial:Soil
MGYS00000763	Soil fungal communities and their contributions to SOM cycling	Quantifying the contribution of EM mycelia to SOM turnover is of critical importance to carbon models . In this study, we evaluated a system to trap enzymatically active EM hyphae under field conditions. Natural-substrate filled mesh bags, surrounded by a sand barrier were effective at trapping EM hyphae while minimizing colonization by obligate saprotrophic fungi. The generated fungal communities were similar in composition to those in the surrounding fermentation/humus layer at both trophic and higher taxonomic levels. Consequently, this system allowed us to study the contribution of EMF mycelia to soil enzyme activity and to SOM-C cycling.	root:Environmental:Terrestrial:Soil
MGYS00000761	Metagenomic analysis of an Arctic soil profile	This is a metagenomic study of the microbial community in an Arctic peat soil profile from a medium-aged drained thaw-lake basin near Barrow, Alaska. Four metagenomic libraries were constructed representing depths of 0-10, 10-20, 20-30 and 30-40 cm. The main goal of this work was to analyze the anaerobic respiratory pathways in this soil, with particular emphasis on microorganisms capable of reducing iron and humic substances in anaerobic respiration.	root:Environmental:Terrestrial:Soil
MGYS00000760	Harvard Forest Chronic Nitrogen Addition Soils Targeted Locus (Loci)	Amplicon sequencing of internal transcribed spacers 1 and 2 and large-subunit D2-D3 region of fungi. Sequences derived from the organic soil horizon of a 20+ year nitrogen enrichment experiment in a northeastern US hardwood forest.	root:Environmental:Terrestrial:Soil
MGYS00000758	Bacteria 16S rRNA amplicon pyrosequencing	Bacteria / white rot fungus interaction during wood decay.	root:Environmental:Terrestrial:Soil
MGYS00000756	Linuron contamination of an on-farm biopurification system	Response of the bacterial community in an on-farm biopurification system to linuron contamination studied in several microcosms.  Soil from an on-farm biopurification system was kept as six microcosms with stable temperature and moisture for 25 days. Three of the six samples were treated with the pesticide linuron (25 mg/g) to select for linuron degrading bacteria and plasmids.	root:Environmental:Terrestrial:Soil
MGYS00000754	Soil DNA Soil Bacteria Amplicon Sequencing	Prairie plant associated soil bacteria.	root:Environmental:Terrestrial:Soil
MGYS00000753	Rock Varnish Metagenome	Rock Varnish and associated soil from Cima Volcanic Field and Darwin Pass.	root:Environmental:Terrestrial:Soil
MGYS00000752	farmland soils Targeted Locus (Loci)	Bacterial community compositions in different soil samples.	root:Environmental:Terrestrial:Soil
MGYS00000750	G1E;G2E;G3E Soil Metagenome	This study presented the eukaryotic diversity of the soil in Grove Mountains, East Antarctica, and provided reference for the investigating of the function of the Antarctic ecosystem.  The Grove Mountains area, located in the interior of East Antarctica, is low in rain and temperature. Soil in this area came into shape slowly and formed cold desert soil. To investigate the microeukaryotic diversity of the cold desert soil from Grove Mountains, three soil samples were collected from the south of Mountain Harding during the 26th Chinese Antarctic scientific expedition. After pyrosequencing with a 454 Life Science GS-FLX sequencer, the V4 region of the 18S rRNA gene sequences were analysed, the microeukaryotic diversity of soil from Grove Mountains was generally achieved.	root:Environmental:Terrestrial:Soil
MGYS00000748	PAHs contaminated soil Metagenome	We also have applied 454 pyrosequencing to explore 66,507,993 bp of metagenomic sequence data from the 24 soil samples. The purpose of this study was to identify the dynamic changes of microbial community structure in degradation with effective degradation bacteria Kocuria sp. P10 strain.	N/A
MGYS00000747	1) Glacier Forefront 2) Fungi and Bacteria Community Targeted Locus (Loci)	Early community assembly of soil microbial communities is an essential process for pedogenesis and development of organic legacies. We examined fungal and bacterial succession along a well-established temperate glacier forefront chronosequence representing ~70 years of deglaciation to determine community assembly. As microbial communities may be heavily structured by establishing vegetation, we included non-vegetated soils as well as soils from underneath four plant species with differing mycorrhizal ecologies (Abies lasiocarpa, ectomycorrhizal; Luetkea pectinata, arbuscular mycorrhizal; Phyllodoce empetriformis, ericoid mycorrhizal; Saxifraga ferruginea, non-mycorrhizal). Our main objectives were to contrast fungal and bacterial successional dynamics and community assembly as well as to decouple the effects of plant establishment and time since deglaciation on microbial trajectories using high throughput sequencing.	root:Environmental:Terrestrial:Soil
MGYS00000746	Soil community for preservation Metagenome	Soil was stored at three temperatures over two weeks to determine the most appropriate method for preserving the soil microbiome.  Soil was collected from the mineral soil surface to a depth of ~6 inches underneath a native riparian California bay tree at California Polytechnic State University (N 35 18'' 46.59'''', W 120 39'' 7.26''''). There was substantial organic matter buildup in this soil, but it is serpentinite in nature with low calcium and high magnesium content.	root:Environmental:Terrestrial:Soil
MGYS00000745	Rice paddy soil Targeted Locus (Loci)	Investigation of Methane Emission and Bacterial and Archaeal Communities in Rice Paddy Soil during Rice Cultivation.	root:Environmental:Terrestrial:Soil
MGYS00000744	Arable soils under rice-wheat cropping system	Fertilization is a common practice to improve plant nutrient and increase crop production, but it can also affect soil bacterial communities. In addition, soil microbial communities are dynamics in seasonal changes. Therefore, this study focuses on the responses of bacterial communities in arable soils under rice-wheat cropping system to different fertilizer regimes and sampling time.	root:Environmental:Terrestrial:Soil
MGYS00000743	Soil sample Metagenome	The study aims to determine factors which determine the diversity and species distribution of fungi (especially ectomycorrhizal fungi) in forest soils.  Pine forest sample - buried mesh bag containing sterile sand and DNA extracted from sand after 2 months burial in forest soil (approx 10 cm depth).	root:Environmental:Terrestrial:Soil
MGYS00000742	PCP contaminated soil samples Metagenome	The main objective of the project was to compare the diversity of soil bacterial communities estimated using the Ion Torrent PGM or a new framework based on DGGE profiling.  Two differently textured soils were divided into 4 subsamples. For each soil, three subsamples were contaminated with pentachlorophenol at concentrations of 300, 900 and 3000 mg/kg.	root:Environmental:Terrestrial:Soil
MGYS00000741	Old Rifle Site metagenome	Metagenomic DNA from soil and from bottle cultures innoculated with soil form the Old Rifle Uranium Mill Tailing site.	root:Environmental:Terrestrial:Soil
MGYS00000739	F1RT Metagenome	Metacellulosomics-driven discovery of bacterial synergism in a soil-derived cellulose-degrading community.	root:Environmental:Terrestrial:Soil
MGYS00000735	Soil microbial communities from the Bolivian Altiplano Targeted Locus (Loci)	Characterize the response of soil fungal and bacterial communities to fallow period length and to a common fallow shrub in the Bolivian Highlands called ''thola''.	root:Environmental:Terrestrial:Soil
MGYS00000733	Arctic soil Metagenome	The study aimed to determine how inhibitors would affect the microbial community structure and hydrocarbon-degrading activity within an Arctic soil.  Bulk Arctic soil treated with diesel and various inhibitor combinations.	root:Environmental:Terrestrial:Soil
MGYS00000732	Cerrado soil Metagenome	Despite the significant ecological and economical importance of the Cerrado, little is currently known about its biodiversity, especially concerning its soil microbial diversity.A still open question is how different land use systems influence the diversity and structure of microbial communities under the same soil type. In this context, the aim of this work was to analyze and compare the soil bacterial communities from Cerrado under different land use systems using high throughput pyrosequencing of 16S rRNA genes.  The research was performed on soil samples from agricultural and natural areas in the Triangulo Mineiro region in the state of Minas Gerais, Brazil, at 1858 S and 4702 W and 939 m above the sea level. A total of 12 soil samples (three for each environment) were chosen for sampling and were taken from four locations under Natural Forest (mesophilic forest comprised by species of Qualea grandifolia, Bowdichia virgilioides, Pterodon pubescens, Caryocar brasiliense, Vatairea macrocarpa, Astronium fraxinifolium, Eugenia dysenterica, and Hymenaea stigonocarpas), Grassland (used for grassing, comprised by Brachiaria decumbens ~ 20 years old), Sugarcane field (monoculture of sugarcane ~15 years old and annually fertilized with P, K and N) and Coniferous Forest (dense forest of Pinus caribaea var. hondurensis with 32 years old; the soil surface presented a 10 cm layer of litter consisting of needles, cones and woodchipsan area).	root:Environmental:Terrestrial:Soil
MGYS00000731	gts.soil.sample Metagenome	Soil fungi in Gutianshan.	root:Environmental:Terrestrial:Soil
MGYS00000729	Soil bacterial diversity shifts after digestate and chemical fertiliser treatments	Comparing the effect of digestate and chemical fertiliser on soil bacteria.	root:Environmental:Terrestrial:Soil
MGYS00000728	The diversity of culturable soil bacterial communities	Understanding the difference in community composition between culturable and unculturable soil bacteria.	root:Environmental:Terrestrial:Soil
MGYS00000726	Soil Targeted Locus (Loci)	Analysis the microbial composition change after co-cultivating with some substrates.  Norway peat soil that has been amended for more than 30 years.	root:Environmental:Terrestrial:Soil
MGYS00000724	Microbial community at industrially contaminated site Metagenome	The taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges.  The soil sample was collected from the contaminated banks of Khari-cut canal.	root:Environmental:Terrestrial:Soil
MGYS00000723	Mars Oasis Metagenome	A random soil sample from Mars Oasis, Antarctica.	root:Environmental:Terrestrial:Soil
MGYS00000722	Bacterial Diversity of the Cold Desert Soil from Grove Mountains, East Antarctica	This study presented the bacterial diversity of the soil in Grove Mountains, East Antarctica, and provided reference for the investigating of the function of the Antarctic ecosystem.	root:Environmental:Terrestrial:Soil
MGYS00000721	Phototrophs Metagenome	454 amplicon pyrosequencing was used to assess bacterial (16S rRNA), fungal (ITS region) and phototroph (23S rRNA genes of plastids) community structure at the soil surface (upper 3mm) of pasture soil following incubation under light (16hr:8hr light:dark cycle) and dark conditions for 80 days.  Phototrophs at Gartenacker soil surface.	root:Environmental:Terrestrial:Soil
MGYS00000717	Soil in greenhouse China Metagenome	This research, by means of 454 pyrosequencing, determined the effects of 1,3-D on the bacterial community. The results of this study will evaluate the effects of 1,3-D on the soil bacterial community of greenhouse vegetable industry and offer a theoretical foundation to the use of 1,3-D on greenhouse vegetable industry.  These soil samples were collected in in a commercial field near Fang county, Taian City, Shandong province, China. The soil at the experimental site was a silt loam, composed of 15% sand, 80% silt, and 5% clay, with an organic matter content of 24.8 g kg-1 of soil, pH 7.2, and a soil density of 1.21 g cm-3	root:Environmental:Terrestrial:Soil
MGYS00000709	Bacterial community diversity and structure of winter wheat-cultivated soils	Bacterial community diversity and structure of two typical grain food rotations of winter wheat-rice and winter wheat-maize soon after wheat harvested are studied. It will help us have a knowledge of sustainable agriculture systems.  In this study, soil samples were collected soon after winter wheat harvest from two typical rotation systems, i. e. winter wheat-rice located in Changshu (CS), Jintan (JT), and Zhangjiagang (ZJG), Jiangsu province and winter wheat-maize located in Dezhou (DZ), Shandong province, and in Quzhou (QZ), Hebei province in China.	root:Environmental:Terrestrial:Soil
MGYS00000708	Peat layer 16S amplicon	Peat-accumulating ecosystems playing a key role in the global carbon and water budget.  Surface and subsurface peat layers of a northen wetland.	root:Environmental:Terrestrial:Soil
MGYS00000707	Soil aquifer treatment site soil samples and simulated conditions Metagenome	Effect of initial concentration of pharmaceuticals and personal care products on their removal in laboratory-scale biofilm columns.  Soil samples taken from soil aquifer treatment site over wetting cycle and simulated soil samples from laboratory columns.	root:Environmental:Terrestrial:Soil
MGYS00000705	Rice paddy soil Targeted Locus (Loci)	To investigated the bacterial and archaeal diversity in the rice paddy soils which have been fertilized for 23 years.	root:Environmental:Terrestrial:Soil
MGYS00000698	Soil samples Targeted Locus (Loci)	Analysis of the taxonomic composition of soil microbiome for the microbiological mapping of the soil types in order to improve agronomic practices.  16S rRNA gene pyrosequencing from the various soil types in Russia.	root:Environmental:Terrestrial:Soil
MGYS00000694	Permafrost soil along CRCOP Metagenome	Bacterial biodiversity was investigated by 454 pyrosequencing of 12 soil samples from 4 different permafrost sites along the China-Russia Crude Oil Pipeline, in order to reveal the background communities for assessing the impact of accidental oil spills on intrinsic bacterial consortia.	root:Environmental:Terrestrial:Soil
MGYS00000693	Soil microbial diversity of 106 samples Metagenome	These data contain the information about the response of soil bacterial diversity and composition to multi-factorial environmental changes, including increased precipitation, rising temperature, adding nitrogen, adding phosphorus, removing plant functional groups, grazing, and some of their combination. Specifically, C8,C10,C12,C32 and C33 represent the treatment of removing no plant functional group; C5,C6,C9,C11,C13,C14,C21,C22,C23,C24,C25,C28,C29,C39 and C40 represent the treatment of removing one plant functional group; C1,C2,C4,C7,C17,C18,C19,C20,C26,C3,C30,C34,C35,C36 and C38 represent the treatment of removing two plant functional groups; and C15,C16,C27,C31,C37 represent the treatment of removing three plant functional groups. Meanwhile, D16,D23,D32,D40,D47,D51 and D64 represent the control; D18,D19,D46,D55,D60 and D9 represent the treatment of warming; D22,D36,D38,D41,D42,D56 and D57 represent the treatment of watering; D15,D31,D37,D39,D4 and D50 represent the treatment of simultaneous warming and watering; D21,D26,D58 and D63 represent the treatment of adding phosphorus; D30,D34,D49 and D65 represent the treatment of adding nitrogen; D14,D35,D45 and D5 represent the treatment of simultaneous adding N and watering; D17,D48,D54 and D6 represent the treatment of simultaneous adding N and P; D25,D62,D66 and D8 represent the treatment of grazing; D11,D2,D43 and D59 represent the treatment of simultaneous grazing and watering; D10,D29,D3 and D44 represent the treatment of simultaneous grazing and adding P; D27,D28,D33 and D7 represent the treatment of simultaneous grazing and adding N; D1,D12,D20 and D52 represent the treatment of simultaneous grazing and adding N and watering; D13,D24,D53 and D61 represent the treatment of simultaneous grazing and adding N and P.	root:Environmental:Terrestrial:Soil
MGYS00000690	An Evaluation of the Impact of Multi-walled Carbon Nanotubes on Soil Microbial Community Structure and Functional Diversity	The goal of this project was to evaluate the effects of multiwalled carbon nanotubes on microbial community in soil (functionality as well as community composition) at different exposure concentration.	root:Environmental:Terrestrial:Soil
MGYS00000673	Mock and soil DNA Targeted Locus (Loci)	Study on the effects of the type of polymerase and PCR cycle number on the accuracy of pyrosequencing analysis of bacterial community.	root:Environmental:Terrestrial:Soil
MGYS00000669	Organic Farm Targeted Locus	16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing based on soil surface samples collected from the first certified organic farm (Tune Farm) in Alabama.	root:Environmental:Terrestrial:Soil
MGYS00000666	PAMPA Dataset: Argentinean agricultural pampean soils Metagenome	Soil microbial communities are among the most diverse and complex environments in the world. Our information about the identity and metabolic capabilities of terrestrial microbes is still scarce. Moreover, although microorganisms in soil are essential for nitrogen, carbon, phosphorous and sulfur cycling as well as plant growth and crop production, only a few microbial species involved in these processes have been described in detail. The future years will face the challenge of increasing agricultural yields conserving soil microbial communities and soil quality. To do so, a better comprehension of micro-ecosystem functioning and microbial description will be needed. As a first modest approach towards the understanding of soil microbial communities and how land use affects them, we have generated a metagenomic dataset obtained by high throughput sequencing of samples from Argentinean Pampas. Three different geographic regions, three different types of land uses and two soil types (bulk and rhizospheric) were analyzed using whole genome shotgun (WGS) and amplicon sequencing. A total of 19 Mi (7.7 Gb) WGS reads and over 1 Mi 16 rRNA pyrotags were generated. Our preliminary results suggest that soil microbial communities are different at both, taxonomic and metabolic level, on each type of tillage system and geographic region in bulk soils. Rhizospheric microbial communities resulted markedly different from those in bulk soils and less sensitive to the type of tillage system. This dataset is the first soil metagenomic study in Argentina and one of the few available in the world. This should be considered as a kick-start for future efforts towards a better comprehension of soil microbial communities in agricultural systems in the Argentinean region and a useful comparison dataset for other regions in the world.	root:Environmental:Terrestrial:Soil
MGYS00000665	Bacterial 16S rRNA genes from heavy-metal contaminted soils Targeted Locus (Loci)	Analysis of bacterial diversity in heavy metal-contaminated soils.	root:Environmental:Terrestrial:Soil
MGYS00000662	Biochar-amended soil Targeted loci environmental	To evaluate the effect of biochar-mineral complexes on organic soil microbial communities.	root:Environmental:Terrestrial:Soil
MGYS00000661	Soil from Cuatro Cienegas Basin, Coahuila, Mexico Targeted Locus (Loci)	The purpose of this study was to follow microbial succession following sterilization of soil plots in arid and humid locations within the Cuatro Cienegas Basin, a desert oasis.	root:Environmental:Terrestrial:Soil
MGYS00000649	Active ammonia oxidizers in an acid soil are phylogenetically closely related to neutrophilic Nitrososphaera viennensis	All cultivated ammonia-oxidizing archaea (AOA) within the Nitrososphaera cluster (former soil group 1.1b) are neutrophilic. Molecular survey also indicates broad existence of Nitrososphaera-like phylotype in acid soil, but its ecological role is poorly understood. In this study, we present molecular evidences for chemolithoautotrophic growth of the Nitrososphaera-like AOA in an acid soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by significant increase in abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis of amoA genes as a function of buoyant density of DNA gradient following ultracentrification of the total DNA extracted from SIP microcosms indicated substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the heavy DNA fractions suggested that archaeal and nitrite-oxidizing bacterial communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that 13CO2 assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting chemolithoautotrophic lifestyle. Sequencing analysis of both amoA and 16S rRNA genes revealed that the 13C-labeled AOA were phylogenetically closely related to neutrophilic strains Nitrososphaera viennensis EN76 and JG1 within the Nitrososphaera cluster. Our results provide strong evidence for the adaptative growth of Nitrososphaera-like AOA in acid soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated.	root:Environmental:Terrestrial:Soil
MGYS00000621	Soil Metagenome	Effects of functionalized multi-walled carbon nanotubes on soil bacterial community composition.	root:Environmental:Terrestrial:Soil
MGYS00000385	Sulfidic cave snottites Metagenome	Snottites are extremely acidic (pH 0-2) biofilms that form on the walls and ceilings of H2S-rich caves. We investigated the community composition, metabolic potential, and biogeochemistry of these biofilms using metagenomics in combination with full-cycle rRNA and other methods.	root:Environmental:Terrestrial:Rock-dwelling (subaerial biofilm)
MGYS00004382	Targeted loci sequencing of anaerobic benzene-degrading enrichment cultures	This project aims to characterize the microbial community of anaerobic benzene-degrading cultures originating from different subsurface environments. In this project, we used 454-based DNA amplicon sequencing targeting v6-v8 region of 16S rRNA genes.	root:Environmental:Terrestrial:Deep subsurface
MGYS00004362	Hot springs Metagenome	Investigation of microbial diversity	root:Environmental:Aquatic:Thermal springs:Sediment
MGYS00004689	Cave sediment Metagenome	Bacterial diversity in Farpuk cave, Mizoram	root:Environmental:Aquatic:Sediment
MGYS00004645	microbial community diversities of Tuosu Lake	Detecting the bacterial, archaeal and fungal population diversities in Tuosu Lake	root:Environmental:Aquatic:Sediment
MGYS00004631	freshwater sediment metagenome Raw sequence reads	horizontal sediment samples in different seasons from Dianchi Lake and Erhai Lake	root:Environmental:Aquatic:Sediment
MGYS00004584	16S sequencing of environmental samples to test the impact of sediment source	The Broad Institute sequenced environmental samples to tests the impact of sediment source, supplemental cellulose source, and depth within Winogradsky columns, on microbial community structure. The study was conducted, in part, within introductory microbiology courses at Vassar College (Poughkeepsie, NY) and Williams College (Williamstown, MA). Sequencing was conducted at the Broad Institute (Cambridge, MA). Winogradsky columns were created from sediment collected near the edge of two small ponds (under approximately 15-30 cm of water) in late October 2008. Ponds were located near the campus of Williams College in Williamstown, Massachusetts: Buxton Pond (N 42.70o (42 o 42 15)  W 73.2114 o (73 o 12 41) and Ephs Pond (N 42.7201o (42 o 43 12)  W 73.1975 o (73 o 11 51).	root:Environmental:Aquatic:Sediment
MGYS00004459	MeHg Coal Ash	Mercury (Hg) associated with coal ash is an environmental concern, particularly if the release of coal ash to the environment is associated with the conversion of Hg to methylmercury (MeHg), a bioaccumulative form of Hg that is produced by anaerobic microorganisms. In this study, sediment slurry microcosm experiments were performed to understand how spilled coal ash might influence MeHg production in anaerobic sediments of an aquatic ecosystem. Two coal ash types were used: (1) a weathered coal ash; and (2) a freshly collected, unweathered fly ash that was relatively enriched in sulfate and Hg compared to the weathered ash. These ash samples were added to anaerobic sediment slurries constructed with a relatively pristine sediment (containing 0.03 mg kg-1 Hg) and a Hg-contaminated sediment (containing 0.29 mg kg-1 Hg). 16S amplicon sequencing of microbial communities in the slurries was done for each microcosm.	root:Environmental:Aquatic:Sediment
MGYS00004419	Lake Washington sediment enrichments	In this study, we addressed the role that provided nitrogen plays in determining the composition of methane-consuming communities and the methane oxidation potential in a well-studied model system. We applied a multi-phase approach combining microcosm enrichments and pure culture studies with methane oxidation potential measurements and high throughput sequencing. We focused on incubation conditions with a limited O2 availability as observed in the natural environment. 16S rRNA gene profiling showed that with N2 as the only available nitrogen source, communities were dominated by Methylomonas species as the major methane-oxidizing bacteria (MOB). In the presence of added nitrate however, Methylobacter species were the dominant MOB. Pure culture studies of Methylomonas and Methylobacter isolated from the same environment and incubated in the same way confirmed that the growth of a Methylomonas strain was not significantly affected when N2 was the only provided nitrogen source, while growth of a Methylobacter strain was negatively impacted. By further exposing long-term methane fed microbial communities to different nitrogen sources, intraspecific dynamics of non-methanotrophic community members were observed, suggesting nitrate as an additional selective factor for co-occurring species. Our results show that provided nitrogen source is an important factor determining specific responses of individual community members and consequently affecting community composition and overall methane consumption.	root:Environmental:Aquatic:Sediment
MGYS00004418	Fluctuating redox regimes raw sequence reads	Evaluate the changes in the active microbial community due to fluctuating, stable oxic and stable anoxic redox conditions.	root:Environmental:Aquatic:Sediment
MGYS00004408	Sediment saline lake Grevelingen (Netherlands) Raw sequence reads	Microbial diversity in sediment of the saline lake Grevelingen (Netherlands)	root:Environmental:Aquatic:Sediment
MGYS00004405	Old Rifle sediment Raw sequence reads	A systematic column study compared the interactive effects of acetate amendment, sediment geochemistry, and bacterial community composition on in-situ bioremediation of U(VI) using sediments from the subsurface at the U.S. Department of Energys Integrated Field Research Challenge site in Rifle, Colorado that were either contaminated or non-contaminated by a uranium plume.	root:Environmental:Aquatic:Sediment
MGYS00004400	Bacterial biogeography of a High Arctic ice cap	This study investigates the roles of dispersal, environmental and biotic filtration in bacterial assemblies, in order to understand the environmental influences in cryoconite ecosystems. Foxfonna dome is used as a model ecosystem to observe the bacterial biogeography of an ice cap.	root:Environmental:Aquatic:Sediment
MGYS00004397	Transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines)	In the Zambales ophiolite range, terrestrial fluid seeps host diverse microbial communities, which may be supported by hydrogen gas generated via serpentinization. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. These data provide context for future serpentinizing seep ecosystem studies, particularly in tropical biomes.	root:Environmental:Aquatic:Sediment
MGYS00004396	Sediment bacterial diversity	This study investigated the effects of salmonid aquaculture on microbial diversity and community composition of sediments in Chiloe, southern Chile using Roche 454 GS-FLX of the 16S ribosomal RNA gene. Bacterial diversity was found to be significantly lower in aquaculture sites than in reference sites. Bacterial communities were found to differ significantly between reference and aquaculture sites, but OTU richness was not significantly different between sites. The bacterial groups significantly enriched in aquaculture sites were genera belonging to Bacteroidetes (Flavobacteria) and Gammaproteobacteria, which play key roles in organic matter mineralization and sulfur oxidation. These findings show that current practices related to Chilean salmonid aquaculture alter the structure and functionality of marine microbial communities in sediments and suggest major changes in the biogeochemical processes.	root:Environmental:Aquatic:Sediment
MGYS00004391	Sewer sediments Targeted loci environmental	16S rRNA gene metagenomic study of sewer sediments	root:Environmental:Aquatic:Sediment
MGYS00004377	Boreal lake sediment 16S rRNA gene amplicon (454-pyrosequencing) raw sequence reads	Boreal lake sediment 16S rRNA gene amplicons	root:Environmental:Aquatic:Sediment
MGYS00004376	Antimony contaminated sediments Raw sequence reads	Water and surface sediments were collected from six sites with different extent of Sb contamination along Chahe watershed and were analyzed for geochemistry as well as bacterial diversity.	root:Environmental:Aquatic:Sediment
MGYS00004364	Deep Subsurface Basalts Targeted Locus (Loci)	Approximately 42% of the continental crust is composed of mafic magmatic rocks, such as basalts. These rocks often manifest themselves as massive areas known as large igneous provinces (LIPs). LIPs cover thousands to millions of square kilometers and thus comprise major portions of the subsurface and the biosphere. LIPs, and more specifically basalts, are known to be chemically reactive and favorable for microbial life due to the abundance of reduced compounds in the rock.  LIPs exist both in marine systems and terrestrial systems. In marine systems, microorganisms are known to extensively interact with minerals in basalt and may play a large role in the global biogeochemical cycles of C, Fe, and S. Sources of energy available to lithoautotrophic microorganisms below the seafloor include minerals containing reduced Fe and S and also H2 generated from water-rock reactions. Hydrogen is of particular interest in terrestrial subsurface basalt systems, where the subsurface lithoautotrophic microbial ecosystem (SLiME) hypothesis originated. SLiMEs are microbial communities that subsist in deep oligotrophic environments without utilizing energy rich reduced organic compounds that originated from photosynthesis. SLiMEs were first hypothesized to exist in the Columbia River Basalt Group (CRBG). Basalt systems also host diverse communities apart from SLiMEs, such as microbial communities consisting of iron reducers, sulfate reducers, acetogens, and methanogens. In the basaltic Snake River Plain Aquifer (SRPA) in Idaho, microbial communities cycle carbon by forming and oxidizing methane.  Today, LIPs are being examined as potential geological storage sites for carbon dioxide in an attempt to sequester CO2 away from the atmosphere to alleviate temperature increases due to climate changes. The Wallula pilot well being used for a geologic carbon sequestration project in eastern Washington State and located in the CRBG provides a window to the subsurface where the microbial diversity of these geologically important regions can be explored. In addition, the well will provide insight into the microbial communities present in the basalts that could play a role in carbon cycling in the deep subsurface where supercritical CO2 (scCO2) is injected.  Analyzing samples from the CRBG using deep DNA sequencing technology will further the understanding of the unique microbial diversity of the subsurface, especially with respect to community composition of LIPS and different members contained in different formations. Pyrosequencing will also establish an important baseline for understanding the microbial communities in the aquifers of the Wallula pilot well prior to the injection of scCO2. These communities will certainly change following the injection and pyrosequencing could play a critical role in the analysis of the samples obtained after the injection of scCO2 into the system. The high resolution associated with deep sequencing technology would allow the detection of shifts in the diversity of the microbial communities.  All samples presented here originated from the Wallula pilot well in eastern Washington State. The well penetrates through three Columbia River Basalt formations, the deepest of which is targeted for carbon sequestration. This study aimed to characterize the microbial community prior to the injection of carbon dioxide to provide a baseline for comparison after carbon has been stored in the basalt. Samples Wal213, Wal220, Wal31, Wal39, and Wal413 were collected from pristine formations as the well was drilled using a progressive drill-and-test technique that provides samples more representative of the formation of origin. Quality of the samples was also ensured due to the use of an underbalanced drilling technique in which water from the formation acted as drilling fluid, as well as the collection of samples after extensive pumping of the well. Sample Wal34 was collected 2 years after the completion of the well. The microbial diversity of other locations in the Colombia River Basalt Group has been investigated previously (Stevens et al., 1993; Stevens and McKinley, 1995; Fry et al., 1997), but not at the location of the Wallula pilot well and not using sequencing technology which provides a more complete picture of the microbial community. A more detailed description of the Wallula pilot well can be found in the 2009 report Preliminary Hydrogeologic Characterization Results from the Wallula Pilot Study by McGrail et al. (report number PNWD-4129).	root:Environmental:Aquatic:Sediment
MGYS00004363	Sippewissett Salt Marsh tide pool sediment Targeted Locus (Loci)	Bacterial community phylogenetic study in sediments of salt marsh	root:Environmental:Aquatic:Sediment
MGYS00004358	KB34 Transcriptome or Gene expression	Eubacterial and archaeal community identification in historically contaminated subsurface sediment and community shift during PHC degradation under given experimental conditions.  Historically contaminated subsurface sediment was used to monitor hydrocarbon degradation behavoir under sulphate reducing and methanogenic conditions over 450 days. Total RNA was isolated from experimental sets and reverse-transcribed to cDNAs. Phylogenetic marker gene 16S rDNA was amplified with eubacterial and archaeal universal primers and amplicons were sequenced on Roche 454 sequencing platform.	root:Environmental:Aquatic:Sediment
MGYS00004353	Salt marshes sediment microhabitats Metagenome	In the present study, microbial communities of bulk and rhizosphere sediments were investigated using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial richness and composition of bulk sediment and two plant species inhabiting salt marsh systems. FLX 454 titanium pyrosequencing study. Note that the sequences submitted are raw sequences after demultiplexing thus without a chimera check and other quality filtering. These will need to be filtered out using, e.g., using qiime scripts such as split_libraries and pick_otus with the usearch_ref argument, which will provide a chimera check and filter out poor quality sequences.	root:Environmental:Aquatic:Sediment
MGYS00004315	Bacterial communities from Thrombolites of Lake Sarmiento	The aim of this study was to examine the bacterial diversity of field (lived) versus cultured (kept in an aquarium system) thrombolites from Sarmineto Lake by sequencing of the V4 hypervariable region of the 16S rRNA gene. We attempt to reveal the chemical composition (before and after culturing) of our samples and to compare the bacterial populations founded with those from worldwide sites where microbialites thrive, in order to discern bacterial communities drivers within similar ecosystems.	root:Environmental:Aquatic:Sediment
MGYS00004285	zooplankton environmental sample Metagenome	COI sequences of Zooplankton in Lake Tai Metagenome	root:Environmental:Aquatic:Sediment
MGYS00004247	Biogeography of subsurface prokaryotic communities along with sediment deposition of sediments	454 pyrosequencing of 16S rRNA gene amplicons were used to investigate the geological distribution of bacteria and archaea along with salinity.	root:Environmental:Aquatic:Sediment
MGYS00004503	Saltern of Margherita di Savoia Metagenome	We analyzed the prokaryotic communities of the Salterns of Margherita di Savoia (Italy).	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
MGYS00004495	Saltern microbial community diversity	Microbial diversity analysis	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
MGYS00004474	Saltern microbial community diversity	Microbial diversity analysis	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
MGYS00004443	Metagenomics Cabo Rojo Salterns	Culture independent study of microbial communities in hypersaline environments in a tropical solar saltern in Cabo Rojo, Puerto Rico. This project aims to determine the diversity present using direct 16S rRNA amplification. A different diversity is expected due to the stable conditions year round which in turn may lead to identification of new species.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
MGYS00004374	Protistan plankton diversity along salt gradient	High-throughput pyro-sequencing was used to investigate protistan diversity in solar saltern ponds	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
MGYS00004314	solar evaporation pond sample Metagenome	metagenomic data of solar evaporation pond of ramnagar, west bengal, india.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
MGYS00001943	Saltern bacteroidetes	Uncultured bacteroidetes were directly recovered from the solar saltern CR30 (Santa Pola, Alicante, Spain) by using fluorescence activated cell sorting and then single cell were lysed and their genomes amplified by multiple displacement amplification. Finally, genomes were sequenced by Illumina technology.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
MGYS00004345	Microbial mats and sediments from Atacama	Atacama region in Chile is one of the most arid locations in the world. Extreme conditions in the area include: high UV irradiation, hypersalinity, drastic temperature changes, and desiccation. Hypersaline lakes can be found in this environment, and therein, bacterial communities thrive, forming different structures and colonizing varied niches. Given that the conditions in the lakes have important seasonal changes, including mainly temperature and dissecation, it is interesting to study the composition and evolution of these communities, and also its influence in the biogeochemical setting. In this dataset of bacterial diversity assessed by pyrosequencing V4 region of 16S rRNA gene, microbial mats and sediments from several lakes in Atacama region in Chile, including Coposa, Pucsa, Llamara, and Cejar, were analyzed.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
MGYS00004343	Llamara 1 evaporites metagenome	Domal evaporitic structures on Salar de Llamara are analyzed to study microbial diversity in the community inhabiting the evaporite.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
MGYS00004308	Raw sequence reads	Archaeal and bacterial 16S rRNA sequence from sediments sampled from Great Salt Lake, Utah, USA	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
MGYS00004304	Hypersaline sapropels Targeted loci environmental	The purpose of the present study was to describe and link the prokaryotic diversity in two disparate hypersaline sapropels (Transylvanian Basin, Central Romania), with nutrient and geochemical data in order to infer the role of the microbiome in their formation.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
MGYS00004555	Socompa Lake Stromatolite Shotgun Metagenomic Sequencing	With the altitude of 3570 m, this is so far the highest site where actively forming non-lithified stromatolites have been found, located at the shore of a volcanic, alkaline lake Socompa (Argentina). These microbial communities are a hotspot of biodiversity thriving under harsh environmental conditions that might be compared to Early Earth. This study uses a WGS strategy to understand the unique community composition and the mechanisms used by their members to withstand the extreme environment.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00004095	Antarctic Lakes Brine Raw sequence reads	The Tarn Flat area is the largest ice-free area (ca. 11  9 km) north to the McMurdo Dry Valley in Victoria Land (Antarctica). The aim was to identify the biodiversity differences in hypersaline brines; understanding the reasons of these differences, considering that brines might contain DNA and RNA molecules that remain trapped inside for long geological eras, thus representing a key to reconstruct past ecosystems.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00000384	Santa Pola Saltern Metagenome	Filtered water samples from hypersaline ponds of Santa Pola Saltern, Spain.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00001497	Soda Lakes Metagenome	The objective of this study was to explore the microbial diversity within the soda lakes in Kenya. Soda lakes represent some of the extreme but highly productive environments on earth. The microbial diversity on these environments is of interest in biotechnological applications. The data presented here give the first detailed study of the microbial taxa resident within lakes Magadi, Elmenteita, Crater Lake Sonachi and Bogoria in Kenya	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline:Sediment
MGYS00004578	Great Sippewissett Marsh Plot nirS Targeted Locus	nirS amplicon sequences from Great Sippewissett Marsh plot fertilization experiments	root:Environmental:Aquatic:Marine:Wetlands:Sediment
MGYS00004544	Biogeography of coastal wetland bacterial communities experiencing sudden vegetation dieoff	This study aims to describe how sediment microbial communities respond to the loss of vegetation through sudden vegetation die off (SVD) in two geographically separated wetlands. Further, samples were collected in the summer and fall to characterize temporal dynamics of the communities.	root:Environmental:Aquatic:Marine:Wetlands:Sediment
MGYS00004451	Sediment metagenome	Anaerobic methane oxidizing enrichment sampled from coastal tropical wetland	root:Environmental:Aquatic:Marine:Wetlands
MGYS00004189	Mud volcano Metagenome	Mud Volcano	root:Environmental:Aquatic:Marine:Volcanic
MGYS00004661	East China Sea environmental 16S rRNA gene pyrosequencing	To study the bacterial community structure of seawater samples of the ECS	root:Environmental:Aquatic:Marine:Sediment
MGYS00004658	cultured bacteria from enrichment culture Raw sequence reads	To targeted culture marine bacteria after enrichment culture	root:Environmental:Aquatic:Marine:Sediment
MGYS00004655	nirS-Encoding and nirK-Encoding Denitrifiers in the Sediment of Daya Bay Raw sequence reads	Surface sediments (upper 2 cm) were collected in spring (March 2016), summer (August 2016) and winter (December 2015) from four different locations in Daya Bay.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004654	A comparison of eukaryote community composition in four contrasting sediments in the Celtic Sea	As part of the NERC funded Shelf Seas Biogeochemistry program, microbial structure, diversity and abundance was compared in four contrasting sediment types, from mud to sand. Samples were collected before (March 2015) and immediately after a spring diatom bloom (May) and also again in late summer (August). These data are 16S rRNA and 18S rRNA gene sequence sets from the four sediment types, and from the three sampling time points. Relative abundance and composition was determined using Illumina MiSeq (MrDNA, TX, USA). The V1V3 region of 16S rRNA was amplified using the PCR primers 27F (Vergin et al., 1998) and 519Rmod (Andreotti et al., 2011) using the PCR and sequencing conditions described in Tait et al. (2015). For 18S rRNA genes, the primers Euk7F and Euk570R were used.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004642	Characteristics of SRB community in Sediments from the East China Sea by high-throughput sequencing	The diversity and composition of SRB in sediments from the East China Sea was investigated based on the high-throughput sequencing analyses of the dsrB gene	root:Environmental:Aquatic:Marine:Sediment
MGYS00004627	marine sediment metagenome Targeted Locus (Loci)	Cores were collected over a year long period from sites associated with three transects in the northern Gulf of Mexico. Surface sediments were analyzed to determine patterns in Bacteria and Archaea within these samples and comparisons made to patterns observed for microeukaryotes. The study aimed to determine how location, season and sediment characteristics influence diversity and community structure. Similarities or differences in patterns among the three domains were identified.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004623	Detection and diversity of nitrite oxidoreductase alpha subunit (nxrA) gene of Nitrospina in the marine sediments	nxrA gene abundance and diversity in sediments	root:Environmental:Aquatic:Marine:Sediment
MGYS00004622	illumina high-throughput sequencing of AOB community	Microbial ecology of AOB community	root:Environmental:Aquatic:Marine:Sediment
MGYS00004621	Pyrosequencing of AOB community	Microbial ecology of ammonia-oxidizing bacteria	root:Environmental:Aquatic:Marine:Sediment
MGYS00004609	Denitrifying communities in marine sediments incubated under different oxygen regimes.	The aim of this study was to understand how oxygen regimes control denitrifying communities with the genetic capacity to reduce nitrous oxide. The study highlights importance of oxygen as a factor influencing the genetic potential for N transformations in marine sediments.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004598	Diversity of methyl alkyl succinate synthase genes in hydrocarbon seep sediments (Raw sequence reads)	In this study, the potential of hydrocarbon biodegradation in marine sediments was determined through the detection of a functional biomarker, the masD gene encoding (1-methyl-alkyl) succinate synthase, the key enzyme of anaerobic alkane degradation. We studied the masD diversity in 12 sampling sites from 7 methane, gas and hydrocarbon seeps differing in water depth, sediment depth, temperature, sulfate reduction rate and hydrocarbon composition (alkanes, aromatics) by parallel 454-tagged sequencing.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004524	marine sample sequencing	microbial diversity	root:Environmental:Aquatic:Marine:Sediment
MGYS00004523	environmental sample sequencing	microbial diversity	root:Environmental:Aquatic:Marine:Sediment
MGYS00004507	Guaymas Basin and Sonora Margin sediment Targeted loci	Our proposed microbial analyses of Guaymas Basin and Sonora Margin subsurface sediments are guided by the working hypothesis that microbial communities will change in composition and metabolic potential, as hydrothermal activity decreases across the ridge flanks, chemical and thermal gradients are attenuated, and substrate availability changes. We propose that the distinctly different lithological and hydrothermal histories of these sediments, and their depositional contexts and changing quality and quantity of buried organic matter will affect the microbial community composition and activity.PI: Andreas Teske	root:Environmental:Aquatic:Marine:Sediment
MGYS00004381	Artificial stream sediment raw sequence reads	This study used artificial stream mesocosms to assess the effects of a single addition of nano-TiO2 (P25 at a final concentration of 1 mg L-1) on the abundance, activity and community composition of sediment-associated bacterial communities. The addition of nano-TiO2 resulted in a rapid (within one day) decrease in bacterial abundance in artificial stream sediments, but bacterial abundance returned to control levels within 3 weeks. Pyrosequencing of partial 16S rRNA genes did not indicate any significant changes in the relative abundance of any bacterial taxa with nano-TiO2 treatment, indicating that nano-TiO2 was toxic to a broad range of bacterial taxa and that recovery of the bacterial communities was not driven by changes in community composition.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004380	Assessing the effects of salmon farming seabed enrichment using bacterial community diversity and high throughput sequencing	16S bacterial sequencing of DNA and RNA taken from around marine sediment under and around salmon farm cages.Published 2015 FEMS	root:Environmental:Aquatic:Marine:Sediment
MGYS00004310	sediment metagenome Metagenome	Benthic communities in the aquatic ecosystem are influenced by both natural and anthropogenic stressors. To understand the ecogenomic responses of sediment communities to the multiple stressors of polluted environments, the bacteria, protistanand metazoan communities in sediments from marine and adjacent riverine areas of North Bohai Sea were characterized by environmental DNA meta-systematics, and their associations with environmental variables were assessed bymultiple statistical approaches. The structures of communities in sediments were shaped by both natural variables and anthropogenic contaminants, including DDTs, PAHs or metals. Particularly, the correlation network of multiple communities was modulated by the concentrationsof Na and DDTs at the family level.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004302	Metagenome microbial communities of bottom sediments of the Kara Sea	Metagenomic analysis of the microbial community in the bottom sediments Kara Sea shelf Yenisei Gulf and Gyda Bay by pyrosequencing	root:Environmental:Aquatic:Marine:Sediment
MGYS00004300	Uncultered bacterium Targeted Locus (Loci)	In the context of global warming in the Arctic environment greater understanding of microbial-driven processes related to sediment and hydric transfers is of major importance where these are linked to erosion processes. To add to the research in this area, we investigated the structure of sedimentary microbial communities from three distinct samples collected along a short Glacier-River-Fjord transect in Kongsfjorden (Fjord of Svalbard) at the beginning of the active thaw using a metagenomic approach. A methodological approach was used based on the pyrosequencing of 16S rRNA genes coupled with multiple DNA extractions to overcome major methodological biases, namely DNA extraction and polymerase chain reaction (PCR).	root:Environmental:Aquatic:Marine:Sediment
MGYS00004282	Illumina high-throughput sequencing of bacterial community	Microbial ecology of bacterial community	root:Environmental:Aquatic:Marine:Sediment
MGYS00004281	Pyrosequencing of bacterial community	Microbial ecology of bacterial community	root:Environmental:Aquatic:Marine:Sediment
MGYS00004272	Marine sediment Raw sequence reads	The microbial community influenced by bioturbation of macrofauna	root:Environmental:Aquatic:Marine:Sediment
MGYS00004255	2011 depth sediment Metagenome	2011 oil spilled sediment	root:Environmental:Aquatic:Marine:Sediment
MGYS00004254	Red Sea sediment 2011 Targeted Locus (Loci)	This study is to determine the eukaryotic microbial community structure in the sediment of Red Sea.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004240	Narragansett Bay, RI Sediments Targeted Locus (Loci)	Goals were to investigate microbial community of sediment samples with acetylene and without	root:Environmental:Aquatic:Marine:Sediment
MGYS00004236	sediment metagenome Raw sequence reads	This study demonstrated that Dehalococcoides could be employed as a promising biomarker to test the present of organohalides in wastestreams or other environmental samples.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004234	Eukaryote diversity assessment of sediments of the Western English Channel	Sediments were collected at monthly intervals from the Western English Channel (site L4) and environmental DNA extracted. The effect of season on the community composition and diversity of eukaryotes was assessed using in depth sequencing of 18S rRNA genes. This data will be compared with traditional techniques used to identify benthic species to assess the efficacy of eDNA biomonitoring as a tool for measuring biodiversity.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004233	Arabian sea sediment samples with protist reads Metagenome	Protist paleome from Arabian sea	root:Environmental:Aquatic:Marine:Sediment
MGYS00004232	Benthic microbial communities in the sediments of the Southern Ocean	To investigation benthic microbial communities in the sediments of the Southern Ocean underlying Phaeocysis bloom.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004230	A comparison of microbial community composition in four contrasting sediments in the Celtic Sea	As part of the NERC funded Shelf Seas Biogeochemistry program, microbial structure, diversity and abundance was compared in four contrasting sediment types, from mud to sand. Samples were collected before (March 2015) and immediately after a spring diatom bloom (May) and also again in late summer (August). These data are 16S rRNA and 18S rRNA gene sequence sets from the four sediment types, and from the three sampling time points. Relative abundance and composition was determined using Illumina MiSeq (MrDNA, TX, USA). The V1V3 region of 16S rRNA was amplified using the PCR primers 27F (Vergin et al., 1998) and 519Rmod (Andreotti et al., 2011) using the PCR and sequencing conditions described in Tait et al. (2015). For 18S rRNA genes, the primers Euk7F and Euk570R were used.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004221	uncultured prokaryote Targeted Locus (Loci)	Analysis of community composition of sulfur-oxidizing bacteria in East China Sea using soxB as a functional molecular marker	root:Environmental:Aquatic:Marine:Sediment
MGYS00004214	Sediment microbial community Random survey	Assessment of Microbial Community Composition in Chesapeake Bay Sediments	root:Environmental:Aquatic:Marine:Sediment
MGYS00004194	La Medee sediment - Microbial Metagenome Metagenome	SSU 16S pyrosequencing project of the microbial metagenome of a DHAB sediment (La Medee) from the Eastern Mediterranean.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004191	Oxic sediment - Extracellular Metagenome	SSU 16S pyrosequencing project of the microbial metagenome of an oxic deep-sea sediment from the Eastern Mediterranean.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004175	Baltic Sea Basin sediments diversity Raw sequence reads	Baltic Sea sediment from IODP X347 active community diversity through 16S RNA sequencing	root:Environmental:Aquatic:Marine:Sediment
MGYS00004174	dsrB gene diversity in marine coastal sediments in Aarhus Bay, Denmark	Sulfate-reducing microorganisms (SRM) are key players in the marine carbon and sulfur cycles, especially in coastal sediments. We identified and characterised SRM using dsrB gene sequencing in a marine coastal sediment in Aarhus Bay, Denmark.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004165	SMAR-T Raw sequence reads	deep-sea sediments	root:Environmental:Aquatic:Marine:Sediment
MGYS00004134	marine sediment Raw sequence reads	surface coastal sediment	root:Environmental:Aquatic:Marine:Sediment
MGYS00004132	Environmental eukaryotes Metagenome	18S sequences from environmental samples using universal eukaryote primers. The goal of the study is to design and test eukaryote specific primers to be used in assessing biodiversity of eukaryotes.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004120	deep marine subsurface Raw sequence reads	The deep sedimentary biosphere, extending hundreds of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea, and microbial eukaryotes. Little is known about microbial eukaryotes in these habitats, however studies suggest that fungi dominate. Here we compared fungal ribosomal RNA signatures present in sediment core samples from 6 and 95mbsf from Peru Margin site 1229A. Fungal-specific PCR primers were used in this study.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004113	Global phylogeography survey of thermophilic spores in marine sediments.	16S rRNA gene-based survey of thermophilic spores in marine sediments from globally distributed locations.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004105	Eastern offshore environmental monitoring of Krishna Godavari Basin Bay of Bengal 2013-2016, Funded by: ONGC India	Environmental monitoring of Krishna Godavari Basin Bay of Bengal	root:Environmental:Aquatic:Marine:Sediment
MGYS00004100	marine sediment metagenome Raw sequence reads	Microbial diversity survey of shallow tropical marine sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004098	Marine sediment amplicon Targeted loci environmental	Marine sediment from Aarhus Bay	root:Environmental:Aquatic:Marine:Sediment
MGYS00004096	Metazoan sequencing	The present study provides a new data on the diversity of nematodes communities in sub-marine canyon.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004093	Microbial diversity of marine sediments	Understanding the microbial diversity of deep sea marine sediments	root:Environmental:Aquatic:Marine:Sediment
MGYS00004091	uncultured eukaryote Raw sequence reads	This study aims to reveal eukaryotic diversity in sediments from the South China Sea.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004086	Microbial community structure of chronically polluted marine sediments from a cold region of the southern hemisphere	This study is part of a larger initiative: Microbial Community Structure and Metabolic Potential of Chronically Polluted Marine Sediments from Cold Regions of the Northern and Southern Hemispheres (CSP-328, JGI-DOE). The goal of this larger project is to increase our understanding of the biogeographic distribution patterns and functional traits of microorganisms in cold, polluted costal sediments. In this study, we analized the structure and diversity of microbial communities of cold polluted coastal sediments from Ushuaia Bay.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004071	surface sediment Raw sequence reads	The study of this paper was to characterize the characterization of depth-related microbial communities and their potential functions in the sediment ecosystem of the East China Sea.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004070	surface sediment Raw sequence reads	This study was to characterize the structure and function of microbial communities in surface sediment from the East China Sea.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004042	marine metagenome Metagenome	Marine microbial diversity study	root:Environmental:Aquatic:Marine:Sediment
MGYS00004035	Microbial communities in deep eastern Mediterranean Sea surface sediments	In order to elucidate spatial distribution of microorganisms in deep sea surface sediments and to reduce the general information deficiency regarding microbial community composition in sediments of the eastern Mediterranean Sea, sequences of surface sediment samples from 9 stations in the Levantine basin were produced by 454 massive tag sequencing and compared to each other.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004029	Sinking bloom influences benthic microorganisms	Here, we analyzed the bacterial community structure of four abyssal sediments and one shallow reference site in the Atlantic sector of the Southern Ocean. The sediments differed in their exposure to phytoplankton blooms to investigate potential links between the blooms and benthic microorganisms. Our main hypotheses were (i) that an extended bloom situation in the surface ocean leads to shifts in the benthic microbial communities with short delay times and (ii) that certain key bacterial clades benefit from the organic matter input.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004025	marine sediment metagenome Raw sequence reads	Environmental parameters driving the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt Region in the Gulf of Mexico	root:Environmental:Aquatic:Marine:Sediment
MGYS00004012	Mid-Atlantic Ridge sediment Raw sequence reads	The objective of this study was to determine the bacterial community structure within deeply buried marine sediments along the western flank of the mid-Atlantic ridge. Samples were collected during Integrated Ocean Drilling Program expedition 336 (Oct-Dec 2011).	root:Environmental:Aquatic:Marine:Sediment
MGYS00003996	marine sediment metagenome Raw sequence reads	Using environmental samples to study the microbial community structure in bohai sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003995	marine sediment metagenome Raw sequence reads	Using environmental samples to study the community structure of anammox bacteria in Bohai sediments.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003994	sediment microorganisms nirK gene Raw sequence reads	We extract total DNA in sediment microorganisms from BoHai sediment, and we use illumina to study the nirK gene in total DNA.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003174	dsrB sequencing of sulfate-reducing microbial communities in Skagerrak and Baltic sediment	Seabed communities of sulfate-reducing microorganisms were profiled by Illumina MiSeq sequencing of the dsrB gene from four different sites up to a depth of 5.3 meters below seafloor.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003171	marine sediment metagenome Raw sequence reads	To investigate the methane-oxidation archaeal communities in the Canadian Beaufort Sea	root:Environmental:Aquatic:Marine:Sediment
MGYS00003170	16S_Sediment_Bolinao	V4-V5 sequences from sediments in Bolinao, Philippines	root:Environmental:Aquatic:Marine:Sediment
MGYS00003128	Studies of marine microbial dark matter	To analyze the culturable mechanisms of enrichment culture, and to establish a sequencing-based workflow that could be used as a platform for the culturing of marine bacteria throught 16S rRNA transcript amplicon sequencing.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003127	resuscitation mechanisms during enrichment culture	To analyze the culturable mechanisms of enrichment culture, and to establish a sequencing-based workflow that could be used as a platform for the culturing of marine bacteria	root:Environmental:Aquatic:Marine:Sediment
MGYS00003124	Microbial Diversity in Antarctic marine sediments (Admiralty Bay and Bransfield Strait)	We assessed the composition and structure of bacterial and archaeal communities at 15 stations in Admiralty Bay and Bransfield Strait, Antarctica.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003120	Archaea diversity in marine sediment	To study archaeal diversity in global marine sediment	root:Environmental:Aquatic:Marine:Sediment
MGYS00003079	marine sediment metagenome Raw sequence reads	to compare the differences among these environmental samples	root:Environmental:Aquatic:Marine:Sediment
MGYS00003070	envinronment Metagenome	We used a 16S and 18S rRNA based pyrosequencing approach to characterize the sediment bacterial and microeukaryote communities in mud volcanoes (MVs) with differential activity in the Gulf of Cadiz	root:Environmental:Aquatic:Marine:Sediment
MGYS00003011	gas hydrate bearing sediment Raw sequence reads	By investigating the microbial community structure in the gas hydrate bearing cores, we can understand some of in situ biochemistry processes. It is useful to get to know how microbial involved in forming high-saturation microbial origin gas hydrates.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003005	Anammox bacteria in surface sediments of South China Sea	Raw sequences of anammox bacteria in South China Sea.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002960	Archaea	archaea communitites	root:Environmental:Aquatic:Marine:Sediment
MGYS00002946	Microbial diversity of marine sediments from Ross Sea	To understand the microbial diversity of marine sediments along the depth	root:Environmental:Aquatic:Marine:Sediment
MGYS00002895	Aarhus Bay sediment PCR amplified product sequencing	To identify acetate-assimilating/utilizing microbes in marine sediments	root:Environmental:Aquatic:Marine:Sediment
MGYS00002894	Nitrate-storing microorganisms in sediments of the Bornholm Basin	The objective of this study is to examine the distribution of nitrate-storing microorganisms along a transect towards deeper water depths in the hypoxic Bornholm Basin. Nitrate-storing microorganisms were identified by amplicon sequencing (Illumina MiSeq) of Eukaryotes and diatoms (18S rRNA gene). The organisms that were identified by sequencing were evaluated in regard to their ability and capacity to store intracellular nitrate.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002891	Queensland Marine Sediment	Characterization of bacterial communities in marine sediments from Gladstone and Heron Island	root:Environmental:Aquatic:Marine:Sediment
MGYS00002887	Deep mud-volcano biosphere in the Nankai accretionary wedge	Submarine mud-volcanoes are globally distributed in the plate convergent margins1,2. The mud-volcanism transports deep-sourced fluids and hydrocarbons to the seafloor3, which upward supply often supports chemosynthetic benthic life and microbial communities that play significant ecological roles in biogeochemical carbon cycle4,5. Yet, geochemical and microbiological characteristics of the deep mud-volcano subsurface remain largely unknown. Here, we studied an active submarine mud-volcano in the Nankai Trough by drilling down to 200 meters from the summit. Cell count and molecular analyses indicate that relatively small (102~105 cells/cm3) but phylogenetically diverse microbial populations are present throughout the cored sediment. In the pore water, carbon isotopic compositions of bicarbonate and acetate are notably 13C-enriched up to the maximum value of +40 and -25, respectively. High concentrations of hydrogen (up to 1,800 nM) are observed, suggesting a thermodynamically feasible condition for microbial acetogenesis via CO2 reduction. Radiotracer experiments consistently showed that acetogenesis activities are generally 2-3 orders of magnitude higher than those of methanogenesis. These data indicate that the deep biosphere in the submarine mud-volcano is characterized by tectonic and sedimentolgoical regimes of the oceanic accretionary wedge, and hence different from the stratified sedimentary biosphere.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002816	Taxonomic study of endospores in a marine sediment	This study mapped the taxonomy and diversity of endospores and vegetative bacteria in a marine sediment. We further investigated potential sources of endospore accumulation in the seabed.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002770	marine sediment metagenome Metagenome	China sediments from the northern slope of the South China Sea archaeal 16S rRNA gene groups, metagenomic data, deep-sea sediments	root:Environmental:Aquatic:Marine:Sediment
MGYS00002735	eDNA_Subseafloor	PMA-DNA study of subseafloor sediment	root:Environmental:Aquatic:Marine:Sediment
MGYS00002668	SCHEMA_Sediment	GoM-SCHEMA: Shipwreck Corrosion, Hydrocarbon Exposure, Microbiology and Archaeology Project	root:Environmental:Aquatic:Marine:Sediment
MGYS00002664	marine sediment metagenome Metagenome	In this study, we investigated marine sediment from around the Okinawan 'Kaichu-Doro' Causeway, which was constructed 44 years ago to connect three islands (Henza-jima, Miyagi-jima, Hamahiga-jima) to Okinawa. The construction of this causeway has been shown to influence the surrounding marine ecosystem via fragmentation and the loss of water circulation. In this research, we collected 10 sediment cores (5 cores from each side) 60-80 cm length from 1 m water depth and divided into layers (each layer 15 cm) to examine differences in environmental DNA from areas around the causeway. We examined the vertical diversity of microbial communities and metabolite to elucidate and estimate the correlation between metabolites and microbial communities among marine sediment layers.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002565	Extracellular DNA marine sediment Targeted Locus (Loci)	To assess the diversity of eukaryotes in Red Sea sediments via amplicon sequencing of extracellular DNA.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002474	Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes	Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO2 in the seabed. The emission of CO2 may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO2 and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO2-seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO2 concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO2 concentration, indicating that microbial activity and community structure are sensitive to CO2 venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (1330?cm in depth) characterized by high CO2. Measurement of the potential sulfate reduction rate at pH conditions of 39 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO2-seep sedimentary environment; however, CO2 and pH in the deep-sea sediment were found to severely impact the activity and structure of the microbial community.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002439	Zostera Marina Ammonification environmental	In the Fall of 2014, Jessica Abbott (from Jay Stachowiczs lab) and Susan Williams performed an ammonification experiment in Bodega Bay, CA. The experiment involved 72 different plots containing either two or six known genotypes of Zostera marina. The rate of ammonification was measured in sediment from these plots at several different time points post field collection. We are working to determine the microbial community composition of this sediment with the goal of identifying which member(s) of the community might be responsible for the ammonification rates observed.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002375	Microbial diversity studies of Arabian Sea sediment	Marine ecosystems are distinctive ecological niche, with a variety of microbes playing important roles in nutrient recycling and other ecological processes, thereby requiring a thorough exploration of their microflora. Similarly Arabian Sea sediments are hotspots for microbial diversity and therefore requires a detailed investigation. Bacterial diversity profiles of marine metagenome were brought to light by the present studies based on Illumina sequencing trageting the V3 regions of 16S rRNA gene, revealing the roles of different bacteria in nutrient cycling and organic matter degradation. The analysis also revealed the existence of many unknown sequences, indicating a large untapped bacterial diversity in these areas.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002373	Characteristics of SOB community in Sediments from the East China Sea by high-throughput sequencing	The diversity and composition of SOB in sediments from the East China Sea was investigated based on the high-throughput sequencing analyses of the soxB gene	root:Environmental:Aquatic:Marine:Sediment
MGYS00002100	marine seawater and sediment Raw sequence reads	bacterial diversity	root:Environmental:Aquatic:Marine:Sediment
MGYS00001948	ANME-2a Genome sequencing	To understand the ecological roles of ANME-2a	root:Environmental:Aquatic:Marine:Sediment
MGYS00004638	Temperature shifts simulating secondary oil recovery	The germination of endospore forming bacteria in response to temperature shifts encountered during secondary oil recovery was investigated. Relevance for the mitigation of reservoir souring.	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00004505	Tyne oil spill snorkels Raw sequence reads	"Bioelectrochemical bioremediation to accelerate hydrocarbon biodegradation in anoxic marine sediments, using ""oil-spill snorkels"". The snorkels (rods of conductive material) were positioned to create an electrochemical connection between the anoxic contaminated sediment and the oxic overlying water. In principle, the snorkel could take advantage of the capability of electro-active bacteria to anaerobically oxidize hydrocarbons with the snorkel serving as a respiratory electron acceptor.Fifty 16S rRNA amplicon libraries were generated representing microbial communities from the snorkel, no oil snorkel, control, no oil control and abiotic experiments at 175, 286 and 466 days during the incubation period, as well as from the initial sediments with and without oil (Time 0)."	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00004442	sediment metagenome Metagenome	Ecological effects assessments of spilled oils	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00002848	Sediment Microcosm Metagenome	Sediment Microcosm - Oil_contaminated*reduced_water_pH	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00002521	Gulf of Mexico open ocean Targeted Locus (Loci)	Influence of dispersants on pelagic microbial oil degraders. Microbial communities from deep seawater at a natural hydrocarbon seep in the northern Gulf of Mexico were exposed to Macondo oil; dispersed oil; or dispersants in laboratory experiments.	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00004591	Survey of xoxF diversity in different marine environments	Methanol dehydrogenase is a key enzyme in methylotrophic bacteria, catalysing the oxidation of methanol to formaldehyde. In many methylotrophs, this is a well-characterised pyrroloquinoline quinone dependent enzyme consisting of two subunits, encoded by the genes mxaFI. A homolog of the large subunit MxaF is also present in most known methylotrophs, encoded by the gene xoxF. In several methylotrophs, this gene was found to be the only putative methanol dehydrogenase, but it is also present in several non-methylotrophs. This has led to a discussion over its potential role in methylotrophy and C1 cycling. This study aims to investigate the presence and diversity of the xoxF gene in the marine environment.	root:Environmental:Aquatic:Marine:Neritic zone
MGYS00002645	Mediterranean Contaminated Pelagic communities	Response of pelagic communities to an input of contaminated elutriate from sediments or to artificial pollution with a mix of pollutants	root:Environmental:Aquatic:Marine:Pelagic
MGYS00004168	Simulated crude oil seepage Caspian Sea Raw sequence reads	The response of the microbial community to a crude oil seepage simulated for 190 days under close-to-in situ conditions in a sediment core from Caspian Sea using a Sediment-Oil-Flow-Through (SOFT) system was studied by NGS sequencing. We hypothesize that specific taxa respond specifically to simulated crude oil seepage by an increase of their cell numbers resulting in a change of community composition.	root:Environmental:Aquatic:Marine:Oil seeps
MGYS00004509	bacterial community in the deep-sea surface sediments	bacterial community in the deep-sea surface sediments of the Eastern Indian Ocean	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00004392	Controls on microalgal community structures in cryoconite holes upon high Arctic glaciers, Svalbard	Glaciers are known to harbor surprisingly complex ecosystems. On their surface, distinct cylindrical holes filled with meltwater and sediments are considered as hot spots for microbial life. The present project addresses possible biological interactions5 within the community of prokaryotic cyanobacteria and eukaryotic microalgae (microal- gae) and relations to their potential grazers, additional to their environmental controls.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00004049	uncultured prokaryote Targeted loci environmental	This study sequenced bacterial 16S ribosomal DNA from subseafloor sediment of the Bering Sea, in an effort to understand diversity in the deep subsurface.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00003119	marine sediment metagenome Raw sequence reads	This dataset contains the bacterial and archaeal 16S rRNA sequence information from the Methane Microbial Observatory for Seafloor Analysis (MIMOSA) deployment at GC600 from October 2013 (PE14-09) to March 2014 (PE14-14). The purpose of the deployment was to examine the in situ degradation of oil. The deployment contained flow-through chambers of sediment, one amended with oil and one unamended. Samples were collected from the beginning and end of the experiment.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00002723	Sediment bacteria in the Southern Ocean	The aim of the study was to investigate bacterial community structures sediment samples taken in the Southern Ocean around Elephant Island and the Antarctic Peninsula. Bacterial community structures were assessed by pyrotag sequencing targeting the bacterial 16S rRNA gene.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00002501	Caspian Sea Sediment - 16S Survey Targeted Locus (Loci)	The Caspian Sea is one of the most polluted seas in the world due to industrial and agricultural effluents as well as extraction of oil and gas reserves. Microbial communities can impact the fate of contaminants and nutrients. However, insight into the microbial ecology of the Caspian Sea significantly lags behind other marine systems. Here we describe the microbial diversity of sediments collected from three sampling stations in the Caspian Sea. This study provides a baseline assessment that may serve as a point of reference as this system changes or as remediation efforts are initiated to reduce pollution.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00003173	Marine sediment Raw sequence reads	A mesocosm-scale experiment to investigate the electrobioremediation of crude oil-contaminated marine sediments.	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated sediments
MGYS00004660	Hydrocarbon biodegradation potential affected by geographical location, tempearture, and nutrient	Surface water samples from three different geographical locations were incubated with oil at a systematic set of temperature and nutrient conditions.	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
MGYS00004659	Dispersant experiment using Pensacola beach water	The project studies the impact of dispersant application in oil-contaminated seawater at environmental-related concentration	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
MGYS00004384	Oil-water intephase microbial community analysis Raw sequence reads	Following the succession of microbial community changes at oil-seawater interphase during oil degradation	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
MGYS00003988	Arctic benthos Targeted Locus (Loci)	Biogeography of Arctic benthic bacteria. This study examines the influence of global change on the structural and functional diversity of microbial communities in Arctic sediments.  Biogeography of Arctic benthic bacteria sampled at the deep-sea, long-term observatory HAUSGARTEN in the Arctic Ocean.	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00002809	Microbial eukaryotes	Little is known about the taxonomic and phylogenetic diversities, and the relative importance of historic processes and environmental gradients underlying the current diversity and community assembly, of single-celled eukaryotes in marine benthic habitats. By pyrosequencing ribosomal RNA genes and characterizing multiple environmental factors, we investigated temporal and spatial patterns of a- and -diversities of microeukaryotes in near-surface sediments of three basins of the Yellow Sea Large Marine Ecosystem.	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00002959	marine sediment metagenome Targeted loci environmental	Abyssal sediments, polymetallic nodules, and water-column samples were collected from the UKSRL1, OMS claim area as well as APEI within the Clarion-Clipperton fracture zone in the Pacific Ocean. The ABYSSLINE 2015 Cruise took place aboard the research vessel Thomas G. Thompson (R/V Thompson) between February 12, 2015 and March 25, 2015, as an expedition jointly funded and supported by Seabed Resources Limited and Ocean Mineral Singapore. The chief objective of the AB02 was to conduct an evaluation of biological and environmental baseline conditions in the UK-1 contract area, and the OMS contract area at depths ranging from 3900 to 4400 meters (m) in the Clarion-Clipperton Zone (CCZ; also known as the Clarion  Clipperton Fracture Zone). Specifically, the study targeted two 30 by 30 kilometer (km) areas; one in the UK-1 contract area and one in the OMS contract area, centered approximately at 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49' N, 116 36' W) and 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49' N, 116 36' W), respectively. This project consists of samples isolated at the sediment sites described above and inoculated into seawater medium in microcosm experiments to evaluate the influence of bicarbonate on community composition.	root:Environmental:Aquatic:Marine:Oceanic:Aphotic zone
MGYS00002814	Microbial Biogeography and Potential Ecological Function Deep Indian Ocean Ridge	The marine microbial biogeography is gradually emerging a consensus. However, knowledge of the biodiversity, the biogeographic patterns and the factors influencing the distribution of deep-marine prokaryotes in distinct habitats at large scale is far from adequate. In this study, 16S rRNA gene Miseq-sequencing was used to survey the diversity and biogeography of prokaryotes from 39 sites across a broad geographic range, containing two obvious different habitats, hydrothermal and non-hydrothermal sediments. The deep marine sediment communities were highly diverse and Proteobacteria, Thaumarchaeota, Planctomycetes, Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae and Bacteroidetes were dominant in both habitats with varied percentages. The composition of prokaryotic communities obviously diverged across environmental heterogeneity and large geographic distances.	root:Environmental:Aquatic:Marine:Oceanic:Aphotic zone
MGYS00004530	pyrosequencing  Raw sequence reads of deep-sea Archaea	water-sediment interface in the slope Mariana Trench	root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
MGYS00002788	Global Malaspina 2010 deep ocean expedition - rRNA pyrotags	Amplicon sequencing of the 16S rRNA of deep oceanic Bacteria and Archaea from Malaspina 2010 Expedition	root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
MGYS00002672	marine sediment metagenome Targeted loci environmental	Abyssal sediments, polymetallic nodules, and water-column samples were collected from the UKSRL1, OMS claim area as well as APEI within the Clarion-Clipperton fracture zone in the Pacific Ocean. The ABYSSLINE 2015 Cruise took place aboard the research vessel Thomas G. Thompson (R/V Thompson) between February 12, 2015 and March 25, 2015, as an expedition jointly funded and supported by Seabed Resources Limited and Ocean Mineral Singapore. The chief objective of the AB02 was to conduct an evaluation of biological and environmental baseline conditions in the UK-1 contract area, and the OMS contract area at depths ranging from 3900 to 4400 meters (m) in the Clarion-Clipperton Zone (CCZ; also known as the Clarion  Clipperton Fracture Zone). Specifically, the study targeted two 30 by 30 kilometer (km) areas; one in the UK-1 contract area and one in the OMS contract area, centered approximately at 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49' N, 116 36' W) and 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49' N, 116 36' W), respectively.	root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
MGYS00002542	Abyssal Baseline Study & Geophysical Survey (ABYSSLINE 02)_AB01_Re-sequenced Targeted loci environmental	Abyssal sediments, polymetallic nodules, and water-column samples were collected from the UKSRL1, OMS claim area as well as APEI within the Clarion-Clipperton fracture zone in the Pacific Ocean. The ABYSSLINE 2015 Cruise took place aboard the research vessel Thomas G. Thompson (R/V Thompson) between February 12, 2015 and March 25, 2015, as an expedition jointly funded and supported by Seabed Resources Limited and Ocean Mineral Singapore. The chief objective of the AB02 was to conduct an evaluation of biological and environmental baseline conditions in the UK-1 contract area, and the OMS contract area at depths ranging from 3900 to 4400 meters (m) in the Clarion-Clipperton Zone (CCZ; also known as the Clarion  Clipperton Fracture Zone). Specifically, the study targeted two 30 by 30 kilometer (km) areas; one in the UK-1 contract area and one in the OMS contract area, centered approximately at 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49 N, 116 36 W) and 13 degrees 49 minutes North, 116 degrees 36 minutes West (13 49 N, 116 36 W), respectively.	root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
MGYS00002488	Microbial communities associated with ferromanganese nodules and the surrounding sediments	The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities.	root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
MGYS00002102	a seamount and adjacent deep-sea plains in the western Pacific Ocean Metagenome	Using high-throughput DNA sequencing, we investigated their diversity and community composition in different sediment layers of a seamount and an adjacent deep-sea plain in the tropical western Pacific Ocean with water depths ranging between 813 m and 4,566 m.	root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
MGYS00004657	marine metagenome Raw sequence reads	the diversity of aoa in the South China Sea	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004637	Marine picocyanobacterial community structure	A surprising recent observation is that one of the smallest types marine phytoplankton, picocyanobacteria of the genus Synechococcus, can contain concentrations of silicon rivaling those found in diatoms. As part of an NSF-funded project exploring the implications of this observation, entitled ''Understanding the Role of Picocyanobacteria in the Marine Silicate Cycle'', we used PacBio sequencing of a PCR-amplified fragment of the petB gene to describe the diversity and structure of the cyanobacterial community in seawater samples collected at several locations in the North Atlantic ocean. We used this information to determine whether there is a relationship between the content of biogenic silica in the <3 micron size fraction and the types of picocyanobacteria present.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004628	dust metagenome Raw sequence reads	Evaluating the impact of atmospheric depositions on dinitrogen fixation in the Eastern Mediterranean Sea- A mesocosm approach	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004490	Protists community in the southern East China Sea	18S rDNA sequences from the southern East China sea	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004485	Microbial communities in the ocean Raw sequence reads	understand the mechanisms that shape microbial diversity in the global-scale ocean ecosystem	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004480	Bacteria community in the southern East China Sea	Bacterial 16S rDNA sequences in the southern East China Sea	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004478	16S marine bacteria Raw sequence reads MEDEA2	dataset includes deep sea bacteria from the deep northern North Atlantic ocean including mesopelagic, and bathypelagic samples.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004436	seawater metagenome Raw sequence reads	The study wants to reveal the influence of solitary wave to bacterial community	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004435	Bacterial community diverisity	Bacterial community diversity of seawater in East China Sea	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004434	marine sediment metagenome Raw sequence reads	South China Sea sediment core microbial diversity	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004420	Sea ice and seawater Raw sequence reads	Fungi are vastly understudied in the marine realm and the extent of their functionality as nutrient cyclers and parasites is constrained by the current understandings of fungal distribution and drivers on global scales. To investigate fungal distributions, high throughput sequencing of the 18S and 28S rRNA genes were examined from across the western Arctic and sub-Arctic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004299	seawater metagenome Metagenome	Microbial dicersity	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004083	Microbial eukaryote Metagenome	The central Arctic Ocean has been covered by heavy sea ice, thus the condition of the underlying ecosystem has remained uncertain. To investigate the microbial eukaryotes diversity in seawater from the central Arctic Ocean, water samples were collected from five stations during the 3rd Chinese Arctic Scientific Expedition in 2008. After pyrosequencing with a 454 Life Science GS-FLX sequencer, the V4 region of the 18S rRNA gene sequences were analysis, the molecular diversity of microbial eukaryotes of sea water from the central Arctic Ocean was generally achieved.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004059	Marine protists Metagenome	A study of the genetic diversity of protists in the central Arctic Ocean in late summer 2011.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004024	Benham Rise 16S raw sequence reads	16S rDNA raw sequencing reads from prokaryotes isolated from the water column of Benham Rise, Philippines	root:Environmental:Aquatic:Marine:Oceanic
MGYS00003175	aquatic bacterial metagenome Raw sequence reads	Bacterioplankton metacommunity structure across thermal effluent gradients	root:Environmental:Aquatic:Marine:Oceanic
MGYS00003125	CTD water column metabarcoding	Water column metabarcoding of 16S rRNA from South Atlantic	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002958	Surface ocean Targeted Locus (Loci)	18S rRNA gene was targeted in environmental samples from surface water in the Chukchi Sea to assess diversity of the eukaryotic protist community.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002947	Ocean Acidification baceria sample Targeted loci environmental	A microcosm experiment was done in the western pacific ocean to investigate the response of bacterial community to the ocean acidification.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002888	Ocean Water Metagenome	"Microbes from water column samples and ""non-lethal"" sediment traps were collected on 0.2 uM micron filters to look at diversity and richness of bacterial community dynamics within an annually recurring spring phytoplankton bloom."	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002786	Green Edge microcosms Raw sequence reads	We investigate the response of Arctic bacterial communities to the addition of phytoplankton derived dissolved organic matter through biodegradation experiments conducted during a cruise in the Baffin Bay in June-July 2016	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002725	16S amplicons Subtropical Frontal Zone New Zealand	This study consists of samples collected from 8 surface water stations along a 48 km transect. Samples were taken between January 2014 and April 2015.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002582	Southern Ocean microorganisms Targeted Locus (Loci)	Bacteria and archaea from filtered Southern Ocean seawater.  Filtered and size-fractionated (0.1 m, 0.8 m, 3.0 m) seawater from the Southern Ocean.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002541	16S rRNA amplicon from marine Bacteria Raw sequence reads	The contribution of different bacterial phylotypes to the ocean biogeochemical cycles depends on their activity and biomass. However, little is known about active bacteria in the deep ocean, the largest habitat on Earth.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002437	DEEPEND: Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples. Cruises DP03 and DP04 from Jan 2016 - December 2016	Seawater will be collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters will be stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable regions will be generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0  1500 m, assess seasonal variation, and examine variation related to nektonic vertical migration. Microbiome analyses will also consider environmental variables unique to the GOM, such as Mississippi river green water inputs, mesoscale features, or microbiomes of associated GOM marine fauna as part of community ecology profiles. When possible, correlations will be made to other environmental factors such as nutrient concentrations.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002381	rDNA amplicon sequencing of Western North Atlantic microbial community	"Targeted amplicon sequencing of the 16S V4 and 18S V4 rRNA genes from microplankton DNA collected via filtration of seawater. Samples obtained from 24 sampling stations across the Western North Atlantic as part of work conducted for NSF Award #1350710: ""Method Development for High-Resolution Underway N2 Fixation Measurements"", with the goal of characterizing the marine microplankton community and relating community structure to measured productivity and nitrogen fixation rates."	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004375	Shallow-water pockmarks diversity Targeted Locus (Loci)	Shallow-water pockmarks are associated with hydrocarbon ascent through the muddy sediment blanjet in world-wide continental shelves. We investigated the prokaryotic diversity in the sediment of several shallow-water pockmarks.	root:Environmental:Aquatic:Marine:Neritic zone:Sediment
MGYS00004590	13C methanol SIP (WCO station L4)	Methanol is a biochemically active, volatile organic compound that plays an important role in tropospheric oxidant photochemistry. It has recently been suggested that the global ocean, where surface methanol concentrations are in the ~30-400 nM range, is a net sink for atmospheric methanol. In the marine environment, this (and other) one-carbon compound is used as an energy and carbon source by bacteria known as methylotrophs. So far, little is known about the identity of the active methanol oxidisers in marine habitats. In this study, Stable Isotope Probing using 13C labelled methanol was combined with 16S rRNA and functional gene amplicon sequencing as well as metagenome sequencing to identify methylotrophic bacteria that are responsible for methanol assimilation in samples obtained from the Western Channel Observatory station L4.	root:Environmental:Aquatic:Marine:Neritic zone
MGYS00002572	California Current Cruise CCE-P1408 Process Cruise #6	Passive sinking of particulate organic matter (POM) is the main mechanism through which the biological pump transports surface primary production to the ocean interior. However, the contribution and variability of different biological sources to vertical export is not fully understood. In this work, we use DNA metabarcoding of 18S rRNA gene and particle interceptor traps (PITs) to characterize the taxonomic composition of particles sinking out of the photic layer in the California Current Ecosystem. The PITs included formalin-fixed and 'live' traps to investigate compositional changes associated with consumption and remineralization processes. Sequences affiliated to Radiolaria, mainly Spumellaria and Acantharia, dominated the eukaryotic assemblage in fixed-traps (90%) with Dinophyta and Metazoa making minor contributions. The prominence of Radiolaria decreased markedly in live-traps (<3%), possibly due to selective consumption by large copepods, heterotrophic nanoflagellates and amoeboid phaeodarians that were heavily enriched in these traps. These patterns were consistent across the coastal-to-open water masses surveyed, despite major differences in productivity and trophic structure of the epipelagic plankton community. Our findings indicate that in addition to more commonly considered phytoplankton and crustacean zooplankton, the role of rhizarians can be significant for POM vertical export and cycling in the CCE and potentially in other oceanic ecosystems.	root:Environmental:Aquatic:Marine:Neritic zone
MGYS00004416	16S rRNA amplicon sequences of Baltic Sea bacterioplankton	The aim of this study was to investigate interactions between bacterioplankton and phytoplankton during the Baltic Sea spring bloom. These datafiles include the 16S rRNA amplicon sequences of the bacterioplankton.	root:Environmental:Aquatic:Marine:Marginal Sea
MGYS00004404	ARMS Jeddah sample Raw sequence reads	To assess cryptic benthic diversity in three reefs in the Jeddah region of the Red Sea we undertook a metabarcoding (using 18S rRNA primers) approach to survey the eukaryotes found in Autonomous Reef Monitoring Structures (ARMS)	root:Environmental:Aquatic:Marine:Marginal Sea
MGYS00003167	A long-standing complex tropical dipole shapes marine microbial biogeography	Dipole eddies are mesoscale oceanographic features consisted of a cyclonic eddy and an anticyclonic eddy that function as a two-way biological pump, accumulating plankton production by pumping nutrient into the euphotic zone and accelerating the transport of organic matter into deep ocean, respectively. Dipoles happened frequently in the ocean with a duration from a few days to several months, resulting in significant impacts on local and global oceanic biological, ecological and geochemical processes. To better understand how dipole shape microbial community, we examined depth-resolved distributions of microbial communities across a dipole in the South China Sea. Our data demonstrated the dipole had a substantial influence on the microbial distributions and community structures both vertically and horizontally. Large Alpha- and Beta- diversity differences were observed between anticyclonic eddy and cyclonic eddy in surface and subsurface layers, consistent with distribution changes of major OTUs in the dipole with effects of uplifted, downward transported, enriched, depleted, horizontally transported. The edge of dipole might also cause strong vertical water movement indicated by Prochlorococcus and Synechococcus. Our findings suggest that dipole with its unique physical features might act as a driver for the distribution and diversity of microbial community.	root:Environmental:Aquatic:Marine:Marginal Sea
MGYS00003078	uncultured marine picoeukaryote strain:Peuk_V4_NWP2 Raw sequence reads	We aim to determine spatial and temporal distribution and diversity of marine picoeukaryotes in marginal seas of the northwestern Pacific Ocean.	root:Environmental:Aquatic:Marine:Marginal Sea
MGYS00003012	Anammox bacteria in sediment cores of Daya Bay, China	16S rRNA gene of anammox bacteria	root:Environmental:Aquatic:Marine:Marginal Sea
MGYS00003010	Marine bacteria metagenome	16S metagenome of marine bacteria from marginal East China Sea	root:Environmental:Aquatic:Marine:Marginal Sea
MGYS00002494	uncultured marine picoeukaryote strain:Peuk_V4_NWP1 Raw sequence reads	We aim to determine spatial and temporal distribution and diversity of marine picoeukaryotes in marginal seas of the northwestern Pacific Ocean.	root:Environmental:Aquatic:Marine:Marginal Sea
MGYS00004535	Microbial community in permeable intertidal sediment	The microbial community in permeable intertidal sediment, Gloucester Point	root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
MGYS00003068	E1 Targeted Locus (Loci)	Reveal the diverse bacterial community in intertidal sediments of Fildes Peninsula	root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
MGYS00002650	Sediment surface microbial community changes due to phytoplankton addition	Changes in microbial community in the sediment surface after addition of phytoplankton biomass.	root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
MGYS00002119	Stromatolite Type 1 HBC Metagenome	Samples were isolated from stromatolitic microbial mats from Bahamas.	root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
MGYS00002117	HBC thrombolite metagenome	Metagenome of a intertidal thrombolitic mat community from Highborne Cay, Bahamas.	root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
MGYS00004702	Sediment Metagenome Raw sequence reads	Metagenomic sequences of Archaea, Bacteria and Eukarya originating from Spiekeroog salt marsh sediment	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00004517	Chandeleur Island 2016 Amplicon Study Raw sequence reads	These amplicon sequences were generated from year 2 of an ongoing study of Chandeleur Islands saltmarsh habitats.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00004388	Bacterial community shift in the coastal Gulf of Mexico salt-marsh sediment microcosm in vitro following exposure to the Mississippi Canyon Block 252 oil (MC252)	Microbial communities play a crucial role in microbial loop process that constitute the foundation of the ecosystem structure and function. The goal of this study was to monitor a shift in the bacterial community following treatment with MC252 oil.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00004242	Salt Marsh Sediments Raw sequence reads	A study looking at the effects of sediment depth and nitrogen enrichment on bacterial communities	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00002571	US East Coast Salt Marshes Targeted Locus (Loci)	This work is aimed at elucidating the extent of microbial diversity and biogeography in US east coast salt marshes using 16s tag sequencing.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00002498	Little Sippewissett Marsh Targeted Locus (Loci)	Anthropogenic impacts and fecal populations at Little Sippewissett Marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00000749	Wetland soil Targeted Locus (Loci)	At the salt marsh Dongtan, the effect of Spartina alterniflora invasion on the structure of archaea were investigated at three points where the first was uninvaded, the second was partially invaded and the third was completely displaced.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00002134	Metagenomic study of Alchichica microbialites	We performed a comparative metagenomic analysis of microbialite samples along a depth gradient to characterise the functional profile of the microbialite-associated microbial communities.	root:Environmental:Aquatic:Marine:Intertidal zone:Microbialites
MGYS00004666	Diversity of denitrifying bacteria in Sanya mangrove sediments	This study aims to evalue the diversity of denitrifying bacteria in Sanya mangrove sediments from China.	root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
MGYS00004665	Diversity of diazotrophic bacteria in Sanya mangrove sediments	This study aims to assess the structure and driving factors of diazotrophic bacteria in Sanya mangrove sediments from China	root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
MGYS00004644	mangrove rhizosphere sediment Metagenome Raw sequence reads	To provide the comprehensive diversity and structure of diazotrophic and bacterial communities in the rhizospheres of mangroves	root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
MGYS00004615	mcrA singapore mangrove Raw sequence reads	Spatial variations of methanogenic communities in the tropical mangroves	root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
MGYS00004540	Fungal diversity in Sanya mangrove sediments, China	This study aims to investigate the diversity pattern and driving factors of fungi in mangrove sediments from Sanya, China.	root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
MGYS00004536	Diversities of bacteria and archaea in Sanya mangrove sediments	Study on the diversities of bacteria and archaea in Sanya mangrove sediments.	root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
MGYS00004394	Enriched mixed culture from mangrove sediment with capability of producing 1,3-PDO from glycerol genome sequencing and assembly	This project investigated the impact of increasing initial concentration of pretreated crude glycerol over the microbial community in mixed culture and metabolic products distribution.	root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
MGYS00004369	South China Normal University mangrove sediment Targeted Locus (Loci)	South China Normal University mangrove sediment samples	root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
MGYS00004348	Cataloging the Microbial Diversity of Sundarbans in the Backdrop of Climate Change	The influence of temporal and spatial variations on the microbial population in sediments of Sundarbans has been assessed using 16S rRNA gene pyrosequencing. The extraction of DNA from the sediment samples collected from the surface (2 cm) and subsurface (16 cm) layers in two seasons (monsoon and post monsoon) and the direct application of the 16S rRNA gene pyrosequencing resulted in approximately 117 Mbp of data from three sampling stations (Jharkhali, Sahidnagar and Godkhali). The taxonomic analysis of the pyrosequencing data grouped the sequences into 24 different phyla. In general, Proteobacteria were the most dominant phyla and further analysis revealed the dominance of Deltaprotaobacteria, Alphaproteobacteria and Gammaproteobacteria within the sediments. To our knowledge, this is the first detailed analysis of the microbial diversity in the world''s largest mangrove sediment of Sundarabns.	root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
MGYS00003074	marine metagenome Raw sequence reads	The microbial community of Sundarban Mangrove marine water samples	root:Environmental:Aquatic:Marine:Intertidal zone:Mangrove swamp
MGYS00004681	Marine planktonic ciliates (phylum Ciliophora, subclasses Oligotrichia and Choreotrichia): SSU rDNA	This study focuses on the richness and taxonomic composition of ciliate protists in marine plankton of a large temperate estuary (Long Island Sound, USA).	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00004224	Benthic Ocean Acidification	Investigation of the impact of elevated CO2 and temperature on microbial community composition within a muddy sediment mesocosm.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00002883	Po river Prodelta and Mar Piccolo of Taranto surface sediments bacterial communities targeted loci		root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00002768	Patagonian fjord prokaryote community	Time series of prokaryote community composition in waters of a Patagonian fjord	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00004487	Coral Spawn Degradation, Bocas del Toro, Panama - Raw sequence reads	The goal of this study was to identify bacterial communities that were labeled with a thymidine analog, bromodeoxyuridine, for investigating active bacterial communities during a coral mass-spawn degradation study off coastal Panama.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00004464	Effects of triclosan on bacterial community composition in natural seawater microcosms	The main objective of this study was to analyze the impact of triclosan on bacterial communities in seawater microcosms from Looe Key Reef, FL, Keys, USA.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00004454	Localized impact of aquaculture effluent on Red Sea coral reef water nutrients and microorganisms	We examined the impact of an aquaculture effluent canal in Al Lith, Saudi Arabia on the nutrients and picoplankton community overlying coral reefs in the Red Sea. Across 24 sites representing 0  21 km from the effluent, we measured nutrient concentrations, quantified microbial cell abundances, and utilized high-throughput sequencing of bacterial and archaeal small subunit ribosomal RNA (SSU rRNA) to examine microbial community composition.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00004163	Fringing reef Metagenome	This study used 16S and 18S rRNA genes pyrosequencing derived metagenomic DNA to obtain the microbial profiles of a marine tropical reef surface of Kham island, Trat province, Thailand	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00004043	Microbiome variation in Agaricia undata with distinct depth distribution ranges	Here, we study the prokaryotic community associated with reef-building coral (Agaricia undata) over a depth gradient (38-80 m)	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00002950	Coral or reef-seawater associated bacteria Targeted Locus (Loci)	SSU rRNA gene amplicons from Ctenactis crassa, Herpolithia limax or reef seawater.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00002778	Environmental zooplankton Targeted Locus (Loci)	This study investigated the diversity of metazoan plankton around three reef systems in the central/southern Red Sea utilising 18S rRNA amplicon sequencing.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00002550	Coral	Characterization of fungal and bacterial communities associated with inlets, ocean water, and coral tissue samples	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00004667	Zhoushan intertidal zone sediments Raw sequence reads	We reported the ANME archaea in the intertidal zone.	root:Environmental:Aquatic:Marine:Intertidal zone
MGYS00004463	sediment metagenome Raw sequence reads	This study focus on the effect of tidal zonation and the rhizosphere on the distribution of microeukaryotes.	root:Environmental:Aquatic:Marine:Intertidal zone
MGYS00002592	Intertidal Mixing Zone Targeted Locus (Loci)	Submarine groundwater must pass through an Fe-mineralized barrier before being discharged to coastal environments. Our goal was to assay the microbial members of this subsurface aquifer environment, looking at both pore water and surface sediments from a shore-perpendicular transect down to 4 m depth.	root:Environmental:Aquatic:Marine:Intertidal zone
MGYS00003121	Hydrothermal Deposit Targeted Locus (Loci)	Understanding the distribution and activity of sulfate reduction at hydrothermal vents requires a more thorough interrogation of the community ecology and metabolic activity of vent hosted microorganisms in the context of the extreme physico-chemical environment.   To date, many studies have quantified rates of sulfate reduction in hydrothermal-influenced sediments and vent isolated microorganisms, but only one study of sulfate reduction exists for hydrothermal deposits.  Here we present rates of microbially-mediated sulfate reduction as determined via 35S tracer studies- from three distinct hydrothermal deposits recovered from the Middle Valley vent field on the Juan de Fuca Ridge.  We further evaluate these rates in the context of the in situ geochemistry and microbial community structure of each chimney to better constrain linkages between phylogeny and function.   Middle Valley hydrothermal deposits Chowder Hill, Dead Dog, and Needles collected July 2010 AT15-67 on Alvin Dive 4625.	root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
MGYS00002884	marine sediment metagenome Targeted loci environmental	Compare the bacterial communities of hydrothermal deposits and other deep-sea sediments in Okinawa Trough	root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
MGYS00002840	Sediment Metagenome	This study presents an evaluation of the impacts of DNA extraction methods, targeted 16S rRNA hypervariable regions and sample origins on the microbial diversity detected by 454-pyrosequencing in sediments from cold seep and hydrothermal vent ecosystems	root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
MGYS00004022	Loihi Seamount Targeted loci environmental	We propose 16s tag sequencing from subsurface fluid samples and microbial mats sampled directly above the venting fluids to further our understanding of subsurface microbial populations in a low sulfide, high iron hydrothermal environment, and to determine the extent of interaction between microbial communities in the subsurface diffuse fluids and seafloor microbial mats. We will test the following hypotheses:1. The subsurface microbial communities in the Hiolo area and Spillway area have different compositions that are related to local fluid chemistry, and2. The dominant species in microbial mats at Loihi Seamount are seeded by subsurface populations present in diffuse flow fluids. It is likely that the dominant mat species are present but not dominant in the subsurface, and bloom in the transition zone at the seafloor where warm, reduced anoxic fluids mingle with cool,oxic seawater.	root:Environmental:Aquatic:Marine:Hydrothermal vents:Microbial mats
MGYS00004222	AT26-10 Crab Spa IGT incubations raw sequence reads	"These are sequences from the final time point of ~24 h incubations of diffuse-flow hydrothermal vent fluids from ""Crab Spa"" (9o50.3981 N, 104o17.4942 W). All but two samples were incubated at 24 C, the remaining two were incubated at 50 C. Further details about sampling and experimental conditions are available in an accepted publication by McNichol et al (2016) entitled ""Assessing Microbial Processes in Deep-Sea Hydrothermal Systems via Incubations at In Situ Temperature and Pressure"" to be published in Deep-Sea Research Part I. A forthcoming publication will also use these data."	root:Environmental:Aquatic:Marine:Hydrothermal vents:Diffuse flow
MGYS00002781	Comparative 16S analysis of hydrothermal vent samples from the Mid-Atlantic Ridge (MAR)	The samples were collected as part of a comparative 16S amplicon sequencing-based analysis of hydrothermal vent samples from the Mid-Atlantic Ridge (MAR)	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00004061	Bacterial community of cold seeps Metagenome	Spatial scaling of bacterial diversity of cold seeps in the deep Eastern Mediterranean sea	root:Environmental:Aquatic:Marine:Cold seeps:Sediment
MGYS00003130	Preservation of ancient eukaryotic DNA in methane hydrate-associated marine sediments.	Ancient eukaryotic DNA in marine sediment can provide valuable information on the paleo-environment. However, labile nucleic acids are generally considered to be microbially degraded in water and sediment columns. Previously, ancient eukaryotic DNA has been retrieved from sediments associated with anoxic water column in lake and semi-closed sea, due to the minimized effect of oxic biodegradation. Cold seep sediment is characterized by high upward flux of methane, where there is the possibility that the excess energy source might suppress the degradation of deposited organic matter including nucleic acids by microbial activity. We investigated the preservation of ancient eukaryotic DNA in marine sediments associated with and without methane hydrate in the eastern Japan Sea, between which the dominant prokaryotic populations are clearly distinct. Marine sediments were retrieved from the eastern Japan Sea during a cruise onboard R/V Marion Dufresne in June 2010. Two-step alkaline DNA extractions were conducted with 0.1 g of marine sediments. DNA from living organisms such as fungi was removed by the first extraction under mildly heated conditions at 65 degrees Celsius, which was followed by the second extraction at 95 degrees Celsius. Triplicate DNA extraction and subsequent clone library analysis were more reproducible for marine sediments associated with methane hydrate. Based on highly variable18S rRNA gene sequences, terrestrial and marine organisms were taxonomically identified at the species level. The diversity of ancient eukaryotic DNA represented by Alveolata, Fungi, Stramenopiles and Viridiplantae was comparable between this study and previous ones. As only 0.1g of g wet sediment is required, the overall methodology developed in this study has great potential to reconstruct terrestrial and marine ecology at high time resolution. In addition, methane hydrate-associated sediments, which are globally distributed along the continental margin, have great potential to reconstruct the past terrestrial and marine ecology around the world over geological timescales.	root:Environmental:Aquatic:Marine:Cold seeps:Sediment
MGYS00002890	archaeal community in Haima cold seep in SCS	archaeal community	root:Environmental:Aquatic:Marine:Cold seeps:Sediment
MGYS00002843	Incubation of marine methane seep sediments with a bioorthogonal amino acid	In marine sediments, anaerobic oxidation of methane (AOM) is primarily catalyzed by syntrophic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). We applied bioorthogonal non-canonical amino acid tagging (BONCAT) using a high-throughput approach to detecting protein synthesis in individual cells, on sediments from deep-sea methane seeps. Sediment samples have been incubated in the presence or absence of methane and a bioorthogonal amino acid. V6 regions of bacterial and archaeal 16S rRNA genes were amplified using general primers, tagged, and analyzed for shifts in the microbial community during time of incubation.	root:Environmental:Aquatic:Marine:Cold seeps:Sediment
MGYS00004432	seawater metagenome	Methane seep mesocosms	root:Environmental:Aquatic:Marine:Cold seeps
MGYS00004137	marine methane seep Targeted Locus (Loci)	Analysis of microbial diversity (e.g., 16S rRNA gene diversity) in folliculinid ciliates found at methane seeps along the Pacific margin.	root:Environmental:Aquatic:Marine:Cold seeps
MGYS00003069	Marine methane seep Targeted Locus (Loci)	Analysis of 16S rRNA gene diversity in methane-derived authigenic carbonate nodules and their host sediments, across two previously established marine methane seep sites off the west coast of North America.	root:Environmental:Aquatic:Marine:Cold seeps
MGYS00002785	Santa Monica Basin seep sediment incubations to assess C and N sources for F430 synthesis	Santa Monica methane seep sediment incubations	root:Environmental:Aquatic:Marine:Cold seeps
MGYS00002772	Hydrate Ridge, OR - Deep sea cold seep ecosystem Targeted Locus (Loci)	The goal of this study was to examine how various sources and scales of heterogeneity within a methane seep ecosystem off the coast of Oregon influenced microbial eukaryote community composition and diversity.	root:Environmental:Aquatic:Marine:Cold seeps
MGYS00002665	16S Amplicon Data from an Antarctic Cold Seep	Benthic fauna from a high Antarctic cold seep	root:Environmental:Aquatic:Marine:Cold seeps
MGYS00002655	Marine methane seep Targeted Locus (Loci)	Microbial 16S rRNA diversity associated with various samples at marine methane seeps along the western North American margin.	root:Environmental:Aquatic:Marine:Cold seeps
MGYS00002653	Heterogeneity of methane seep microbiomes in the NE Pacific	Data from 16S rRNA sequencing of marine sediment samples collected from both methane seep and reference sediments along the Cascadia Margin (NE Pacific) during three separate research cruises. Included 8 newly discovered seeps, 2 known seeps, and 2 reference sediments.	root:Environmental:Aquatic:Marine:Cold seeps
MGYS00004653	Denitrification bacteria in sediment cores of Daya Bay, China	nirS gene	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004625	Microbial ecology of AOA community in sediment from adjacent waters of Rushan Bay	Microbial ecology of AOA community	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004624	Microbial ecology of AOB community in sediment from adjacent waters of Rushan Bay	Microbial ecology of AOB community	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004600	coastal sediment Raw sequence reads	Diversity of Rhodopirellula and related planctomycetes. This study investigates the diversity of Rhodopirellula and related planctomycetes in an intertidal sediment of Sylt island, Germany, employing carB gene, coding for the large subunit of carbamoylphosphate synthetase, as a marker gene.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004513	Microbial diversity before and after tidal re-instatement	Microbial community diversity from four surface sediment sites collected in duplicates. Two of the sites are below sea level and two are above sea level. The data set includes samples before and after a tidal re-instatement project. Greenhouse gas fluxes, water levels, and salinity were also collected to identify the potential of blue carbon in coastal wetlands.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004504	Bacterial community structure and their predicted functions in coastal sediments	The main objectives of the present study were investigation of bacterial community compositions and their predicted functions in coastal sediments, considering the impacts of natural processes and anthropogenic activities.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004460	seawater bacterial community Raw sequence reads	We report the sediment derived dissolved organic matter degradation in incubation experiment with the overlying seawater, shifts in microbial community structure during the incubation were investigated. Microbial genomic DNA was extracted from the polycarbonate membranes (microbial cells filtered) and the 16S rRNA gene sequences (v3+v4) were amplified by PCR.We classified the OTUs based on their phylogenetic affiliations and determined their relative proportions on the total number of sequencing reads.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004444	Coastal Sediment Bacterial Community Alterations in Association with Sudden Vegetation Dieback	This study analyses the alterations in the sediment microbial communities in a coastal wetland in response to the die off of the dominant plant, Spartina alterniflora	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004425	Microbial ecology of archaeal community in sediment from adjacent waters of Rushan Bay	Microbial ecology of archaeal community	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004424	Microbial ecology of bacteiral community in sediment from adjacent waters of Rushan Bay	Microbial ecology of bacterial community	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004395	coastal sediment diversity study	The main objectives of the present study were the in-depth characterization of bacteria and archaea diversity and community distribution in the coastal sediments along a pollution gradient subject to costal anthropogenic disturbances and the riverine input.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004360	Comparative analysis of bacterial community-metagenomics in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252)	Microbial communities play a crucial role in microbial loop process that constitute the foundation of the ecosystem structure and function. The goal of this study was to monitor microbial community shift in the Gulf of Mexico coastal sediments following exposure to MC252 oil in a laboratory microcosm experiment. We used bacterial tag encoded FLX pyrosequencing (bTEFAP) approach targeting the 16S rRNA gene. We also studied the presence of the biodegradative genes in pure cultures of bacteria from oil-treated sediments samples.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004251	Microbial diversity of Oslo Fjord Pockmark sediments	The non-active pockmarks of the Oslo Fjord are excellent seabed features for studying the effects of geology on the microbial diversity. Geological features such as pockmarks effect the waterflow over the seabed. Here we studied the microbial communities from pockmarks sediments to understand how the diversity is affected by these structures.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004210	Mudflat sediment Metagenome	Microorganisms are important in gulf ecosystem, they are more sensitive to environmental changes and are better indicators for environmental quality assessment. Therefore, understanding the microbial community compositions is important to improve the environmental assessment indicators.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004058	Marine Sediment Targeted Locus	Marine sediment samples collected from the Bay of Fundy, New Brunswick.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00003001	Comparison of marine sediments from the Beguela upwelling zone	Comparing the microbial communities present in the marine sediments off the coast of Namibia and their relationship to phosphogensis.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00002724	Development and validation of a multi-trophic metabarcoding biotic index for benthic organic enrichment biomonitoring using a salmon farm case-study.	Salmon farms are often associated with strong benthic enrichment gradients. Routine monitoring is usually required by regulation, and has traditionally been based on benthic macrofaunal communities. This is reliant on taxonomic expertise, excludes analsyis of micro-organisms and turn-around times can be slow, limiting opportunities for adaptive management. Environmental metabarcoding is a powerful high-throughput sequencing-based technique that is promising for identifying and quantifying assemblages of benthic organisms for biomonitoring. Previous studies have demonstrated relationships between specific taxonomic groups (e.g., bacteria, foraminifera or other eukaryotes) and anthropogenic effects. However, there is uncertainty around applicability at larger spatial and temporal scales, and the absence of fixed categorical scales makes the use of data challenging for routine biomonitoring. In this study, we analysed 105 sediment samples collected over three years from three salmon farms spanning two separate bioregions. Environmental DNA and RNA (eDNA/eRNA) metabarcoding of three taxonomic groups (foraminifera [For], bacteria [Bac], and general eukaryotes [Euk]) was undertaken in parallel with traditional macrofaunal and biochemical analysis (which were used to calculate an Enrichment Stage [ES] index for each sample). The most abundant 200 to 250 Operational Taxonomic Units in each taxonomic group were assigned to Eco-Groups (EG) using a quantitative, quality-based method. These were then used to develop a Metabarcoding Biotic Index (MBI) for each group individually (For-MBI, Bac-MBI, and Euk-MBI) and in combination (multi-trophic MBI; mt-MBI). Based on our assessment criteria we robustly allocated ca. 500 EG to a wide range of known and unknown taxa. Using both the development (year 1 [Y1] and 2 [Y2]) and independent validation (year 3) datasets the weakest correlation was between For-MBI and ES (eDNA/RNA, R2 = 0.731 to 0.850), whereas strong correlations were obtained between the mt-MBI and, or when just Bac and Euk data (mt[Bac+Euk]-MBI) were combined (eDNA/RNA, R2 > 0.900). Consequently, we suggest that foraminifera be excluded from the mt-MBI, which will reduce analytical time and costs. The strong correlations obtained between the mt-MBI and ES confirms that it has the potential to complement or even replace current fish farm biomonitoring techniques in the near future.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00001043	Mangrove soil sediment Targeted Locus (Loci)	Biodiversity is at present receiving increasing attention due to need of conservation and sustainable utilization. Proper sampling and identification of organisms at the baseline is prerequisite to monitor any disturbances in future. This is particularly significant in the context of sea level rise and climate changes. The Indian coastal and marine habitat includes near shore, creeks, tidal flats, mud flats, coastal dunes, mangroves, seaweed, sea grass beds and coral reefs. These marine habitats are potential natural resources playing significant role in ecological and economic stabilities of the country. The present study aims at to inventorize the present microbial diversity on Indian coast and construct a detailed strategy for bridging the gaps with sampling plan for creating a database available in public domain.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004543	UCYN-A diversity in the Pacific	UCYN-A nifH amplicons were recovered from a coastal and oligotrophic site in the Pacific to characterize the diversity of UCYN-A sublineages.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004520	Effects of different types of wastewater on microbial degradation of 2,2'',4,4''-tetrabromodiphenyl ether (BDE-47) in anaerobic sediment.	Surface sediments (from 0 to 10 cm depth) were collected from the southern coastal area (30.9844? N, 120.1411? E) at Taihu Lake, with a low-level of PBDE contamination as reported previously.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004519	Future climate change affects the microbiome and condition of habitat-forming kelp	Climate change can cause effect on marine ecosystem. As a result, higher temperature and enrichment of carbon dioxide of seawater would be expected in the future scenario. In this study, we experimentally investigated the independent and interactive effects of warming and acidification on the habitat-forming kelp Ecklonia radiata and its associated microbiome, then 16S rRNA sequencing data of microbial communities associated with E. radiata on healthy and blistered samples under current and future environmental conditions were collected.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004502	Marine Bacteria 16S V4 Raw sequence reads	Analysis of Bacterioplankton Community Distribution Pattern in Bohai Bay	root:Environmental:Aquatic:Marine:Coastal
MGYS00004500	Metagenomics of Jacarepagua Lagoon	"The Jacarepagua lagoon is a coastal shallow water body in the Rio de Janeiro city (Brazil) historically contaminated by Microcystins (""MCs"" - toxin produced by cyanobacteria with carcinogenic potential for mammals). These molecules are stable and resistant to variation in some physical and chemical factors (i.e. temperature, pH) and some common proteases. Besides, many studies have evidenced the process of bioaccumulation of MCs in different organisms, its adsorption to sediment particles and also its biodegradation by microorganisms from the environment. Previously, we evaluated the removal of MC from water by microorganism assemblages and biodegradation process was observed in the sediment as well as in the interstitial water. Furthermore, we analysed the microbial community through sequencing 16S rDNA by Illumina and showed the differences between these two microbiomes. Moreover, major identified phyla were Chloroflexi, Proteobacteria, Firmicutes, OP3 and the identified OTUs several genera described as MC-degraders were detected"	root:Environmental:Aquatic:Marine:Coastal
MGYS00004457	water sample Raw sequence reads	seawater bacterial diversity in Dongji Island	root:Environmental:Aquatic:Marine:Coastal
MGYS00004433	Microbial community diversity in Arctic marine sediments and Planktonic microbial	This study assessed the microbial community composition in Arctic marine sediments by 454 pyrosequencing of the 16S rRNA gene and planktonic microbial community composition in an Arctic fjord by 454 pyrosequencing of the 16S rRNA and 18S rRNA genes.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004407	coastal suspended particulate matter North Sea surface Raw sequence reads	Microbial diversity in the North Sea coastal surface water during an annual cycle	root:Environmental:Aquatic:Marine:Coastal
MGYS00004287	seawater PCC7002M CCMP1334M Raw sequence reads	publish a paper	root:Environmental:Aquatic:Marine:Coastal
MGYS00004099	Coastal Marine Environment Targeted loci environmental	Marine protist samples were taken from Tolo Harbour in Hong Kong, before during and after a severe hypoxic episode.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004094	Metagenome from mudbank Area,Alappuzha Kerala India	The Water samples are collected from 3 locations in the Coastal waters of Alappuzha during the monsoon and pre-monsoon period.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004088	Marine sample from an Antarctic Bay Raw sequence reads	Describe microbial diversity	root:Environmental:Aquatic:Marine:Coastal
MGYS00004087	Marine waters Raw sequence reads	Microbial community structure of ballast and harbor waters	root:Environmental:Aquatic:Marine:Coastal
MGYS00004051	Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site	High-throughput sequencing of ocean biomes has revealed vast eukaryotic microbial diversity, asignificant proportion of which remains uncharacterized. Here we use a temporal approach tounderstanding eukaryotic diversity at the Scripps Pier, La Jolla, California, USA, via high-throughput amplicon sequencing of the 18S rRNA gene, the abundances of both Synechococcusand Synechococcus grazers, and traditional oceanographic parameters. We also exploit ourability to track OTUs temporally to evaluate the ability of 18S sequence-based OTU assignmentsto meaningfully reflect ecological dynamics. The eukaryotic community is highly dynamic interms of both species richness and composition, though proportional representation of higher-order taxa remains fairly consistent over time. Synechococcus abundance fluctuates throughoutthe year. This study has resulted in a temporal dataset of eukaryotic 18S sequences that cover a wide range of taxa and offers insights into the pier microbial community and how it changes with time.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004031	Protists in Havre-aux-Maisons Lagoon, Magdalen Islands, Quebec, Canada	Seasonal monitoring, 454-sequencing 18S rDNA V4 region	root:Environmental:Aquatic:Marine:Coastal
MGYS00003165	the assembly of abundant and rare bacterioplankton subcommunities in three subtropical bays	Contribution of selective and neutral processes to the assembly of abundant and rare bacterioplankton subcommunities	root:Environmental:Aquatic:Marine:Coastal
MGYS00003013	Microbial diversity in the Tongyeong-Geoje coastal area of Korea	Investigate the potential interactions among the bacterial species, phytoplankton, and environmental parameters	root:Environmental:Aquatic:Marine:Coastal
MGYS00002769	Distribution of the Roseobacter clade	The aim of this study was to investigate the distribution of the Roseobacter clade in water and sediment samples which were taken along a latitudinal gradient from Germany to Norway.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002765	Coastal seawater influenced by the municipal effluents Raw sequence reads	Coastal seawater influenced by the municipal effluents	root:Environmental:Aquatic:Marine:Coastal
MGYS00002647	Microbial diversity in the Tongyeong-Geoje coastal area of Korea2	Investigate the potential interactions among the bacterial species, phytoplankton, and environmental parameters	root:Environmental:Aquatic:Marine:Coastal
MGYS00002646	Microbial diversity in the Tongyeong-Geoje coastal area of Korea	Investigate the potential interactions among the bacterial species, phytoplankton, and environmental parameters	root:Environmental:Aquatic:Marine:Coastal
MGYS00002544	Temporal dynamics of the particle-attached and free-living microbial communities from coastal seawater	We examined the particle-attached and free-living microbial communities from coastal seawater at the Pivers Island Coastal Observatory (PICO) monthly from July 2013-August 2014. Partial 16S rRNA gene libraries were used to identify bacteria found in four size fractions of seawater >63m (zooplankton and large particles), 63-5m (particles), 5-1m (small particles/ dividing cells) and <1m (free-living bacteria).	root:Environmental:Aquatic:Marine:Coastal
MGYS00002486	Distributions and Abundances of Sublineages of the N2-Fixing Cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) in the Noumea Lagoon	UCYN-A sequences from the Noumea Lagoon time-series (July 4, 2012 - April 3, 2014).	root:Environmental:Aquatic:Marine:Coastal
MGYS00002376	Nahant Collection	This collection includes whole genome sequences of purified isolates of marine bacteria, isolated on Vibrio-selective media, and viruses infecting a subset of these strains. All derive from seawater collected in the marine littoral zone at Canoe Cove in Nahant, MA, USA.	root:Environmental:Aquatic:Marine:Coastal
MGYS00005082	seawater metagenome Metagenome	Environmental metagenomic dataset originating from seawater collected near Anvers Island (Antarctic Peninsula). Dataset consist of short reads produced via the Illumina HiSeq 2500 platform. The complete dataset was used to assess metazoan community composition through the application of environmental DNA (eDNA).	root:Environmental:Aquatic:Marine
MGYS00004664	marine metagenome Raw sequence reads	Raw bacterial 16S rRNA sequences from 3 North Atlantic water masses, amended and unamended with high molecular weight organic matter (cruise EN584).	root:Environmental:Aquatic:Marine
MGYS00004648	marine plankton metagenome Targeted loci environmental	Study the pigmentation composition and taxonomic composition of Synechococcus communities in the South China Sea and East China Sea	root:Environmental:Aquatic:Marine
MGYS00004641	microbes in coastal sea	microbial biogeography	root:Environmental:Aquatic:Marine
MGYS00004636	Diazotroph Community Structure and Distribution in the Kuroshio Current along the Tokara Strait Raw sequence reads	Diazotroph Community Structure and Distribution in the Kuroshio Current along the Tokara Strait	root:Environmental:Aquatic:Marine
MGYS00004635	Niche separation of ammonia-oxidizing archaea by the Kuril Islands in the subarctic Northwestern Pacific		root:Environmental:Aquatic:Marine
MGYS00004632	Picocyanobacterial diversity in spring in the East China Sea and the East Sea (Targeted loci environmental)	To understand a distribution pattern of picocyanobacterial diversity during spring season in seas around Korean peninsula, their genetic diversity were studied using barcoded amplicon sequencing approaches in the East Sea and the East China Sea.	root:Environmental:Aquatic:Marine
MGYS00004607	Assessing the microbial diversity in Cape Comorin ocean water	Cape Comorin is a site located at the southern-most point of the Indian Peninsula, where the Bay of Bengal, Arabian Sea and the Indian Ocean meet. This study aims to explore the microbial diversity present in the ocean water at this site.	root:Environmental:Aquatic:Marine
MGYS00004601	North Sea plastic incubation and reference communities, raw sequence reads	The study investigated the influence of seasonal and biogeographical factors on composition and structure of microbial communities colonizing plastic water bottles in the North Sea. Additionally, glass slides and background seawater were sampled.	root:Environmental:Aquatic:Marine
MGYS00004592	Marine bacterium Metagenome	Analyze the potential utilization of EPS	root:Environmental:Aquatic:Marine
MGYS00004588	Surface samples of the NW Pacific Ocean Targeted Locus (Loci)	Diversity of DMS-producing dddP genes in the NW Pacific Ocean	root:Environmental:Aquatic:Marine
MGYS00004582	ETSP OMZ nirS Metagenome	nirS amplicon sequences from the Eastern Tropical South Pacific	root:Environmental:Aquatic:Marine
MGYS00004576	Picocyanobacterial diversity in temperate marginal seas	To elucidate the seasonal and spatial changes in picocyanobacterial diversity in temperate waters, baccoded amplicon pyrosequencing of 16S-23S internal transcribed spacer sequences was applied.  Synechococcus and Prochlorococcus diversity in the East Sea and the East China Sea.	root:Environmental:Aquatic:Marine
MGYS00004573	Bacteria community in the southern East China Sea	Bacterial community analysis in the southern East China Sea.  V6 region of 16s rRNA amplification for bacterial community in the southern East China Sea.	root:Environmental:Aquatic:Marine
MGYS00004534	Phaeobacter inhibens host-attached and free-living communities	The aim of the study was to investigate the microbial communities succession on the surface of a diatom and the surroundings	root:Environmental:Aquatic:Marine
MGYS00004528	Particulate methane monooxygenase diversity on an Arctic shelf	Analysis of particulate methane monooxygenase diversity from natural seawater and methane-ammended sea water incubations via amplicon sequencing of the pmoA subunit.	root:Environmental:Aquatic:Marine
MGYS00004511	microbial diversity Raw sequence reads	microbial diversity of Bohai Sea	root:Environmental:Aquatic:Marine
MGYS00004508	18S-V4 amplification of dinoflagellate cyst communities in the South China Sea	We employed both the newly developed high-throughput sequencing-based metabarcoding method and traditional morphological identification to characterize dinocyst communities collected from the South China Sea.	root:Environmental:Aquatic:Marine
MGYS00004501	seawater metagenome Genome sequencing and assembly	particle-attached and free-living bacteria	root:Environmental:Aquatic:Marine
MGYS00004493	Microbial communities in the phycosphere environment	understand the mechanisms that shape microbial diversity in the algal bloom process	root:Environmental:Aquatic:Marine
MGYS00004244	Herbicide-incubated GBR lagoon microbiomes Targeted loci environmental	Year-long incubation of microbiomes from the Great Barrier Reef lagoon using the diuron herbicide. Profiling using 16S rRNA amplicon profiling.	root:Environmental:Aquatic:Marine
MGYS00004229	marine metagenome	23 seawater microbiomes collected from the aquaculture areas, Laoshan Bay, the Yellow Sea, China	root:Environmental:Aquatic:Marine
MGYS00004227	Microbial diversity	Analysing microbial diversity	root:Environmental:Aquatic:Marine
MGYS00004226	Diatom Community Composition CCS Diel	Diatom and other Stramenopile community composition from targeted amplicon sequencing of V4 region of 18S from incubated seawater collected in upwelled waters off the coast of Oregon. Incubation treatments included UV and no UV natural light treatments as well as dark treatments and were collected at 3 time points.	root:Environmental:Aquatic:Marine
MGYS00004223	Marine biomonitoring: predicting biotic indices from eDNA metabarcoding	We investigated the possibility of using supervised machine learning (SML) algorithms to build predictive models from eDNA metabarcoding data targeting groups that are not commonly used for benthic monitoring. We tested our approach on benthic foraminifera, a group of unicellular eukaryotes known to be sensitive to organic enrichment associated with marine aquaculture	root:Environmental:Aquatic:Marine
MGYS00004220	Arctic sea-ice and sub-ice seawater raw sequence reads	Arctic sea-ice and sub-ice seawater crude oil microcosms	root:Environmental:Aquatic:Marine
MGYS00004218	Vertebrate eDNA survey in nearshore marine environment	This study compared the presence/absence and relative abundance of marine fishes and mammals in different nearshore habitats using environmental DNA (eDNA) versus visual surveys (SCUBA). We determined the spatial resolution of eDNA as well as the false-negative rate compared to the dive surveys.	root:Environmental:Aquatic:Marine
MGYS00004217	Characterization of bacterial communities associated With toxic Dinoflagellates: pyrodinium bahamense Var. compressum	The publication should report the findings of bacteria communities associated with toxic dinoflagellate, pyrodinium bahamense Var. Compressum based on 16S rRNA Metagenomic sequencing	root:Environmental:Aquatic:Marine
MGYS00004211	Bacterial community composition in the naturally iron-fertilized region off Kerguelen Island (Southern Ocean). Targeted Locus (Loci)	The KEOPS2 cruise sampling strategy covered spatially diverse iron-fertilized stations at early bloom stages in the Kerguelen plateau and ocean region (Oct-Nov 2011). KEOPS2 data showed that natural iron fertilization of the Southern Ocean at the scale of hundreds of thousands km2 produced a mosaic of blooms, and that the biological and biogeochemical response to fertilization was diverse. The objective of this study was to explore the bacterial community structure using 16S rRNA gene tag pyrosequencing during the onset of spring phytoplankton blooms in the context of natural Fe fertilization of the Southern Ocean.	root:Environmental:Aquatic:Marine
MGYS00004209	Microbial eukaryote community structure during early phytoplankton blooms in the naturally iron-fertilized Kerguelen area (Southern Ocean) Targeted Locus (Loci)	The KEOPS2 cruise sampling strategy covered spatially diverse Fe-fertilized stations at early bloom stages in the Kerguelen plateau and ocean region (Oct-Nov 2011). KEOPS2 data showed that natural iron fertilization of the Southern Ocean at the scale of hundreds of thousands km2 produced a mosaic of blooms, and that the biological and biogeochemical response to fertilization was diverse. The objective of this study was to explore the microbial eukaryotic community structure using 18S rRNA gene tag pyrosequencing during the onset of spring phytoplankton blooms in the context of natural Fe fertilization of the Southern Ocean. The hypothesis tested was that the protistan communities would differ between the Fe-fertilised blooms and the HNLC waters and also between the blooms. The use of pyrotags provided a unifying approach for assessing the breadth of protistan communities including the groups that are quasi impossible to characterize using traditional approaches of microscopy and culture (e.g MAST, MALV, Fungi..).	root:Environmental:Aquatic:Marine
MGYS00004207	DOM nutrient stress experiment bacterial communities	These sequences include bacterioplankton 16S rDNA amplicons both environmental samples from the Santa Barbara Channel, CA, USA, and from subsequent remineralization bioassays. Bioassays were amended with dissolved organic carbon from nutrient-stressed diatoms.	root:Environmental:Aquatic:Marine
MGYS00004206	Santa Barbara Channel cruise SBDOM11 bacterioplankton 16S rDNA	This sample includes environmental bacterioplankton DNA from the SBDOM11 cruise in the Santa Barbara Channel, California, USA, in May 2011, as well as associated experimental samples from remineralization bioassays. This project traced the bacterial response to the DOM produced by an upwelling-driven phytoplankton bloom, from recently upwelled water through the onset of nutrient stress.	root:Environmental:Aquatic:Marine
MGYS00004205	Microbial community of Red Sea (16S amplicon) Targeted Locus (Loci)	16S pyro-sequencing of samples from multiple places in Red Sea	root:Environmental:Aquatic:Marine
MGYS00004203	Nanticoke Harbour, ON, Canada (plankton SSU 454 sequencing)		root:Environmental:Aquatic:Marine
MGYS00004202	Bayside Harbour, NS, Canada (plankton SSU library 454 sequencing)		root:Environmental:Aquatic:Marine
MGYS00004200	Marine phytoplankton Metagenome	Marine phytoplankton in the northern ECS and coastal waters near Jeju from April 24~30th, 2011	root:Environmental:Aquatic:Marine
MGYS00004187	Ascidian and Seawater Metagenome	Diversity, structure and host-specificity of microbial associates in ascidians (tunic tissue).	root:Environmental:Aquatic:Marine
MGYS00004173	Microbial eukaryotes in an Arctic under-ice spring bloom north of Svalbard.	In this study, we investigated microbial eukaryote diversity and community compositional differences in an under-ice spring bloom north of Svalbard. Our mainobjectives were to: 1) Identify the community of microbial eukaryotes in two ice-coveredstations, 2) to unravel the influence of water masses of different characteristics and historyversus local processes on the composition of the microbial protist communities, and 3) tostudy the metabolically active fraction of the community by comparing inventories based onrRNA and the rRNA gene.	root:Environmental:Aquatic:Marine
MGYS00004170	Characteristics of eukaryotic plankton community in the Coastal Waters of Rongcheng by Illumina sequencing	Plankton community structure and diversity in the coastal waters of Rongcheng, China	root:Environmental:Aquatic:Marine
MGYS00004167	marine metagenome Targeted Locus (Loci)	The goal of this project is to examine and integrate taxonomic, genetic, and functional diversity in marine lakes in Palau and Indonesia. Samples have been collected at multiple depths in multiple lakes since 2010. DNA was extracted from filtered water samples, and archaeal/bacterial 16S rRNA genes were amplified and then sequenced (using 454 in 2010 and Illumina thereafter).	root:Environmental:Aquatic:Marine
MGYS00004162	Polyamine-transforming bacterioplankton in seawater	This study investigated the taxonomic compositions of PA-transforming bacterioplankton in surface seawater collected from nearshore to shelf break stations on the South Atlantic Bight of the United States.	root:Environmental:Aquatic:Marine
MGYS00004161	Surface water bacteria Targeted Locus (Loci)	Study of diversity and community composition of bacterioplankton in surface waters of the Southern Adriatic sub-basin (SAd) in the Mediterranean Sea, across an environmental gradient from coastal to offshore stations	root:Environmental:Aquatic:Marine
MGYS00004159	Marine plankton Metagenome	Changes of Bacteria community composition in the water column of Igoumenitsa Gulf, Ionian Sea, Greece, over a year	root:Environmental:Aquatic:Marine
MGYS00004156	Bacteria Metagenome	This study presented the bacterial diversity in sea water from Greatwall cove and Ardley cove, Fildes Peninsula, and provided reference for the investigating of the function of the Antarctic ecosystem.	root:Environmental:Aquatic:Marine
MGYS00004155	Canada Basin Metagenome	The Canada Basin is a deep oceanic basin within the Arctic Ocean. To investigate the bacterial diversity in seawater from the Canada Basin, water samples were collected from five stations in the Canada Basin during the 3rd Chinese Arctic Scientific Expedition in 2008. After pyrosequencing with a 454 Life Science GS-FLX sequencer, the V3 region of the 16S rRNA gene sequences were analyzed, the bacterial diversity of sea water from the Canada Basin was generally achieved.	root:Environmental:Aquatic:Marine
MGYS00004154	Microbial eukaryotes Metagenome	This study presented the molecular diversity of microbial eukaryotes in sea water from Greatwall cove and Ardley cove, Fildes Peninsula, and provided reference for the investigating of the function of the Antarctic ecosystem.	root:Environmental:Aquatic:Marine
MGYS00004153	Plankton sample collected from Nanaimo Harbour Targeted Locus (Loci)	Nanaimo Harbour, BC, Canada (plankton SSU library 454 sequencing)	root:Environmental:Aquatic:Marine
MGYS00004146	Active picoeukaryotes in the Eastern Mediterranean Sea	Response of active picoeukaryotes to the deposition of Saharan dust and European aerosols in the Eastern Mediterranean Sea revealed by 454 pyrosequencing	root:Environmental:Aquatic:Marine
MGYS00004144	Enrichment metagenome	Genetic and Cultured diversity of free living marine Spirochaetes	root:Environmental:Aquatic:Marine
MGYS00004141	Amplicon-Based Illumina Sequencing Reveals High Diversity of Phytoplankton in the Coastal Waters of Qinhuangdao	plankton community structure and diversity in the coastal waters of Qinhuangdao	root:Environmental:Aquatic:Marine
MGYS00004140	Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding	This study compared the presence/absence of marine fishes and mammals at 10 different sites in the Monterey Bay National Marine Sanctuary. We tested for differences in marine vertebrate communities at different water sampling depths and whether a station was located on the shelf or in a canyon on Monterey Bay. We also compared OTUs identified in biological triplicates.	root:Environmental:Aquatic:Marine
MGYS00004136	marine metagenome	Romanian coastal Black Sea Bacteria	root:Environmental:Aquatic:Marine
MGYS00004135	May 2013 DNA-SIP marine seawater bacteria metagenomic assembly	Illumina bacteria and archaea 16S rRNA genes	root:Environmental:Aquatic:Marine
MGYS00004133	Meiobenthos nSSU metagenetic meiobenthic data	nSSU meiobenthic diversity - nSSU meiobenthic samples from UK, EU and Gambia from 454 GS FLX.	root:Environmental:Aquatic:Marine
MGYS00004131	Island Metagenome	Actinobacterial Diversity	root:Environmental:Aquatic:Marine
MGYS00004130	Seawater sample Targeted Locus (Loci)	Heterotrophic nanoflagellate (HNF) grazing is one of the main factors shaping the structure of the prokaryotic communities in the marine environments as an important source of microbial mortality. It strongly affects prokaryotic abundance, diversity and taxonomic composition. We analyzed the effects of predation exerted by heterotrophic nanoflagellates (HNF) on bacterioplankton assemblages from a surface coastal station in the North Adriatic Sea, evaluating also the effects of smaller HNF (<3 m) which are known to constitute an important link between bacteria and larger protists. We coupled the traditional dilution method with 454 sequencing of 16S rRNA gene, providing qualitatively and quantitatively evaluations of the grazing process occurring in marine microbial communities.	root:Environmental:Aquatic:Marine
MGYS00004128	ETNP Targeted Locus (Loci)	Bacterial communities in filtered seawater isolated from the Eastern Tropical North Pacific (ETNP).	root:Environmental:Aquatic:Marine
MGYS00004127	Metagenetic analysis of copepod community in the tropical and subtropical Pacific	A large-scale biogeographic study of copepods is challenging in the tropical and subtropical Pacific due to inaccessibility, high species diversity and limitation by morphological identification. In this study, spatial patterns of epipelagic copepod community structure was revealed using 28S metagenetic method at 19 stations in Kuroshio, North Pacific subtropical gyre, eastern tropical Pacific and South Pacific subtropical gyre. The copepod communities were the most correlated to chlorophyll a, and community structure in subtropical gyres was different from those in Kuroshio and eastern tropical Pacific. The metagenetic analysis also could detect copepod diversity, and high copepod diversity was observed in oligotrophic North and South Pacific subtropical gyres with peak in North Pacific subtropical gyre. This is first metagenetic study of copepods covering wide-area and could serve as a basis of the understanding of diversity and biogeography of copepods in the tropical and subtropical Pacific.	root:Environmental:Aquatic:Marine
MGYS00004126	A metagenetic approach for revealing community structure of marine planktonic copepods	Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We developed a method for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) through analysis of an artificial copepod community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. The number of sequence reads per MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. MOTUs were successfully classified at the family level at 97% similarity; similar patterns of species richness and biomass within families were revealed with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass-dominant species in each field-collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.	root:Environmental:Aquatic:Marine
MGYS00004125	California Current System Long Term Ecological Research P1604 (CCS_LTER_P1604) Targeted loci environmental	Using metabarcoding of 16S and 18S rRNA, we evaluate variability of prokaryotic and protistan communities in the water column and on particles collected in sediment traps across an inshore-offshore environmental gradient in the California Current System.	root:Environmental:Aquatic:Marine
MGYS00004121	uncultured prokaryote Raw sequence reads	To study the 16S phylogeny in the upwelling water, which was caused by the intrusion of Kuroshio Current	root:Environmental:Aquatic:Marine
MGYS00004119	Spatial variation of bacterioplankton in south Atlantic Bight	The continental shelf ecosystem off the Georgia coast i.e., the South Atlantic Bight (SAB), is among the most productive marine environments that hosts many hard or live bottom areas and are homes to large number of phytoplankton, sponges, corals and many species of tropical and subtropical fishes. From the Georgia bank seaward, the coastal, shelf, slope and Gulf Stream waters represent a natural gradient of many environmental parameters, including decreased nutrients and increased salinity. Extensive efforts have surveyed the major macroorganisms in the region, however, little is known yet on the dynamics of bacteria, which are the major conduits in the energy and nutrient flow within the system. This study investigated the spatial and temporal dynamics of bacterioplankton community composition along transects from the coast bank of Georgia to Gulf Streams on the SAB.	root:Environmental:Aquatic:Marine
MGYS00004117	Seawater free living bacterioplankton	To study the relationships between bacterioplankton community composition and environmental factors between different sampling scales.	root:Environmental:Aquatic:Marine
MGYS00004115	ARK26/3_Station212 Targeted Locus (Loci)	ARK26/3_Station212_Protist	root:Environmental:Aquatic:Marine
MGYS00004101	Santa Barbara Basin Raw sequence reads	Microbial community of the benthic boundary layer of the Santa Barbara Basin.	root:Environmental:Aquatic:Marine
MGYS00004075	Eastern Mediterranean Sea Lignin and Xylan enrichments	A set of microcosms inoculated with a consortia of microbes from the eastern Mediterranean sea and incubated with lignin and xylan as a sole carbon source in artificial seawater medium. Consortia was investigated for their potential to produce lignin degrading enzymes.	root:Environmental:Aquatic:Marine
MGYS00004074	Pyrosequencing, the South Sea, May 2009	Analysis of microbial diversity and spatial distribution patterns of microbial community structure in seawater samples	root:Environmental:Aquatic:Marine
MGYS00004073	sea water bacteria Raw sequence reads	Here, we use high throughput sequencing to investigate bacterial diversity and community structure in seawater of the of Zhoushan archipelago. The large amount of data that was obtained and will lay foundations for further biological research in the east china sea.	root:Environmental:Aquatic:Marine
MGYS00004069	water sample Raw sequence reads	water microbial diversity in the Zhoushan Archipelago Sea Area	root:Environmental:Aquatic:Marine
MGYS00004068	Ecological Genomics of the Eastern Tropical South Pacific Oxygen Minimum Zone Metagenome	Oxygen minimum zones (OMZs) are oxygen deficient regions of the ocean that are hotspots for nutrient and climate active trace gas cycling. Forming at intermediate depths (~1001000 m) in response to high biological oxygen demand and reduced ventilation, OMZs occur naturally in regions of high productivity and nutrient-rich upwelling. Global climate change and enhanced run-off from our farms and cities also contributes to OMZ formation and expansion. An expansive and permanent OMZ persists in the Eastern Tropical South Pacific (ETSP) along the coast of northern Chile and Peru. Studies in the ETSP-OMZ have been critical in charting the microbial communities and metabolic processes driving coupled biogeochemical cycling in coastal and open ocean OMZs throughout the global ocean.	root:Environmental:Aquatic:Marine
MGYS00004065	Magadalen Islands Spatio Temporal (MIST) Large Fraction	Farm and control large fraction protists samples pyrosequencing 454 raw sequence reads	root:Environmental:Aquatic:Marine
MGYS00004041	Copepod induced bacterial community Raw sequence reads	Live copepods from the North Atlantic subtropical gyre were collected and rinsed to be used in bioassay-type experiments. Bacteria present in various seawater and copepod treatments were analyzed by targeting the 16S rRNA V3-V4 region. In this study, copepods were observed to increase growth of bacteria which were released to their surroundings. Additionally, copepods may be responsible for inhibiting or inducing growth of specific bacterial groups.	root:Environmental:Aquatic:Marine
MGYS00004030	Sea microbial community Metagenome	Taxonomic description of the Azov Sea microorganisms	root:Environmental:Aquatic:Marine
MGYS00004028	Amplicon sequences from naphthalene biodegradation in Arctic and temperate seawater	Seawater samples from Arctic and temperate area were collected and used directly as inoculum for microcosm scale (1 L) biodegradation experiments. Two set of naphthalene biodegradation experiments were carried out at four different incubation temperatures (0.5, 4, 8, 15 C) with Arctic and temperate seawater. DNA was extracted and amplicon libraries were prepared from the two original seawater samples and one exposed sample at each incubation temperature.	root:Environmental:Aquatic:Marine
MGYS00004023	marine plankton metagenome Raw sequence reads	To understand the succession of phytoplankton-associated bacteria in correlation with phytoplankton bloom	root:Environmental:Aquatic:Marine
MGYS00004021	Marine photic zone, New Caledonia Lagoon raw sequence reads, nitrogenase amplicons	The VAHINE mesocosm experiment, conducted in the low-nutrient low-chlorophyll waters of the Noumea Lagoon (coastal New Caledonia) was designed to trace the incorporation of nitrogen (N) fixed by diazotrophs into the food web, using large volume (50 m3) mesocosms. This experiment provided a unique opportunity to study the succession of N2-fixing microorganisms (diazotrophs) and calculate in situ net growth and mortality rates in response to fertilization with dissolved inorganic phosphate (DIP) over a 23-day period, using both polymerase chain reaction (PCR) amplification of nitrogenase genes (nifH) and quantitative PCR (qPCR) assays targeting known marine diazotroph lineages.	root:Environmental:Aquatic:Marine
MGYS00004016	Antarctic Hypersaline Brine Raw sequence reads	Antarctic brine sampled in the Boulder Clay site (74  44 ''S, 164  01'' E), located in Northern Victoria Land. The aim was to identify the biodiversity differences in hypersaline brines; understanding the reasons of these differences, considering that brines might contain DNA and RNA molecules that remain trapped inside for long geological eras, thus representing a key to reconstruct past ecosystems.	root:Environmental:Aquatic:Marine
MGYS00004015	16S rDNA amplicon of Bacteria and Archaea Metagenome	16S rDNA sequencing of Bacteria and Archaea in the NW Mediterranean sea (transect from coast to open ocean and vertical profiles)	root:Environmental:Aquatic:Marine
MGYS00004014	The Nanoeukaryotic plankton Raw sequence reads	This research in molecular biology techniques for research method, on the east sea tiny eukaryotic analyze and evaluate the diversity of plankton, using multidisciplinary technology to create a data platform, environmental impact factors of miniature eukaryotic phytoplankton were discussed.	root:Environmental:Aquatic:Marine
MGYS00004013	atmospheric depositon effect on bacterial diversity	Atmospheric inputs from mineral and anthropogenic sources are nowadays increasing globally due to desertification in one hand and industrialization on the other. In this context, it is important to understand how atmospheric particles can favor the growth of certain bacterioplankton groups of the ocean over others, as these changes will affect the ratio between primary and heterotrophic production, and consequently the concentration of atmospheric carbon that can be fixed (or released) in the surface layer of the ocean. As aerosol composition varies seasonally and locally, we evaluated the effect of both types of atmospheric particles on different locations of the northwestern Mediterranean and at different times of the year.	root:Environmental:Aquatic:Marine
MGYS00004010	Marine eukaryotes Targeted loci environmental	18S rRNA gene was targeted in environmental samples from the subsurface chlorophyll maximum (SCM) in the Arctic Ocean and the Atlantic (Scotian Shelf) to assess diversity of the eukaryotic protist community.	root:Environmental:Aquatic:Marine
MGYS00004009	Spatial and environmental variation in whole microbial communities in Fildes Bay, King George Island, Antarctica Raw sequence reads	To explore the photosynthetic eukaryotic and bacterial diversity using NGS, statistics analysis and ecological studies in Fildes Bay, King George Island, Antarctica.	root:Environmental:Aquatic:Marine
MGYS00004005	Marine Samples Targeted Locus (Loci)	This project examines the effects of        inorganic phosphorus addition to water column (within water tanks)        bacterioplankton community structure.  All samples from all tanks and experimental days.  Control mesocosm 1, experimental day zero - Control mesocosm 2, experimental day zero.  Samples were collected from seawater in Eastern        Mediterranean from polluted and nearby unpolluted coastal areas.	root:Environmental:Aquatic:Marine
MGYS00003169	SAR amplicon from community incubated with various nanophytoplankton in microcosm	To address the impact of prey (bottom-up) on protist communities, we combine insights from two methods  DGGE to assess abundant ciliates, and HTS sequencing of SAR (Stramenopila, Alveolata, Rhizaria) communities  in marine microcosms. Here are the resulting read generated for this project with our SAR primers.	root:Environmental:Aquatic:Marine
MGYS00003131	Seawater bacteria Metagenome	The study goal is the investigate the bacteria genera and species changes with small peptide incubation in seawater.	root:Environmental:Aquatic:Marine
MGYS00003129	suspended particulate matter Raw sequence reads	Analysis of microbial diversity in the Black Sea water column	root:Environmental:Aquatic:Marine
MGYS00003126	White sea picoplankton Metagenome	Phototrophic picoeukaryotes are important constituents of marine ecosystems. The aim of this study was to determine the molecular diversity and community structure of phototrophic picoeukaryotes in the water and ice of the White Sea in different seasons.	root:Environmental:Aquatic:Marine
MGYS00003090	Microcosms Metagenome	Interactive effects	root:Environmental:Aquatic:Marine
MGYS00003077	Marine Metagenome	16S Barcode pyrosequence	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00003019	AllDist Targeted Locus (Loci)	All samples from all sites	root:Environmental:Aquatic:Marine
MGYS00003003	Trichodesmium spiralis associated microbiome Targeted loci	We sequenced 16S rRNA gene amplicons of samples collected from Trichodesmium spiralis colonies and filtered seawater obtained concomitantly to determine the microbiome of this Cyanobacterium in comparison with the community structure of the surrounding seawater.	root:Environmental:Aquatic:Marine
MGYS00003000	Species-specific associations between bacterioplankton and photosynthetic picoeukaryotes	We used flow cytometry sorting of raw seawater to identify novel bacterial phylotypes found in physical association with photosynthetic picoeukaryotes. In total, five samples were collected at the Santa Cruz wharf on Monterey Bay during summer and fall, 2014. The phylogeny of associated microbes was assessed through Illumina MiSeq sequencing of amplicons of the 16S rRNA gene from unsorted seawater <10 m >0.2 m as well as triplicate samples of 1000 sorted photosynthetic picoeukaryote cells.	root:Environmental:Aquatic:Marine
MGYS00002957	Sea water microorganisms Raw sequence reads	To investigate the microbial diversity at the SEATS station in South China Sea.	root:Environmental:Aquatic:Marine
MGYS00002956	blocking PCR amplification of metazoan DNA for protistan diversity	Protists form the basis of marine food webs. However, the understanding of protistan diversity is typically impeded by the predominance of metazoans, especially when employing universal primers in samples from large size fractions. In order to block the amplification of metazoan DNA in PCR, we designed 3 blocking primers and tested the performance using pure cultures and environmental samples. Furthermore, blockimg primers were applied to samples from a large size fraction, which is insufficiently studied due to the dominance of metazoans.	root:Environmental:Aquatic:Marine
MGYS00002955	sea water Picoeukaryotic Community Raw sequence reads Raw sequence reads	Little is known regarding the diversity and distribution of picoeukaryotes in the east China Ocean, although these organisms are vital components of their environment. Here, we used High throughput sequencing technology to assess the seasonal 18S r RNA diversity of picoeukaryotes at six sampling sites in Carbon sink Time Series Station at Zhoushan	root:Environmental:Aquatic:Marine
MGYS00002951	Magdalen Island Spatio Temporal (MIST) Raw sequence reads	Mussels culture impact on protists community in Magadlen Islands Havre-aux-Maisons lagoon (Gulf of St-Lawrence, Canada) in 2010	root:Environmental:Aquatic:Marine
MGYS00002945	SCS SEATS Raw sequence reads	Marine Group II only dominated shallow water column (<75 m) at the central basin (SEATS) station and was replaced by the dominance of Marine Group I in deeper water, which has commonly been observed in global oceans.	root:Environmental:Aquatic:Marine
MGYS00002939	Mesocosm Targeted Locus (Loci)	Mesocosm experiment with water from Bothnian Bay: the effect of temperature and terrestrial DOC	root:Environmental:Aquatic:Marine
MGYS00002936	16S rRNA sequences of bacterioplankton spatial distributions in the Baltic Proper	The overall goal of this spatial sampling of marine bacterioplankton was to observe the distribution of populations from coastal to offshore. In relation to bacterial production and primary production such information is relevant for investigating coastal to offshore food web efficiency and the role of bacterioplankton community composition in food web dynamics.	root:Environmental:Aquatic:Marine
MGYS00002892	Oceanic microplankton do not adhere to the latitudinal diversity gradient	A latitudinal biodiversity gradient has captivated ecologists for years, and has become a widely recognized pattern in biogeography, manifest as an increase in biodiversity from the poles to the tropics. Oceanographers have attempted to discern whether these distribution patterns are shared with marine biota, and a lively debate has emerged with regard to the global distribution of microbes. Limitations in sampling resolution for such large-scale assessments have often prohibited definitive conclusions. This investigation has evaluated microbial planktonic communities along a ~15,400 km Pacific Ocean transect with DNA from samples aquired every 2 degrees of latitude within a three month period between late August to early November, 2003. Next generation sequencing targeted Bacteria, Archaea, and Eukarya rDNA sequences.Beta analysis of ~10.8 million high quality sequences showed significant geographic patterns of microbial communities, primarily the Bacteria and Archaea domains. Despite regional clustering, none of the domains exhibited a unimodal pattern of alpha-diversity with respect to latitude. Bacteria communities increased in richness from Arctic to Antarctic waters; whereas Archaea and Eukarya communities showed no latitudinal or polar trends. Based on these analyses, constraints on macrofaunal response to factors related to latitude may not be defining prokaryotic and eukaryotic microorganism diversity patterns in the global ocean.	root:Environmental:Aquatic:Marine
MGYS00002889	marine Archaea metagenome	Vertical profiles of archaeal diversity in water columns	root:Environmental:Aquatic:Marine
MGYS00002886	Bacterial communities from the water column and the surface sediments along a transect in the East Sea (Sea of Japan)	We determined the composition of water and sediment bacterial assemblages from the East Sea using 16S rRNA gene sequencing. Total bacterial reads were greater in surface waters (<100 m) than in deep seawaters (>500 m) and sediments. However, total OTUs, bacterial diversity, and evenness were greater in deep seawaters than in surface waters with those in the sediment comparable to the deep sea waters. Proteobacteria was the most dominant bacterial phylum comprising 67.3% of the total sequence reads followed by Bacteriodetes (15.8%). Planctomycetes, Verrucomicrobia, and Actinobacteria followed all together consisting of only 8.1% of the total sequence. Candidatus Pelagibacter ubique considered oligotrophic bacteria, and Planctomycetes copiotrophic bacteria showed an opposite distribution in the surface waters, suggesting a potentially direct competition for available resources by these bacteria with different traits. The bacterial community in the warm surface waters were well separated from the other deep cold seawater and sediment samples. The bacteria exclusively associated with deep sea waters was Actinobacteriacea, known to be prevalent in the deep photic zone. The bacterial group Chromatiales and Lutibacter were those exclusively associated with the sediment samples. The overall bacterial community showed similarities in the horizontal rather than vertical direction in the East Sea.	root:Environmental:Aquatic:Marine
MGYS00002885	water Raw sequence reads	microbial diversity in the water	root:Environmental:Aquatic:Marine
MGYS00002842	Eukaryotic natural population from Northern Baffin Bay - Raw sequence reads	This BioProjects contain raw sequences reads of 18S rRNA and rDNA from natural populations in Northern Baffin Bay from surface and 20m depth.	root:Environmental:Aquatic:Marine
MGYS00002821	Microbial diversity associated with copepods in the North Atlantic subtropical gyre	To characterize microscale spatial heterogeneity, microbial community composition of microzooplankton, primarily small copepods, was investigated in comparison to bacterioplankton in surrounding seawater from the oligotrophic open ocean. Zooplankton individuals were collected at or above the deep chlorophyll maximum in the North Atlantic Subtropical Gyre, and the diversity of microbial communities was investigated using 16S rRNA gene amplicon pyrosequencing targeting the V5-V9 region. Zooplankton studied included the copepods Undinula vulgaris, Pleuromamma spp., Sapphirina metalina, Pseudocalanus spp., and Tigriopus sp., and an amphipod, Phrosina semilunata. High -diversity was observed among samples, with zooplankton taxa-specific bacterial communities distinct from the communities in the surrounding seawater. The taxonomic composition of the microbial communities suggests both external and internal associations are present. Copepod association is a unique microbial niche that may play a role in biogeochemical cycling in the oligotrophic open ocean.	root:Environmental:Aquatic:Marine
MGYS00002815	15N methylamine SIP (WCO station L4)	Methylated amine compounds such as methylamine are important sources of nitrogen for microorganisms in marine habitats. Methylamine is a volatile organic compound generated by degradation of organic matter. The biodegradation of methylamine by marine microorganisms is a major factor modulating the emission of this compound into the atmosphere, where methylamine influences global climate processes. As methylamine contains carbon as well as nitrogen, it can serve as a source of both elements for microorganisms So far, little is known about the identity of the active methylamine oxidisers in marine habitats, especially regarding organisms that use methylamine as a nitrogen source. In this study, Stable Isotope Probing using 15N labelled methylamine was combined with 16S rRNA and functional gene amplicon sequencing as well as metagenome sequencing to identify bacteria that are involved in methylamine degradation or assimilation of methylamine derived nitrogen in samples obtained from the Western Channel Observatory station L4.	root:Environmental:Aquatic:Marine
MGYS00002813	Microbial associations in temperate marine copepods from the Gulf of Maine	16S rRNA amplicon sequencing with the Illumina MiSeq platform on seawater and copepods from the Gulf of Maine.	root:Environmental:Aquatic:Marine
MGYS00002811	Northern Gulf of Mexico Hypoxic Zone Raw sequence reads	Northern Gulf of Mexico Hypoxic Zone. Water column samples collected July 2013. Average depth 18 m.	root:Environmental:Aquatic:Marine
MGYS00002783	Water and Sediment samples Targeted loci environmental	Water and Sediments samples from multiple locations in Panama	root:Environmental:Aquatic:Marine
MGYS00002777	INVESTIGATING THE MICROBIAL EUKARYOTIC COMMUNITIES IN THE SURFACE WATERS OF THE ARAFURA SEA AND CORAL SEA	WE INVESTIGATED THE DIVERSITY OF MICROBIAL EUKARYOTES IN THE SURFACE WATERS OF THE ARAFURA SEA, TORRES STRAIT AND CORAL SEA, USING FLOW CYTOMETRY AND HIGH-THROUGHPUT SEQUENCING OF THE V9 REGION OF THE 18S rRNA GENE.	root:Environmental:Aquatic:Marine
MGYS00002714	ocean bacteria Metagenomic assembly	Bacterial DNA was isolated from two water samples: 1 location in the Bering Strait from the chlorophyll max layer (7m depth) and 1 location in the Chukchi Sea from bottom water (55m depth). The samples were collected with the purpose of sequencing the metagenome to serve as a protein identification database for a metaproteomics study.	root:Environmental:Aquatic:Marine
MGYS00002669	Vibrio-specific 16S rRNA sequences from seawater, sediment, and oyster hatchery samples	Vibrionaceae rRNA sequences from seawater, sediment, and oyster hatchery samples. Vibrio-specific 16S rRNA genes were amplified using VF169 and 680R primers (Yong et al. 2006, Thompson et al. 2004) and sequenced on the Illumina MiSeq.	root:Environmental:Aquatic:Marine
MGYS00002661	Bacterial Diversity in the East China Sea	This study aims to determine bacterial community structures using illumina MiSeq paired-end sequencing (for 16S rDNA) in the East China Sea.	root:Environmental:Aquatic:Marine
MGYS00002657	Sea water sample Targeted Locus (Loci)	Study of spatial and temporal variation in marine bacterial communities.	root:Environmental:Aquatic:Marine
MGYS00002585	Protist Diversity in the East China Sea	This study aims to determine protist community structures using illumina MiSeq paired-end sequencing (for 18S rDNA) in the East China Sea.	root:Environmental:Aquatic:Marine
MGYS00002564	Sea spray aerosols at Three California Beaches	While the diversity and identity of microorganisms in water and sand at the beach have been well documented, few studies have investigated microorganisms in sea spray aerosols (SSA) at the beach. We characterized the microbial communities in SSA, water, and sand of three beaches in central California (Cowell Beach, Baker Beach, and Lovers Point) by sequencing the V4 region of the 16S rRNA gene.	root:Environmental:Aquatic:Marine
MGYS00002545	IMPACT OF SAHARAN DUST DEPOSITION ON BACTERIOPLANKTON IN MARINE SURFACE WATER	Microcosm Experiments Performed in Florida Keys, field season 2015	root:Environmental:Aquatic:Marine
MGYS00002520	Marine metagenome Targeted loci environmental	The main goals of this study were to establish a baseline of the microbial organisms present in surface water samples in Port Everglades Inlet in Fort Lauderdale, FL	root:Environmental:Aquatic:Marine
MGYS00002496	Gulf Oil Spill underwater oil plume samples Targeted Locus (Loci)	During late spring and summer of 2010, the Northern Gulf of Mexico (GoM) was exposed to an oil spill different in magnitude and scope from any previous spill. The Deepwater Horizon, an ultra-deep, offshore drilling platform, began working GoM oil fields in 2001. While working a well in Mississippi Canyon on April 20, 2010, a bolus of methane gas ascended the drill pipe and exploded at the surface. Two days later the platform sank and since then, substantial quantities of oil and gas have leaked from the damaged wellhead. This work addressed the offshore oceanic impacts of the BP spill.  Sediment microbial mediated processes are capable of oxidizing oil and methane in the environment. The PI''s examined the impacts of the Deepwater Horizon Oil Spill on microbially mediated processes in the deep waters and sediments in the vicinity of the spill site. The work complemented several funded or planned geochemical and microbiological sampling programs focused on the oil spill response. PI''s evaluated rates of water column methane oxidation and sediment sulfate reduction and methanogenesis at multiple sites around the spill site. Additional experiments quantified the impact of nutrients, oxygen and substrate concentrations on these important microbially mediated processes.  The Joye group participated in six research cruises during 2010 and received samples from another six cruises from the study area. On all cruises, water samples were collected using a CTD rosette and Niskin or Go-Flo bottles. Sediment samples were obtained by box coring, multi-coring, or using the manned submersible ALVIN.  The PI''s extended the monitoring/assessment program that was initiated through the NOAA National Institute of Undersea Science and Technology (NIUST) funded cruise and further leveraged by NOAA/NIUST (cruises in July 2010, October 2010) by conducting three major expeditions in 2010. This RAPID project directly supported the PI''s efforts for cruises in May/June 2010 (NSF Joye chief scientist); August 2010 (NSF Montoya, chief scientist); November/December 2010 (NSF Joye chief scientist); and July 2011 (NSF Montoya, chief scientist)	root:Environmental:Aquatic:Marine
MGYS00002481	Western Antarctic Peninsula Microbial Community Assembly		root:Environmental:Aquatic:Marine
MGYS00002477	Protistan communities of the upper Arctic Ocean (18S SSU-rRNA Targeted Locus)	Protistan communities of the upper Arctic Ocean (18S SSU-rRNA Targeted Locus), sampled during the MALINA cruise, August 2009.	root:Environmental:Aquatic:Marine
MGYS00002374	Seawater Metagenome	Microbial community in seawater sample	root:Environmental:Aquatic:Marine
MGYS00002372	UK coast natural seawater Genome sequencing	the aim of the project is to determine the effect of plastics on marine bacterial community	root:Environmental:Aquatic:Marine
MGYS00002108	Red Sea metagenomes	An expedition spanning nearly the entire eastern Red Sea. We sampled at eight stations along this route, sampling from the surface down to 500m.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00002105	Baltic Sea Surface Water Metagenome	Surface water collected in the Baltic Proper, 10 km east of Oland in the Baltic Proper (N 5655.851, E 1703.640)	root:Environmental:Aquatic:Marine
MGYS00001945	seawater sample Metagenome	Ocean Acidification: microbes as sentinels of adaptive responses to multiple stressors: contrasting estuarine and open ocean environments Seawater samples collected from the Gulf of Mexico	root:Environmental:Aquatic:Marine
MGYS00001941	Hawaii Dissolved Organic Matter (HIDOM) microcosm perturbation experiments	Marine dissolved organic matter (DOM) contains nearly as much carbon as the Earths atmosphere. To investigate the roles of planktonic marine microbes in the biogeochemical cycling of DOM, we followed the transcriptional responses of a surface water microbial assemblage to DOM derived from an axenic culture of Prochlorococcus marinus and high-molecular weight DOM concentrated from nearby surface waters.	root:Environmental:Aquatic:Marine
MGYS00001932	Gulf of Mexico water and sediments Metagenome	Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km SW of the wellhead), one water column reference station outside of the affected area (37.77 km SE of the wellhead), and deep-sea sediments near the wellhead (3.66 km SE of the wellhead) were sampled one year after the capping of the well.	root:Environmental:Aquatic:Marine
MGYS00001539	Marine water Metagenome	Examine viral communities in ballast and harbor waters	root:Environmental:Aquatic:Marine
MGYS00001428	Marine eukaryotic metatranscriptomes	Metatranscriptome data	root:Environmental:Aquatic:Marine
MGYS00000546	Metagenome sequencing of marine membrane vesicles	Sequencing of DNA amplified from membrane vesicles isolated from the oceans	root:Environmental:Aquatic:Marine
MGYS00004606	sediment metagenome metagenome L-T	The objectives of this investigation were to assess TCS removal mechanisms in sediments from surface flow constructed wetlands planted with Lemnaminor.	root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
MGYS00004605	sediment metagenome Metagenome	The objectives of this investigation were to assess TCS removal mechanisms in sediments of surface flow constructed wetlands planted with Hornwort	root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
MGYS00004604	Sediment microbial communities from Cattail constructed wetlands, Jinan, China - C-T Metagenome	The objectives of this investigation were to assess TCS removal mechanisms in sediments from surface flow constructed wetlands planted with emergent plant (Cattail)	root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
MGYS00004423	XRCWU sediment metagenome Metagenome	To investigate the influence of wetland types on the composition and structure of microbial communities.	root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
MGYS00004422	XRCWD sediment metagenome Metagenome	To investigate the influence of wetland types on the composition and structure of microbial communities.	root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
MGYS00004421	XRM sediment metagenome Metagenome	To investigate the influence of wetland types on the composition and structure of microbial communities.	root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
MGYS00004643	Coastal marsh sediment alkB, pmoA, and P450 gene survey	This dataset includes high-throughput amplicons for alkane dehydrogenase (alkB) genes, particulate monooxygenase (pmoA) genes, and cytochrome P450, encoded by CYP153, genes amplified and sequenced from subtidal sediment and inland soil samples collected biannually (September 2011 to October 2014) from a marsh near Grand Isle, Louisiana. This marsh was affected by oil deposition following the Deepwater Horizon oil spill in 2010. The goals of this dataset are to 1) track changes in the phylogenetic diversity of genes that code for a key enzymes used for bacterial alkane oxidation, short and long chain, from the oil impacted sediments and soil, and 2) to contribute to an understanding of bacterial functional role in the degradation of weathered oil residues in a natural marsh system.	root:Environmental:Aquatic:Freshwater:Wetlands:Marsh
MGYS00004488	Temporal effect of plant diversity and oiling on nitrogen cycling in marsh sediments	The effect of plant diversity on ecosystem recovery from oil spills and temporal effects on biogeochemical cycles needs to be investigated to identify key ecosystem processes as well as the various challenges associated with coastal ecosystem recovery. Oil spill effects on nitrogen cycling caused by either changes in species composition of primary producers or microbial community composition have also been documented. Although low to moderate oiling of coastal wetlands has been shown to impact ecosystem functions, studies focused on determining long term impacts of oil spills on marsh vegetation, microbial community composition and associated effects on nitrogen cycling are relatively limited. This project investigated temporal effects of plant diversity on denitrification and microbial community dynamics through mesocosm experiments. The mesocosms consisted of the black mangrove, Avicennia germinans, along with either a monoculture or polyculture of the smooth cord grass, Spartina alterniflora. The results presented were obtained using DNA extracted from replicate sediment cores sampled in April 2016, 6 months after the mesocosms were treated with oil to achieve a final concentration of 4000 ppm.	root:Environmental:Aquatic:Freshwater:Wetlands:Marsh
MGYS00004449	sediment metagenome Raw sequence reads	The goal of the project is to differentiate storm and tsunami deposits by characterizing the microbial assemblage found in them.	root:Environmental:Aquatic:Freshwater:Storm water
MGYS00004619	microbial community in an integrated constructed wetland Raw sequence reads	microbial community in an integrated constructed wetland	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004616	lake sediment Raw sequence reads	methanotrophs diversity in lake sediments	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004585	Amplicon sequencing of gyrA and parC in Escherichia communities in river/lake sediments	To describe the abundance of fluoroquinolone resistance mutations in environmental Escherichia communities, and investigate the link between abundance of resistance mutations and fluoroquinolone pollution.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004583	Robertson Glacier Targeted Locus (Loci)	cbbL transcript amplicons from Robertson Glacier, Alberta, Canada subglacial sediment sampled in 2010	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004456	Freshwater sediment Raw sequence reads	The study aims to find out the changes in microbial community structure of anode biofilm and sediment in sediment microbial fuel cells. The samples include original freshwater sediment that used in SMFCs and anode biofilm of SMFCs in which worms were observed or not.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004455	Studies on archaeal communities from freshwater sediments based on 16S rRNA gene biomarker	Study of the abundance and diversity of archaeal communities inhabiting freswater sediments in basis of the 16S rRNA gene biomarker.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004402	Sediment samples Raw sequence reads	the Sediment samples and background Environmental microbial diversity	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004370	Enhanced pyrene and benzo[a]pyrene degradation by plant root and SMFC	Toward Understanding Complex Interaction between Roots of Macrophyte Sweet Flag Acorus calamus and Anode of Microbial Fuel Cell for Pyrene and Benzo[a]pyrene Degradation in Freshwater Sediments	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004357	Molecular Characterization of the Structural and Functional Microbial Community in Sediments of a Northern Utah, Basin-Fill Aquifer	Characterization of arsenic and Fe(III) reducing microbial communities at the cache valley sites	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004355	Uranium reducing microbial consortia, under alkaline conditions relevent to geological disposal	Uranium reducing microbial consortia, under alkaline conditions relevent to geological disposal, assessed by 16S rRNA gene pyrosequencing	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004349	Vertical profiles of bacterial community diversity in a drinking water reservoir	Bacterial community diversity in a drinking water reservoir	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004259	CPN Metagenome	Paired end illumine sequencing of V4 region of the 16S rRNA gene along with biolog ecoplate has been performed to systematically evaluate the bacterial community and their metabolic activity of cave sediments in Meghalaya, India	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004258	Svalbard Targeted Locus (Loci)	This study compared microbial communities in sediments in streams that drain glaciated and unglaciated catchments in Svalbard	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00002104	Yangtze River bacteria Raw sequence reads	Abstract: the bacteria in the Yangtze River	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00001837	Brazoria Sediment Inocula and Fermentations of Carboxylate Biofuels Platform Targeted Locus (Loci)	Comparison of community compositions of different fermentation screen approaches conducted simultaneously with a shared inoculum source. Chemical engineers at Texas A&M use three fermentation screens to evaluate and model community performance at different scales, times, substrate concentrations, and product concentrations. To date, these screens have been used sequentially to optimize different features of the process while the inoculum has undergone selective pressure from storage conditions. We used four fresh, environmentally distinct, previously characterized sediment sources collected from Brazoria National Wildlife Refuge to simultaneously inoculate the three screens. We sequenced the communities in each screen to compare the communities that establish across the manipulated parameters.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00004379	Pond sediments Metagenome	Diversity of Bacterial and Archaeal 16S rRNA genes in sediment samples collected from biological stabilization ponds across different latitudes of China	root:Environmental:Aquatic:Freshwater:Pond:Sediment
MGYS00004372	magnetite Targeted Locus (Loci)	Pond sediment magnetite grains show a distinctive microbial community	root:Environmental:Aquatic:Freshwater:Pond:Sediment
MGYS00004649	Arctic Microbial response to oil and Corexit	The fate of oil and oil spill response chemicals in the Arctic is of critical importance as marine shipping and oil exploration are increasing due to receding sea ice cover. Using indigenous Arctic marine organisms in freshly collected seawater, we identified of bacterial taxa that increase in relative abundance in response to both oil and Corexit in Arctic seawater, suggesting that some taxa biodegrade components of both oil and dispersant. We then paried these microbial analyses with the chemical loss of oil and the surfactant components of Corexit 9500. These results allow for the first comparison between Arctic and temperate environments in regards to the fate of Corexit and the microbes involved in biodegrading dispersants and oil.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004647	Hangzhou-sediment-sample Raw sequence reads	This is the result of amplicon sequencing of multiple microbial functional genes in sediment samples	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004618	ZRCWU sediment metagenome Metagenome	To investigate the influence of wetland types on the composition and structure of microbial communities.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004617	River sediments Metagenome	Mining activities have introduced contamination to surrounding aquatic and terrestrial environments, causing adverse impacts to human health and the environment. Indigenous microbial communities are responsible for biogeochemical cycling in diverse environments, indicating the potential to remediate the contamination introduced by the mining activities. Antimony has been extensively mined in China and Sb contamination in mining areas has been frequently encountered. However, the microbial composition and structure in response to antimony contamination has remained overlooked. Here we selected a watershed heavily contaminated by an antimony tailing from an upstream mine. We obtained comprehensive geochemical data (specifically, physical-chemical properties and different antimony extraction fractions) from river water and sediments at different depths. In addition, the indigenous microbial communities were profiled by high-throughput sequencing from 16 sediment samples (535,390 valid reads).	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004613	sediment metagenome B2 Metagenome	The objectives of this investigation was to assess archaeal community and diversity in sediments from natural wetlands.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004612	sediment metagenome metagenome A2	The objectives of this investigation was to assess archaeal community and diversity in sediments from natural wetlands.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004611	sediment metagenome B1 Metagenome	The objectives of this investigation was to assess archaeal community and diversity in sediments from natural wetlands.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004529	16S rDNA sequencing	Bacteria communiy abundance during PAHs degradation	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004526	Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania	The goal of this study were to determine how hydraulic fracturing impacts bacteria in nearby streams by analyzing 16S rRNA data. Overall diversity and interactions among bacteria were examined to see how hydraulic fracturing may impact bacterial communities. Analysis was also done to identify pathways that were potentially enriched in streams near hydraulic fracturing and taxa that could be potential biomarkers for impacted streams. Therefore, this study generated data that increase our understanding of how hydraulic fracturing affects the surrounding environment.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004510	Variation in freshwater stream sediment community 16S rRNA profiles along an urbanization gradient	We examined bacterial community change along an urbanization gradient in NE Ohio, USA to assess the effects on urbanization on bacterial community diversity.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004483	Sediment river Genome sequencing and assembly	Bacterial community composition in sediment discharge at upper and lower reaches of Puyang river	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004481	Microbial diversity in benthic stream sediment	The goal of this sequencing project is to identify putative methanotrophic organisms in benthic stream sediments.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004468	Marine sediment metagenome	Study of bacterial diversity of Bhitarkanika sediment	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004447	Enrichment of organohalide respiring bacteria	Organohalide respiring bacteria are difficult to enrich and isolate, which can limit research on these important organisms. The goal of this research was to develop a method to rapidly (minutes to days) enrich these organisms from a mixed culture or sediment sample. The method presented herein was based on the hypothesis that organohalide respiring bacteria would be more hydrophobic than other bacteria as a result of their niche dehalogenating hydrophobic compounds. To test this hypothesis, a method was developed to separate putative organohalide respiring bacteria at the interface between a hydrophobic organic solvent and aqueous media. This novel separation technique was tested with a sediment-free culture, a tetrachloroethene-enriched digester culture, and sediment from an uncontaminated lake.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004445	Study of microbial diversity from sediment samples of the SaiGon-DongNai system	The main goal is to study the microbial diversity in polluted river affected by urban and industrial activities.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004415	XRU sediment metagenome Metagenome	To investigate the influence of wetland types on the composition and structure of microbial communities.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004414	ZRCWD sediment metagenome Metagenome	To investigate the influence of wetland types on the composition and structure of microbial communities.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004412	ZRD sediment metagenome Metagenome	To investigate the influence of wetland types on the composition and structure of microbial communities.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004411	ZRM sediment metagenome Metagenome	To investigate the influence of wetland types on the composition and structure of microbial communities.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004410	ZRU sediment metagenome Metagenome	To investigate the influence of wetland types on the composition and structure of microbial communities.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004409	PAH-contaminated sediment from the Lagos Lagoon, Nigeria	sediment metagenome	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004385	Lakes ediments of the Amazon River system Raw sequence reads	There is a paucity of information on the composition of the methanogenic microbial communities in tropical lake sediments, and we decided to study methanogenic lake sediments from the Amazon in more detail.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004337	Rifle sediment bacterial community Targeted Locus (Loci)	The objective of the research at the Rifle site is to gain a comprehensive and mechanistic understanding of the microbial factors and associated geochemistry controlling uranium mobility at the field scale so that DOE can confidently remediate uranium plumes as well as support stewardship of uranium-contaminated sites.  This subproject focuses on near-full-length amplification, high-throughput sequencing, and assembly of the bacterial 16S rRNA gene for community characterization.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004313	the under-explored coal gangue and the adjacent acid mine drainage creek soil Raw sequence reads	Microbial communities inhabiting the acid mine drainage (AMD) have been extensively studied. However, the microbial communities in the coal gangue that may generate the AMD and function as the seed bank of microbiota for AMD-related environments are still under-explored. In this study, we characterized the microbial communities within these under-explored extreme habitats and compared with those in the downstream AMD creek. In addition, the interplay between the microbiota and the environmental parameters was statistically investigated.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004312	Appliaction of metagenomic technique for isolation of microbes from mangroves for potential use in biofertilization and bioremediation	The sequences submitted are the fingal ITS metagenomic. The mangrove ecosystem of Goa forms a very important bio-repository. Therefore, the ITS metagenomic DNA sequences obtained from Goa coastline will help to develop a gross idea about the fungal community members present in the mangrove sediments of North and South Goa. This is the first report of fungal metagenomic sequences for Mandovi &amp; Zuari mangrove ecosystem obtained through illumina Miseq platform.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004286	microbial communities in long-term e-waste contaminated river sediments	The release of toxic organic pollutants and heavy metals by primitive electronic waste (e-waste) processing to waterways has raised significant concerns, but little is known about their potential ecological effects on aquatic biota especially microorganisms. We characterized the microbial community composition and diversity in sediments sampled along two rivers consistently polluted by e-waste, and examined how community functions respond to the complex combined pollution. High throughput 16S rRNA sequencing showed that Proteobacteria (particularly Deltaproteobacteria) dominated the sediment microbial assemblages followed by Bacteroidetes, Acidobacteria, Chloroflexi, and Firmicutes. PICRUSt metagenome inference provided an initial insight into the metabolic potentials of these e-waste affected communities, with genes encoding key enzymes (including dioxygenase, dehydrogenase, aldolase, decarboxylase, hydroxylase and hydrolase) in organic pollutants-degradation pathways largely harbored by some of the dominant genera (such as Sulfuricurvum, Thiobacillus and Burkholderia) detected in situ. Statistical analyses revealed that toxic organic compounds contributed more to the observed variations in sediment microbial community structure and function (24.68% and 8.89%, respectively) than heavy metals (12.18% and 4.68%), and BaP, available lead and EC were the key contributors. Given the ecological significance of microbes in sediments, long-term e-waste pollution has the potential to alter nutrient cycling and contribute to functional perturbation of freshwater systems.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00002099	Archaeal Raw sequence reads	Abstract: Archaeal is very important in the nitrogen cycle.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00002098	Taihu Raw sequence reads	Abstract: AOA and AOB were the important nitrogen microbes	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00002097	bacterial diversity of lake sediments	To determine influence of inflow-rivers on bacterial community of the lake	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004477	Prokaryotic microbial communities structure in the  headwater watchment of Dongjiang River in the south of China	Prokaryotic microbial communities structure in the headwater watchment of Dongjiang River in the south of China	root:Environmental:Aquatic:Freshwater:Lotic
MGYS00004475	Eucaryotic microbial communities structure in the  headwater watchment of Dongjiang River in the south of China	Eucaryotic microbial communities structure in the headwater watchment of Dongjiang River in the south of China	root:Environmental:Aquatic:Freshwater:Lotic
MGYS00004577	Bacterial and fungal diversity in Ashumet Pond, MA (USA), and prevalence of manganese-oxidizing isolates	Distinct black manganese oxide mineral coatings have long been observed on a portion of the shores of Ashumet Pond, a freshwater pond impacted by heavily contaminated groundwater emanating from a nearby decommissioned wastewater treatment facility. The goal of this study is to identify the microbial communities contributing to the biogeochemical cycling of Mn, and thus to the remediation of metals and organics in this environment.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004531	Microbial community in PAH-contaminated riverine sediments	Co-occurrence patterns of microbial community	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004518	Lake sediment sequencing	This study can provide novel insights into basin pollution control in plain river networks	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004506	Surface Diatom Sediments of Deep Freshwater Lake Baikal	In this work we analyzed the structure and diversity of bacterial and archaeal communities in the surface sediment core. Microscopy has shown that this core is rich in siliceous diatom valves (frustules), whose degrees of preservation varied with the depth and diatom species as revealed by SEM. Pyrosequencing targeting bacterial V3-V4 and archaeal V1-V3 regions of 16S rRNA were performed to profile procaryotic community structure.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004476	Archaea microbial communities structure in the  sediment and downarea soil of the Fengshuba Reservoir in the Guangdong Provinve, South China	Archaea microbial communities structure in the sediment and downarea soil of the Fengshuba Reservoir in the Guangdong Provinve, South China	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004361	Qinghai Lake sediments Metagenome	Investigation of microbial diversity	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004350	Anaerobic Photosynthetic Consortia 16s rRNA profiling	Anaerobic photosynthetic consortia that degrade cellulose and fix nitrogen.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004306	sediment microorganism Metagenome	Using the method of massively parallel sequencing (Roche 454 platform used) studied the diversity and abundance of microbial communities in sediments site Posolskay Banka, of Lake Baikal	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004303	rRNA, rDNA bacteria thaw ponds Targeted loci environmental	Present (rDNA) and active (rRNA) arctic bacterial communities under an increased temperature incubation	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004284	freshwater sediment metagenome Metagenome	To investigate the influence of nitrate on soil microbial communities.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004278	Lonar sediment Raw sequence reads	Identifying total microbiota of the extreme ecosystem	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004267	Surface sediment raw sequence reads 1	Diversity of bacteria in surface sediment from Lake Bosten in xinjiang Province, China	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004261	Swan lake bacteria Raw sequence reads	bacterial 16S V3 region sequences	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004260	Baikal Archaea Metagenome	Using the method of massively parallel sequencing (Roche 454 platform used) studied the diversity and abundance of archaeal communities in methane hydrate- and oil bearing sediments, c different component composition of pore water in six districts of Lake Baikal	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004257	Characteristics of bacterial communities in the deep sediment Lake Baikal from the regions with oil and gases discharging	Using the method of massively parallel sequencing (Roche 454 platform used) studied the diversity and abundance of bacterial communities in methane hydrate- and oil bearing sediments, c different component composition of pore water in six districts of Lake Baikal.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004252	Thermokarst ponds Targeted Locus (Loci)	The objective of our study was to evaluate the release and potential for GHG emissions in the poorly studied runnel ponds compared with polygonal ponds of northeastern Canada. Archaeal community composition in the sediments was analyzed with high-throughput 16S rRNA gene pyrosequencing.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00002103	bacterial diversity of lake sediment	To determine influence of allochthonous rivers on bacterial communities of the lake	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004273	Sediment Raw sequence reads	to study the denitrifying microorganisms in Lake Taihu	root:Environmental:Aquatic:Freshwater:Lentic
MGYS00004668	Marine (Aarhus) and freshwater (Lake Constance) sediment Raw sequence reads	General marine and freshwater sediment community in low iron environment; Distribution, abundance and activity of iron metabolizers	root:Environmental:Aquatic:Freshwater:Lake
MGYS00004390	Amino acid addition experiment Metagenome	Amino acid addition experiments using freshwater lake bacterioplankton	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001410	Freshwater microbial communities from Lake Mendota, WI - 17MAY2012 deep hole epilimnion metagenome		root:Environmental:Aquatic:Freshwater:Lake
MGYS00001408	Freshwater microbial communities from Trout Bog Lake, WI - 28MAY2007 hypolimnion metagenome		root:Environmental:Aquatic:Freshwater:Lake
MGYS00001407	Freshwater microbial communities from Trout Bog Lake, WI - 22MAY2008 epilimnion metagenome		root:Environmental:Aquatic:Freshwater:Lake
MGYS00001406	Freshwater microbial communities from Trout Bog Lake, WI - 29MAY2008 epilimnion metagenome		root:Environmental:Aquatic:Freshwater:Lake
MGYS00001405	Freshwater microbial communities from Lake Mendota, WI - 05MAY2012 deep hole epilimnion metagenome		root:Environmental:Aquatic:Freshwater:Lake
MGYS00001404	Freshwater microbial communities from Lake Mendota, WI - 03MAY2011 deep hole epilimnion metagenome		root:Environmental:Aquatic:Freshwater:Lake
MGYS00001403	Freshwater microbial communities from Lake Mendota, WI - 18MAY2011 deep hole epilimnion ns metagenome		root:Environmental:Aquatic:Freshwater:Lake
MGYS00001402	Freshwater microbial communities from Lake Mendota, WI - 18MAY2010 deep hole epilimnion ns metagenome		root:Environmental:Aquatic:Freshwater:Lake
MGYS00001401	Freshwater microbial communities from Lake Mendota, WI - 20MAY2010 deep hole epilimnion metagenome		root:Environmental:Aquatic:Freshwater:Lake
MGYS00004469	Effect of climate-change induced glacier melting on the benthic prokaryotic diversity in the West Antarctic Peninsula	West Antarctic Peninsula (WAP) is recognized as one of the fastest warming area on Earth. Climate change and the consequent warming of the oceans has reduced the polar icecaps resulting in a change of the regulation of the biological pump, with altered conditions of primary production and nutrient cycling and circulation. Moreover, the increased melting of coastal glacier and scouring events may have a strong impact on local communities, potentially affecting the local biodiversity and ecosystem functioning. We investigated community structure and diversity of benthic prokaryotes in a fast warming region of the WAP.	root:Environmental:Aquatic:Freshwater:Ice:Glacier
MGYS00004352	Cryoconite sediments Targeted Locus (Loci)	Biological processes on glacier surfaces affect the physical behaviour of glaciers and ice sheets and carbon and nutrient fluxes in the cryosphere. Changes in rates of biological processes are often associated with changes in diversity, yet there is little knowledge of the diversity of active microbes on glacier surfaces and its controls. We examined the microbial abundance, community structure, and the proportion of the active microbes at two contrasting surface sites located at the margin and in the interior of the Greenland ice sheet over the course of a melting season, using DNA and RNA co-extraction from the same samples, quantitative PCR and pyrosequencing of 16S rRNA and rDNA. Whereas the rDNA abundances were similar at both sites (108  109 copies g-1), the rRNA abundance was significantly higher in the interior (1010 copies g-1). Significant differences in diversity were found between the sites, with the DNA diversity significantly higher at the margin and the RNA diversity higher at the interior site. The bulk of the active communities at both sites comprised Cyanobacteria and Alpha- and Betaproteobacteria, suggesting a truncated food web structure dominated by few bacterial primary producers and decomposers. We suggest that the ice sheet margin contains a more diverse but less active assemblage of microbes while the interior harbours a less diverse but well-adapted active community. We propose that the process of community assembly at the surface of the GrIS can be understood as species sorting from a metacommunity of airborne microbes which land on the ice surface.	root:Environmental:Aquatic:Freshwater:Ice:Glacier
MGYS00004340	Aldegondabreen cryoconite Targeted Locus	The aggregation of surface debris (cryoconite) on melting glaciers into larger may provide microenvironments for various microorganisms and metabolic processes. Here we investigate the microbial community on the surface of Aldegondabreen, a valley glacier in Svalbard which is supplied with carbon and nutrients from different sources across its surface, including colonies of seabirds. We used a combination of geochemical analysis (surface debris, ice and meltwater), quantitative PCR (targeting the 16S rRNA and amoA genes), pyrosequencing and multivariate statistical analysis to better understand the ecology of prokaryotic microbes on the surface on Aldegondabreen and their role in nitrogen cycling. The combination of high nutrient input, supraglacial melt water flow and the presence of fine, claylike particles supports the formation of cmscale cryoconite aggregates in some areas of the glacier surface. We show that a diverse microbial community is present, dominated by the cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria, that are wellknown in supraglacial environments. Allochthonous material including plant tissuederived chloroplasts was also identified in the molecular analysis. Importantly, ammonia oxidizing archaea (AOA) were detected in the aggregates for the first time on an Arctic glacier.	root:Environmental:Aquatic:Freshwater:Ice:Glacier
MGYS00004462	16S rDNA metagenomes of Western Balkans glacial lakes sediments	Since the Balkan Peninsula is situated in the climatic transition between the temperate zone and Mediterranean conditions, it can be assumed that this region will become dryer and warmer in the course of global climatic change. Potential vanishing of glaciers in this part of Europe could endanger existing glacial lakes, which points to the need of conservation and biodiversity studies of this ecological niche. The studies of microbial communities in glacial lakes, especially in southeast Europe are rare and even neglected. It is well recognized that unexplored ecological niches and metabolic potential as well as new molecular frameworks of their microbial communities could be a gold mine of secondary metabolites with importance for biotechnology, medicine and pharmacy. Our goal was to assess the bacterial communities from selected Western Balkans glacial lakes. Selection of lakes was based on exposure to anthropological influences. Thus we analyzed bacterial communities from Plav lake (designated as D in the project, located in the town of Plav), Black lake (designated as C in the project, outside of human settlements but tourist attraction) and Donje Bare lake (isolated lake without significant human impact, designated as Z in the project).	root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
MGYS00003658	VAG Mine Pit Pond Metagenome	The Vermont Asbestos Group (VAG) mine provides an experimental model to investigate resident microbial communities exposed simultaneously to multiple environmental stressors. The VAG Pit Pond and its Outlet present an alkaline aquatic environment, contaminated with asbestos-laden mine tailings and a variety of heavy metals.As no information is available on the microbial community structure of this aquatic ecosystem, our first goal was to characterize the taxonomic profile of its resident microorganisms. Investigations of human-induced perturbation have provided little understanding of microbial community dynamics. The overarching goal of this project is to expand our knowledge of these microbial community interactions using a combination of sequence-based and function-based methodologies. The work lays the foundation for study of microbial dynamics in ecological and geochemical processes of human-impacted environments.	root:Environmental:Aquatic:Freshwater:Groundwater:Mine drainage
MGYS00004439	Bacterial community profiles in  a bioreduced uranium contaminated site after reoxidation	A site contaminated with uranium was bioreduced through multiple injections of ethanol to immobilize the uranium in situ. Then it was allowed to reoxidize via the invasion of low-pH , high-nitrate groundwater back into the reduced zone for about 4 years. To examine the biogeochemical response, high-throughput sequencing were applied to characterize bacterial population shifts.	root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
MGYS00004387	Long distance electron transfer by cable bacteria in aquifer sediments	Investigation of BTEX contaminated groundwater sediments for the abundance of cable bacteria which could enhance biodegradation by long distance electron transfer at the plume fringes	root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
MGYS00004341	Aquifer sediment nitrate reducing community change	Microbial community composition change over the course of a heterotrophic nitrate reducing enrichment. Sediments used in this experiment were collected from a nitrate contaminated shallow aquifer at a depth of 58-61ft from Alda, NE. Illumina sequencing of the V5 hypervariable region of the 16S rRNA gene is used.	root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
MGYS00004467	Impacts of crude oil and chemical dispersant exposure on marine microbial biofilm formation and steel corrosion	The release of hydrocarbons and dispersants in the marine environment may place at risk the preservation of historic steel shipwrecks on the seafloor. In this study, we exposed steel biofilm communities to crude oil and dispersants and monitored compositional and functional changes after exposure, and the impact of oil exposure on steel corrosion processes.	root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
MGYS00004401	Sediment of acid mine drainage Targeted loci environmental	Sediments from an ancient gold mine in La Carolina, San Luis, Argentina.	root:Environmental:Aquatic:Freshwater:Groundwater:Acid Mine Drainage
MGYS00004486	Uncultured Environmental Isolate Targeted loci environmental	This study highlights the potential for microbial activity to help remove chelating agents and radionuclides from groundwater during radioactive waste geodisposal.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00003122	Groundwater microbiome		root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00002071	hospital shower hose biofilms metagenomes	Drinking water (DW) biofilms are well known to harbor opportunistic pathogens, however, these biofilm communities remain poorly characterized by culture-independent approaches that circumvent the limitations of conventional monitoring efforts. In this study we characterize the composition of microbial communities growing on five hospital shower hoses using shotgun metagenomics.	root:Environmental:Aquatic:Freshwater:Drinking water
MGYS00000836	Biofoam biofilm sample 16S rRNA gene libraries	Small scale biosand filters (BSFs) utilized as point of use (POU) water treatment technologies can provide quality drinking water in arid regions. In this current study, biofilms within a novel biologically active POU technology that removes pathogens from water were studied. The biofilms develop across porous foam cartridge filters termed biofoam, and were assayed for community membership. Biofilms within the POU filter medium were developed at three different locations in the US using three different surface waters. Biofilm microbial communities that developed on biofoam were analyzed utilizing 454 pyrosequencing of the 16S rDNA genes, and showed a remarkable degree of shared community membership among the three locations. A large, diverse shared microbiome was found as defined by the top 100 shared operational taxonomic units (OTUs) at 0.03 cut off (97% similarity). This represented 280,000 of the 306,000 sequences (>90%). Of those, 25% were classified within the genus Pseudomonas. Members of the microbial communities found within the shared microbiome of the biofoam were closely associated with organisms commonly found in activated sludge, drinking water biofilms, rhizosphere, phyllosphere, and soil ecosystems. The biofoam provides a unique and effective porous matrix for biofilm formation, which appears to allow for the establishment of consistent microbial communities, even when developed at different locations utilizing different water sources. Improving our understanding of the biofoams microbial ecology may provide insights into mechanisms of pathogen removal, and allow development of customized biofilms for targeted remediation projects, as part of a lightweight and energy efficient water filtration system.	root:Environmental:Aquatic:Freshwater:Drinking water
MGYS00004626	Sundarbans estuarine ecosystem Metagenome	This work will provide a model for the large-scale extension of molecular phylogenetic-type analysis of direct study, characterization, and secondary metabolite biosynthetic gene clusters that remain hidden in soil microbiomes of Sundarbans. Genome base study with the theoretical prediction of structures will provide importance for the discovery of natural products in the future from Sundarbans ecosystem. The expansion of the genomic sequence will exhibit potential route for synthetic biology approaches and metabolic research. Preliminary data on this screening will demonstrate great economic interest.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004593	Ammonia monooxygenase biogeography and sequence diversity in the Cape Fear Estuary	This project is focused on exploring the spatial and temporal distribution of microbes involved in nitrification within the sediments of the Cape Fear Estuary. 454 Sequencing of both bacterial and archaeal amoA genes was conducted with DNA extracts obtained from estaurine surface sediment samples. Spatial patterns were evaluated by collecting sediment along the salinity gradient of the estuary. Temporal patterns were evaluated by collecting sediment samples seasonal over a three year period. The interaction of community composition with environmental conditions was evaluated using in situ sediment transplant experiments within the estuary, where sediment bundles were moved from one location in the estuary to another and changes in the microbial community were observed over time following transplantation. These data are relevant to understanding the diversity and distribution of microbes involved in microbial nitrogen cycling and how the diversity of these functional groups interact with environmental conditions within an estuary.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004580	Chesapeake Bay Sediment nirS Metagenome	Amplicon sequences of nirS, encoding nitrite reductase	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004575	Estuarine wetland Targeted Locus (Loci)	At the salt marsh Dongtan, the effect of Spartina alterniflora invasion on the structure of bacteria were investigated at three points where the first was uninvaded, the second was partially invaded and the third was completely displaced.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004574	Estuarine wetland Targeted Locus (Loci)	This study aimed to understand the abundance and diversity of methanogens in salt marsh sediments with S. alterniflora invasion.  mcrA of methanogens collected by 454-pyrosequencing from Dongtan salt marsh.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004466	sediment metagenome Raw sequence reads	It was used to reflect the microbial community diversity for the sediment samples collected from the Yellow River Estuary.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004453	estuary metagenome Raw sequence reads	Anaerobic Dechlorination of Tetrachlorobisphenol A	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004430	estuary metagenome Raw sequence reads	Continent-wide Pollution of Estuaries with Antibiotic Resistance Genes	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004393	Microbial communities in estuarine sediments	Microbial communities from estuarine sediments differing in anthropogenic contamination	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004368	Newfoundland sediment pyrosequencing	16S rRNA gene sequencing for bacterial community composition of sediment collected on the West coast of Newfoundland, Canada	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004367	Microbial eukaryote 454 Roche sequencing in estuarine ecosystems	Using 454 Roche sequencing of the 18S nSSU taxonomy marker, we investigate which of the focal natural drivers are most strongly associated with microbial metazoan and sampled protist diversity across the full salinity gradient of estuarine ecosystems. The data cover two geographically proximate estuaries (Thames and Mersey, UK) with contrasting histories of anthropogenic stress.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004354	Pearl River Estuary sediments Targeted Locus (Loci)	Archaea are widespread and play an important role in the global carbon and nitrogen cycles. However, we still have limited knowledge about how the function of Archaea in varying habitats. The goal of this study was to examine the change in community structure of Archaea in the sediments collected from the lower Pearl River, its estuary, and coastal South China Sea in order to evaluate how archaeal ecological function changes along the salinity gradient. Pyrosequencing of the 16S rRNA gene of Archaea was performed on sediment samples from Feilaixia Dam to Wanshan islands, which have a salinity range of 0.11 to > 31.27. Methanogens like Methanoregula, Methanosaeta, Methanosarcina and ammonia-oxidizing Archaea like Nitrososphaera were abundant in freshwater sediments of the Pearl River whereas Methanococcoides and Nitrosopumilus were abundant in the estuary and coastal South China Sea. This study provides the initial observation of the changing archaeal community structure from the lower Pearl River, its estuary and coastal South China Sea, which will aid the understanding of ecological functions of Archaea in the dynamic continental margins such as the South China Sea.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004351	PREsediment Targeted Locus (Loci)	Microbial community of sediment of Pearl estuary	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004297	The effect of salinity in prokaryotic communities in an estuary	The goal of this project is to understand the effect of a salinity gradient in an estuary on prokaryotic communities and nitrifying communities	root:Environmental:Aquatic:Estuary:Sediment
MGYS00002666	Effects of Fecal Input, Environmental Conditions, and Environmental Sources on Enterococci Concentrations in an Estuarine Ecosystem	To determine major factors influencing enterococci concentrations seen in an estuary and marine beach setting. More specifically delineating fecal input, environmental conditions and environmental reservoirs to determine their combined impact on enterococci concentrations.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004532	the diversity of anammox bacteria in the subterranean estuary	The microbial diversity, distribution pattern of anammox in the subterranean estuary	root:Environmental:Aquatic:Estuary
MGYS00004652	eDNA barcoding of protists for environmental monitoring of aquafarming activities	Goal of the study is the evaluation of protistan eDNA meta barcodes from environmental samples as indicators for environmental quality. The impact includes the implementation of protistan eDNA barcoding in routine environmental monitoring programs	root:Environmental:Aquatic:Aquaculture
MGYS00004539	Seawater metagenome Targeted loci environmental	Red conger eel (Genypterus chilensis, Guichenot) is a native Chilean species whose meat is characterized by high gastronomic demand and is now part of the Chilean aquaculture diversification program. Two disease outbreaks derived from its intensified aquaculture farming have been reported and were associated with Vibrio spp. and Tenacibaculum spp. However, the role of individual species is not clear because there is a lack of information about the bacterial community composition associated with the rearing environment of healthy specimens of this fish species. This study examined the microbial community in the seawater of a G. chilensis aquaculture facility using both culture-based methods and 16S rRNA amplicon sequencing of the V4V5 region using Illumina MiSeq.	root:Environmental:Aquatic:Aquaculture
MGYS00004699	NEW-2	environmental research	root:Environmental:Aquatic
MGYS00004662	Tyrolerfjord-Young Sound 16S raw sequence reads	V1-V2 region of 16S rRNA genes sequenced using Illumina; samples were collected from three rivers and in the fjord of the Tyrolerfjord-Young Sound system.	root:Environmental:Aquatic
MGYS00004293	NEW-1	environmental research	root:Environmental:Aquatic
MGYS00004292	DSW-2	environmental research	root:Environmental:Aquatic
MGYS00004104	Eukaryotic protists Metagenome	Spatial differences in beta diversity between the open ocean, outer shelf, Inner shelf and estuarine waters experiencing different hydrography and biogeochemistry reflect diverse communities of heterotrophic protists. Gradients in Chlorophyll a, temperature, salinity, nitrate, nitrite and dissolved oxygen may serve as barriers to the distribution of heterotrophic protists, enabling selection and diversification of distinctive communities. The present study provides the base line information that can allow comparison of diversity metrics with world ocean sites. This work examines spatial changes in protist communities associated with various low oxygen sites.	root:Environmental:Aquatic
MGYS00002849	Thermophilic endospores in temperate sediments	Sediment heating experiments were performed with freshwater, brackish and marine sediments to investigate the dispersal of microorganisms in aquatic environments	root:Environmental:Aquatic
MGYS00004697	Natural seawater bacterial community in exopolysaccharides utilization	We report the microbial EPS degradation in incubation experiments with seawater from estuarine and open ocean sites (surface and deep water), shifts in microbial community structure during the incubation were investigated. Microbial genomic DNA was extracted from the polycarbonate membranes (microbial cells filtered) and the 16S rRNA gene sequences were amplified by PCR. To understand the changes in the bacterial community structure during the early stage of the incubations, we classified the OTUs based on their phylogenetic affiliations and determined their relative proportions on the total number of sequencing reads.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00004696	Fungal communities across four coastal marine habitats in North Carolina, USA	Despite nearly a century of study, the diversity of marine fungi remains poorly understood. Historical surveys utilizing microscopy or culture-dependent methods suggest that marine fungi are relatively species-poor, predominantly Dikarya, and localized to coastal habitats. However, the use of high-throughput sequencing technologies to characterize microbial communities has challenged traditional concepts of fungal diversity by revealing novel phylotypes from both terrestrial and aquatic habitats. Here, I used ion semiconductor sequencing (Ion Torrent) of the ribosomal large subunit (LSU/28S) to explore fungal diversity from water and sediment samples collected from four habitats in coastal North Carolina. The dominant taxa observed were Ascomycota and Chytridiomycota, though all fungal phyla were represented. Diversity was highest in sand flats and wetland sediments, though benthic sediments harbored the highest proportion of novel sequences. Most sequences assigned to early-diverging fungal groups could not be assigned beyond phylum with statistical support, suggesting they belong to unknown lineages.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004692	Microbial diversity and skin mucosal microbiota in farmed Atlantic salmon with ulcerative disorders, raw sequence reads	The Norwegian aquaculture of Atlantic salmon Salmo salar is hampered by ulcerative disorders associated with bacterial infections. Studying the composition of microbial communities on skin mucus, and how the microbiota is structured in ulcers will enhance our understanding of ulcer etiology. To achieve this we used seawater farmed Atlantic salmon and sampled the base and edge of ulcers at the end of winter (April) and at the end of summer (September), in addition to skin-mucus of healthy individuals. In order to assess microbiota associated to the host and to get a better insight into the environmental ecology we additionally sampled the seawater column and sediment layer underneath the farm facility in addition to the distal intestine of Atlantic salmon.	root:Environmental:Aquatic:Aquaculture
MGYS00004691	Microbial Diversity in the Southwest Atlantic Ocean and Patagonian Freshwater Bodies	The Southwest Atlantic Ocean (SAO) has one of the largest and most productive continental shelves of the World, notwithstanding which microbiological studies of this region are rather scarce. Likewise, the majority of Continental Patagonian (CP) lakes, rivers and other water bodies remain as pristine as microbiologically unstudied. This project constitutes an initiative aimed to contribute to surveying, systematizing and understanding the dynamics (i.e. ecology and evolution) of microbial communities from this region.	root:Environmental:Aquatic:Freshwater:Pond
MGYS00004688	SJP and SJUP Metagenome	SJP- Uranium polluted sediment sample collected from Cauvery bank of Kokarayanpettai, Erode District. SJUP- Unpolluted sample collected from agriculture field of Bhavani, Erode District.	root:Environmental:Terrestrial:Soil:Uranium contaminated
MGYS00004676	uncultured prokaryote Metagenome	In the present study, microbial communities ofsponges, Sediments and Seawater inhabitingcoral reef ecosystems were investigated usingbarcoded pyrosequencing of 16S rRNA geneamplicons. Our main goals were to compare thebacterial and archaeal richness and composition ofsponge species, sediment and seawaterinhabiting coral reef systems. FLX 454 titanium pyrosequencing study.	root:Environmental:Aquatic:Marine
MGYS00004672	Zooplankton microbiome of the Amazon River Plume and western trophic North Atlantic	The goal of this study was to investigate if mesozooplankton grazers in the Amazon River plume-influenced western trophic North Atlantic directly grazed upon diazotrophic organisms.	root:Environmental:Aquatic:Marine
MGYS00004669	microbial community composition of marine water and sediment	To study the diversity and composition of water and sediment microbial community in seaweed cultivation zone and natural sea zone.	root:Environmental:Aquatic:Marine:Coastal
MGYS00000805	Dehalococcoides-containing environmental samples and enrichment cultures Metagenome	The organohalide respiring bacteria, Dehalococcoides mccartyi, are pertinent to bioremediation of perchloroethene (PCE) and trichloroethene (TCE), due to their unique metabolic capability to transform chlorinated ethenes to the non-toxic, ethene. Despite their widespread environmental distribution, biostimulation of Dehalococcoides in soil/sediment microcosm studies and during in situ bioremediation has failed to consistently promote reductive dechlorination of PCE/TCE beyond cis-dichloroethene (cis-DCE), commonly attributing this observation to the lack of strains with cis-DCE and vinyl chloride-reducing abilities. Consistent with this observation, in our study, microcosms established with garden soil and mangrove sediment stalled at cis-DCE, even after an extended incubation (200 days) and multiple biostimulation events. Only microcosms containing PCE-contaminated groundwater sediment produced ethene as the end-reduced product. Transfers from cis-DCE stalled microcosms to fresh medium in the absence of soil or sediment, however, yielded complete dechlorination of TCE to ethene, thus, unveiling the true biological potential of the endogenous Dehalococcoides. We hypothesized that biostimulation of Dehalococcoides in our cis-DCE-stalled microcosms was impeded by soil or sediment components serving as terminal electron acceptors for growth of microbes competing with Dehalococcoides for electron donor (H2). Therefore, dilution of the soil/sediment and competing microorganisms fostered the growth of Dehalococcoides and the production of ethene in the microcosm transfers. Our findings support this hypothesis through several lines of evidence. We found that i) Proteobacteria classes which dominated soil/sediment microbial communities became undetectable in the enrichment cultures, ii) the enrichment cultures developed contained up to 109 Dehalococcoides mccartyi cells mL-1 and achieved close to dechlorination of 0.5 mmol L-1 TCE to >80% ethene in 1.7 days, iii) methanogenesis drastically decreased in the enrichment cultures, and iv) garden soil and mangrove sediment microcosms bioaugmented with their respective enrichment cultures produced ethene. Our results provide an alternate explanation to unsuccessful microcosm experiments, providing a new perspective from which to better understand contaminated site assessments and to improve the bioremediation process.	root:Environmental
MGYS00000774	Bacterial, IncP-1 and merA diversity in soil and wastewater	The diversity of bacterial 16S rRNA gene, IncP-1 replication (trfA) gene and mercuric reductase (merA) gene in two different soils (forest soil and copper, chrome and arsenic contaminated soil) and wastewater studied by amplicon pyrosequencing. Three replicates were collected from each location.	root:Environmental:Terrestrial:Soil
MGYS00003674	wastewater Metagenome	Investigating the prevalence of antibiotic resistance genes and heavy metal resistance genes along with bacterial community in wastewater treatment plant	root:Engineered:Wastewater:Water and sludge
MGYS00004521	Sand sample from sand bioreactor treating high salt turkey processing wastewater	Sand samples were taken from sand bioreactors treating turkey processing wastewater with added salt from 6 g/L NaCl to 35 g/L NaCl.	root:Engineered:Wastewater:Industrial wastewater:Agricultural wastewater
MGYS00004060	Saltwater aquarium tank mesocosm vertebrate 12S ribosomal locus	A 4.5-million liter aquarium tank was used as a mesocosm to test whether environmental DNA can be used to reconstruct the known vertebrate community within the tank. This tank is part of a flow through system circulating water from Monterey Bay, CA. Water samples were collected and probed for a mitochondrial DNA locus (12S ribosomal gene) that is conserved across vertebrates.	root:Engineered:Wastewater:Industrial wastewater:Agricultural wastewater
MGYS00004472	Altavista VA wastewater lagoon sediment microorganism Raw sequence reads	The main goal of this study is to investigate the microbial communities in sediments from a wastewater lagoon with polychlorinated biphenyl (PCB) contamination. Our study helped better understand the effect of PCB contamination on microbial communities and in situ microbial PCB degrading potential.	root:Engineered:Wastewater:Industrial wastewater
MGYS00003490	Identification of filamentous Chloroflexi morphotypes in Activated sludge plants	This study reports the identification of the Eikelboom morphotypes type 0041 and type 0675. Because these morphotypes differ only in their filament diameters, they are often considered together in surveys based on microscopic identifications. Here we show that they are phylogenetically distinct, and so should be viewed no longer as morphological variants of a single population. Amplicon sequencing data of Australian EBPR plant biomass containing types 0041 and 0675 was utilized to achieve this. Roche 454 amplicon data generated by the Australian Genome Research Facility (AGRF) V1-V3 region of the 16S rRNA gene. Analysis and FISH probes designed against several of these amplicon sequences indicated that these two morphotypes were members of the phylum Chloroflexi. Subsequent surveys of full-scale plant biomass samples showed these two filaments were common in these systems. However, considerable further diversity appears to exist and therefore should be a subject of further research.	root:Engineered:Wastewater:Activated Sludge
MGYS00001277	Shotgun sequencing on multiple activated sludge samples	We performed massive shotgun-sequencing on activated sludge samples from four full-scale industrial and two municipal wastewater treatment plants, each sampled at two different times and with two technical replicates, to determine the functional potential of sludge metagenomes.	root:Engineered:Wastewater:Activated Sludge
MGYS00001276	Bacterial survey in industrial activated sludge through 454 pyrosequencing	We performed 16S-rRNA gene pyrosequencing on activated sludge of different industrial wastewater treatment plants.	root:Engineered:Wastewater:Activated Sludge
MGYS00001166	Activated sludge Metagenome	In order to control biofilm formation in wastewater treatment	root:Engineered:Wastewater:Activated Sludge
MGYS00004373	Sewage sediments Targeted Locus (Loci)	This study reflects on the relationship between microbial groups and sewage operation environments.	root:Engineered:Wastewater
MGYS00000830	Shanghai Laogang landfill leachate	investigate the bacterial and archael community composition in landfill and assess the variation of the bacterial and archael compositions in refuse decomposition process.	root:Engineered:Wastewater
MGYS00001800	Microbial Community Structure of a Pilot Scale Thermophilic Anaerobic Digester Treating Poultry Litter	16s rRNA bacterial survey of anaerobic digester	root:Engineered:Solid waste:Composting:Bioreactor
MGYS00004639	CPM-2	environmental investigation	root:Engineered:Solid waste:Composting
MGYS00004295	FPM-1	environmental investigation	root:Engineered:Solid waste:Composting
MGYS00004289	FPM-2	environmental research	root:Engineered:Solid waste:Composting
MGYS00004288	DSW-1	environmental research	root:Engineered:Solid waste:Composting
MGYS00001814	compost Metagenome	the metagenome of wheat straw compost	root:Engineered:Solid waste:Composting
MGYS00001631	Persistence or attenuation of antibiotic resistance genes during full-scale swine manure vermicomposting via housefly larvae (Musca domestica)	The widespread use of antibiotics in the swine industry has the potential to exert selective pressure for antibiotic resistance genes (ARGs) in both swine-associated microbiota and the bacterial communities in associated environments, posing a potential threat to public health. Full-scale vermicomposting utilizes housefly larvae (Musca domestica) to remove water and aid decomposition of swine manure. Here we determined the prevalence and persistence of ARGs in larvae-associated bacterial communities undergoing ecological succession. The concentrations of four classes of antibiotics, comprising 17 different compounds, and the abundance of their corresponding ARGs, were assessed. Most tetracyclines and sulfadiazine compounds were significantly (p< 0.05) attenuated, while quinolones showed no degradation and were the dominant antibiotics detected in unprocessed manure. Correspondingly, genes encoding tetracycline resistance (tetM, tetO, tetQ, and tetW) were depleted over the course of the study, while two quinolone resistance genes (qnrA and qnrS) were persistent. Interestingly, while sulfonamide was barely detected in late stages of vermicomposting, 2genes encoding sulfonamide resistance (sul1 and sul2) were shown to increase in abundance. While no significant difference in phylum-level bacterial community structure was observed, diversity and species richness did significantly decrease as a result of an increase in abundance of certain taxa, e.g. the relative abundance of a Flavobacteriaceae genus increased 100x, probably representing an excreted intracellular larval symbiont. The persistence of qnrA and qnrS maybe closely related an increase in the relative abundance of certain genera, which responded to shifts in the physicochemical characteristics of the manure (water content, total nitrogen, temperature and pH). The observed sustained bacterial sulfonamide resistance in manure should be a major concern as treated manure is applied to farmland as fertilizer.	root:Engineered:Solid waste:Composting
MGYS00004527	Bacterial community in the solid and liquid wastes of Mizoram, India		root:Engineered:Solid waste
MGYS00001755	Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing	The goal of this work is to develop and test synthetic 16S rRNA gene spike-in standards for use in high-throughput 16S rRNA gene amplicon sequencing experiments. The newly developed spike-in standards were tested using mock community mixtures and environmental microbiome samples.	root:Engineered:Modeled:Simulated communities (sequence read mixture)
MGYS00002999	Synthetic marine metagenome high-throughput sequencing	Study the bacterial community structure and discuss the environmental relatedness.  Collected from seawater and sediment from the ECS.	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00001765	5 bacterial species mock community genome sequencing	Sequencing a mock community consisting of T. roseus DSM 18391, C. akajimensis DSM 45221, P. stutzeri DSM 4166, P. inhibens DSM17395, and G. obscurus DSM 43160 for a comparative analysis of multiple displacement amplification performed in standard bulk reactions or in emulsions. Samples also include unamplified controls and no template negative controls.	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00001675	Quantifying Bias in 16S rRNA Experiments due to DNA Extraction, PCR Amplification, and Sequencing and Classification	The goals of this project are to quantify and characterize bias in 16S rRNA Studies due to a particular choice of DNA extraction, PCR amplification, and sequencing and taxonomic classification protocols. Labs will make choices in protocol based on the environment of interest, but bias will always remain. This experiment is designed to quantify the differences between actual and observed community compositions when equal numbers of 1) cells, 2) DNA, and 3) PCR product are blended. By comparing the results of the experiments, one can quantify the contribution to bias of each step. Also, one can build models to predict true community composition based on the observed community composition.	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00000638	Synthetic microbial community partial 16S rRNA amplicons and metagenomes from synthetic microbial community	Next generation sequencing has dramatically changed the landscape of microbial ecology, large scale and in depth diversity studies being now widely accessible. Determining the accuracy of taxonomic and quantitative inferences and comparing results obtained with different approaches are complicated by incongruence of experimental and computational data types and by lack of knowledge of the true ecological diversity. Here we used highly diverse bacterial and archaeal synthetic communities assembled from pure genomic DNAs to compare inferences from metagenomic and SSU rRNA amplicon sequencing. Both Illumina and 454 metagenomic data outperformed amplicon sequencing in quantifying the community diversity but the outcome was dependent on analysis parameters and platform. New approaches in processing and classifying amplicons can reconstruct the taxonomic composition of the community, but all tested primers lead to significant taxon-specific biases. Controlled synthetic communities assembled to broadly mimic the phylogenetic richness in target environments can provide important validation for fine-tuning experimental and computational parameters used to characterize natural communities.	root:Engineered:Modeled:Simulated communities (DNA mixture)
MGYS00004143	Study of bacterial communities in microcosms amended with brown algae	Marine minimum medium was amended with brown algal biomass and antibiotics (kanamycin and streptomycin), and inoculated with a WT or alyA1-deficient strain of Z. galactanivorans. Bacterial communities were characterized by Miseq 16S rRNA-gene sequencing.	root:Engineered:Lab enrichment:Defined media:Marine media
MGYS00004494	Uncultured Environmental Isolate Targeted loci environmental	Safe disposal of nuclear waste necessitates a thorough understanding of the role microorganisms play on the fate of the waste materials over time. In this study we conducted enrichment experiments to assess the potential for plasticised PVC, commonly used in the nuclear industry, to fuel nitrate reduction by a high pH-adapted microbial community at pH 10. Non-plasticised PVC powder served as an additive-free control, and samples of both materials were gamma irradiated (1 MGy) under hyperalkaline conditions, representative of conditioned nuclear waste, to assess the effect of irradiation on bioavailability.	root:Engineered:Lab enrichment
MGYS00002563	marine sediment metagenome Targeted loci environmental	Difficulties in studying growth dynamics of marine sediment microbial populations in a natural setting limits the ability to identify functions in novel populations, assess competition mechanisms, and extrapolate from growth dynamics in pure cultures. We used qPCR and 16S rRNA gene tag libraries to measure relative growth rates of a microbial community from Cape Lookout Bight, NC, in a laboratory mesocosm. Homogenized sediments were incubated for 122 days, hydrogen concentrations were consistent with thermodynamic control by sulfate-reducing prokaryotes during the sulfate-reducing phase and methanogenesis commenced when hydrogen increased above the methanogen thermodynamic maintenance. Uncultured clades of Methanosarcinales and Methanomicrobiales grew during the methanogenic phase with doubling times ranging from 15-46 days, considerably slower than those grown in pure cultures. An uncultured archaeal group, Kazan-3A-21, also increased with methane production. The majority of the population were from deeply-branching uncultured groups and, like the majority of the putative sulfate reducers, were mostly unresponsive to the shift from sulfate reduction to methanogenesis. We conclude that marine sediment methanogens grow more slowly than cultures, once thermodynamic inhibition by sulfate reducers is alleviated; and the majority of the diversity present in marine sediments grow or die more slowly than could be observed in our 122 day incubation.	root:Engineered:Lab enrichment
MGYS00001848	High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-9-D metagenome		root:Engineered:Lab enrichment
MGYS00003132	Desalination process Targeted Locus/Loci	Water samples were collected from a desalination plant, which were seawater, pretreated seawater, brine of reverse osmosis process and fouled reverse osmosis membranes.  Microbial community differences were determined from intake to fouling communities during desalination process.   1) seawater: intake seawater which provided to desalination process.  2) filter treated seawater: after pretreatment (multimedia filter, MF, UF).  3) Biofouling1 : on reverse osmosis  membrane 1 (front located face to inflow). 4) Biofouling2 : on reverse osmosis membrane 2 (last located). 5) Brine: the concentrated water after reverse osmosis process.	root:Engineered:Industrial production
MGYS00001795	Organic and Non-Organic Wine Targeted Locus (Loci)	Samples taken during fermentation of organic and non-organic wine	root:Engineered:Food production:Fermented beverages
MGYS00001159	Pit mud of Chinese liqour fermentation reactorMetagenome	Chinese liquor is produced by a solid-state fermentation process used for hundreds of years. The process is carried out in rectangular soil pits, whose walls have been layered with a fermentation mud. The age of these this layer is believed to influence final liquor quality and the microbes resident here form the inoculum for fermentation. Microbial diversity in these layers is poorly understood. This is the first report which describes a deep metagenomic sequencing based study to reveal the microbial diversity from 24 pits of varying ages, 20, 30, 50, 140, 220, 350, 400 and 440 years.	root:Engineered:Food production:Fermented beverages
MGYS00001747	Listeria monocytogenes Genome sequencing	Quasi-metagenomics for rapid trace-back of pathogens from complex matrices: a case study with Listeria monocytogenes from ice-cream linked to an outbreak	root:Engineered:Food production:Dairy products
MGYS00001176	Cotija cheese metagenome	Cotija cheese is a Mexican dairy product of spontaneous fermentation with a particular sensorial profile and an indisputable microbiological quality. In this study we analysed bacterial Cotija cheese metagenome in order to get a complete picture of bacterial diversity as well as metabolic potential of consortium related to flavour and odour compound production as well as gene related with bacteriocins production.	root:Engineered:Food production:Dairy products
MGYS00001170	Medium-ripened pasta-filata cheese metatranscriptome Transcriptome or Gene expression	Microbial metatranscriptome (RNA-seq) during manufacturing and ripening of Caciocavallo cheese (a traditional Italian pasta-filata cheese)	root:Engineered:Food production:Dairy products
MGYS00001154	raw sequence reads from analysis of red-smear-cheese	The cheese smear of a Swiss semi-hard red-smear cheese variety was analyzed for comparison of the microbial surface smear community patterns of cheeses differing in their smear quality.	root:Engineered:Food production:Dairy products
MGYS00001153	ITS2-based metagenomic study of twelve French cheese varieties		root:Engineered:Food production:Dairy products
MGYS00001152	Medium-ripened pasta-filata cheese Targeted loci environmental	16S rRNA sequencing (cDNA) of Caciocavallo cheese during manufacturing and ripening	root:Engineered:Food production:Dairy products
MGYS00001151	food metagenome Targeted loci environmental	The aim of the experiment is to assess the microbial communities of spoiled hard cheese using Illumina MiSeq high-throughput sequencing technologies	root:Engineered:Food production:Dairy products
MGYS00001150	Mozzarella cheese Targeted Locus (Loci)	Mozzarella cheese microbiota	root:Engineered:Food production:Dairy products
MGYS00001149	Metagenome from Piedmontese cheese	After total bacterial RNA extraction directly from Piedmontese cheese and cDNA syntesis, V1-V3 region of the 16S rRNA were amplified	root:Engineered:Food production:Dairy products
MGYS00001148	Cheese Targeted Locus (Loci)	V1-V3 rRNA gene amplicons from Fontina PDO cheese	root:Engineered:Food production:Dairy products
MGYS00001147	Canestrato cheese Targeted Locus (Loci)	Canestrato Pugliese PDO cheese metagenome	root:Engineered:Food production:Dairy products
MGYS00001146	Cheese Product Targeted Locus (Loci)	The goal are to explore and study the microbial diversity in cheese samples from Herve region in Belgium.	root:Engineered:Food production:Dairy products
MGYS00001126	Mexican cheese microbiota 18S	Yeast diversity in traditional mexican cheeses	root:Engineered:Food production:Dairy products
MGYS00001125	Mexican cheese microbiota 16S	Microbial diversity of traditional mexican cheeses	root:Engineered:Food production:Dairy products
MGYS00001123	cheese whey bioreactor Metagenome	microbial community of cheese whey	root:Engineered:Food production:Dairy products
MGYS00001121	Ricotta cheese microbiome	Ricotta cheese microbial community evolution during shelf life.	root:Engineered:Food production:Dairy products
MGYS00001113	Cheese Targeted Locus (Loci)	Microbiota of curds and natural whey cultures from Grana Padano, Parmigiano Reggiano and Mozzarella cheese manufactures	root:Engineered:Food production:Dairy products
MGYS00001842	food contamination metagenome Metagenome	fresh bagged spinach spiked with STEC	root:Engineered:Food production
MGYS00001838	Viral metagenomics of US store bought beef, pork, chicken	We describe here the metagenomics-derived viral sequences found in beef, pork, chicken purchased from supermarkets in San Francisco. Meat and meat products can be the source of numerous enteric infections in humans. A library was then constructed using Nextera XT DNA Sample Preparation Kit (Illumina) and then sequenced using the Miseq Illumina platform with 250 bases paired ends with a distinct molecular tag for each pool.	root:Engineered:Food production
MGYS00001804	Metagenome of the microbiota  of wild lavender honey		root:Engineered:Food production
MGYS00001797	Metagenome of the microbiota of lavandin honey		root:Engineered:Food production
MGYS00001773	Dietary supplements Metagenome	Dietary supplements with live microbials.	root:Engineered:Food production
MGYS00001754	Beef metagemome	Exploring the sources of beef microbial contamination and study the beef microbiota evolution after aerobic storage at 4C.	root:Engineered:Food production
MGYS00004734	ISS Metagenomes	Metagenomes created from samples collected from the International Space Station	root:Engineered:Built environment
MGYS00002607	Marine Aggregates Metagenome	Analyze the bacterial community composition of artificially produced marine aggregates on a geometric time series and associate it with the surrounding water.	root:Engineered:Built environment
MGYS00001840	Sugarcane filter cake compost raw sequence reads	Amplicon and shotgun sequencing of microbiome in two sugarcane filter cake compost piles were carried out to analyse the dynamics of fungal and bacterial communities along the process and biomass degrading profile for second generation bioethanol.	root:Engineered:Biotransformation:Mixed alcohol bioreactor
MGYS00001806	Paper sludge microbial community	Recycled paper sludge microbial community as a potential source of enzymes	root:Engineered:Biotransformation
MGYS00000703	Botany Membrane bioreactor, groundwater, granular activated carbon and soil samples 16S Tag Pyrosequencing of Metagenomic DNA.	Bacterial 16S Tag Pyrosequencing of a Membrane Bioreactor and Associated Units during Adaptation to Bioremediation of 1,2-dichloroethane.	root:Engineered:Bioremediation
MGYS00004620	AOB Genome sequencing and assembly	It is able to fixed nitrogen	root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum
MGYS00001855	Continuous culture enrichments from intertidal sediment - Metagenomes, Metatranscriptomes and 16S tag sequencing	A continuous culture was inoculated with intertidal sediment from the German Wadden Sea, and introduced with artificial seawater and a mimicked tidal condition. Natural selection on the microbial community and redox processes were investigated in the culture. Three samples for DNA extraction and four samples for RNA extraction were taken from the culture during the last three weeks of the experiment. Whole DNA shotgun metagenomes were sequenced and the reads were assembled into contigs. Enriched total mRNA was used for transcriptome sequencing. Another 14 samples at different time points were taken for 16S tag sequencing.	root:Engineered:Bioreactor:Continuous culture:Marine intertidal flat sediment inoculum
MGYS00002822	Marine sediment microorganisms Raw sequence reads	Marine sediment incubations with different substrates	root:Engineered:Bioreactor:Continuous culture
MGYS00002722	Temperature controls crystalline iron(III) oxide utilization by microbial communities in ferruginous marine sediment incubations	e carried out Incubation experiments with deep ferruginous sediments from the Helgoland Mud Area, German Bight of the North Sea. Samples were collected using a gravity corer (5 m core length) during RV HEINCKE research expedition HE 443 (54 05.23'' N; 007 58.04'' E) in May 2015. In the laboratory, these sediments were stored under anoxic conditions at 4 oC until slurry incubations were. Anoxic 50-mL slurry incubations were made in 120-ml serum vials with sediment from 416  441 and 441  466 cm depths and anoxic sulphate-free artificial sea water (ASW; composition [L-1]: 26.4 g NaCl, 11.2 g MgCl2.6H2O, 1.5 g CaCl2.2H2O and 0.7 g KCl) at a ratio of 1:3 (w/v) under a headspace of N2. Incubations (n=9) were supplemented by adding iron(III) oxides (hematite or magnetite; LanXess, Germany; 30 mol l-1) and glucose (2 mM) as electron donor. Control incubations (glucose only, n = 9) were supplemented with 2 mM glucose only. The potential for reduction of amended hematite (HG) or magnetite (MG) was evaluated by comparing the amount of Fe2+ formed in crystalline iron(III)-treated incubations to those of the glucose only control (G). Triplicates of each treatment set were incubated statically in the dark at 4 oC, 10 oC, or 30 oC. Supplementary incubations were set up at 30 oC, for testing the effect of 2-bromoethanesulfonate (BES) on methanogenesis and iron reduction in the presence of crystalline iron oxides. For molecular analysis, one millilitre of slurry from individual incubations, at specific time points as stated in each sample description, was used for nucleic acid extraction following a modified protocol from Lueders et al (2004). A two-step PCR approach for Illumina amplicon sequencing described by Herbold et al (2015) was adopted for amplification of Bacteria and Archaea 16S rRNA genes. Amplicon library was sequenced using the Miseq Illumina sequencing platform at University of Bremen, Germany. Sequence analysis of forward reads was performed on the QIIME 1.8.0 platform (Caporaso et al., 2010) based on the 16S rRNA gene profiling analysis pipeline recommended by Pylro et al (2014) with modifications. A Total Sum Scaling approach was used to identify dominant members of the microbial communities in each sample. The resulting article written on the project reported relative abundance of 16S rRNA sequences of Bacteria and Archaea that dominated the microbial communities in each sample.	root:Engineered:Bioreactor:Continuous culture
MGYS00001844	High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-10-D metagenome		root:Engineered:Lab enrichment
MGYS00001843	High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-8-D metagenome		root:Engineered:Lab enrichment
MGYS00001839	Methanogenic digester communities Raw sequence reads	Studies of microbial communities and antibiotic resistance genes	root:Engineered:Bioreactor
MGYS00001751	Methanogen diversity in the rumen in vitro fermentation culture	methanogen diversity in the rumen in vitro fermentation culture	root:Engineered:Bioreactor
MGYS00001815	Substrate variations triggered the emergent of different active bacterial and archaeal assemblages during biomethane production	Biomethane has been regarded as one of the promising renewable energy supplies. However, the microbial communities involved in methane synthesis have not been fully characterized. By examining the bacterial and archaeal 16S rRNA genes in the DNA and RNA using barcoded 454 pyrosequencing, the composition of a methane-generating microbial community and the corresponding active members during the transformation of three target substrates (food waste, cellulose, xylan) were determined. By assigning sequences to their respective taxonomies, substrate-dependent variations in the composition and relative abundance of the active microbial community members were detected. Results from this study suggest that the vast diversity of the microbial community enabled adaptation and transformation of multiple amended substrates, and a subset of the populations became active and altered in relative abundance during methane production. Overall, insights gained from high-throughput sequencing of the metabolically-active populations under different conditions should facilitate the optimization of biomethane systems.	root:Engineered:Biogas plant:Wet fermentation
MGYS00001772	bioethanol fermentation Metagenome	This project investigated the bacterial contents of yeast-based bioethanol fermentation. Bacteria are known to impact the success of bioethanol fermentation, but little is known about bacterial community structure and dynamics during the course of fermentation. Here we used 16S rRNA gene amplicon sequencing to probe community structure during multiple fermentations from multiple facilities across the United States.	root:Engineered
MGYS00000383	Lonar Lake sediment Metagenome	Understanding the relevance of bacterial and archaeal diversity in the soda lake sediments by the culture independent approach using bTEFAP.  Lonar Lake is a saline soda lake located at Lonar in Buldana district, Maharashtra State, India, which was created by a meteor impact.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline:Sediment
MGYS00005126	Postnatal gut immunity and microbiota development is minimally affected by prenatal inflammation in preterm pigs	Chorioamnionitis (CA), resulting from intra-amniotic inflammation, is a frequent cause of preterm birth and exposes the immature intestine to bacterial toxins and/or inflammatory mediators before birth via fetal swallowing. This may affect intestinal immune development, interacting with the effects of enteral feeding and gut microbiota colonization just after birth. Using preterm pigs as model for preterm infants, we hypothesized that prenatal exposure to gram-negative endotoxin influences postnatal bacterial colonization and gut immune development. Pig fetuses were given intra-amniotic lipopolysaccharide (LPS) 3 d before preterm delivery by cesarean section, and were compared with litter-mate controls (CON) at birth and after 5 d of formula feeding and spontaneous bacterial colonization. Amniotic fluid was collected for analysis of leukocyte counts and cytokines, and the distal small intestine was analyzed for endotoxin level, morphology and immune cell counts. Intestinal gene expression and microbiota were analyzed by transcriptomics and metagenomics, respectively. At birth, LPS-exposed pigs showed higher intestinal endotoxin, neutrophil/macrophage density and shorter villi. About 1.0% of intestinal genes were affected at birth and DMBT1, a regulator of mucosal immune defense, was identified as the hub gene in the co-expression network. Genes related to innate immune response (TLR2, LBP, CD14, C3, SFTPD), neutrophil chemotaxis (C5AR1, CSF3R, CCL5) and antigen processing (MHC II, CD4) were also affected and expression levels correlated with intestinal neutrophil/macrophage density and amniotic fluid cytokine levels. On day 5, LPS and CON pigs showed similar necrotizing enterocolitis (NEC) lesions, endotoxin levels, morphology, immune cell counts, gene expressions and microbiota (except for difference in some low-abundant species). Our results show that CA markedly affects intestinal genes at preterm birth, including genes related to immune cell infiltration. However, a few days later, following the physiological adaptations to preterm birth, CA had limited effects on intestinal structure, function, gene expression, bacterial colonization and NEC sensitivity. We conclude that short-term, prenatal intra-amniotic inflammation is unlikely to exert marked effects on intestinal immune development in preterm neonates beyond the immediate neonatal period.	root:Host-associated:Mammals:Digestive system
MGYS00005125	Metagenomic analysis of the cervicovaginal microbiome in women with systemic lupus erythematosus: A new insight into sex and ethnic differences	Non-Lactobacillus dominant cervicovaginal microbiomes have been associated with vaginal and auto-immune diseases such as bacterial vaginosis and systemic lupus erythematosus (SLE). Using a deep sequencing approach, the microbial composition and structure of the cervicovaginal metagenomes of a group of Afro-Caribbean women (with and without SLE) asymptomatic for vaginal disease were analysed. Community state type (CST) IV predominated the metagenomes of the Afro-Caribbean women. In the healthy group Gardnerella (16.37%) and Prevotella (11.3%) species were more abundant than Lactobacillus (5.06%). Whereas, in women with SLE the most abundant species was Prevotella (17.66%) followed by Lactobacillus (13.60%) and Gardnerella (5.73%). These findings suggest that vaginal health is not strictly dependent on the relative abundance of Lactobacillus species. Additionally, some low abundant pathobionts were 5 to 23 times more common in the SLE cohort. This study offers a new postulate into sex and ethnic differences in the prevalence of SLE.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00005124	Metagenomic analysis of the cervicovaginal microbiome in women with systemic lupus erythematosus: A new insight into sex and ethnic differences	Non-Lactobacillus dominant cervicovaginal microbiomes have been associated with vaginal and auto-immune diseases such as bacterial vaginosis and systemic lupus erythematosus (SLE). Using a deep sequencing approach, the microbial composition and structure of the cervicovaginal metagenomes of a group of Afro-Caribbean women (with and without SLE) asymptomatic for vaginal disease were analysed. Community state type (CST) IV predominated the metagenomes of the Afro-Caribbean women. In the healthy group Gardnerella (16.37%) and Prevotella (11.3%) species were more abundant than Lactobacillus (5.06%). Whereas, in women with SLE the most abundant species was Prevotella (17.66%) followed by Lactobacillus (13.60%) and Gardnerella (5.73%). These findings suggest that vaginal health is not strictly dependent on the relative abundance of Lactobacillus species. Additionally, some low abundant pathobionts were 5 to 23 times more common in the SLE cohort. This study offers a new insight into sex and ethnic differences in the prevalence of SLE.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00005123	Ocean Sampling Day (OSD) data from North Adriatic Sea	Ocean Sampling Day (OSD) data from North Adriatic Sea	root:Environmental:Aquatic:Marine
MGYS00005122	CAECAL METAGENOMICS	CAECAL METAGENOMICS IN DIFFERENT FEEDING CONDITIONS	root:Host-associated:Birds:Digestive system
MGYS00005120	Space environmental factor impacts upon murine colon microbiota and mucosal homeostasis	We report how high and low linear energy transfer (LET) radiation, microgravity, and elevated dietary iron affect colon microbiota (determined by 16S rDNA pyrosequencing) and colon function. Three independent experiments were conducted: 1) fractionated low LET ? radiation (137Cs, 3 Gy, RAD), high Fe diet (IRON) (650 mg/kg diet), and a combination of low LET ? radiation and high Fe diet (IRON+RAD) in male Sprague-Dawley rats; 2) high LET 38Si particle exposure (0.050 Gy), 1/6 G partial weight bearing (PWB), and a combination of high LET38Si particle exposure and PWB in female BalbC/ByJ mice; and 3) 13 d spaceflight in female C57BL/6 mice. For each experiment, the colon was resected and feces removed for microbial sequencing analysis on a Roche 454 Genome Sequencer  FLX Titanium instrument (Microbiome Core Facility, Chapel Hill NC) using the GS FLX Titanium XLR70 sequencing reagents and protocols. Analysis of amplicon sequencing data was carried out using the QIIME pipeline. Low LET radiation, high iron diet, and spaceflight increased Bacteroidetes and decreased Firmicutes. Low LET radiation, high Fe diet, and spaceflight did not significantly affect diversity or richness, or elevate pathogenic genera. Spaceflight increased Clostridiales and decreased Lactobacillales, and similar trends were observed in the experiment using a ground-based model of microgravity, suggesting altered gravity may affect colonic microbiota. Microbiota characteriztion in these models is a first step in understanding the impact of the space environment on intestinal health. Overall design: Phylogenetic characterizaiton of fecal microbiota from a total of 49 mouse and rat fecal samples (18 and 31 samples, respectively, no replicates)	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00005110	Spatiotemporal dynamics in the metagenomes of biofouling microbial communities residing in district cooling basins	Metagenomic datasets for biofouling biofilm samples collected from the water cooling tower basins of two district cooling plants.	root:Environmental:Aquatic:Freshwater
MGYS00005114	The effect of viruses on the dynamics of harmful algal blooms	Surface water from areas experiencing harmful algal blooms were collected either at the beginning or during the termination of the bloom. The water was size fractionated, and metagenomes were produced for the host and viral fractions.	root:Environmental:Aquatic:Marine
MGYS00005113	Dysbiosis associated with acute helminth infections in herbivorous youngstock - observations and implications	This study investigates, for the first time, the associations between acute infections by GI helminths and the faecal microbial and metabolic profiles of a cohort of equine youngstock, prior to and following treatment with parasiticides (ivermectin).	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005111	wrasseeggs16s	wrasseeggs16s	root:Host-associated:Fish
MGYS00005112	Mussels larvea 16S	Mussels larvea 16S	root:Host-associated:Mollusca
MGYS00005108	SHAMAN: a user-friendly website for meta-taxonomic analysis from raw reads to statistical analysis	Profiling differences in microbiome composition regarding a healthy or a disease phenotype is central in microbiome research. It typically involves the sequencing, the data processing, the statistical analysis and the graphical representation of the detected signatures. This process is currently addressed through several separated applications that requires expertise for installation, data pre-processing and in some case, programming skills. We present SHAMAN, which is an interactive web application that facilitates the use of a workflow for OTU calculation, the robust statistical modelling proposed by the DESeq2 package and provides more than ten interactive visualisations. It also implements new normalization methods which account for the sparsity of metagenomic data. %which is relevant for the DESeq2 approach.SHAMAN is primary designed for biologist with no experience in metagenomics, but can also meet the needs of specialist who can easily access to the configuration of processed tools and packages. It is freely accessible at http://shaman.pasteur.fr/, but also work as a standalone application with docker (aghozlane/shaman) or in R with packrat. The source code is written in R and is available at https://github.com/aghozlane/shaman. Using a mock community sequencing and a published 16S metagenomic dataset, we show here that SHAMAN allows to perform a complete meta-taxonomic analysis.	root:Engineered:Modeled:Simulated communities (sequence read mixture)
MGYS00005106	The_role_of_the_receptors_of_IL_10_superfamily_members_on_epithelial_cells_during_whipworm_infection_and_immunity	The role of the receptors of IL-10 superfamily members on epithelial cells during whipworm infection and immunity	root:Host-associated:Mammals
MGYS00005105	The impact of anthelmintic treatment on human gut microbiota in western Kenya: Cross-sectional and pre-post deworming comparisons	Murine studies suggest that the presence of some species of intestinal helminths is associated with changes in host microbiota composition and diversity. Some changes are even found in anatomic locations remote from where these helminths reside and may persist after helminth clearance. However, studies in humans have produced varied conclusions and the impact appears to vary widely depending on the helminth species present. To demonstrate how molecular approaches to the human gut microbiome can provide insights into the complex interplay among disparate organisms, DNA was extracted from cryopreserved stools collected from residents of 5 rural Kenyan villages prior to, 3 weeks and 3 months following albendazole (ALB) therapy. Samples were analyzed by qPCR for the presence of 8 species of intestinal parasites, and by MiSeq 16S rRNA gene sequencing. Based on pre-treatment results, the presence of neither Ascaris lumbricoides (Al) nor Necator americanus (Na) infection significantly altered the overall diversity of the microbiota in comparison with age-matched controls. Following ALB therapy and clearance of soil-transmitted helminths (STH), there were significant increases in the proportion of the microbiota made up by Clostridiales (p=0.0002, average fold change 0.57), and reductions in the proportion made up by Enterobacteriales (p=0.0004, average fold change -0.58). There were additional changes in the microbiota that appear to be related to ALB administration, suggesting that these antimicrobial effects must be considered in any post-treatment setting. Nevertheless, the helminth-associated changes in Clostridiales and Enterobacteriales suggest that clearance of STH, and Na in particular, alters the gut microbiota.  This submission was done on behalf of Thomas B. Nutman (Principal Investigator) and Alice V. Easton.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005100	Mucosal Barrier and Th2 Immune Responses are Enhanced by Dietary Inulin in Pigs Infected with Trichuris suis	Diet composition may play a crucial role in shaping host immune responses and commensal gut microbiota populations. Bioactive dietary components, such as inulin, have been extensively studied for their bioactive properties, particularly in modulating gut immune function and reducing inflammation. It is has been shown that colonization with gastrointestinal parasitic worms (helminths) may alleviate chronic inflammation through promotion of T-helper cell type (Th) 2 and T-regulatory immune responses and alterations in the gut microbiome. In this study, we investigated if dietary inulin could modulate mucosal immune function in pigs during colonization with the porcine whipworm, Trichuris suis. T. suis infection induced a typical Th2-biased immune response characterised by transcriptional changes in Th2- and barrier function-related genes, accompanied by intestinal remodelling through increased epithelial goblet and tuft cell proliferation. We observed that inulin also up-regulated Th2-related immune genes (IL13, IL5), and suppressed Th1-related pro-inflammatory genes (IFNG, IL1A, IL8) in the colon. Notably, inulin augmented the T. suis-induced responses with increased transcription of key Th2 and mucosal barrier genes (e.g. IL13, TFF3), and synergistically suppressed pro-inflammatory genes such as IFNG and CXCL9. 16S rRNA sequencing of proximal colon digesta samples revealed that inulin supplementation reduced the abundance of bacterial phyla linked to inflammation, such as Proteobacteria and Firmicutes, and simultaneously increased Actinobacteria and Bacteroidetes. Interestingly, pigs treated with both inulin and T. suis displayed the highest Bacteroidetes: Firmicutes ratio and the lowest gut pH, suggesting an interaction of diet and helminth infection that stimulates the growth of beneficial bacterial species. Overall, our data demonstrate that T. suis infection and inulin co-operatively enhance anti-inflammatory immune responses, which is potentially mediated by changes in microbiota composition. Our results highlight the intricate interactions between diet, immune function and microbiota composition in a porcine helminth infection model. This porcine model should facilitate further investigations into the use of bioactive diets as immunomodulatory mediators against inflammatory conditions, and how diet and parasites may influence gut health.	root:Host-associated:Mammals:Digestive system
MGYS00005097	Shrimp aquaculture	Shrimp aquaculture metagenome	root:Environmental:Aquatic:Aquaculture
MGYS00005095	Comparison of soil bacterial communities in crop rotations with different levels of intensification (i.e. number of crops per year), in Oliveros, Santa Fe, Argentina	Comparison of soil bacterial communities in crop rotations with different levels of intensification (i.e. number of crops per year), in Oliveros, Santa Fe, Argentina	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00005090	EMG produced TPA metagenomics fasta_path of the Longitudinal_Nasopharyngeal_Microbiome_Dynamics_in_Infants_from_the_Maela_ARI_Birth_Cohort (PRJEB25223) data set.	The PRJEB25223 Third Party Annotation (TPA) fasta_path was derived from the primary whole genome shotgun (WGS) data set: PRJEB25223.  This project includes samples from the following biomes: root:Host-associated:Human:Skin:Naris.	root:Host-associated:Human:Skin:Naris
MGYS00005088	EMG produced TPA metagenomics fasta_path of the Novel gut-microbiota based metagenomic signature for advanced fibrosis in nonalcoholic fatty liver disease (PRJNA373901) data set.	The PRJNA373901 Third Party Annotation (TPA) fasta_path was derived from the primary whole genome shotgun (WGS) data set: PRJNA373901.  This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005087	EMG produced TPA metagenomics fasta_path of the Cow-to-mouse fecal transplantation established intestinal microbiota as cause of cow mastitis (PRJNA357148) data set.	The PRJNA357148 Third Party Annotation (TPA) fasta_path was derived from the primary whole genome shotgun (WGS) data set: PRJNA357148.  This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00005086	EMG produced TPA metagenomics fasta_path of the Gut metagenomes of rural populations in Cameroon (PRJEB27005) data set.	The PRJEB27005 Third Party Annotation (TPA) fasta_path was derived from the primary whole genome shotgun (WGS) data set: PRJEB27005.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005084	Natural Bacterial Communities Associated with Emiliania huxleyi	Coccolithophores are photosynthetic marine microorganisms that cover their eukaryotic cells with calcium carbonate disks. They are of great importance in earth's biogeochemical cycles of oxygen, carbon and sulfur and are essential in marine primary production. The species Emiliania huxleyi is the most abundant coccolithophore micro-alga in modern-day oceans. It creates vast annual blooms that stretch for thousands of square kilometers and can be viewed by satellites from space. These dense blooms end after several weeks with the collapse of the algal population. The collapse of the bloom is usually attributed to viral infections or environmental changes. Recent studies demonstrated that bacteria play an important role in the life and death of E. huxleyi populations. In controlled laboratory experiments, it was shown that the bacterium Phaeobacter inhibens has a dynamic mutualistic-pathogenic interaction with the alga. In a co-culture model system, the microbes first exchange beneficial metabolites, however once the alga ages, the bacterium kills its algal partner. This interaction might contribute to the known E. huxleyi bloom dynamics. Nevertheless, in order to interpret data acquired in the lab, a combination between laboratory findings and field studies will be most beneficial in bridging the complex natural environment of E. huxleyi with the laboratory model system. In this current research I intend to link between lab observations and the marine environment. In order to do so, the identity and relative abundance of bacteria that naturally associate with a stable E. huxleyi population in the gulf of Aqaba will be assessed seasonally in order to account for possible seasonal changes in bacterial composition. In understating who are the bacterial key players in the natural environment of E. huxleyi I hope to attain a wide and unbiased comprehensive view of natural algal-bacterial interactions.	root:Host-associated:Algae
MGYS00005081	METAGENOMIC STUDY OF PANCHGAVYA	Panchgavya is a term used to describe five major substances, obtained from cow, which include cow's urine, milk, ghee, curd and dung.	root:Host-associated:Mammals
MGYS00004995	Trial B 2019	Trial B 2019	root:Host-associated:Birds:Digestive system
MGYS00005078	Turf_Chronosequence_16S_ITS	soil 16S and ITS amplicon from different ecosystems	root:Environmental:Terrestrial:Soil
MGYS00005077	CEFS_16S_ITS	soil 16S and ITS amplicon from different ecosystems	root:Environmental:Terrestrial:Soil
MGYS00005076	obesity_all	obesity_all	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00005071	IBK Shotgun Metagenomics Analysis Sample B7	IBK Shotgun Metagenomics Analysis Sample B7	root:Host-associated:Mammals
MGYS00005070	IBK Shotgun Metagenomics Analysis Sample B6	IBK Shotgun Metagenomics Analysis Sample B6	root:Host-associated:Mammals
MGYS00005069	IBK Shotgun Metagenomics Analysis Sample B5	IBK Shotgun Metagenomics Analysis Sample B5	root:Host-associated:Mammals
MGYS00005068	IBK Shotgun Metagenomics Analysis Sample B4	IBK Shotgun Metagenomics Analysis Sample B4	root:Host-associated:Mammals
MGYS00005067	IBK Shotgun Metagenomics Analysis Sample B3	IBK Shotgun Metagenomics Analysis Sample B3	root:Host-associated:Mammals
MGYS00005066	IBK Shotgun Metagenomics Analysis Sample B2	IBK Shotgun Metagenomics Analysis Sample B2	root:Host-associated:Mammals
MGYS00005065	IBK Shotgun Metagenomics Analysis Sample B1	IBK Shotgun Metagenomics Analysis Sample B1	root:Host-associated:Mammals
MGYS00005064	IBK Shotgun Metagenomics Analysis Sample A8	IBK Shotgun Metagenomics Analysis Sample A8	root:Host-associated:Mammals
MGYS00005050	Passalid Beetle2	Metagenomic characterization of the 4 gut regions (FG, MG, AHG, PHG) of the passalid beetle Odontotaenius disjunctus. The four gut regions of 4 beetles were paired-end sequenced using the Illumina platform.	root:Host-associated:Insecta:Digestive system
MGYS00005052	Tucurui_Metagenoma_MGRAST	Functional and taxonomic analysis of samples from the hydroelectric lake of Tucurui.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00005061	Metagenomic characterization of dietary changes effects on the gut microbiome in smallholder dairy cattle	Assessment of changes in microbial diversity in rumen liquor and fecal samples from three breeds of dairy cattle fed on an increasing concentrate diet	root:Host-associated:Mammals:Digestive system
MGYS00005063	Resistflow-INF-EFF-RNA data	Ju F, Beck K, Yin X, McArdell Christa, Singer H, Johnson D, Zhang T, Buergmann H *. 2018. Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange and up-regulated expression in the effluent. The ISME Journal (in press)	root:Engineered:Bioreactor
MGYS00005062	Resistflow-NFC-DNF-RNA data	Ju F, Beck K, Yin X, McArdell Christa, Singer H, Johnson D, Zhang T, Buergmann H *. 2018. Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange and up-regulated expression in the effluent. The ISME Journal (in press)	root:Engineered:Bioreactor
MGYS00005060	RM_CSULB	Grass Rhizosphere	root:Host-associated:Plants:Rhizosphere
MGYS00005059	Artificial mix of real bacterial sequences	Mixes of 15 bacterial DNA samples in different known proportion. Used to evaluate the prediction accuracy for 16S and WGS data	root:Engineered:Modeled:Simulated communities (sequence read mixture)
MGYS00005058	Resistflow-EFF-DNA data	Ju F, Beck K, Yin X, McArdell Christa, Singer H, Johnson D, Zhang T, Buergmann H *. 2018. Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange and up-regulated expression in the effluent. The ISME Journal (in press)	root:Engineered:Wastewater
MGYS00005057	Resistflow-DNF-DNA data	Ju F, Beck K, Yin X, McArdell Christa, Singer H, Johnson D, Zhang T, Buergmann H *. 2018. Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange and up-regulated expression in the effluent. The ISME Journal (in press)	root:Engineered:Bioreactor
MGYS00005056	Resistflow-INF-DNA data	Ju F, Beck K, Yin X, McArdell Christa, Singer H, Johnson D, Zhang T, Buergmann H *. 2018. Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange and up-regulated expression in the effluent. The ISME Journal (in press)	root:Engineered:Wastewater
MGYS00005055	Resistflow-NFC-DNA data	Ju F, Beck K, Yin X, McArdell Christa, Singer H, Johnson D, Zhang T, Buergmann H *. 2018. Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange and up-regulated expression in the effluent. The ISME Journal (in press)	root:Engineered:Wastewater:Water and sludge
MGYS00005054	Indian_sediments	Shotgun metagenomics - sediments contaminated by pharmaceutical discharges. This project contains 11 samples (paired-end 101 bp metagenomic libraries) and sequenced on Illumina HiSeq2000  platform. The raw sequence data of read 1 and read 2 (paired-end) from each metagenome has been uploaded individually.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00005053	Comparative metagenome analysis of normal and arsenic contaminated soils from ballia district, Uttar Pradesh, India	Metagenome of normal soil and arsenic contaminated soil of different agricultural field from Ballia district, Uttar Pradesh, India	root:Environmental:Terrestrial:Soil
MGYS00005051	Enriched_Iron_Ore_metagenome	study of Enriched iron ore metagenome	root:Environmental:Terrestrial:Soil
MGYS00005049	Joined_Deer	Joined_Deer	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00005048	Deer_Metagenomics	Deer_Metagenomics	root:Host-associated:Mammals
MGYS00005047	Passalid Beetle	Metagenomic characterization of the 4 gut regions (FG, MG, AHG, PHG) of the passalid beetle Odontotaenius disjunctus. The four gut regions of 4 beetles were paired-end sequenced using the Illumina platform.	root:Host-associated:Arthropoda:Digestive system:Gut
MGYS00005046	Palazzo_Ducale_SS	Latrine inside an old palace (18th century) (Sassari - Italy)	root:Engineered:Wastewater
MGYS00005004	EMG produced TPA metagenomics assembly of the Thermophilic enriched microbial communities from mini bioreactor at UC Davis - Sample SG0.5JP960 metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA337831.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00005044	Metagenomic analysis of marine coastal waters	Marine coastal environment hosts a complex diversity of bacteria and archaea. Here we studied the spatial and temporal dynamic of their genomes populations and functions using metagenomic analysis.	root:Environmental:Aquatic:Marine:Coastal
MGYS00005043	Characterisation of gut microbiome of sheep experimentally infected with the parasitic nematode Teladorsagia circumcincta	Characterisation of gut microbiome of (i) sheep experimentally infected with the parasitic nematode Teladorsagia circumcincta, i.e. the primary cause of parasitic gastroenteritis in small ruminants in the UK; (ii) sheep immunised against T. circumcincta with an effective sub-unit vaccine developed by collaborators at the MRI; and (iii) immunologically naïve, uninfected control sheep.	root:Host-associated:Mammals:Digestive system
MGYS00005036	EMG produced TPA metagenomics assembly of the Urban Enviromental Genomics Project () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA415974.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Bioremediation:Terephthalate:Wastewater
MGYS00005035	EMG produced TPA metagenomics assembly of the samples from sewage Raw sequence reads (wastewater metagenome) data set.	The wastewater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA388734.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00005033	EMG produced TPA metagenomics assembly of the Comparison between mouse caecal contents and faeces (Mouse_caecal_contents_vs_faeces) data set.	The Mouse_caecal_contents_vs_faeces Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB15341.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Large intestine, Fecal.	root:Host-associated:Mammals:Digestive system
MGYS00005032	EMG produced TPA metagenomics assembly of the Marine sediment trap metagenomes (marine sediment metagenome) data set.	The marine sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA270248.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00005031	EMG produced TPA metagenomics assembly of the Gut microbiome profiling of pediatric patients undergoing stem cell transplantation (gut metagenome) data set.	The gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA283642.  This project includes samples from the following biomes: Host-associated, Human, Digestive system.	root:Host-associated:Human:Digestive system
MGYS00005030	EMG produced TPA metagenomics assembly of the Metagenomic analysis of thiocyanate and cyanide biodegrading microbial consortia Metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA279279.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00005029	EMG produced TPA metagenomics assembly of the Microbial metagenome (DNA-seq) of fermented sausages during ripening (food fermentation metagenome) data set.	The food fermentation metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA352236.  This project includes samples from the following biomes: Engineered, Food production.	root:Engineered:Food production
MGYS00005028	EMG produced TPA metagenomics assembly of the mouse gut metagenome Metagenome (mouse gut metagenome) data set.	The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA341282.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system.	root:Host-associated:Mammals:Digestive system
MGYS00005027	EMG produced TPA metagenomics assembly of the Antimicrobial resistance of urban water samples (freshwater metagenome) data set.	The freshwater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA400857.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater.	root:Environmental:Aquatic:Freshwater
MGYS00005026	EMG produced TPA metagenomics assembly of the Metagenomics of chicken manure composts (compost sample) data set.	The compost sample Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA433771.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00005025	EMG produced TPA metagenomics assembly of the BPA degrading microbial community Raw sequence reads (BPA degrading microbial community) data set.	The BPA degrading microbial community Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA450306.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00005024	EMG produced TPA metagenomics assembly of the metagenomic sequencing on sediments of Xiaomei River (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA382755.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lotic, Sediment.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00005022	EMG produced TPA metagenomics assembly of the Rapid Sand Filter Metagenome Genome sequencing and assembly (biofilter metagenome) data set.	The biofilter metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA384587.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Groundwater.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00005021	EMG produced TPA metagenomics assembly of the epibiont metagenome Raw sequence reads (epibiont metagenome) data set.	The epibiont metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330990.  This project includes samples from the following biomes: Host-associated, Microbial, Bacteria.	root:Host-associated:Microbial:Bacteria
MGYS00005020	EMG produced TPA metagenomics assembly of the Candidatus Accumulibacter enrichment culture Metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA386410.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00005019	EMG produced TPA metagenomics assembly of the Genome-resolved metagenomics of marine perchlorate-reducing communities (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA387015.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00005018	EMG produced TPA metagenomics assembly of the Metagenomic shotgun sequences of the five doenjang samples (traditional Korean fermented soybean paste) () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB19846.  This project includes samples from the following biomes: Engineered, Food production, Fermented vegetables.	root:Engineered:Food production:Fermented vegetables
MGYS00005017	EMG produced TPA metagenomics assembly of the Bioreactor inoculated with intertidal sediment - Metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA226580.  This project includes samples from the following biomes: Engineered, Bioreactor, Continuous culture, Marine intertidal flat sediment inoculum, Wadden Sea-Germany.	root:Engineered:Bioreactor:Continuous culture:Marine intertidal flat sediment inoculum:Wadden Sea-Germany
MGYS00005016	EMG produced TPA metagenomics assembly of the An overview of the virome in wastwater in Brasilia, Brazil by High-throughput sequencing () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA395784.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00005015	EMG produced TPA metagenomics assembly of the Identification of nitrogen-fixing Bradyrhizobium associated with roots of field-grown sorghum by metagenome analyses (root metagenome) data set.	The root metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB6691.  This project includes samples from the following biomes: Host-associated, Plants, Root.	root:Host-associated:Plants:Root
MGYS00005014	EMG produced TPA metagenomics assembly of the Hawaiian Estuary Metagenome () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA429238.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary, Sediment.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00005013	EMG produced TPA metagenomics assembly of the Mesophilic microbial community from rice straw/compost enrichment Sample: eDNA_1 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336844.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00005012	EMG produced TPA metagenomics assembly of the cassava fermentation tank metagenomes (fermentation metagenome) data set.	The fermentation metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA296369.  This project includes samples from the following biomes: Engineered, Food production, Fermented vegetables.	root:Engineered:Food production:Fermented vegetables
MGYS00005011	EMG produced TPA metagenomics assembly of the activated sludge metagenome Raw sequence reads (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA397656.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00005010	EMG produced TPA metagenomics assembly of the Grape berry microbiota cultivar Corvina withering process Metagenomic assembly (food metagenome) data set.	The food metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA289617.  This project includes samples from the following biomes: Engineered, Food production.	root:Engineered:Food production
MGYS00005009	EMG produced TPA metagenomics assembly of the Dechlorination Culture CG-3 and SG-1 Metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA286891.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00005008	EMG produced TPA metagenomics assembly of the Metagenomic analysis of 1,2,3,4-tetrachlorodibenzo-p-dioxin dechlorinating enrichment cultures () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA395380.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lotic, Sediment.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00005007	EMG produced TPA metagenomics assembly of the Thermophilic enrichment culture from UC Davis - Sample SG0.5Z960 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA337828.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00005006	EMG produced TPA metagenomics assembly of the activated sludge Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA295114.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00005005	EMG produced TPA metagenomics assembly of the Metagenome from Paralichthys olivaceus (food metagenome) data set.	The food metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDA53873.  This project includes samples from the following biomes: Engineered, Food production.	root:Engineered:Food production
MGYS00005003	EMG produced TPA metagenomics assembly of the Baikal Rift Zone hot springs metagenome sequencing (hot springs metagenome) data set.	The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA427880.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00005002	EMG produced TPA metagenomics assembly of the Wastewater bioreactor microbial communities from Cape Town, South Africa - Thiocy_cont_750_plan metagenome (wastewater metagenome) data set.	The wastewater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA377107.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00005001	EMG produced TPA metagenomics assembly of the Wastewater bioreactor microbial communities from Cape Town, South Africa - Thiocy_cont_750_biof metagenome (wastewater metagenome) data set.	The wastewater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA377106.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00005000	EMG produced TPA metagenomics assembly of the Pelagic Microbial community sample from North Sea - COGITO 998_met_08 Metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA266685.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004999	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Canada - AD_UKC130_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340509.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004992	EMG produced TPA metagenomics assembly of the Feedstock adapted compost microbial communities from Newby Island compost facility, Milpitas, CA, USA - starting DNA metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA337767.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00004991	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F08 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405741.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004990	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage3 60B metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405728.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004989	EMG produced TPA metagenomics assembly of the Active sludge microbial communities from Klosterneuburg, Austria, studying microevolution and ecology of nitrifiers - Klosterneuburg WWTP active sludge metagenome KNB14_bulk metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375322.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004988	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage3 60A metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405727.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004987	EMG produced TPA metagenomics assembly of the Active sludge microbial communities from Klosterneuburg, Austria, studying microevolution and ecology of nitrifiers - Klosterneuburg WWTP active sludge metagenome KNB19-Kit metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375321.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004986	EMG produced TPA metagenomics assembly of the Microbial communities from bioreactor (seeded with sewage sludge) at LBNL, California, USA - Biofuel metagenome 5 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366160.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004985	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC097_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340755.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004984	EMG produced TPA metagenomics assembly of the Feedstock adapted compost microbial communities from Newby Island compost facility, Milpitas, CA, USA - Passage 4_MCC metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336699.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00004983	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Canada - AD_UKC129_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340508.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004982	EMG produced TPA metagenomics assembly of the riverine metagenome Duhaney River surface sample (riverine metagenome) data set.	The riverine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA475764.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lotic.	root:Environmental:Aquatic:Freshwater:Lotic
MGYS00004981	EMG produced TPA metagenomics assembly of the Anaerobic ammonium oxidizing microbial communities from anammox membrane bioreactor (MBR) in UC Berkley, California, United States - LAC_MetaG_1 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA439836.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004980	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, USA - P5_32mM MetaG metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406753.  This project includes samples from the following biomes: Host-associated, Algae.	root:Host-associated:Algae
MGYS00004979	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, USA - P5_8mM MetaG metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406751.  This project includes samples from the following biomes: Host-associated, Algae.	root:Host-associated:Algae
MGYS00004978	EMG produced TPA metagenomics assembly of the bioreactor metagenome Raw sequence reads (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA415892.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004977	EMG produced TPA metagenomics assembly of the compost enrichment single cell ciliate 20uM2 metagenome N17 metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366634.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00004976	EMG produced TPA metagenomics assembly of the Cellulose adapted compost microbial communities from Newby Island Compost Facility, Milpitas, CA, USA - Passage2 37B metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366613.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00004975	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 12_48_3.3_201_A2 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406033.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004974	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 11_42_5_180_A3 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406032.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004973	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 4_13_20_68_A1 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405535.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004972	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 7_21_20_110_A3 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406028.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004971	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 5_19_20_110_A1 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405536.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004970	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 9_31_10_142_A3 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406030.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004969	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 8_30_10_142_A2 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406029.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004968	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 3_6_20_6_A3 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405534.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004967	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage D2F12 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405752.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004966	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage D2F04 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405749.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004965	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F15 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405747.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004964	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage D2F06 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405750.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004963	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage D2F10 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405751.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004962	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage D2F03 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405748.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004961	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F10 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405743.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004960	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F14 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405746.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004959	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F13 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405745.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004958	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F11 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405744.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004957	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F07 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405740.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004956	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F09 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405742.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004955	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F06 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405739.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004954	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F04 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405737.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004953	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F05 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405738.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004952	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F03 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405736.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004951	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F02 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405735.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004950	EMG produced TPA metagenomics assembly of the Denitratation Metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA389994.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004949	EMG produced TPA metagenomics assembly of the Active sludge microbial communities from Klosterneuburg, Austria, studying microevolution and ecology of nitrifiers - Klosterneuburg WWTP active sludge metagenome KNB14_supernatant metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375324.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004948	EMG produced TPA metagenomics assembly of the Active sludge microbial communities from Klosterneuburg, Austria, studying microevolution and ecology of nitrifiers - Klosterneuburg WWTP active sludge metagenome KNB5-Kit metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375320.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004947	EMG produced TPA metagenomics assembly of the Guchuan gaed pit mud Transcriptome and Genome Sequencing (food fermentation metagenome) data set.	The food fermentation metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA380044.  This project includes samples from the following biomes: Engineered, Food production, Fermented beverages.	root:Engineered:Food production:Fermented beverages
MGYS00004946	EMG produced TPA metagenomics assembly of the Iron sulfur acid spring bacterial and archeal communities from Banff, Canada, to study Microbial Dark Matter (Phase II) - Paint Pots PPM 11 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365563.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004945	EMG produced TPA metagenomics assembly of the High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-1-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365931.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004944	EMG produced TPA metagenomics assembly of the Ionic liquid and high solid enriched microbial communities from the Joint BioEnergy Institute, USA - AR20-6-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366885.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004943	EMG produced TPA metagenomics assembly of the Ionic liquid and high solid enriched microbial communities from the Joint BioEnergy Institute, USA - AR20-3-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366882.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004942	EMG produced TPA metagenomics assembly of the Ionic liquid and high solid enriched microbial communities from the Joint BioEnergy Institute, USA - AR20-4-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366883.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004941	EMG produced TPA metagenomics assembly of the Ionic liquid and high solid enriched microbial communities from the Joint BioEnergy Institute, USA - AR20-2-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366881.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004940	EMG produced TPA metagenomics assembly of the Sewage sludge biodrying material Metagenome (sludge metagenome) data set.	The sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA360876.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004939	EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R1 time_0 SIP DNA metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340518.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004938	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC071_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340772.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004937	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_STIC12_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340501.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004936	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC083_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340783.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004935	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC125_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340771.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004934	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_STIC08_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340499.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004933	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNMR2_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340765.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004932	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC045_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340786.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004931	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNAS2_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340506.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004930	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Hong Kong - AD_UKC107_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340746.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004929	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC052_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340502.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004928	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC032_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340789.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004927	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC030_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340788.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004926	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Hong Kong - AD_UKC117_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340743.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004925	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNHG3_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340761.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004924	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNHG1_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340759.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004923	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNHG2_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340760.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004922	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNAS3_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340507.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004921	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Hong Kong - AD_UKC105_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340745.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004920	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNTR3_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340757.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004919	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNMR1_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340764.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004918	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNMR3_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340766.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004917	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_STIC10_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340500.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004916	EMG produced TPA metagenomics assembly of the Feedstock adapted compost microbial communities from Newby Island compost facility, Milpitas, CA, USA - Passage 4_IL metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA337762.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00004915	EMG produced TPA metagenomics assembly of the Feedstock adapted compost microbial communities from Newby Island compost facility, Milpitas, CA, USA - Passage 4_SG metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA337761.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00004914	EMG produced TPA metagenomics assembly of the AK-R09 Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA261473.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004913	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from China - AD_SCU001_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340751.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004912	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC085_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340784.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004911	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNAS1_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340505.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004910	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC073_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340773.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004909	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC057_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340497.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004908	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC087_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340785.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004907	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNHW1_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340762.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004906	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC055_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340496.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00004905	EMG produced TPA metagenomics assembly of the Thermal compost microbial communities from rain forest in Puerto Rico metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA337811.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00004904	EMG produced TPA metagenomics assembly of the ZCTH02 compost metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA324718.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00004903	EMG produced TPA metagenomics assembly of the L2-AK-MG Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA261476.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00004902	EMG produced TPA metagenomics assembly of the H2-AK-MG Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA261477.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00004901	EMG produced TPA metagenomics assembly of the H1-AK-MG Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA261475.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00004900	EMG produced TPA metagenomics assembly of the AK-R08 Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA261472.  This project includes samples from the following biomes: Engineered, Wastewater, Industrial wastewater.	root:Engineered:Wastewater:Industrial wastewater
MGYS00004899	EMG produced TPA metagenomics assembly of the AK-R07 Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA261471.  This project includes samples from the following biomes: Engineered, Wastewater, Industrial wastewater.	root:Engineered:Wastewater:Industrial wastewater
MGYS00004898	EMG produced TPA metagenomics assembly of the AK-R06 Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA261470.  This project includes samples from the following biomes: Engineered, Wastewater, Industrial wastewater.	root:Engineered:Wastewater:Industrial wastewater
MGYS00004897	EMG produced TPA metagenomics assembly of the AK-MG-013 Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA261481.  This project includes samples from the following biomes: Engineered, Wastewater, Industrial wastewater.	root:Engineered:Wastewater:Industrial wastewater
MGYS00004896	EMG produced TPA metagenomics assembly of the AK-MG-012 Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA261480.  This project includes samples from the following biomes: Engineered, Wastewater, Industrial wastewater.	root:Engineered:Wastewater:Industrial wastewater
MGYS00004895	EMG produced TPA metagenomics assembly of the L1-AK-MG Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA261478.  This project includes samples from the following biomes: Engineered, Wastewater.	root:Engineered:Wastewater
MGYS00004894	EMG produced TPA metagenomics assembly of the Anaerobic thermophilic cellulolytic sludge Metagenome (bioreactor sludge metagenome) data set.	The bioreactor sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA171369.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004893	EMG produced TPA metagenomics assembly of the Metagenome of Two novel Accumulibacter clades (bioreactor sludge metagenome) data set.	The bioreactor sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA81811.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004892	EMG produced TPA metagenomics assembly of the Marine sediment microbial community from Union City, CA, USA - Pond 1C Sediment 1 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366574.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lotic, Sediment.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004891	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_120524 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365023.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Pelagic.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00004890	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_120503 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365022.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Pelagic.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00004889	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110407 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365008.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Pelagic.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00004888	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110414 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365009.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Pelagic.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00004886	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1551A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367303.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary, Sediment.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004885	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic Ocean, analyzing organic carbon cycling - Bottom_A/KNORR_S2/LV metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365943.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004884	EMG produced TPA metagenomics assembly of the Hot spring sediment microbial communities from Zodletone spring, Oklahoma to study Microbial Dark Matter (Phase II) - Zodletone Spring source 0.5m metaG metagenome (hot springs metagenome) data set.	The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364989.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00004883	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1549B-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367298.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary, Sediment.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00004882	EMG produced TPA metagenomics assembly of the landfill metagenome Riverton City dump (landfill metagenome) data set.	The landfill metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA475763.  This project includes samples from the following biomes: Engineered, Solid waste, Landfill.	root:Engineered:Solid waste:Landfill
MGYS00004881	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110321 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365004.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Pelagic.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00004880	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1552A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367305.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00004879	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - C0912_C27A4_35 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330318.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004878	EMG produced TPA metagenomics assembly of the Sediment microbial communities from Great Boiling Springs, Gerlach, Nevada, United States - GBS 60_MetaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA442909.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lentic, Sediment.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004877	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWA TP1 #1 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441393.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004876	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWA TP1 #3 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441395.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Coastal
MGYS00004875	EMG produced TPA metagenomics assembly of the Marine sediment microbial community from Union City, CA, USA - Pond 2C Sediment 2 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366577.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004874	EMG produced TPA metagenomics assembly of the Marine sediment microbial community from La Parguera, Puerto Rico - PR Tt Sediment 3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366477.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004873	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110516 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365015.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004872	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110509 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365013.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004871	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110506 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365012.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004870	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110421 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365010.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004869	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110328 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365005.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004868	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_100430 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365002.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004867	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_100423 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365001.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004866	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_100420 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365000.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004865	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_100330 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367463.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004864	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_100413 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367464.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004862	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary, USA - metaG S.757 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375310.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00004860	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S23_td_Bottom_ad_3770_LV_A metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375515.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004859	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S23_td_NADW_ad_2500m_LV_B metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375514.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004858	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S15_td_NADW_ad_2500m_LV_A metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375456.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004857	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S15_td_O2min_ad_340m_LV metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375454.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004856	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S15_td_DCM_ad_63m_LV_B metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375453.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004855	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S7_td_NADW_ad_2505m_LV_A metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375450.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004854	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S7_td_Bottom_ad_4513_LV_A metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375451.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004853	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1563A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365264.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00004852	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1558A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365256.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00004851	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1561A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365260.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00004850	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1556A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365250.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00004849	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - CAN11_18_M0_10 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366971.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004848	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - CAN11_17_M020 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366970.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004847	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - CAN11_08_M0_20 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366969.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004846	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - CAN11_04_M0_20 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366968.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004845	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in the Saanich Inlet - ESP_161SG_22_DNA metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365966.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004844	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in the Saanich Inlet - ESP_116LU_22_DNA metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365962.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004843	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in the Saanich Inlet - ESP_105LU_22_DNA metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365960.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004842	EMG produced TPA metagenomics assembly of the Lake sediment bacterial and archeal communities from Gulf of Boni, Indonesia to study Microbial Dark Matter (Phase II) - ?I19B2 metaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364777.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lentic, Sediment.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004841	EMG produced TPA metagenomics assembly of the Lake sediment bacterial and archeal communities from Gulf of Boni, Indonesia to study Microbial Dark Matter (Phase II) - ?I18A1 metaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364776.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lentic, Sediment.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004840	EMG produced TPA metagenomics assembly of the Hot spring microbial communities from Elkhorn Slough, Monterey Bay, USA - CD6A metagenome (hypersaline lake metagenome) data set.	The hypersaline lake metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336658.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00004839	EMG produced TPA metagenomics assembly of the Marine sediment microbial community from Union City, CA, USA - Pond 1C Sediment 3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336785.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Pond, Sediment.	root:Environmental:Aquatic:Freshwater:Pond:Sediment
MGYS00004838	EMG produced TPA metagenomics assembly of the Marine microbial community from Union City, CA, USA - Pond 2C Liquid 2 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336786.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Pond.	root:Environmental:Aquatic:Freshwater:Pond
MGYS00004837	EMG produced TPA metagenomics assembly of the Marine microbial community from Union City, CA, USA - Pond 2C Liquid 3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336787.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Pond.	root:Environmental:Aquatic:Freshwater:Pond
MGYS00004836	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - C0912_C27A4_80 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330315.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00004835	EMG produced TPA metagenomics assembly of the Cellulose adapted compost microbial communities from Newby Island Compost Facility, Milpitas, CA, USA - Passage2 60A metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366683.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00004834	EMG produced TPA metagenomics assembly of the Agave microbial communities from Guanajuato, Mexico -  Mg.Sf.rz (plant metagenome) data set.	The plant metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340600.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00004828	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_138 metaG metagenome (plant metagenome) data set.	The plant metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA444460.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00004827	EMG produced TPA metagenomics assembly of the Rhizosphere microbial communities from Sorghum bicolor, Mead, Nebraska, USA - 072115-104_1 MetaG metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406787.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004826	EMG produced TPA metagenomics assembly of the Rhizosphere microbial communities from Sorghum bicolor, Mead, Nebraska, USA - 072115-103_1 MetaG metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406786.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004825	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.10.yng.090610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406165.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004824	EMG produced TPA metagenomics assembly of the Mouse cecum microbial communities from Vienna, Austria - Inoculum for glucosamine and mucus D2O microcosms metagenome (mouse gut metagenome) data set.	The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375352.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Large intestine, Cecum.	root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
MGYS00004823	EMG produced TPA metagenomics assembly of the Mouse cecum microbial communities from Vienna, Austria - Glucosamine amended microcosms incubated with D2O metagenome (mouse gut metagenome) data set.	The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375353.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Large intestine, Cecum.	root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
MGYS00004822	EMG produced TPA metagenomics assembly of the Metagenome analysis of fecal microbiota from mouse which was promoted longevity, spatial learning and memory (mouse gut metagenome) data set.	The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB1459.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00004793	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Cvi.4.yng.030610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406169.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004792	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Oy.3.yng.090410 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406171.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004791	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Oy.2.yng.040610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406173.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004790	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Cvi.7.yng.070610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406168.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004789	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Cvi.2.yng.030610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406167.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004788	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.7.yng.070610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406164.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004787	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Oy.9.old.080610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406154.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004786	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Oy.3.old.270510 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406153.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004785	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Oy.7.old.040610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406151.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004784	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Oy.6.old.040610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406150.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004783	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Oy.5.old.040610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406149.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004782	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Cvi.4.old.130510 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406147.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004781	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.9.old.080610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406142.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004780	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.2.old.270510 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406141.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004779	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Cvi.2.old.240510 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406145.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004778	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.4.old.080610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406140.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004777	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.5.old.080610_R metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406139.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004776	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - RS_199 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365239.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004775	EMG produced TPA metagenomics assembly of the Metagenome analysis of fecal microbiota from mouse which was promoted longevity, spatial learning and memory (mouse gut metagenome) data set.	The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB1462.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00004774	EMG produced TPA metagenomics assembly of the Biogas fermentation microbial communities from Germany - Plant 1 DNA1 metagenome (biogas fermenter metagenome) data set.	The biogas fermenter metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA311382.  This project includes samples from the following biomes: Engineered, Biogas plant, Wet fermentation.	root:Engineered:Biogas plant:Wet fermentation
MGYS00004773	EMG produced TPA metagenomics assembly of the Oil polluted marine microbial communities from Coal Oil Point, Santa Barbara, California, USA - Sample 3 Metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA249643.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Oil-contaminated.	root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
MGYS00004772	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Ebb tide ETM metaG S.759 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365270.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00004771	EMG produced TPA metagenomics assembly of the Biogas fermentation microbial communities from Germany - Plant 2 DNA1 metagenome (biogas fermenter metagenome) data set.	The biogas fermenter metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA311380.  This project includes samples from the following biomes: Engineered, Biogas plant, Wet fermentation.	root:Engineered:Biogas plant:Wet fermentation
MGYS00004770	EMG produced TPA metagenomics assembly of the Metagenome analysis of fecal microbiota from mouse which was promoted longevity, spatial learning and memory (mouse gut metagenome) data set.	The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB1461.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00004769	EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R2_B C12 SIP DNA metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340517.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004768	EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R1_A C12 SIP DNA metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340512.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004767	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Hong Kong - AD_UKC115_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340750.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004766	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNNA7_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340768.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004765	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC075_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340774.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00004764	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.4.yng.040610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406163.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004763	EMG produced TPA metagenomics assembly of the Metagenome analysis of fecal microbiota from mouse which was promoted longevity, spatial learning and memory (mouse gut metagenome) data set.	The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB1464.  This project includes samples from the following biomes: Host-associated, Mammals, Respiratory system.	root:Host-associated:Mammals:Respiratory system
MGYS00004758	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.2.yng.030610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406161.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004757	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.3.yng.040610 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406162.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004756	EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Cvi.2.old.130510 metagenome (rhizosphere metagenome) data set.	The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406144.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.	root:Host-associated:Plants:Rhizosphere
MGYS00004755	EMG produced TPA metagenomics assembly of the Mouse cecum microbial communities from Vienna, Austria - Mucus amended microcosms incubated with D2O metagenome (mouse gut metagenome) data set.	The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375354.  This project includes samples from the following biomes: Host-associated, Mammals, Respiratory system.	root:Host-associated:Mammals:Respiratory system
MGYS00004754	EMG produced TPA metagenomics assembly of the Metagenome analysis of fecal microbiota from mouse which was promoted longevity, spatial learning and memory (mouse gut metagenome) data set.	The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB1463.  This project includes samples from the following biomes: Host-associated, Mammals, Respiratory system.	root:Host-associated:Mammals:Respiratory system
MGYS00004753	EMG produced TPA metagenomics assembly of the Metagenome analysis of fecal microbiota from mouse which was promoted longevity, spatial learning and memory (mouse gut metagenome) data set.	The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB1460.  This project includes samples from the following biomes: Host-associated, Mammals, Respiratory system.	root:Host-associated:Mammals:Respiratory system
MGYS00004752	EMG produced TPA metagenomics assembly of the Ionic liquid and high solid enriched microbial communities from the Joint BioEnergy Institute, USA - AR20-5-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366884.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004748	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - RS_92 metaG metagenome (plant metagenome) data set.	The plant metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA444456.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00004747	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - RS_213 metaG metagenome (plant metagenome) data set.	The plant metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA444455.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00004746	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_167 metaG metagenome (plant metagenome) data set.	The plant metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA444459.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00004745	EMG produced TPA metagenomics assembly of the Ionic liquid and high solid enriched microbial communities from the Joint BioEnergy Institute, USA - AR20-1-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366880.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004744	EMG produced TPA metagenomics assembly of the Biogas fermentation microbial communities from Germany - Plant 4 DNA1 metagenome (biogas fermenter metagenome) data set.	The biogas fermenter metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA311376.  This project includes samples from the following biomes: Engineered, Biogas plant.	root:Engineered:Biogas plant
MGYS00004743	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1550B-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367302.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00004742	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1550B-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367300.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00004741	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1370A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367270.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00004740	EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R1_A C13 SIP DNA metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340510.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00004738	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, USA - P5_0mM MetaG metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406749.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00004737	EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R2_B C13 SIP DNA metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340515.  This project includes samples from the following biomes: Engineered, Biogas plant.	root:Engineered:Biogas plant
MGYS00004736	EMG produced TPA metagenomics assembly of the Analysis of Microbial Diversity of Kombucha () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA382626.  This project includes samples from the following biomes: Engineered, Food production, Fermented beverages.	root:Engineered:Food production:Fermented beverages
MGYS00004735	EMG produced TPA metagenomics assembly of the Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Dewar Creek DC2 2012 metaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375326.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Sediment.	root:Environmental:Aquatic:Thermal springs:Sediment
MGYS00004732	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1449B-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367276.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00004728	Inflammation, Antibiotics, and Diet as Concurrent Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease	Dysbiosis in the human intestines, an alteration in the normal composition of the microbiota, characterizes a wide spectrum of diseases, such as infections, irritable bowel syndrome, Crohn's disease. Dysbiosis has been studied extensively but typically characterized cross-sectionally and as alterations in bacterial taxonomic proportions.  The longitudinal contributions of diet, antibiotic use, and inflammation on the evolution of dysbiosis during therapy for Crohn's disease have not been well characterized. Here we used shot-gun metagenomic sequencing of fecal samples collected from a longitudinal prospective cohort of pediatric Crohn's disease subjects to analyze the representation and gene content of all types of organisms present, including bacteria, fungi, archaea and viruses.  Patients initiated treated with either antibodies directed against tumor necrosis factor alpha or enteral nutrition per the treating physician.  Multivariate analysis showed that microbiome composition was associated with three environmental stressors--intestinal inflammation, antibiotic use, and diet.  Bacterial gene signatures suggested that communities in Crohn's samples were responding to oxidative stress. Antibiotic use was associated with a more dysbiotic composition of the bacterial microbiota as well as a distinctive increase in fungal organisms and human DNA content. In contrast, the abundance of tailed phage and archaea was similar in feces of children with Crohn's disease and healthy controls.  Composition of the bacterial and fungal communities were highly correlated. Dysbiosis in bacterial and fungal communities was reduced in patients with reduction of intestinal inflammation by either therapy. Diet had an independent and rapid effect on gut microbiota composition within one week of initiation. Evidently dysbiosis characteristic of Crohn's disease results in part from inflammation and antibiotic use, and involves correlated changes in bacterial and eukaryotic community members.  Notably, the three stressors were independently associated with different bacteria and different gene pathways, reflecting concurrent disruption of normal homeostasis by multiple mechanisms. Thus, while dysbiosis in general is common to multiple disease states, the nature of the dysbiosis is unique to the environmental stressor.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00004726	WINOGRADSKY PLASTIC LOWER LEVEL	The Winogradsky column is a simple device for culturing a large diversity of microorganisms.	root:Engineered:Lab enrichment:Defined media
MGYS00004725	WINOGRADSKY PLASTIC UPPER LEVEL	The Winogradsky column is a simple device for culturing a large diversity of microorganisms.	root:Engineered:Lab enrichment:Defined media
MGYS00004724	WINOGRADSKY MONOCROTOPHOS LOWER LEVEL	The Winogradsky column is a simple device for culturing a large diversity of microorganisms.	root:Engineered:Lab enrichment:Defined media
MGYS00004723	WINOGRADSKY MONOCROTOPHOS UPPER LEVEL	The Winogradsky column is a simple device for culturing a large diversity of microorganisms.	root:Engineered:Lab enrichment:Defined media
MGYS00004722	WINOGRADSKY QUINALPHOS LOWER LEVEL	The Winogradsky column is a simple device for culturing a large diversity of microorganisms.	root:Engineered:Lab enrichment:Defined media
MGYS00004721	WINOGRADSKY QUINALPHOS UPPER LEVEL	The Winogradsky column is a simple device for culturing a large diversity of microorganisms.	root:Engineered:Lab enrichment:Defined media
MGYS00004720	WINOGRADSKY CONTROL LOWER LEVEL	The Winogradsky column is a simple device for culturing a large diversity of microorganisms.	root:Engineered:Lab enrichment:Defined media
MGYS00004719	WINOGRADSKY CONTROL UPPER LEVEL	The Winogradsky column is a simple device for culturing a large diversity of microorganisms.	root:Engineered:Lab enrichment:Defined media
MGYS00004718	METAGENOMIC STUDY OF WAF	The Indian wild ass (Equus hemionus khur) also called the Ghudkhur, Khur or Indian onager in the local Gujarati language, is a subspecies of the onager native to Southern Asia. It is currently listed as Near Threatened by IUCN.	root:Engineered:Lab enrichment:Defined media
MGYS00004717	SHEEP FAECAL METAGENOME	"Sheep wool has a distinctive ""dry"" texture, a little like linen, typical of wool from this area.  Because the wool yarn is hand spun, the cloth has a wonderfully irregular texture, full of movement."	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00004716	METAGENOME ANALYSIS OF SABARMATI RIVER	The Sabarmati river is one of the major west-flowing rivers in India. It originates in the Aravalli Range of the Udaipur District of Rajasthan and meets the Gulf of Khambhat of Arabian Sea.	root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems
MGYS00004715	KHAJOD WASTE WATER	"Wastewater is any water that has been affected by human use. Wastewater is ""used water from any combination of domestic, industrial, commercial or agricultural activities, surface runoff or stormwater, and any sewer inflow or sewer infiltration"". Therefore, wastewater is a byproduct of domestic, industrial, commercial or agricultural activities. The characteristics of wastewater vary depending on the source. Types of wastewater include: domestic wastewater from households, municipal wastewater from communities (also called sewage) or industrial wastewater from industrial activities. Wastewater can contain physical, chemical and biological pollutants."	root:Engineered:Wastewater
MGYS00004714	COW DUNG ANALYSIS	GIRCOW DUNG HOST ORGANISMS ANALYSIS	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00004712	(1) Personalized microbiome and host features resist gut mucosal colonization by empiric probiotics; (2) Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT	Abstract (1):Empiric probiotics are commonly consumed in healthy individuals as means of life quality improvement and disease prevention. However, evidence of probiotic gut mucosal colonization efficacy remains sparse and controversial. We metagenomically characterized the murine and human mucosal-associated gastrointestinal microbiome and found it to only partially correlate with stool microbiome. A sequential invasive multi-omics measurement at baseline and during consumption of an 11-strain probiotic combination or placebo, demonstrated that probiotics remain viable upon gastrointestinal passage. In colonized, but not germ-free mice, probiotics encountered a marked mucosal colonization resistance. In contrast, humans featured a person-, region- and microbial-specific mucosal colonization patterns, hallmarked by differential baseline host and microbiome features, but indistinguishable by probiotics presence in stool. Consequently, probiotics induced a transient, highly-individualized impact on mucosal community structure and gut transcriptome. Collectively, empiric probiotics supplementation may be limited in universally and persistently impacting the gut mucosa, meriting development of new personalized probiotic approaches.Abstract (2):Probiotics are widely prescribed for prevention of antibiotics-associated dysbiosis and related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut mucosal host-microbiome niche remains elusive. We invasively examined the effects of multi-strain probiotics or autologous fecal microbiome transplantation (aFMT) on post-antibiotic reconstitution of the murine and human mucosal microbiome niche. Contrary to homeostasis, antibiotic perturbation enhanced probiotics colonization in the human mucosa, but only mildly improved colonization in mice. Compared to spontaneous recovery, probiotics induced a markedly delayed and persistently-incomplete indigenous stool/mucosal microbiome reconstitution and gut transcriptome recovery to steady-state configuration, while aFMT induced a rapid and near-complete recovery within days of administration. In-vitro, Lactobacillus-secreted soluble factors contributed to probiotics-induced microbiome inhibition. Collectively, potential post-antibiotic probiotic benefits may be offset by a compromised microbiome and host recovery, highlighting a need of developing aFMT or personalized probiotic approaches achieving mucosal protection, without compromising microbiome recolonization in the antibiotics-perturbed host.	root:Host-associated:Human:Digestive system
MGYS00004709	Structure and function of picoplankton and virus communities along zonal gradients in the South Pacific Ocean	Picoplankton (0.2-2.7 µm fraction) and virus (<0.22 µm fraction) samples were obtained on the BiG-RAPA (Biogeochemical Gradients Role in Arranging Planktonic Assemblages) expedition in the late austral spring of 2010. Additional samples obtained during this expedition include whole community biomass (>0.22 µm fraction) samples that profile a deep (150 m) subsurface chlorophyll maximum in the South Pacific Gyre. High throughput, short read, shotgun sequencing was used to produce metagenomic data from the extracted DNA of these samples. These data enable the assessment of how picoplankton and viral populations are structured along strong physical and chemical gradients on a zonal transect from the upwelling along the western coast of South America to the oligotrophic gyre in the South Pacific.	root:Environmental:Aquatic:Marine
MGYS00004708	Strain-Level Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis	Cystic fibrosis (CF) is a life-threatening genetic disorder accompanied by chronic lung infections and respiratory complications that arise from the accumulation of viscous mucus in the airways. In the clinic, cultures of microbes isolated from the coughed-up lung sputum are used to decide on the CF management strategy. The approach, however, frequently misses non-typical microbes and provides limited strain-level resolution. In the study, we applied an unbiased sequencing approach to lung sputum samples in order to gain a more complete picture of the lung microbiome. We explored changes in the lung microbiome composition over time, particularly during exacerbations and antibiotic treatments. Moreover, we distinguished between evolution of internal strains and introduction of external strains from the environment. To do this, we followed four CF patients displaying extreme clinical phenotypes over the course of two years. During each exacerbation or routine clinical visit, the lung sputum from these patients was taken for shotgun sequencing. Reads not mapping to the host were subjected to assembly, taxonomic profiling, strain typing, and variant analysis. Sequencing revealed the presence of several microbes missed by culture, particularly anaerobes. It allowed us to identify dominant strains of abundant microbes, and to correct mistakes in taxonomic assignment from culture. Finally, after analysing variation on the genome level, we describe multiple events such as a battle for dominance between multiple strains of Pseudomonas aeruginosa in the same patient. This study provides a first insight into the advantages of assessing the complete lung microbiome over time.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00004707	Microbiome of two predominant seagrass species of the Kenyan coast, Enhalus acoroides and Thalassodendron ciliatum	Background. Metagenomics studies have reported on the complexity of microbiomes associated with seagrass and can provide critical insights into the sustainable use and conservation of seagrasses. Recent conservation activities in Kenya focused mainly on coral reefs and mangrove forests with little direct action taken to conserve seagrass meadows. Pollution, over-exploitation of marine resources and minimal efforts towards enforcement of conservation laws of marine environments, have caused degradation and defoliation of seagrass habitats. Little is known about the microbes associated with seagrass species in Kenya and this study aimed to characterize the genetic diversity of the microbiomes of two prominent seagrass species, Enhalus acoroides and T. ciliatum, which is the most commonly occurring species.Methods. Replicate microbiome samples were collected from leaves, roots, sediment and water columns associated with two seagrass species from two sites on the Kenyan coast. The microbial communities of the samples were characterized and compared using 16S ribosomal RNA gene PCR and sequencing. Microbiome features including diversity and taxonomic composition were used to compare within and between sample types and sites.Results. Leaf samples from both E. acoroides and T. ciliatum had significantly different microbial communities comparted to root and sediment samples, revealing a diversity gradient with lowest diversity in water samples and highest in sediment. There were no significant variation in seagrass microbial composition associated with leaf and rhizosphere microbiomes of either E. acoroides or T. ciliatum. However, we did see a difference between water samples associated with each seagrass species.Discussion.This study of the microbial microbiomes associated with the sediments, roots, leaves and surrounding water of E. acoroides and T. ciliatum, included a limited number of samples from a small geographic area, providing a valuable first assessment of the microbial diversity of seagrass beds on the Kenyan coast. We found no significant differences between the plant-associated bacterial communities of the two-seagrass species investigated. Significant differences however, were observed amongst leaf-, root-, sediment- and water-associated bacterial communities. This work will contribute to understanding the dynamic environment of seagrass beds and will contribute to helping conserving and re-establishing seagrass beds degraded by due to anthropogenic activities.	root:Host-associated:Plants
MGYS00004706	Microorganisms related to Ethanol fermentation	The aim of this study is to identify, by metabarcoding approaches, the microorganisms of a ethanol fermentation industry.	root:Engineered:Industrial production
MGYS00004705	Metagenomic Analysis of the Marine Sponge, Cinachyrella keukenthali: Insights into an Emerging Model Sponge	Cinachyrella keukenthali is quickly emerging as a model sponge. Its small size makes it ideal for laboratory sized aquaria and long-term experiments. It is also on the Global Invertebrate Genome Alliance's priority list for genome sequencing. Other experiments have also included a focused amplicon sequencing experiment wherein, two subtypes of Cinachyrella keukenthali may be present in the environment based on microbiome results and some of the ongoing efforts of the global sponge microbiome project. What is poorly understood is the functional potential of the sponge microbiota. We analysed two metagenomes of C. keukenthali to determine non-PCR biased taxonomic makeup, functional potential, metabonomic analysis, and an early look into the microeukaryotes that might be present in the sponge	root:Host-associated:Porifera
MGYS00004687	Microbial diversity in four Mediterranean irciniid sponges	The examined host species, all collected from Crete, Greece, are Ircinia fasciculata, I. oros, I. variabilis, and Sarcotragus spinosulus. In this study we have tried to answer some specific questions such as: a) Is there a host species specific footprint on microbial communities, b) if there is an East versus West Mediterranean footprint, c) if there are similarities or differences on the composition of Ircinia species and non-Ircinia species (species specificity, sponge specificity) and finally whether there is a tissue specific patterning effect of the symbiotic microbial communities of sponges under study	root:Environmental:Aquatic:Marine:Coastal
MGYS00004680	Bacterial ecology of sponges from Irish Waters	The bacterial communities associated with the marine sponges Raspailia ramosa and Stelligera stuposa, collected from Irish Waters, were examined through 454 sequencing and analysis of the V1-V3 region of the 16S genes amplified from sponge metagenomic DNA	root:Environmental:Aquatic:Marine
MGYS00004679	A metagenetic approach for revealing community structure of marine planktonic copepods using Illumina MiSeq	Metagenetic approach is rapidly developing method for revealing community structure from bulk environmental samples. Marine planktonic copepods are diverse and abundant groups in the marine pelagic environments, and the metagenetic method using Roche 454 was constructed for copepods. However, Illumina MiSeq, which can produce more than ten times as many sequence reads as Roche 454, has been getting common sequencing platform. Here, we re-evaluated metagenetic method approach for revealing community structure of marine planktonic copepods using Illumina MiSeq. Because Illumina MiSeq can produce much more sequence reads, the developed method would be helpful for monitoring copepod community and dietary study in the future.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004670	Bacteria of the genus Endozoicomonas dominate the microbial communities of the Mediterranean gorgonian soft coral Eunicella cavolini	Forming dense beds that provide the structural basis of a distinct ecosystem, the gorgonian Eunicella cavolini (Octocorallia) is an important species in the Mediterranean Sea. Despite the importance and prevalence of this temperate gorgonian, little is known about its microbial assemblage although bacteria are well known to be important to hard and soft coral functioning. Here, we used massively parallel pyrosequencing of 16S rRNA genes to determine the composition and relative abundances of bacteria associated with E. cavolini collected from different depths at a site on the French Mediterranean coast. We found that whereas the bacterial assemblages of E. cavolini were distinct and less diverse than those of the surrounding water column, the water depth did not affect the bacterial assemblages of this gorgonian. Our data show that E. cavolini's microbiome contains only a few shared species and that it is highly dominated by bacteria from the genus Endozoicomonas, a gamma-Proteobacteria that is frequently found to associate with marine invertebrates.	root:Environmental:Aquatic:Marine
MGYS00004663	Bacterial communities in sediments of a boreal stream	Here we study the  bacterial communities in sediments of a boreal stream. Bacterial communities were studied by NGS (454 pyroseq) of bacterial 16S rRNA, nirK, nirS and nosZ genes.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004634	Fe3+ and Mn4+ - induced changes in microbial communities of boreal lake sediments	Here we study the structure of bacterial and archaeal communities in sediments of two boreal lakes (littoral site in one lake and profundal site in another lake) . We specifically focused on community changes induced by increased availability of Fe3+ and Mn4+, which were studied by laboratory incubation of sediment samples collected from the profundal site. Microbial communities were studied by NGS (Ion Torrent) of bacterial and archaeal 16S rRNA genes as well as archaeal mcrA genes and mcrA-transcripts.	root:Environmental:Aquatic:Sediment
MGYS00004571	PCE/TCE dechlorinating microbial community and dehalogenase genes from Wonju Stream, South Korea	Groundwater at an industrial complex in Wonju remains contaminated with TCE despite several attempts at remediation over the last 15 years. Since the microbial dechlorination intermediates cis-DCE and VC were detected in the down-stream groundwater, we investigated whether the indigenous microbial communities could convert chloroethenes to ethene making bioremediation potentially feasible. Pyrosequencing of the 16S rRNA genes showed that Geobacter, Desulfuromonas, and Dehalococcoides populations grew significantly during the time PCE and TCE were converted to ethene. Most 16S rRNA sequences of Dehalococcoides spp. were phylogenetically close to known Dehalococcoides sp. strains, however about 10% of sequences were quite distant from the previously characterized Dehalococcoides sp. (97% or less sequence identity). Bellininea and Longilinea populations, which belong to Chloroflexi, also grew during the dechlorination phase.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00004569	Marine sediment metagenome ICM_CRS	Diversity and structure of the microbial community in tropical coral reef sediments.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004563	Deep sequencing of a DMSP-degrading gene (dmdA) in a coastal bacterioplankton community	Ten primer pairs targeting environmental clades of the dimethylsulfoniopropionate (DMSP) demethylase protein, DmdA, were designed using an iterative bioinformatic approach that took advantage of >1700 dmdA sequences captured in marine metagenomic datasets.  Using the bioinformatically-optimized primer pairs, dmdA genes were amplified from free-living coastal bacterioplankton samples and sequenced using 454 technology.  An average of 6,400 amplicons per primer pair represented almost 800 clusters of environmental dmdA sequences, with clusters defined conservatively at >90% nucleotide sequence identity (~95% protein identity).  Systematic comparisons of primer performance showed that degenerate and inosine-based primers did not perform better than specific primer sets in retrieving dmdA diversity, and sometimes captured a lower diversity of sequences from the same DNA sample.  The specific primer sets were used to compare dmdA diversity in free-living versus particle-associated bacteria in southeastern U.S. coastal waters.  Hundreds of different dmdA clusters were found in both size fractions, with Roseobacter-like and SAR11-like sequences dominating both. The free-living fraction had a higher diversity of dmdA clusters overall, though clusters retrieved by a given primer set were largely shared (52-88%) across the two size fractions, and most sequences were affiliated with these shared clusters (~90%). Despite evidence from 16S rRNA-based taxonomic surveys that free-living bacterioplankton are a considerably less diverse subset of particle-associated bacteria at this site, this seems not to be the case for a widespread bacterial gene mediating sulfur transformations.	root:Environmental:Aquatic:Marine
MGYS00004562	Methanogens and iron-reducing bacteria are major contributors to mercury methylation in boreal lake sediments	Methylmercury is a potent human neurotoxin easily biomagnified in aquatic food webs. Anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, but the diversity of microbial mercury methylating communities in the environment remains largely unexplored. The diversity of mercury methylating microbial communities in boreal lake sediments, encompassing a wide range of mercury methylation rates, was characterized using barcoded amplification and high throughput sequencing of 16S rRNA and hgcA genes. Previously, most studies in aquatic ecosystems have implicated sulphate-reducing bacteria as the main mercury methylators. Here we demonstrate that Methanomicrobiales contribute significantly to the hgcA gene pool in boreal lake sediments. Experimental mercury isotope tracer incubations confirmed that, while sulphate-reducers contribute to mercury methylation, methanogens and iron reducers are also quantitatively important for the process. Our results change the way we perceive the local and global diversity of mercury methylating microbial communities in boreal lake sediments and call for further studies on the environmental factors regulating mercury methylation.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004557	Intergenerational Lizard Lounges do not Explain Variation in the Gut Microbiomes of Green Iguanas	These samples represent the hindgut swabbings of 76 Green Iguanas (66 hatchlings, three subadults, seven adults), with hatchlings from nine sites (Gamboa, Panama and eight sites on or around Barro Colorado Island, Panama). We included an equal number of hatchlings from each site when possible. Hatchling social behavior (i.e., size of group, proximity to others) was observed haphazardly for individuals for about 60 days post-emergence over two years. (Adults and subadults were sampled and included whenever possible.) We primarily included samples taken about 4-6 weeks into the season for direct comparisons across sites and social levels. We have multiple samples (mean 3 per lizard) for 12 hatchlings spanning several days to several weeks between samples.	root:Host-associated:Reptile
MGYS00004553	Diamante Lake viral metagenome	"Diamante Lake, located inside the Galan Volcano crater and placed at 4589m above sea level (coordinates: 26°00'51.04""S , 67°01'46.42""O), presents multiple extreme conditions that include: High UV radiation, salinity and arsenic, low oxygen pressure and a hydrothermal vent input. Red biofilm samples (mixed with sediments) from Diamante Lake were resuspended in PBS, cleared by centrifugation, and viral particles were purified using a CsCl gradient and ultracentrifugation. The total DNA of the purified viral fraction was then extracted using a Roche Viral DNA purification kit. Sequencing libraries were prepared using the Nextera library preparation kit from Promega and sequenced at 2x250bp using a Illumina MiSeq machine."	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00004552	Severino orchard metagenome	The total DNA sample from Severino orchard was extracted using a MoBio Powersoil DNA Isolation Kit and sequenced at 2x250bp using a Illumina MiSeq machine, to prepare a Metagenomic Shotgun Library.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00004551	Yucra orchard metagenome	The total DNA sample from Yucra orchard was extracted using a MoBio Powersoil DNA Isolation Kit and sequenced at 2x250bp using a Illumina MiSeq machine, to prepare a Metagenomic Shotgun Library.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00004550	Metagenomics of Ojo de Campo	Water samples from Ojo de Campo Lake were sequenced and analyzed	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00004549	Metagenomics of Pozo Bravo microbial mats	Microbial mats from Pozo Bravo Lake were sequenced and analyzed	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00004548	Diamante Lake Metagenome	"Diamante Lake, located inside the Galan Volcano crater and placed at 4589m above sea level (coordinates: 26°00'51.04""S , 67°01'46.42""O), presents multiple extreme conditions that include: High UV radiation, salinity and arsenic, low oxygen pressure and a hydrothermal vent input. Total DNA from Diamante Lake Red Biofilm was extracted using a Fast Spin Kit for Soil (MP Biomedicals) and sheared by sonication with a target fragment size of ~ 400 bp. DNA fragment distribution was confirmed in a Fragment Analyzer (Advanced Analytical) and libraries were constructed using Illumina TruSeq DNA kit 2x300 bp as per manufacturer's instructions. Libraries were multiplexed and ran in a Illumina MiSeq machine."	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00004547	Metagenomics of Brava and Tebenquiche lakes microbial mats	Atacama region in Chile is one of the most arid locations in the world. Extreme conditions in the area include: high UV irradiation, hypersalinity, drastic temperature changes, and desiccation. Hypersaline lakes can be found in this environment, and therein, bacterial communities thrive in microbial mats and other structures. WGS metagenomics allows to analyze the genes in the environment and infer functional and taxonomic diversity, and also their influence in the biogeochemical setting. In the datasets from this project, two microbial mats from lakes Brava and Tebenquiche, in Atacama region in Chile, were analyzed.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Saline:Microbial mats
MGYS00004484	Methane and dissolved organic carbon fueled microbial loop supports a tropical subterranean estuary ecosystem	Here we demonstrate that a microbial loop shuttles CH4 and DOC to higher trophic levels of the anchialine food web in the Yucatan Peninsula (Mexico). Methane and DOC production and consumption within the coastal groundwater correspond with a microbial community capable of methanotrophy, heterotrophy and chemoautotrophy, based on characterization by 16S rRNA amplicon sequencing and respiratory quinone composition. This study reveals a heretofore unrecognized subterranean methane sink and contribute to our understanding of the carbon cycle and ecosystem function of karst subterranean estuaries.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00004446	Genetic potential for pentachlorophenol degradation at historically contaminated groundwater sites	Novel primers for pcpB  allowed us for the first time to investigate the genetic potential for degradation of the priority pollutant pentachlorophenol (PCP) in situ. We assessed whether pcpB is detectable at chlorophenol-polluted groundwater sediments at two sites, and if its abundance reflects differences in PCP concentration. We also sought correlations between the abundance and diversity of pcpB and sphingomonads that might indicate host specificity. pcpB was highly abundant, with copy numbers of up to 7% of bacterial 16S rRNA gene copies, and its relative abundance was linked to spatial or temporal differences in groundwater PCP concentration at two historically polluted sites, indicating ecological relevance of the pathway in situ. pcpB abundance was associated with sphingomonad abundance, but independent of sphingomonad community composition. This provides the first culture-independent support for widespread horizontal transfer of PCP degradation potential among sphingomonads in chlorophenol-polluted groundwaters.	root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
MGYS00004441	Microbial community response on waste water discharge in recipient freshwater sediments	In this study, we examined how nitrified wastewater affects the microbiology of boreal lakes sediments. Microbial community compositions were assessed with next generation sequencing of the 16S rRNA gene	root:Environmental:Aquatic:Sediment
MGYS00004335	Novel Biphenyl Oxidizing Bacteria and Dioxygenase Genes from a Korean Tidal Mudflat	Gene-targeted FLX titanium pyrosequencing integrated with 13C-stable isotope probing (SIP) revealed that tidal mudflat sediments harbor for novel aerobic biphenyl degradative bacteria and aromatic ring hydroxylating dioxygenases (ARHD). Known terrestrial biphenyl oxidizing bacteria and dioxygenase genes were rare in 13C-biphenyl enriched bacterial community. Instead, more than 80% of the detected ARHD genes are not in the public databases.	root:Environmental:Aquatic:Marine:Wetlands:Sediment
MGYS00004334	Stratification of anaerobic methanotrophs in cold-seep sediments	Methane seepages typically harbor communities of anaerobic methane oxidizers (ANME), however knowledge about fine-scale vertical variation of ANME in response to geochemical gradients is limited. Here we investigate microbial communities in sediments at two different locations at thge Nyegga field; (1) a push-core below a white microbial mat in the G11 pockmark, and (2) a Gravity-core at CNO3. Both experiments were analysed using 16S rRNA gene tag pyrosequencing and real time quantitative PCR.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004332	MiSeq 16S rRNA gene (prokaryotic 16S rRNA gene) sequences of 33 Mai Po sediments, including 18 samples from winter and 15 samples from summer	DNA from 33 Mai Po sediments have been extracted and amplified by 515F/909R primer pairs (for prokaryotic 16S rRNA gene). The prokaryotic communities of these 33 samples were obtained.	root:Environmental:Aquatic:Marine:Wetlands:Sediment
MGYS00004331	MiSeq 16S rRNA gene (archaeal 16S rRNA gene) sequences of 33 Mai Po sediments, including 18 samples from winter and 15 samples from summer	DNA from 33 Mai Po sediments have been extracted and amplified by 21f/958r & Arch347F/Arch806R primer pairs (for archaeal 16S rRNA gene). The archaeal communities of these 33 samples were obtained.	root:Environmental:Aquatic:Marine:Wetlands:Sediment
MGYS00004330	Funtonal metagenomic of salt resistance	Hypersaline environments are considered some of the most extreme habitats on earth and microorganisms have developed diverse molecular mechanisms of adaptation to withstand these conditions. The present study was aimed at identifying novel genes involved in salt resistance from the microbial communities of brines and the rhizosphere of the halophyte Arthrocnemum from the Es Trenc saltern (Mallorca, Spain). The bacterial and archaeal diversity assessed by pyrosequencing of 16S rRNA gene libraries revealed the presence of microbial communities that are typical in such environments. Metagenomic libraries were constructed with DNA from brine and rhizosphere samples, they were transferred to the osmosensitive strain Escherichia coli MKH13, and screened for salt-resistant clones. As a result, a total of eleven genes that confer salt resistance were identified, some of which encode for well known proteins previously related to osmoadaptation as a glycerol and a proton pump, whereas other genes encode for proteins not previously related to this function as RNA and DNA helicases, an endonuclease III (Nth) and hypothetical proteins of unknown function. Furthermore, four of the retrieved genes were cloned and expressed in Bacillus subtilis and interestingly, three of them exhibited also salt resistance in this bacterium, broadening the spectrum of bacterial species where these genes can operate. This is the first report of salt resistance genes recovered from different metagenomes of a hypersaline environment, which will help to further elucidate novel molecular mechanisms of salt resistance.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00004329	Cellar age related dynamics of prokaryotic community in pit muds	Microbes in pit mud (PM) play key roles in the liquor quality. We investigated prokaryotic community structure and diversity in PM samples with different cellar ages (1, 10, 25 and 50 years) using 454 pyrosequencing technique based on 16S rRNA gene. We selected 5 fermentation pits for each cellar age. Samples were collected from upper, middle and lower part locations as replicate samples for every pit.	root:Engineered:Food production:Fermented beverages
MGYS00004328	Taxonomic composition of microbial communities in coastal Arctic sediments	The taxonomic composition of microbial communities was examined in two sediment cores taken off the coast of Alaska in the Beaufort Sea in 2009.  One of the cores (PC10) had low methane concentrations while the deep depths of the other core (PC12) had high concentrations.  To examine community composition, variable regions V6-V8 of 16S rRNA genes were amplified using primers 926F and 1392R and the products were sequenced by pyrosequencing.  The analyses indicated that bacteria made up >95% of all sequences while eukaryotes contributed about 3% of the total. Less than 1% of all sequences could be assigned to archaea.  Archaea were relatively more abundant in the methane-rich core than in the methane-poor core.  Deltaproteobacteria were most abundant in the surface layer of both cores, then decrease in relative abundance as depth increased.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004327	A diverse and metabolically active microbial community persists in deep subsurface clay borehole water	The Boom Clay layer in Belgium is investigated in the context of subsurface nuclear waste storage, making use of the underground laboratory HADES. The HADES facility offers a rather unique access to a subsurface microbial community, in an environment of which all geological and geochemical characteristics are being thoroughly studied. This study presents the first elaborate description of a subsurface clay microbial community, residing in Boom Clay borehole water. Using an integrated approach of microscopy, metagenomics, activity screening and cultivation, the presence and activity of this community is disclosed. Despite the low energy environment, the microscopy and molecular analyses show a surprisingly large bacterial diversity and richness, tending to correlate positively with the organic matter content of the environment. Among different samples, a core bacterial community comprising seven bacterial phyla is defined, including both aerobic and anaerobic genera with a range of metabolic preferences. In addition, when using the appropriate media, a considerably large fraction of this community is found cultivable, active in situ and matching the metagenomic data. In conclusion, this study shows the possibility of a microbial community of relative complexity to actively persist in subsurface Boom Clay.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004326	Targeted analyses of Dehalococcoidetes (phylum Chloroflexi) diversity and community structures in marine subsurface sediments.	Bacteria of the class Dehalococcoidetes (phylum Chloroflexi) are widely distributed in the subsurface and are especially prevalent in the deep marine subsurface. Nevertheless, little is known about the specific distributions of DEH, the extent of DEH diversity and the variability of DEH sub-group distributions at different sites and depths. Therefore, this study specifically examined the distribution and diversity of DEH through depths of various marine sediment cores by 454 pyrosequencing using newly designed 16S rRNA gene targeting primers to generate amplicons for sequencing. The data reveals Dehalococcoidetes diversity is more pronounced than previously recognized, and that distributions of Dehalococcoidetes changes through depths of marine sediments, suggesting varied metabolic properties in different sub-groups within this clade.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004325	A combined massive parallel sequencing-indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities	A combined massive parallel sequencing-indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities	root:Engineered:Bioremediation
MGYS00004321	Microbial community in on-site tsunami sediment caused by the Great East Japan Earthquake	In this project, we investigated microbial communities in the tsunami sediment at Dec. 2011, Mar. 2012 and Oct. 2013 to clarify time-course change of microbial communities and compare those in the surface (0-2 mm indepth) and core (20-40 mm in depth) sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004318	Microbial community structure or iron oxyhydroxides rich mound in Satsuma Iwo-jima, Japan	Iron oxyhydroxides rich mounds are observed at the bottom of Nagahama bay where iron and silica rich thermal fluid is discharged. The microbial community structure was investigated using V4 region of 16S rRNA gene.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004250	Pelagic Sediment Metagenome	Deep sea water sludge of about 1000 m depth was collected from Andaman Sea.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004249	How much do we know about marine metazoan biodiversity? Recent disclosures using second generation sequencing.	In response to contemporary threats to biodiversity, accurate and objective methods of species or operational taxonomic unit (OTU) assessment are fundamental to our understanding of mechanistic links among ecosystem components and resilience. Second generation sequencing approaches have been especially insightful for biodiversity analyses of the microbial biosphere, but to date, such approaches have not been used to study Metazoan phyla. Here, we utilize second generation sequencing for interpreting the relative richness of multiple metazoan phyla inhabiting the marine benthos. We identify (a.) comparative and substantial levels of unrecorded richness, that refute currently accepted paradigms of phylum rank abundance, (b.) ecosystem-level community composition at fine level spatial hierarchical scales and (c.) sequences derived from putative metazoan taxa that bear little genetic resemblance to any phylum that has been sequenced previously. These findings suggest that such techniques will provide a valuable addition to the exploratory tool-box for rapidly and simultaneously documenting the identity, composition and potential function of hitherto intractable, but ecologically important, communities.	root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
MGYS00004241	Time course change of microbial community in tsunami sediment caused by the Great East Japan Earthquake	In this project, we investigated microbial communities in the tsunami sediment collected on Nov. 2012 and incubated under atmosphere in laboratory to clarify time-course change of microbial communities and compare those in the surface (0-2 mm in depth) and core (12-16 mm in depth) sediment.	root:Environmental:Aquatic:Sediment
MGYS00004239	Organic matter from melting Arctic sea ice triggers bacterioplankton activity and diversity	As Arctic multiyear ice is being replaced with first-year sea ice, a key question pertains to the cycling and fate of the increasingly dominant first-year ice carbon upon its release into the water column during melt. In this study, we experimentally tested the hypothesis that changes in sea ice dissolved organic matter (DOM) fractions affect the response of under-ice microbial communities and, as a corollary, the cycling of sea ice carbon in surface waters.Size-fractionated DOM fractions were isolated from first-year ice, producing three pools of dissolved organic carbon comprising the full DOM spectrum, large exopolymeric substances (EPS > 100 KDa molecular weight), and small EPS (< 100 KDa and > 10 KDa molecular weight). Enrichment experiments with these fractions revealed, over a 216 h period, significant and contrasting changes in prokaryotic abundance and production, substrate utilization rates, and microbial diversity between enrichments. The different DOM fractions differed in terms of molecular composition, elemental ratios and carbohydrate contribution, with the full DOM spectrum showing the highest proportion of carbohydrates and highest number of low-molecular weight unique compounds. Despite an abundance of low-molecular weight compounds in the DOM enrichment, the EPS fractions induced the strongest and fastest response of underice microbial communities, with highest growth rates and substrate utilization for the small EPS fraction. Shifts in microbial diversity were also observed over the course of the experiment, resulting in different community composition between enrichments. Notably, the EPS and DOM enrichments led to a dominance of Colwellia and Psychromonas, respectively.The results support our hypothesis, showing the fundamental role of the composition of the sea ice dissolved organic matter (DOM) pool and its dual impact, through changes in microbial diversity and substrate utilization, on organic matter cycling at the sea-ice interface. These findings have far-reaching consequences in terms of the cycling and export of sea ice associated carbon in the climatically-impacted Arctic and its role in global biogeochemical cycles.	root:Environmental:Aquatic:Marine
MGYS00004238	Microbial processes in iron-rich sediments of Lake Towuti, Indonesia: Disentangling the methane and iron cycles	Lake Towuti is a ferruginous basin with anoxic conditions below 130 m water depth. Due to these special settings, the lake is ideal to study early diagenesis in iron-rich sediments such as those that generated ancient iron formations during the Archean and Proterozoic. We investigated microbial populations present in the sediments, their role in iron cycle and any cryptic link to other elements. For this purpose, we worked on samples from short cores that were retrieved from Lake Towuti by our scientific team from the German Research Centre for Geosciences (Potsdam, Germany) and the University of British Columbia (Vancouver, Canada). This project was supported by the ICDP priority program of the Deutsche Forschungsgemeinschaft through grants to Jens Kallmeyer (KA 2293/8-1) and Aurèle Vuillemin (VU 94/1-1); the Swiss National Science Foundation (grant no. P2GEP2_148621 to Aurèle Vuillemin); the German Research Centre for Geosciences through an expedition grant to Jens Kallmeyer and Dirk Wagner; and an Natural Sciences and Engineering Research Council of Canada Discovery grant (no. 0487) to Sean A. Crowe.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00004186	Active microbial eukaryotes amidst a marine subsurface RNA paleome	During the first RNA-based survey of subsurface eukaryotes in a globally distributed sample collection, we detected metazoan, plant, and diatom rRNA signatures in sediments up to 2.7 million years old. The recovery of RNA from those taxa is consistent with burial in sub-seafloor environments during sedimentation, and subsequent preservation of those nucleic acids.  Extensive controls indicate that the recovered RNA does not derive from seawater or aerosol contaminants, supporting the authenticity of an RNA-based subsurface eukaryotic paleome. This paleome has the potential to inform our understanding of environmental conditions at the time of deposition. Within this same dataset, a high diversity of fungi in ocean sediments was found up to 48 meters below seafloor (mbsf) exhibiting statistically significant correlations with total organic carbon  (TOC), sulfide, and dissolved inorganic carbon (DIC). We interpret these correlations, together with the uniqueness of fungal profiles in the subsurface, and microscopic observations of filamentous fungi, yeasts, and spores as indicators of subsurface fungal activity	root:Environmental:Aquatic:Marine:Sediment
MGYS00004185	Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns	Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterised by strong thermo-halo stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S ribosomal RNA genes (rRNA genes) revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were the features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces were significantly higher in cell count, compared with the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we move from the Alphaproteobacteria-dominated deep-sea to the Planctomycetacia or Deferribacteres-dominated interfaces to the Gammaproteobacteria-dominated brine layers. The archaeal marine group I was dominant in the deep-sea water and interfaces; whilst several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II; despite the near-identical populations in the overlaying deep-sea waters. The lowest convective layers harboured interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.	root:Environmental:Aquatic:Marine
MGYS00004183	Microbial communities in sponge samples from Gulf of Mexico	454 pyrosequencing of v5 v6 regions of 16s rRNA genes	root:Host-associated:Porifera
MGYS00004182	Pronounced Seasonal Dynamics of Freshwater Chitinase Genes	Chitinase and 16S ribosomal RNA genes from Lake Erken derived from a seasonal survey.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00004181	16S rRNA gene pyrosequencing and clone library revealed highly diverse microbial communities in natural marine biofilms	Microbial communities in biofilms have been suggested to mediate a wide spectrum of ecological functions. However, the underlying mechanism of most of the mediations is still unresolved mainly because of the uncertainty in characterizing members in the communities using existing 16S rRNA gene-based molecular methods. In this study, a newly developed method – barcoded 16S rRNA gene pyrosequencing – was employed to provide a detailed characterization of the bacterial communities in intertidal and subtidal marine biofilms developed in two seasons. This method has high sensitivity to detect low-abundance taxa and is able to generate a large amount of highly reliable data in a very short period of time. Our results revealed highly diverse biofilm bacterial communities varied with season and tidal level. Over 6,000 OTUs with species estimates of up to 15,000 were recovered in a biofilm sample, which is by far the highest record in sub-tropical marine biofilms and is much greater than biofilms developed in certain natural habitats. Nineteen phyla were found in the biofilm samples, for which Cyanobacteria and Proteobacteria were the most abundant phylum dominating the intertidal and subtidal biofilms, respectively. Apart from these two phyla, Actinobacteria, Bacteroidetes, and Planctomycetes were found to be the major groups recovered in both intertidal and subtidal biofilms, yet their relative abundance varied among samples. Full-length 16S rRNA gene clone library was constructed for the 4 biofilm samples and showed similar results with pyrosequencing. The relationship of bacterial community and settlement of larvae of a marine invertebrate is discussed.	root:Environmental:Aquatic:Marine
MGYS00004180	Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea	Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to deeply investigate the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri, and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1,000 microbial OTUs and an estimate of up to 2,000 species. Altogether 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding seawater and 4 of which were recorded in sponges for the first time. Up to 100 OTUs with an estimate of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest diversity ever recorded for sponges. A non-negligible proportion of unclassified reads in sponges may represent the presence of novel species. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations although they varied to certain degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned into one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently diverged from those in the surrounding seawater. Our results suggested the Red Sea sponges possess highly sponge-species specific microbial communities which are resistant to environmental influence. Although sponges have been regarded as microbial fermenters with a huge microbial diversity being reported among the animal kingdom, much of their microbial diversity remains to be explored.	root:Environmental:Aquatic:Marine
MGYS00004179	Characterization of Microbial Community Structure and Population Dynamics of Tetrachloroethene-Dechlorinating Tidal Mudflat Communities using a Multipronged Approach	A multipronged approach comprising microcosm studies, Titanium pyrosequencing, 16S rRNA gene clone libraries, and dechlorinator-targeted quantitative real-time PCR (qPCR) characterized reductive dechlorinating activities and populations in tidal flat sediments collected from South Korea's central west coast near Kangwha.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004178	Marine metagenome ICM_DOF	454 Tagging of Deep Ocean Flux Material.	root:Environmental:Aquatic:Marine
MGYS00004152	Archaeal diversity of Loki's Castle black smokers at the Arctic Mid-Ocean Ridge	Hydrothermal vent systems harbor rich microbial communities ranging from aerobic  mesophiles to anaerobic hyperthermophiles. Among these, members of the archaeal domain  dominate the microbial communities in such extreme environments, partly because of their  temperature- and mechanically-resistant membrane lipids. In this study, we use geochemical  and molecular microbiological methods to investigate the abundance and diversity of archaea  in black smoker chimneys from the newly discovered Loki's Castle hydrothermal vent field  on the Arctic Mid-Ocean Ridge (AMOR) with vent fluid temperatures of 317°C and pH of  5.5. Archaeal glycerol dialkyl glycerol tetraether lipids (GDGTs) with 0 to 4 cyclopentane  moieties were dominant in all sulfide samples and are most likely derived from both  (hyper)thermophilic Euryarchaeota and Crenarchaeota, which are presumably involved in  sulfur and iron reduction, as well as methanogenesis. GDGTs with an additional covalent  bond between the isoprenoid hydrocarbon chains, so-called H-shaped GDGTs and also  containing 0 to 4 cyclopentane rings, were present with similar abundances. These lipids are  not often reported, but may be derived from sulfur-reducing members of the  Thermococcaceae. Crenarchaeol has been detected in samples derived from the chimney  exterior indicating the presence of Thaumarchaeota, involved in ammonia-oxidation (AOA)  at lower ambient temperatures. Our observations based on 16S rDNA-based taxonomy and  biomarker lipid analysis provide insight into microbial communities thriving within the  porous sulfide structures of an active deep-sea hydrothermal vent, where microbial cycling of  sulfur, hydrogen and methane predominantly by archaea may be the prevailing  biogeochemical processes.	root:Environmental:Aquatic:Marine:Hydrothermal vents:Black smokers
MGYS00004151	Marine microbial eukaryote community analysis in Korea	To investigate marine microbial euakryote community in Korea, we used the pyrosequencing technology.	root:Environmental:Aquatic:Marine
MGYS00004150	Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing	The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water columns overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (20 m and 50 m) and deeper layers (200 m and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations, which are 7.4 km apart. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. Our results indicate that the microbial communities sampled in this study are different from those identified in water columns in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea.	root:Environmental:Aquatic:Marine
MGYS00004149	Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 sequencing-by-synthesis	Information on genetic diversity of picoeukaryotes (<2 to 3 µm) comes mainly from traditional gene cloning and sequencing. However, the method suffers from cloning biases and limited throughput. We studied the composition and genetic diversity of picoeukaryotes off the subtropical western Pacific coast using cloning-independent and massively parallel 454 pyrosequencing of the hypervariable V4 region of the 18S rRNA gene. The approach gave a high coverage of the community at genetic difference >=5% but still underestimated the total diversity at genetic difference <=2%. Picoeukaryotic assemblage in the eutrophic site was less diverse than that with low chlorophyll a biomass. Stramenopiles, dinoflagellates, ciliates and prasinophytes were the dominant groups, comprising approximately 29, 19, 11 and 11% of the picoeukaryotes respectively. A differential spatial distribution of high-level taxonomic groups and phylotype OTUs of picoeukaryotes was observed between samples. Our study represents the most comprehensive examination of marine picoeukaryotic diversity to date, using the 454 sequencing-by-synthesis technology for the first time.	root:Environmental:Aquatic:Marine
MGYS00004108	MiSeq 16S rRNA gene (archaeal 16S rRNA gene) sequences of 4 SCS sediments	DNA from 4 SCS sediments have been extracted and amplified by 21f/958r & Arch347F/Arch806R primer pairs (for archaeal 16S rRNA gene). The archaeal communities of these 4 samples were obtained.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004107	Identification and activity of acetate-assimilating microorganisms in diffuse hydrothermal fluids	In diffuse hydrothermal fluids concentrations of organic compounds such as acetate can be significant. To date knowledge about mixo- and heterotrophic microorganisms in hydrothermal systems is derived from pure cultures only. We set out to identify acetate-consuming microorganisms in diffuse fluids from two distinct hydrothermal systems using cultivation-independent approaches. For this purpose we combined a characterization of the microbial community in fluids with short-term incubations (8-12 h) using 13C-labeled acetate at low concentrations (10 or 30 µM). We followed cell growth and assimilation of 13C into single cells by nanoSIMS combined with fluorescence in situ hybridization (FISH). In 55°C fluids from the Menez Gwen system, Mid-Atlantic Ridge, a novel epsilonproteobacterial group related to Nautiliales accounted for nearly all acetate-assimilating cells. In contrast, in 4°C and 37°C fluids from the Manus Basin (Papua New Guinea) Gammaproteobacteria dominated the 13C-acetate-assimilating community, which was supported by 16S rRNA sequences related to Marinobacter and Alteromonas. We also detected yet unidentified, weakly acetate assimilating cells in 72°C fluids (Manus Basin) that were presumably related to Acinetobacter. In particular in the 37°C and 55°C incubations the microbial communities differed from those in native fluids indicating rapid growth of heterotrophic organisms. The instant response suggests that acetate-consumers in diffuse fluids are r-strategists, which quickly exploit their food sources whenever available under the spatially and temporally highly fluctuating conditions at hydrothermal vents. Our data provide first insights into a largely under-investigated part of microbial carbon cycling at hydrothermal vents and reveals potential roles of known and yet unknown heterotrophic microorganisms in these systems.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00004082	Variable Loading Conditions Influence Charge and Current Generation in Multi-Anode Environmental Microbial Fuel Cells	The role of operating conditions, specifically duty cycling, on microbial fuel cell (MFC) performance has only recently been studied. This study uses an environmental MFC containing multiple anodes, positioned in chambered anoxic seawater overlying marine sediments, to explore how varying the time an anode is connected and disconnected from a cathode influences cumulative charge, and finds that a switching interval of 15 seconds when duty cycling among the anodes results in the greatest normalized current density (amps per unit time connected). Further studies demonstrate the overall electrode reaction resistance increases with shorter disconnection times, and there is a minimum time below which current decreases significantly. Microbial diversity analyses reveal a substantial enrichment in sulfur-cycling microbes on the anodes compared to the sediment, though no measurable change in community composition among operational anodes. Based on these data, we posit that, in environmental MFCs, replenishment of depleted chemical species within the biofilm and surrounding diffusion layer is necessary for maximum charge transfer, and that proton flux is not limiting in highly buffered systems. These data underscore the importance of considering all factors, including diffusion and migration flux, microbial community composition, and resting time, when optimizing MFC performance.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004081	Microbial Community Diversity Response to a Changing Arctic Ocean	Increasing global temperatures are having a profound impact in the Arctic, including the dramatic loss of multiyear sea ice in 2007 that has continued to the present. The majority of life in the Arctic is microbial and the consequences of climate-mediated changes on microbial marine food webs, which are responsible for biogeochemical cycling and support higher trophic levels, are unknown. We examined microbial communities over time by using high-throughput sequencing of microbial DNA collected between 2003 and 2010 from the subsurface chlorophyll maximum (SCM) layer of the Beaufort Sea (Canadian Arctic). We found that overall this layer has freshened and concentrations of nitrate, the limiting nutrient for photosynthetic production in Arctic seas, have decreased. We compared microbial communities from before and after the record September 2007 sea ice minimum and detected significant differences in communities from all three domains of life. In particular, there were significant changes in species composition of Eukarya, with ciliates becoming more common and heterotrophic marine stramenopiles (MASTs) accounting for a smaller proportion of sequences retrieved after 2007. Within the Archaea, Marine Group I Thaumarchaeota, which earlier represented up to 60% of the Archaea sequences in this layer, have declined to <10%. Bacterial communities overall were less diverse after 2007, with a significant decrease of the Bacteroidetes. These significant shifts suggest that the microbial food webs are sensitive to physical oceanographic changes such as those occurring in the Canadian Arctic over the past decade.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004080	Marine sediment metagenome ICM_DSE	Using 454 sequencing technology to explore eukaryotes diversity in the polar deep-sea sediments.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004079	Minor impact of ocean acidification to the structure of an Arctic sediment microbial community	Effects of ocean acidification on the diversity and structure of Arctic surface sediment bacterial and archaeal community was analysed in detail using 16S rRNA 454 pyrosequencing. Intact sediment cores were collected and exposed to one of five different pCO2 concentrations (380 (present day), 540, 750, 1120 and 3000 µatm) and RNA extracted after a period of 14 days exposure. Measurements of diversity and multivariate similarity indicated very little difference between pCO2 treatments. Only when the highest and lowest pCO2 treatments were compared were significant differences evident, namely increases in the abundance of the Halobacteria and differences to the presence/absence structure of the Planctomycetes. Members of the Planctomycetia also increased with increasing pCO2 concentration, particularly the Planctomyces, Schlesneria, Pirellula, Blastopirellula, Rhodopirellula and the Pir4 lineage, indicating that these groups may be able to take advantage of changing pH or pCO2 conditions. The modest response of the microbial communities associated with these sediments may be due to the low pore-water pH already experienced by sediment microbes or be a result of the high buffering capacity of marine sediments.	root:Environmental:Aquatic:Marine:Sediment
MGYS00004078	"Specialists instead of generalists oxidize alkanes in anoxic marine
                hydrocarbon seep sediments"	"The anaerobic oxidation of non-methane hydrocarbons mediated by
                sulfate-reducing bacteria (SRB) is a major process of organic matter degradation at
                marine hydrocarbon seeps. Several SRB have been successfully cultured, however,
                knowledge about in situ active organisms is still very limited. Here, we identified
                alkane-degrading key players from two contrasting seeps at the Mediterranean Amon
                Mud Volcano (Amon MV) and Guaymas Basin in the Gulf of California using
                complementary stable-isotope probing (SIP) techniques. Anoxic sediments were
                incubated with 13C-labeled butane or dodecane under close to in situ conditions.
                DNA- and RNA-based SIP in combination with 454-pyrosequencing (PYRO-SIP) allowed the
                identification of four phylogenetically distinct deltaproteobacterial groups of
                alkane-oxidizing SRB within the family Desulfobacteraceae. We named the groups
                degrading short-chain alkanes ‘SCA-SRB1' and ‘SCA-SRB2' and those degrading
                long-chain alkanes ‘LCA-SRB1' and ‘LCA-SRB2'. CARD-FISH with newly developed
                specific probes revealed a high relative in situ abundance of SCA-SRB1 and SCA-SRB2
                with 2% of the total community, while groups LCA-SRB1 and LCA-SRB2 were below 1% of
                total cells. Protein-based SIP (Protein-SIP), which enables to trace stable isotopes
                from substrate to protein, confirmed alkane-degrading key players of the family
                Desulfobacteraceae. In addition, Protein-SIP indicated additional carbon sources for
                13C biosynthesis besides alkanes, and gave insights into possible metabolic
                pathways: (1-methylalkyl)succinylation as initial step of butane degradation and the
                oxidative Wood–Ljungdahl pathway as terminal point of alkane
                degradation."	root:Environmental:Aquatic:Marine:Sediment
MGYS00004057	Development and validation of a marine experimental life support system for accessing synergistic effects of climate change and oil pollution on microbial communities	A state of the art marine experimental life support system framework was developed to perform microcosms experiments of climate change and anthropogenic pollutants effects on marine microbial communities. The system can be build with commercially available materials, enabling the reproduction of the same experiment in several locations worldwide. Here the system was validated for microbial ecology studies by comparing the bacterial composition of environmental and microcosm samples with a RNA-based barcode pyrosequencing approach. The OTU composition shift towards anaerobic bacterial groups in manipulates samples, witch can be explained with the operational programme executed. Replicate microcosm maintained a high OTU composition stability, with similar variability to the environmental samples.  This system can be use to establish cause-effect relationships into the effects of climate change and other anthropogenic stressors on specific marine microbial communities. Moreover, the marine experimental life support system versatile design enables its use on ecotoxicology tests.	root:Environmental:Aquatic:Marine
MGYS00004056	Marine metagenome ICM_SSD	Spatial Scaling of Microbial Diversity	root:Environmental:Aquatic:Marine:Sediment
MGYS00004055	Structuring effect of environmental variables on protistan diversity patterns in two anoxic marine basins	The tenet that 'everything is everywhere, but the environment selects' has influenced microbiology for several decades, and is still debated controversially. However, the proof or disproof of the hypothesis still remains difficult. Scant data from prokaryotic studies suggest that at least over large distances historical separation may overwhelm environmental effects, challenging the above mentioned hypothesis. Though, at smaller spatial scales, environmental effects seem to dominate diversity patterns, while distance effects are of secondary importance. We tried to contribute to the ongoing discussion by investigating patterns of protistan diversity from two geographically separated marine anoxic basins (Cariaco Basin, Venezuela, Framvaren Fjord, Norway). To take distance and environmental effects into account, each basin was sampled at two different locations along an environmental gradient. Biodiversity patterns were analyzed by applying the 454 sequencing technique. Resulting data sets were used to examine overall diversity of samples under study and to compare recorded community patterns based on taxonomic composition and similarity indices. By combining our results with contextual data from both sampling sites we tested for distance effects in relation to contemporary environmental effects.	root:Environmental:Aquatic:Marine
MGYS00004053	Metagenomic approach for studying picoeukaryotes in a extreme oligotrophic marginal sea (South Adriatic Sea) during winter mixed conditions	This study investigates this smallest plankton fraction (cells ≤ 3µm) in both prokaryotic and eukaryotic perspective considering changes of the community in the photic zone from coastal to open sea during mixed winter conditions. Using high-throughput sequencing of 16S and 18S rRNA genes along with flow-cytometry counts of bacteria, cyanobacteria and photosynthetic picoeukaryotes (PPEs) we described picoplanktonic community in the oligotrophic ecosystem. With pigment and lipid analyses of picoplankton community, we characterized PPEs and detected specific events in microbial loop. Prokaryotic community was dominated by Alphaproteobacteria, mainly SAR11 clade (44.91%), followed by Gammaproteobacteria (Oceanospirillales and Pseudomonadales, 14.96%), Bacteroidetes, mainly Flavobacteriales (13%), Cyanobacteria (Prochlorococcus and Synechococcus, 9.52%), Marinimicrobia, SAR406 clade (7.97%), Deltaproteobacteria (3.83%), Actinobacteria (2.24%) and Chloroflexi (1.90%). Picoeukaryotes, although the drivers of photosynthetic activity in oligotrophic systems, in this study were dominated by heterotrophic counterparts: Syndiniales, parasitic dinoflagellates (79.67%), other Dinophyta (8.7%) and on two depths Collodaria, family Sphaerozoidae (22.1%) and Polycistinea, Spumellarida (5.0%), while total photoautotrophic fraction of picoeukaryotes were represented with Mamiellophyceae, Stramenopiles, photoautotrophic Cryptophyta and some Haptophyta, together not exceeding 5% of total sequences. Heterotrophic bacteria and cyanobacteria, separated into populations of Prochlorococcus and Synechococcus, had abundances up to 7×105; 2.3×104 and 2.5×104 cells mL-1, respectively. Photoautotrophic picoeukaryotes were most abundant at P600-25m with 3×103 cells mL-1. According to pigment composition, the most prevalent phototrophs in picoplankton were Cyanobacteria and green algae.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00004037	Ecological succession leads to chemosynthesis in mats colonizing wood in sea water	We used amplicon and metagenomic sequencing combined with fluorescence in situ hybridization (FISH) to test whether a microbial succession occurs during mat formation and whether the wood fall mats present chemosynthetic features	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00004020	Spatially differing bacterial communities in water columns of the northern Baltic Sea	The Baltic Sea is a large, shallow and strongly stratified brackish water basin. It suffers from eutrophication, toxic cyanobacterial blooms and oxygen depletion, all of which pose a threat to local marine microbial communities. In this study, the diversity and community structure of the northern Baltic Sea bacterial communities in the water column were − for the first time − thoroughly studied by 454-sequencing. The spring and autumn bacterial communities were one order of magnitude less diverse than those in recently studied oceanic habitats. Patchiness and strong stratification were clearly detectable, since only less than 1% of OTUs were shared among eleven samples. The community composition was more uniform horizontally (at a fixed depth) at different sites than vertically within one sampling site. Taxonomic affiliations revealed a total of 23 bacterial classes and 169 genera, and five percent of the sequences were assigned unclassified. The cyanobacteria constituted less than two percent of the sequences and potentially toxic cyanobacterial genera were practically absent during the sampling seasons.	root:Environmental:Aquatic:Marine
MGYS00004004	Diversity and population structure of Marine Group A in the oxygen minimum zone of the Northeast subarctic Pacific Ocean	NONE	root:Environmental:Aquatic:Marine
MGYS00004002	Marine sediment metagenome ICM_CFU	Investigation of prokaryote diversity in the sub-seafloor biosphere by 16S rRNA gene tag (V6) sequencing.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003998	MiSeq 16S rRNA gene (Thaumarchaeota 16S rRNA gene) sequences of 12 SCS sediments	DNA from 12 SCS sediments have been extracted and amplified by THAUM494/958R primer pairs (for Thaumarchaeota 16S rRNA gene). The Thaumarchaeota communities of these 12 samples were obtained.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003997	MiSeq 16S rRNA gene (archaeal 16S rRNA gene) sequences of 12 SCS sediments	DNA from 12 SCS sediments have been extracted and amplified by 21f/958r & Arch347F/Arch806R primer pairs (for archaeal 16S rRNA gene). The archaeal communities of these 12 samples were obtained.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003981	Microbial Community Assembly in Soybean	Soybean has great economic and social importance for Brazil, and nitrogen, the most required nutrient by plants, is fully supplied by bacteria symbiosis. In order to guarantee the biological process maximization, it is necessary to inoculate strains of efficient and competitive bacteria, that accompany the technological development of new cultivars	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00003978	EMG produced TPA metagenomics fasta_path of the Shotgun metagenomic analysis of Lake Paajarvi sediment microbes. (PRJEB29513) data set.	The PRJEB29513 Third Party Annotation (TPA) fasta_path was derived from the primary whole genome shotgun (WGS) data set: PRJEB29513.  This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lentic:Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00003977	The gut microbiota distinguishes GI-healthy and -unhealthy captive colobineprimates - Hale folivorous primates (HiSeq)	This study focuses on the gut microbe populations of the Guizhou snub-nosed monkey, Rhinopithecus brelichi.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00003973	Latitudinal surveys of algal-associated microorganisms	Over the last decade, disease has emerged from being a long overlooked factor in natural communities to become an increasing focus for ecological research in terrestrial and marine ecosystems. There is also major concern that global warming and other anthropogenic stressors may be responsible for the spread of pathogens, enhanced virulence and decreased resilience of hosts. This project focuses on macroalgae or seaweeds, the dominant habitat-forming organisms in temperate rocky reef communities worldwide. They are the trees of temperate coastal ecosystems. Anthropogenic stressors can have dramatic effects on the health and persistence of large macroalgae and are responsible for extensive losses of habitat-forming algae. Importantly, declines in habitat-forming macroalgae not only impact the algae themselves, but have major effects on the diversity and abundance of associated organisms. During this project, we aim to characterise microbial communities associated with the surfaces of dominant seaweed species on temperate Australian coasts, from northern New South Wales, south to Tasmania and also along the western Australian coastline. Furthermore, we aim to identify potential pathogens associated with stressed specimens and quantify their abundance at different sites and different times and correlate microbial data with various physico-chemical information from each site and specimen. This work will provide baseline data on algal-bacterial associations on a latitudinal scale and may also provide information on the distribution and abundance of potential algal pathogens. We hope also to understand how different environmental conditions influence algal-associated microorganisms and predict how environmental change may affect interactions between these microbes and their hosts.	root:Host-associated:Algae
MGYS00003964	Functional description of microbial communities  from biochemical passive reactors treating synthetic Acide Mine Drainage	This study aims to stablish the link between the dynamics of microbial communities with the stability of process and functions of biochemical passive bioreactors for AMD-bioremediation. Dynamics of microbial communities can be simulated at different resolutions, depending on the approximation used to define the interacting units, here we are going to describe the bioreactors microbiome through two of the most common approaches: (1) using 16S rRNA gene data to simulate the dynamics of microbial communities in terms of interactions between taxa; and (2) using the whole metagenome sequencing  to characterize the whole community as a supra-organism performing various functions.	root:Engineered:Bioreactor
MGYS00003963	Influence of tillage practices on soil microbial diversity and activity in a long-term corn experimental field under continuous maize production	It is well known that an intensive conventional farming and continuous use of land resources can lead to a decrease of soil sustainability. The aim of this study was to compare the impact of four different tillage practices (minimum tillage MT, shallow ploughing SP, ripper subsoiling RS and conventional tillage DP) on soil profile under both continuous and rotating (wheat, bean, maize) maize production since 1970. The field study was conducted on 24 experimental plots on a loam soil of Fagna, Tuscany (Italy), where soil samples were collected at four different layers of 10 cm each, up to a total depth of 40 cm (0-10, 10-20, 20-30 and 30-40 cm in triplicate) and of 20 cm (0-10 and 10-20 cm) from continuous and rotating maize fields respectively, in order to measure the effect of the different tillage practices on soil organic matter, microbial diversity and microbial activity.	root:Environmental:Terrestrial:Soil:Loam:Agricultural
MGYS00003957	Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample - 3 prime	"The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known ""mock communities"" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution."	root:Mixed
MGYS00003954	EMG produced TPA metagenomics assembly of the EMOSE (2017) Inter-Comparison of Marine Plankton Metagenome Analysis Methods (BZZ_CAA_CAN) data set.	The BZZ_CAA_CAN Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB87662.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003952	Song whitehead bats	Seba's short-tailed bat, Carollia perspicillata, is a frugivorous bat that feeds mainly on the fruits of plants of the genus Piper, serving as important dispersers of their seeds. However, Piper species are known to contain secondary metabolites that are often toxic or distasteful to some consumers and also function to protect the plant from attack by microbes and insects. Piperine is one such metabolite (an alkaloid) found in Piper species that has been shown to have both antibacterial and antifungal activity. One study showed that supplementation of fruit with piperine resulted in decreased consumption by C. perspicillata. These studies suggest that a tradeoff may exist between the potential benefits and disadvantages to the host of consuming such metabolites. We propose to determine whether piperine consumption affects the composition of the microbial communities that inhabit the gut of this bat species.	root:Host-associated:Mammals
MGYS00003951	Gut microbiome of hibernating bears	I hypothesize that the colon microbiome of the hibernating black bears is a unique assemblage of bacteria that performs functions vital for hibernation, giving bears the unique ability to survive for months without eating or urinating. The first step in studying this phenomenon is to identify the bacteria that comprise this microbiome using 16S amplicon data. My colleagues and I have collected samples from the colons of 17 hibernating American black bears (Ursus americanus) in Minnesota, USA. We used three methods of collection that sampled from 10.5cm to 40cm proximal to the anus, for a total of 49 samples. DNA has been extracted, using EMP standard protocols, at the Biofrontiers Institute, Knight lab, in Boulder, Colorado.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00003950	The gut microbiota distinguishes GI-healthy and -unhealthy captive colobineprimates - Hale folivorous primates (MiSeq)	I currently have a total of 160 DNA samples (from feces) that represent the following species: wild Rhinopithecus brelichi (Guizhou snub nosed monkey, 3 wild Macaca thibetana (Tibetan macaque),10 captive Rhinopithecus brelichi (Guizhou snub nosed monkey),3 captive Rhinopithecus roxellana (Sichuan snub nosed monkey, 2 captive Colobus guereza (Eastern black and white colubus monkey),16 captive Nasalis larvatus (Proboscis monkey);-8 captive Pygathrix nemaeus nemaeus (Red shanked douc langur), 11 captive Trachyipthecus auratus (Javan langur), 3 captive Trachypithecus vetulus vatulus/nestor (Purple faced langurs), 1 pooled sample from Ateles geoffroyi (Spider monkeys). These samples were collected by Chia Tan (San Diego Zoo) and myself from the Fanjingshan National Nature Reserve (Guizhou, China), the Panxi Breeding Center (Guizhou, China), the Singapore Zoo (Singapore), and the Columbian Park Zoo (Lafayette, Indiana, USA). All samples amplified on a gel after performing PCR with 16srRNA primers. MiSeq data trimmed to 100bp in the study)	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00003946	Seyler North Atlantic water column	CLIVAR (Climate Variability and Predictability) is a core component of the World Climate Research Program (WCRP). CLIVAR's objective, as stated on their website (www.clivar.org) is to describe and understand the ocean-atmosphere processes responsible for climate variability and predictability on seasonal, interannual, decadal, and centennial time-scales, through the collection and analysis of observations and the development and application of models of the coupled climate system, in cooperation with other relevant climate-research and observing activities. In April-May 2012, we participated in a research cruise as part of the US CLIVAR/CO2 Repeat Hydrography program, onboard the UNOLS ships R/V Atlantis. The cruise was a repeat of World Ocean Circulation Experiment (WOCE) line A20 (longitude 52W), previously conducted in 2003. 10-L water samples were collected at a total of 83 stations at varying depth intervals, using a 36-Niskin bottle rosette. We took 0.5-1.0 L samples from the rosette roughly once per day at 16 stations throughout the cruise. At each station, water was taken from at least three distinct zones in the water column, based on data from the CTD: the middle of the mixed layer, the local oxygen minimum, and the middle of the bathypelagic zone. At 7 stations, samples were also drawn from the bottom-most bottle. Biomass was immediately collected on 0.2 um filters under vacuum filtration. SIP microcosms were set up at 13 stations using 13C sodium acetate, 13C urea, 13C sodium bicarbonate, 13C algal lipid/pigment extract, and 15N algal protein extract. The samples submitted to the Earth Microbiome Project represent T=0 time points for the SIP microcosms (before amendment) and extra samples taken for RNA/DNA analysis. Results from SIP are currently being processed.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00003943	Metagenomic analysis of some key samples from anaerobic digestion of high salt and sulphate waste.	The waste stream generated by our industrial partner, MARA/AO3, during the production of omega3 fatty acids from marine algae is very large and still rich in nutrients and solid cellular material.The generated wastewater contains amino acids, metals, sulphate and high salt concentration. Discharge or treatment of this waste has an associated cost, both fiscal and environmental. Anaerobic digestion of this waste has the potential to reduce costs, recover value and resources and reduce environmental impact. This project explored whether a salt-tolerant microbial community can carry out effective anaerobic digestion of this high-salt waste stream. We additionally investigated whether the used of molybdate as an inhibitor of sulphate reduction can increase the methane production potential of the sulphate-rich AO3 waste.	root:Engineered:Bioreactor
MGYS00003940	Acidobacterial EPS degraders uraveled by stable isotope probing - Shotgun Metagenomics sequencing	Stable isotope probing was used to evaluate which microorganisms, bacteria and fungi, were involved in the assimilation of an exopolysaccharide (EPS) produced by the acidobacterial strain Granulicella WH15. The strain was grown in culture medium with labeled glucose, in order to produce labeled EPS. The EPS was extracted, the polysaccharide purified and incubated with soil. This is the shotgun metagenomics data derived from this study	root:Engineered:Solid waste:Composting
MGYS00003939	Caprobiome_2	Samples come from inoculum (anaerobic sludge) and UASB reactor fed with acid whey containing mostly ethanol or lactate.	root:Engineered:Wastewater
MGYS00003937	Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils	A 12-year sample archive of DNA from Alaskan arctic tundra ecosystems are available to the Earth Microbiome Project for comparison of microbial diversity across a range of arctic environments from soils to water to sediments. These samples were preserved and extracted using a method that differs from that of the EMP. Therefore, we must test how the extraction method used to extract our archived samples compares with those methods used by the EMP. The samples for this test were collected during the summer of 2011 at the Toolik Field Station. Each site was sampled in triplicate and samples were divided and preserved for extraction using our standard protocol (three replicates), and for extraction using the EMP protocol (three replicates). Half of the samples are from the epilimnion and hypolimnion of ultra-oligotrophic Toolik Lake collected over the course of the summer, and the rest are from different environments associated with a headwater stream that lies upslope of Toolik Lake. The data from these samples will allow us to test whether our extraction protocol yields results that are similar to the EMP extraction protocol, to investigate how replicates compare, and to determine how the microbial community and its metagenome changes over the course of the summer in Arctic tundra waters. LTRB, Long Term Ecological Research. The samples from this study were provided to the EMP for amplification with the EMP protocols	root:Mixed
MGYS00003933	Impact of Plant Development on Structure and Function of Rhizosphere Microbial Community associated with Groundnut (Arachis hypogaea L.)	Impact of Plant Development on Structure and Function of Rhizosphere Microbial Community associated with Groundnut (Arachis hypogaea L.).Present study investigates changes in microbiome of Groundnut rhizosphere throughout the development of plant from pre-sowing to post-harvest.	root:Environmental:Terrestrial:Soil
MGYS00003932	IBK Shotgun Metagenomics Analysis Sample A3	IBK Shotgun Metagenomics Analysis Sample A3	root:Host-associated:Mammals
MGYS00003925	Knight skin biogeography comparison	Knight_skin_biogeography - Comparison of skin samples from a rat (mammal), cyclostomid (fish), iguana (reptile), bull frog (amphibian) and a bird (pigeon) to determine if the site chosen to sample on different animals are dependent on site selection.	root:Host-associated:Animal
MGYS00003924	The oral and skin microbiomes of captive Komodo Dragons are significantly shared with their habitat.	Here we collect saliva, skin, and fecal samples from captive Komodo dragons (V. komodoensis) and other captive varanids (V. olivaceus, V. indicus, V. rudicollis) in the first-ever culture-independent assessment of the varanid microbiome. Environmental samples were also collected to characterize host-environment microbiome sharing. This study adds crucial information to our understanding of captive Komodo dragon microbial ecology.	root:Mixed
MGYS00003923	Gut microbiota of phyllostomid bats that span a breadth of diets	The microbial communities that inhabit the gut of animals play essential roles in host biology including nutrient provisioning, regulation of tissue development, and immune system development. Both ecological and evolutionary forces are thought to have shaped these communities. However, previous efforts to quantify the extent to which different factors contribute to the structure of gut bacterial communities have targeted either a range of host diversity too narrow to analyze ecological drivers of community structure, or so wide that diet and phylogeny are tightly correlated, and thus difficult to disentangle. In order to assess the relative contribution of host ecology (including dietary specializations) and evolution (phylogenetic relationships) in shaping gut microbiome diversity we have chosen to study the phyllostomid bats (Chiroptera: Phyllostomidae). Phyllostomid bats span almost the entire dietary diversity known for terrestrial mammals, with omnivorous, insectivorous, carnivorous, hematophagous, nectarivorous, and frugivorous species. Crucially, there is a robust phylogenetic framework for this group that indicates dietary specialization has evolved multiple times from insect-feeding ancestors. Nectar feeding and carnivory have each evolved twice, the inclusion of some fruit in the diet has evolved 5 times, and blood-feeding and extreme frugivory have evolved one time each. Repeated instances of the evolution of dietary specializations enable analyses that separate host diet and environment from phylogeny as drivers of bacterial community structure. To date, we have collected 96 fecal samples for 38 species that span the dietary diversity of the clade. All of these samples were collected in the field in Belize and Ecuador, and thus represent the microbiome of these bats in their natural habitat. We would like to generate 16S and shotgun metagenomic sequences for these samples to assess community membership and function. This project represents a significant step forward in the characterization of vertebrate microbiome because it enables hypotheses on the relative importance of different factors in structuring bacterial communities to be explicitly tested. These data will also provide insight into the role the gut microbial community plays in adaptation to novel diets.	root:Host-associated:Mammals:Digestive system
MGYS00003922	A combination of biochar-mineral complexes and compost improves soil bacterial processes, soil quality, and plant properties	Biochar is derived from the oxygen-limited pyrolysis of organic matter (e.g. agricultural or municipal waste) and constitutes for complex structure of recalcitrant, porous carbon and well as mobile minerals and nutrients. Several studies have shown that the addition of biochar improves agricultural yields and performance in a way comparable to classical NPK or urea-based fertilisers. Biochar is therefore an emerging and attractive replacement for classical farming practices with the additional benefit of sequestering carbon that would otherwise be burnt or composted. The mechanisms behind the beneficial properties of biochar are not well understood, but initial work has shown that its amendment to soil impacts on microbial community composition. To better understand these processes, this project will obtain a comprehensive picture of the microbial community in bulk soil, roots and biochar particles in agricultural soils that were supplemented with various amounts of biochar as part of a field trial executed by the New South Wales Department of Primary Industries (DPI). A total of 253 samples will be analysed, that constitute a design that will allow us to understand where the most pronounced microbial changes occur (e.g. biochar particle versus soil) and what changes in the microbial communities occur over time.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00003921	Agricultural intensification and the functional capacity of soil microbes on smallholder African farms -swkenya	Since 2005, the Africa Green Revolution has aimed to increase crop yields on small-scale farms in sub-Saharan Africa by promoting the increased use of mineral fertilizers. Microbial ecologists have begun to understand the relationship between nutrient enrichment and bacterial community composition but little-to-no work has been done to understand the effects of different agricultural management practices on microbial diversity and function in tropical systems. For this study, we collected soil samples from 21 farms of three management types, high mineral fertilizer use, low mineral fertilizer use, and improved fallow.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00003920	Panama Precip Grad Soil	The effect of precipitation in structuring soil microbial communities has not been extensively explored in lowland tropical rain forests. Across the Isthmus of Panama, there is a precipitation gradient ranging from 1600 mm MAP to less than 3000 mm MAP with several other biotic and abiotic factors found to co-vary with MAP. The Smithsonian Tropical Research Institute has established more than 40 plots (1 ha each) in which all trees 10cm dbh have been identified to species and mapped.	root:Environmental:Terrestrial:Soil
MGYS00003919	Malaysia Pasoh Landuse Logged Forest	In Malaysia and much of Southeast Asia the major drivers of deforestation are logging and expansion of oil palm agriculture. Forests regenerating from logging have been found to support relatively high levels of biodiversity for some larger taxa, while oil palm plantations have been shown to harbor a very small fraction of biodiversity that would otherwise be observed in primary forest. However, no studies have evaluated the belowground communities in these mosaics across the tropical landscape.	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00003918	Malaysia Lambir Soils	Lambir Hills National Park is located in Sarawak, Malaysia on the island of Borneo. The Center for Tropical Forest Science (http://www.ctfs.si.edu/) established a permanent 52-ha research plot at this site in 1991 and mapped, tagged, and identified all trees 1cm dbh (recensuses occur every 5 years). Of all the CTFS plots established to date (&gt;40 across the world), Lambir Hills is the most diverse in terms of tree species with &gt;1000 species found to be coexisting. One of the major drivers of high tree diversity at this site is thought to be the soil heterogeneity. There are four distinct soil types at this site ranging from low to high fertility.	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00003917	Agricultural intensification and the functional capacity of soil microbes on smallholder African farms - kakamenga	For the previous 2-3 years, soils from a chronosequence of farms along the edge of the Kakamega forest in Kenya along with soils from adjacent forested plots were sampled for trace gas fluxes and nitrogen cycling processes. This project sampled soils from the same plots to evaluate the effects of land use change and farm age on the bacteria responsible for key nitrogen cycling processes.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00003916	Friedman Alaska peat soils	The samples are from Cornell University in the lab of Lars Angenent, and are soils and biofilms from tundra ecosystems outside Barrow, AK.	root:Environmental:Terrestrial:Soil
MGYS00003915	Urban stress is associated with variation in microbial species composition, but not richness, in Manhattan	Green roof and city park samples. In urban environments, green roofs provide a number of potential benefits, including decreases in urban heat island effects and reduced energy costs for buildings. However, they may also serve as habitat islands for maintaining biodiversity across the landscape, similarly to city parks. In this project, eleven experimental green roofs were sampled in addition to five city parks. The green roofs were spread across all five boroughs of New York City and were established in 2010 on top of select recreation centers run by the New York City Department of Parks and Recreation. All experimental green roofs were planted with the same density of native plant communities from the greater New York area and had identical soil substrate and planting box dimensions. The five city parks chosen for sampling included Central Park, the largest park in New York City, and the High Line, which is the newest large park established in the city. From each green roof, six composite soil cores (0-10 cm) were taken from six planting boxes (each box 4 m X 2 m) for a total of six representative samples per green roof. On three of the green roofs, we sampled in a spatially-explicit manner to capture fine-scale heterogeneity in microbial composition. For these samples, 10 individual soil cores were collected from three planting boxes for a total of 30 soil cores per roof. From each city park, three plots (20 m X 20 m) were sampled and five soil cores (0 to 10 cm) were composited as a representative sample for each plot. In Central Park, five plots were sampled rather than three plots due to the larger size of the park. Research questions: Do green roofs planted with native plants in New York City function as biodiversity reservoirs for bacteria, is there significant heterogeneity in microbial community composition at fine spatial scales within individual green roofs, based on the fine-scale spatial heterogeneity of green roof soil bacteria, how many samples are necessary to collect as a representative sample for each green roof, how much overlap is there in microbial community composition of the green roof substrates and city park soils and is there evidence for biogeographical structuring of green roof microbial communities across New York City.	root:Environmental:Terrestrial:Soil
MGYS00003914	Mission Bay Sediment Viromes	Mission Bay Sediment Viromes	root:Environmental:Aquatic:Marine:Sediment
MGYS00003913	Marine mammal skin microbiomes	Skin samples from 139 animals, encompassing 12 species, have already been collected in collaboration with marine mammal scientists. These samples include skin biopsies from free-ranging animals from offshore Hawaii, field-captured and released animals from coastal Massachusetts and stranded and by-caught animals, primarily from Cape Cod. Samples are from the following species are currently stored in my lab at -80C: short-beaked common dolphin (Delphinus delphis), Atlantic white-sided dolphin (Lagenorphynchus acutus), rough-toothed dolphin (Steno bredanensis), bottlenose dolphin (Tursiops truncates), pantropical spotted dolphin (Stenella attenuata), harbor porpoise (Phocoena phocoena), short-finned pilot whale (Globicephala macrorhynchus), sperm whale (Physeter macrocephalus), melon headed whale (Peponocephala electra), minke whale (Balaenoptera acutorostrata), harbor seal (Phoca vitulina), and grey seal (Halichoerus grypus). Additionally, skin samples have been committed to me from 3 other species: fin whales (Balaenoptera physalus) and sei whales (Balaenoptera borealis) from offshore Massachusettes, and free-ranging beluga whales (Delphinapterus leucas) from Alaska. The skin samples were obtained from free-ranging, beach stranded, or recently deceased animals. The majority of the free-ranging animals were observed to be in apparently good health condition, while those stranded on the beach (samples obtained from both live and dead animals) are considered to be health-compromised.	root:Host-associated:Mammals:Skin
MGYS00003912	Recovery of biological soil crust-like microbial communities in previously submerged soils of Glen canyon	In 1963 the Glen Canyon Dam was completed and Lake Powell began to fill. After recent, successive years of drought in the Colorado River upper basin the water level in Lake Powell has been steadily declining, and is now approximately 100 ft below the high water line. Here we present a survey of soil microbial communities at three sites in Glen Canyon, each spanning a transect from just below the current water level to above the high water line in steps of 10 vertical feet. Approximately 100 samples were collected, and archaeal and bacterial 16S rRNA was sequenced on the Illumina HiSeq2000 platform to a median sampling depth of approximately 81,000 sequences per sample. We show that the phylogenetic composition of the submerged and exposed soil microbial communities are distinct, and that with time since reemergence microbial communities of exposed soils have become more similar to those of biological soil crusts, which typify undisturbed soils of the area. Our results suggest that as the water level of Lake Powell recedes, the microbial communities of Glen Canyon soils are dynamically recovering from flood disturbance.	root:Environmental:Terrestrial:Soil
MGYS00003911	Ercolini whole grain feces	Whole grains contain numerous physiologically bioactive compounds, a key group being polyphenolic compounds (such as ferulic acid). These compounds were shown to have potent antioxidant activity. Limited evidence exists regarding the bioavailability of the whole grain bioactive compounds and their physiological impact on health outcomes in humans such as the CVD risk, body weight and abdominal circumference. Evidence from animal and few human studies indicated that prebiotic dietary fibre ameliorates metabolic syndrome and controls body weight through reduction of inflammation. This study aims to evaluate the bioavailability WG polyphenols, the effect of WG on body weight, circumferences and composition, and to clarify the underlying mechanisms. A commercial WG product, having prebiotic properties and a high amount of polyphenols bound to dietary fibre, was selected. Eighty healthy overweight subjects will be enrolled. Forty volunteers will be asked to change their habitual diet only replacing equicaloric portions of specific foods with 68 g WG per day for 8 weeks; the other half will include a placebo. At baseline, and after 4 and 8 weeks, measure of body weight, waist and hip circumferences, bioimpedance analysis and blood, urine and feces collection will be performed. Markers linked to antioxidant status (serum ferulic acid, beta-carotene and FRAP), to inflammatory status (several cytokines by multiplexed immunometric assay), to lipid and glucose metabolism as well as to the overall nutritional status and appetite, will be measured.	root:Host-associated:Human:Digestive system
MGYS00003909	Brazelton LostCity chimney biofilm	The Lost City Hydrothermal Field, an ultramafic-hosted system located 15 km west of the Mid-Atlantic Ridge, has experienced at least 30,000 years of hydrothermal activity. Previous studies have shown that its carbonate chimneys form by mixing of round 90C, pH 9-11 hydrothermal fluids and cold seawater. Flow of methane and hydrogen-rich hydrothermal fluids in the porous interior chimney walls supports an archaeal biofilm dominated by a single phylotype of Methanosarcinales. We have a collection of 40 carbonate chimney samples, most of which have been dated with uranium-thorium isotopic systematics. The resulting ages range from 34 to 145,000 years. Previous 16S rRNA pyrotag sequencing of 4 of these samples revealed that rare sequences in young chimneys were often more abundant in older chimneys, indicating that species can remain rare in a chimney for &gt;100 years before blooming and becoming dominant when the environmental conditions allow. These results suggest that a long history of selection over many cycles of chimney growth has resulted in numerous closely related species at Lost City, each of which is pre-adapted to a particular set of re-occurring environmental conditions. Due to the unique characteristics of the Lost City Hydrothermal Field, these data offer an unprecedented opportunity to study the dynamics of a microbial ecosystem's rare biosphere over thousands of years.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00003907	Faecal microbiota of Schistosoma mansoni-infected mouse	Monitoring of changes in the gut microbiota of mouse along the infection with Schistosoma mansoni	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00003906	Microbial community in A2O or A2O-MBR	Microbial community in A2O or A2O-MBR	root:Engineered:Wastewater:Water and sludge
MGYS00003895	The commensal helminth Hymenolepis diminuta ameliorates chemically induced colitis in a rat model system	Hymenolepis diminuta infection in rats is an attractive model for a therapeutic helminthbecause the long-term and stable infection resembles the long-term associations humanshistorically had with helminths and offers the possibility of long-term treatment. Here weinvestigate the ability of H. diminuta to protect rats against colitis induced through applicationof the haptenizing agent DNBS directly to the colon. We test the ability of immature H.diminuta to ameliorate the effects of colitis during the prepatent period, when H. diminutainduces a type 2 immune response. We also test mature H. diminuta (patent period) againstboth moderate (single DNBS application) and severe (two DNBS applications) colitis, a modeldeveloped in this study to assess the effects of H. diminuta on longer-term disease. We monitorthe gut bacterial microbiota over time, as well as measures of rat health and TNFα expression.We show that mature H. diminuta results in lower inflammation, faster recovery and lesserpathology from severe colitis, but has little impact on moderate colitis. Immature H. diminutainduce elevated IL-10 expression, but do not protect against severe colitis. The gut microbiotais disrupted during colitis and does not appear to play an overt role in H. diminuta mediatedprotection.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00003892	Mediterranean Bathypelagic Habitat	"In general, a remarkable number of similarities were found with the deep meso-pelagic Pacific and a convergence at the level of taxa found and types of metabolism with the soil microbiota is starting to be perceived. The authors use the term ""invisible soil"" paraphrasing the ""invisible forest"" coined by Paul Falkowski to refer to the hidden but gigantic primary productivity found in the photic zone. The diversity of metabolic enzymes involved in resilient organic compounds degradation was very high. However, many microbes could complement their heterotrophic metabolism with chemolithotrophic energy supplies and, specifically in the Mediterranean, the oxidation of carbon monoxide, probably released by tectonic activity, could be important. There is also evidence that the microbes rarely live isolated. The free living planktonic lifestyle is probably not very popular in this extremely depleted environment. Quorum sensing genes indicate that instead, microbes tend to aggregate in particles and they could become luminescent maybe to attract and be eaten by animals. This strategy could provide the cells with a sporadic visit to the nutritious oasis of an animal gut. Overall, this paper shows that the deep ocean possesses a rich and mostly unknown microbiota that deserves much more studies.

A recent analysis of a metagenomic library from the deep Mediterranean shows a surprising high number of quorum sensing or lux genes that are only expressed when bacteria live in colonies. The deep ocean might be too depleted in resources for microbes to live independently. Instead the association to detritus particles might give them a rich microenvironment. Now, some of the genes detected have been positively identified as luxA, directly involved in bioluminescence.

Why would deep sea bacteria be luminescent? One possible explanation is that they become attractive to animals that at these depths are very photosensitive. Being swallowed by one of these creatures would give the bacteria a temporary oasis of nutrient-rich conditions before another long dip in the abyssal black."	root:Environmental:Aquatic:Marine:Oceanic
MGYS00003871	The gut microbiota distinguishes GI-healthy and -unhealthy captive colobineprimates	Despite concerted efforts to improve the conservation status of Asian primates,conditions in their natural habitats continue to worsen. As a result, captive breeding programs may become increasingly important to ensure species survival. Nevertheless, maintaining healthy captive populations of Asian primates can be difficult, particularly for primates of the Colobinae subfamily that commonly suffer from morbidity and mortality due to gastrointestinal (GI) distress of unknown cause. While there is speculation that this GI distress may be associated with a dysbiosis of the gut microbiota, no study has directly examined the role of the gut microbiota in colobine GI health. Hi Seq data	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00003870	Temple TX native exotic precip study	Bacterial biodiversity between native and novel exotic-dominated communities exposed to irrigation treatment In many systems, novel exotic-dominated plant communities are replacing native plant communities. We experimentally compared species diversity decline between nine-species grassland communities under field conditions to test whether bacterial diversity differed between communities containing all exotic or all native plant species, using a pool of 40 plant species. Mixtures (64) were established with equal functional group proportions using a paired species approach that controlled for phylogeny and growth form between pairs of native and exotic plant species. Origin (native vs. exotic) was crossed with summer irrigation treatments. Here we examine weather changes in climate, plant biomass and plant diversity affect bacterial community composition. Aboveground biomass was greater in exotic than native plots, and this difference was larger in mixtures than in monocultures. Plant species diversity declined more in exotic than native plant communities. Using 16S rDNA, we will determine if soil microbial communities are sensitive to changes in irrigation and plant communities, or if soil microbial communities are resilient, resulting in minimal changes in soil bacterial community composition.	root:Environmental:Terrestrial:Soil
MGYS00003869	A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA	With an unprecedented decade-long time series from a temperate eutrophic lake, we analyzed bacterial and environmental co-occurrence networks to gain insight into seasonal dynamics at the community level. We found that (1) bacterial co-occurrence networks were non-random, (2) season explained the network complexity and (3) co-occurrence network complexity was negatively correlated with the underlying community diversity across different seasons. Network complexity was not related to the variance of associated environmental factors. Temperature and productivity may drive changes in diversity across seasons in temperate aquatic systems, much as they control diversity across latitude. While the implications of bacterioplankton network structure on ecosystem function are still largely unknown, network analysis, in conjunction with traditional multivariate techniques, continues to increase our understanding of bacterioplankton temporal dynamics.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00003868	Marine CDOM accumulation during a coastal Arctic mesocosm experiment: No response to elevated pCO2 levels	Metagenome and transcriptome of filtered sea water samples from mesocosms under different CO2 partial pressure. CO2 pressures were increased in multiple mesocosms and samples within each were taken during an elongated period of time.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00003867	Bergen Ocean Acidification Mesocosms	Water samples were obtained from a replicated mesocosm study (two treatments, each in triplicate) established in coastal waters of a fjord close to Bergen, Norway (60.27 N: 5.22 E). Each mesocosm contained 11,000 L of coastal water and two of the six mesocosms were sampled for this study. To induce the phytoplankton bloom, nitrate and phosphate were added. Water samples were taken at the peak and immediately following the collapse of the phytoplankton bloom from both a high CO2 and control mesocosm. Water samples were collected in May 2006. Metagenomic and Metatranscriptomics data has already been published. These data presented here are 16S rRNA V3-V4 Illumina amplicon data.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00003866	Polluted Polar Coastal Sediments	With the goal of increasing our understanding of the biogeographic distribution and functional traits of microorganisms from cold, polluted coastal sediments, we are performing a comprehensive characterization of the structure and function of microbial communities from sediments of four hydrocarbon-polluted cold regions (Potter Cove, Antarctic Peninsula; Ushuaia Bay, Tierra del Fuego Island; Vertahamnen, Baltic Sea; Adventfjord, Svalbard Archipelago). At each site, replicate samples were collected from polluted sediments and from unpolluted sediments for comparison. This project is the result of an international collaboration between researchers of Argentina, USA, Sweden and Norway, and has been funded by the Community Sequencing Program of the Joint Genome Institute (JGI-DOE, USA). The project PIs are Hebe Monica Dinoisi (CENPAT-CONICET, Argentina) and Janet K. Jansson (LBNL).	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00003865	Laboratory Directed Research and Development Biological Carbon Sequestration	Californian_Grassland_soil_incubated_with_pyrolized_plant_material. LDRD biosequestration research: (1) to understand the mechanisms of soil carbon stabilization and how to influence them; (2) to understand how to enhance or influence different means of biologically capturing CO2 in ecological and industrial environments; and (3) to understand and evaluate strategies to increase sequestration of atmospheric carbon and minimize loss of already sequestered carbon. The context for this action is the understanding that sequestering carbon through biological capture of CO2 and stabilization in soils is one of the approaches being considered for reduction of atmospheric carbon loads. Soils are a promising reservoir for sequestration, because soil organic carbon residence times are up to tens of thousands of years, and soil carbon is less vulnerable to disturbance than is above ground biomass.	root:Environmental:Terrestrial:Soil
MGYS00003864	Great Lake Microbiome	Microbial diversity analysis at different depths and stations in great lakes of the US (Michigan, Superior)	root:Environmental:Aquatic:Freshwater:Lake
MGYS00003863	Rio de Janeiro Coastline	Although Brazil is well known for the great biodiversity within its flora and fauna, the microbial diversity has been poorly characterized. The geographic formation of Rio de Janeiro results in a combination of distinct environments near the coastal Atlantic Ocean, such as Atlantic rain forest, restingas, estuaries, bay areas, hypersaline lagoons and freshwater lakes. All together make the surrounding areas of Rio de Janeiro coastline a microbial diversity hotspot. These tropical regions are of enormous interest since they are considered an important source of novel and unique microorganisms for bioremediation and for biotechnological industries. However, the adjacent areas present either a deficient sewage treatment or/and a busy industrial park that can severely impact the environment. Therefore, the aim of this study is to characterize the microbial community and the functional diversity from pristine and contaminated aquatic environments from Rio de Janeiro coastline. Studying the microbial and functional distributions associated with environmental data, we will be able to identify the effect of environmental factors on the microbial community. This information will be useful to preserve the natural conditions of these tropical areas.	root:Environmental:Aquatic
MGYS00003862	Microbial communities of the deep unfrozen: Do microbes in taliks increase permafrost carbon vulnerability?	Microbial life in the nutrient-limited aThe vast frozen terrain of northern latitude ecosystems is typically thought of as being nearly biologically inert for the winter period. Yet deep within the frozen ground of northern latitude soils reside microbial communities that can remain active during the winter months. As we have shown previously, microbial communities may remain active in permafrost soils just below the freezing point of water. Though perhaps more importantly, microbial communities persist in unfrozen areas of water, soil, and sediment beneath water bodies the entire year. Microbial activity in taliks may have significant impacts on biogeochemical cycling in northern latitude ecosystems because their activity is not limited by the winter months. Here we present compositional and functional data, including long term incubation data, for microbial communities within permafrost landscapes, in permafrost and taliks, and the implications of these activities on permafrost carbon decomposition and the flux of CO2 and CH4. Our experiment was conducted at the Alaska Peatland Experiment (APEX) within the Bonanza Creek LTER in interior Alaska. Our site consists of a black spruce forest on permafrost that has degraded into thermokarst bogs at various times over the last five hundred years. We assume the parent substrate of the deep (1-1.5m) thermokarst peat was similar to the nearby forest soil and permafrost C before thaw. At this site, flux tower and autochamber data show that the thermokarst bog is a sink of CO2 , but a significant source of CH4. Yet this does not tell the whole story as these data do not fully capture microbial activity within the deep unfrozen talik layer. There is published evidence that within thermokarst bogs, relatively rapid decomposition of old forest floor material may be occurring. There are several possible mechanisms for this pattern; one possible mechanism for accelerated decomposition is the overwintering activities of microbial communities in taliks of thermokarst soils. To test this idea, we conducted anaerobic incubations of deep (1m) bog soils at two different temperatures to determine microbial temperature response functions. We also measured soil profile CO2 and CH4 concentrations and functional gene assays of the deep bog microbial community. Incubation data in combination with overwinter temperature profiles show that the talik has high potential rates of CO2 and CH4 production compared to the mass of C from forest floor and permafrost C to 1m depth. Results highlight the potential importance of taliks affecting the vulnerability of permafrost carbon to decomposition and reduction to methane.nd low-permeability continental crystalline crust is abundant but remains relatively unexplored. Using high-throughput sequencing to assess the 16S rRNA gene diversity, we found diverse bacterial and archaeal communities along a 2516-m-deep drill hole in continental crystalline crust in Outokumpu, Finland.	root:Environmental:Terrestrial:Soil
MGYS00003861	Myrold Alder Fir	Replacement Series. This well-designed experiment was established in the mid-1980s to evaluate competition between various mixtures of red alder and Douglas-fir. Experimental plots were established at two locations in Oregon: the Cascade Head Experimental Forest, a high-productivity site in the Coast Range and Site 1 of the Oregon Transect, and the H.J. Andrews Experimental Forest, a low-productivity site in the western Cascade Mountains similar to Site 3 of the Oregon Transect and an NSF LTER site. Both sites were clear-cut and burned in 1984 (Knowe and Hibbs, 1996). Cascade Head was planted the following year and the H.J.Andrews was planted in 1987. Both sites were planted with a design consisting of a replacement series of red alder and Douglas-fir planted on a 10-by-10 grid at 3-m spacing. Of the several mixtures available, we will use the 100 percent red alder and 100percent Douglas-fir plots. Each mixture is replicated three times within a site in a randomized complete block design. These sites have been studied intensively and significant metadata is available, including some information about microbial communities (Boyle et al., 2008; Boyle-Yarwood et al. 2008; Selmants et al., 2005; Vermes and Myrold, 1992; Yarwood et al., 2010). A total of 12 plots (2 sites, with 3 blocks per site, with each block containing plots of 2 tree species) will be sampled.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00003860	Spatial variation in arctic soil microbial communities in fire impacted permafrost ecosystems	Spatial variation in arctic soil microbial communities in fire impacted permafrost ecosystems	root:Environmental:Terrestrial:Soil
MGYS00003859	Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome	This is a preliminary study to examine the microbiota associated with the Cannabis plant. Soils samples from the bulk soil, soil associated with the roots, and the rhizosphere were extracted and the DNA sequenced. Roots from three independent plants of different strains were examined. These roots were obtained November 11, 2011 from plants that had been harvested in the summer. Future studies will attempt to analyze the soils and rhizospheres from the same location at different time points in the plant lifecycle.	root:Mixed
MGYS00003858	Spatial scale drives patterns in soil bacterial diversity.	Most soil processes, including microbial diversity and CO2 efflux, are extremely variable across spatial scales. The destructive and labor-intensive nature of traditional soil sampling and processing methods have hampered broad investigation of spatial heterogeneity in soil function. We collected microsamples of soil (&lt;3 g each) that provided enough material for DNA extraction to characterize the microbial community while reducing sample processing time that can result in DNA degradation and will dramatically enhance the spatial resolution of the of the diversity metrics. We collected twenty-five soil samples (0.7 cm dia X 5 cm deep) in a 10x10 cm grid at five points along a 36 m transect in each of six 36 x 20 m plots representing a low-diversity perennial grassland dominated by Panicum virgatum (fertilized and unfertilized treatments). The aim is to correlate microbial community structure with abiotic factors, which will help build a mechanistic understanding of feedbacks between soil microbes and ecosystem C fluxes.	root:Environmental:Terrestrial:Soil
MGYS00003857	Whole-grain wheat consumption reduces inflammation in a randomized controlled trial on overweight and obese subjects with unhealthy dietary and lifestyle behaviors: role of polyphenols bound to cereal dietary fiber	The study aims at characterizing the microbiota of the saliva in obese patients and in a randomly selected population of normal weight individuals. The overall scope is to explore the possibility that a peculiar microbial ecology characterizes the saliva of obese people and thus start wondering whether this can have any meaning on the pathology occurrence and development.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00003856	Viral communities associated with algal/coral interactions	Coral competition with benthic algae has been shown to alter the bacterial communities associated with the coral. Certain groups of algae lead to an increase in potential pathogens, potentially shifting the competitive advantage away from the coral and to the alga, while others do not. Here we investigate the changes in the viral communities associated with corals competing with different types of benthic algae to determine if similar changes occur in the viral component of the coral holobiont. We expect that algae that cause stress to corals will lead to the induction of eukaryotic viruses (e.g. infecting coral and/or zooxanthellae) and pathogen-associated phage, while algae that are inferior competitors to corals will not.	root:Mixed
MGYS00003855	Anaerobic ammonium-oxidizing bacteria in marine environments: widespread occurrence but low diversity	The respiratory reduction of nitrate (denitrification) is acknowledged as the most important process that converts biologically available nitrogen to gaseous dinitrogen (N2) in marine ecosystems. Observations during the last decade, however, indicate that anaerobic ammonium oxidation by nitrite (anammox) may be an important pathway for N2 formation and N removal in coastal marine sediments and in anoxic water columns of the oceans (e.g. Hulth et al., 2005). For about a decade we have explored this mechanism during N mineralization by a wide range of biogeochemical and molecular tools including e.g. benthic flux measurements and high resolution imaging of solute distributions, 15N amendments (single and coupled additions of 15NH4+, 14NO3- and 15NO3-), polymerase chain reaction (PCR), and qualitative and quantitative fluorescence in situ hybridization (FISH) (e.g. Brandsma et al., 2011; Schmid et al., 2007; Engstrom et al., 2005; Jetten et al., 2003). The present study focuses on benthic N-cycling in the deepest trough of a Swedish fjord where the anammox reaction contributes up to 79% of total N2 production. The relative importance of anammox for N2 release was directly correlated with a variety of biogeochemical parameters. The observed correlations indicated a competition between reductants for pore water nitrite during early diagenesis, and that additional factors (e.g. availability of Mn-oxides), superimposed on overall patterns of diagenetic activity, are important for determining absolute and relative rates of anammox in coastal marine sediments. Insight in the metagenome of the microbial community in this complex benthic environment would provide complementary and critical information to further understand N cycling in marine environments.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003854	Kilauea geothermal soils and biofilms	Examination of geothermal sites on Kilauea. One site involves a steaming tumulus that supports a stratified biofilm at about 50 C. The site other involves a forest that was destroyed by sub-surface heating. What exists at present are heated soils and biofilms that develop on steaming tree trunks. The latter include anoxygenic chloroflexi plus a variety of CO oxidizers.	root:Mixed
MGYS00003853	magnificent mongolian microbes	How the microbial ecology of the Mongolian Steppe shifts with climate change is a central question under investigation in the five-year PIRE Mongolia Project (Partnerships in International Research and Education, mongolia.bio.upenn.edu). Through this project, plant ecologists, biogeochemists, soil scientists, and climate modelers, are empirically documenting the effects of climate and land-use change on this arid ecosystem. Though many global change studies strive to link ecosystem shifts to microbial mechanisms, few have integrated edaphic, floristic and climatic data with microbial community data produced by Next-Generation Sequencing techniques, as is being done in the PIRE Mongolia Project. Moreover, the experimental design is comparable to numerous other climate change studies, allowing for the production of globally relevant data. Presently, 16S pyrosequencing data is being analyzed from the soil microbial community of this well replicated, multi-factorial experiment, which includes warming, watering, grazing and topography treatments. The average annual temperature at the Lake Hvsgl Long-Term Ecological Research (LTER) site has increased by 1.7C since 1963, and some of the greatest projected increases in temperature are associated with northern Mongolia. Hence, this site is therefore ideally suited for studying ecological shifts driven by climate change. One of the initial hypotheses in this moisture-limited system is that microbial diversity will decrease with warming and increase with watering. In order to unravel the microbial community composition of the system, 16S data will be integrated with spatial and temporal data that includes information on carbon and nitrogen fluxes, changes in plant phenology and shifts in climate.	root:Environmental:Terrestrial:Soil
MGYS00003852	Examination of Microbial Communities through a Freshwater/saltwater Transition Zone in Cenotes, Yucatan, Mexico	We have groundwater samples from karst sinkholes (cenotes) from Yucatan Peninsula, Mexico. Since the groundwater is permanently stratified, we have samples from fresh water, saline water, and the fresh-saline water interfaces from three different cenotes plus a control site that is an abandoned drinking water well at a hotel territory. Our three cenotes differ by depth (20-150 m), the amount carbon input from organic matter, light input, and proximity to the coast (increased influence from marine as well as anthropogenic sources). We have samples from the cenotes Xcolac, Calica and the hotel well from both dry and rainy seasons. In addition, we have dry season sediment samples from cenotes Xcolac and Calica.	root:Environmental:Aquatic
MGYS00003851	Gibbons tongue river 16S	The samples are river sediment particles (1.75-2.36 mm in diameter) taken from the top 20 cm of the river bed. For each sampling, we measured the coordinates, water temp, pH, dissolved oxygen percent, conductivity, whether the water was upwelling or downwelling.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00003814	Prokaryote populations of extant microbialites along a depth gradient in Pavilion Lake, British Columbia, Canada	The Pavilion Lake Research Project (PLRP) is an international, multi-disciplinary, science and exploration effort to explain the origin of freshwater microbialites in Pavilion Lake, British Columbia, Canada. Fossil microbialites represent some of the earliest remnants of life on ancient Earth, and were common from ~2.5 billion to 540 million years ago. Today, microbialites are found in environments where conditions are often too harsh for most organisms. However, the microbialites in both Pavilion and Kelly lakes have provided a new environment for the scientific community to study. These lakes demonstrate that large and uniquely shaped structures can also occur in non-extreme environments that also support fish, plants and other species. The microbialites of these modern lakes are relevant to our understanding of ancient microbiaites that were once common and diverse on early Earth, as such, Pavilion Lake has become an exciting field site for Earth scientists and astrobiologists who are interested in the application of the PLRP research to the search for life in our solar system and beyond. The PLRP was founded in 2004, and has grown in exciting new directions ever since. During the 2004 field season, PLRP scientists discovered microbialites in Kelly Lake, which is approximately 20 km NW from Pavilion Lake. The PLRP team will be taking their DeepWorker Science and Exploration (DSE) program to Kelly Lake in 2011. These research activities complement those that have taken place at Pavilion Lake since 2008, and will help to broaden our understanding of modern microbialite-rich environments. Further to these science activities, the PLRP supports a thriving human exploration research component. The focus of this program element is the development of operational technologies and strategies that facilitate scientific productivity and efficiency for future human scientific exploration of our Solar System.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00003813	NEON: Directions and resources for long-term monitoring in soil microbial ecology	The EMP_Pilot represents a subset of soil samples from the National Ecological Observatory Network (NEON) microbe prototype project. The EMP_Pilot was designed as a cross-facility comparison to quantify variation in sample processing and outputs from two sequencing facilities (Argonne National Labs, Lawrence Berkeley Labs) for quality assurance. The twelve soil samples that comprise the EMP-Pilot were collected in 2009 from four NEON core domain sites in Alaska, Florida,Utah, and Hawaii and represent gradients in ecosystem and soil properties. Information regarding the NEON Domain sites can be found at www.neoninc.org/science/domains. In 2013, soil biochemical, phospholipid fatty acid (PLFA), and targeted gene sequence data associated with the EMP-Pilot samples will be available through NEON's data sharing system.	root:Environmental:Terrestrial:Soil
MGYS00003812	Jurelivicius Antarctic cleanup	Antarctic Clean Up Project. Microcosms constructed at Brazilian Antarctic Station. Comandante Ferraz using diesel-oil contaminated soil. The contamination was caused by a blast and fire at the station in Ferbruary of 2012	root:Environmental:Terrestrial:Soil:Sand:Oil-contaminated
MGYS00003811	Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters.	Temporal and spatial variation of samples from a slow sand filter water purification system. This is illumina repeat of 454 data	root:Mixed
MGYS00003810	Diversity of carbonate deposits and basement rocks in continental and marine serpentinite seeps.	Biogeography of serpentinite-hosted microbial communities Microbial habitats hosted in ultramafic rocks constitute substantial, globally-distributed portions of the subsurface biosphere, occurring both on the continents and beneath the seafloor. The aqueous alteration of ultramafics, in a process known as serpentinization, creates energy rich, high pH conditions, with low concentrations of inorganic carbon which place fundamental constraints upon microbial metabolism and physiology. Despite their importance, very few studies have attempted to directly access and quantify microbial activities and distributions in the serpentinite-hosted ecosystems. We have initiated microbiological studies of alkaline springs and their associated carbonate deposits at three separate continental sites of serpentinization in Newfoundland, Italy, and California, and we are comparing these results to previous analyses of the Lost City hydrothermal field, near the Mid-Atlantic Ridge. We anticipate that the data from these samples will yield insight into the biogeography of serpentinite-hosted microbial communities and provide targets for further investigation of important biogeochemical processes.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00003809	Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments	Investigation into the effects of ocean acidification on microbial community structure and diversity in bioturbated coastal marine sediments. Samples taken from surface sediments and sediment from the burrow walls of Upogebia deltaura, a bioturbating shrimp species. Sediments were subjected to 5 different pH levels over a 14-week exposure period. Bacterial and archaeal 16S genes were sequenced.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003808	The role of macrobiota in structuring microbial communities along rocky shores	I hypothesize that microbial populations of the rocky intertidal of the northeast Pacific should be related to the nitrogen sources available to them, particularly the presence of animals and gradients in animals abundance. I thus have 48 collections for 16s analyses through the EMP at Argonne Labs (Gilbert Lab) designed to test whether microbial diversity increases in proximity to ammonium-excreting animals and whether the presence and absence of the abundant California mussel is a determinant of microbial diversity. All samples come from the coast of Washington state in 2009 and 2010, including 2 locales: Tatoosh Island and Second Beach. Microbial populations of the rocky intertidal areas of the northeast Pacific are little described compared to their open ocean counterparts. Thus, the work will be a novel investigation into diversity of this area as well as determinants of diversity.	root:Mixed
MGYS00003807	Canadian MetaMicroBiome Initiative samples from	Microbial communities harbor immense genetic diversity with enormous promise for applications in bioproduct synthesis and green chemistry. Metagenomic libraries provide a window into this largely untapped reservoir of nucleic acid diversity and individual libraries have been generated from a variety of terrestrial and aquatic environments. A limitation is that metagenomic libraries are typically project-specific and maintained in isolation. In an effort to enable the sharing of genetic material from environmental samples for the benefit of the scientific community, we are establishing the Canadian MetaMicroBiome Library. This repository will house composite soil samples that are characterized by extensive 16S rRNA gene and whole-genome sequencing, generating taxonomic profiles and metabolic pathway reconstructions for each sample. The sequence data will be submitted to existing public databases and linked with detailed physical, chemical and geographic characterization of the samples according to established metagenomic standards. Sample DNA will be used to construct high quality libraries in cosmid vectors, allowing for phenotypic screening in a broad range of microbial surrogate hosts. Phenotypic screening of metagenomic libraries provides access to truly novel functions that would otherwise be missed by sequence-based surveys of bulk community DNA or metagenomic libraries. MetaMicroBiome is being initiated with soil samples collected from across Canada, and initial libraries are being screened for novel glycoside hydrolase activities in multiple surrogate hosts. Once MetaMicroBiome is established, contributions of samples from other environments will be accepted for inclusion. The resulting resource will provide the international scientific community with access to a common collection of thoroughly characterized community-contributed genetic material in clone library format for custom phenotypic screens.	root:Environmental:Terrestrial:Soil
MGYS00003806	Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin	The Ocean Drilling Program (ODP) was funded by the U.S. National Science Foundation and 22 international partners (JOIDES) to conduct basic research into the history of the ocean basins and the overall nature of the crust beneath the ocean floor using the scientific drill ship JOIDES Resolution. Joint Oceanographic Institutions, Inc. (JOI), a group of 18 U.S. institutions, was the Program Manager. Texas A&amp;M University, College of Geosciences was the Science Operator. Columbia University, Lamont-Doherty Earth Observatory provided Logging Services and administered the Site Survey Data Bank. Any opinions, findings, and conclusions or recommendations expressed in these documents are those of the author(s) and do not necessarily reflect the views of the National Science Foundation, the participating agencies, Joint Oceanographic Institutions, Inc., Texas A&amp;M University, or Texas A&amp;M Research Foundation.Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100 to 2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00003800	Dominguez sleep deprived flies	The sleep deprivation experiment was done in wild flies or in pumilio knockdown expression (using RNA interference). Pumilio seems critical for the homeostatic response to sleep deprivation.When wild flies are sleep deprived, they respond by sleeping more after the deprivation stimulus is removed. Pumilio RNAi (expression knockdown) sleep less after sleep deprivation. Analyzing these samples, we can see if sleep deprivation leads to the disregulation of intestinal microbes, and if pumilio plays a role on this regulation.	root:Host-associated:Insecta
MGYS00003798	The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys (NZTABS)	Terrestrial Antarctic Biocomplexity Survey. The New Zealand Terrestrial Antarctic Biocomplexity survey (NZTABS) is the largest and most comprehensive landscape scale biological study ever undertaken. The Antarctic Dry Valley system offers unprecedented access to a trophically simple biological system that appears to be solely structured by abiotic environmental drivers. The primary biology in this system is microbial. Linking a range of high-resolution remote sensing data with over 600 person days in the field, the 220 km2 3 valley NZTABS survey now includes over 650 spatially strategic soil samples targeting the diversity habitats in the system. Each sample and site has been analyzed for a range of geochemistry as well as a comprehensive survey of biology (all visible vegetation, insects, all infauna and flora (nematodes, rotifers, tartigrades), and microbiology). The initial microbial surveys (Bacteria, Cyanobacteria, fungi) were carried only using DNA fingerprinting analysis. All of the information has been placed into and interactive GIS framework allowing direct relationships between all parameters to be queried. The central objective of the survey is to determine the primary environmental drivers for structuring the biology to enable us to develop a model that can predict the distribution of biology across the entire Dry Valley system (6500 km2) using only remote sensing. Ultimately we hope that the model will be able to identify areas of sensitivity or unusual complexity that should be protected.	root:Mixed
MGYS00003793	McGuire Nicaragua coffee soil	Coffee plantations in northern Latin America coincide with areas of extremely rich biodiversity. Recent advances by fair trade organizations have stimulated sustainable agriculture in the form of shade coffee plantations as a way of reconciling economic and conservation targets; however, the shade management techniques vary between sites and result in different canopy assemblies across farms over time. The effect of differing canopy regimes on microbial communities are poorly understood but guide nutrient cycling, crucial for both agriculture and the maintenance of ecosystem diversity. The goal of this project is to explore the relationship between managed canopies, land use history, and soil microbial communities in Nicaraguan shade-coffee plantations, and use this information to develop a set of guidelines for soil management to improve soil quality.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00003786	Environmental metagenomic interrogation of Thar desert microbial communities	Interrogation soil microbial community from arid and semiarid regions of the Thar Desert is essential. Until recently the studies on Thar desert soil microbes mostly focused on cultivation alone. Here we use culture independent approach. T-RFLP result shows that there is a significant difference among arid and semiarid soil bacterial communities, they clustered according to the sample type arid-soil, semi-arid soil, sand dune. Our clone library showed difference in the bacterial communities among arid-soil, semi-arid soil, sand dune respectively.	root:Environmental:Terrestrial:Soil:Desert
MGYS00003785	Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm.	Soil pH effect on soil metagenome Craibstone, Scotland soil maintained at different pH levels (4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5) and harvested in 2006 and 2007	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00003783	Protist diversity in a permanently ice-covered Antarctic Lake during the polar night transition	The McMurdo Dry Valleys of Antarctica harbor numerous permanently ice-covered lakes, which provide a year-round oasis for microbial life. Microbial eukaryotes in these lakes occupy a variety of trophic levels within the simple aquatic food web ranging from primary producers to tertiary predators. Here, we report the first molecular study to describe the vertical distribution of the eukaryotic community residing in the photic zone of the east lobe (ELB) and west lobe (WLB) of the chemically stratified Lake Bonney. The 18S ribosomal RNA (rRNA) libraries revealed vertically stratified populations dominated by photosynthetic protists, with a cryptophyte dominating shallow populations (ELB-6m; WLB-10m), a haptophyte occupying mid-depths (both lobes 13m) and chlorophytes residing in the deepest layers (ELB-18 and 20m; WLB-15 and 20m) of the photic zone. A previously undetected stramenopile occurred throughout the water column of both lobes. Temporal variation in the eukaryotic populations was examined during the transition from Antarctic summer (24-h sunlight) to polar night (complete dark). Protist diversity was similar between the two lobes of Lake Bonney due to exchange between the photic zones of the two basins via a narrow bedrock sill. However, vertical and temporal variation in protist distribution occurred, indicating the influence of the unique water chemistry on the biology of the two dry valley watersheds.	root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
MGYS00003780	Catlin Arctic Survey 2010 L3	The Catlin Arctic Surveys deployed an Explorer Team (years 2009, 2010, 2011) and Ice Base (years 2010, 2011), to examine sea ice thickness (addressing the rate of loss), and the phenomena of ocean acidification and thermohaline destabilisation (two key consequences of sea ice loss). The climate change-driven themes of the Catlin Arctic Surveys introduced each year (sea-ice loss, 2009, ocean acidification, 2010, thermohaline destabilisation, 2011) are inter-related, with potential global effects. These samples are from the 2010 expedition.	root:Environmental:Aquatic:Marine
MGYS00003773	Rees Vulcano island MedSea	A survey was performed in nearshore waters of the Island of Vulcano, Italy during May 2011 to investigate the impact of elevated CO2 from volcanic vents on the phytoplankton in local seawater populations. Samples were collected onto sterivex filters on two days at a range of 4 pH levels on each day.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00003772	New Zealand Free Air Carbon dioxide Enrichment soil samples	Rhizosphere soil samples from Rings 1-6 of NZ FACE (New Zealand Free Air Carbon Dioxide Enrichment) experiment. Each ring pasture has an atmosphere that is either enriched with 475 ppm CO2 or ambient atmospheric CO2 throughout the photoperiod and throughout the photoperiod since 1997. Each sample also comes from either an area exposed to warming treatment since 2009 or an area with no warming treatment.	root:Environmental:Terrestrial:Soil
MGYS00003769	Chu Changbai mountain soil	We have collected 24 soil samples in different elevations in Changbai Mountain, northeastern China, and investigated the distributions of microbial communities and functions along elevation. Climate warming often results in increased forest fire. We have collected 60 soil samples in Greater Khingan Mountains, northern China, and investigated microbial response to forest fire and microbial succession after post-fire.	root:Environmental:Terrestrial:Soil
MGYS00003765	Halophilic Communities as a Source for Novel Lignocellulolytic Enzymes	The goal of my project has been to identify microbes and enzymes tolerant of varying levels of salinity. The driving hypothesis for this work is that salt tolerance correlates with ionic liquid tolerance. Ionic liquids are presently the best means of pretreating lignocellulosic biomass to better enable its biological conversion into useful products at biorefineries. Ionic liquid tolerance enzymes and microbes with help consolidate the various steps in the production of biofuels and reduce the impact of residual ionic liquids in feedstock materials, thereby reducing processing costs. We have collected samples from Puerto Rico and the San Francisco Bay in California from environments representing a gradient of salinities. Both sediment-associated and planctonic microbial community samples were collected and enrichments have been prepared from some of the samples. Each of the environments samples are also of great interest to the broader environmental microbiology scientific community including planctonic samples from the Bioluminescent Bay near La Parguera, PR and sediment samples from Thalassia testudinum beds near the bay.	root:Mixed
MGYS00003759	Distinct microbial communities associated with buried soils in the Siberian tundra.	Around 1700 Gt carbon are stored in the Northern latitude permafrost regions (Schuur et al, BioScience 2008). This is more than double the size of the atmospheric carbon pool but the estimates are still quite uncertain and might be even higher. It is however estimated that 25 percent of this large carbon pool in Arctic soils will be lost by the end of the 21st century and will be released to the atmosphere as CO2 (Gruber et al., 2004). The subduction of organic-rich material from the surface to deeper layers caused by repeated freezing and thawing of the active layer during Arctic summer is assumed to be a major mechanism of carbon storage in the Arctic. These cryoturbations are spatially widely distributed and store high amounts of soil organic carbon (SOC). Decomposition of recent cryoturbated carbon is strongly retarded thereby essentially taking out this fraction of SOC from the current carbon cycle. Todays primary concern and research focus is the vulnerability of cryoturbated SOC due to global warming which is predicted to lead to intensified decomposition and elevated greenhouse gas emissions. Here we present a study that aims to provide a comprehensive picture of the microbial community structure of permafrost-affected and cryoturbated soils of different Northern latitude permafrost regions in Siberia and Greenland. For this purpose, soil samples were collected in northeast Siberia in a transect along the upper Kolyma river, and in the Zackenberg region, Greenland. The sampling scheme covered several bioclimatic subzones and vegetation types. We are currently analysing data retrieved from SSU amplicon sequencing, the quantification of several functional groups involved in carbon cycling and physico-chemical analyses in order to predict potential microbial regulators in SOC storage. This study is part of the multinational CryoCARB project (for further information, see: www.cryocarb.net).	root:Environmental:Terrestrial:Soil
MGYS00003754	Brazilian Antarctic cleanup 16S	Contaminated soil collected near from Brazilian Antarctic Station Comandante Ferrar after fire led to an explosion with diesel contamination of soil/tundra in February 2012	root:Environmental:Terrestrial:Soil
MGYS00003750	Defining seasonal marine microbial community dynamics	In order to facilitate conservation of biological diversity we require comprehensive knowledge of the microbial ecology of an ecosystem. As the vast majority of microbes are not readily culturable, we must use molecular tools to investigate their diversity and function in marine ecosystem. However, it is still difficult to understand their role in ecological processes. Here we present a study to characterize changes in the diversity and metabolic activity of the heterotrophic bacterial community over an annual cycle in the Western English Channel. For this purpose, surface water samples were collected from the sampling station, L4, every week for a year. The respiration rate of the heterotrophic microbial community was determined from the decrease in dissolved oxygen content of the less than 0.8m size-fraction of the sea water. We are currently analyzing captured DNA using 16S rRNA amplicon and shotgun metagenomic pyrosequencing to determine the diversity and functional profile of the active bacteria in order to characterize annual changes in the active bacterial community. This dataset sits within the larger framework of the Western English Channel bacterial diversity time series (2003-2009) and the seasonal metagenomic and metatranscriptomic studies associated with this site. We demonstrate that respiration rates are characterized by specific microbial diversity and function at different times of year, highlighting seasonal fluctuation in this ecosystem.	root:Environmental:Aquatic:Marine
MGYS00003748	Song Colorado freshwater fish	Microbiota of slime and gut samples from different species of freshwater fish from the Colorado River.	root:Mixed
MGYS00003736	Microbial Community and Ovine Host Responses to Early and Late Haemonchus contortus Infection	This work seeks to explore the impact of early and late Haemonchus infection on abomasal and ruminal microbial community, and ovine host. Overall, these results indicate that Haemonchus infection plays a crucial role for shaping abomasal and ruminal microbial community composition, and diversity.	root:Host-associated:Mammals:Digestive system:Stomach
MGYS00003735	Migratory locust	Migratory locust gut microbiome isolated from Saudia Arabia	root:Host-associated:Insecta:Digestive system
MGYS00003732	Single Batch Fermentation System Simulating Human Colonic Microbiota_Ulcerative colitis	KUHIMM	root:Engineered:Lab enrichment
MGYS00003731	Gut microbiome response to short term dietary intervention in reactive hypoglycemia subjects	Gut microbiome response to short term dietary intervention in reactive hypoglycemia subjects	root:Host-associated:Human:Digestive system:Intestine
MGYS00003730	YWI microbiome study	Anaerobic digestion process in waste water treatment plants is a well-established method of converting organic material to a biogas. However, the microbiomes involved in AD are not fully understood highlighting the importance of community profiling study for getting essential information on how the communities are structured. Here, we profiled microbial communities of fifteen full-scale anaerobic digesters operated by regional waste water treatment company. Using amplicon 16S sequencing of V4 regions, we observed a presence of highly diverse microbiomes and differences between samples associated with digesters operational status and feedstock pre-treatment. Most abundant phyla and their members were revealed showing the presence of a core microbiome in these reactors.	root:Engineered:Wastewater:Water and sludge
MGYS00003729	Research on Airborne Ice Nucleating Species	Research on Airborne Ice Nucleating Species	root:Environmental:Air
MGYS00003727	The study aims to study the transcriptional response of soil communities to the artificial pollution with toluene	This study project for a complete characterization and interpretation of the functional response of local microbial communities present in different type soils upon contamination of toluene.	root:Environmental:Terrestrial:Soil:Clay
MGYS00003726	Core MV1012-46.9-JPC2 aDNA metagenomes and negative control	Illumina 4000 sequencing of MV1012-46.9-JPC2 sediment core	root:Environmental:Aquatic:Marine:Sediment
MGYS00003724	Resistflow-WWTPs-16S DNA data (unpublished)	This is unpublished data. Any use of the data in a publication, meta-analysis, or global survey should get the approval from the corresponding author (helmut.buergmann@eawag.ch). RESIST-Flow: Understanding resistance gene flow during passage of wastewater treatment	root:Engineered:Wastewater
MGYS00003721	photoautotrophic_biofilm	Samples of this study were collected of a super-intensive shrimp culture using photoautotrophic biofilm as complementary aquafeed	root:Environmental:Aquatic
MGYS00003720	Microbial community response to different substrates during anaerobic digestion	This study investigated the changes of microbial community response to anaerobic digestion of pig manure, chicken manure, sewage sludge, sterilized pig manure, sterilized chicken manure and sterilized sewage sludge. The authors tried to clarify the role of the substrate microbial community on the fate of ARGs during anaerobic digestion.	root:Engineered:Wastewater:Water and sludge
MGYS00003718	Lane 6 Analysis	Negative control lane for ancient DNA taken from core MV1012 46.9	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00003715	LogMPIE: Landscape Of Gut Microbiome - Pan India Exploration	LogMPIE is an observational, multi-center, cross geography and age-group study. The primary objective of the study was to report the microbiome baseline across India. The study reported data from over 1000 subjects. Additionally, for individual subjects, factors such as BMI, lifestyle, dietary habits and gender were recorded.  The study was conducted by Tata Chemicals Limited.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003712	The fecal microbiota in L-DOPA naive PD patients	Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both, the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naïve PD patients might also serve as a biomarker.We thus compared the fecal microbiomes of 31 early stage, L-DOPA-naive PD subjects to 28 age matched controls by metagenomic analysis.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003709	Ammonia effect on food waste anaerobic digestion	Food waste has high organic content that enables it to become an attractive feedstock for anaerobic digestion. However, food waste anaerobic digestion often suffers from a poor performance and instability caused by a high ammonium concentration resulted from a high nitrogen content in the feedstock. This study aimed to trace dynamic changes in microbial populations during food waste digestion adapted to increasing ammonium concentration, using both biofunctional information obtained from radioactive isotope tracer technique, analysis of 16S rRNA amplicons and fluorescence in situ hybridisation.	root:Engineered:Wastewater:Water and sludge
MGYS00003708	Catchment sources of microbes	We will undertake the first ever large-scale microbiome exploration in Melbourne water catchments to provide a baseline dataset on the composition of microbial communities in animals, water and the environment to underpin drinking water quality management.	root:Host-associated:Mammals:Digestive system
MGYS00003707	Puerto Rico and Plantanal	Part of the Western acculturation project - Plantanal and D1-30 longitudinal babies from PR	root:Host-associated:Mammals
MGYS00003706	Peralta starlings	We explored how experimental changes in humidity and temperature affect female incubation performance and nest environment and bacterial community on eggshells. We also explored the relationship between bird ectoparasites and egg colour, with bacterial load on eggshells and hatching success.	root:Host-associated:Birds
MGYS00003705	Microbiome of honey bees from Puerto Rico	Samples of bees, royal jelly from honey bees (Apis mellifera) in Puerto Rico. Includes whole head, whole larva, whole pupa, whole gut and royal jelly. Effect of Tetracycline application.	root:Host-associated:Insecta
MGYS00003702	Effect of natural additives on the rumen microbiome following feeding of beef cattle with a blend of natural additives	The indiscriminate use of antibiotics in animal production and human consumption is related to the increase of microorganisms resistant to a wide class of chemical compounds. Thus, alternatives are sought for the use of growth promoters and antimicrobials in animal production. Recent research demonstrates the potential of applying essential oils (OEs) in several areas as potential substitutes for antibiotics. This is because they have characteristics similar to these products. However, there are few data in the literature regarding the actions of OEs in axenic cultures of anaerobic ruminal microorganisms. Thus, a project is proposed to: evaluate the efficacy of essential oils from the sequencing of rumen microorganisms of finished cattle in confinement; determine the genes expressed by the ruminal microbiota; identify pure cultures affected by the presence of OEs; to observe the effect of OEs on ruminal bacteria by electron microscopy; to evaluate the microbial resistance of OEs in ruminal bacteria; and evaluate the metatranscriptome of axenic culture of ruminal bacteria cultured with OEs. It is expected to identify species strongly affected by OEs and metabolic routes and mechanisms used by ruminal microorganisms to deal with the presence of OEs and their active compounds. Queen's University of Belfast is part of the Russel Group, which contains the 24 best institutions in the UK. An important part of Queen's University's research is related to food safety. Thus, the university has highly qualified equipment and technical staff for research related to the entire food production chain.	root:Host-associated:Animal:Digestive system
MGYS00003699	Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau	Continent-scale biogeography has been extensively studied in soils and marine systems, but little is known about biogeographical patterns in non-marine sediments. We used barcode pyrosequencing to quantify the effects of local geochemical properties and geographic distance for bacterial community structure and membership, using sediment samples from 15 lakes on the Tibetan Plateau (4–1670 km apart). Bacterial communities were surprisingly diverse, and distinct from soil communities. Four of 26 phyla detected were dominant: Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria, albeit 20.2% of sequences were unclassified at the phylum level. As previously observed in acidic soil, pH was the dominant factor influencing alkaline sediment community structure, phylotype richness and phylogenetic diversity. In contrast, archaeal communities were less affected by pH. More geographically distant sites had more dissimilar communities (r = 0.443, P = 0.030). Variance partitioning analysis showed that geographic distance (historical contingencies) contributed more to bacterial community variation (12.2%) than any other factor, although the environmental factors explained more variance when combined (28.9%). Together, our results show that pH is the best predictor of bacterial community structure in alkaline sediments, and confirm that both geographic distance and chemical factors govern bacterial biogeography in lake sediments.	root:Environmental:Aquatic:Sediment
MGYS00003698	Hawaii Kohala Volcanic Soils	We are studying a network of sites along an extreme rainfall gradient that ranges from 200 mm to 3500 mm/year over a short distance of 12 km due to orographic moisture interception by Kohala Mountain in Hawaii. This climate sequence is ideal for studying soil development because the effects of rainfall on soil properties can be isolated from other environmental factors. Unlike most gradients that span arid to wet tropical climates, soil forming factors other than rainfall vary minimally across these sites: Parent material and topography are constant and there is minimal variation in vegetation and climate factors other than rainfall. These unique circumstances make this gradient a powerful model field system to understand the effects of rainfall variation on soil development and ecosystem biogeochemistry, as demonstrated by the seminal work done in these areas by our collaborators Peter Vitousek (Stanford) and Oliver Chadwick (UCSB). In spite of the wealth of ecosystem and soils research conducted at these sites, there is little known about soil microorganisms in these soils and no community characterization using DNA sequencing. We will sequence soil 16S rRNA genes from 13 different locations along the gradient. At each location we have samples from each of three depths (0-15 15-30, 30-50 cm) and four field replicates for each depth at most locations.	root:Mixed
MGYS00003691	Long Term Soil Productivity project	The Long-Term Soil Productivity (LTSP) study was established to demonstrate how alteration of soil porosity and organic matter (two of the more alterable soil properties) would affect soil processes and site productivity throughout forest lands of North America. The experimental design is a 3 x 3 factorial with 3 levels of organic matter loss and 3 levels of soil compaction. The organic matter (OM) treatments include stem-only harvest, whole-tree harvest, and forest floor displacement to mineral soil. The compaction treatments include no compaction, light compaction (2 cm impression), and heavy compaction (4 cm impression). In BC, we have three replicate blocks in the Sub-Boreal Spruce (SBS) biogeoclimatic zone, three in the Boreal White and Black Spruce (BWBS) biogeoclimatic zone, three in the Interior Douglas-fir (IDF) biogeoclimatic zone on common, acidic forest soil, three in the IDF on sensitive calcareous soils, and two replicates have been installed in the Interior Cedar Hemlock (ICH) biogeoclimatic zone that complete an installation initiated by the USDA Forest Service in Idaho.	root:Environmental:Terrestrial:Soil
MGYS00003688	Myrold Oregon transect	OTTER. The Oregon transect consists of sites that follow a gradient of net primary productivity from the highest productivity forests in the world (coastal Sitka spruce) to semi-arid juniper woodlands (Fig. 1). This gradient represents the range of net primary productivity found in North America (Runyan et al., 1994). In addition to differences in productivity and vegetation composition, these sites also display a range of soil types. Extensive metadata are available for these sites (Gholz, 1982; Myrold et al., 1989; Runyan et al., 1994; Stark and Hart, 1997; daac.ornl.gov), but no information is available on the microbial communities of these soils. A total of 6 sites will be studied, with 3, 30-by-30 m plots established at each site to provide some information about within site variability, which will result in 18 samples for analysis.	root:Environmental:Terrestrial:Soil
MGYS00003687	Biodiversity and Functional Patterns of Microbial Assemblages in Postglacial Pond Sediment Profiles	The purpose of this project is to characterize biodiversity and functional patterns of microbial assemblages in sediment profiles of postglacial ponds that have experienced different histories of human land-use change, and to compare these patterns with a suite of temporal, biological and geochemical markers.	root:Environmental:Aquatic:Sediment
MGYS00003684	Spirito monensin cow hindgut	This study aims to investigate the effect of monensin (Rumensin, Elanco-Eli Lilly Co.) on the microbial community structure of the cow hindgut. Monensin is an ionophore antibiotic administered to cattle and dairy cows to increase their feed efficiency by altering rumen fermentation. Monensin acts by changing the activity of specific metabolic pathways, leading to an increase in propionate concentrations and a decrease in acetate and butyrate concentrations in the cow rumen. Previous studies conducted on the effect of monensin on rumen microbial community structure have led to differing conclusions. In addition, few studies have been conducted to assess the effect of monensin on the microbial community structure elsewhere in the cow digestive tract, such as in the cow hindgut. For the current study, manure was collected, over a period of three months, from eight dairy cows housed at the Teaching and Research Center at Cornell University. Four of the cows were fed a control diet containing no monensin. The other four cows were fed a diet with measured incrementally increasing amounts of monensin. To investigate the effect of monensin on the microbial community composition of the cow hindgut, a total of 184 rectal grab samples were collected from the eight cows over the three month period. Once collected, the samples were processed and stored in a -80degreeC freezer for later microbial community composition analysis. The samples were then extracted using the MO BIO Powersoil-htp 96 Well Soil DNA Isolation Kit and frozen at -80degreeC until they could be sent for further processing and sequencing.	root:Host-associated:Animal:Digestive system:Fecal
MGYS00003681	Garcia bird gut microbiome	Characterization of bird gut microbiome - gizzard, upper intestine, lower intestine from birds in Venezuela. With Maria -Gloria Dominguez Bello	root:Host-associated:Birds:Digestive system
MGYS00003677	Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography	Interactions between hosts and associated microbial communities can fundamentally shape the development and ecology of 'holobionts', from humans to marine habitat-forming organisms such as seaweeds. In marine systems, planktonic microbial community structure is mainly driven by geography and related environmental factors, but the large-scale drivers of host-associated microbial communities are largely unknown. Using 16S-rRNA gene sequencing, we characterized 260 seaweed-associated bacterial and archaeal communities on the kelp Ecklonia radiata from three biogeographical provinces spanning 10° of latitude and 35° of longitude across the Australian continent. These phylogenetically and taxonomically diverse communities were more strongly and consistently associated with host condition than geographical location or environmental variables, and a 'core' microbial community characteristic of healthy kelps appears to be lost when hosts become stressed. Microbial communities on stressed individuals were more similar to each other among locations than those on healthy hosts. In contrast to biogeographical patterns of planktonic marine microbial communities, host traits emerge as critical determinants of associated microbial community structure of these holobionts, even at a continental scale.	root:Host-associated:Plants
MGYS00003675	Growth phase-associated changes in the transcriptome of Pseudomonas veronii 1YdBTEX2 in minimal media with toluene.	To study which genes are specifically induced during the different growth phases in toluene, which could indicate the changes in BTEX metabolism as well as the biological processes affected during the different growth phases, a controlled RNA-seq transcriptome analysis was carried out. Gene expression levels were analyzed from cultures upon inoculation (T0), after 4(T4) and 24(T24) hours after inoculation in minimal medium with toluene.	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00003673	Microbial community of the bulk soil and rhizosphere of rice plants over its lifecycle	Soil and rhizosphere samples from 4 cultivars of Japanese rice from planting to harvest	root:Mixed
MGYS00003670	Ezenwa Cape Buffalo	Cape Buffalo in South Africa were sampled (fecal) in 2011	root:Host-associated:Mammals:Digestive system
MGYS00003668	AD-culturomics	Metagenomic studies on microbial ecosystems provide in silico confirmation that these communities consist of thousands of microbial species of which the majority remains poorly characterised and/or uncultured. Specifically, in anaerobic microbial communities that govern conversion of organic matter to biogas, isolation approaches are limited. Following this notion, the project proposes to isolate, identify and archive novel microorganisms from anaerobic digesters (AD) using the isolation chips technique. “Artificial” seed communities could then be created to enhance energy recovery from AD systems by increasing production of biogas.	root:Engineered:Wastewater:Water and sludge
MGYS00003666	Bird Egg Shells from Spain	Study of bird egg shells from Spain	root:Host-associated:Birds
MGYS00003659	Longitudinal analysis of microbial interaction between humans and the indoor environment	The Home Microbiome Project was a seed funding initiative to generate exploratory data on the dynamic microbial relationships between people and their homes. The proposal aimed to tackle two core hypotheses: 1-The dominant microbiota associated with human skin is rapidly transferred to surfaces in a home, masking microbiota signatures left from previous interactions with the surface, 2-The composition and relative abundance of members of the dominant microbial community associated with human skin are maintained following transfer to a surface. To test these hypotheses the project aimed to generate 16S rRNA data from hand, foot and gut samples of 18 individuals in seven representative groups. In addition, we proposed to collect surface samples from two internal door knobs, a kitchen counter, the bedroom and bathroom floors and a light switch from each surveyed home, every-other day for two weeks prior to moving in and four weeks following the move into a new home (Table 1). The Home Microbiome Study collected a total of 1,609 microbial samples from seven houses, 18 people, three dogs, and one cat. The people comprised 3 children under 10 years old, and 15 adults over 20 years old. The children comprised 2 males and 1 female in separate houses. The adults comprised 7 females and 8 males. Metadata regarding basic demographics of the individuals and temp, humidity and dew point for each room being analyzed.	root:Mixed
MGYS00003656	EMG produced TPA metagenomics assembly of the Thermophilic AOM enrichment (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA286178.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine
MGYS00003655	EMG produced TPA metagenomics assembly of the Baltic marine sediment metagenome (marine sediment metagenome) data set.	The marine sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA308531.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003654	EMG produced TPA metagenomics assembly of the Chandeleur Islands 2015 Metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA390775.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary, Sediment.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00003652	EMG produced TPA metagenomics assembly of the Anammox enrichment reactor metagenome () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA383778.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003651	EMG produced TPA metagenomics assembly of the Biogas fermentation microbial communities from Germany - Plant 4 DNA2 metagenome (biogas fermenter metagenome) data set.	The biogas fermenter metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA311383.  This project includes samples from the following biomes: Engineered, Biogas plant, Wet fermentation.	root:Engineered:Biogas plant:Wet fermentation
MGYS00003650	EMG produced TPA metagenomics assembly of the Biogas fermentation microbial communities from Germany - Plant 2 DNA2 metagenome (biogas fermenter metagenome) data set.	The biogas fermenter metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA311379.  This project includes samples from the following biomes: Engineered, Biogas plant.	root:Engineered:Biogas plant
MGYS00003649	EMG produced TPA metagenomics assembly of the Initial activated sewage sludge GCZ12 Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA268585.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003648	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 14_58_20_212_A1 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406035.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003647	EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R2 time_0 SIP DNA metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340519.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003646	EMG produced TPA metagenomics assembly of the Stanley AS Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA273520.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003645	EMG produced TPA metagenomics assembly of the Cellulose adapted compost microbial communities from Newby Island Compost Facility, Milpitas, CA, USA - Passage2 60B metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366478.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00003644	EMG produced TPA metagenomics assembly of the Evaluation of Enriched Background Microflora of Raw Milk Cheese Spiked with E. coli O157:H7 and E. coli O103 using Next-Generation Sequencing Technology (E.coli O157 and E.coli O121 spiked in cheddar cheese) data set.	The E.coli O157 and E.coli O121 spiked in cheddar cheese Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA430402.  This project includes samples from the following biomes: Engineered, Food production, Dairy products.	root:Engineered:Food production:Dairy products
MGYS00003643	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1555A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365247.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003642	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1546B-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367282.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003641	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1449A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367275.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003640	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Flood tide non-ETM metaG S.545 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365283.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003639	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Flood tide ETM metaG S.725 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365282.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003638	EMG produced TPA metagenomics assembly of the Marine microbial community from La Parguera, Puerto Rico - BB Mangrove B Liquid metagenome (marine sediment metagenome) data set.	The marine sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336774.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal, Sediment.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00003637	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - C0912_C33A6_35 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330319.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003636	EMG produced TPA metagenomics assembly of the Oceanic oxygen minimum zone microbial communities that regulate carbon cycling - Sample ETNP201406SV203 (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA323948.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00003635	EMG produced TPA metagenomics assembly of the Pelagic Microbial community sample from North Sea - COGITO 998_met_04 Metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA266676.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003634	EMG produced TPA metagenomics assembly of the High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-6-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365936.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003633	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P5a_0mM metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441889.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003632	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P3_4mM metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441895.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003631	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P5a_16mM metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441892.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003630	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P5a_4mM metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441890.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003629	EMG produced TPA metagenomics assembly of the High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-5-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365935.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003628	EMG produced TPA metagenomics assembly of the High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-4-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365934.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003627	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_224 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365236.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00003626	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_187 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365232.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00003625	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_208 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365233.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00003624	EMG produced TPA metagenomics assembly of the Metagenome of the microbiota of Chestnut honey from a  bio-diversified environment (Metagenome of the microbiota of Chestnut honey from a bio-diversified environment) data set.	The Metagenome of the microbiota of Chestnut honey from a bio-diversified environment Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA358537.  This project includes samples from the following biomes: Engineered, Food production.	root:Engineered:Food production
MGYS00003623	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNNA4_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340769.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003622	EMG produced TPA metagenomics assembly of the Agave microbial communities from Guanajuato, Mexico -  At.P.e (plant metagenome) data set.	The plant metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340603.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00003621	EMG produced TPA metagenomics assembly of the Final activated sewage sludge GCZ13 Metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA268638.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003620	EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R2_A C13 SIP DNA metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340514.  This project includes samples from the following biomes: Engineered, Biogas plant.	root:Engineered:Biogas plant
MGYS00003618	EMG produced TPA metagenomics assembly of the compost enrichment single cell ciliate 20uM1 metagenome N11 metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366625.  This project includes samples from the following biomes: Engineered, Solid waste, Composting, Bioreactor.	root:Engineered:Solid waste:Composting:Bioreactor
MGYS00003617	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1556B-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365251.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003616	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1547B-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367288.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003614	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWPA TP2 #1 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441402.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Brackish
MGYS00003613	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWPA TP1 #2 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441400.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Brackish
MGYS00003612	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWP TP1 #2 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441397.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Brackish
MGYS00003611	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - fosmids plate 3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330365.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003609	EMG produced TPA metagenomics assembly of the A plaque on both your houses: Exploring the history of urbanisation and infectious diseases through the study of archaeological dental tartar.	The A plaque on both your houses: Exploring the history of urbanisation and infectious diseases through the study of archaeological dental tartar Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12831.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00003607	EMG produced TPA metagenomics assembly of the compost enrichment single cell ciliate 20uM1 metagenome O22 metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366627.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00003605	Shotgun metagenomic analysis of Lake Paajarvi sediment microbes.	We analyzed microbes in the sediments of a boreal nitrate-rich Lake Paajarvi using shotgun metagenomics.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00003604	EMG produced TPA metagenomics assembly of the Metagenomic data simulated to represent a complex microbial community (SimulatedMG) data set.	The SimulatedMG Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB27585.  This project includes samples from the following biomes: Host-associated, Human, Digestive system.	root:Engineered:Bioreactor
MGYS00003601	EMG produced TPA metagenomics assembly of the Metagenomic analysis of the Binga Hot Springs in Zimbabwe for Microbial Diversity and Hydrolytic Enzymes (Binga Hot Springs) data set.	The Binga Hot Springs Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB7848.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs.	root:Environmental:Aquatic:Thermal springs
MGYS00003600	EMG produced TPA metagenomics assembly of the PHOTOHETEROPHY IN A MESOSCALE ANTICYCLONIC EDDY IN THE EASTERN MEDITERRANEAN SEA (Mesoscale_eddy) data set.	The Mesoscale_eddy Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6559.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic, Photic zone.	root:Environmental:Aquatic:Marine:Oceanic:Photic zone
MGYS00003599	EMG produced TPA metagenomics assembly of the Coral microbial communities from La Bocana,Puerto Morelos, Mexico - Diploria C A metagenome metagenome (coral metagenome) data set.	The coral metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364874.  This project includes samples from the following biomes: Host-associated, Invertebrates, Cnidaria, Coral.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00003597	EMG produced TPA metagenomics assembly of the Oral Microbiome (human oral metagenome) data set.	The human oral metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA230363.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00003596	EMG produced TPA metagenomics assembly of the Microbial organisms associated to corals Metagenome (coral metagenome) data set.	The coral metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA246443.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Coral reef	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00003595	EMG produced TPA metagenomics assembly of the Yilgarn Craton Acid Salt Lake Sediment Metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA260488.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lotic, Acidic.	root:Environmental:Aquatic:Freshwater:Lotic:Acidic
MGYS00003594	EMG produced TPA metagenomics assembly of the 5m sample from a Rifle, CO sediment metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA263282.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lotic, Sediment.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00003592	EMG produced TPA metagenomics assembly of the human gut metagenome (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA324672.  This project includes samples from the following biomes: Host-associated, Human, Digestive system.	root:Host-associated:Human:Digestive system
MGYS00003591	EMG produced TPA metagenomics assembly of the sediment metagenome Raw sequence reads (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330825.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lotic, Sediment.	root:Environmental:Aquatic:Freshwater:Lotic:Sediment
MGYS00003590	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MMD3.0 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330130.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003581	EMG produced TPA metagenomics assembly of the Healthy human gut virome (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA308867.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system
MGYS00003580	EMG produced TPA metagenomics assembly of the Fecal Microbiota Transplantation experiments () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA353655.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00003579	EMG produced TPA metagenomics assembly of the Hot spring microbial mat communities from California, USA to study Microbial Dark Matter (Phase II) - Cone Pool mat layer C metaG metagenome (hot springs metagenome) data set.	The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364778.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00003578	EMG produced TPA metagenomics assembly of the Environmental DNA from seawater and marine sediment Metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA373808.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment, Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003577	EMG produced TPA metagenomics assembly of the Functional dynamics of the elderly gut microbiome during probiotic consumption (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA298362.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003574	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in the Saanich Inlet - ESP_153SG_22_DNA metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365964.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003573	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1557A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365255.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003572	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Eden Landing Ponds, California, USA - A23 P3 (4) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366524.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003571	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and P1 (3) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366518.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003570	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and P1 (4) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366523.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003569	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and P2 (1) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366670.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003566	EMG produced TPA metagenomics assembly of the sediment bacteria metagenome Metagenome (sediment bacteria) data set.	The sediment bacteria Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA338830.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Hydrothermal vents, Sediment.	root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
MGYS00003565	EMG produced TPA metagenomics assembly of the Microbial communities from multiple species of Shipworm: Sample from Bankia setacea gill BSg4 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336724.  This project includes samples from the following biomes: Host-associated, Mollusca.	root:Host-associated:Mollusca
MGYS00003564	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - CAN11_03_M0_10 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366973.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003563	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in the Saanich Inlet - SI037_S2LV_130m_DNA metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366995.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003562	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Ebb tide non-ETM metaG S.715 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365276.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003561	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1547A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367289.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003560	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1562A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365262.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003559	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1563A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365265.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003558	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1569-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365269.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003557	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Eden Landing Ponds, California, USA - A23 M3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366385.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003556	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Eden Landing Ponds, California, USA - A23 E2 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366481.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003555	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and P2 (3) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366673.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003554	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and M1 (2) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366515.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003553	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Eden Landing Ponds, California, USA - A23 E3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366390.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003552	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - fosmids plate 4 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330366.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003551	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in the Saanich Inlet - ESP_90LU_22_DNA metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365958.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003550	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Freshwater metaG S.703 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365285.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003549	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1548B-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367292.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003548	EMG produced TPA metagenomics assembly of the Methane-oxidizing microbial communities from mesocosms in the Hudson Canyon - EN10B Hudson Canyon metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365094.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003547	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S7_td_SurfaceA_ad_6m_LV_A metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375449.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003546	EMG produced TPA metagenomics assembly of the Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Dewar Creek DC9 2012 metaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375329.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Sediment.	root:Environmental:Aquatic:Thermal springs:Sediment
MGYS00003545	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_100511 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365003.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Pelagic.	root:Environmental:Aquatic:Marine:Pelagic
MGYS00003544	EMG produced TPA metagenomics assembly of the Marine sediment microbial community from Fremont, CA, USA - Pond A23 Sediment 1 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366548.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003543	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Eden Landing Ponds, California, USA - A23 P3 (3) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366517.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003542	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and M1 (3) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366516.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003541	EMG produced TPA metagenomics assembly of the particle-associated bacteria from the Mediterranean Sea (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA318731.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003540	EMG produced TPA metagenomics assembly of the tailing ponds sediment Raw sequence reads (tailing ponds sediment) data set.	The tailing ponds sediment Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA431952.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Pond, Sediment.	root:Environmental:Aquatic:Freshwater:Pond:Sediment
MGYS00003539	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - fosmids plate 5 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330367.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003538	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - Fosmid plate 7 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329904.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003537	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S15_td_SurfaceA_ad_5m_LV_A metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375452.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003535	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - Fosmid plate 8 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329905.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003534	EMG produced TPA metagenomics assembly of the Subseafloor sediment microbial communities from Guaymas Basin, Gulf of California, Mexico - Guay17, Core 4571-4, 12-15 cm metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406720.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003533	EMG produced TPA metagenomics assembly of the Impact of the Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition (DNA Isolation Methodology for Microbiome Genomics) data set.	The DNA Isolation Methodology for Microbiome Genomics Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14814.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal, Engineered, Modeled, Simulated communities (microbial mixture), Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00003532	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC059_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340498.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003531	EMG produced TPA metagenomics assembly of the Biogas fermentation microbial communities from Germany - Plant 1 DNA2 metagenome (biogas fermenter metagenome) data set.	The biogas fermenter metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA311381.  This project includes samples from the following biomes: Engineered, Biogas plant.	root:Engineered:Biogas plant
MGYS00003530	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 16_60_3.3_214_A3 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406037.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003529	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 6_20_20_110_A2 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405537.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003528	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNNA5_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340767.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003527	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1555B-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365245.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003526	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1554B-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367310.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003525	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1553A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367307.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003524	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Freshwater metaG S.541 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365287.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003523	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Flood tide ETM metaG S.705 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365279.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003522	EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R1_B C12 SIP DNA metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340513.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003521	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNTR4_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340758.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003520	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC078_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340504.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003519	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P3_0mM metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441894.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003518	EMG produced TPA metagenomics assembly of the Evaluation of Enriched Background Microflora of Wheat flour Spiked with E. coli O157 and E. coli O121 through metagenomics (E.coli O157 and E.coli O121 spiked in wheat flour) data set.	The E.coli O157 and E.coli O121 spiked in wheat flour Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA430401.  This project includes samples from the following biomes: Engineered, Food production.	root:Engineered:Food production
MGYS00003517	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, USA - P5_16mM MetaG metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406752.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003516	EMG produced TPA metagenomics assembly of the Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage D2F08 metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367151.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003514	EMG produced TPA metagenomics assembly of the anaerobic reactor metagenome for  ARGs (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA399632.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003513	EMG produced TPA metagenomics assembly of the CSTR anaerobic reactor Raw sequence reads (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA303948.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003512	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Hong Kong - AD_UKC113_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340749.  This project includes samples from the following biomes: Engineered, Wastewater, Industrial wastewater.	root:Engineered:Wastewater:Industrial wastewater
MGYS00003509	Description of the bacterial microbiota of EntomoPathogenic Nematodes (EPNs)of Steinernema genus	Entomopathogenic nematodes from the genus Steinernema are used in biological control of insect pests. The free form of the nematode (infective juvenile) is in closed symbiotic association with the intestinal bacteria Xenorhabdus (Enterobacteriaceae). In the well-studied Steinernema carpocapsae - Xenorhabdus nematophila couple, it was largely shown that the bacterial symbiont played an important role in the death of the insect and in the elimination of the microbial competitors inside the insect cadaver. However, in addition to symbiotic bacteria, other cultivable bacteria have been regularly isolated from infective juveniles nematodes.In this study,we used both culture-dependent and multigenic metabarcoding methods to obtain a comprehensive survey of S. carpocapsae bacterial microbiota. We used two markers, the V3-V4 region of the 16S rRNA gene and a region of the rpoB gene, for which a database was built. We identified a core-microbiota of about 10 OTUs that were present in more than 70% of the samples. Representative bacterial strains of the core-microbiota were tested for their insecticidal performances and their ability to produce antimicrobial molecules.	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00003508	The process-related dynamics of microbial community during the fermentation of Chinese strong-flavored liquor	Chinese strong-flavored liquor (CSFL) is one of the most typical representatives of Chinese liquor. It is brewed by multiple-microorganism consortia in a special fermention pit (FT). However, the fermentation process was not fully understood owing to its complicated metabolisms involved many microorganisms. In this study, we investigated the process-related dynamics of microbial communities and main flavor compounds during the 70-day fermentation process using MiSeq-sequencing method. Results showed that during the early fermentation period (1-23 days), the prokaryotic diversity decreased significantly, Lactobacillaceae (Lactobacillus) gradually dominated in prokaryotic community. By contrast, the eukaryotic diversity raise remarkably. Thermoascus, Aspergillus, Rhizopus and unidentified Saccharomycetales were dominant eukaryotic members. Glucose was produced from macromolecular carbohydrates (e.g., starch) in the fermentation. During the middle fermentation period (23-days), microbial diversity did not change significantly. Prokaryotic community was almost dominated by Lactobacillaceae (Lactobacillus), while eukaryotic community was mainly comprised of Thermoascus, Emericella and Aspergillus. Glucose concentration decreased significantly, while the concentrations of lactate acid, propanoic acid and ethanol increase constantly. During the later fermentation period (48-70 days). Microbial community kept relative constant. The ester acetate, ethyl lactate and ethyl hexanoate began to be produced. Canonical correspondence analysis (CCA) showed that Lactobacillaceae, Bacilli, Botryotinia, Aspergillus, unidentified Pleosporales, and Capnodiales  were positively correlative to the producion of organic acids and ethyl ester ( P<0.05 ). Additionally, Saccharomycetales, Monascus, and Rhizopus were positive corelative  to glucose production ( P<0.05 ), highlighting their roles in the degradation of carbohydrates. This study contributes to our understanding of microbial community composition, successsion and their function in the fermentation process of CSFL fermentation.	root:Engineered:Food production:Fermented beverages
MGYS00003505	Prior dietary practices and connections to a human gut microbial metacommunity alter responses to diet interventions	It is unclear how to ensure that the gut microbiota of individuals with disparate dietary practices (DPs) respond consistently to prescribed dietary interventions. To address this, we identified DP-associated gut bacterial taxa in individuals either practicing chronic calorie restriction with adequate nutrition (CRON) or without dietary restrictions (AMER). Transplanted into gnotobiotic mice, AMER and CRON microbiota responded predictably to CRON and AMER diets but with variable response strength. Individual microbiota exist within a population of host communities (metacommunity) connected by microbial exchange. Sequentially cohousing AMER-colonized mice with two different groups of CRON-colonized mice emulated metacommunity effects, resulting in enhanced responses to a CRON diet intervention and changes in several metabolic features in AMER animals. This response was driven by an influx of CRON DP-associated taxa. Certain DPs may impair responses to dietary interventions, necessitating introduction of absent diet-responsive bacterial lineages present in other individuals and identified using the strategies described.	root:Host-associated:Animal:Digestive system:Fecal
MGYS00003504	Carrot juice fermentations as man-made microbial ecosystems dominated by lactic acid bacteria	During the present study, the microbial characteristics of carrot juice fermentations were evaluated via combined culture-dependent, culture-independent, and metabolite target analysis approaches. In total, the dynamics of more than 200 fermentation samples from a Michelin star chef, laboratory fermentations, and a citizen science fermentation project, were analyzed.	root:Engineered:Food production:Fermented vegetables
MGYS00003503	Biodiversity-function relationships in methanogenic communities	Methanogenic communities play a crucial role in carbon cycling and biotechnology (anaerobic digestion), but our understanding of how their diversity, or composition in general, determines the rate of methane production is very limited. Studies to date have been correlational because of the difficulty in cultivating their constituent species in pure culture. Here we investigate the causal link between methanogenesis and diversity in laboratory anaerobic digesters by experimentally manipulating the diversity of cultures by dilution and subsequent equilibration of biomass. This process necessarily leads to the loss of the rarer species from communities. We find a positive relationship between methane production and the number of taxa, with little evidence of functional saturation, suggesting that rare species play an important role in methane producing communities. No correlations were found between the initial composition and methane production across natural communities, but a positive relationship between species richness and methane production emerged following ecological selection imposed by the laboratory conditions. Our data suggest methanogenic communities show little functional redundancy, hence any loss of diversity– both natural and resulting from changes in propagation conditions during anaerobic digestion – is likely to reduce methane production.	root:Engineered:Bioreactor
MGYS00003502	Characterization of archaeal and bacterial communities in UASB reactors fed pig manure supernatant, operated at high ammonia concentrations	Four UASB reactors fed pig manure supernatant were operated at two ammonium concentrations (1.9 and 3.7 g L-1 for LA and HA reactors, respectively) and at variable temperatures over 358 days. The granules used as inoculum originated from a UASB reactor treating pulp and paper process wastewater. The reactors were all operated at HRT 1.0 day. The organic loading rate (OLR) was 16±2 g COD L-1 d-1 for the entire experiment. Archaeal and bacterial communities were characterized by Illumina sequencing of 16S rRNA amplicons covering the v3 and v4 regions.	root:Engineered:Bioreactor
MGYS00003501	Acetate- and glucose-fed microbial fuel cells. Samples of bioanodes as well as biomass not associated with electrodes.	We operated microbial fuel cells (MFCs) on acetate or glucose and investigated the responses to starvation, exposure to alternative electron donors, and conversion of the bioanodes into biocathodes. Samples for DNA extraction, PCR of the V4 region of the 16S rRNA gene, and Illumina MiSeq sequencing was carried out on samples collected from three acetate-fed and three glucose-fed MFCs. Samples were collected from the bioanodes, liquid, and biofilm growing on non-conductive areas of the MFCs.	root:Engineered:Bioreactor
MGYS00003499	The microbial communities in anaerobic digesters	Anaerobic digestion is regarded as a key environmental technology in the present and future bio-based economy. The microbial community completing the anaerobic digestion process is considered complex, and several attempts already have been carried out to determine the key microbial populations. However, the key differences in the anaerobic digestion microbiomes, and the environmental/process parameters that drive these differences, remain poorly understood. In this research, we hypothesized that differences in operational parameters lead to a particular composition and organization of microbial communities in full-scale installations. A total of 38 samples were collected from 29 different full-scale anaerobic digestion installations, showing constant biogas production in function of time. Microbial community analysis was carried out by means of amplicon sequencing and real-time PCR. The bacterial community in all samples was dominated by representatives of the Firmicutes, Bacteroidetes and Proteobacteria, covering 86.1 ± 10.7% of the total bacterial community. Acetoclastic methanogenesis was dominated by Methanosaetaceae, yet, only the hydrogenotrophic Methanobacteriales correlated with biogas production, confirming their importance in high-rate anaerobic digestion systems. In-depth analysis of operational and environmental parameters and bacterial community structure indicated the presence of three potential clusters in anaerobic digestion. These clusters were determined by total ammonia concentration, free ammonia concentration and temperature, and characterized by an increased relative abundance of Bacteroidales, Clostridiales and Lactobacillales, respectively. None of the methanogenic populations, however, could be significantly attributed to any of the three clusters. Nonetheless, further experimental research will be required to validate the existence of these different clusters, and to which extent the presence of these clusters relates to stable or sub-optimal anaerobic digestion.	root:Engineered:Wastewater:Water and sludge
MGYS00003498	nirs nirK nosZ batch tests transcripts	nirs nirK nosZ batch tests transcripts	root:Engineered:Wastewater:Water and sludge
MGYS00003497	Microbiology of portuguese WWTP	Microbiology of portuguese WWTP	root:Engineered:Wastewater:Activated Sludge
MGYS00003496	Influence of electron acceptors in transcript diversity of active members of the denitrifying community	The aim of this work was to study the effect of various combinations of electron acceptors, nitrate (NO3-), nitrite (NO2-) and N2O, on the denitrification pathway of a d-EBPR system. Batch tests were performed with different electron acceptor combinations, to explore the denitrification pathway. The changes in community structure were evaluated by MiSeq Illumina high throughput sequencing.	root:Engineered:Wastewater:Activated Sludge
MGYS00003495	Metagenomic analysis of microbial psychrotolerant consortia leaching of metal sulfides at low temperatures.	The bioleaching processes are limited by the availability of O2 and low temperatures (3°C to 15°C) in Andean mining zones. These parameters limit bacterial leaching operations because decrease the rate of iron oxidation by mesophilic microorganisms. This study aimed to isolate and characterize microbial psychrotolerant consortia leaching (MPCL) that can be used in industrial processes for metal recovery units at high altitude mining operation. We collected and cultured 11 samples of acidic water from the Volcan mining company (4261 m.a.s.l) located in the city of Cerro de Pasco, the Huarón mine (4534 m.a.s.l) located in the district of Huayllay, and Yanamate Lake (4358 m.a.s.l) located at the southeast of Cerro de Pasco city. We obtained 6 MPCL that oxidized copper sulfide 0.5%(w/v) and zinc sulfide 0.5%(w/v) at 5ºC. Growth kinetics of the 6 MPCL were evaluated and doubling times of 49.5 hours for CuS and 60.8 hours for ZnS were obtained. The release of copper kinetics on a sulphide ore and synthetic sulphide (CuS) were evaluated, obtaining better results in CuS, where copper (II) was released to 1.51 mg/L for every 10^5 cells/ml. Metagenomic DNA of the 6 consortia were extracted. The amplicons libraries were built and sequenced using 27F and 518R primers. The consortia were mostly composed for the genus Acidithiobacillus sp. and only in one of them Leptospirillum ferroxidans was present.	root:Engineered:Bioreactor
MGYS00003494	M'thermobacter and ex situ biogas upgrading	Ex situ biomethanation is a cost-effective modification of anaerobic digestion, in which hydrogenotrophic methanogens are provided excess hydrogen (H2) and carbon dioxide (CO2) in the absence of a solid biogas feedstock, placing both the process and metabolic emphasis on near-total conversion of CO2 and H2 to biomethane. The concept can be applied ex situ as ‘biological upgrading' to biogas from anaerobic digestion, and is usually carried out at thermophilic temperatures (>50°C) in order to accelerate methanogenesis. The ex situ methanogenic community responsible for this upgrading is currently poorly characterised but is expected to feature abundant methanogens specialising in fixation of CO2 and H2 to CH4. Given the lack of a digestion feedstock, the importance of bacteria in an upgrading community is less clear. In this study, the methanogenic and microbial communities involved in thermophilic ex situ upgrading of a 1 CO2 : 4 H2 mix were characterised during disruption and restoration of biogas production due to a process shift to higher temperatures (55°C to 65°C). Although DGGE, 16S clone library and 16S pyrosequencing approaches showed Methanothermobacter to be the dominant methanogen throughout operation, no relationship was evident between decreased upgrading function and Methanothermobacter abundance. Instead, it is possible that biogas production was restored through addition of organic and/or inorganic substrate in a re-inoculation event. This implies a role for the ex situ bacterial community, the majority of which (>50% reads) belong to uncharacterised Firmicutes taxa, in particular the MBA03 group.	root:Engineered:Biogas plant
MGYS00003493	Microbial structure of intermittently aerated sequencing batch reactor (IASBR) treating dairy processing wastewater.	This study investigated the application of an intermittently aerated sequencing batch reactor (IASBR) to the biorremediation of synthetic dairy processing wastewater. Aeration rates conditions were varied in the bioreactor to determine the impacts on IASBR microbial community structure and orthophosphate (PO4-P) and ammonium (NH4-N) removal efficiencies. Bacterial communities of the IASBR were described through 16S rRNA metagenomic analyses by high-throughput pyrosequencing procedure (454 pyrosequencing, Roche) using V5-V9 primers. Sequencing data were analysed by using Quantitative Insights Into Microbial Ecology (QIIME) pipeline.	root:Engineered:Wastewater
MGYS00003492	TE supplementing Grass silage Anaerobic Digestion (TE-GAD)	Wall et al. (2014) attempted to determine the optimal mix of silage/slurry in biomethane based AD. Trials showed that although BioMethane Potential (BMP) was highest in 100% silage tests, generation of biomethane was more stable with a 20% inclusion of dairy slurry (by VS%). At higher loading rates BM output in 100% silage (R-G) and 80%silage:20% slurry (R-SG) reached parity, possibly an effect of incomplete degradation of solids within the retention time, but may also be imformed by the microbial community created by increased rate of feedstock addition.Another trend documented both in the original study  and more broadly  is the decline in reactor stability with increased organic loading rate (OLR), as measured by the FOSTAC ratio (effectively the reactor's buffering capability and frequently an indicator for process stability). Increases in OLR from 2.5 to 3 kgVS/m3/d led to rapid accumulation of VFAs (AcO, PrO) in R-G, while no issue was observed over the course of R-SG operation. Due to the constant turnover of organic material and active biology of the reactor community, issues with reactor operation are frequently linked to limiting concentrations of trace elements such as Fe, Co, Ni, etc.. However it is not externally apparent which portions of the community are restricted by the lack of trace elements (TE) - this study aims to characterise the communities stressed by Wall et al., 2014, and determine which populations relate to bottlenecking of (TE).The two reactors characterised in this study (R-G,R- SG) were sampled over 68 and 65 weeks respectively after being seeded from the same sludge inoculum, fed 100% silage and 80:20% silage:slurry, and operated along the same design principles. R-G was sampled at week 1, 20, 37, 40, 43, 49, 54, 64, 65, 68. R-GS was sampled at week 01, 20, 37 and 65 to act as a positive control for R-G.	root:Engineered:Bioreactor
MGYS00003491	Follows soon	Follows soon...	root:Engineered:Biogas plant
MGYS00003489	EMG produced TPA metagenomics assembly of the Pit mud of Chinese liqour fermentation reactorMetagenome (fermentation metagenome) data set.	The fermentation metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA260163.  This project includes samples from the following biomes: Engineered, Food production, Fermented beverages.	root:Engineered:Food production:Fermented beverages
MGYS00003488	Gut microbiomes from 359 European pig and poultry herds (EFFORT)	Antimicrobial resistance (AMR) in bacteria and associated morbidity and mortality is increasing. Use of antimicrobials for livestock selects for AMR that can subsequently be transferred to the human reservoir. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (http://www.effort-against-amr.eu/), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 Gigabases of DNA sequence, using shotgun metagenomics. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several newly described, critical AMR genes, including mcr-1 and optrA, which differed both between host species and countries. We found that the total AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns have similar resistomes.	root:Host-associated:Animal:Digestive system:Fecal
MGYS00003486	EMG produced TPA metagenomics assembly of the Campus Antibiotics Virome Study () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA327423.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Oral, Host-associated, Human, Digestive system.	root:Host-associated:Human:Digestive system
MGYS00003484	LSA-COMPARE FOOD TRIAL	LSA-COMPARE FOOD TRIAL	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003480	EMG produced TPA metagenomics assembly of the Choice of method for purification of bacterial DNA from faecal material influences community structure as detected by next generation sequencing (gut metagenome) data set.	The gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA243036.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003479	EMG produced TPA metagenomics assembly of the Evaluating the Potential of using Next-Generation Sequencing for Direct Clinical Diagnostics of Faecal Samples from Patients with Diarrhoea () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14038.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003478	EMG produced TPA metagenomics assembly of the Athlete Microbiome Project (AMP) (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA305507.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003476	EMG produced TPA metagenomics assembly of the Metagenomics of Japanese gut microbiomes (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB3601.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.	root:Host-associated:Human:Digestive system
MGYS00003472	Habitat Selection Effects on Brent Goose Gut Microbiomes	We quantified the microbial community structure and function of gut microbiomes of migratory light-bellied Brent geese in Iceland in May. We classified birds based on whether they were feeding on terrestrial grass, marine mudflats, or both.	root:Host-associated:Animal:Digestive system:Fecal
MGYS00003470	EMG produced TPA metagenomics assembly of the Raw DNA sequence of sludge samples from FO-AnMBR () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA317285.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003469	EMG produced TPA metagenomics assembly of the An integrated catalog of reference genes in the human gut microbiome (IGC) data set.	The IGC Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB5224.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003467	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNTR2_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340756.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003466	EMG produced TPA metagenomics assembly of the compost enrichment single cell ciliate 20uM2 metagenome J21 metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366630.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00003465	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWPA TP0 #3 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441399.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Brackish
MGYS00003464	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S23_td_SurfaceB_ad_5m_LV_B metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375509.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003462	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - C0912_C43A7_35 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330317.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003460	Schistosoma mansoni infection is associated with quantitative and qualitative modifications of the mammalian intestinal microbiota	In spite of the extensive contribution of intestinal pathology to the pathophysiology of schistosomiasis, little is known of the impact of schistosome infection on the composition of the gut microbiota of its mammalian host. Here, we characterised the fluctuations in the composition of the gut microbial flora of the small and large intestine, as well as the changes in abundance of individual microbial species, of mice experimentally infected with Schistosoma mansoni with the goal of identifying microbial taxa with potential roles in the pathophysiology of infection and disease. Bioinformatic analyses of bacterial 16S rRNA gene data revealed an overall reduction in gut microbial alpha diversity, alongside a significant increase in microbial beta diversity characterised by expanded populations of Akkermansia muciniphila (phylum Verrucomicrobia) and lactobacilli, in the gut microbiota of S. mansoni-infected mice when compared to uninfected control animals. These data support a role of the mammalian gut microbiota in the pathogenesis of hepato-intestinal schistosomiasis and serves as a foundation for the design of mechanistic studies to unravel the complex relationships amongst parasitic helminths, gut microbiota, pathophysiology of infection and host immunity.	root:Host-associated:Mammals:Digestive system
MGYS00003442	Broiler caecal metagenomics	The caecum of broiler chickens were analysed using metagenomics	root:Host-associated:Animal:Digestive system
MGYS00003439	Alterations in the colon microbiota induced by the gastrointestinal nematode Trichuris suis	Helminth parasites have evolved to regulate host immunity to ensure their survival through mechanisms that dampen host inflammation. These properties have been recently exploited therapeutically to treat human diseases. The bio-complexity of the intestinal lumen would suggest that interactions between parasite and intestinal microbiota would also influence inflammation.  In this study, we characterized the porcine proximal colon microbiota in response to Trichuris suis (whipworm) infection using 16S rDNA-based and whole genome shotgun (WGS) approaches.  A 21-day T. suis infection in pigs induced a profound change in the composition of the proximal colon microbiota. The abundance of four of the 15 phyla identified, such as Proteobacteria, was changed in infected pigs. Approximately 10% of genera were significantly altered by infection. Notably, reduced Succinivibrio abundance in infected pigs implied that T. suis infection altered carbohydrate metabolism in the proximal colon microbial ecosystem. Conversely, Mucispirillum was significantly increased in infected pigs suggesting that mucosal disruption induced by parasitic infection and feeding perturbed this ecological niche. Infection led to a significant shift in the metabolic potential of the proximal colon microbiota. Approximately 26% of all metabolic pathways indentified were affected by infection. Two important functional categories repressed by infection were carbohydrate metabolism and lysine biosynthesis. Furthermore, changes in pathogen associated pathways suggested that T. suis infection could impact subsequent infection and modulate host-pathogen interactions. Our findings should facilitate development of strategies for parasitic control in pigs and humans and optimize successful helminth therapy to reduce inflammation.	root:Host-associated:Mammals:Digestive system
MGYS00003416	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC096_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340754.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003415	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 13_49_3.3_201_A3 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406034.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003414	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 10_41_5_180_A2 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406031.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003413	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNNA6_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340770.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003412	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_174 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365230.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003411	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 15_59_3.3_214_A2 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406036.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003410	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC077_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340503.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003409	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1555C-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365246.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003408	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1555A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365244.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003407	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1550A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367299.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003406	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1546A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367281.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003405	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1449C-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367277.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003404	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1371A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367272.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003403	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1370B-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367269.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003402	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1371B-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367274.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003401	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1370A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367268.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003400	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Freshwater metaG S.747 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365286.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003399	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Ebb tide ETM metaG S.573 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365271.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary
MGYS00003398	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Southern Atlantic ocean transect to study dissolved organic matter and carbon cycling - Knorr_S7_td_250_ad_252m_LV_B metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365636.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00003397	EMG produced TPA metagenomics assembly of the Pelagic Microbial community sample from North Sea - COGITO 998_met_09 Metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA266687.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003396	EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R1_B C13 SIP DNA metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340511.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003395	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Hong Kong - AD_UKC111_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340748.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003394	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P3_16mM metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441897.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003393	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P3_32mM metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441898.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003392	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P3_8mM metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441896.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003391	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, United States - P5a_8mM metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441891.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003390	EMG produced TPA metagenomics assembly of the High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-7-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365937.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003389	EMG produced TPA metagenomics assembly of the High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-3-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365933.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003388	EMG produced TPA metagenomics assembly of the High solid enriched microbial communities from the Joint BioEnergy Institute, USA - SP1-2-D metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365932.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Bioreactor
MGYS00003387	EMG produced TPA metagenomics assembly of the Cellulose adapted compost microbial communities from Newby Island Compost Facility, Milpitas, CA, USA - Passage2 37A metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366677.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00003386	EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Washington, USA - P5_4mM MetaG metagenome (mixed culture metagenome) data set.	The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406750.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003385	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - RS_189 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365238.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00003384	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_91 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365237.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00003383	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_222 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365235.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00003382	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_219 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365234.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00003381	EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_186 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365231.  This project includes samples from the following biomes: Host-associated, Plants.	root:Host-associated:Plants
MGYS00003380	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC048_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340495.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003379	EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC028_MetaG metagenome (activated sludge metagenome) data set.	The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340787.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00003378	EMG produced TPA metagenomics assembly of the compost enrichment single cell ciliate 20uM2 metagenome O9 metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366631.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00003376	EMG produced TPA metagenomics assembly of the compost enrichment single cell ciliate 20uM2 metagenome J15 metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366629.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00003375	EMG produced TPA metagenomics assembly of the compost enrichment single cell ciliate 20uM2 metagenome J5 metagenome (compost metagenome) data set.	The compost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366628.  This project includes samples from the following biomes: Engineered, Solid waste, Composting.	root:Engineered:Solid waste:Composting
MGYS00003374	EMG produced TPA metagenomics assembly of the Artificial metagenome assembled from nine heterogeneous microorganisms (synthetic metagenome) data set.	The synthetic metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA218588.  This project includes samples from the following biomes: Engineered, Lab Synthesis, Genetic cross.	root:Engineered:Lab Synthesis:Genetic cross
MGYS00003373	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 2_5_20_6_A2 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405533.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Biogas plant:Wet fermentation
MGYS00003372	EMG produced TPA metagenomics assembly of the Switchgrass degrading microbial communities from high solid loading bioreactors in New Hampshire, USA - 1_4_20_6_A1 metaG metagenome (bioreactor metagenome) data set.	The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405532.  This project includes samples from the following biomes: Engineered, Bioreactor.	root:Engineered:Biogas plant:Wet fermentation
MGYS00003371	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110331 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365006.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003370	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG S.751 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365291.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003369	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWPA TP2 #2 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441403.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Coastal
MGYS00003367	EMG produced TPA metagenomics assembly of the Severe gut microbiota dysbiosis is associated with poor growth in patients with short bowel syndrome (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA311208.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003366	EMG produced TPA metagenomics assembly of the Sediment microbial communities from Great Boiling Springs, Gerlach, Nevada, United States - GBS 85_MetaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA442911.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Sediment.	root:Environmental:Aquatic:Thermal springs:Near-boiling (>90C):Alkaline
MGYS00003365	EMG produced TPA metagenomics assembly of the Sediment microbial communities from Great Boiling Springs, Gerlach, Nevada, United States - GBS 70_MetaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA442910.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Sediment.	root:Environmental:Aquatic:Thermal springs:Near-boiling (>90C):Alkaline
MGYS00003364	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWPA TP2 #3 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441404.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Brackish
MGYS00003363	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWPA TP0 #1 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441398.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Brackish
MGYS00003362	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWA TP1 #2 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441394.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Brackish
MGYS00003361	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - Fosmid plate 11 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329910.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003360	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - fosmids plate 1 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330363.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Lentic:Brackish
MGYS00003359	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWPA TP1 #3 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441401.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Brackish
MGYS00003358	EMG produced TPA metagenomics assembly of the Coastal seawater microbial communities from Marineland, Florida, United States - SWA TP2 #1 metagenome (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA441396.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Brackish
MGYS00003357	EMG produced TPA metagenomics assembly of the Synechococcus and Synechococcus-associated heterotrophic bacteria genome sequencing (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA445564.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Brackish
MGYS00003356	EMG produced TPA metagenomics assembly of the Subseafloor sediment microbial communities from Guaymas Basin, Gulf of California, Mexico - Guay15, Core 4569-2, 21-24 cm metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406718.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00003355	EMG produced TPA metagenomics assembly of the Marine microbial communities from the West Antarctic Peninsula - Coastal water metaG108-DNA metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375608.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Brackish
MGYS00003354	EMG produced TPA metagenomics assembly of the sediment metagenome Metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA341273.  This project includes samples from the following biomes: Environmental, Aquatic, Marine,Oceanic, Sediment.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00003353	EMG produced TPA metagenomics assembly of the xiaobaijiao Raw sequence reads (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA298307.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003352	EMG produced TPA metagenomics assembly of the Gulf Coast Oil Spill Metagenomic Project (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA53921.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic, Oil-contaminated.	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
MGYS00003351	EMG produced TPA metagenomics assembly of the Metagenomic profiles of samples from aquaculture systems (Metagenomic analysis of antibiotic resistance genes in conventional and recirculating aquaculture systems) data set.	The Metagenomic analysis of antibiotic resistance genes in conventional and recirculating aquaculture systems Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB22134.  This project includes samples from the following biomes: Environmental, Aquatic, Aquaculture.	root:Environmental:Aquatic:Aquaculture
MGYS00003350	EMG produced TPA metagenomics assembly of the Marine microbial communities from the West Antarctic Peninsula - Coastal water metaG017-DNA metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375604.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003349	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - Fosmid plate 10 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329909.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003348	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - Fosmid plate 9 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329906.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003347	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - fosmids plate 6 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330368.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003346	EMG produced TPA metagenomics assembly of the Human fecal microbiome before and after consumption of AH1206 - Raw sequence reads (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA324129.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003345	EMG produced TPA metagenomics assembly of the Subseafloor sediment microbial communities from Guaymas Basin, Gulf of California, Mexico - Guay13, Core 4488-10 , 4-6 cm metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406717.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003344	EMG produced TPA metagenomics assembly of the Marine sediment microbial community from Fremont, CA, USA - Pond A23 Sediment 2 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366549.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary, Sediment.	root:Environmental:Aquatic:Marine
MGYS00003342	EMG produced TPA metagenomics assembly of the Continental margin sediment microbial communities from China - ANME2c_DSS_Sorted metaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364899.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00003340	EMG produced TPA metagenomics assembly of the Marine microbial communities from the West Antarctic Peninsula - Coastal water metaG029-DNA metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375605.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Coastal
MGYS00003339	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary, USA - metaG S.535 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375312.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00003337	EMG produced TPA metagenomics assembly of the Methane-oxidizing microbial communities from mesocosms in the Hudson Canyon - EN1E Hudson Canyon metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365091.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003336	EMG produced TPA metagenomics assembly of the sediment metagenome Metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340165.  This project includes samples from the following biomes: Environmental, Aquatic, Sediment.	root:Environmental:Aquatic:Sediment
MGYS00003335	EMG produced TPA metagenomics assembly of the Metagenome sequences from enrichment cultures of Trichodesmium erythraeum IMS101 Metagenome (Trichodesmium erythraeum IMS101) data set.	The Trichodesmium erythraeum IMS101 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA328268.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003334	EMG produced TPA metagenomics assembly of the nanhaiyihao Raw sequence reads (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA298308.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003333	EMG produced TPA metagenomics assembly of the Deep igneous marine biosphere Metagenome (marine sediment metagenome) data set.	The marine sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA264811.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003330	EMG produced TPA metagenomics assembly of the Marine algal microbial communities from Sidmouth, United Kingdom - Sidmouth_Asex2 metaG metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365149.  This project includes samples from the following biomes: Host-associated, Algae, Red algae.	root:Host-associated:Algae:Red algae
MGYS00003327	EMG produced TPA metagenomics assembly of the Marine microbial communities from the West Antarctic Peninsula - Coastal water metaG058-DNA metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375606.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Coastal.	root:Environmental:Aquatic:Marine:Coastal
MGYS00003326	EMG produced TPA metagenomics assembly of the Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Dewar Creek DC16 2012 metaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375330.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Sediment.	root:Environmental:Aquatic:Thermal springs:Sediment
MGYS00003324	EMG produced TPA metagenomics assembly of the Methane-oxidizing microbial communities from mesocosms in the Hudson Canyon - EN4B Hudson Canyon metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365092.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003323	EMG produced TPA metagenomics assembly of the Methane-oxidizing microbial communities from mesocosms in the Hudson Canyon - EN8B Hudson Canyon metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365093.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003322	EMG produced TPA metagenomics assembly of the Methane-oxidizing microbial communities from mesocosms in the Hudson Canyon - EN8C Hudson Canyon metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365089.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003321	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1562A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365263.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003320	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1550A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367301.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003319	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1549B-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367296.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003318	EMG produced TPA metagenomics assembly of the seawater metagenome Genome sequencing and assembly (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA320927.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic, Oil-contaminated.	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
MGYS00003317	EMG produced TPA metagenomics assembly of the Marine algal microbial communities from Porto, Italy - Porto_4 metaG metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365151.  This project includes samples from the following biomes: Host-associated, Algae, Red algae.	root:Host-associated:Algae:Red algae
MGYS00003316	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1546C-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367286.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003315	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1370B-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367271.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003314	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Ebb tide non-ETM metaG S.555 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365273.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003313	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and E2 (1) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366671.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003312	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and P2 (2) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366672.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003311	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and M2 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366537.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003310	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and E1 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366675.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003309	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Eden Landing Ponds, California, USA - A23 M2 (2) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366485.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003308	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Eden Landing Ponds, California, USA - A23 E3 (4) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366386.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003307	EMG produced TPA metagenomics assembly of the Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Dewar Creek DC8 2012 metaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375327.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00003306	EMG produced TPA metagenomics assembly of the Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Dewar Creek DC4 2012 metaG metagenome (sediment metagenome) data set.	The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375328.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00003305	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1568-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365267.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003304	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1558A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365257.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003303	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1561A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365261.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003302	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1560A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365259.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003301	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1556B-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365253.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003300	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1555C-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365249.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003299	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1555B-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365248.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003298	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1554A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367311.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003297	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1554B-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365243.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003296	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1553A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367308.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003295	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1552A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367306.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003294	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1551A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367304.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003293	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1549A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367295.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003292	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1548B-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367294.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003291	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1548A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367293.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003290	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1548A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367291.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003289	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1547B-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367290.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003288	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1547A-3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367287.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003287	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1546B-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367285.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003286	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1546A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367284.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003285	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1449C-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367280.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003284	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1449B-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367279.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003283	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1449A-02 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367278.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003282	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG S.737 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365290.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003281	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - High salinity metaG S.579 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365289.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003280	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Ebb tide non-ETM metaG S.753 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365278.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003279	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Ebb tide non-ETM metaG S.571 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365275.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003278	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Ebb tide non-ETM metaG S.709 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365274.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003277	EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Ebb tide non-ETM metaG S.689 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365272.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003276	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - CAN11_66_BLW_10 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366975.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003275	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - CAN11_48_BLW_10 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366974.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003274	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - CAN11_07_M0_10 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366972.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003273	EMG produced TPA metagenomics assembly of the Marine hydrothermal vent microbial communities from Guaymas Basin, Gulf of California to study Microbial Dark Matter (Phase II) - Marker 14 Mat core 4571-4 33-36 cm metaG metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365033.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Coral reef.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00003272	EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in the Saanich Inlet - SI037_S4LV_200m_DNA metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366996.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00003271	EMG produced TPA metagenomics assembly of the North Pond site U1382 metagenome (marine sediment metagenome) data set.	The marine sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA360271.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003270	EMG produced TPA metagenomics assembly of the Marine microbial community from Cabo Rojo, Puerto Rico -PR CR 10% Liquid 2 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA337757.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003268	EMG produced TPA metagenomics assembly of the Marine microbial community from Union City, CA, USA - Pond 1C Liquid 3 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336779.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003267	EMG produced TPA metagenomics assembly of the Microbial communities from multiple species of Shipworm: Sample from Bankia setacea gill BSg1 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336867.  This project includes samples from the following biomes: Host-associated, Mollusca.	root:Host-associated:Mollusca
MGYS00003266	EMG produced TPA metagenomics assembly of the Microbial communities from multiple species of Shipworm: Sample from Bankia setacea gill BSg2 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336726.  This project includes samples from the following biomes: Host-associated, Mollusca.	root:Host-associated:Mollusca
MGYS00003265	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - C0912_C49A8_80 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329533.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003264	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - C0912_C49A8_35 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330316.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003252	EMG produced TPA metagenomics assembly of the Oceanic oxygen minimum zone microbial communities that regulate carbon cycling - Sample ETNP201406SV69 (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA323946.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003251	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and P1 (2) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366501.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003250	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and M2 (2) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366381.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003249	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and E1 (2) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366502.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003248	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Eden Landing Ponds, California, USA - A23 M2 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366383.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003247	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Eden Landing Ponds, California, USA - A23 M3 (2) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366483.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003246	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Eden Landing Ponds, California, USA - A23 E3 (3) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366384.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Salt marsh.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003245	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and E2 (3) metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366504.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003244	EMG produced TPA metagenomics assembly of the Aerobic enrichment media from Bioluminiscent Bay, La Parguera, Puerto Rico - Tt and P1 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366674.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003243	EMG produced TPA metagenomics assembly of the Ammonia-oxidizing marine microbial communities from Monterey Bay, California, USA - CAN11_54_BLW_10 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366976.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003242	EMG produced TPA metagenomics assembly of the Freshwater microbial mat bacterial communities from Lake Vanda, McMurdo Dry Valleys, Antarctica - Oligotrophic Lake LV.19.MP7.G1 metagenome (microbial mat metagenome) data set.	The microbial mat metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA368330.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lake.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00003241	EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110519 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365016.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003240	EMG produced TPA metagenomics assembly of the Human gut microbiome in AS (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA353560.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.	root:Host-associated:Human:Digestive system
MGYS00003219	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP2098 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330087.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003218	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Pacific Ocean - MP2097 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330118.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003205	EMG produced TPA metagenomics assembly of the Marine microbial communities from the Deep Atlantic Ocean - MMD0.2 metagenome (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330084.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00003204	EMG produced TPA metagenomics assembly of the human oral metagenome Raw sequence reads (human oral metagenome) data set.	The human oral metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA292588.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00003203	EMG produced TPA metagenomics assembly of the Human sputum and synthetic metagenomic samples (synthetic metagenome) data set.	The synthetic metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA287929.  This project includes samples from the following biomes: Engineered, Modeled, Simulated communities (DNA mixture), Host-associated, Human, Digestive system, Oral.	root:Host-associated:Human:Digestive system:Oral
MGYS00003202	EMG produced TPA metagenomics assembly of the Great Barrier Reef lagoon metagenomic survey (seawater metagenome) data set.	The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA276060.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Brackish.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00003201	EMG produced TPA metagenomics assembly of the Genome sequence of Blattabacterium cuenoti str. BPAY (Blattabacterium cuenoti BPAY) data set.	The Blattabacterium cuenoti BPAY Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB1602.  This project includes samples from the following biomes: Host-associated, Insecta, Digestive system	root:Host-associated:Insecta:Digestive system
MGYS00003199	EMG produced TPA metagenomics assembly of the gut microbiota from an obese human (SRP012035) data set.	The SRP012035 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: SRP012035.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003198	EMG produced TPA metagenomics assembly of the Impact of LAB supplementation in drinking water on chicken crop and ceca (LSA LAB in drinking water) data set.	The LSA LAB in drinking water Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB17637.  This project includes samples from the following biomes: Host-associated, Birds, Digestive system, Crop, Lumen.	root:Host-associated:Birds:Digestive system:Ceca
MGYS00003192	Parasitic nematodes modulate the expression of IL-17-associated genes through host type 2 immunity-dependent inhibition of segmented filamentous bacteria	Immune modulation by helminth (worm) parasites could protect the host against autoimmune diseases. We report that the parasitic nematode Nippostrongylus brasiliensis induces changes in the expression of antimicrobial peptides that are associated with marked microbial composition shifts, including reductions of segmented filamentous bacteria (SFB), a group of Gram-positive, anaerobic, spore-forming Clostridia, in ileal, jejunal, colon and fecal samples. SFB reduction correlates with decreased intestinal expression of T helper 17 (Th17) cell response markers. While infection of mice genetically deficient in the type 2 response-inducing signature cytokine IL-13 and the STAT6-activated cell signaling pathway failed to reproduce these phenotypes, administration of the type 2 response-inducing cytokine IL-25 activated a similar response in wild type mice as infection with N. brasiliensis. The reduced capacity to evoke Th17 responses resulted in increased susceptibility of N. brasiliensis-infected mice to co-infection with the bacterial pathogen Citrobacter rodentium. Our results demonstrate that helminth parasite infection alters the intestinal microbiota with SFB functioning as an immune-modulatory target for a Th17-dependent anti-inflammatory mechanism.	root:Host-associated:Animal:Digestive system
MGYS00003184	Kallisti Limnes subsea pools Metagenome Study	Metagenome studies of the Kallisti Limnes, carbon dioxide-accumulating subsea pools	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00003181	Gut microbiota of yellow-necked mouse (Apodemus flavicollis)	Microbiota variation in five gut sections of yellow-necked mouse (Apodemus flavicollis) was analyzed using pyrosequencing of V1-V3 16s rRNA.	root:Host-associated:Animal:Digestive system
MGYS00003179	Microbiota Dogs	Microbiota Dogs	root:Host-associated:Animal:Digestive system:Fecal
MGYS00003164	Impact of a major inflow event on the composition and distribution of bacterioplankton communities in the Baltic Sea	Major Baltic inflow (MBI) events carry highly saline water from the North Sea to the central Baltic Sea and thereby affect both the environmental conditions and the biota in the Baltic's deeper layers. While bacterioplankton communities in the Baltic Sea are strongly structured by its salinity, how MBIs impact the composition and distribution of those communities is unknown. However, insights into this relationship were afforded by an exceptional MBI in 2014 that brought saline and oxygenated water into the basins of the central Baltic Sea. Following this event, we analyzed bacterioplankton community composition in the inflowing water and in the uplifted former bottom water at stations in the Western and central Baltic Sea that were reached by the MBI. Bacterial diversity data were compared with data on the respective communities obtained during a previous non-inflow situation involving the same locations. In contrast to the broad taxonomic changes in bacterial community composition that are generally associated with changes in salinity, significant changes following the 2014 MBI were mainly at the genus level. The relative similarity of the bacterial communities in the inflowing and uplifted waters as well as the results from an inflow-simulating numerical model indicated that the inflowing water did not originate directly from the North Sea but mostly from adjacent areas in the Baltic Sea. These findings further suggested that the inflow event led to a series of shifts in Baltic Sea water mass among the Baltic Sea basins and a gradual mixing of the water bodies. Dramatic changes in bacterial community composition between inflowing and uplifted waters did become visible when the bottom-water inflow reached the anoxic, sulfidic deep basins, resulting in an uplifting of the former anoxic bacterial community, dominated by the Epsilonproteobacterium Sulfurimonas spp., to water depths within the oxygenated layer. Our study of the impact of MBIs on bacterioplankton communities therefore highlights two relevant underlying mechanisms that impact the distribution and possibly also the activities of planktonic bacteria in the Baltic Sea: the successive dilution of inflowing North Sea with ambient waters and the uplifting of former bottom-water communities to higher water strata.	root:Environmental:Aquatic:Marine:Marginal Sea
MGYS00003148	A comprehensive analysis of the faecal microbiome and metabolome of Strongyloides stercoralis infected volunteers from a non-endemic area	A comprehensive analysis of the faecal microbiome and metabolome of Strongyloides stercoralis infected volunteers from a non-endemic area	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003147	Infections by human gastrointestinal helminths are associated with changes in faecal microbiota diversity and composition	Investigations of the impact that patent infections by soil-transmitted gastrointestinal nematode parasites exert on the composition of the host gut commensal flora are attracting growing interest by the scientific community. However, information collected to date varies across experiments, and further studies are needed to identify consistent relationships between parasites and commensal microbial species. Here, we explore the qualitative and quantitative differences between the microbial community profiles of cohorts of human volunteers from Sri Lanka with patent infection by one or more parasitic nematode species (H+), as well as that of uninfected subjects (H-) and of volunteers who had been subjected to regular prophylactic anthelmintic treatment (Ht). High-throughput sequencing of the bacterial 16S rRNA gene, followed by bioinformatics and biostatistical analyses of sequence data revealed no significant differences in alpha diversity (Shannon) and richness between groups (P = 0.65, P = 0.13 respectively); however, beta diversity was significantly increased in H+ and Ht when individually compared to H-volunteers (P = 0.04). Among others, bacteria of the families Verrucomicrobiaceae and Enterobacteriaceae showed a trend towards increased abundance in H+, whereas the Leuconostocaceae and Bacteroidaceae showed a relative increase in H- and Ht respectively. Our findings add valuable knowledge to the vast, and yet little explored, research field of parasite – microbiota interactions and will provide a basis for the elucidation of the role such interactions play in pathogenic and immune-modulatory properties of parasitic nematodes in both human and animal hosts.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003143	Pilot study to compare the effects of high carbohydrate and high fat diets on gut microbiome	Diet has been shown to affect microbiome, but effects of diet composition is less clear.We have shown that the relative content of protein, fat and carbohydrate in the diet is key to modulating calorie intake and affects metabolic changes. We wanted to explore the effects on gut microbiome.In this pilot study we selected 6 patients from a larger clinical trial currently underway.Each patient had detailed biometric and dietary data collected, then was changed to a carefully designed, isocaloric diet for 4 weeks.Prior to intervention, all 6 patients were on a normal omnivorous diet.3 patients were changed to an oral high carbohydrate (OHC) diet.3 patients were changed to an oral high fat (OHF) diet.Stool was collected at baseline (BL) and then a second final sample (FL) was collected after 4 weeks of diet change.Stool was stored immediately at 4 degrees, frozen within two hours of collection and stored at -80 degrees Celsius.DNA was extracted from the stool using a QIAGEN, AllPrep PowerFecal DNA/RNA kit.Illumina Sequencing was performed.Project: CAGRF18283Sample Preparation: Illumina TruSeq DNA NanoSequencing: HiSeq Paired End Cluster Kit v4 cBotReads were trimmed for adapters using Trimmomatic v 0.36	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003141	Metagenomic data simulated to represent a complex microbial community	Metagenomic data simulated with grinder to represent a complex microbial community composed of 22 organisms with different relative abundances	root:Engineered:Bioreactor
MGYS00003139	Global surveillance of antimicrobial resistance - Batch June 2017	Global surveillance of antimicrobial resistance June 2017	root:Engineered:Wastewater
MGYS00003137	To determine whether there are differences in the intestinal microbiome between treatment-naïve Multiple Sclerosis (MS) subjects and controls, and between Caucasian (CA), Hispanic (HA), and African American (AA) MS subjects.	In this study focused on newly diagnosed treatment-naïve MS patients, we found increased relative abundance of Clostridia in all three patient cohorts compared to controls, with consistent and more detailed findings from the metagenomic analyses.  This work provides a candidate for further study for a role in early MS, at the least as a biomarker for the disease.  In addition, we found differences between the microbiomes of ethnic subgroups of MS patients that merit further study.	root:Host-associated:Human:Digestive system:Intestine
MGYS00003135	Human_infections_with_the_whipworm__Trichuris_trichiura__are_not_associated_with_alterations_in_the_faecal_microbiota_	"Materials and Methods: We carried out the study in two rural communities 
in Esmeraldas Province, Ecuador. School-age children were screened for 
the presence of STH infections and allocated to one of 3 groups: 
uninfected, T. trichiura only, and mixed infections with T. trichiura 
and Ascaris lumbricoides. A sample of uninfected children and those with 
T. trichiura infections only were treated with albendazole (800 mg/day 
for 3 days) and ivermectin (single dose of 200 ug/kg), and stool samples 
were collected 3 weeks post-treatment. Bacterial DNA was extracted using 
the FastDNA Spin kit for soil, and bacterial community profiles were 
studied by 454 pyrosequencing of 16S rRNA genes. This generated 999,796 
sequences, which were processed and analysed using mothur.

Results: Microbiota analyses were done using stool samples from 97 
children aged 8-14 years of whom 30 were not infected, 17 were infected 
with T. trichiura alone, and 50 had mixed infections with both T. 
trichiura and A. lumbricoides. Post-treatment samples were analyzed for 
14 of the 17 children initially infected with T. trichiura alone and 21 
of 30 uninfected children. Treatment resulted in 100% cure of STH 
infections. Comparisons of the microbiota at different taxonomic levels 
showed no statistically significant differences in composition between 
uninfected children and those with T. trichiura infections. A surprising 
finding was a decreased proportional abundance of a few bacterial genera 
from the clostridia class of Firmicutes, in tandem with a reduced 
overall bacterial diversity, among children with mixed infections 
compared to either uninfected children or those with T. trichiura 
infections only, indicating a specific effect of A. lumbricoides 
infection on intestinal microbiota.  Anthelmintic treatment of children 
with T. trichiura did not appear to alter composition of faecal microbiota.

Discussion: This is the first molecular study to analyse the effect of 
whipworm infection on the human intestinal microbiota. Our data indicate 
that T. trichiura infections alone have no effect on the faecal 
microbiota of children living in endemic communities, but that A. 
lumbricoides colonisation might be associated with a disturbed 
microbiota. Our results also catalogue the microbiota that is present in 
rural Ecuadorians, and indicate that there are differences between this 
cohort and individuals from more urban, industrialised societies."	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00003088	Marine sediment metagenome ICM_GMS	Microbial Census of Marine Methane Seeps: Initial Results	root:Environmental:Aquatic:Marine:Cold seeps
MGYS00003087	Marine sediment metagenome ICM_NZS	Physical and Microbial Characterisation of Marine Sediment from Two Contrasting Oceanographic Areas in New Zealand.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00003083	Marine metagenome ICM_GPS	Global Protistan Survey: Comparison of High-Throughput ''454'' Pyrosequencing vs. ''Deep'' Sanger Sequencing of 18S rRNA genes in Arctic (Chukchi Sea) and Antarctic (Ross Sea) ecosystems.	root:Environmental:Aquatic:Marine
MGYS00003082	Bacterial diversity in the South Adriatic Sea during winter of 2016	Bacteria represent the most important microorganisms in the world oceans comprising up to 75% of the total biomass at surface and playing fundamental processes for biogeochemistry. Along the water column, they are useful markers of the trophic state of water masses, therefore representing useful ecological indicators in the surveyed areas. In this study in the southern Adriatic Sea bacteria were quantified by flow cytometry and their diversity assessed by high-throughput sequencing (HTS). In addition, the most represented bacterial groups were quantified by qPCR. The samples were collected from the surface to the seabed, at a total of 16 different depths at four stations in the southern Adriatic Sea, during the late winter BIOTA (BIO-Tracing Adriatic water masses) cruise conducted in 2016. The investigated area showed an unusual circulation characterized by a mixed layer down to 200 m, which differed from the usual winter convection conditions, typical of middle-altitude ecosystems and important for the seasonal picoplankton dynamics in the South Adriatic Sea. Heterotrophic bacteria were separated into HNA (relative High Nucleic Acid content) and LNA (Low Nucleic Acid content) subpopulations with abundances up to 1.8 x 105 and 8.8 x 105 cells/mL, respectively. HNA populations dominated at offshore stations reaching their maximum at depths below the euphotic zone. The bacterial community was dominated by Alphaproteobacteria accounting for > 40% of the total, represented by the SAR11 clade (90.84%), followed by Marinimicrobia (18% of the total), mainly represented by clade SAR406 (8.44%). However, distinctive bacterial groups were found in euphotic layer (Bacteroidetes and Actinobacteria) and aphotic layer samples (Deltaproteobacteria, Marinimicrobia, Chloroflexi, Acidobacteria and Planctomycetes). qPCR assays confirmed HTC results with abundances of targeted bacterial groups found to vary between different sampling points and sampling depths and values ranging from 8.7 x 103 to 9.13 x 105 copy number/mL for Alphaproteobacteria, from 1.44 x 104 to 5.11 x 105 copy number/mL for Gammaproteobacteria and from 1.8 x 103 to 2.4 x 105 copy number/mL for Bacteriodetes. For all targeted taxa higher abundances were found in the euphotic than in the aphotic zone. Introducing of different methodological approaches to the study allowed us to get better insight into the structure of the bacterial assemblages in the South Adriatic.	root:Environmental:Aquatic:Marine:Marginal Sea
MGYS00003081	MiSeq 16S rRNA gene (prokaryotic 16S rRNA gene) sequences of 16 SCS sediments	DNA from 16 SCS sediments have been extracted and amplified by 515F/909R primer pairs (for prokaryotic 16S rRNA gene). The prokaryotic communities of these 16 samples were obtained.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003075	Distribution and composition of thiotrophic mats in the hypoxic zone of the Black Sea (150-170m water depth, Crimea margin)	Distribution and composition of thiotrophic mats were analyzed using high-resolution biogeochemical and community fingerprinting at the outer shelf of the Northwestern Black Sea. Dives with the submersible JAGO showed accumulations of organic matter forming dark patches on the seafloor, which were covered by mat-forming whitish microbial filaments. Where the Black Sea chemocline met the seabed (between 150 - 170 m), these mats covered between 25 to 55 % of the seafloor, and appeared to form a belt of 3 km width. The mats were composed of Beggiatoa-like large filamentous sulfur bacteria based on 16S rRNA sequences from the mat. The microbial community under the mats was enriched with taxa affiliated with polymer degrading, fermenting and sulfate reducing microorganisms. Under the mats, higher organic matter accumulation, as well as higher remineralization and sulfate reduction rates were measured compared to outside the mat. Mat-covered and mat-free sediments showed similar degradability of the bulk organic matter pool, suggesting that the higher sulfide fluxes and subsequent development of the thiotrophic mats in the patches are consequences of the accumulation of organic matter rather than its qualitative composition. Our observations suggest that the key factors for the distribution of thiotrophic mat-forming communities near to the Crimean shelf break are (1) hypoxic conditions repressing grazers and favoring thiotrophic bacteria and (2) the specific seafloor topography that enhances the accumulation of labile organic matter.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003067	16S rRNA metagenomic investigation of arsenotrophic bacteriome of ground water and soil from arsenic-prone area of Bangladesh	In order to characterize the microbial biodiversity of arsenic contaminated water and surrounding soil a metagenomic approach by sequencing six hypervariable regions of 16S rRNA gene has been performed.	root:Environmental:Terrestrial:Soil
MGYS00003066	16S rRNA metagenomic investigation of arsenotrophic bacteriome of ground water and soil from arsenic-prone area of Bangladesh	In order to characterize the microbial biodiversity of arsenic contaminated water and surrounding soil a metagenomic approach by sequencing six hypervariable regions of 16S rRNA gene has been performed.	root:Environmental:Terrestrial:Soil
MGYS00003025	The effect of lifetime nutrition on the rumen microbiome and how this effects the lifetime performance and meat quality of aberdeen angus cattle	Aberdeen angus cattle have been raised on diets to promote different growth speeds; concentrate only diet for fast growth, high abundance of high quality forage (perennial ryegrass) for medium growth and restricted low quality forage grazing for slow growth. Once cattle had reached pre determined fat grade they were slaughtered and the meat was analysed for factors including fatty acid content, taste and shelf life. Alongside this rumen fluid samples were taken at slaughter for metagenomic analysis using full metagenome shotgun sequencing. This metagenome data will be compared with the meat analysis and other performance data taken throughout the experiment to assess the effect of nutrition on the rumen microbiome and how that effects the phenotype of the animal.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00003018	Diversity and composition of sediment microbial assemblages in an Atlantic port environment	Under the framework of the PORTONOVO cooperation which endeavors to enhance monitoring of environmental quality in ports along the Atlantic coast of Europe, we assessed microbial diversity and composition in a Portuguese port environment (Ria de Aveiro). Samples were collected in five locations: two within the port, two along the channel adjacent to the port and one in a relatively undisturbed reference location. Bacterial composition differed significantly among locations with the most pronounced difference being recorded between samples from the reference site versus both port locations. Samples taken from the channel adjacent to the port were intermediate in composition. The port samples were, furthermore, associated with higher values of nitrates, phosphates and total organic carbon; abundant bacterial OTU's (= 50 sequences) were also much more prevalent. Dominance as indicated by the relative abundance of the most abundant OTU was also pronounced in samples from port locations. Port and channel locations were associated with higher relative abundances of Actinobacteria, Deltaproteobacteria (particularly Desulfobacterales) whereas non-port locations had higher relative abundances of Flavobacteria and Rhodobacterales. Our results indicate that the port environment has a pronounced effect on bacterial composition, with sediment from areas under intense port activity displaying a dominance of the Desulfobacterales order.	root:Environmental:Aquatic:Marine:Sediment
MGYS00003017	Bacterial communities in sandy sediment at submarine volcanic vents off Panarea Island (Italy)	"Benthic bacterial communities composition at submarine natural CO2 vents were investigated to
            assess the effect of CO2 leakage and consequent seawater acidification on benthic marine microbial
            assemblages. Sandy sediment samples were collected off Basiluzzo Islet (Panarea Island, Italy) both at CO2
            venting areas and at CO2 not impacted area, and DNA was extracted from two different sediment layers (0-2 cm
            and 4-6 cm). Bacterial communities was described using 454-Massively Parallel Tag Sequencing (454-MPTS)."	root:Environmental:Aquatic:Marine:Sediment
MGYS00003007	Habitat and host related variation in sponge bacterial communities in Indonesian coral reefs and marine lakes	Marine lakes are very rare and unique global ecosystems. Isolated from the surrounding marine habitat, many now house numerous endemic species. In the present study, we compare the bacterial communities of two sponge species, Suberites diversicolor and Cinachyrella australiensis, found inside and outside the lakes. Both species housed unique bacterial assemblages, dominated by Proteobacteria and with high concentrations of Cyanobacteria (the most abundant taxon related to Synechococcus) in one of the marine lakes. Other bacterial phyla were much less prevalent or even completely absent from both species. At the class level, Alphaproteobacteria dominated the communities of Suberites whereas Gammaproteobacteria dominated communities of C. australiensis. There was no discernible difference between bacterial communities hosted by S. diversicolor inside and outside the lake. The bacterial community of this species was, furthermore, dominated by three very closely-related Alphaproteobacterial taxa that together made up 64% of all sequences. C. australiensis, in contrast, hosted markedly different bacterial communities inside and outside the lakes with very few shared abundant taxa. Dominant OTU's in C. australiensis were closely-related to taxa known to be involved in nitrogen fixation, ammonia-oxidation and sulphur-oxidation, an indication that the sponge may be an important component of nutrient cycling inside and outside of marine lakes.	root:Environmental:Aquatic:Marine:Brackish
MGYS00002998	The ecology of microbial communities associated with Macrosystis pyrifera	Bacteria control major nutrient cycles and directly influence plant, animal and human health. However, we know relatively little about the forces shaping their large-scale ecological ranges, community assembly and stability over time. As for many living surfaces in the marine environment, the epiphytic bacterial biofilm communities on macro algae such as Macrocystis pyrifera, and the mechanisms that drive their assembly are poorly understood, apart from the magnitude and diversity of their composition. This biodiversity is not lacking for possible explanations, from colonization to dispersal, succession and persistence by competition. High throughput sequencing has contributed to a variety of potential mechanisms being proposed to characterize the assembly of these microbial communities. We used 454 parallel tag pyrosequencing of the 16s rna gene to better explore the diversity, stability and specificity of the microbial communities associated with the dominant kelp species in Monterey Bay. We also compared the kelp-associated communities with those present in the surrounding seawater to assess the influence of environmental conditions. Our results reveal patterns in the distribution of individual bacterial members at multiple levels of phylogenetic resolution within and around a M. pyrifera ecosystem suggesting the lack of a proposed stable core community of species associated with marine macro algae across space and time (Tujula et al., 2010). M. pyrifera harbors species-specific and temporally adapted epiphytic bacterial biofilms on their surfaces, and the most cosmopolitan taxa are also the most abundant in individual assemblages. Since several of the kelp-specific bacteria identified were highly similar to other bacteria known to either avoid subsequent colonization by eukaryotic larvae or to exhibit antibacterial activities, host-specific bacterial associations might play an important role for M. pyrifera. This study reports on the first published in-depth assessment of the diversity and phylogenetic profile of the bacterial communities associated with M. pyrifera.	root:Host-associated:Algae:Brown Algae
MGYS00002996	CCA_pathobiome	Coralline algae are major benthic calcifiers that play crucial roles in coral reef ecosystems. In this study, we provide data from the first investigation of the bacterial communities associated with healthy and diseased corallines. We target two diseases?Coralline White Band Syndrome (CWBS) and Coralline White Patch Disease (CWPD)?and show that they are associated with different pathobiomes, which indicates different disease causations.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00002961	Culture-enriched human gut microbiomes reveal core and accessory resistance genes	In this study, we used culture enrichment of stools to reveal lower abundance bacteria by high-throughput sequencing. We sequenced fecal bacteria growing under four culture conditions from 24 individuals, before and after use of antibiotics (day 0 and day 7). Overall, 187 species of bacteria had an assembly size greater than 1 million nucleotides, 67 species achieved it only under culture conditions and 22 only in culture-independent fecal microbiomes.The four culture conditions are : (i) MCDA maximum enrichment broth anaerobic culture (MEB-ANA)(ii) MCDA maximum enrichment broth aerobic culture (air enriched with 5% CO2) (MEB-CO2), (iii) MCDA anaerobic culture in presence of 32µg/ml cefoxitin (FOX-ANA)(iv) MCDA aerobic (with 5% CO2) culture in presence of 32µg/ml cefoxitin (FOX-CO2)	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002953	16S data describing Antarctic benthic sediment	Here, we collected twenty-four sediments samples over a 5,500 km transect of western Antarctica that spans the Ross Sea up to the Weddle Sea.  Diversity data from all three domains of life were collected via next-generation DNA sequencing and numerous geochemical and nutrient data were also collected, which greatly contributes to the existing understanding of benthic Antarctic sediments communities.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002948	Diversity of bacterioneuston and bacterioplankton in coastal waters of Misaki, Japan	Deep sequencing of environmental DNA from surface microlayer obtained using polycarbonate membrane (depth= 33 micrometer), glass plate (depth=42 micrometer) and drum sampler (depth=35 micrometer). The bacterial communities obtained using these three surface microlayer samplers were compared to control underlying water obtained from the depth of 20 cm.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002944	Life in a toxic environment	Monitoring of microbial groups along redox gradients in different marine environments.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002943	Metagenome analysis of picoeukaryotes from surface seawater	Surface seawater was collected at two sampling sites in Sendai Bay (C5: 141.083W, 37.976N; C12: 141.317W, 37.974N), Miyagi, Japan on October 7 and December 1 in 2013. Suspended particles were concentrated to 100 fold and divided into two subsamples: (1) mixied with DMSO(5%) and frozen to sore in liquid nitrogen, (2) kept non-frozen. Picophytoplankton cells were sorted by flow cytometry. The genomic DNA was extracted and amplified by whole genome amplification. Partial 18S rRNA gene of the eukaryotes was amplified and sequenced using GS junior.	root:Environmental:Aquatic:Marine
MGYS00002940	Xylophaga in situ Eclusion Experiment	We tested the effect of the presence of Xylophaga sp. on the microbial community and on the hydrogen sulfide concentration during a 85 days experiment at 500m deep. We validate the ability of wood falls microbial community to produce a significant amount of hydrogen sulfide in the absence of Xylophaga sp. during the first months of wood falls colonization	root:Environmental:Aquatic:Marine
MGYS00002937	Arctic first-year drift ice and under-ice water bacterial communities	Arctic first-year drift ice and under-ice water bacterial communities (16S rRNA gene) were studied with Illumina MiSeq.	root:Environmental:Aquatic:Marine
MGYS00002905	Atlantic salmon microbiota	Atlantic salmon skin mucus and surrounding water have been sampled at production facilities both in freshwater and after transfer to seawater. Extracted DNA is sequenced using barcoded 16S primers using PacBio SCC.	root:Environmental:Aquatic
MGYS00002904	Multimodal assessment of flax dew-retting and functional impact on short fiber polymer composites	We have undertaken a dynamic analysis of flax retting combining chemical, spectroscopic, microscopic and targeted-metagenomics characterizations of flax straw collected in the field at different periods after harvest.	root:Host-associated:Plants
MGYS00002902	Preliminary analysis into the metagenome of the marine fire sponge, Tedania ignis, using assembly independent methods	Tedania ignis, or the mangrove fire sponge is a common species throughout the Caribbean and south Florida. It is well known for the intense burning sensation upon contact with skin. The microbiome of T. ignis was recently sequenced as part of the Sponge Microbiome project, but not much is known of the functional potential of these microbial communities, or the taxonomic domain make-up of this species. Metabolites from T. ignis have been found to have potent anti-cancer properties, but the producing symbiont or symbionts have not been determined. In this study, we show the domain makeup of this species, the functional potential of the sponge, and the taxonomic makeup from assembly-free metagenomes.	root:Host-associated:Porifera
MGYS00002882	Coastal eutrophication controls the bacterial community composition in different reef habitats of the Spermonde Archipelago, Indonesia.	Coastal eutrophication is a key driver of shifts in bacterial communities, but related knowledge is very scarce. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments and mucus of the hard coral genus Fungia, along that cross-shelf environmental and water quality gradient. The main research questions were: (1) How do bacterial communities respond to changes in water quality along a spatial gradient? (2) Which water quality parameters influence the  bacterial community composition? (3) Are there bacteria community differences between the different investigated microbial habitats? For this purpose a range of key water parameters were measured at 8 stations in distances from 2 to 55 km from urban Makassar. This was supplemented by sampling of bacterial communities of important microbial habitats using 454 pyrosequencing. Findings revealed that the population center Makassar had a strong effect on the concentrations of Chlorophyll a, suspended particulate matter (SPM) and transparent exopolymer particles (TEP), which were all significantly elevated at the inshore compared the other 7 sites. Shifts in the bacterial communities were specific to each sampled habitat. In the water column, the relative abundance of Gammaproteobacteria increased with distance from Makassar, while that of Alphaproteobacteria decreased.In the sediments, there was a pronounced dominance of Gammaproteobacteria at the inshore site, which decreased along the gradient. There was no gradual shift in bacterial classes for samples obtained from the Fungia mucus. We observed a strong positive correlation between Bacteroidia, Chlamydiia and Acidobacteria_Gp6 and chlorophyll a, TEP and SPM. Deinocooci, Verrumicrobiae and Alphaproteobacteria were, on the other hand, positively correlated to DOC concentrations. In addition, we observed very distinct communities between the investigated habitats. Our data shows strong changes in the bacterial community composition at the inshore site for water column and sediment samples. Alarmingly, this led to a much higher prevalence of potentially pathogenic bacteria at the chronically impacted site closest to Makassar.	root:Environmental:Aquatic:Marine
MGYS00002845	Interkingdom signaling: Modulation of bacterial colonization by quorum sensing interference of Aurelia aurita	Host-derived interference with bacterial communication (quorum quenching, QQ) to modulate microbial colonization of the moon jellyfish Aurelia aurita.	root:Host-associated:Cnidaria
MGYS00002820	Variations in prokaryotic community assembly and predicted metabolic potential of surface sediments with geography in the coastal northern Zhejiang, East China Sea	The coastal marine area of northern Zhejiang (East China Sea) is important to regional development in the southeast of China. Marine sediment prokaryotes play crucial roles in regional biogeochemical cycling. However, the sediment prokaryotic community assembly and metabolic potential in this ecosystem had not been revealed on an extended spatial scale. We collected surface sediment samples across sixe typical zones (Yushan, Xiangshan Harbor, Hangzhou Bay, eastern Zhoushan Islands, eastern Xiangshan, and Sanmen Bay) of this area and combine 16S rRNA gene sequencing, community-level metabolic reconstruction, and sediment physicochemical measurement to investigate the variations in taxonomic composition and metabolic gene family composition with geography and related environmental conditions. Geographic distance effect won the arm-race in shaping beta-diversity pattern with the major environmental drivers such as oil, temperature, texture, sulfide, and water depth, but left larger proportion of unexplained variation, suggesting the effects of unmeasured factors and stochastic process. We found discriminant assemblages across the zones, suggesting some provincial distributions of prokaryotes. On the other hand, the predicted metabolic potential structure slightly but significantly shifts with geography. The key roles of sulfide and oil in shaping metabolic potential structure suggested the importance of sulfur (S) metabolism in biogeochemical cycling here. Particularly, we found that sulfate reduction was the dominant pathway in S-metabolism in the Yushan sediments as indicated by the evidences from taxonomic composition, predicted enzyme-level gene, and metabolic product. This study provides the first insight into the regional turnover of sediment prokaryotic diversity and metabolic potential in this ecosystem.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002817	Cascading influence of inorganic nitrogen sources on DOM production composition lability and microbial community structure in the open ocean	We evaluated the potential for abrupt increases in inorganic N sources to induce cascading effects on DOM and microbial communities in the surface ocean. We collected water from 5 m depth in the central North Pacific and amended duplicate 20 L polycarbonate carboys with nitrate or ammonium, tracking planktonic carbon fixation DOM production DOM composition and microbial community structure responses over 1 week relative to controls	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002808	Dissolved compounds excreted by copepods reshape the diversity and the activity of marine bacterioplankton community	Copepods are important suppliers of bioreactive compounds for marine bacteria through fecal pellet production, sloppy feeding and excretion. However, the interaction between copepods and bacteria is poorly understood in the marine environment. Herein, we investigated the nitrogen and phosphorus compounds excreted by copepods fed by two size fractions of natural food (<20 µm and 20-150 µm) in the upwelling zone of central south of Chile in late summer and spring. We then assessed the biogeochemical response of the bacterial community and their structure, in terms of total and active cells, to the addition of these dissolved compounds. Results revealed that copepods actively excreted nitrogen and phosphorus compounds, mainly in the form of ammonium and dissolved organic phosphorus (DOP), reaching excretion rates up to 2.6 µmol L-1 h-1 and 0.05 µmol L-1 h-1, respectively, in spring. The high accumulation of excreted nitrogen and phosphorus was associated in both periods with the 20-150 µm size fraction of food, which coincided with the main food item available for copepods in the field. Variation in the abundance (contribution to total bacterial sequences) of bacteria taxa was characterized by a decrease of Bacteroidetes and Cyanobacteria, and an increase of Proteobacteria, mainly Alphaproteobacteria and Gammaproteobacteria depending on treatment. Some orders, such as Flavobacteriales presented a rapid response to the products excreted by copepods, increasing their abundance between 3 to 10% in the first four hours of the experiment evolution. Moreover, the specific bacterial activity (16S rRNA: rDNA) suggested a differential response associated with the two size fractions of food provided to copepods, Alphaproteobacteria was stimulated in the treatment enrichment with excretion products by copepods fed with <20 µm size fraction, but inhibited at the 20-150 µm size fraction in March. In December, Alphaproteobacteria was active in both treatments, but in the treatment enriched with excretion products by copepods fed with <20 µm size fraction was higher than the treatment enriched with excretion products by copepods fed with 20-150 µm size fraction. Our findings indicate that the different size fractions of food provided to copepods have an impact on the main products excreted by copepods and showed that bacterial community can respond in a short period of time (<4 h) to excreted organic and inorganic substrates.	root:Environmental:Aquatic:Marine
MGYS00002784	Limited influence of primary treated sewage waters on bacterial abundance, production and community composition in coastal seawaters	The response of bacteria in terms of abundance, production and community structure to changes induced by the discharge of primary treated sewage waters was investigated combining microbiological, chemical and molecular tools. The primary treatment did not affect substantially the bacterial community structure in wastewaters and did not reduce the concentrations of fecal indicators. The spatial distribution of the sewage plume was governed by vertical stratification and currents. Bacterial abundance and production in the sea receiving waste waters depended predominantly on environmental conditions. In the waters with the highest concentration of fecal pollution indicators the bacterial community was characterized by allochthonous bacteria belonging to Epsilonproteobacteria, Firmicutes, Gammaproteobacteria and Bacteroidetes. The latter two taxa were also present in unpolluted waters but had a different structure, typical for oligotrophic environments. Although the impact of primary treated sewage waters was limited, a sanitary risk persisted due to the relevant presence of potentially pathogenic bacteria.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002771	Metagenomic community analysis of marine zooplankton using two plankton nets	Metagenomic analysis was conducted to evaluate effects of plankton nets on marine zooplankton community. Zooplankton samples were collected in the coastal water off Japan, using two types of plankton nets.  PCR was performed to amplify 18S V7-V9 regions, and the 454-pyrosequencing run was carried out .	root:Environmental:Aquatic:Marine:Coastal
MGYS00002764	Latitudinal diversity patterns of pelagic copepods in the Pacific using metagenetic analysis	Latitudinal diversity patterns of pelagic copepods in the Pacific were investigated from 40?S to 68?N along 170?W using metagenetic analysis of nuclear large subunit ribosomal DNA.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002734	Seasonal and spatial diversity of bacterial communities in marine sediments of Ningbo Xiangshan Coastal Ocean	With the rapid development of social economy, East China Sea has suffered from excess nutrient emissions, organic pollutants and heavy metals, and formed a complex marine ecological environment in the past decades. The bacterial biogeographic pattern in marine sediments can reflect the time variation and biological processes of the local ecological environment quickly and accurately. In this study, we collected sediment samples of the two seasons of winter and summer in coastal area of East China Sea at 7 stations from the near to the distant for investigating bacterial community with 16S rRNA gene high-throughput sequencing.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00002715	Metagenomics of soil	Analysis of the microbial communities of different soils	root:Environmental:Terrestrial:Soil
MGYS00002713	Effect of genetics and environment on gut bacteria in Anopheles and Aedes mosquitoes.	The aim was to investigate the effect of genetics and environment on gut bacteria in adult Anopheles and Aedes mosquito. The mosquitoes were both co-reared and reared separately. Larval water, sugar feeding source and adult mosquito-guts were analysed for bacteria.	root:Engineered:Lab enrichment:Defined media
MGYS00002710	Microbial community structure and dynamics in the oxygen minimum zone of the Northeast subarctic Pacific Ocean	NONE	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002708	Microbiome of St. Lawrence estuary sediments	The myxobacteria are a widely dispersed group of Gram-negative bacteria known for their elaborate fruiting bodies. Principally soil bacteria, they are key players in the breakdown and processing of organic compounds in terrestrial soils, acting as both primary cellulose degraders and bacterial predators. While easily cultivated from soil, isolation of myxobacteria from lakes, rivers and oceans is rare, and for many years it was thought that myxobacteria were incapable of surviving in aquatic environments. We recently conducted a metagenomics analysis of several sites in the Gulf of St. Lawrence, examining the bacteria found free-living in the water column and attached to suspended marine sediment. While sequences corresponding to myxobacteria were not prevalent in the water column, they were widely dispersed in the sediments, forming up to 3-4 % of the active bacterial community in some cases. To determine the role of myxobacteria in the St. Lawrence estuary ecosystem, and to isolate any therapeutically relevant natural products that they may produce, we will pinpoint samples rich in myxobacteria via metagenomics. This will allow us to see how myxobacterial species prevalence changes as we move from freshwater to saltwater sediments.	root:Environmental:Aquatic:Estuary:Sediment
MGYS00002707	Dynamics of bacterial communities mediating the treatment of an as-rich acid mine drainage in a field-scale pilot	Passive treatment based on iron biological oxidation is a promising strategy for As-rich acid mine drainage (AMD) remediation. The present study aimed at the characterization of the bacterial diversity in a field-pilot bioreactor treating extremely As-rich AMD in situ. Inside the bioreactor, the bacterial communities responsible for iron and arsenic removal formed a biogenic precipitate. These communities evolved from a structure at first similar to the one of the feed water used as an inoculum to a structure similar to the natural ecosystem developing in situ in the AMD. Diverse FeOB populations largely dominated the bioreactor including: Gallionella, Ferrovum, Leptospirillum, Acidithiobacillus, Ferritrophicum,… Notable shifts were observed in the distribution of these populations inside the bioreactor. Appreciable arsenite oxidation occurring in the bioreactor could be linked to the presence of Thiomonas related bacteria. The spatio-temporal dynamics of the whole communities were tightly linked to variations in the physico-chemistry of the AMD water transiting inside the bioreactor. The main parameters that proved to exert a control on the bacterial communities potentially involved in the water treatment process were: DO, temperature, pH, dissolved sulfates, arsenic and Fe(II) concentrations and redox potential. The ubiquity and the physiological diversity of the bacteria identified (including the genus of biotechnological relevance Ferrovum) suggested that this treatment system could be easily adapted to the treatment of AMD with a large range of physico-chemical characteristics.	root:Engineered:Wastewater:Industrial wastewater:Mine water
MGYS00002706	VETII samples	The samples relate to the Danish VETII project regarding the relationship between antimicrobial usage in finishing pigs and antimicrobial resistance in their gut microbiome. Five different sub-projects are included; 1. Pilot project containing 10 farms (P), 2. Observational project containing 83 farms, 3. Rearing time related longitudinal study in 6 of the 83 farms, thus both weaners (W) and finishing pigs were sampled in those farms. 4. 2x2 split (A,B) sampling project in 4 of the 83 farms, and 5. Production cycle longitudinal study in 52 of the 83 farms, thus the second sampling was performed two finishing pig production cycles after the first sampling. Sampling took place from Marts 2014 to July 2016. Each faeces sample from a farm consists of 30 individual pig faeces samples pooled into one.	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00002703	Anaerobic digestion of phenol rich influent	Aims of this study were (1) to investigate the phenol-degrading anaerobic population in operationally identical reactors in order to identify key players involved in phenol degradation and resistance in AD reactors and (2) to determine the impact of the inoculum in shaping the structure of the phenol-degrading community. It was tested whether different starting communities, adapted to different phenolic compounds, were as effective in treating a mixture of dairy and phenolic wastewater.Four different inocula were studied in triplicate lab-scale reactors run over a period of 180 to 265 days. The reactors were operated at mesophilic conditions with a mixture of a synthetic dairy and phenol wastewater.	root:Engineered:Bioremediation:Persistent organic pollutants (POP)
MGYS00002701	Airway metagenome of children in Kilifi, Kenya	Naso- and oropharyngeal samples were collected from children with different manifestations of respiratory infection as well as from well controls. Upper airway microbiota were characterised by sequencing the V3/V4 hypervariable region of the bacterial 16S rRNA gene on the Illumina MiSeq platform.	root:Host-associated:Human:Respiratory system
MGYS00002698	Microbial induced mineral precipitations caused by nitrate treatment for souring control during microbial enhanced oil recovery (MEOR)	Microbiologically active environments, like oil reservoirs, can suffer different a range of problems due to the presence of sulfate-reducing microorganisms. These includeing, but are not limited to: H2S formation, souring and corrosion caused mainly by sulfate-reducing microorganisms. To prevent biogenic sulfate reduction, nitrate can be used as an environmentally friendly alternative to biocides. However, side effects of nitrate injection are sometimes observed but not well understood. In our study, we used original water from an onshore reservoir, where a microbial enhanced oil recovery (MEOR) application is planned, and investigated the effects of nitrate addition on H2S generation, mineral precipitation and microbiology. We observed that nitrate did inhibit H2S formation in most, but not all cases while available in the medium. During nitrate reduction, iron and calcite minerals precipitated over short- and long-term (10 or 160 days) incubations. This was caused by a nitrate-reducing group of bacteria belonging to the family Deferribacteraceae. Using dynamic sandpack setups and numerical modeling approaches with the simulator TOUGHREACT, we observed significant reduction in permeabilities (~44x) suggesting injectivity issues over time in case nitrate is continuously added to the reservoir. Our study shows that nitrate-dependent processes, which were described separately for pure-cultures before, are also valid for natural mixed communities present in oil fields and underlines the complex interplay of microbial metabolisms associated with those communities.	root:Environmental:Terrestrial:Oil reservoir
MGYS00002691	Commensal viruses maintain intraepithelial T cells via non-canonical RIG-I signaling	Much attention has been focused on the role of commensal bacteria in health and disease, but the role of commensal viruses is understudied. Metagenomic analysis shows that the intestine of humans and animals harbors various commensal viruses and the dysbiosis is often associated with intestinal infection and inflammatory diseases, but the role and mechanism of commensal viruses in the homeostasis of intestinal immune system remain unexplored. Here, we show that commensal viruses are essential for the homeostasis of intestinal intraepithelial lymphocytes (IELs). The cytosolic viral RNA sensing receptor RIG-I in antigen presenting cells can recognize commensal viruses and maintain IELs via an interferon-independent, but MAVS-IRF1-IL-15 axis dependent manner. Notably, the recovery of IELs restores the colitis susceptibility of commensal viruses-depleted mice to dextran sulfate sodium. Collectively, our results indicate that commensal viruses can support the homeostasis of IELs and regulate mucosal immunity via non-canonical RIG-I signaling.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00002690	EMG produced TPA metagenomics assembly of the Infant fecal microbiome related to eczema (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA272371.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002689	EMG produced TPA metagenomics assembly of the Alkaline Insect Gut Metagenome Project (SRP010470) data set.	The SRP010470 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: SRP010470.  This project includes samples from the following biomes: Host-associated, Arthropoda, Digestive system.	root:Host-associated:Arthropoda:Digestive system:Gut
MGYS00002687	EMG produced TPA metagenomics assembly of the Human Faecal Samples Raw sequence reads (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA308846.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002685	EMG produced TPA metagenomics assembly of the Metagenomics analysis of donor and recepient samples from fecal transplant for Recurrent Clostridium difficile infection () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA339012.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002682	Biomethanization of CO2 via ex-situ application	In recent years several studies investigated a potential of biogas upgrading to high quality biomethane using biological biomethanization of CO2 approach. Resulting biomethane can be used as a substitute of a natural gas in the National Grid or serve as a gaseous biofuel for transportation. In this study, eight lab scale reactors were inoculated with waste water treatment plant sludge and acclimatised for a period of time prior H2 injection. The conversion rate of hydrogen was monitored to determine kinetics rate. Samples were also collected to establish the microbial community structure in response to hydrogen injection using metagenomic analysis.	root:Engineered:Biogas plant
MGYS00002681	16S amplicon study of compost tea, teku kana and litters	A metagenomic study, using 16S amplicon approach, has been performed to analyze bacterial communities of compost tea, teku kana and litter used to produce it.	root:Engineered:Solid waste:Composting
MGYS00002678	EMG produced TPA metagenomics assembly of the Hot spring microbial communities from South Africa to study Microbial Dark Matter (Phase II) - Sagole hot spring metaG metagenome (hot springs metagenome) data set.	The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364998.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00002677	EMG produced TPA metagenomics assembly of the preterm infant gut metagenomes (NIH Y4 Cohort) (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA396794.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002676	EMG produced TPA metagenomics assembly of the Dissecting effects of community context on a gut pathobiont in a model of childhood undernutrition (Host-pathobiont-microbiota interactions in undernutrition) data set.	The Host-pathobiont-microbiota interactions in undernutrition Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB9703.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00002674	EMG produced TPA metagenomics assembly of the Cotija cheese metagenome (food metagenome) data set.	The food metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA286900.  This project includes samples from the following biomes: Engineered, Food production, Dairy products.	root:Engineered:Food production:Dairy products
MGYS00002673	Convergence of gut microbiomes in myrmecophagous mammals	Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant- and termite-eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins, and aardwolves thus provide a model system for understanding the potential role of gut microbiota in the convergent adaptation to myrmecophagy. Here, we expand upon previous mammalian gut microbiome studies by using high-throughput barcoded Illumina sequencing of the 16S rRNA gene to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples. We confirm that both diet and phylogeny drive the evolution of mammalian gut microbiota, with cases of convergence in global composition, but also examples of phylogenetic inertia. Our results reveal specialized placental myrmecophages as a spectacular case of large-scale convergence in gut microbiome composition. Indeed, Neighbor-Net networks and beta diversity plots based on UniFrac distances show significant clustering of myrmecophagous species (anteaters, aardvarks, and aardwolves) even though they belong to phylogenetically distant lineages representing different orders. The aardwolf, which diverged from carnivorous hyenas only in the last 10 million years, experienced a convergent shift in the composition of its gut microbiome to become more similar to other myrmecophages. These results confirm diet adaptation to be a major driving factor of convergence in gut microbiome composition over evolutionary timescales. This study sets the scene for future metagenomic studies aiming at evaluating potential convergence in functional gene content in the microbiomes of specialized mammalian myrmecophages.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00002671	Biological Impacts of Ocean Acidification	Impacts of ocean acidification and warming on marine macroalgae and its microbiota	root:Environmental:Aquatic:Marine
MGYS00002662	Biomethanization of CO2 in AD plants - amplicon study	Anaerobic digestion uses a variety of organic wastes (domestic, industrial, agricultural) to produce biogas – a mixture of carbon dioxide and methane. Biogas is often used on the industrial application to generate heat and power but can also be upgraded to biomethane and injected directly into the National Grid as a substitute for natural gas. Currently, the upgrading step limits the wider use of biomethane as a gaseous biofuel. In order to increase the biomethane potential, biomethanization can be applied either by adding H2 to the reactor and converting it to methane in presence of endogenous (in-situ) or exogenous (ex-situ) CO2 by the resident microbiome.  Here, we upgraded biogas to biomethane using in-situ biomethanization. Using DNA sequencing approaches such as metagenomics and 16S amplicon sequencing the identity of microbial members of the enriched community and their functional potential was uncovered leading to better understanding on how the AD biomethanization process can be manipulated and improved.	root:Engineered:Biogas plant:Wet fermentation
MGYS00002656	Meta_Kosmos	Bacterial diversity patterns in response to ocean acidification.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002654	Zooplankton communities in the coastal water of northeastern Hokkaido	Monitoring zooplankton communities is important to understand changes in the marine ecosystem. In this study, total 101 zooplankton samples were collected weekly in 2014 and 2015 at the Okhotsk tower in Mombetsu city, Hokkaido, Japan. A metagenetic analysis of the 18S region was conducted to reveal seasonal changes of zooplankton diversity and community in the coastal water of northeastern Hokkaido along the Okhotsk Sea.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002643	Biological Impacts of Ocean Acidification	Restructuring of epibacterial communities on Fucus vesiculosus forma mytili in response to elevated pCO2 and increased temperature levels	root:Host-associated:Algae:Brown Algae
MGYS00002608	Lactobacillus dominate in the intestine of Atlantic salmon fed dietary probiotics.	Probiotics are live microbial strains incorporated as dietary supplements in feeds and are known to provide health benefits to the host. These live microbes manipulate the gut microbes by suppressing the growth and competing with other intestinal microbes. Lactic acid bacteria (LAB) are potential probiotics that have been widely studied; in this study, we have elucidated the effects of two LAB types (LAB1 & LAB2) isolated from the intestinal content of farmed healthy juveniles of rainbow trout on the distal intestinal microbial communities of Atlantic salmon (Salmo salar). We employed high-throughput 16S rRNA gene amplicon sequencing technique to investigate the intestinal bacterial communities harbouring in the distal intestinal content and mucus of the 3 groups of Atlantic salmon fed diets-devoid of or diets-containing LABs. Our results show that LAB shifts the intestinal microbial profile; LAB supplementation did not show any significant alterations in the alpha diversity of the three groups. However, LAB2 feeding increased the bacterial diversity in the distal intestinal mucus of the fish. Beta diversity analysis showed a significant difference between control and LAB-fed groups. We found intestinal Lactobacillus abundant and dominant in the LAB-fed fish. In addition, few members of the phyla Tenericutes, Actinobacteria, and Spirochaetes were also found to be abundant in the LAB-fed groups. Furthermore, the bacterial association network analysis showed that in the LAB1-fed group significantly abundant and relevant OTUs are closely linked suggesting that they may be highly interactive. We did not find any evidence on cooperation-related runaway effect. These results indicate that dietary probiotics modulate the distal intestinal microbiota of Atlantic salmon. These results are intended to improve the understanding of the modulations and interactions of gut microbiota under the influence of selected probiotic species.	root:Host-associated:Fish:Digestive system:Foregut
MGYS00002603	Diet analysis of Japanese sardine and Pacific round herring larvae	A successful feeding on preferred prey is important for survival of fish larvae; however, it is difficult to obtain high taxonomic resolutions from damaged gut contents by morphological classification. In this study, <10 mm early post-larvae of Japanese sardine (Sardinops melanostictus) and Pacific round herring (Etrumeus teres) were collected in Tosa Bay (Japan) during their major spawning period. Their diet and environmental plankton communities were  investigated using metagenetic analysis of 18S V9 region.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002593	Diversity, Ecology and Biogeochemistry of cyst-forming acantharia (Radiolaria) in the oceans	Marine planktonic organisms that undertake active vertical migrations over their life cycle are important contributors to downward particle flux in the oceans. Acantharia, globally distributed heterotrophic protists that are unique in building skeletons of celestite (strontium sulfate), can produce reproductive cysts covered by a heavy mineral shell that sink rapidly from surface to deep waters. We combined phylogenetic and biogeochemical analyses to explore the ecological and biogeochemical significance of this reproductive strategy. Phylogenetic analysis of the 18S and 28S rRNA genes of different cyst morphotypes collected in different oceans indicated that cyst-forming Acantharia belong to three early diverging clades from the orders Chaunacanthida and Holacanthida that are mainly heterotrophic. Environmental high-throughput V9 tag sequences and clone libraries showed that the three clades are widely distributed in the Indian, Atlantic and Pacific Oceans at different latitudes, but seem more abundant in regions of higher primary productivity. Moreover, sequences of cyst-forming Acantharia were distributed evenly in both the photic and mesopelagic zone, a vertical distribution that we attribute to their life cycle where flagellated swarmers are released in deep waters from sinking cysts. Bathypelagic sediment traps in the subantarctic and oligotrophic subtropical Atlantic Ocean showed that downward flux of Acantharia was only large at high-latitudes and during a phytoplankton bloom. High organic carbon export in cold waters would be a putative nutritional source for non-symbiotic juveniles ascending in the water column. This study improves our understanding of the life cycle and biogeochemical contribution of Acantharia, and brings new insights into a remarkable reproductive strategy in marine protists	root:Environmental:Aquatic:Marine
MGYS00002590	This workpackage details only the prokaryote (Archaea and Bacteria) analyses for the MicroPolar project.	DNA and cDNA (derived from total RNA) were amplified with primers for Illumina sequencing of the 16S rDNA gene.	root:Environmental:Aquatic:Marine
MGYS00002589	Bioaccumulation and gut microbiome response in the great pond snail Lymnaea stagnalis exposed to PBDEs in the presence and absence of nylon microplastics	It is recognised that microplastics will associate with persistent organic chemicals within the environment, potentially changing their bioavailability and the interaction of organisms with these chemicals. The aims of this study were to investigate how the presence of microplastics affect PBDE bioaccumulation and the gut microbiome in the great pond snailLymnaea stagnalis. Snails were exposed to microplastics and PBDEs independently and in combination for 96 hours. Microplastic particles (13-15 µm nylon powder) were mixed with quartz sand sediment at 1% w/w. A PBDE mix (containing BDE-47, 99, 100, 153 and PBB-153) was added to the sediment-microplastic mix in glass vessels at six environmentally relevant concentrations (94, 188, 375, 750, 1500, 3000 ng g-1 each PBDE), with six replicates consisting of one snail per treatment. There was no significant mortality observed in any of the treatments after 96 hours exposure. Of the six snails per treatment, three were analysed for PBDE tissue concentration and three were analysed for gut microbiome composition. The presence of microplastics did not significantly change PBDE bioaccumulation. However, our data indicate that that the presence of microplastics did influence gut microbial community diversity. In snails exposed to microplastics only (without PBDEs), microbial diversity was lower compared to those not exposed to microplastics. In the presence of microplastics, with increasing PBDE concentration, gut microbial diversity increased. In comparison, when microplastics were absent microbial communities were less diverse at the higher concentrations. A similar trend is reflected in the community composition data. These data imply that microplastics alone can influence the gut microbial community and they can also alter the effects of PBDEs on the gut microbiome. Given the importance of the gut microbiome for nutrition, metabolic function and immunity, such perturbation to the microbial community may have implications for organism health and fitness.	root:Host-associated:Mollusca:Digestive system
MGYS00002587	Microbiome of supragingival plaque from healthy volunteers	Microbiome of supragingival plaque from healthy volunteers	root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
MGYS00002586	Development and acquisition of the microbiota across multiple body sites in preterm infants at risk of NEC and sepsis	Premature infants are at a high risk of developing necrotising enterocolitis. A microbial element of the condition has been confirmed, however exact aetiology remains enigmatic and ‘typical' microbiota development remains undefined. To characterise establishment of the severely preterm infant gut microbiota we employed targeted sequencing of the bacterial 16S rRNA gene. Sample types included oral and endotracheal swabs, stool and breast milk, collected from 7 patients over the first 2 months, postnatally (n = 158 samples). Propidium monoazide treatment was combined with targeted sequencing of the V4 region of the 16S rRNA gene to identify viable bacterial communities. Significantly lower alpha diversity was observed in stool than upstream mucosae (P < .005). Homogenising dispersal of dominant taxa was identified across all body-sites within the first week of life and persisted throughout the sampling period for all infants. Beta diversity was lowest immediately following birth and between proximal sampling sites. Oral microbiota showed the greatest similarity to stool (R2 = .73, P < 0.05), however the composition of stool microbiotas diverged from upstream mucosae over time (67% at WoL 1 vs 20% at WoL 8). We suggest a temporal pattern of gut microbiota development where speciation and divergence increase over time.	root:Host-associated:Human
MGYS00002562	Bacterial communitiy compositions on natural and artificial substrates in the Spermonde Archipelago, Indonesia	Populations on small islands surrounded by coral reefs often heavily depend on these reefs. The health and recovery of reefs are strongly influenced by recruitment of coral larvae. Their settlement relies on cues such as those emitted from bacterial communities forming biofilms on reef surfaces. Environmental conditions can change these bacterial community compositions (BCC) and may in turn affect settlement of coral larvae. We investigated BCC and coral larvae settlement at three small inhabited islands with different distance from the mainland in the Spermonde Archipelago, Indonesia. BCC and recruitment were analyzed on artificial ceramic tiles after 2-8 weeks exposure time and on natural reef substrate. Environmental analysis showed a clear separation in water parameters between inshore and near-shore/mid-shelf sites, as well as distinct benthic communities at all of the three sites. No coral recruitment was observed at the inshore site with highest anthropogenic impact. At the other two sites coral recruitment occurred on natural surfaces (recruits per 100 cm2: 0.73 ± 1.75 near-shore, 0.90 ± 1.97 mid-shelf), but there was no significant difference between the two sites. On artificial substrates coral recruitment differed between these two sites, with tile orientation and with exposure time of the tiles in the reef. The most abundant bacteria on both substrates were Gammaproteobacteria, Alphaproteobacteria and Cyanobacteria. BCC was strongly correlated with water quality and significant differences in BCC between the inshore site and near-shore/mid-shelf were found. On artificial substrates there was a significant difference in BCC with exposure time in the reef. Furthermore, bacterial communities on artificial tiles showed changes in their composition after being subjected to higher water temperatures in an experimental setting. We demonstrate how changes in water quality and temperature can affect BCC in coral reefs, which in turn could affect coral recruitment. Small islands such as these investigated feature a high spatial variability, as seen e.g. in environmental gradients, differences in BCC or in coral recruitment. Our study highlights the value of taking both BCC and coral recruitment into account in addition to the environmental conditions, when considering the recovery potential of coral reefs.	root:Environmental:Aquatic:Marine
MGYS00002543	Bacterial diversity in snow from mid-latitude mountain areas: Alps, Eastern Anatolia, Karakoram and Himalaya.	Snow can be considered an independent ecosystem that hosts active microbial communities. Snow microbial assemblages have been extensively investigated in the Arctic and in the Antarctica, but rarely in mid-latitude mountain areas. In this study, we investigated the bacterial communities of snow collected in four glacierized areas (Alps, Eastern Anatolia, Karakoram and Himalaya) by high-throughput DNA sequencing. We also investigated the origin of the air masses that produced the sampled snowfalls by reconstructing back-trajectories. A standardized approach was applied to all the analyses in order to ease comparison among different communities and geographical areas. The bacterial communities hosted from 25 to 211 Operational Taxonomic Units (OTUs), and their structure differed significantly between geographical areas. This suggests that snow bacterial communities may largely derive from ‘local' air bacteria, maybe by deposition of airborne particulate of local origin that occurs during snowfall. However, some evidence suggest that a contribution of bacteria collected during air mass uplift to snow communities cannot be excluded, particularly when the air mass that originated the snow event is particularly rich in dust.	root:Environmental:Aquatic:Freshwater:Ice
MGYS00002531	A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes	Massively parallel pyrosequencing of amplicons from the V6 hypervariable regions of small-subunit (SSU) ribosomal RNA (rRNA) genes is commonly used to assess diversity and richness in bacterial and archaeal populations.  Recent advances in pyrosequencing technology provide read lengths of up to 240 nucleotides. Amplicon pyrosequencing can now be applied to longer variable regions of the SSU rRNA gene including the V9 region in eukaryotes. We present a protocol for the amplicon pyrosequencing of V9 regions for eukaryotic environmental samples for biodiversity inventories and species richness estimation. The International Census of Marine Microbes (ICoMM) and the Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites (MIRADA-LTERs) projects are already employing this protocol for tag sequencing of eukaryotic samples in a wide diversity of both marine and freshwater environments.	root:Environmental:Aquatic:Marine
MGYS00002528	Short-term interaction of pyrene and cadmium in prokaryotic community in coastal sediment microcosms	Acute ecological impact of co-contamination of polycyclic aromatic hydrocarbons (PAHs) and heavy metals and their short-term interaction on diversity and composition of coastal benthic prokaryotes were unclear. We took pyrene (Pyr) and cadmium (Cd) as the representatives and mimicked an eight-week exposure of moderate and high levels of Pyr, Cd and their mixtures. 16S rRNA amplicon sequencing was used to investigate interaction of the contaminants in temporal succession of prokaryotes.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00002511	Prokaryotic community response to microalgal lysates	Changes in the community structure of heterotrophic prokaryotes in the open tropical Pacific in response to dissolved organic matter derived from microalgal lysates	root:Environmental:Aquatic:Marine:Oceanic
MGYS00002506	Biomethanization of CO2 in anaerobic digestion plants	Anaerobic digestion uses a variety of organic wastes (domestic, industrial, agricultural) to produce biogas – a mixture of carbon dioxide and methane. Biogas is often used on the industrial application to generate heat and power but can also be upgraded to biomethane and injected directly into the National Grid as a substitute for natural gas. Currently, the upgrading step limits the wider use of biomethane as a gaseous biofuel. In order to increase the biomethane potential, biomethanization can be applied either by adding H2 to the reactor and converting it to methane in presence of endogenous (in-situ) or exogenous (ex-situ) CO2 by the resident microbiome.  Here, we upgraded biogas to biomethane using in-situ biomethanization. Using DNA sequencing approaches such as metagenomics and 16S amplicon sequencing the identity of microbial members of the enriched community and their functional potential was uncovered leading to better understanding on how the AD biomethanization process can be manipulated and improved.	root:Engineered:Biogas plant
MGYS00002504	Shotgun Metagenome Sequencing of Lake Soyang	The lakewater samples were collected from different depths and differnet seasons. The DNA was extracted after filtration through 0.2 um pore-size membrane.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00002502	Bacterial communities collected on the surface of stainless steels samples exposed to seawater heated from 30°C to 40°C.	Stainless steels exposed to seawater undergo a several hundred millivolt increase of the open circuit potential called ennoblement.That phenomenon is caused by the bacteria present on the surface of the stainless steel.There is a critical temperature of 38°C above which the ennoblement is inhibited despite the presence of bacteria. We collected bacteria from samples exposed to a range of temperature: 30°C, 33°C, 36°C, 38°C and 40°C in order to compared the conditions leading to ennoblement (under 40°C).We find the presence of the electro-active bacteria Candidatus Tenderia electrophaga, an electro-autotrophic bacteria able to use an electrode as an electron donor to reduce oxygen. We propose a model for which electrotroph bacteria are responsible for the ennoblement.	root:Engineered:Lab enrichment:Defined media:Marine media
MGYS00002480	Association of metformin administration with gut microbiome dysbiosis in healthy volunteers	Metformin is a widely used first-line drug for treatment of type 2 diabetes. Despite its advantages metformin has variable therapeutic effects, contraindications, and side effects. Here, for the very first time, we investigate the short term effect of metformin on the composition of healthy human gut microbiota.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002479	Actinobacterial endophytes of medicinal plant Melia toosendan	DNA was extracted from Melia toosendan plant bark, fruit, leaf, root and stem samples. Actinobacterial endophytes were analyzed using 16S rRNA targeted amplicon sequencing using actinobacteria specific primers.	root:Host-associated:Plants
MGYS00002475	Metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene of a mixed zooplankton assemblage was carried out using the 454 pyrosequencing platform.	Background: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae.  However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. Methodology/Principle Findings: Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. Conclusions: Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta.  It also reveals rare species and parasites.  We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.	root:Environmental:Aquatic:Marine
MGYS00002462	Effect of size fractionation and DNA extraction on the diversity and composition of prokaryotic and eukaryotic plankton community	We determined the effect of sample size fractionation (5 size fractions) and DNA extraction (2 methods) on the composition of the prokaryotic (16s) and eukaryotic (18s) plankton community composition	root:Environmental:Aquatic:Marine
MGYS00002452	Pelagic Microbiome: viruses to protists. 16S and 18S data from oceanic samples collected at the chlorophyll maximum.	We collected environmental samples during the second cruise of the project “The Great Southern Coccolithophore Belt” collecting samples in the South Indian Ocean and Southern Ocean; during the RSS James Clark Ross Cruise JCR271 as part of the project on Arctic Ocean Acidification collecting samples in the Arctic; finally we collected two costal samples off the coast of South Africa during algal bloom events. Samples included 16S, 18S  amplicons and metagenomic data.	root:Environmental:Aquatic:Marine
MGYS00002451	16S and 18S sequences from the epiphytic biofilm on leaves of Enhalus acroides	Seagrass meadows are a crucial component of tropical marine reef ecosystems. The seagrass plants are colonized by a multitude of epiphytic organisms that contribute to determining the ecological role of seagrasses. To better understand how environmental changes like ocean acidification might affect epiphytic assemblages, the microbial community composition of the epiphytic biofilm of Enhalus acroides was investigated at a natural CO2 vent in Papua New Guinea using molecular fingerprinting and next generation sequencing of 16S and 18S rRNA genes. Both bacterial and eukaryotic epiphytes formed distinct communities at the CO2-impacted site compared to the control site. This site-related CO2 effect was also visible in the succession pattern of microbial epiphytes. We further found an increased abundance of bacterial types associated with coral diseases at the CO2-impacted site (Fusobacteria, Thalassomonas) whereas eukaryotes such as certain crustose coralline algae commonly related to healthy reefs were less diverse. These trends in the epiphytic community of E. acroides suggest a potential role of seagrasses as vectors of coral pathogens and may support previous predictions of a decrease in reef health and prevalence of diseases under future ocean acidification scenarios.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002447	Specific gut microbiome members are associated with distinct immune markers in allogeneic hematopoietic stem cell transplantation	"Background:
Increasing evidence shows the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic hematopoietic stem cell transplantation, (HSCT), i.e. a replacement of the cellular part of the patients' immune system with that of a foreign donor. HSCT is employed as curative immunotherapy for a number of non-malignant and malignant hematologic conditions, including acute lymphoblastic leukemia. The procedure can be accompanied by severe side effects such as infections, acute graft-versus-host disease (aGvHD), and death. Here, we performed a longitudinal analysis of immunological markers, immune reconstitution and gut microbiota composition in relation to clinical outcomes in children undergoing HSCT. Such an analysis could reveal biomarkers, e.g. at the time point prior to HSCT, that in the future could be used to predict which patients are of high risk in relation to side effects and clinical outcomes and guide treatment strategies accordingly. 

Results:
In two multivariate analyses (sparse partial least squares regression and canonical correspondence analysis), we identified three consistent clusters: (1) High concentrations of the antimicrobial peptide human beta-defensin 2 (hBD2) prior to the transplantation in patients with high abundances of Lactobacillaceae, who later developed moderate or severe aGvHD and exhibited high mortality. (2) Rapid reconstitution of NK and B cells in patients with high abundances of obligate anaerobes such as Ruminococcaceae, who developed no or mild aGvHD and exhibited low mortality. (3) High inflammation, indicated by high levels of C-reactive protein, in patients with high abundances of facultative anaerobic bacteria such as Enterobacteriaceae. Furthermore, we observed that antibiotic treatment influenced the bacterial community state.

Conclusions: 
We identify multivariate associations between specific microbial taxa, host immune markers, immune cell reconstitution and clinical outcomes in relation to HSCT. Our findings encourage further investigations into establishing longitudinal surveillance of the intestinal microbiome and relevant immune markers, such as hBD2, in HSCT patients. Profiling of the microbiome may prove useful as a prognostic tool that could help identify patients at risk of poor immune reconstitution and adverse outcomes, such as aGvHD and death, upon HSCT, providing actionable information in guiding precision medicine."	root:Host-associated:Human:Circulatory system:Blood
MGYS00002445	COMPARE Food Ring Trial - wet	Due to the importance of foods in the transmission of zoonotic agents, within COMPARE Task 2.7 framework a food metagenomic proficiency test was organised between April and June, 2018. The aim of the proficiency test waa to compare microorganisms identity and corresponding abundances in a food matrix tested by shotgun metagenomic sequencing. The food matrix was smoked salmon spiked with a mock community containing bacteria, viruses and parasites. The food matrix was dispatched to each proficiency test participant frozen, including a thermo-logger to monitor the shipping temperature. It was expected that each Participant received the spiked smoked salmon shipped from DTU on April 24 2018, performed nucleic acid extraction and shotgun metagenomic sequencing and upload sequencing data.	root:Engineered:Food production
MGYS00002444	Microbial diversity in the Benguela coastal upwelling system as derived from 16S rRNA sequencing and RNA Stable Isotope Probing (SIP)	Sediment microbial diversity was assessed in samples retrieved from four sampled transects. 16S metagenomics was used to characterize microbial structure in the sediments of the different sampling stations. Furthermore, stable isotope probing was employed in samples from certain stations in an attempt to link the function and identity of the microorganisms of the sediment samples. Two microcosm experiments were conducted with one involving the addition of nitrate as substrate and the other one sulphate. In both experiments the provided electron donor was acetate.	root:Environmental:Aquatic:Marine:Sediment
MGYS00002443	Deep-amplicon sequencing as a powerful new tool to screen for sequence polymorphisms associated with anthelmintic resistance in parasitic nematode populations	Parasitic gastrointestinal nematodes contribute to significant human morbidity and cause billions of dollars per year in lost agricultural production. Control is dependent on the use of anthelmintic drugs, which in the case of livestock parasites, are severely compromised by the widespread development of drug resistance. More recently, there are concerns regarding the emergence of anthelmintic resistance in human parasitic nematodes in response to the selection pressure resulting from mass drug administration (MDA) programs. Consequently, there is an urgent need for sensitive, scalable and accurate diagnostic tools to detect the emergence of anthelmintic resistance.. Detecting and measuring the frequency of resistance-associated mutations in parasite populations has the potential to provide sensitive and quantitative assessment of resistance emergence from an early stage.  We describe the development and validation of deep-amplicon sequencing as a powerful new approach to detect and quantify the frequency of single nucleotide polymorphisms (SNPs) associated with benzimidazole resistance. We have used parasite communities in sheep, to undertake a proof-of-concept study of this approach. Sheep provide an excellent host system, as there are multiple co-infecting trichostrongylid nematode species, each with varying prevalence of benzimidazole resistance. We demonstrate that the approach provides an accurate measure of resistance allele frequencies, and can reliably detect resistance alleles down to a frequency of 0.1%, making it particularly valuable for screening mutations in the early stages of resistance. We illustrate the power of the technique by screening UK sheep flocks for benzimidazole resistance-associated SNPs at three different codons of the β-tubulin gene, in seven different parasite species from 164 populations (95 from ewes and 69 from lambs) in a single MiSeq sequencing run.  This approach provides a powerful new tool to screen for the emergence of anthelmintic resistance mutations in parasitic nematode populations of both animals and humans.	root:Host-associated:Animal
MGYS00002441	EMG produced TPA metagenomics assembly of the doi: 10.3389/fmicb.2016.00579 We employed shotgun metagenome and 16S rDNA gene amplicon sequencing of topsoil samples to robustly compare the taxonomic and functional gene content (Oklahoma and Alaska 1-Year Soil Warming Experiment) data set	The Oklahoma and Alaska 1-Year Soil Warming Experiment Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB10725. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00002438	Abundance, diversity and distribution of Legionellales in wet environments in Sweden	In this study, 57 samples from water, soil and sediments were collected in different wet environments in Uppland, Sweden. 45 of them were taken from natural reserves, and 12 from a silver mine. The main objective was to study the abundance, diversity and distribution of members of the gammaproteobacterial order Legionellales.	root:Environmental
MGYS00002436	EMG produced TPA metagenomics assembly of the Characterization of the distal gut microbiota in obese patients following a weight-loss intervention using whole metagenome shotgun sequencing (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA290729.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002434	DEHP Alters Gut Microbiota in Human Neonates	Postnatal exposure to DEHP is associated the development of allergic diseases later in life. The objectives of this study is to investigate whether iatrogenic DEHP exposure affected the gut microbiota pattern in newborns and linked to allergic lung inflammation development as the child gets older.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002431	EMG produced TPA metagenomics assembly of the The fecal microbiota in L-DOPA naive PD patients (PD-GER) data set.	The PD-GER Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB17784.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002430	EMG produced TPA metagenomics assembly of the Gut microbiome development along the colorectal adenoma-carcinoma sequence (AT_CRC) data set.	The AT_CRC Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB7774.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002421	Prokaryotic microbiota associated to the digestive cavity of the jellyfish Cotylorhiza tuberculata	The microbiota associated to the gastric cavity of four exemplars of the jellyfish Cotylorhiza tuberculata has been studied by means of cultured-dependent and –independent methods. The pyrosequencing approach rendered a very reduced diversity of Bacteria in where four major groups were shared by the four exemplars and made up to 95% of the total diversity. The culturing approach recovered low abundant organisms but detected by the pyrosequencing approach. The major key organisms were related to the genera Spiroplasma, Thalassospira, Tenacibaculum (from the pyrosequencing data), and Vibrio (from the cultivable fraction). Altogether the results indicate that C. tuberculata contains an autochtonous microbiota of very reduced diversity that may have established a beneficious mutualist relation with the host. On the other hand, some of the major key players may be potential pathogens and the host may serve as dispersal mechanism.	root:Host-associated:Invertebrates:Cnidaria
MGYS00002419	EMG produced TPA metagenomics assembly of the Microbiome study of the RISK cohort (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA237362.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002418	EMG produced TPA metagenomics assembly of the Durable coexistence of donor and recipient strains after fecal microbiota transplantation (Impact of faecal microbiota transplantation on the intestinal microbiome in metabolic syndrome patients) data set.	The Impact of faecal microbiota transplantation on the intestinal microbiome in metabolic syndrome patients Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12357.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002417	EMG produced TPA metagenomics assembly of the Reproducibility of associations between the human gut microbiome and colorectal cancer assessed in a patient population from Washington, DC, USA (Colorectal cancer and the human gut microbiome) data set.	The Colorectal cancer and the human gut microbiome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12449.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002415	EMG produced TPA metagenomics assembly of the Metagenomic analysis of fecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer (Metagenomic analysis of fecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer) data set.	The Metagenomic analysis of fecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB10878.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002413	Alginate oligosaccharide-induced shift in the intestinal microbiota of salmon.	Prebiotics are food/feed additives intended to sculpt gut microbial communities as they are selectively utilized by the microorganisms to exert beneficial health effects on hosts. Macroalga-derived oligosaccharides are potential prebiotics, and herein, we determined the effects of Laminaria sp.-derived alginate oligosaccharide (AlgOS) on the distal intestinal microbiota of Atlantic salmon (Salmo salar). Using a high-throughput 16S rRNA gene amplicon sequencing technique, we investigated the microbiota harboured in the intestinal content and mucus of Atlantic salmon offered feeds supplemented with 0.5 and 2.5% AlgOS. We found that AlgOS shifts the intestinal microbiota profile; alpha diversity was significantly reduced with 2.5% AlgOS while with 0.5% AlgOS the alteration occurred without impacting the bacterial diversity. Beta diversity showed a significant difference between control and AlgOS-fed groups. AlgOS supplementation facilitated the dominance of Proteobacteria and Spirochaetes, promoting the growth of presumed butyrate producers in the intestine. In addition, 0.5% AlgOS stimulated certain bacteria belonging to Proteobacteria, Spirochaetes and Actinobacteria. This indicates that the low inclusion of AlgOS can plausibly induce a prebiotic effect on the distal intestinal microbiota of Atlantic salmon. These results are expected to generate further interest in the potential of macroalgae-derived oligosaccharides as prebiotics for food and feed applications.  	root:Host-associated:Fish:Digestive system:Intestine
MGYS00002411	EMG produced TPA metagenomics assembly of the human gut Metagenome (human gut metagenome) data set.	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375935.  This project includes samples from the following biomes: Host-associated, Human, Digestive system.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002408	Pilot study comparing yield from 16srRNA sequencing from frozen tissue vs. formalin-fixed paraffin-embedded (FFPE) tissue from the ileum and colon	Introduction: Next generation sequencing have made it possible to examine the microbiome of the GI tract without culture dependent methods. 16srRNA sequencing is currently the most frequently used sequencing method to examine the microbiome in the GI tract. As sequencing costs continues to decrease, thorough investigations of the microbiome in the GI tract is now easily accessible. However, several studies have shown large variation between the mucosal and fecal microbiome in humans. In inflammatory bowel disease (IBD), the mucosal microbiome is considered to be the most relevant for the pathogenesis. Mucosal tissue is only accessible during colonoscopy or surgery, and the availability of colon or ileum tissue is therefore the most important limiting factor in microbiome research in IBD. However the access to FFPE-tissue is immense compared to the availability of fresh tissue samples. Aims and methods: To compare the yield from 16srRNA sequencing on frozen tissue vs. FFPE from the same patient. Two patients scheduled for bowel resection because of cancer in the right hemicolon were included in this pilot study. Paired tissue biopsies were taken from the colon and ileum in both patients immediately after surgical bowel resection. One biopsy in the pair was frozen on liquid nitrogen and in -80 C and the other put on formalin for subsequent DNA isolation and sequencing analysis. DNA isolation were performed using Qiagen, QIAamp DNA mini kit for the frozen the tissue and Qiagen, QIAamp DNA FFPE tissue kit for FFPE tissue. 16srRNA sequencing, using Illumina Miseq platform were performed on both frozen tissue and FFPE tissue.	root:Host-associated:Human:Digestive system
MGYS00002407	Metagenome from an acidogenic thermophilic anaerobic reactor	Metagenome from an acidogenic thermophilic anaerobic reactor	root:Engineered:Bioreactor:Continuous culture
MGYS00002406	Pooled sputum DNA extracts from patients with severe asthma who received either placebo or azithromycin for 48 weeks	Pooled sputum DNA extracts from patients with severe asthma who received either placebo or azithromycin for 48 weeks (AMAZES trial)	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00002404	Yarwun Port Curtis Sediment Bacterial 16S rRNA (V6) 454 sequence	Samples were collected from the top 10cm of marine sediment from Port Curtis, Gladstone, Queensland, Australia. Sampling occurred over two tropical wet seasons (October to May) and two tropical dry seasons (June to September) between 2008 and 2010. Whole microbial DNA was extracted from subsamples and the V6 region of the bacterial 16S rRNA gene was sequenced by 454 pyrosequencing.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00002400	Comparison of DNA extraction methods for oral bacterial 16S rRNA-V4 sequencing using healthy Japanese adult samples	The project contains bacterial partial 16S rRNA V4 sequencing data of supragingival plaque samples pooled from multiple teeth of 12 healthy Japanese adults. The partial 16S rRNA V4 region (typically 259 base pairs) was PCR-amplified and sequenced using the Illumina MiSeq platform. Paired-end sequencing and dual index tag techniques were applied. All relevant research protocols and procedures were approved by Ethics Committee of Tohoku University School of Medicine, Sendai, Japan. All subjects provided written informed consent.	root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
MGYS00002399	oxidative stress Methanoperedens nitroreducens	‘Candidatus Methanoperedens nitroreducens' is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In this study we investigated the effect of oxygen exposure on an enrichment culture dominated by ‘Ca. M. nitroreducens' (83% enrichment). In batch activity assays supplemented with 5% oxygen in headspace we monitored the methanotrophic activity of both anaerobic and aerobic methanotrophs and investigated the gene expression of ‘Ca. M. nitroreducens'.	root:Engineered:Bioreactor:Continuous culture
MGYS00002398	Metagenomic sequencing of water samples	Amplicon sequencing of urban water samples by Illumina technology	root:Engineered:Wastewater
MGYS00002397	Mucosal microbiome and 5-ASA concentration in the left hemicolon and rectum in patients with quiescent ulcerative colitis	Introduction: 5- aminosalicylic acid (5-ASA) is the mainstay of treatment of patients with ulcerative colitis (UC). 5-ASA acts locally in the colonic mucosa and mucosal concentrations of 5-ASA are inversely correlated to disease activity. Previous studies have found large inter-individual variations in mucosal 5-ASA concentrations. Several explanatory models have been proposed, but is remains unintelligible why some patients have high 5-ASA concentrations, while others have low. Previous findings suggest that treatment with Asacol (pH-dependent release formulation) yields higher mucosal 5-ASA concentrations than Pentasa (time-dependent release formulation). The mucosal bacterial composition and fermentation products, such as short chain fatty acids, greatly impact pH-value in the colon and might therefore be correlated to 5-ASA concentration. Aim and method: In this cross-sectional non-randomized study, we have measured mucosal concentration of 5-ASA and its inactive metabolite acetyl-5-ASA (Ac-5-ASA) in the left hemicolon and rectum in patients with quiescent UC taking Mezavant, Asacol or Pentasa. Patients with quiescent UC using oral mesalazine monotherapy in the maximal dose recommended by the manufacturers (4.0-4.8g o.d.) were included. Eight hours after ingestion of mesalazine, patients underwent blood sample collection, followed by bowel preparation with enema and sigmoidoscopy. A total of six mucosal biopsies were collected 10, 25 and 40 cm from the anal verge. 5-ASA and Ac-5-ASA concentrations were measured in five biopsies and serum by high-performance liquid chromatography. The mucosal and fecal microbiome was explored using 16srRNA sequencing. Disease activity was assessed by Mayo score (MS), Geboes histological score (GS) and measurement of plasma ESR, CRP, blood leukocytes and fecal calprotectin concentrations.	root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon
MGYS00002396	Oral bacterial 16S rRNA-V4 sequencing of three Japanese adults sampled in multiple time points during a day	The project contains bacterial partial 16S rRNA sequencing data of 81 supragingival plaque samples of incisor, premolar, and molar teeth. Samples were taken from three adult Japanese males for multiple time points during a day (forenoon, evening, and night for three days). Partial bacterial 16S rRNA V4 region (typically 258 or 259 base pairs) was amplified and sequenced based on the Illumina MiSeq paired-end read sequencing protocol. Ninety-six combinations of dual index tags (Illumina D-series) were utilized. The project also contains data of four sequencing replicates for a part (4/81) of DNA samples by an independent sequencer run. All relevant research protocols and procedures were approved by Ethics Committee of Tohoku University School of Medicine, Sendai, Japan. All subjects provided written informed consent.	root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
MGYS00002393	Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae	This study was conducted to assess the temporal dynamics of rhizosphere and root microbiota during the development of Plasmodiophora brassicae in root hairs of Chinese cabbage (Brassica rapa subsp. pekinensis). After inoculation (or not) with P. brassicae, disease was assessed at five sampling date during the vegetative stage of plant growth. The first symptom of clubroot disease appeared 14 days after inoculation (DAI) and increased drastically between 14 and 35 DAI. The structure of microbial communities associated to rhizosphere soil and root samples was assessed at each sampling date through sequencing of bacterial (16S) and fungal (18S) molecular markers. Proteobacteria and Bacteroidetes bacterial phyla dominate the Chinese cabbage rhizosphere and root microbiota. Rhizosphere bacterial communities also contained Actinobacteria and Firmicutes to a higher extend than in the roots. Moreover, a dramatic shift of fungal communities of non-inoculated plants occurred between the two last sampling dates, especially in plant roots but also in their rhizosphere. Most of Ascomycota fungi dominant until then were replaced by a fungus assigned to the Chytriomycota phylum. Parasitic invasion by P. brassicae disrupted the rhizosphere and root-associated community assembly during the vegetative stage of plant growth. These effects occurred late during the secondary cortical infection stage of clubroot disease in plant roots. At this stage, Flavisolibacter and Streptomyces in the rhizosphere, and Bacillus in the roots, were drastically less abundant upon parasite invasion. Rhizosphere of plants colonized by P. brassicae was significantly more invaded by the Chytriomycota fungus, which could reflect a mutualistic relationship in this compartment between these two microorganisms.	root:Host-associated:Plants:Rhizosphere
MGYS00002391	A practical introduction to microbial molecular ecology through the use of iChips	In the context of anti-microbial resistance as one of the most serious issues faced globally by health providers, we explored a practical introduction to molecular microbial ecology. We designed field work and practical experiments for third year members of a four year undergraduate Masters Programme in which the students employed traditional and novel isolation techniques to identify antimicrobial activities from soil dwelling microorganisms. Students gained experience in isolating DNA from complex microbial communities, amplifying 16S rRNA genes and applied richness / diversity indices as well as principal coordinates analyses to the interpretation of the data they obtained from high throughput sequencing. Our results confirmed that isolation chips (iChips) facilitate the growth of a greater diversity and different species subset from the complex soil microorganism community than traditional plate spreading techniques. However, rarefaction of 16S rRNA amplicon sequencing data showed that the majority of observed species in soil remain unculturable by current methods. Based on the written reports produced by the students carrying out the work, we concluded that the described protocols are robust and informative, that these activities provide a good practical introduction to the theories and practice of molecular ecology and can be easily deployed to groups of six or more students in a cost-effective manner.	root:Environmental:Terrestrial:Soil:Loam
MGYS00002390	Coix seed helps mice to lose weight and it is associated with the regulation of the gut microbiota.	Coix seed is commonly used as food material and herbal medicine in Asian countries. Evidence showed it has hypolipidemic activity, and can decrease the level of serum lipid. But whether Coix seed takes effect by modulating the composition of the gut microbiota remains unknown. In our study, 44 mice were randomly allocated to three groups, receiving Chow, high fat, and high fat added Coix seeds diet for 5 weeks, respectively. Mice who received the high fat diet demonstrated significant increasing in body weight and fat mass compared with the Chow groups. Complementing Coix seed could help mice lose weight, and reduce the fat mass and total cholesterol. Through sequencing of the V4-V5 regions of 16S rRNA genes in fecal samples, we found the gut microbiota had a distinct change in HF diet group comparing to Chow group. Coix Seeds can regulate the abundance of serveral bacteria, which are probably contributed to losing weight and preventing diabetes.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00002389	It was verified the impact of irrigation treatments (wet, optimal, dry and very dry) and three potato cultivars on soil microbial community.	The water management was classified into four soil water matric potential mean: -15 kPa (Wet), -25 kPa (Optimal), -30 kPa (Dry) and -45 kPa (Very Dry). The three potato cultivars used were Goldrush (most cultivated mid-season variety in Quebec), Envol (popular early variety), and Red Maria (mid-late to late variety).	root:Environmental:Terrestrial:Soil:Crop
MGYS00002388	Antibiotic-induced acceleration of Type 1 diabetes alters intestinal innate pathway maturation	The early-life intestinal microbiota plays a key role in shaping host immune system development. We found that a single early-life antibiotic course (1PAT) accelerated Type 1 diabetes (T1D) development in male NOD mice. The single course had strong and persistent effects on the intestinal microbiome, selecting for a highly metabolically active metagenome, with altered hepatic and serum metabolites. The exposure led to differential ileal and hepatic histone modification, and perturbed ileal gene expression, strongly affecting the normal maturational pattern. Earliest effects involved specific genes in innate immune pathways, with later effects on adaptive immunity. Microbiome analysis revealed four potential T1D-protective taxa and four T1D-accelerating taxa, and a network linking specific microbial taxa to differences in ileal gene expression was identified. This simplified animal model has improved understanding of the mechanisms by which early-life gut microbiome perturbations alter host intestinal responses, contributing to T1D.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00002387	Investigation of the microbial diversity and metabolic function of microorganisms in dust as compared to soil in dust source regions.	Deserts are known to be major sources of dust, which is transported as aerosols across regional and even transcontinental scales. Dust has been shown to have negative effects on human well-being, as it has been associated with inducing respiratory, allergic, and cardiovascular diseases. Dust particles are known to serve as carrier for microorganisms, such as fungal spores, viruses, bacteria, archaea, and protozoa. The aim of this study is to examine the microbial composition and metabolic potential of filter-, soil-dust-, and biocrusts samples collected on Barbados, on Cyprus, Sahara desert and during Air Quality and Climate Change in the Arabian Basin (AQABA) ship expedition leading through the Mediterranean Sea and around the Arabian Peninsula.	root:Environmental:Terrestrial:Soil
MGYS00002386	differential metatranscriptomics of bulk soil and compost	3 bulk soil samples and 3 compost samples have been sequenced to determine the functional differences of the microbial communities.	root:Environmental:Terrestrial:Soil:Loam
MGYS00002385	in situ v. ex situ biogas upgrading	This study compares the upgrading communities between in situ and ex situ operation during increasing flow rates of H2 and CO2, showing that the presence (in situ) or absence (ex situ) of feedstock strongly delineates these communities. This in turn governs community response to rates of H2 supply, with in situ communities showing a far greater susceptibility to inhibition, population flux, and displacement of methanogens (Methanothermobacter). In comparison, ex situ upgrading communities saw little change at much higher H2 flow rates, and instead encouraged larger populations of closely related methanogens (Methanobacterium). These large ex situ hydrogenotrophic populations were significantly associated with smaller, ‘satellite' populations of hydrogen-producing bacteria, indicating a thermophilic upgrading community centred on biogas metabolism.	root:Engineered:Bioreactor:Continuous culture
MGYS00002384	Microbiota of Citrus sinensis plants affected by Citrus Decline Disease	Citrus Decline Disease was recently-reported affecting several citrus species in Iran when grafted on a local rootstock variety, Bakraee. Preliminary studies found ‘Candidatus Phytoplasma aurantifoliae' and ‘Candidatus Liberibacter asiaticus' as putative etiological agents, but were not ultimately able to determine which one, or if an association of both, were causing the disease. The current study has the aim of characterizing the microbiota of citrus plants that are either asymptomatic, showing early symptoms, or showing late symptoms through amplification of the V1-V3 region of 16S rRNA gene using an Illumina sequencer in order to (i) clarify the etiology of the disease, and (ii) describe the microbiota associated to different symptom stages.	root:Host-associated:Plants
MGYS00002383	Antibiotic manufacturing effluent enriches resistance genes and alter the structure of microbial communities	In this work, we have examined sludge samples from a Croatian azithromycin production plant using shotgun metagenomics, to better understand the full diversity of known resistance genes, mobile genetic elements and the impact on taxonomic composition caused by extensive antibiotic selection pressures. We compare this data to sludge from a wastewater treatment plant receiving municipal sewage. We find that the sludge from pharmaceutical production harbors around three times as much resistance genes as the municipal sewage sludge, with particularly large enrichments of aminoglycoside, amphenicol and sulfonamide resistance genes. The findings highlight that antibiotic production does contribute to the development of antibiotic resistance also in European settings and indicate a large potential for co-selection of resistance genes to a variety of antibiotic classes.	root:Engineered:Wastewater:Activated Sludge
MGYS00002382	Investigating short- and long-term genome evolution of commensal bacteria using the Oligo-MM community	The functionality of the mammalian intestinal ecosystem is influenced by various host and external factors, affecting the composition, gene expression and evolution of the microbial community over time. In particular, bacterial genome evolution is mostly driven by small additive mutations and horizontal gene transfer (HGT), events which are normally selected for in the course of environmental changes.We have previously established a defined consortium of 12 cultivable murine isolates (Oligo-MM) in a gnotobiotic mouse model to study the role of the gut microbiota and its association with diseases. We now aim to use this model for investigating short- and long-term genome evolution of commensal bacteria, and for delineating microbiota-associated functions and metabolic potential in their natural host.	root:Host-associated:Mammals:Digestive system
MGYS00002377	Environmental DNA profiles capture the influence of treated wastewater effluent on water column bacterial composition in headwaters of the Rhine River	Rivers receive a wide range of micro-pollution from wastewater treatment plants (WWTPs). WWTP effluent adds nutrients and chemicals into streams and follows well-documented hydrological mixing patterns based on dilution. However, the hydrological mixing of planktonic microbial communities is less well-documented. We tested whether environmental DNA (eDNA) sampled from 24 headwater streams and WWTP effluent flowing into the economically important Rhine River followed predicted dilution patterns and characterized the bacterial communities using 16S rRNA amplicon sequencing. Total eDNA recovered from the effluent lacked a quantitative mixing relationship with receiving streams, suggesting that eDNA is influenced by more than hydrological dilution. The downstream 16S profiles highlighted a decrease in Cyanobacteria and Proteobacteria taxa and an increase in Firmicutes and TM7 taxa compared to the upstream. All resulting sequences were assigned in silico habitat descriptors, and these habitat descriptors matched expected values for the effluent (e.g., “wastewater”) and upstream (e.g., “freshwater lake”, “river”) for most streams, whereas the downstream habitat descriptors were a mixture between the two. Thus, we demonstrate that effluent alters water column bacterial communities in receiving streams. This qualitative alteration of bacterial communities warrants further investigation into how bacterial pollution from WWTPs affects ecosystem function and stress.	root:Engineered:Wastewater:Industrial wastewater
MGYS00002371	Porcupine Seabight 16S Ribosomal RNA	Porcupine Seabight 16S Ribosomal RNA	root:Environmental:Aquatic:Marine:Sediment
MGYS00002370	Prospecting of extreme microbial ecosystems associated to minerals (microbialites, microbial mats and endoevaporites) in Puna, Wetlands and Salars of Argentina, Chile and Bolivia	Puna wetlands and salars are unique extreme environments since they are located in high altitude saline deserts, largely influenced by volcanic activity. UV radiation, arsenic content, high salinity, and low dissolved oxygen content, together with extreme daily temperature fluctuations and oligotrophic conditions comprise an environment that recreates the early Earth and even extraterrestrial conditions.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Saline
MGYS00002369	This is a repeat of previous analysis but with human reads filtered out.	This is a repeat of previous analysis but with human reads filtered out.	root:Mixed
MGYS00002368	Metatranscriptome sequencing from  samples corresponding to size fractions for protists.	Metatranscriptome sequencing from  different depths to retain small and large cell size (Protists Organisms). The RNA was extracted and submitted to high throughput sequencing.	root:Environmental:Aquatic:Marine
MGYS00002367	In-planta sporulation mediates host-partner interactions in the alder-Frankia-ectomycorrhizae tripartite symbiosis	In-planta sporulation mediates host-partner interactions in the alder-Frankia-ectomycorrhizae tripartite symbiosisfastq files from metabarcoding on nifH gene.primer GCIWTHTAYGGIAARGGIGGIATHGGIAAATIGCRAAICCICCRCAIACIACRTCnifH barcode  TATGTCAG TATGTCAGSTR1barcode  TATGTCAG TAGTCGCASTR2barcode  TATGTCAG TACTATACSTR3barcode  TATGTCAG ACTAGATCSLB1barcode  TATGTCAG GATCGCGASLB2barcode  TATGTCAG CGCTCTCGSLB3barcode  TAGTCGCA ACACACACSOR1barcode  TAGTCGCA ACAGCACASOR2barcode  TAGTCGCA GTGTACATSOR3barcode  TAGTCGCA TATGTCAGSFF1barcode  TAGTCGCA TAGTCGCASFF2barcode  TAGTCGCA TACTATACSFF3barcode  TAGTCGCA ACTAGATCSTO1barcode  TAGTCGCA GATCGCGASTO2barcode  TAGTCGCA CGCTCTCGSTO3barcode  TACTATAC ACACACACSXF1barcode  TACTATAC ACAGCACASXF2barcode  TACTATAC GTGTACATSXF3barcode  TACTATAC TATGTCAGAgTR1barcode  TACTATAC TAGTCGCAAgTR2barcode  TACTATAC TACTATACAgTR3barcode  TACTATAC ACTAGATCAgLB1barcode  TACTATAC GATCGCGAAgLB2barcode  TACTATAC CGCTCTCGAgLB3barcode  ACTAGATC ACACACACAgXF1barcode  ACTAGATC ACAGCACAAgXF2barcode  ACTAGATC GTGTACATAgXF3barcode  ACTAGATC TATGTCAGAgFF1barcode  ACTAGATC TAGTCGCAAgFF2barcode  ACTAGATC TACTATACAgFF3barcode  ACTAGATC ACTAGATCAiTR1barcode  ACTAGATC GATCGCGAAiTR2barcode  ACTAGATC CGCTCTCGAiTR3barcode  GATCGCGA ACACACACAiLB1barcode  GATCGCGA ACAGCACAAiLB2barcode  GATCGCGA GTGTACATAiLB3barcode  GATCGCGA TATGTCAGAiXF1barcode  GATCGCGA TAGTCGCAAiXF2barcode  GATCGCGA TACTATACAiXF3barcode  GATCGCGA ACTAGATCAiFF1barcode  GATCGCGA GATCGCGAAiFF2barcode  GATCGCGA CGCTCTCGAiFF3barcode  CGCTCTCG ACACACACAvFF1barcode  CGCTCTCG ACAGCACAAvFF2barcode  CGCTCTCG GTGTACATAvFF3barcode  CGCTCTCG TATGTCAGAvXF1barcode  CGCTCTCG TAGTCGCAAvXF2barcode  CGCTCTCG TACTATACAvXF3	root:Host-associated:Plants
MGYS00002366	Feeding sows resistant starch during gestation and lactation impacts their faecal microbiota and milk composition but shows limited effects on their progeny	Establishment of a beneficial microbiota profile for piglets as early in life as possible is important as it will impact their future health. In the current study, we hypothesized that resistant starch (RS)  provided in the maternal diet during gestation and lactation will be fermented in their hindgut, which would favourably modify their milk and/or microbiota composition and that it would in turn affect piglets' microbiota profile and their absorptive and immune abilities. In this experiment, 33% of pea starch was used in the diet of gestating and lactating sows and compared to control sows. Their microbiota and milk composition were determined and the microbiota, short-chain fatty acids (SCFA) production and gut health related parameters of the piglets were measured two days before weaning.  In addition, their overall performances and post-weaning faecal score were also assessed. The RS diet modulated the microbiota of the sows during gestation, increasing the Firmicutes:Bacteroidetes ratio and the relative abundance of beneficial genera like Bifidobacterium but these differences disappeared during lactation and were not transmitted to the offspring. Milk protein and lactose concentrations were impacted by the diet, without an impact on piglets' bodyweight or diarrhoea frequency post-weaning.  Moreover, the intestinal morphology measured as villus height and crypt depths, and the inflammatory cytokines in the intestine of the piglets were not differentially expressed between maternal treatments.  Only ZO-1 was more expressed in the ileum of piglets born from RS sows, suggesting a better closure of the mucosa tight junctions. It is concluded that changes in the microbiota transferred from mother to piglets due to the inclusion of RS in the maternal diet are rather limited even though milk composition was affected.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00002365	De novo whole metagenome sequencing studies	A comparative study between control and disease condition metagenome sampples.	root:Environmental:Aquatic:Freshwater:Pond
MGYS00002360	Flores_tongue_EBI	SMP - tongue samples from Flores_SMP ID:	root:Host-associated:Human:Digestive system:Oral:tongue dorsum
MGYS00002359	Human identification through analysis of the salivary microbiome	Human identification has played a prominent role in forensic science for the past two decades and will continue to do so.  The development of techniques to exploit samples, which cannot be satisfactorily analysed at present, is driving the field.  High-throughput sequencing techniques have been available for a few years however there are very few examples of their application in forensic science.   This study investigates the potential for bacteria found in the salivary microbiome to be used in a new method for human identification. Two different targets (16S RNA and rpoB) were chosen to maximise coverage of the salivary microbiome and when combined, they increase the power of identification. Paired-end Illumina high-throughput sequencing was used to analyse the bacterial composition of saliva from two different people at four different time points (t=0 and t=28 days and then one year later at t=0 and t=28 days).   Five major phyla dominate the samples: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Streptococcus, a firmicute, is one of the most abundant genera found in saliva and targeting Streptococcus rpoB has enabled a deeper characterisation of the different streptococci species otherwise impossible with 16S rRNA alone. We have observed that samples from the same person group together regardless of time of sampling. However, samples taken one month apart group closer together than those taken one year apart. The results indicate that it is possible to distinguish two people using the bacteria found in their saliva.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002358	Core function of microbiota in peri-implantitis and periodontitis	Eleven patients who have peri-implantitis and periodontitis were selected. They were evaluated based on the clinical examination and radiographic data. Sub-gingival and sub-mucosal biofilm samples were taken from the deepest pockets of each site, and we characterized bacterial community of 16S rRNA and 16S rRNA genes (rDNA) using Illumina miseq.	root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
MGYS00002357	Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood	Variation in the human oral microbial community composition in health and disease has been observed, but factors associated with this variation remain largely unstudied. We characterized inter- and intra-individual variation of microbial communities in the largest cohort to date (264 saliva samples), using culture-independent 16S rRNA pyrosequencing. We followed the temporal dynamics of their salivary microbiota over 10 years spanning adolescence, and determined the influence of human genotype, gender, age, puberty, and weight class on the microbial communities. Participants included 107 healthy individuals sampled mainly at ages 12-13, 17-18 and 22-24, with a few sampled as early as 8 years of age. In contrast to gut or skin microbiomes, there is a core genus-level salivary microbiome; individuals are more similar to themselves and their co-twins in the 12-17 and in the 17-22 cohorts than to the whole sample population, but not over the 10 years from 12 to 22; and human genotype has no significant role in the oral bacterial composition. The data are most consistent with shared environment serving as the main determinant of microbial populations. Twins resemble each other more closely than the whole population at all time-points, but become less similar to each other when they age and no longer cohabit. Several organisms have age-specific abundance profiles, including members of the genera Veillonella, Actinomyces, and Streptococcus. There is no clear effect of weight class, puberty, and gender. The results of this work will provide a basis to further study oral microbes and human health.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002356	Oral bacterial 16S rRNA-V4 sequencing of four Japanese adults in multiple conditions of sample storage	The project contains bacterial partial 16S rRNA sequencing data of 66 supragingival plaque samples of upper molar teeth. Samples were taken from four adult Japanese males on September 7, 2013. Partial bacterial 16S rRNA V4 region (typically 259 base pairs) was amplified and sequenced based on the Illumina MiSeq paired-end read sequencing protocol. Maximum 96 combinations of dual-index tags (Illumina D-series) were used. All relevant research protocols and procedures were approved by Ethics Committee of Tohoku University School of Medicine, Sendai, Japan. All subjects provided written informed consent.	root:Host-associated:Human:Digestive system:Oral:Supragingival plaque
MGYS00002355	Population-based study on salivary microbiome of Japanese adults	We collected saliva from Japanese adults aged over 40 years inhabiting Hisayama town, Fukuoka, Japan in a health examination performed as a part of the follow-up survey of the Hisayama cohort study on 2007. The V1-V2 region of 16S amplicon sequence of human salivary microbiome were analyzed using Ion PGM. The project goal is to identify core and pan salivary microbiome in Japanese adults and to clarify the relationship with host''s health and health-related conditions.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002354	Salivary microbiota of Japanese orally healthy adults, pool 4	V1-V2 region of 16S amplicon sequence of human salivary microbiome from 63 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002353	Salivary microbiota of Japanese orally healthy adults, pool 5	V1-V2 region of 16S amplicon sequence of human salivary microbiome from 66 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002352	Salivary microbiota of Japanese orally healthy adults, pools 1 and 2	V1-V2 region of 16S amplicon sequence of human salivary microbiome from 37 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002351	Salivary microbiota of Japanese orally healthy adults, pool 3	V1-V2 region of 16S amplicon sequence of human salivary microbiome from 51 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002350	Salivary microbiota of orally healthy adults in South Korea	V1-V2 region of 16S amplicon sequence of human salivary microbiome from 52 orally-healthy South Korean adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002349	sputum from patients with severe asthma who received either placebo or azithromycin for 48 weeks	sputum from patients with severe asthma who received either placebo or azithromycin for 48 weeks	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00002348	Simulated oral microbiome with artificial duplicates	This study includes multiple samples simulating a human oral community with 13 bacterial species and different levels of artificial duplicates. Reads have been simulated using BBmap.	root:Engineered:Modeled:Simulated communities (sequence read mixture)
MGYS00002347	Effect of OEA on gut microbiota in mice	The lipid sensor oleoylethanolamide (OEA), an endogenous high-affinity agonist of peroxisome proliferator-activated receptor-α (PPAR-α) secreted in the proximal intestine, is endowed with several distinctive homeostatic properties, such as control of appetite, anti-inflammatory activity, stimulation of lipolysis and fatty acid oxidation. When administered exogenously, OEA has beneficial effects in several cognitive paradigms; therefore, in all respects, OEA can be considered a hormone of the gut-brain axis. Here we report an unexplored modulatory effect of OEA on the intestinal microbiota and immune response.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00002346	Human endocarditis	Identification of the causative agent of infectious endocarditis	root:Host-associated:Human:Circulatory system
MGYS00002342	Genome-wide association study of Medicago truncatula rhizosphere microbial communities and plant nutritional strategies	Coming Soon	root:Host-associated:Plants:Rhizosphere
MGYS00002341	Exploring the native habitat and wild relatives of common bean (Phaseolus vulgaris) for ‘missing plant microbes'	The rhizosphere microbiome is important for plant growth and health, contributing to nutrient acquisition and (a)biotic stress tolerance. Rhizosphere microbiome composition is shaped in part by the plant genotype, but the underlying genetic basis is largely unknown. Going back to the roots, we investigated how plant domestication affected rhizosphere microbiome assembly of common bean (Phaseolus vulgaris), a key food crop worldwide. DArT genotyping and plant phenotyping showed substantial genetic diversity and root architectural differences between ancestral and modern bean accessions grown in Colombian field soil. Bean genotypes affected rhizosphere microbiome composition, with Bacteroidetes and Verrucomicrobia enriched on roots of ancestral beans and Actinobacteria more prevalent on modern beans. Genome-wide association mapping pinpointed single nucleotide polymorphisms (SNPs) in the bean genome associated with the abundance of specific rhizobacterial families. SNPs identified in chromosomes 3 and 4 were positioned at loci associated with signaling, lignin biosynthesis and pathogen resistance.	root:Host-associated:Plants:Rhizosphere
MGYS00002339	EMG produced TPA metagenomics assembly of the The microbial colonization of the intestine during the first months of life constitutes the most important process for the microbiota-induced host-homeostasis.	The Rotavirus vaccine on infants gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6972.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002338	EMG produced TPA metagenomics assembly of the Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide.	The Mgwas study of LC Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6337.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002337	EMG produced TPA metagenomics assembly of the Platygyra carnosa metagenome Raw sequence reads (coral metagenome) data set.	The coral metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA302351.  This project includes samples from the following biomes: Host-associated, Invertebrates, Cnidaria, Coral.	root:Host-associated:Invertebrates:Cnidaria:Coral
MGYS00002336	EMG produced TPA metagenomics assembly of the Banana aphid (Pentalonia nigronervosa) haemolymph Metagenome (insect metagenome) data set.	The insect metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA268300.  This project includes samples from the following biomes: Host-associated, Insecta.	root:Host-associated:Insecta
MGYS00002335	EMG produced TPA metagenomics assembly of the High fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice (mice obesity) data set.	The mice obesity Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB10308.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00002333	EMG produced TPA metagenomics assembly of the Bacteria Genome sequencing and assembly (Bacteria) data set.	The Bacteria Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA326914.  This project includes samples from the following biomes: Host-associated, Arthropoda, Digestive system, Gut.	root:Host-associated:Insecta
MGYS00002332	EMG produced TPA metagenomics assembly of the Geospatial distribution of viral communities in tropical freshwater ecosystems (freshwater metagenome) data set.	The freshwater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA400853.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater.	root:Environmental:Aquatic:Freshwater
MGYS00002331	EMG produced TPA metagenomics assembly of the Compositional_dynamics_of_intestinal_spore_forming_bacteria (Compositional_dynamics_of_intestinal_spore_forming_bacteria) data set.	The Compositional_dynamics_of_intestinal_spore_forming_bacteria Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB20539.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Intestine.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002330	EMG produced TPA metagenomics assembly of the Hot spring microbial streamer communities from Conch Spring, Yellowstone National Park, USA - C T=80-84 metagenome (hot springs metagenome) data set.	The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336661.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00002326	EMG produced TPA metagenomics assembly of the Hot spring microbial communities from South Africa to study Microbial Dark Matter (Phase II) - Tshipise hot spring metaG metagenome (hot springs metagenome) data set.	The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364997.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00002324	EMG produced TPA metagenomics assembly of the Hot spring and microbial mat streamer communities from Octopus Spring Streamers, Yellowstone National Park, USA - T=80-84 metagenome (hot springs metagenome) data set.	The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336655.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00002323	EMG produced TPA metagenomics assembly of the Hot spring microbial communities from Great Boiling Spring, Nevada - cellulolytic enrichment S 77C Metagenome (hot springs metagenome) data set.	The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA279023.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C):Sediment
MGYS00002322	EMG produced TPA metagenomics assembly of the Resistome of effluents of wastewater treatment plants () data set.	The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA413894.  This project includes samples from the following biomes: Engineered, Bioremediation, Terephthalate, Wastewater.	root:Engineered:Wastewater:Water and sludge
MGYS00002321	EMG produced TPA metagenomics assembly of the freshwater metagenome Raw sequence reads (freshwater metagenome) data set.	The freshwater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA335374.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lake.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00002320	EMG produced TPA metagenomics assembly of the freshwater sediment metagenome Raw sequence reads (freshwater sediment metagenome) data set.	The freshwater sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA320875.  This project includes samples from the following biomes: Environmental, Aquatic, Freshwater, Lentic, Sediment.	root:Engineered:Bioremediation:Hydrocarbon
MGYS00002318	EMG produced TPA metagenomics assembly of the Hot Lake Unicyanobacterial Consortia (microbial mat metagenome) data set.	The microbial mat metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA283228.  This project includes samples from the following biomes: Environmental, Aquatic, Non-marine Saline and Alkaline, Hypersaline, Microbial mats.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline:Microbial mats
MGYS00002317	EMG produced TPA metagenomics assembly of the Hot spring microbial communities from Grendel Spring, Yellowstone National Park, USA - T=76-80 metagenome (hypersaline lake metagenome) data set.	The hypersaline lake metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336649.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00002314	EMG produced TPA metagenomics assembly of the Metagenome sequencing of a chitin enriched culture (Metagenome sequencing of a chitin enriched culture) data set.	The Metagenome sequencing of a chitin enriched culture Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6317.  This project includes samples from the following biomes: Environmental, Terrestrial, Soil.	root:Environmental:Terrestrial:Soil
MGYS00002313	EMG produced TPA metagenomics assembly of the Metagenomic analysis of microbial mat of hot springs (Metagenomic analysis of microbial mat of hot springs) data set.	The Metagenomic analysis of microbial mat of hot springs Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14856.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs.	root:Environmental:Aquatic:Thermal springs
MGYS00002312	EMG produced TPA metagenomics assembly of the Manikaran hot springs water metagenome (Water metagenome) data set.	The Water metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB19501.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs.	root:Environmental:Aquatic:Thermal springs:Near-boiling (>90C)
MGYS00002311	"EMG produced TPA metagenomics assembly of the Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge (Genome sequence for Ca. ""Promineofilum breve"" Cfx-K) data set"	"The Genome sequence for Ca. ""Promineofilum breve"" Cfx-K Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11413. This project includes samples from the following biomes : Sludge."	root:Engineered:Wastewater:Activated Sludge
MGYS00002310	"EMG produced TPA metagenomics assembly of the Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge (Genome sequence for Ca. ""Promineofilum breve"" Cfx-K) data set"	"The Genome sequence for Ca. ""Promineofilum breve"" Cfx-K Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11413. This project includes samples from the following biomes : Sludge."	root:Engineered:Wastewater:Activated Sludge
MGYS00002308	EMG produced TPA metagenomics assembly of the Metagenome sequencing of marine membrane vesicles (marine metagenome) data set.	The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA222589.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.	root:Environmental:Aquatic:Marine
MGYS00002307	EMG produced TPA metagenomics assembly of the Experimental trial using phytase in the diet for broiler (Phytase) data set.	The Phytase Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12987.  This project includes samples from the following biomes: Birds.	root:Host-associated:Birds
MGYS00002306	EMG produced TPA metagenomics assembly of the Metagenome on soil background with high concentration of arsenic and antimon Genome sequencing (soil metagenome) data set	The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA239941. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00002305	EMG produced TPA metagenomics assembly of the Wetland samples Metagenome (soil metagenome) data set	The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA227301. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00002303	Microbiome profiling Schlöppnerbrunnen peat cores from different depths	Microbiome profiling of Schlöppnerbrunnen peat cores collected from different depths ranging from 0-30 cm.	root:Environmental:Terrestrial:Soil
MGYS00002302	Development of an in-vitro, three stage model of the equine hindgut, inoculated with faeces.	An in-vitro model of the equine hindgut was developed to aid with the understanding of the bacteria that reside within the large intestine horses. This model utilises the bacteria in faeces to initiate bacterial populations, so that there is no need for invasive sample collection. These are the sequencing files from the sequencing of the 16S rRNA gene of samples from the gut model and gastrointestinal content that accompany the journal paper for the validation of our equine hindgut model.	root:Host-associated:Mammals:Digestive system
MGYS00002299	This study includes multiple samples simulating a human oral community with 13 bacterial species	This is a simulation study. Reads have been simulated using BBmap.	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00002298	Bacteria in Anopheles darlingi breeding sites in Manaus, the Amazon, Brazil	In this study bacterial community composition in Anopheles darlingi breeding waters was investigated. Four sites in Manaus Brazil were sampled by taking surface water. The water samples were DNA extracted and 16S rRNA genes were amplified and sequenced by MiSeq. The reads were then analysed and compared between the sites.	root:Environmental:Aquatic:Freshwater:Lotic
MGYS00002297	JoanneHStudy	JoanneHStudy	root:Mixed
MGYS00002296	Defining the microbial response to colitis through integrated host and microbiome profiling: Replication data set	This is a replication study of E-MTAB-3562  ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3562/ ) and  complementary transcription profiling data from the mouse hosts have also been deposited at ArrayExpress under accession number E-MTAB-3590 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3590/ )	root:Host-associated:Mammals:Digestive system
MGYS00002294	Soil microbial response to organic disturbances	We employed a deep 16S amplicon sequencing approach to evaluate the recovery of the native soil microbiome after multiple disturbances caused by the application of organic vinasse residue, inorganic nitrogen (N) or a combination of both during the sugarcane crop-growing season.	root:Environmental:Terrestrial:Soil:Loam:Contaminated
MGYS00002293	Breast Cancer Metagenomics	Breast Cancer Metagenomics	root:Host-associated:Human:Skin
MGYS00002286	Metagenomic investigation of six depths from the anchialine Bundera sinkhole	Bundera sinkhole is an anchialine ecosystem located in north-western Australia. It has a highly stratified physico-chemical profile which is reflected in the microbial community structure of each strata. This study is the first to perform shotgun metagenomics on communities inhabiting a selection of depths: 2, 8, 17, 18, 22 and 28 m.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002285	Microbial community in Trachea-oropharynx of Diabetic patient was compared with healthy controls and bacterial pneumonia	The aim of this study is to produce a healthy control metataxonomic data of bacterial community in tracheal-oropharynx using endotracheal tube which can be used for sputa studies which would involve various pathological conditions including bacterial infectious pneumonia. Furthermore, we also investigated samples from diabetic patients as infection-free risk group which is frequently requested patients in clinical environment.	root:Host-associated:Human:Respiratory system
MGYS00002284	Plant nutrient resource use strategies shape active rhizosphere microbiota through root exudation	Plant nutrient resource strategies have the potential to strongly influence plant-microorganism interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether plant nutrient use strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil and inhabiting the root tissues.	root:Host-associated:Plants:Rhizosphere
MGYS00002283	Effect of short- and medium- chain fatty acids on gut microbiome of gilthhead sea bream (Sparus aurata)	This study aimed to evaluate the potential beneficial effects of SCFAs, used as a feed additive, on intestinal microbiota composition. For this purpose, a specific combination of short and medium chain fatty acids was tested in juvenile gilthead sea bream (Sparus aurata) fed a plant-based diet. The Illumina MiSeq platform for high-throughput amplicon sequencing of 16S rRNA gene, and QIIME pipeline were used to analyse and characterize the whole microbiome associated to both, feeds and S.aurata intestine. In summary our findings clearly indicated that SCFAs positively modulated the fish intestinal microbiota by increasing the number of beneficial lactic acid bacteria, namely Lactobacillus, and reducing Gammaproteobacteria that include several potential pathogenic bacteria.	root:Host-associated:Fish:Digestive system:Intestine
MGYS00002282	Antarctic Snow Algae 2014/15 16S and 18S Illumina Seq of snow algae communities around Ryder Bay, Antarctica	Antarctic Snow Algae 2014/15 16S and 18S Illumina Seq of snow algae communities around Ryder Bay, Antarctica. DNA extracted from green phase dominant and red phase dominant blooms on the snow surface. Field samples collected by Matt Davey (Univeristy of Cambridge, Department of Plant Sciences).	root:Environmental:Aquatic:Freshwater:Ice
MGYS00002281	There are 3 zooplankton samples from 3 different ponds, we collected sample and use the fresh samples to do DNA extraction directly, then mix them with adjustment guided by the number of species within each of them. At last, use Hiseq-2599 PE-150 to do NGS work	These 3 samples come from 3 different freshwater ponds. Our lab used the fresh sample to easy the DNA extraction pipeline.  Our primary goal of this experiment is testing the mitochondrial metagenomic strategy in zooplankton, for phylogenetic diversity and molecular ecology research	root:Environmental:Aquatic:Freshwater:Pond
MGYS00002279	Root Herbivory Shapes The Dynamic Of Oilseed Root And Rhizosphere Microbial Communities Through Chemical Changes	Interactions between plants and herbivorous insects are known to influence the evolution of plant defenses. Recent studies are unravelling the impact of microorganisms from the rhizosphere on such interactions and are gradually changing our perception, but the reverse effect has seldom been investigated. Herbivore attacks on plants could represent important perturbations for belowground communities. Our study aimed at determining how plant herbivory influences resistance and resilience of root and rhizosphere microbial community assemblages and whether potential changes in root metabolites and elemental compounds during herbivory can explain microbial community dynamics. We further questioned the influence of initial soil microbial diversity on these interactions. We conducted our study on a crop plant, oilseed rape (Brassica napus) and one of its major belowground pest, the cabbage root fly (Delia radicum). Soils of different initial microbial diversity were obtained through a removal-recolonization method. Root and rhizosphere sampling targeted different stages of the herbivore development: i) the hatching stage which corresponds to the initiation of herbivory, ii) the third larval instar which corresponds to the peak of herbivory and iii) adult emergence which corresponds to the end of herbivory. Bacterial communities were more affected by herbivory than fungi communities, which appeared very variable. Herbivory was associated to an increase of γ-Proteobacteria and of 5 bacterial dominant genera belonging to this phylum and Firmicutes. Root communities were more resilient than rhizosphere communities. This resilience was partly visible at the root metabolite and nutrient level, which reached back a more stable state at the end of herbivory. But herbivory also induced an increase of sulfur-containing compounds, as well as a couple amino acids and sugars. Three bacterial genera were positively correlated to most metabolites and negatively to nutrients. Further researches would help to identify the biological function of the microbial genera impacted by plant infestation and their potential implication in the plant defense.	root:Host-associated:Plants:Rhizosphere
MGYS00002278	Endocarditis due to Cardiobacterium hominis	We report a metagenomic analysis of a heart valve community acquired from a patient with blood culture negative infective endocarditis due to Cardiobacterium hominis.	root:Host-associated:Human
MGYS00002275	Effect of chewing gum on the oral microbiome	Characterisation of the human plaque microbiota before and after the administration of maltitol chewing gums or base chewing gums for two weeks. Study subjects are healthy individuals or patients with caries. Microbiome analysis is performed by 16S profiling of variable regions V1-V2 using Roche 454 GS-FLX sequencing.	root:Host-associated:Human:Digestive system:Oral
MGYS00002271	Oral and Vaginal Microbiota of Mother''s and Their Infant and Toddler Daughters	Using high-throughput sequencing of the 16s rRNA gene, we studied the oral and vaginal microbiome of girls less than 15 months of age and compared those sites to those of their mothers.	root:Host-associated:Human
MGYS00002255	Hydraulic retention time affects bacterial community structure in an As-rich acid mine drainage (AMD) biotreatment process	Arsenic removal consecutive to microbiological iron oxidation and precipitation is an effective process for treating As-rich acid mine drainage (AMD). Here, we  studied the effect of hydraulic retention time (HRT) - a key operating parameter that drives water treatment process performances - on water physico-chemistry, precipitate mineralogy, and bacterial community that develops in a bench-scale bioreactor treating AMD from the Reigous Creek (Carnoulès mine, France). System efficiency regarding Fe(II) and As(III) oxidation and As removal was monitored during 19 days. At the end, the mineralogy (As and Fe bearing phases) and bacterial communities in the biogenic precipitate were analyzed by X-ray absorption spectroscopy and high-throughput 16S rRNA gene sequencing, respectively. The percentage of Fe(II) oxidation (10–47 %) and As removal (19–37 %) increased with increasing HRT. Arsenic was trapped in the biogenic precipitates as As(III)-bearing schwertmannite and amorphous ferric arsenate, with a decrease of As/Fe ratio with increasing HRT. The bacterial community in the biogenic precipitates differed widely from that of the original feed water. Fe-oxidizing bacteria were dominant whatever the HRT but the proportion of Gallionella and Ferrovum genera shifted notably, from respectively 65 and 12 % at low HRT, to 23 and 51 % at high HRT. This shift was associated with physicochemical changes in pH, dissolved oxygen and Fe(III) concentrations in the treated water. A genetic potential for As(III) oxidation was evidenced through the detection of aioA genes at all HRT and As-oxidizing Thiomonas genera was always present as a minority member of the community but HRT did not appear to control As(III) oxidation in the present experiment. To our knowledge, this is the first evidence of the role of HRT as a driver of bacterial community structure in bioreactors exploiting the microbial Fe(II) oxidation process for AMD treatment.	root:Environmental:Aquatic:Freshwater:Groundwater:Acid Mine Drainage
MGYS00002254	Immediate transcriptional response of microbial communities present in soil to the presence of toluene and Pseudomonas veronii inoculation	This study project for a complete characterization and interpretation of the functional response of local microbial communities present in different type soils upon contamination of toluene.	root:Environmental:Terrestrial:Soil:Oil-contaminated
MGYS00002253	Compilation of different anaerobic digester microbial communities analysed through 16S rRNA gene amplicon sequencing during continuous and long term operation for conversion of non pre-treated microalgae into biogas	Microbial communities have an indigenous and strong potential to acclimatize to different substrates. Anaerobic bioreactors can be used for not only treating several waste streams, but also converting them into valuable products including energy. The resulting product of anaerobic reduction of the organic matter is biogas, whose high content in methane provides it a high energetic potential. Among the different sources of organic matter that can be converted into energy are the microalgae. These microorganisms are a promising renewable source as a biofuel as their culture has a low environmental footprint. The main bottleneck for their use in full scale biogas-producing systems is their disruption, as their cell wall bodies are often hard to hydrolyze. This study focuses on the analysis of different anaerobic bioreactors treating microalgae biomass. Microbial analysis of the communities involved in this process provides valuable information about relevant microorganisms that enhance the microalgae disruption. Several phylotypes have been revealed in this study after taxonomic assignment of the open reference clusters found after 16S rRNA gene amplicon sequencing analysis.	root:Engineered:Biogas plant:Wet fermentation
MGYS00002252	Gut microbiome changes in IL10 -/- mice fed westernized diet	IL10-/- Balb/c mice (enterocolitis model) fed with a high fat, high sucrose or control diet for 16 weeks. Feces samples taken at start, then every 4 weeks. Monitored for colitis.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00002245	Development of an oral mucosa model to study host-microbiome interactions during wound healing	Crosstalk between the human host and its microbiota is reported to influence various diseases such as mucositis. Fundamental research in this area is however complicated by the timeframe restrictions during which microbe-host interactions can be studied in vitro. The model proposed in this paper consists of an oral epithelium and biofilm to study microbe-host crosstalk in vitro in non-infectious conditions up to 72 h. Microbiota derived from oral swabs were cultured on an agar/mucin layer and challenged with monolayers of keratinocytes grown on plastic or collagen type I layers embedded with fibroblasts. The overall microbial biofilm composition in terms of species diversity remained representative for the oral microbiome, whilst the epithelial cell morphology and viability were unaffected. Applying the model to investigate wound healing revealed a reduced healing of 30% in presence of microbiota, which was not caused by a reduction of the proliferation index (52.1–61.5) or a significantly increased number of apoptotic (1-1.13) or necrotic (32-30.5%) cells. Since the model allows the separate study of the microbial and cellular exometabolome, the biofilm and epithelial characteristics after co-culturing, it is applicable for investigations within fundamental research and for the discovery and development of agents that promote wound healing.	root:Host-associated:Human:Digestive system:Oral
MGYS00002242	16S amplicon sequence analysis of microbial communities in the oral cavity, stomach and gut	The V1 and V2 region of the 16S ribosomal RNA gene. 45 individuals (18 PPI-users and 22 PPI-nonusers) in total.	root:Host-associated:Human:Digestive system
MGYS00002241	MICROBIOLOGICAL AND BIOINFORMATICS ANALYSIS OF PRIMARY SJOGREN'S SYNDROME PATIENTS WITH NORMAL SALIVATION	"Background: Reduced salivation is considered a major clinical feature of most but not all cases of primary Sjögren's syndrome (pSS). Reduced saliva flow may lead to changes in the salivary microbiota. These changes have mainly been studied with culture that typically recovers only 65% of the bacteria present.

Objective: This study was to use high throughput sequencing, covering both cultivated and not-yet-cultivated bacteria, to assess the bacterial microbiota of whole saliva in pSS patients with normal salivation.

Methods: Bacteria of whole unstimulated saliva from nine pSS patients with normal salivation flow and from nine healthy controls were examined by high throughput sequencing of the hypervariable region V1V2 of 16S rRNA using the 454 GS Junior system. Raw sequence reads were subjected to a species-level, reference-based taxonomy assignment pipeline specially designed for studying the human oral microbial community. Each of the sequence reads was BLASTN-searched against a database consisting of reference sequences representing 1,156 oral and 12,013 non-oral species. Unassigned reads were then screened for high-quality non-chimeras and subjected to de novo species-level operational taxonomy unit (OTU) calling for potential novel species. Downstream analyses, including alpha and beta diversities, were analyzed using the Quantitative Insights into Microbial Ecology (QIIME) pipeline. To reveal significant differences between the microbiota of control saliva and Sjögren's saliva, a statistical method introduced in Metastats www.metastats.cbcb.umd.edu was used.

Results: Saliva of pSS patients with normal salivation had a significantly higher frequency of Firmicutes compared with controls (p=0.004). Two other major phyla, Synergistetes and Spirochaetes, were significantly depleted in pSS (p=0.001 for both). In addition, we saw a nearly 17% decrease in the number of genera in pSS (25 vs. 30). While Prevotella was almost equally abundant in both groups (25% in pSS and 22% in controls), about a twofold increase in pSS of Streptococcus (28% vs. 17%) and Veillonella (26% vs. 12%) was detected. Prevotella melaninogenica was the major species in controls (13%) while Veillonella atypica and the Veillonella parvula groups dominated in patient samples (14 and 14%). The scarcity in bacterial species in pSS compared with controls was also demonstrated by alpha and beta diversity analyses, as well as read abundance depicted in a phylogenetic tree.

Conclusions: While Firmicutes was significantly higher in pSS patients than in controls, Synergistetes and Spirochaetes were significantly lower. The number of bacterial genera and species was also lower. These data showed that microbial dysbiosis is another key characteristic of pSS whole saliva which can occur independent of hyposalivation."	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002239	Temporal stability of the salivary microbiome and its association with salivary markers of oxidative stress	Salivary markers of oxidative stress are associated with periodontal status and are altered in patients with periodontitis or caries. It has been hypothesized that the composition of oral microbiome and the presence of specific bacterial species might be associated with some salivary markers of oxidative stress. The day to day variability of salivary markers of oxidative stress has been described. More detailed studies are needed for the assessment of salivary microbiome stability. The objective of the present study is to study temporal stability of saliva microbiome and to analyze its association to variations of salivary markers of oxidative stress.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00002216	Effect of oral immunization with the Ty21a typhoid vaccine on local and systemic immune responses and the gut microbiota in adults	The resident microbial consortia of the human gastrointestinal tract play an integral role in modulating the immune response both locally and systemically. However, detailed information regarding the correlates of protective immunity after vaccine administration in relation to the gastrointestinal microbiota is absent. In this study, the licensed oral attenuated typhoid vaccine Ty21a was administered in a clinical study to investigate whether oral immunization resulted in alterations of the microbiota and identify immune responses that may alter microbiota composition. The gastrointestinal microbiota was characterized from stool samples by pyrosequencing of the bacterial 16S ribosomal gene.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002215	Human oral microbiome (root canal, apical abscess, and oral cavity) Targeted Locus	Background: Endodontic infections are a leading cause of oro-facial pain and tooth loss in western countries, and may lead to severe life-threatening infections.  These infections are polymicrobial with high bacterial diversity.  Understanding the spatial transition of microbiota from normal oral cavities through the infected root canal to the acute periapical abscess can improve our knowledge of the pathogenesis of endodontic infections and lead to more effective treatment. We obtained samples from the oral cavity, infected root canal and periapical abscess of 8 patients (5 with localized and 3 with systemic infections). Microbial populations in these samples were analyzed using next-generation sequencing of 16S rRNA amplicons. Bioinformatics tools and statistical tests with rigorous criteria were used to elucidate the spatial transition of the microbiota from normal to diseased sites. Results: On average, 10,000 partial 16S rRNA gene sequences were obtained from each sample.  All sequences fell into 11 different bacterial phyla.  The microbial diversity in root canal and abscess samples was significantly lower than in the oral samples.  Streptococcus was the most abundant genus in oral cavities while Prevotella and Fusobacterium were most abundant in diseased samples.  Root canal and periapical abscess microbiota were more similar to each other than to the oral cavity microbiota. Using rigorous criteria and novel bioinformatics tools, we found that Granulicatella adiacens, Eubacterium yurii, Prevotella melaninogenica, Prevotella salivae, Streptococcus mitis, and Atopobium rimae were over-represented in diseased samples.  Conclusions: We used a novel approach and high-throughput methodologies to describe microbial transition from normal to diseased oral sites in the same individuals    Eight patients with root canal infections (5 with systemic infections and 3 with localized infection) undergone treatment. Samples were obtained from three sampling sites in each patient. Oral (OS): samples collected from the subjects by rubbing 3 fine paper points against patient''s cheek mucosa, lateral boarder of the tongue and supragingival plaque at the contra lateral side away from the affected tooth. Root Canal (RC): samples collected from the root canal space of the diseased tooth using 3 fine paper points. Abscess Aspiration (AS): the area of the swelling was aspirated with a syringe that has a 16 gauge needle, and expressed into a sterile vial.	root:Host-associated:Human:Digestive system:Oral
MGYS00002214	Using High Throughput Sequencing to Understand the Biodiversity of Oral Bacterial Communities	High throughput sequencing of 16S rRNA amplicons is a cost-effective method for evaluation of bacterial communities associated with oral diseases. However, before undertaking large-scale studies, it is necessary to understand the technique-associated limitations and intrinsic variability of the oral ecosystem, which may affect our ability to discover disease-associated biomarkers. In this work we evaluated bias in species representation using an in vitro-assembled mock community of oral bacteria. We then sequenced the salivary and buccal mucosa bacterial communities of five healthy subjects to investigate their diversity and differences within and between subjects. Mock community analysis revealed primer and DNA isolation biases and an overestimation of diversity that was reduced after eliminating singleton operational taxonomic units (OTUs). Sequencing of salivary and mucosal communities revealed 455 OTUs (0.3% dissimilarity) across all samples with only 78 of the OTUs present in all subjects. Salivary communities were more diverse, with 120-318 OTUs per subject, while in mucosa each subject had 63-136 OTUs. Total OTUs per subject estimated using CatchAll (an estimator that performed well in evenly distributed salivary and also in uneven mucosal communities), ranged from 145-369 for saliva and 111-377 for mucosa. Inter-subject variability in community structure was lower than site differences between salivary and mucosal communities within subjects. These differences were evident even at very low sequencing depths and were mainly explained by an over-representation of Streptococcus mitis and Gemella haemolysans in mucosa, while several taxa from the genera Neisseria, Porphyromonas, Prevotella, Fusobacterium, among others, showed higher affinity for saliva. In summary, we present an experimental and data analysis framework that will facilitate the design and interpretation of pyrosequencing-based studies of the oral flora. Despite challenges associated with this technique, we demonstrate its power for the evaluation of oral diversity and biogeography patterns.	root:Host-associated:Human:Digestive system:Oral
MGYS00002213	Oral cavity microbiome analysis vs. pneumonia risk	16S rRNA gene sequencing to compare the oral microbial profiles in community dwelling adults with those residing in healthcare environments that are known to have high epidemiologic risk for pneumonia (i.e., nursing home residents, and mechanically ventilated patients in intensive care units).  Our goal was to determine if there was an association between the oral microbial profile and subsequent development of pneumonia.   Using sterile cotton applicators, oral cavity samples were obtained and pooled for each subject from the anterior and posterior gingival crevice of each tooth, buccal mucosa, tongue, and the soft and hard palate. Using sterile cotton applicators, oral cavity samples were obtained with two swabs from the: 1) anterior and posterior gingival crevice of each tooth; and 2) buccal mucosa, tongue, and the soft and hard palate.	root:Host-associated:Human:Digestive system:Oral
MGYS00002212	Defining a core microbial community of healthy human oral cavity	The aim of this study was to define the healthy oral microbiome. We sampled and sequenced the V5-V6 hypervariable region of 16S rRNA from microbiomes obtained at several intraoral niches (dental surfaces, cheek, hard palate, tongue and saliva) in three healthy Caucasian male adults with no dental caries, no periodontal disease and no antibiotic use in the past three months. Samples were collected in the morning, 12 hours after tooth brushing and 2 hours after the last food and/or drink intake.	root:Host-associated:Human:Digestive system:Oral
MGYS00002211	Oral and nasal microbiome in Parkinson's disease	Parkinson's disease (PD) is associated with neurodegeneration in olfactory and gastrointestinal nervous tissues. Accordingly, PD patients frequently suffer from hyposmia, hyposalivation, and dysphagia. Since hyposmia and gastrointestinal dysfunction are frequently premotor symptoms, it has been speculated that an external, for example microbial, agent could trigger the pathologic process in the corresponding tissues with subsequent spreading to the central nervous system. We recently demonstrated that fecal microbiota of PD patients differ from those of control subjects. Based on these findings and the involvement of nasal and perioral tissues in PD, we compared the oral and nasal bacterial communities of 76 PD patients and 76 control subjects using a 16S rRNA gene sequencing approach. The sequencing was performed in a MiSeq machine.	root:Host-associated:Human
MGYS00002210	This study develops a framework for exploiting the oral microbiome for monitoring oral cancer development, progression and recurrence.	Individual bacteria and shifts in the composition of the microbiome have been associated with human diseases including cancer.  To investigate changes in the microbiome associated with oral cancers, we profiled cancers and anatomically matched contralateral normal tissue from the same patient by sequencing 16S rDNA hypervariable region amplicons.  In cancer samples from both a discovery and a subsequent confirmation cohort, abundance of Firmicutes (especially Streptococcus) and Actinobacteria (especially Rothia) was significantly decreased relative to contralateral normal samples from the same patient.  Significant decreases in abundance of these phyla were observed for pre-cancers, but not when comparing samples from contralateral sites (tongue and floor of mouth) from healthy individuals.  Weighted UniFrac principal coordinates analysis based on 12 taxa separated most cancers from other samples with greatest separation of node positive cases.  These studies begin to develop a framework for exploiting the oral microbiome for monitoring oral cancer development, progression and recurrence.	root:Host-associated:Human:Digestive system:Oral
MGYS00002207	The intestinal microbiota predisposes to the occurrence of traveller's diarrhoea and to the carriage of multidrug-resistant Enterobacteriaceae after travelling to tropical regions.	The risk of acquisition of multidrug-resistant Enterobacteriaceae (MRE) and of occurrence of diarrhea is particularly high when travelling to tropical regions, likely owing to suboptimal hygiene living conditions and uncontrolled antibiotic usage. To date, the link between MRE acquisition, traveller's diarrhoea and the microbiota composition in healthy people has not been addressed. Therefore, we analysed the composition of metabolically active microbiota by sequencing the total cDNA from faecal samples before and after the travelling.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002199	Comparison of copper contaminated soils, with similar uncontaminated controls.	Two sites of long-term copper polluted soil were sampled, along with nearby uncontaminated controls. All treatments were carried out and sampled in triplicate. A third site was samples at a copper mine, though the control site was of a dissimilar soil type and only single samples of each were taken.Marker taxa and gene functional groups will be identified between polluted and control soils.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00002193	16S Amplicon sequencing of northwestern argentinian artisanal cheeses gDNA using V4 primers	The Northwest argentinian artisanal cheese is a handcrafted product made from raw cow milk. The ripening process occurs spontaneously and, probably, it is influenced by environmental conditions. Its sensory characteristics and safety are probably the result of the balance between microbial populations and their metabolic capacity. The 16S amplicon sequencing of three DNA samples (and their corresponding replicates) from different Northwest argentinian artisanal cheeses, was used to assess the taxonomic affiliation of the bacterial populations in that type of cheeses. The samples were processed using 16S amplicon sequencing on a  Mi-seq sequencer with 515/806 primers to V4 region, this was carried out at Molecular Research (MR DNA) service provider (www.mrdnalab.com, Shallowater, TX, USA) following the manufacturer's guidelines.	root:Engineered:Food production:Dairy products
MGYS00002192	Metagenomic data from an northwestern argentinian artisanal cheese	The Northwest argentinian artisanal cheese is a handcrafted product made from raw cow milk. The ripening process occurs spontaneously and, probably, it is influenced by environmental conditions. Its sensory characteristics and safety are probably the result of the balance between microbial populations and their metabolic capacity. A metagenome-based approach was used to assess the taxonomic affiliation and function potential for bacteriocin production of the bacterial populations in this type of cheese. The DNA sample was subjected to shot-gun sequencing based on ion semiconductor technology using an IonTorrent PGM system, this was carried out at Molecular Research (MR DNA) service provider (www.mrdnalab.com, Shallowater, TX, USA) following the manufacturer's guidelines.	root:Engineered:Food production:Dairy products
MGYS00002190	Microbial biogeography of French caves	Diversity comparison of four pristine caves with five anthropized caves in Dordogne region (France).	root:Environmental:Terrestrial:Deep subsurface
MGYS00002189	Endocarditis due to Neisseria meningitidis	We report a metagenomic analysis of a heart valve community acquired from a patient with blood culture negative infective endocarditis due to Neisseria meningitidis.	root:Host-associated:Human:Circulatory system
MGYS00002188	Community structure analysis in chronic periodontitis and novel oral sampling sites for detecting disease indicators	Periodontitis is an infectious and inflammatory disease of polymicrobial etiology that can lead to the destruction of bones and tissues that support the teeth. The management of chronic periodontitis (CP) relies heavily on elimination or at least control of known pathogenic consortia associated with the disease. Until now, microbial plaque obtained from the subgingival (SubG) sites has been the primary focus for bacterial community analysis using deep-sequencing. In addition to the use of SubG plaque, here we investigated whether plaque obtained from supragingival (SupG) and tongue dorsum sites can serve as alternatives for monitoring CP-associated bacterial biomarkers. Using SubG, SupG, and tongue plaque DNA from 11 healthy and 13 diseased subjects, we sequenced V3 regions (~200 bases) of the 16S rRNA gene using Illumina sequencing. For the first time, this study demonstrates that SupG and tongue dorsum plaque can serve as alternative sources for detecting and enumerating known and novel bacterial biomarkers of CP. This finding is clinically important because, in contrast with SubG sampling that requires trained professionals, obtaining plaque from SupG and tongue sites is convenient, minimally-invasive, and offers a novel means to track CP-biomarker organisms during treatment outcome monitoring.	root:Host-associated:Human:Digestive system:Oral
MGYS00002185	metagenome	metagenome	root:Engineered
MGYS00002184	Moving pictures of the human microbiome	Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease, and malnutrition. Sequencing and computational technologies however have been a limiting factor in performing dense timeseries analysis of the human microbiome. Here we present the largest human microbiota timeseries analysis to date, covering two individuals at four body sites over 396 timepoints. Results: We find that despite stable differences between body sites and individuals, daily fluctuations in an individual's microbiota appear characteristic. Additionally, only a small fraction of the total within body site microbial communities appears to be present across all time points, suggesting that if a core temporal microbiome exists it is small. Many more taxa appear to be persistent but non-permanent community members. DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and for assessing responses to therapeutic interventions.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002183	Bacteria in domestic water-storage containers with or without mosquito larvae	In this study, bacteria in domestic water-storage containers in an Indian village were analysed. Bacteria were identified by 16S rRNA gene amplicon sequencing and identified bacteria were correlated to the presence of vector mosquitoes.	root:Environmental:Aquatic:Freshwater:Drinking water
MGYS00002182	Microbial modulations using fecal microbiota transplantation improves cerebral amyloidosis, taupathy and gliosis in ADLPAPT transgenic mice.	Cerebral amyloidosis and severe tauopathy in the brain are key pathological features of Alzheimer's disease (AD), resulting in reactive gliosis and behavioral abnormalities of learning and memory. Despite a strong influence of the intestinal microbiota on neurodevelopment and neurological disorders, a functional link between the gut microbiota and AD remains unknown. Using a newly developed ADLPAPT transgenic mouse model that overexpresses human mutant APP/PS1 and mutant tau, we examined the impact of the gut microbiota on AD pathogenesis. The composition of the gut microbiota in ADLPAPT mice differed from that of healthy wild type (WT) mice; these differences appeared in early life of ADLPAPT mice before AD pathogenesis. Also, ADLPAPT mice showed low-grade inflammation, high gut permeability and metabolic endotoxemia. RNA-Seq analysis of colonic tissue revealed that aging-related tissue degeneration and macrophage dysfunction occurred earlier in ADLPAPT mice, compared to WT mice. Interestingly, frequent transfer of fecal microbiota from the WT mice into ADLPAPT mice ameliorated Aβ plaque, neurofibrillary tangle formation and glial reactivity, thereby improving learning behavior in recipient mice. In addition, abnormalities in colonic gene expressions were recovered by fecal microbiota transfer. These findings suggest that gut microbial dysbiosis and gut microbiota-derived factors contribute to the development of AD.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00002180	sputum from patients with bronchiectasis pooled together and sequenced for the purpose of investigating the effect of erythromycin on antibiotic resistance carriage	Determining the effects of antimicrobial therapies on airway microbiology at a population-level is essential. Such analysis allows, for example, surveillance of antibiotic-induced changes in pathogen prevalence, the emergence and spread of antibiotic resistance, and the transmission of multi-resistant organisms. However, current analytical strategies for understanding these processes are limited. Culture- and PCR-based assays for specific microbes require the a priori selection of targets, while antibiotic sensitivity testing typically provides no insight into either the molecular basis of resistance, or the carriage of resistance determinants by the wider commensal microbiota. Shotgun metagenomic sequencing provides an alternative approach that allows the microbial composition of clinical samples to be described in detail, including the prevalence of resistance genes and virulence traits. While highly informative, the application of metagenomics to large patient cohorts can be prohibitively expensive. Using sputum samples from a randomised placebo-controlled trial of erythromycin in adults with bronchiectasis, we describe a novel, cost-effective strategy for screening patient cohorts for changes in resistance gene prevalence. By combining metagenomic screening of pooled DNA extracts with validatory quantitative PCR-based analysis of candidate markers in individual samples, we identify population-level changes in the relative abundance of specific macrolide resistance genes. This approach has the potential to provide an important adjunct to current analytical strategies, particularly within the context of antimicrobial clinical trials.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00002179	Responses in Methane Production, Rumen metabolism and Microbial Community in Tropical Adapted Cattle Fed 3-Nitrooxypropanol	The aim of this study was to investigate the effects of 3-nitrooxypropanol (3-NOP) and chloroform on methane and hydrogen production, rumen metabolites and microbial community structure in cattle fed a tropical roughage diet. Eight rumen-fistulated steers were fed a roughage hay diet (Rhode grass; Chloris gayana). Four animals received the antimethanogenic compound chloroform (1.6 g choloroform-cyclodextrin /100 kg LW) while the other four received 3-NOP (2.5 g 3-NOP/ animal/ day) for 21 days. Methane reduction compared with control period was similar for both treatments (30 to 38 %) with no differences of H2 expelled between controls and treatments. Daily weight gain was significantly increased when animals were treated with 3-NOP compared with chloroform and control. Regarding the rumen fermentation parameters increases in ammonia, acetate and branched chain fatty acids were observed with both compounds compared with the controls. Also, methylamines, alcohols and dimethylsulfone concentrations were significantly increased with the treatments compared with control. The rumen microbiome analyses revealed a similar profile for both treatments, with a shift in operational taxonomic units (OTUs) assigned to the Prevotellaceae and Campylobacteraceae family. Moreover, major archaeal OTUs associated with Methanobrevibacter and Methanosphaera were significantly affected to varying extents based on the inhibitory treatments compared to the control. Also the abundance of the Methanobrevibacter spp was decreased by 3-NOP and chloroform, while the Methanomassiliicoccaceae family was inhibited only by 3-NOP. The results suggest that despite the specific mode of action of 3-NOP on methanogens, inhibition of methanogenesis by both compounds resulted in similar responses in metabolism and microbial community structure in the rumen. We hypothesized that these changes were driven by the redirection of metabolic hydrogen by both treatments. Therefore results from previous publications using chloroform as an inhibitor of methanogenesis may be useful in predicting rumen microbiome and fermentation responses to 3-NOP.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00002178	Ring Test for fecal DNA extraction protocols in pigs	The PiGutNet COST action organised a ring test to evaluate different DNA extraction protocols for porcine gut microbiota. A set of pooled samples were distributed to several laboratories along Europe and each group performed a set of extraction protocols. Extracted DNA was subjected to 16S sequencing (V3-V4 region) in an Illumina MiSeq instrument.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00002162	Characterization of microbial communities during a Ground Tire Rubber (GTR) desulfurization process	The present study aims at evaluating the effectiveness of bioreactor-based ground tire rubber (GTR) biodesulfurization process using two bacterial strains in two different bioreactors: i) Gordonia desulfuricans DSM 44462T, and ii) Rhodococcus sp. AF21875. Automated ribosomal inter-genic spacer analysis (ARISA), and High Throughput Sequencing of 16S rRNA gene amplicons were used to analyze samples collected from the bioreactors over time to detect the persistence of the inoculated bacteria within the autochthonous communities, and to compare communities in the bioreactors. Furthermore, the abundance of total bacteria (16S rRNA gene) and biodesulfurization potential (dszA) were estimated using qPCR, in the bioreactors and on GTR before the treatment. ARISA showed that G. desulfuricans DSM 44462T was able to persist, while there are no clear evidences of Rhodococcus sp AF21875 persistence into the bioreactor due to the presence of matching ARISA fragments in the untreated GTR. In both bioreactors, a high abundance of genus Gordonia and Rhodococcus was observed, with an increase of dszA copy numbers over time. Vulcanizates containing biodesulfurized GTRs showed better mechanical and rheological properties than an untreated GTR vulcanizate and even comparable with a natural rubber reference.	root:Engineered:Bioreactor
MGYS00002157	Blue Mountains Swamp Archaea	Blue Mountains Swamp Archaea	root:Environmental:Aquatic:Freshwater:Wetlands:Swamp
MGYS00002150	Microbiome of deep dentinal caries lesions associated with symptomatic irreversible pulpitis	This study used a next-generation sequencing approach to identify the bacterial taxa occurring in the advanced front of caries biofilms associated with pulp exposure and irreversible pulpitis.	root:Host-associated:Human:Digestive system:Oral
MGYS00002146	Distinct and Complex Bacterial Profiles in Human Periodontitis and Health  Revealed by 16S Pyrosequencing	Periodontitis has a polymicrobial etiology within the framework of a complex microbial ecosystem. With advances in sequencing technologies comprehensive studies to elucidate bacterial community differences have recently become possible. We used 454 sequencing of 16S rDNA to compare subgingival bacterial communities from 29 periodontally healthy controls and 29 subjects with chronic periodontitis. Amplicons from both the V1-2 and V4 regions of the 16S gene were sequenced, yielding 1,393,579 sequences. They were identified by BLAST against a curated oral 16S database, and mapped to 16 phyla, 106 genera, and 596 species. 81% of sequences could be mapped to cultivated species. Differences between health- and periodontitis-associated bacterial communities were observed at all phylogenetic levels, and UniFrac and PCoA showed distinct community profiles in health and disease. Community diversity was higher in disease, and 123 species were identified that were significantly more abundant in disease, and 53 in health. Spirochaetes, Synergistetes, and Bacteroidetes were more abundant in disease, while the Proteobacteria were found at higher levels in healthy controls. Within the phylum Firmicutes, the class Bacilli was health-associated, while the Clostridia, Negativicutes, and Erysipelotrichia were associated with disease. These results implicate a number of taxa that will be targets for future research. Some, such as Filifactor alocis and many spirochetes were represented by a large fraction of sequences as compared to previously identified targets. Elucidation of these differences in community composition provides a basis for further understanding the pathogenesis of periodontitis.	root:Host-associated:Human:Digestive system:Oral
MGYS00002143	Coral and human-associated micro-eukaryotes.	Coral and human-associated micro-eukaryotes. PIs Javier del Campo and Patrick J. Keeling.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002139	DNA isolation and sampling kits comparison	Intestinal microbiome plays a key role in shaping human health. In large cohort microbiome studies a comfortable sampling kit is crucial for good compliance of volunteers. The kit should also provide material of good quality for sequencing. Also, different DNA isolation kits provide varying results due to different lysis procedures. We compared multiple sampling and DNA isolation kits to assess their applicability in cohort studies.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002138	Effect of Yoga and low-FODMAP diet in the intestinal microbiota of patients with IBS	Background & Aims: Irritable bowel syndrome (IBS) is unlinked to a pathophysiology, but lowering stress (e.g. by yoga) or a low-carbohydrate diet (i.e. low-FODMAP diet, LFD) relief symptoms. The effects of yoga or LFD intervention on the gut microbiota in patients with irritable bowel syndrome was examined for correlations between both treatment options.Methods: Fifty-nine patients with IBS undertook a single-blind, randomized controlled trial involving a yoga or LFD intervention. Bacterial abundance was analyzed by 16S rRNA gene amplicon sequencing at baseline and after 12 weeks using operational taxonomic units (OTUs). Results: LFD resulted in reduction of the overall relative abundance of Firmicutes, especially of the genus Blautia. This was matched by an increase in the relative abundance of bacteria belonging to the phylum Bacteroidetes. This observation appears also as a weak, but not statistically significant trend in the yoga group. Few OTUs showed a similar response to yoga and LFD. The most pronounced was a decrease observed in the family Lachnospiraceae, namely Eubacterium hallii, Blautia wexlerae and Fusicatenibacter saccharivorans.Conclusions: This study suggests that both, yoga and LFD can change the microbiota for some OTUs in a similar way. The reduction in the abundance of Firmicutes in LFD might unfold its effects through a direct change in the gut bacteria composition. In constrast, yoga might indirectly act on the microbiome through the parasympathetic nervous system, which paralleled the effects of LFD for some Lachnospiraceae species. The underlying mechanism of both interventions are open for future research.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002137	Raw sequences of mock communities sequenced by the Langille Lab.	All of the raw sequence data for the mock communities that have been sequenced by the Langille Lab.	root:Engineered:Modeled:Simulated communities (sequence read mixture)
MGYS00002120	Metagenomic Shotgun of EPS-cultivated microorganisms	Metagenomic Shotgun of Microorganisms grown in culture medium with acidobacterial EPS as sole carbon source.	root:Engineered:Lab enrichment:Defined media
MGYS00002118	Metagenomic analysis of the minke whale (Balaenoptera acutorostrata) gut microbiome	No maximum limits (ML) for e.g. PCB or Hg in whale products exists in Europe, possibly due to the embargo on whale products by the EU in the beginning of the 80's. European and Norwegian ML for PCB6 in marine oils, which may be used as a proxy indicator ML for blubber, is 0.2 mg/kg fat, and the ML for Hg is 0.5 mg/kg wet weight for fillets of most fish. Norwegian whale is legally exported to other whale hunting nations like Japan, which have ML for both Hg and total PCB, which are 0.4 mg/kg and 0.5 mg/kg, respectively. Microbes are central players in geochemical cycles, including cycling of metals and other elements, which may affect seafood safety by e.g. by mercury methylation. Microbial analyses of intestinal microbiota may reveal the potential for transformation/methylation of mercury (Hg) to methyl mercury (MeHg).	root:Host-associated:Mammals:Gastrointestinal tract:Intestine
MGYS00002116	Bulk and rhizosphere soil microbial communities in wheat fields	The study aims to investigate functional activities of soil microbial communities surrounding wheat crops that are associated with higher yields. Two wheat fields were sampled for bulk and rhizosphere soil at three different wheat growth and development stages (March, June and July 2017). We used 16S rRNA sequencing to identify and compare bacteria present in these soil samples.	root:Environmental:Terrestrial:Soil:Loam:Agricultural
MGYS00002114	microbiome profile of fungivorous thrips Hoplothrips carpathicus	microbiome profile of fungivorous thrips Hoplothrips carpathicus	root:Host-associated:Insecta:Digestive system
MGYS00002113	Metagenome assembly of a bacterial community from an acidogenic thermophilic anaerobic reactor	Metagenome assembly of a bacterial community from an acidogenic thermophilic anaerobic reactor	root:Engineered:Bioreactor
MGYS00002112	Effect of infection with and treatment of sensitive and resistant strains of Teladorsagia circumcincta on the ovine intestinal microbiota	The pathogenic nature of gastro-intestinal round worms has a significant effect on absorption in the gut. However, quantifying precisely the dynamics of the microbial community has not been possible until the advent of culture-independent 16S rDNA-based sequence analysis and whole genome shot gun high throughput sequencing.  In this study, Illumina MiSeq technology was used to sequence amplicons of the V4 region of the 16S rRNA gene, to determine the inherent variability of the gut microbiota between samples obtained from two different areas of the intestinal tract (rectal and terminal ileum) in six identically treated sheep.  The same approach was used to further define the effect of infection with and treatment of sensitive and resistant strains of T.circumcincta on the ovine intestinal microbiota, and rectal faecal composition.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00002111	Complete BK Polyomavirus genome sequences from patients with urinary tract infections.	We report BK Polyomavirus genome sequences assembled from shotgun metagenomic sequencing data of patient urine samples previously tested for urinary tract infection. Variation and phylogenetic analysis is used to characterise the virus diversity from this patient cohort from the East of England, UK.	root:Host-associated:Human:Excretory system:Urethra:Urine
MGYS00002110	Metagenomic Analysis of soil microbial community of the western high land	In this study soil was collected from the western high land of Saudi Arabia. The samples were analyzed using next generation sequencing.	root:Environmental:Terrestrial:Soil
MGYS00002096	Targeted metagenomics of perchlorate reducing bacteria	We performed microfluidic enrichment and sequencing of environmental DNA based on the presence of the chlorite dismutase gene	root:Engineered:Lab enrichment
MGYS00002095	River Ganges Microbiome Project	River Ganges Water and Soil Community Structure	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00002092	Herbal Formula-3 alleviates food allergy in mice by modulating the composition of the gut microbiota	Formula-3, an herbal medicine formula, had been demonstrated to inhibit food allergy in rats by stabilizing mast cells. However, it is not clear how Formula-3 modulates the composition of the intestinal microbiota and alleviates food allergy. We performed 16S rDNA sequencing of gut metagenome in fecal samples, and investigated the effect of Formula-3 on healthy mice and food allergy (FA) mice. We found  that Formula-3 decreased gut community richness, increased Lactobacillus and the Bacteroides-to-Prevotella ratio in mice. Additionally, it altered the functional pathways such as energy metabolism and transport system metabolism. It will provide insights into the interaction between herbal formula and gut microbiota, and the potential mechanism of TCMs for disease alleviations.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00002091	The effect of mixed probiotics on fecal microbiota of farmed raccoon dogs	Probiotics could be used as an alternative for improving host health, in this study, mixed probiotics were used to feed farmed raccoon dogs for 12 weeks, the fecal microbiota were investigated with Illumina MiSeq sequencing.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00002090	The effect of mixed probiotics on fecal microbiota of farmed fox	Antibiotics had potentially negative effects on host health and environment. Probiotics could be an alternative for improving host health. In this study, mixed probiotics were used to added in the diet of farmed fox. High-through put sequencing was used to investigated the 16S rRNA gene of fecal microbiota.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00002089	Impact of GOS on chicken gut	Impact of GOS on chicken gu	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00002088	Metagenome data from DNA stable isotope probing of Stiffkey saltmarsh sediment microcosms to investigate methanogenesis from choline	Coastal saltmarsh sediments represent an important source of natural methane emissions, much of the methanogenesis originates from quaternary and methylated amines, such as choline and trimethylamine. However, the key microbes involved in choline-dependent methanogenesis remain poorly characterized and the metabolic pathways by which the saltmarsh microbes degrade choline and form methane are yet to be determined. In this study, we combined DNA stable isotope probing microcosms with high throughput sequencing of 16S rRNA genes and 13C2-choline enriched metagenomes, followed by binning of the microbial population genomes to identify the microbes responsible for methanogenesis. Microcosm incubation with 13C2-choline leads to the formation of trimethylamine and subsequent methane production, suggesting that choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate. Amplicon sequencing analysis identified Deltaproteobacteria, of the genera Pelobacter and Desulfuromonas were the major choline-utilizers. The methanogenic Archaea, of the genera Methanococcoides became enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of the microbial population genomes from metagenomic DNA resulted in the identification of bins that are classified as Pelobacter, Desulfuromonas, Methanococcoides and their associated viruses. Analyses of these bins revealed that Pelobacter and Desulfuromonas have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00002087	Common swift feather microbiota described by high throughput DNA sequencing	We provide the first-ever investigation of feather microbiota by high throughput DNA sequencing for any bird species by describing bacteria found on the innermost tertial feather of 22 adult Common swifts (Apus apus). We found feather microbiomes with large abundance of Bacillales, Actinomycetales, Burkholderiales, Sphingobacteriales, Sphingomonadales, Rhizobiales, Pseudomonadales, Clostridiales, Rubrobacterales and Lactobacillales. Bacterial communities did not change with any feature of individuals we measured. Network and cluster analysis of feather microbiomes disclosed three clusters , characterized by bacteria typical of seawater, plants and soil, and unrelated to conditions at the breeding grounds. We hypothesized that feather microbiomes may reflect, at least partially, airborne bacterial communities of the environments where individuals spent non-breeding periods, or of those they crossed during migration, rather than breeding environment. If confirmed, this evidence may disclose the possibility to use feather bacteria as intrinsic marks for tracing non-breeding origin and routes of migratory birds.	root:Host-associated:Birds
MGYS00002086	Impact of different diets on gut microbiomes: correlation with inflammation and metabolism	Rats were fed 3 different diets (one negative control), stools were collected and 16S gene analysed by V4 region Illumina MiSeq technology	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00002085	First insight into microbial communities associated with species belonging to orders Coleoptera and Thysanura inhabiting anthills of Formica rufa and F. polyctena	In the present study we used Next Generation Sequencing (NGS) in 16S rRNA gene analysis to define microbial communities of seven insect species (Atelura formicaria, Dedrophilus pygmaeus, Leptacinus formicetorum, Monotoma angusticollis, Myrmechixenus subterraneus, Ptenidium formicetorum and Thiasophila angulata) inhabiting anthills of two ant species: Formica rufa and F. polyctena. Moreover, we analyzed obtained microbiome profiles to verify the presence of known endosymbionts.	root:Host-associated:Insecta
MGYS00002084	Weaning transition microbiota and blood types in pig	The host-gut microbiota interplay is well recognized as a key factor for the homeostatic maintenance, for the pathological events control and for growth performances of the animals. The weaning transition represents a moment of drastic changes, which also have a strong impact on the gut microbial community leading to a high risk of dysbiotic events. The adhesion of bacteria on intestinal mucosa is mediated by molecules which compose the glycocalyx on epithelium surface and which act as specific receptors determining the structure of the mucosal bacterial community. Some of these receptors are the mucosal blood type antigens which are genetically determined in the host. The association between ABO blood groups and intestinal microbial profile has been tested in human with contrasting results. For the pig there are no studies on the relationship between blood groups and gut microbiota, however, in our previous study we reported some differences in the glycomic pattern of the jejunal mucosa and in the adhesion of E. coli, associated with the porcine blood groups A0. In the present study we followed the changes in faecal microbiota of piglets from the lactation to 2 weeks after weaning testing the hypothesis that the blood types may impact on its structure. No differences were reported for the A0 blood types. The metagenomic predictions revealed a shift from fatty acid degradation to fatty acid biosynthesis in bacterial community between pre- and post-weaning.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00002083	Bacterial communities associated with Phormidium (cyanobacteria) dominated biofilms	The aim of the study was to investigate the spatial and temporal variation of the structure of bacterial communities associated with Phormidium in river biofilms. This work was performed in one French (Tarn River) and eight New Zealand rivers, which enabled us to compare several communities from local to intercontinental scales. We used high-throughput sequencing of 16S rRNA gene fragment including the V4-V5 variable regions.	root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
MGYS00002081	WGS data from FMT trial for the treatment of recurrent Clostridium difficile infection	Fecal microbiota transplantation (FMT) is a treatment for microbiome-associated diseases in which gut microbiota are transferred from a healthy donor to a patient. Although the success of FMT requires donor bacteria to engraft in the patient's gut, the forces governing bacterial engraftment in humans are unknown. Here, we use a vast, ongoing clinical experiment - the treatment of recurrent Clostridium difficile infection with FMT - to uncover the rules of engraftment in humans. First, we built a machine learning model that accurately predicts which bacterial species will engraft in a given host. We then developed a maximum-likelihood strain inference method, Strain Finder, allowing us to infer the genotypes of donor strains and to track them through patients' guts over time. Surprisingly, engraftment could be predicted largely from the abundance and phylogeny of bacteria in the donor and the pre-FMT patient. We also found that donor strains within a species engraft in an all-or-nothing manner and that previously undetected strains frequently colonize the patient after FMT. We validated these findings in another disease context, metabolic syndrome, suggesting that the same principles of engraftment extend to other indications. These findings may guide the design of bacterial therapeutics that target diseases ranging from ulcerative colitis to cancer.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002080	Faecal metagenomes of healthy pigs	Faecal samples from 16 healthy pigs were analysed using metagenomics, 16S rRNA microbiome amplicon sequencing and qPCR analysis for relative quantities of antibiotic resistance genes.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00002072	Longitudinal study of the diabetic skin and wound microbiome	Background: Type II diabetes is a chronic health condition which is associated with skin conditions including chronic foot ulcers and an increased incidence of skin infections.  The skin microbiome is thought to play important roles in skin defence and immune functioning.  Diabetes affects the skin environment, and this may perturb skin microbiome with possible implications for skin infections and wound healing.  This study examines the skin and wound microbiome in type II diabetes. Results: Ten type II diabetic subjects with chronic foot ulcers were followed over a time course of 10 weeks, sampling from both foot skin (swabs) and wounds (swabs and debrided tissue) every two weeks. A control group of 8 non-diabetic subjects was also followed over 10 weeks, and skin swabs collected from the foot skin every two weeks.  The diabetic skin microbiome was significantly less diverse than non-diabetic skin.  Community composition was also significantly different between diabetic and non-diabetic skin, however the most abundant taxa were similar between groups, with differences driven by very low abundant members of the skin communities. Chronic wounds were generally colonized by the most dominant skin Staphylococcus, along with other taxa that generally different by patient. No significant correlations were found between wound duration or healing status and the abundance of any particular taxa, while wound size was positively correlated with the dominant skin Staphylococcus.   Conclusions: The major difference observed in this study of the skin microbiome associated with diabetes was a significant reduction in diversity.  The long-term effects of reduced diversity are not yet well understood, but are often associated with disease conditions.	root:Host-associated:Human:Skin
MGYS00002070	EMG produced TPA metagenomics assembly of the ASS lime injection - injection site (ASS lime injection - injection site) data set	The ASS lime injection - injection site Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6137. This project includes samples from the following biomes :Grassland .	root:Environmental:Terrestrial:Soil:Clay
MGYS00002069	EMG produced TPA metagenomics assembly of the Bacterial diversity in various environments such as cultivated soil, alpine soil,  semi-arid soil (Soil diversity) data set	The Soil diversity Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB14534. This project includes samples from the following biomes :Soil .	root:Environmental:Terrestrial:Soil
MGYS00002068	EMG produced TPA metagenomics assembly of the Wisconsin, Continuous corn soil metagenome reference core Project (Soil 402460) data set	The 402460 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set SRP008617. This project includes samples from the following biomes :Soil .	root:Environmental:Terrestrial:Soil
MGYS00002067	EMG produced TPA metagenomics assembly of the RA Metagenome (soil metagenome) data set	The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA188489. This project includes samples from the following biomes :Soil .	root:Environmental:Terrestrial:Soil
MGYS00002066	EMG produced TPA metagenomics assembly of the Sheep rumen microbiome (gut metagenome) data set	The gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA202380. This project includes samples from the following biomes :Mammal (non-human) .	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00002065	Rainbow trout raised in two rearing water systems	In a crossover design feeding experiment in two rearing water, trout was fed two non-aquatic alternative protein diets to understand the effect of the water systems on trout performance and gut bacterial composition.	root:Host-associated:Fish:Digestive system
MGYS00002064	16S data from FMT trial for the treatment of recurrent Clostridium difficile infection	Fecal microbiota transplantation (FMT) is a treatment for microbiome-associated diseases in which gut microbiota are transferred from a healthy donor to a patient. Although the success of FMT requires donor bacteria to engraft in the patient's gut, the forces governing bacterial engraftment in humans are unknown. Here, we use a vast, ongoing clinical experiment - the treatment of recurrent Clostridium difficile infection with FMT - to uncover the rules of engraftment in humans. First, we built a machine learning model that accurately predicts which bacterial species will engraft in a given host. We then developed a maximum-likelihood strain inference method, Strain Finder, allowing us to infer the genotypes of donor strains and to track them through patients' guts over time. Surprisingly, engraftment could be predicted largely from the abundance and phylogeny of bacteria in the donor and the pre-FMT patient. We also found that donor strains within a species engraft in an all-or-nothing manner and that previously undetected strains frequently colonize the patient after FMT. We validated these findings in another disease context, metabolic syndrome, suggesting that the same principles of engraftment extend to other indications. These findings may guide the design of bacterial therapeutics that target diseases ranging from ulcerative colitis to cancer.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002063	EMG produced TPA metagenomics assembly of the human salivary and gut microbiomes, as well as a microflora colonized on the surface of marine kelp Metagenome (terrestrial metagenome) data set	The terrestrial metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA357324. This project includes samples from the following biomes : Human gut, Human Oral.	root:Host-associated:Human
MGYS00002060	EMG produced TPA metagenomics assembly of the Human Gut Microbiome Metagenome (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA299502. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002059	EMG produced TPA metagenomics assembly of the Biochar-amended soil Targeted loci environmental (soil metagenome) data set	The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA297134. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil
MGYS00002057	EMG produced TPA metagenomics assembly of the Evaluation of vertical transmission between mother-infant (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA287207. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002056	EMG produced TPA metagenomics assembly of the Homo sapiens fecal metagenome Raw sequence reads (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA279580. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002055	EMG produced TPA metagenomics assembly of the Metagenome study of rice samples under various conditions (soil metagenome) data set	The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA271842. This project includes samples from the following biomes : Plant.	root:Environmental:Terrestrial:Soil
MGYS00002054	EMG produced TPA metagenomics assembly of the Municipal Pensacola Beach Sand Metagenome (beach sand metagenome) data set	The beach sand metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA260285. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil:Sand
MGYS00002052	EMG produced TPA metagenomics assembly of the Gut metagenome from two premature infants (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA221723. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002051	EMG produced TPA metagenomics assembly of the Oklahoma soil 10 year warming Metagenome (soil metagenome) data set	The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA219368. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil
MGYS00002049	EMG produced TPA metagenomics assembly of the DG Metagenome (soil metagenome) data set	The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA188490. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil
MGYS00002048	EMG produced TPA metagenomics assembly of the Kansas, Cultivated corn soil metagenome reference core Project (402463) data set	The 402463 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set SRP008742. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00002047	EMG produced TPA metagenomics assembly of the Central Alaskan Permafrost Metagenome (permafrost metagenome) data set	The permafrost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA72925. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00002046	EMG produced TPA metagenomics assembly of the DIPP Diabetes Microbiome (DIPP Diabetes Microbiome) data set	The DIPP Diabetes Microbiome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set SRP006764. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002044	EMG produced TPA metagenomics assembly of the Metagenomic, Metatranscriptomic and Metviriomic analysis of samples collected at four time points during a single day at the Gulf of Aqaba in the Red Sea. (Red Sea Diel) data set	The Red Sea Diel Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19060. This project includes samples from the following biomes : Marine.	root:Environmental:Aquatic:Marine
MGYS00002043	EMG produced TPA metagenomics assembly of the Molecular study on haloarchaea producing industerially important enzymes (Molecular study on Haloarchaea) data set	The Molecular study on Haloarchaea Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB18746. This project includes samples from the following biomes : Aquatic.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline
MGYS00002042	EMG produced TPA metagenomics assembly of the Oyster and water samples from Texas bays. (Texas Bay Metagenomes) data set	The Texas Bay Metagenomes Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB16362. This project includes samples from the following biomes : Marine, Mollusca.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002041	EMG produced TPA metagenomics assembly of the Study of the changes in the metagenome of the groundwater community at (Metagenomics of a radioactive legacy site) data set	The Metagenomics of a radioactive legacy site Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB14718. This project includes samples from the following biomes : Freshwater.	root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
MGYS00002037	EMG produced TPA metagenomics assembly of the Comparison of two soil microbiomes with different organic matter content (Restinga experiment) data set	The Restinga experiment Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB12940. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil
MGYS00002036	EMG produced TPA metagenomics assembly of the Mining for novel cellulase genes from different ecosystem metagenomes (Mining for novel cellulase genes) data set	The Mining for novel cellulase genes Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB12864. This project includes samples from the following biomes : Aquatic.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline:Sediment
MGYS00002033	EMG produced TPA metagenomics assembly of the The Pig's other genome: a reference gene catalogue of the gut microbiome (A catalog of the pig gut metagenome) data set	The A catalog of the pig gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11755. This project includes samples from the following biomes : Mammal (non-human).	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00002032	EMG produced TPA metagenomics assembly of the Chinese Poyang Lake resistant genes from soil metagenome (Chinese Poyang Lake resistant genes from soil metagenome) data set	The Chinese Poyang Lake resistant genes from soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9412. This project includes samples from the following biomes : Freshwater.	root:Environmental:Terrestrial:Soil
MGYS00002031	EMG produced TPA metagenomics assembly of the Subseafloor microbes at Mid-Cayman Rise (Mid-Cayman Rise FS848 and FS856 metagenomes) data set	The Mid-Cayman Rise FS848 and FS856 metagenomes Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9204. This project includes samples from the following biomes : Hydrothermal vents.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00002030	EMG produced TPA metagenomics assembly of the Coupled metagenomic and metatransciptomic study of the Columbia River coastal margin salinity gradient (Columbia River coastal margin 'omics) data set	The Columbia River coastal margin 'omics Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9136. This project includes samples from the following biomes : Marine.	root:Environmental:Aquatic:Marine:Coastal
MGYS00002029	EMG produced TPA metagenomics assembly of the MiDAS DNA Extraction metagenomics and metatranscriptomics (ena-STUDY-AALBORG UNIVERSITY-27-02-2015-09:25:27:418-237) data set	The ena-STUDY-AALBORG UNIVERSITY-27-02-2015-09:25:27:418-237 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8669. This project includes samples from the following biomes : Sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00002028	EMG produced TPA metagenomics assembly of the Forest harvesting reduces the soil metagenomic potential for biomass decomposition (Forest harvesting reduces the soil metagenomic potential for biomass decomposition) data set	The Forest harvesting reduces the soil metagenomic potential for biomass decomposition Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8420. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00002027	EMG produced TPA metagenomics assembly of the The initial state of the human gut microbiome determines its reshaping by antibiotics (Impact of cefprozil on the gut microbiome of healthy individuals) data set	The Impact of cefprozil on the gut microbiome of healthy individuals Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8094. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002026	EMG produced TPA metagenomics assembly of the BASE – Biomes of Australian Soil Environments (BASE) data set	The BASE Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB7626. This project includes samples from the following biomes : Soil.	root:Environmental:Terrestrial:Soil
MGYS00002025	EMG produced TPA metagenomics assembly of the Metagenomic analysis of sediments along a uranium gradient (Metagenomic analysis of sediments along a uranium gradient) data set	The Metagenomic analysis of sediments along a uranium gradient Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6942. This project includes samples from the following biomes : Freshwater.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00002021	EMG produced TPA metagenomics assembly of the Metagenomic analysis of infant stool sample (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA60717. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002018	We employed shotgun metagenome and 16S rDNA gene amplicon sequencing to robustly compare the taxonomic and functional gene content variability between two key soil ecosystems for climate change, an Alaskan tundra permafrost (AK) and a natural prairie temperate soil in Oklahoma (OK).	"Please see: Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem. Johnston et al. 2016. Frontiers in Microbiology.
doi: 10.3389/fmicb.2016.00579

How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1–2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100–530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that Alaska tundra microbial communities are less diverse and more homogenous across spatial scales than previously anticipated, and provided DNA sequences of abundant populations and genes that would be relevant for future studies of the effects of environmental change on tundra ecosystems."	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00002017	BBSRC Main Experiment Shotgun Study	There is rich genetic diversity in India's native poultry breeds, and the hybrid exotic lines often used in Indian commercial production are distinct from the majority of poultry reared in the UK. The prevalence and dynamics of gastrointestinal infection at farm-level has a direct bearing on economic risk to individual farmers and contributes to overall global concerns of food security and food safety.Changes to diet, use of vaccines or antimicrobials, and flock-level interventions such as ‘thinning', can have profound effects on intestinal health and the evolution and spread of disease-causing microbes and may be amplified by genetic variation in host and microbe populations. Whilst major advances in genomics and genotyping of commercial poultry lines is facilitating the identification of loci linked to susceptibility or resistance, the impact of host and pathogen diversity on disease and production outcomes remains largely unexplored.	root:Host-associated:Birds:Digestive system:Ceca
MGYS00002015	EMG produced TPA metagenomics assembly of the Lime was injected to acid sulfate soils with aim to balance the acidity. The indigenous microbial communities before and after injection were investigated. (Effects of lime injection on the microbial community in acid sulfate soils) data set	The Effects of lime injection on the microbial community in acid sulfate soils Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6125. This project includes samples from the following biomes : Grassland.	root:Environmental:Terrestrial:Soil
MGYS00002014	EMG produced TPA metagenomics assembly of the Raw reads of the microbiota of premature infant mouth, skin, and gut (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA327106. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human
MGYS00002013	EMG produced TPA metagenomics assembly of the Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India (Antibiotic resistance genes in a polluted lake) data set	The Antibiotic resistance genes in a polluted lake Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6102. This project includes samples from the following biomes : Freshwater.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00002011	EMG produced TPA metagenomics assembly of the Microbial Community of Mobilong Acid Sulfate Soil depth profile using Metagenomics (Mobilong Soil Profile) data set	The Mobilong Soil Profile Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB5872. This project includes samples from the following biomes : Grassland.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00002010	EMG produced TPA metagenomics assembly of the Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount, 2011-2012 (Axial Seamount Metagenomes 2011-2012) data set	The Axial Seamount Metagenomes 2011-2012 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB5293. This project includes samples from the following biomes : Hydrothermal vents.	root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
MGYS00002007	EMG produced TPA metagenomics assembly of the A human gut microbial gene catalog established by deep metagenomic sequencing (MetaHIT) data set	The MetaHIT Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB2054. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002006	EMG produced TPA metagenomics assembly of the Symptomatic atherosclerosis gut metagenome. (gut metagenome) data set	The gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA177201. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system
MGYS00002003	Metagenomics of camel tuberculosis	Tuberculosis is the most important zoonotic disease in the world.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00002002	microbiom of B. reticulatus	microbiom of B. reticulatus	root:Host-associated:Fungi
MGYS00002001	Desert Fairy Circles	The formation of fairy circles, circular patches without vegetation in the center but with perennial grasses at the margin, is investigated.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00002000	Study of the microbial assembly of lab-scale biofilter media	Little is known about the forces that determine the assembly of diverse bacterial communities inhabiting drinking water treatment filters and how this affects drinking water quality. Two contrasting ecological theories can help to understand how natural microbial communities assemble; niche theory or neutral theory, where environmental deterministic factors or stochastic factors predominate respectively. This study investigates the development of the microbial community on two common contrasting filter materials (quartz sand and granular activated carbon-GAC), to elucidate the main factors governing their assembly, through the evaluation of environmental (i.e. filter media type) and stochastic forces. Laboratory-scale filter columns were used to mimic a rapid gravity filter; the microbiome of the filter materials and of the filter influent and effluent was characterised using next generation 16S rRNA gene amplicon sequencing and flow-cytometry. Chemical parameters (i.e. dissolved organic carbon, trihalomethanes formation) were also monitored to assess the final effluent quality.  The filter media communities seemed to be strongly assembled by selection rather than stochastic immigration, with only 28% of those OTUs shared with the source water detected on the filter media and following predictions using a neutral community model. GAC hosted a phylogenetically more diverse community than sand. The two filter media communities seeded the effluent water, triggering differences in both water quality and community composition of the effluents. Overall, GAC proved to be better than sand in controlling microbial growth, by promoting higher bacterial decay rates and hosting less bacterial cells, and showed better performance for putative pathogen control by leaking less Legionella cells into the effluent water.	root:Environmental:Aquatic:Freshwater:Drinking water:Delivery networks
MGYS00001998	A large-scale field study of bacterial communities in cereal aphid across Morocco	Insects are frequently associated with bacteria that can have significant ecological and evolutionary impacts on their hosts. Much progress has been made to unravel the diversity and effects of obligate and facultative endosymbionts. Nevertheless, few studies have examined the influence of environmental factors to microbiome composition of aphids. The current work assessed the diversity of bacterial communities of five cereal aphid species collected across Morocco and covering a wide range of environmental conditions. Deep 16S rRNA sequencing enabled us to identify 17 bacterial Operational Taxonomic Units (OTU). Facultative endosymbionts were totally absent in D. noxia, R. maïdis and R. padi, whereas a high relative prevalence of R. insecticola and S. symbiotica was observed in S. avenae and S. maydis, respectively. In addition to these symbiotic partners, Pseudomonas, Acinetobacter, Pantoea, Erwinia and Staphyloccocus were also identified in the aphid species R. padi, R. maïdis and S. avenae, suggesting that the aphid microbiome is not limited to the presence of endosymbiotic bacteria. Beside the significant association between host species and bacterial communities, a significant inverse correlation was also found between altitude and α-diversity.	root:Host-associated:Insecta:Digestive system
MGYS00001997	First insight into microbiome profile of fungivorous thrips Hoplothrips carpathicus (Insecta: Thysanoptera) at different developmental stages	In the present study we used Next Generation Sequencing (NGS) in 16S rRNA gene analysis to define whether the bacterial composition varies among the different developmental stages of H. carpathicus. We analyzed obtained microbiome profiles to verify the presence of known endosymbionts. Moreover, we delineate metabolic potentials of the microorganisms associated with different developmental stages of H. carpathicus.	root:Host-associated:Insecta
MGYS00001996	16S RNA  high-throughput sequencing of the gut microbiota from chronic exposed Sprague-Dawley rats.	A growing body of research suggests that dysbiosis of the gut microbiota induced by environmental pollutants, such as pesticides, could have a role in the development of metabolic disorders.  We have examined the long-term effects of 3 doses of the Roundup herbicide (made of glyphosate and formulants) on the gut microbiota in male and female Sprague-Dawley rats. A total of 141 bacteria families were identified by a high-throughput sequencing metagenomics approach. An OPLS-DA analysis revealed an increased Bacteroidetes family S24-7 and a decreased Lactobacillaceae in 8 out of the 9 females treated with Roundup. These effects were confirmed by repetitive sequence-based PCR fingerprinting showing a clustering of treated females. A traditional culture-based method showed that Roundup had a direct effect on rat gut microbiota. Cultivable species showed different sensitivities to Roundup, including the presence of a high tolerant strain identified as Escherichia coli by 16S rRNA sequencing. The high tolerance of this E. Coli strain was explained by the absence of the EPSPS gene (coding glyphosate target enzyme) as studied by DNA amplification. Overall, these gut microbiome disturbances showed a substantial overlap with those associated with liver dysfunction in other studies. In conclusion, we revealed that environmental concentrations of R have a sex-dependent impact on rat gut microbiome composition and thus warrant further investigations.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00001992	Microbiota broiler carcasses	Microbiota broiler carcasses	root:Host-associated:Birds
MGYS00001991	Metagenomic characterization of the human intestinal microbiota in faecal samples from STEC-infected patients	The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatics approaches, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with STEC infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Regardless of the bioinformatic procedure used, a good resolution of the taxonomic profiles of the samples was achieved. The faeces collected from the STEC infected patients showed a lower intestinal abundance of the beneficial microorganisms Bifidobacterium and Clostridiales spp. in comparison to controls where those microorganisms predominated. These differences were observed with both bioinformatic approaches used and seemed to be related with the STEC infection although the variation in the relative abundance of the members of the Bifidobacterium genus could have also been associated with the dysbiotic status following the diarrhoea.Finally, the metagenomic sequencing allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001990	Blue Mountains Swamp Bacteria	Blue Mountains Swamp Bacteria	root:Environmental:Aquatic:Freshwater:Wetlands:Swamp
MGYS00001986	EMG produced TPA metagenomics assembly of the Linking Lifestyle to the Oral and Gut Microbiota in a Large Prospective Cohort (human gut metagenome) data set	The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA188481. This project includes samples from the following biomes : Human gut.	root:Host-associated:Human:Digestive system
MGYS00001976	Metagenome Analysis of palm oil mill effluent	Metagenome Analysis of palm oil mill effluent	root:Engineered:Wastewater:Industrial wastewater:Agricultural wastewater
MGYS00001972	16S rRNA gene sequencing (Primers 518F and 806R, Illumina MiSeq 150pb-PE) of SIP fractions following glucose amendment in Organic vs Conventional management systems and annual vs perennial crops.	16S rRNA gene sequencing (Primers 518F and 806R, Illumina MiSeq 150pb-PE) of SIP fractions following glucose amendment in Organic vs Conventional management systems and annual vs perennial crops.	root:Environmental:Terrestrial:Soil:Crop
MGYS00001970	characterization of gut microbiota profiles in nod2-/- and nod2+/+ mice and effect of genotype and environment on severity of colitis	characterization of gut microbiota profiles in nod2-/- and nod2+/+ mice and effect of genotype and environment on severity of colitis	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001968	Microbial communities in drinking water systems	Microbial communities in drinking water systems	root:Environmental:Aquatic:Freshwater:Drinking water
MGYS00001967	metagenomes from three stations	metagenomes from three stations	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00001965	Shotgun Metagenomic Analysis of Microbial Composition of Kombucha	Shotgun Metagenomic Analysis of Microbial Composition of Kombucha	root:Engineered:Food production:Fermented beverages
MGYS00001963	New species of Methylomirabilis	New species of Methylomirabilis	root:Host-associated:Microbial
MGYS00001962	Dietary fat-induced gut barrier dysfunction and pathobiont expansion aggravate experimental colitis	Dietary fat-induced gut barrier dysfunction and pathobiont expansion aggravate experimental colitis	root:Host-associated:Mammals:Digestive system
MGYS00001961	Gut bacteria from giant stick insect guts	Gut bacteria from giant stick insect guts	root:Host-associated:Insecta:Digestive system
MGYS00001960	Library of 16S RNA, amplicon, from microbial community	Library of 16S RNA, amplicon, from microbial community	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001958	Skin microbiota of Scinax alcatraz	Skin microbiota of Scinax alcatraz	root:Host-associated:Amphibia
MGYS00001957	soil microbiota in 2 different forest	soil microbiota in 2 different forest	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00001956	skin microbiota in infected frogs	skin microbiota in infected frogs	root:Host-associated:Amphibia
MGYS00001953	Variations on the diversity of amphibian skin microbiota across forests fragments	Variations on the diversity of amphibian skin microbiota across forests fragments	root:Host-associated:Amphibia
MGYS00001952	Diversity of  Picoeukaryotic community in the Gulf of Gabès (south-eastern Mediterranean)	Diversity of  Picoeukaryotic community in the Gulf of Gabès (south-eastern Mediterranean)	root:Environmental:Aquatic:Marine
MGYS00001951	The rumen microbial metagenome associated with high methane production in cattle	The rumen microbial metagenome associated with high methane production in cattle	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00001949	gut microbiota of mice treated with ag-nanoparticles	gut microbiota of mice treated with ag-nanoparticles	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001946	DeepHotMicrobe - genomic clues on microbial adaptation to life in deep bedrock	DeepHotMicrobe - genomic clues on microbial adaptation to life in deep bedrock	root:Environmental:Aquatic:Freshwater:Groundwater:Cave water
MGYS00001939	Metatranscriptome analysis of maize rhizosphere microbiome under nanosilver exposure	Metatranscriptome analysis of maize rhizosphere microbiome under nanosilver exposure	root:Host-associated:Plants:Rhizosphere
MGYS00001933	The diversity of bacteria in marine sediments of the Barents Sea	The diversity of bacteria in marine sediments of the Barents Sea	root:Environmental:Aquatic:Marine:Sediment
MGYS00001928	Hot water plumbing microbiome	Hot water plumbing microbiome	root:Engineered:Built environment
MGYS00001926	Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2015	Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2015	root:Environmental:Aquatic:Marine:Hydrothermal vents:Diffuse flow
MGYS00001918	Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for small DNA viruses.	Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for small DNA viruses.	root:Environmental:Aquatic:Marine
MGYS00001916	Pilot Study DBT-BBSRC	Pilot Study DBT-BBSRC	root:Host-associated:Birds
MGYS00001912	Classification and quantification of commensal lysogens and induced prophages in the gut bacterial and phage metagenomes	Classification and quantification of commensal lysogens and induced prophages in the gut bacterial and phage metagenomes	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001911	This project studies the global transcriptional changes of P. veronii 1YdBTEX once it is introduced in different soils which contain a establish resident microbial community. We would like to characterize the response from the resident community members to the introduced strain.	This project studies the global transcriptional changes of P. veronii 1YdBTEX once it is introduced in different soils which contain a establish resident microbial community. We would like to characterize the response from the resident community members to the introduced strain.	root:Environmental:Terrestrial:Soil
MGYS00001910	The influence of sludge retention time on the  expressed functional diversity of and biotransformation rates of micropollutants performed by a community originating from wastewater activated sludge	The influence of sludge retention time on the  expressed functional diversity of and biotransformation rates of micropollutants performed by a community originating from wastewater activated sludge	root:Engineered:Wastewater:Activated Sludge
MGYS00001909	Metagenomic study on pasturelands chronically exposed to pesticides	Metagenomic study on pasturelands chronically exposed to pesticides	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00001908	Correlation between gut microbiota and presence of fecal fungal isolates in Crohn's disease patients.	Correlation between gut microbiota and presence of fecal fungal isolates in Crohn's disease patients.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001906	Host-microbiome interactions	Host-microbiome interactions	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00001903	wastewater metagenomics Orsay site 01	wastewater metagenomics Orsay site 01	root:Engineered:Wastewater
MGYS00001902	Aortite	Aortite	root:Host-associated:Human:Circulatory system
MGYS00001901	16S data - Multi-omics Differentially Classify Disease State and Treatment Outcome in Pediatric Crohn's Disease	16S data - Multi-omics Differentially Classify Disease State and Treatment Outcome in Pediatric Crohn's Disease	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001899	Benguela Upwelling sediments metagenome study	Benguela Upwelling sediments metagenome study	root:Environmental:Aquatic:Marine:Sediment
MGYS00001898	Small mammal faecal metagenome and its relevance in emerging zoonotic infections.	Small mammal faecal metagenome and its relevance in emerging zoonotic infections.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001897	A/B testing for colon model	A/B testing for colon model	root:Host-associated:Human
MGYS00001896	Tick	Tick	root:Host-associated:Insecta
MGYS00001895	Respiratory tract metagenomics for Respiratory Disease Complex in Poultry	Respiratory tract metagenomics for Respiratory Disease Complex in Poultry	root:Host-associated:Birds:Respiratory system
MGYS00001894	Pesticide degrading bacterial populations on glacier	Pesticide degrading bacterial populations on glacier	root:Environmental:Aquatic:Freshwater:Ice:Glacier
MGYS00001893	ICU_metagenomics_Using_16S_rRNA_analysis_for_assessing_the_respiratory_bacterial_infection_threat_to_immunocompromised_patients_within_Intensive_Care_Units	ICU_metagenomics_Using_16S_rRNA_analysis_for_assessing_the_respiratory_bacterial_infection_threat_to_immunocompromised_patients_within_Intensive_Care_Units	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001892	Human fecal microbiome	Human fecal microbiome	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001889	Nitrogen utilization by marine prokaryotes revealed using stable isotope probing coupled with tag sequencing (Tag-SIP)	Nitrogen utilization by marine prokaryotes revealed using stable isotope probing coupled with tag sequencing (Tag-SIP)	root:Environmental:Aquatic:Marine
MGYS00001888	Bacterial communities in two seasons	Bacterial communities in two seasons	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00001887	Metagenomics 1st 5 data	Metagenomics 1st 5 data	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001886	The_mechanism_of_nutritional_therapy_for_Paediatric_Crohn_s_disease	The_mechanism_of_nutritional_therapy_for_Paediatric_Crohn_s_disease	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001885	Temperature and nutrients as drivers of microbially mediated arsenic oxidation and removal from Acid Mine Drainage	Temperature and nutrients as drivers of microbially mediated arsenic oxidation and removal from Acid Mine Drainage	root:Environmental:Aquatic:Freshwater:Groundwater:Acid Mine Drainage
MGYS00001884	Effects of seasonality and previous logging on wild lemur gastrointestinal microbial composition, nematode infections and their interactions	Effects of seasonality and previous logging on wild lemur gastrointestinal microbial composition, nematode infections and their interactions	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001882	Effects of milk on gut microbiome	Effects of milk on gut microbiome	root:Host-associated:Mammals:Milk
MGYS00001880	Euprymna scolopes accessory nidamental gland and egg jelly coat bacterial communities	Euprymna scolopes accessory nidamental gland and egg jelly coat bacterial communities	root:Host-associated:Mollusca
MGYS00001879	Community composition and ultrastructure of a continuous bioreactor enrichment culture, in which anaerobic methane oxidation (AOM) was coupled to nitrate reduction.	Community composition and ultrastructure of a continuous bioreactor enrichment culture, in which anaerobic methane oxidation (AOM) was coupled to nitrate reduction.	root:Engineered:Bioreactor:Continuous culture
MGYS00001878	Amplicon sequencing of 16S rRNA of bacterial communities from deep-sea surface sediments in pressure and food source experiments	Amplicon sequencing of 16S rRNA of bacterial communities from deep-sea surface sediments in pressure and food source experiments	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00001877	Modulation of the piglets' microbiota: differential effects by a high wheat bran maternal diet during gestation and lactation	Modulation of the piglets' microbiota: differential effects by a high wheat bran maternal diet during gestation and lactation	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001876	Structure and function of epispheric microbial communities from Warszawa, Białowieża and Bóbrka	Structure and function of epispheric microbial communities from Warszawa, Białowieża and Bóbrka	root:Host-associated:Plants:Phylloplane
MGYS00001868	the relationships between gut microbiome and environmental chemicals	the relationships between gut microbiome and environmental chemicals	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001866	We studied the effect of different zinc sources on the intestinal microbiome in weaned pigs	We studied the effect of different zinc sources on the intestinal microbiome in weaned pigs	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001863	Metatranscriptome reveals the function shifts of the vaginal microbiome during the treatment of bacterial vaginosis	Metatranscriptome reveals the function shifts of the vaginal microbiome during the treatment of bacterial vaginosis	root:Host-associated:Human:Reproductive system:Vagina
MGYS00001861	TSLR sequencing of landsort deep oxycline	TSLR sequencing of landsort deep oxycline	root:Environmental:Aquatic:Marine
MGYS00001860	Metagenomic study from hydrothermal sediments retrieved from Menez Gwen and Rainbow deep-sea vents.	Metagenomic study from hydrothermal sediments retrieved from Menez Gwen and Rainbow deep-sea vents.	root:Environmental:Aquatic:Thermal springs:Sediment
MGYS00001859	Area of habitation strongly influences faecal microbial composition of wild lemurs	Area of habitation strongly influences faecal microbial composition of wild lemurs	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001858	Study of bacteriome from urban sediment: behavior according chemical and physical variables	Study of bacteriome from urban sediment: behavior according chemical and physical variables	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00001857	gut mcrobiome research	gut mcrobiome research	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001856	Poly iron sulfate flocculant as an effective additive for improving the performance of microbial fuel cells	Poly iron sulfate flocculant as an effective additive for improving the performance of microbial fuel cells	root:Engineered:Lab enrichment
MGYS00001854	16S rRNA gene amplicon sequences of high-pressure bioelectrode microbiotas	16S rRNA gene amplicon sequences of high-pressure bioelectrode microbiotas	root:Engineered:Bioreactor
MGYS00001853	Bacterial communities in kimchi manufacturing process	Bacterial communities in kimchi manufacturing process	root:Engineered:Food production:Fermented vegetables
MGYS00001852	Anaerobic digester microbiome in Stickney WRP	Anaerobic digester microbiome in Stickney WRP	root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
MGYS00001851	Heterotrophic methanogens dominate in anaerobic digesters	Heterotrophic methanogens dominate in anaerobic digesters	root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
MGYS00001850	Evaluation of the potential for ammonia biofiltration using mature composts based on bacteriome analyses targeting 16S rRNA genes	Evaluation of the potential for ammonia biofiltration using mature composts based on bacteriome analyses targeting 16S rRNA genes	root:Engineered:Solid waste:Composting
MGYS00001849	Effects of NaCl concentrations on anode microbes in microbial fuel cells inoculated with mangrove soils	Effects of NaCl concentrations on anode microbes in microbial fuel cells inoculated with mangrove soils	root:Engineered:Bioreactor:Continuous culture:Marine intertidal flat sediment inoculum
MGYS00001847	Bacterial community of Korean traditional fermented foods	Bacterial community of Korean traditional fermented foods	root:Engineered:Food production:Fermented vegetables
MGYS00001846	food metagenome Metagenome	food metagenome Metagenome	root:Engineered:Food production:Fermented seafood
MGYS00001836	4 samples from Pacific Ocean uncultured phage metagenome	 Anaerobic oil degrading sediment metagenome - anaerobic subsurface sediments containing Monterey Formation oil and hydrocarbon gasses; sample description: Shane Seep; Coal Oil Point hydrocarbon seep field, offshore Goleta, CA.  0.22 micron filtered; CsCl-gradient; DNAse treatment.      <p>  ANME metagenome - carbonate mound formed by hydrate crystalization and expansion;  actively releasing methane from sediments; sample description: 0.22 micron filtered; CsCl-gradient; DNAse treatment, amplified via MDA with phi29 polymerase.     <p>  Methanogenic sediments metagenome - anoxic sediments from center of Santa Barbara Basin. Basin water exhibits suboxic conditions at sampling depth.  Subsurface environment detailed in refs 1&2.  Methanogenesis confirmed through intermittent incubation headspace analyses; sample description: 0.22 micron filtered; CsCl-gradient; DNAse treatment.     <p>  Benthic methanotrophic mats metagenome - sample cultivated ~1 month above active hydrocarbon gas vent; sample description: 0.22 micron filtered; CsCl-gradient; DNAse treatment.   	root:Environmental:Aquatic:Marine:Oceanic
MGYS00001835	Bioreactor scalability: laboratory-scale bioreactor design influences bioreactor performance, ecology and community physiology in expanded granular sludge bed bioreactors	Feasibility studies of new biotechnologies inevitably begin with laboratory-scale trials however rarely do we determine whether laboratory-scale results reflect full-scale performance or ecology. This study aims to bridge that knowledge gap using the expanded granular sludge-bed bioreactor (EGSB), a high-rate anaerobic digester type, as a model for study.Two laboratory-scale idealizations of the EGSB – a one-dimensional and a three- dimensional scale-down of a full-scale design – were built and operated in triplicate under near-identical conditions to a full-scale EGSB. The laboratory-scale bioreactors were seeded using biomass obtained from the full-scale bioreactor, and, spent water from the distillation of whisky from maize was applied as substrate at both scales. Over 70 days, bioreactor performance, microbial ecology and microbial community physiology were monitored at various depths in the sludge-beds using 16S rRNA gene sequencing (V4 region), specific methanogenic activity (SMA) assays and a range of physical and chemical monitoring methods.SMA assays indicated dominance of the hydrogenotrophic pathway at full-scale whilst a more balanced activity profile developed during the laboratory-scale trials. At each scale, Methanobacterium was the dominant methanogenic genus present. Bioreactor performance overall was better at laboratory-scale than full-scale.  We observed that bioreactor idealization at laboratory-scale significantly influenced spatial distribution of microbial community physiology and taxonomy in the bioreactor sludge-bed, with 1-D bioreactor types promoting stratification of each. In the 1-D laboratory bioreactors, increased abundance of Firmicutes was associated with both granule position in the sludge bed and increased activity against acetate and ethanol as substrates. We further observed that stratification in the sludge-bed in 1-D laboratory-scale bioreactors was associated with increased richness in the underlying microbial community at species (OTU) level and improved overall performance.	root:Engineered:Bioreactor:Continuous culture
MGYS00001834	The microbial content of raw and pasteurised cow's milk as determined by molecular approaches including sequencing	The microbial composition of raw and pasteurised milk is assessed by industry on a daily basis. However, many such tests are culture-dependent and thus bacteria that are present at sub-dominant levels and/or that cannot be easily grown in the laboratory may be overlooked. To address this potential bias, we have employed a number of culture-independent techniques, including flow cytometry, real-time qPCR and high throughput sequencing, to assess the microbial population of milk from a selection of commercial milk producers, pre- and post-pasteurisation. The combination of techniques employed reveals the presence of a previously unrecognised and diverse bacterial population in unpasteurised cow's milk. Most notably, the use of high throughput sequencing resulted in a number of bacterial genera being identified in milk samples for the first time. These included Bacteroides, Faecalibacterium, Prevotella and Catenibacterium. Our culture-independent analyses also indicate that the bacterial population of pasteurised milk is more diverse than previously appreciated but that non-thermoduric bacteria within these populations are likely to be in a damaged, non-culturable form. It is thus apparent that the application of state-of-the-art approaches can provide a detailed insight into the bacterial composition of milk and could potentially be employed in the future to investigate the factors that influence the composition of these populations.	root:Engineered:Food production:Dairy products
MGYS00001833	Volatile fatty acids (VFAs) production through anaerobic fermentation	Volatile fatty acids (VFAs) production through anaerobic fermentation is an effective way. Microbes in active sludge play key roles in VFAs production. In present study, VFAs were produced by sludge from five representative waste organic materials. We investigated prokaryotic community structure and diversity in sludge samples using 454 pyrosequencing technique based on 16S rRNA gene. Samples were collected as replicate samples for every waste organic material.	root:Engineered:Wastewater:Activated Sludge
MGYS00001832	Dynamics tracheal intubation airway microbiota of ventilated patients at continuous time points via metagenomic sequencing	Abstract  Background: The use of an endotracheal tube may influence the tracheal  microbiota compositions of ventilator patients which may be the leading cause of mortality in hospital intensive care units. Our primary objective is totrack the diversity and dynamics of bacterial communities within or between the patients, and to determine whether antibiotic therapy and adrenal corticosteroids treatment might influence the harbor of human bacterial pathogens..  Methods: The samples were obtained from eight patients of ventilator with endotracheal tube from Peking University People's Hospital in Respiratory Intensive Care Unit (RICU) during a period of 15 days. The microbiota of tracheal aspirates samples from day0, 1, 3, 5,7,10 and 14 were analyzed using 454 pyrosequencing. The primers: 341F and 805R, complemented with 454 adapters and sample specific barcodes were used for PCR amplification of the 16S rRNA genes.   Results: Analysis of 736,495 high-quality sequences (92,061 reads per patient) revealed a wide range of aerobic, anaerobic, pathogenic, opportunistic, novel and uncultivable bacterial species. The composition of microbiota species were significantly distinguished between the day0 and the day14 of tracheal aspirate samples (Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and Streptococcus pneumoniae). On the individual basis, the microbiota was, however, relatively stable over time. Treatment with antibiotics and adrenal corticosteroids indeed influenced the global composition of the microbiota. CONCLUSION: These results support the phenomenon of dynamics diversification of airway microbiota  in ventilated patients with tracheal intubation. Antibiotics and adrenal corticosteroids therapy may contribute to the alternation of microbiota.	root:Host-associated:Human:Respiratory system:Pulmonary system
MGYS00001831	co-fermentation of straw and swine manure with cattle swine-seeded inoculum	The spatial and temporal dynamics of microbial community in the straw and sludge, and their correlations to bioreactor performance remain to be unveiled. To address these questions, we investigated the microbial compositions and the dynamics of microbiota associated to straw and sludge during co-fermentation of straw and swine manure with cattle swine-seeded inoculum by using 16S rRNA amplicon pyrosequencing technique. There are 18 samples in total, including 9 and 9 independent samples associated with straw and sludge, respectively. each of straw or sludge associated samples includes 3 sampling time point representing different fermentation process.	root:Engineered:Bioreactor
MGYS00001830	anaerobic co-fermentation of straw and swine manure	The spatial and temporal dynamics of microbial community in the straw and sludge, and their correlations to bioreactor performance remain to be unveiled. To address these questions, we investigated the microbial compositions and the dynamics of microbiota associated to straw and sludge during co-fermentation of straw and swine manure using 16S rRNA amplicon pyrosequencing technique. There are 17 samples in total, including 9 and 8 associated with straw and sludge, respectively. each of straw or sludge associated samples includes 3 sampling time point representing different fermentation process.	root:Engineered:Bioreactor
MGYS00001829	Biofilm-forming microbiota of a full-scale biogas reactor	Biogas is a flexible carrier of renewable energy, since methane can partly substitute fossil fuels for both heat and power generation and as fuel. Anaerobic digestion of biowastes in a full-scale biogas reactor was improved by the addition of straw, while the organic loading rate (OLR) could be increased in order to gain higher methane production. The composition of microbial community on straw as biofilm carrier and in fluid reactor content was analyzed by a 16S rDNA 454 pyrosequencing. The microorganisms Candidatus Cloacomonas acidaminovorans and the methanogenic archaeum Methanoculleus dominated the biofilm on straw. Most likely a syntrophic interaction between C. acidaminovorans and the hydrogenotrophic Methanoculleus is responsible for the achievable higher biogas yield after straw addition.	root:Engineered:Biogas plant
MGYS00001828	Anaerobic enrichment culture affected by heat shock	Sludge from anaerobic digester in municipal wastewater treatment process was enriched with benzoate for over three years. This methanogenic enrichment culture was exposed to different levels of heat shock (temperature and duration). Distinct methane production profiles and microbial community structures were observed after heat shock.	root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
MGYS00001827	Electricity generation from rice bran in microbial fuel cells	Laboratory-scale single-chamber microbial fuel cells (MFCs) were inoculated with paddy-field soil and supplied with rice bran for electricity generation. Power outputs and microbiome compositions were compared between MFCs containing pure water as the liquid phase (MFC-W) and those containing mineral solution (MFC-M).	root:Engineered:Lab enrichment:Defined media
MGYS00001826	16S rRNA pyrosequencing of bacterial community associated with lightly pickled vegetables	16S rRNA pyrosequencing of bacterial community associated with lightly pickled vegetables was performed to determine the effect of the revision of prerequisite program for those minimally-processed fresh produce.	root:Engineered:Food production:Fermented vegetables
MGYS00001825	Bacterial community of Korean fish sauce	The metagenome data of Korean fish sauce were obtained by the 454 GS FLX Titanium. This metagenome data contains 19,420,342 bp. Detailed genomic analysis will give further information and insight for bacterial community of Korean fish sauce.	root:Engineered:Food production:Fermented seafood
MGYS00001824	prokaryotic community and assembly in fermentation pit muds	The raw sequences, obtained from illumina MiSeq sequencing, were processed (e.g. trimming, denoising, chimeras removing, etc.). A total of 170098 effective sequences from all (fermentation pit mud) FPM samples remained and the number of reads per sample ranged from 13613 to 14653. Based on 97% similarity of 16S rRNA gene sequences, they distributed into 4927 OTUs and each sample contained 774 to 1453 OTUs. Moreover, the coverage of effective reads per sample was higher than 94% (ranged from 94.3% to 96.4%).For the general phylogenetic composition of FPM community, a total of 33 phyla including 31 bacterial and 2 archaeal phyla, with relative abundance per sample ranged from 90.96-98.44%, were observed. Among them, 20 phyla were commonly shared by all of the FPMs, with abundances accounted for 89.21-98.34%. The dominant phyla (>10%, of total effective sequences) were Firmicutes (58%), Euryarchaeota (19%) and Bacteroidetes (11%).	root:Engineered:Solid waste:Solid animal waste
MGYS00001823	Phylogenetic identification of a hydrogel complex composed of microbially reduced graphene oxide and sewage sludge	Graphene oxide (GO) was recently shown to be an excellent anode substrate for exoelectrogens, such as Geobacter species. The enrichment of exoelectrogenic bacteria can be achieved on GO by using an electron acceptor, together with the acetate oxidization, which leads to the formation of a self-aggregated hydrogel anode with the microbially reduced GO (rGO). We investigated the applicability of GO as the anode for electricity recovery from sewage wastewaters. The project investigated prokaryotic composition of the electrically polarized two different anode-microbes complexes. i.e. rGO-micobes complex and graphite felt-microbes complexes.	root:Engineered:Lab enrichment
MGYS00001822	Phylogenetic identification of GO-reducing bacteria enriched from freshwater environments	This project conducted the phylogenetic identification of bacteria capable of respiration with an extracellular electron acceptor, graphene oxide (GO). GO is the oxidized form of graphene, a 2D honeycomb lattice of carbon. GO can be reduced to the reduced GO (rGO) by bacteria via extracellular electron transferring. Ant the rGO can facilitate the recovering electricity from bacteria. A variety of microorganisms potentially ability to reduce GO, while the reduction of GO was demonstrated by only Schewanella spp. This study enriched GO respiring bacteria from fresh water environments, and identified the enriched GO respiring bacteria by pyrosequencing targeting V4 region of 16SrRNA gene.	root:Engineered:Lab enrichment
MGYS00001821	Microbial community analysis of methanogenic enrichments	To define syntrophy-associated microbial communities, this study enriched methanogenic communities with propionate, butyrate, benzoate, acetate, formate, and H2 from two different inocula.	root:Engineered:Lab enrichment:Defined media
MGYS00001820	An innovative bioelectrochemical-anaerobic digestion-coupled system for counteracting ammonia toxicity by in-situ ammonia recovery: process performance and microbial ecology	The bacterial and archaeal communities in a bioelectrochemical-anaerobic diegstion-coupled system were sequenced by Ion Torrent Personal Genome Machine	root:Engineered:Biotransformation
MGYS00001819	Protist community structure in several habitats of the Central Arctic Ocean in summer 2011 and 2012	Protists form a major part of the Arctic ecosystem and are of great importance for biodiversity and productivity of the Central Arctic Ocean (CAO). The sea ice is considered as one of the main factors that influence protist communities. Current changes in sea ice conditions are assumed to alter protist community biodiversity and composition in ice-influenced habitats with further implications for the overall productivity of the CAO and carbon sequestration to the deep sea. We investigated the environmental factors driving protist community structure and the potential consequences of sea ice retreat on protists in the CAO. Samples were collected from the deep-chlorophyll maximum water and sea ice during August and September in 2011 and 2012. In addition, we sampled melt pond water and under-ice water during record sea ice minimum in 2012 to analyze the exchange of protist communities (i.e. number of shared operational taxonomic units, OTUs) between the different habitats under several sea ice conditions.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00001818	Impact of the Mk VI SkinSuit on skin microbiota of terrestrial volunteers and an International Space Station-bound astronaut	Microgravity induces physiological deconditioning due to the absence of gravity loading, resulting in bone mineral density loss, atrophy of lower limb skeletal and postural muscles, and lengthening of the spine. SkinSuit is a lightweight compression suit designed to provide head-to-foot (axial) loading to counteract spinal elongation during spaceflight. As synthetic garments may impact negatively on the skin microbiome, we used 16S ribosomal RNA (rRNA) gene amplicon procedures to define bacterial skin communities at sebaceous and moist body sites of five healthy male volunteers undergoing SkinSuit evaluation. Each volunteer displayed a diverse, distinct bacterial population at each skin site. Short (8 h) periods of dry hyper-buoyancy flotation wearing either gym kit or SkinSuit elicited changes in the composition of the skin microbiota at the genus level but had little or no impact on community structure at the phylum level or the richness and diversity of the bacterial population. We also determined the composition of the skin microbiota of an astronaut during pre-flight training, during an eight-day visit to the International Space Station involving two 8 h periods of SkinSuit wear, and for one month after return. Changes in composition of bacterial skin communities at five body sites were strongly linked to changes in geographical location. A distinct ISS microbiome signature was found which reversed to a pre-flight profile on return. No changes in microbiome complexity or diversity were noted, with little evidence for colonisation by potentially pathogenic bacteria. We conclude that short periods of SkinSuit wear do not compromise the healthy skin microbiome.	root:Host-associated:Human:Skin
MGYS00001817	Microbiota of caloric restricted mice by 16S	We explored the effect of caloric restriction on fecal and cecal microbiota in mice.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001816	Characterization of tissue microbiota using the Illumina MiSeq sequencing technology after pipeline validation on Mock communities	Characterization of tissue microbiota using 16S metagenomic sequencing by Illumina MiSeq of:  - feces  - ileum  - adipose tissue   - heart  - liver  - brain  - muscle The validation of the sequencing pipeline was also assessed using Mock communities.	root:Host-associated:Mammals
MGYS00001812	metabarcoding data from marine samples	The data regards the study of polluted samples from the Mediterranean sea. The bacterial community of the samples were analysed by a 454 pyrotag experiment targetting the 16S rRNA gene partial sequences (length >100 nucleotides). The of the study was to unravel, categorize, and catalogue the diversity and ecology of microorganisms thriving in four major oil refinery polluted sites on the coastlines of Morocco, Tunisia, Egypt and Greece and three Northern polluted sites at Gulf of Genoa, strait of Messina and Syracuse.	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
MGYS00001810	Role of Tissue-specific Microbiota in Initial Establishment Success of Pacific oysters (Crassostrea gigas)	We transplanted oysters from two invasive, genetically distinct invasive populations of the Wadden sea (Texel, Netherlands and Sylt, Germany, and monitored the short term microbiota shifts and colonization in different tissues during the initial phases of establishment in the new habitat. To manipulate the microbiome mismatch we treated half of the oyster with antibiotics in order to minimize the interactions between resident microbiota and new colonizers, while the other half was transplanted with their natural resident microbiome. We followed oyster survival and changes in diversity, composition and abundance of oyster-associated bacterial communities as a whole and Vibrionaceae and Arcobacter in particular, over the first five days in the new habitat. In this way, we could estimate how the composition and diversity of microbiota in different tissues contribute to success of oyster establishment in the new environment.	root:Host-associated:Mollusca
MGYS00001809	Randomized controlled trial on the impact of early live intervention with bifidobacteria on the healthy infant fecal microbiota and metabolite profile	Background: Early life colonization of the intestinal tract is a dynamic process influenced by numerous factors. The impact of probiotic-supplemented infant formula on the composition and function of the infant gut microbiota is not well defined. Objective:To determine the effect of a bifidobacteria-containing formula on the healthy human intestinal microbiome during the first year of life.Design: Double-blinded, randomized and placebo-controlled study with newborn infants assigned to a standard whey-based formula containing a total of 10(8) cfu/g of Bifidobacterium bifidum, B. breve, B. longum, B. longum subsp. infantis (intervention), or to control formula without bifidobacteria (placebo). Breast-fed controls were included. Diversity and composition of fecal microbiota were determined by 16S rRNA gene amplicon sequencing and metabolite profiles were analysed by UHP-LC mass spectrometry over a period of two years. Results: One hundred six infants were randomized to the interventional (n=48) or placebo (n=49) group; 9 infants were solely breast-fed throughout the entire intervention period of 12 months. Infants exposed to bifidobacteria-supplemented formula showed decreased occurrence of Bacteroides and Blautia spp. associated  with changes in lipids and unknown metabolites at month 1. Microbiota and metabolite profiles converged during the intervention period and long-term colonization (24 months) of the supplemented Bifidobacterium strains was not detected. Significant differences in microbiota and metabolites were detected between infants fed by breast or formula (p<0.005) and between infants born by vaginal and caesarean birth (p<0.005). No significant differences were observed between infant feeding groups regarding growth, antibiotic uptake, or other health variables (p>0.05).Conclusions: The supplementation of bifidobacteria to infant diet can modulate the occurrence of specific bacteria and metabolites during early life with no detectable long-term effects.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001808	Microbial community of PM microbiome	We investigate the community of the PM using MiSeq-sequencing of 16S rDNA and rRNA	root:Engineered:Solid waste:Composting
MGYS00001807	Tropical urban market crop waste composting in Uganda	n a composting study as a management option for urban market crop wastes in Uganda, the population of microorganisms involved in composting were evaluated. The study covered bacteria and fungi. Bacteria were studied by means of pyrosequencing of SSU rDNA and fungi by ITS rDNA.	root:Engineered:Solid waste:Composting
MGYS00001805	Appraisal of the important PAO and GAO communities of fullscale EBPR wastewater treatment systems	The current study collectively assessed the abundance and diversity of all proposed PAO and GAO in 18 Danish fullscale wastewater treatment  plants with biological nutrient removal over a period of 9 years using 16S rRNA gene amplicon sequencing. The microbial community structure in all plants exhibited a large temporal stability during this period. Evidence for the role of the proposed PAO and GAO in EBPR varies and is critically assessed, in light of their calculated amplicon abundances, to indicate which of these are important in full-scale systems.	root:Engineered:Wastewater:Nutrient removal:Biological phosphorus removal:Bioreactor
MGYS00001803	Low FODMAP diet and probiotics in irritable bowel syndrome: a 2x2 factorial design, randomised, placebo-controlled trial	Background and aims: Feeding studies demonstrate the clinical potential of restriction of fermentable carbohydrates (low FODMAP diet, LFD) in irritable bowel syndrome (IBS). However, a placebo-controlled dietary advice study has not been conducted and the diet leads to a potentially detrimental shift in microbiota composition.Methods: A 2x2 factorial trial was undertaken in the tertiary care setting. Patients aged 18-65 years with Rome III IBS were recruited. Patients were randomised 1:1 for four weeks to a diet (sham diet vs LFD) and supplement (placebo vs probiotic), resulting in four different groups. The sham diet was equivalent in dietary restriction compared with LFD. The probiotic was multistrain (VSL#3). Patients were masked to the interventions. The primary endpoints were adequate relief of symptoms and stool Bifidobacteria abundance at four weeks. Results: 104 patients were randomised. 27 were allocated to sham diet/placebo, 26 to sham diet/probiotic, 24 to LFD/placebo and 27 to LFD/probiotic. There was no interaction between the interventions. In the intention-to-treat analysis, adequate symptom relief was higher for LFD (57%) versus sham (38%), although did not reach statistical significance (p=0.051), whereas in the per protocol analysis the higher proportion for LFD (61%) versus sham (39%) was statistically significant (p=0.043). Bifidobacteria were lower after LFD versus sham (8.8 vs 9.2 16S rRNA genes/g, p=0.008) and higher after probiotic versus placebo (p=0.019). There was no effect of LFD on microbiota diversity.Conclusions: This is the first placebo-controlled study of LFD advice in IBS, reporting adequate symptom relief that approached significance together with significantly reduced symptom scores compared with placebo.  Probiotic co-administration ameliorated the diet-induced decline in Bifidobacteria abundance.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001802	Phloroglucinol degradation in the rumen promotes the redirection of hydrogen when methanogenesis is suppressed	Strategies to manage metabolic hydrogen ([H]) in the rumen should be considered when reducing ruminant methane emissions. However, little is known about the use of dietary treatments to stimulate rumen microorganisms capable of capturing the [H] available when methane is inhibited in vivo. The effects of a phenolic compound (phloroglucinol) on methane production, [H] flows and subsequent responses in rumen fermentation and microbial community composition when methanogenesis is inhibited were investigated in cattle. Eight rumen fistulated Brahman steers fed ad libitum with a ratio 60:40 forage:concentrate were randomly allocated in two groups receiving chloroform as antimethanogenic compound for 21 days. Following that period one group received the chloroform + phloroglucinol, whilst the other group just received the chloroform for 16 days. The chloroform treatment resulted in an increase in H2 expelled as methane production decreased with a shift in rumen fermentation towards propionate and formate at day 21 of treatment. Also OTUs assigned to Prevotella were promoted whilst archaea OTUs were decreased with the chloroform treatment as expected. The addition of phloroglucinol in the rumen resulted in a decrease of H2 expelled (g) per kg of DMI and moles of H2 expelled per mol of methane decrease compared with the chloroform only-treated animals. A shift towards acetate and a decrease in formate were observed on the phloroglucinol-treated animals. These changes in the rumen fermentation were accompanied by an increase of OTUs assigned to Coprococcus spp., which could suggest the genus is a significant contributor to the metabolism of this phenolic compound in the rumen. This study demonstrates for the first time in vivo that under methanogenesis inhibition, H2 gas accumulation can be reduced by redirecting [H] towards alternative sinks through the nutritional stimulation of microbial groups that generates metabolites of value to the host and also it might help to decrease the partial pressure of H2 in the methane-inhibited rumen.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00001801	Metagenomic analysis sweet wort	Metagenomic analysis of ivorian sweet wort(tchapalo processing)	root:Engineered:Food production:Fermented beverages
MGYS00001799	Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life	The gastrointestinal tracts of mammalians are sterile in utero and colonized by microorganisms immediately after delivery. The subsequent development of the infant gut microbiota involves a complex succession of microbes, driven by factors such as gestational age, mode of delivery, antibiotic use, hygiene, geographical zone and type of feeding.	root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon
MGYS00001798	Bacterial community diversity and variation in spray water sources and the tomato phyllosphere	Tomato (Solanum lycopersicum) consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water) when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato phyllosphere and the water sources commonly used in commercial vegetable production.    The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The phyllosphere bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both phyllosphere environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant.    Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato phyllosphere. This study has provided the first next-generation sequencing database describing the bacterial communities living in the phyllosphere of a tomato crop under two different spray water regimes, and therefore represents an important step forward towards the development of science-based metrics for Good Agricultural Practices.	root:Engineered:Food production
MGYS00001796	A longitudinal study of the feline faecal microbiome identifies changes into early adulthood irrespective of sexual development	Companion animals provide an excellent model for studies of the gut microbiome because potential confounders such as diet and environment can be more readily controlled for than in humans. Additionally, domestic cats and dogs are typically neutered early in life, enabling an investigation into the potential effect of sex hormones on the microbiome. In a longitudinal study to investigate the potential effects of neutering, neutering age and gender on the gut microbiome during growth, the faeces of kittens (16 male, 14 female) were sampled at 18, 30 and 42 weeks of age. DNA was shotgun sequenced on the Illumina platform and sequence reads were annotated for taxonomy and function by comparison to a database of protein coding genes. In a statistical analysis of diversity, taxonomy and functional potential of the microbiomes, age was revealed as the only factor with significant effects on the variation observed. No significant effects were detected for gender, neutering, or age when neutered (19 or 31 weeks). At 18 weeks of age the microbiome was dominated by the genera Lactobacillus and Bifidobacterium (35% and 20% average abundance). Structural and functional diversity was significantly increased by week 30 but there was no further significant increase. At 42 weeks of age the most abundant genera were Bacteroides (16%), Prevotella (14%) and Megasphaera (8%). Significant differences in functional potential included an enrichment for genes in energy metabolism (carbon metabolism and oxidative phosphorylation) and depletion in cell motility (flagella and chemotaxis). We conclude that the feline faecal microbiome is predominantly determined by age when diet and environment are controlled for. We suggest this finding may also be informative for studies of the human microbiome, where control over such factors is usually limited.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001793	Experimental challenge of poultry feces	Poultry feces have been spiked with known concentration of bacteria and stored at different times and temperatures before DNA extraction	root:Host-associated:Birds:Digestive system:Fecal
MGYS00001792	Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak	The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidifications on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 µatm) and those exposed to present day CO2 conditions.	root:Environmental:Aquatic:Marine:Coastal
MGYS00001788	Semi-synthetic marine metagenomes for metagenomic pipeline assessment	As part of ELIXIR project, six different semi-synthetic marine metagenomes were created to analyse and evaluate the available metagenomic tools/pipelines.	root:Engineered:Modeled
MGYS00001787	Handley et al. demonstrate that vaccination against SIV infection in Rhesus macaques prevents alterations in the gastrointestinal virome and bacterial microbiome that are typically associated with poor disease outcome.	Pathogenic simian immunodeficiency virus (SIV) infection is associated with AIDS, expansion of the eukaryotic enteric virome, consequent intestinal epithelial damage, translocation of viral and bacterial components into the circulation and systemic immune activation. Here we characterized changes in the enteric virome and bacterial microbiome during pathogenic SIV infection, and determined whether vaccine-mediated protection altered these disease manifestations. Vaccine-associated protection against SIV infection prevented expansion of the enteric virome. Overall gastrointestinal bacterial community structure was indistinguishable in protected and unprotected animals, however, animals that ultimately succumb to AIDS related disease had altered levels of several bacterial taxa including an increased abundance of many disease-associated bacteria. These data suggest that immune control of SIV-induced immunodeficiency aids in the maintenance of a normal fecal microbiome and ameliorates SIV-associated systemic inflammation.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001786	Sialylated milk glycans promote growth in gnotobiotic mice and pigs with a stunted Malawian infant gut microbiota	Identifying interventions that more effectively promote healthy growth of children with undernutrition is a pressing global health goal. Analysis of human milk oligosaccharides (HMOs) from 6-month postpartum mothers in two Malawian birth-cohorts revealed that sialylated HMOs are significantly less abundant in mothers with severely stunted infants. To explore this association, we colonized young germ-free mice with a consortium of bacterial strains cultured from the fecal microbiota of a 6-month old stunted Malawian infant and fed recipient animals a prototypic Malawian diet with or without purified sialylated bovine milk oligosaccharides (S-BMO). S-BMO produced a microbiota-dependent augmentation of lean body mass gain, changed bone morphology and altered liver, muscle and brain metabolism in ways indicative of a greater ability to utilize nutrients for anabolism. These effects were also documented in gnotobiotic piglets using the same consortium and Malawian diet. These preclinical models establish a causal microbiota-dependent relationship between S-BMO and growth promotion.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001785	Arsenophonus and Sodalis Symbionts in Louse Flies: an Analogy to the Wigglesworthia and Sodalis System in Tsetse Flies	Symbiosis between insects and bacteria result in a variety of arrangements, genomic modifications, and metabolic interconnections. Here, we present genomic, phylogenetic, and morphological characteristics of a symbiotic system associated with Melophagus ovinus, a member of the blood-feeding family Hippoboscidae. The system comprises four unrelated bacteria representing different stages in symbiosis evolution, from typical obligate mutualists inhabiting bacteriomes to freely associated commensals and parasites. Interestingly, the whole system provides a remarkable analogy to the association between Glossina and its symbiotic bacteria. In both, the symbiotic systems are composed of an obligate symbiont and two facultative intracellular associates, Sodalis and Wolbachia. In addition, extracellular Bartonella resides in the gut of Melophagus. However, the phylogenetic origins of the two obligate mutualist symbionts differ. In Glossina, the mutualistic Wigglesworthia appears to be a relatively isolated symbiotic lineage, whereas in Melophagus, the obligate symbiont originated within the widely distributed Arsenophonus cluster. Although phylogenetically distant, the two obligate symbionts display several remarkably similar traits (e.g., transmission via the host's “milk glands” or similar pattern of genome reduction). To obtain better insight into the biology and possible role of the M. ovinus obligate symbiont, “Candidatus Arsenophonus melophagi,” we performed several comparisons of its gene content based on assignments of the Cluster of Orthologous Genes (COG). Using this criterion, we show that within a set of 44 primary and secondary symbionts, “Ca. Arsenophonus” is most similar to Wigglesworthia. On the other hand, these two bacteria also display interesting differences, such as absence of flagellar genes in Arsenophonus and their presence in Wigglesworthia. This finding implies that a flagellum is not essential for bacterial transmission via milk glands.	root:Host-associated:Insecta:Digestive system
MGYS00001784	Temporal dynamics of the toxic cyanobacterial community composition and toxin presence in two South German lakes	Bacterioplankton plays an essential role in aquatic ecosystems, and cyanobacteria are an influential part of the microbiome in many water bodies. In freshwaters used for recreational activities or drinking water, toxic cyanobacteria cause concerns due to the risk of intoxication with cyanotoxins, such as microcystins. In this study, we aimed to unmask relationships between toxicity, cyanobacterial community composition, and environmental factors. At the same time, we assessed the suitability of a genetic marker to serve as toxicity proxy and aimed to expose the main microcystin producer bacterium. We used Illumina MiSeq sequencing to assess bacterioplankton and perform an in depth analysis of the cyanobacterial community composition in two recreational lakes in South Germany during the cyanobacterial bloom period. We quantified a microcystin biosynthesis gene (mcyB) using qPCR and linked this information with microcystin concentration using HPLC and ELISA to assess toxicity. Microcystin biosynthesis gene (mcyE)-clone libraries were used to determine the origin of toxicity genes. Both lakes displayed distinct bacterial community compositions during the sampling period despite sharing a large fraction of their microbiome (about three quarters of all bacterial OTUs). Proteobacteria, Actinobacteria, and Cyanobacteria dominated Lake Klostersee while Cyanobacteria prevailed in Lake Bergknappweiher. The cyanobacterial community composition was highly dynamic in both lakes, and temporal variations were most evident at the lowest taxonomic level. In both lakes, we witnessed a diversification of dominant cyanobacterial genera. Microcystin concentration correlated positively with total phosphorus and mcyB copy number. However, mcyB copy number was not a reliable signal for bloom toxicity. We identified low abundant Microcystis sp. as the only microcystin producer in both lakes. Therefore, risk assessment efforts need to take into account the fact that dominant cyanobacterial taxa did not contribute to the microcystin contamination of the blooms observed.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001782	Microbiota of caloric restricted mice by WMGS	We explored the effect of caloric restriction on fecal and cecal microbiota in mice.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001781	Whole shotgun metagenome sequencing of AD micro biome	The microbial community responsible for the biogas-producing anaerobic digestion (AD) process used to recover energy from waste is poorly characterised and likely contains many organisms not required for gas generation. Metagenomics approaches offer insights into AD communities that could potentially be exploited to improve the conversion of biomass to biogas, but distinguishing between the biological and technical variability of samples from different sources makes generalisation of results challenging. To determine how different DNA extraction methodologies and sequencing approaches influence the perceived microbiome, we analysed technical replicates of 16S rRNA amplicons and whole shotgun metagenomes from different AD systems. Here we show that diversity measurements of the microbiome in AD samples were strongly influenced by extraction regimes and analysis methodology. 16S rRNA amplification resulted in over- and under-estimation of several taxonomic phyla compared to a PCR-free metagenomics approach. Samples extracted using mechanical methods displayed significantly lower diversity and fewer observed phylotypes than samples extracted by chemical and thermal lysis, which produced higher molecular weight DNA and showed the greatest diversity in community profiles. Our results highlight that the most commonly used extraction and analysis protocols provide a skewed view of the diversity and species richness of the AD microbiome which is likely to extent to other samples. We suggest that methodological differences could be a significant source of variability among AD, and other, metagenomics studies.	root:Engineered:Biogas plant:Wet fermentation
MGYS00001780	16S and 18S amplicon sequencing of compost wheat straw composting microbial community	This study investigated the microbial community structure  of wheat straw derived composting microbial community using 16S and 18S amplicon sequencing.	root:Engineered:Solid waste:Composting
MGYS00001779	Detection of bacterial pathogens from broncho-alveolar lavage by next-generation sequencing	The application of culture-free methods, notably whole-metagenome shotgun (WMGS) sequencing, in routine clinical analysis is still limited although they have some advantage over culture-based approach. A combination of an appropriate DNA extraction procedure, sequencing and bioinformatics tools is essential for removal of human DNA and improved bacterial species identification. We tackled these issues by applying a specifically-designed clinical metagenomics pipeline, from DNA extraction to bioinformatics methods, on a broncho-alveolar lavage (BAL) sample from a severely immunocompromised patient who developed an atypical nosocomial pneumonia.	root:Host-associated:Human:Respiratory system:Pulmonary system
MGYS00001778	Microbiome of anaerobic digesters in municipal wastewater treatment plants	Anaerobic digestion (AD) is a promising biotechnology that simultaneously achieves waste treatment and energy recovery simultaneously. For the purpose of improving operation performance, previous researches have attempted to define the core microbiota of AD, but due to the complexity of the microbial ecology and limited sampling size of the diverse type of digesters, our understanding remains insufficient. In this study, we performed a comprehensive microbial community survey by using 16S rRNA gene-based sequencing of 148 digester sludge samples from 90 full-scale digesters at 51 municipal wastewater treatment plants from North America, Europe, and East Asia. Among the samples, eight different types of community structures were identified, among which the largest one could serve as a model structure of digester microbiome. Relatively mild community changes were induced by moderate temperature fluctuation, while drastic community changes were caused by pretreatment, high salinity and high temperature. Within each type, we identified the signature microbial populations that were associated with the operating conditions. By performing pairwise comparisons between the microbiomes in the feed to and within the digesters, microbial populations that were likely resides as result of incomplete digestion were identified. Overall, this study elucidates of microbial ecology in AD and provides a basis for further investigations into the functions of poorly defied microorganisms, which could ultimately enable improvement of digestion performance.	root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
MGYS00001776	Extraction and sequencing methodology affects perceived microbiome	The microbial community responsible for the biogas-producing anaerobic digestion (AD) process used to recover energy from waste is poorly characterised and likely contains many organisms not required for gas generation. Metagenomics approaches offer insights into AD communities that could potentially be exploited to improve the conversion of biomass to biogas, but distinguishing between the biological and technical variability of samples from different sources makes generalisation of results challenging. To determine how different DNA extraction methodologies and sequencing approaches influence the perceived microbiome, we analysed technical replicates of 16S rRNA amplicons and whole shotgun metagenomes from different AD systems. Here we show that diversity measurements of the microbiome in AD samples were strongly influenced by extraction regimes and analysis methodology. 16S rRNA amplification resulted in over- and under-estimation of several taxonomic phyla compared to a PCR-free metagenomics approach. Samples extracted using mechanical methods displayed significantly lower diversity and fewer observed phylotypes than samples extracted by chemical and thermal lysis, which produced higher molecular weight DNA and showed the greatest diversity in community profiles. Our results highlight that the most commonly used extraction and analysis protocols provide a skewed view of the diversity and species richness of the AD microbiome which is likely to extent to other samples. We suggest that methodological differences could be a significant source of variability among AD, and other, metagenomics studies.	root:Engineered:Biogas plant:Wet fermentation
MGYS00001775	discovery of GH genes using metatranscriptomic approach	discovery of GH genes from enrichment culture using metatranscriptomic approach	root:Engineered:Solid waste:Composting
MGYS00001774	Microbial diversity in high-nitrate wastewater bioreactor	Denitrification of high concentration of nitrate wastewater was investigated in expanded granular sludge bed (EGSB) reactor with sodium acetate as the carbon source. The optimal parameters were achieved with C/N mole ratio of 2.0, liquid up-flow velocity (Vup) of 3.0 m/h and pH of 6.2–8.2. Complete denitrification can be achieved even with nitrate nitrogen concentration as high as 14000 mg/L. Furthermore, 454-pyrosequencing technology was used to analyze bacterial diversity. Results showed that a total of 5573 sequences were obtained which could be affiliated to 6 phylogenetic groups, including Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Chloroflexi and unclassified phylum. Proteobacteria (84.53%) was the dominant microbial population, followed by Firmicutes (13.24%) and Actinobacteria (0.38%). The dominate phylum was different from that in other anaerobic system.	root:Engineered:Wastewater:Water and sludge
MGYS00001768	ECOLOGICAL AND MOLECULAR ASPECTS OF LIGNOCELLULOSE DIGESTION IN NEOTROPICAL HIGHER TERMITES	Due to their ability in digesting lignocellulose, termites are key organisms in the ecosystems that maintain carbon balance and incorporate organic matter into the soil. They are also considered the world's smallest bioreactors. The evolution of termites was marked by modifications on symbiont composition and acquisition of new feeding strategies that improved the digestion of lignocellulose resulting in the diversification of food sources. Nevertheless, some aspects of lignocellulose digestion in neotropical species are poorly known and studies are necessary to further comprehend their impact on the environment and their potential in the new bioeconomy. The aim of this proposal will be to study the digestion of lignocellulose and the community structure of the symbiotic microbiota in six species of neotropical higher termites by integrating ecological and molecular analyses. We will first compare microbiota functions of Cornitermes cumulans based on metagenomics and metatranscriptomic analyses. Then we will evaluate the activity of lignocellulases and the microbial community composition by six species of higher termites with different feeding strategies using enzymatic assays and 16S and ITS sequencing. We suggest that C. cumulans stores food in order to facilitate the digestion of lignocellulose by soil microorganisms before ingestion. In addition, both lignocellulose digestion and microbiota functional composition will be different according to termite feeding specialization. The results of this study will be significant to further understand the symbiotic relationship between the microbiota and termites.	root:Host-associated:Insecta
MGYS00001766	Clinical study of saliva metabolomics and microbiomics in respiratory diseases	Chronic and acute respiratory diseases represent major challenges for clinicians with incidence rates continuing to rise throughout the world.  It is important to develop approaches to accurately and rapidly diagnose the types and stages of respiratory disease.  Many approaches are focusing on such as serum or sputum as the basis of a screening programme. Many biomolecules found within human saliva have their origins in the circulatory system and thus, saliva offers a non-invasive diagnostic tool for a number of diseases.  In this study, we assessed how far saliva could be used to reveal key changes. In particular, we have used metabolomics whereby the chemical components of a sample (1000s of biochemicals) can be accurately quantified in a matter of minutes – to assess salvia samples from 93 samples. Saliva has also been used as a biofluid for metabolomics previously used to identify specific oral, breast and pancreatic cancer profilesThe sampled population encompassed 53 COPD patients from Prince Phillip, Gwangli and Bronglais Hospitals in the Hywel Dda Health Board Area. These consisted of 38 age-matched volunteer controls, 8 lung cancer patients and 18 with a range of respiratory diseases.  The samples consisting of 50 L of saliva were analysed using metabolomic approaches involving the use of Electrospray Ionisation Mass Spectrometry (FIE-MS) to produce a large dataset 169 samples x 6500 metabolites.  Application of “multivariate” statistical approaches allowed the identification of metabolites that are different in particular sample classes.   Using statistically approaches such as Principal Component Analysis (PCA) we demonstrate that saliva could distinguish between samples from each clinical classification compared to controls.  These results were validated using a cross-validated Receiver operating characteristic (ROC) curve which indicated a diagnostic accuracy of > 0.70. Individual chemicals which are the sources of variation between the sample sets have been identified. Further, we have discovered clear differences in the saliva metabolome of COPD patients at different disease severity as defined by Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage classification.  Therefore, this innovative application of “big-data” based analyses has yield potential biomarkers that could be exploited to inform future clinical practice.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00001764	Bacterial community composition in coking wastewater treatment bioreactor sludge	This study aims to illustrate the microbial community in bioreactors of coking wastewater treatment by pyrosequencing.	root:Engineered:Wastewater:Industrial wastewater
MGYS00001763	bacterial community of chinese soybean pastes	Fermented soybean foods contain high nutritious and health beneficial component including easily digestible peptide, cholesterol-free oils, minerals, and vitamins. Various types of fermented soybean foods have been developed and largely consumed as a flavoring condiment in wide Asian regions. While the quality of fermented soybean foods is largely affected by microorganisms participated in the fermentation process, our knowledge about microorganisms of soybean pastes manufactured in the Northeast area of China is still limited.    In the current study using culture-independent massive sequencing analysis, 6,3399 high quality sequences were derived from sixteen soybean paste samples collected from Northeast area of China by a barcoded pyrosequencing method targeting hyper-variable regions V1/V2 of the 16S rRNA gene. Soybean pastes of Korean minority of china (SPKM), Hun Chinese (SPHC) and Korean doenjang showed largely different shape of bacterial community. Overall compositions of bacterial community between groups were clearly separated in Clustering analysis. In addition, each soybean pastes contained representative bacterial species significantly different between each other as follows: Bacillus subtilis in SPKM, Tetragenococcus halophilus in SPHC, and Enterococcus durans in Korean doenjang. In this study, a massive sequencing approach was applied for the first time to analyze the microbial communities of soybean pastes manufactured in Northeast area of China and clearly revealed that different shapes of microbial communities in soybean pastes were affected by manufacturing process along with manufacturing regions.	root:Engineered:Food production:Fermented vegetables
MGYS00001762	Metatranscriptomics analysis of a benzene-degrading enrichment culture under denitrifying conditions	Benzene is the risk-determining compound in oxygen-depleted subsurface environments contaminated by fuel hydrocarbons. Although anaerobic benzene degradation from benzoyl-CoA as a key aromatic central intermediate is well-known, the initial steps of benzene activation in absence of oxygen and its funneling towards benzoyl-CoA remains ill-defined. Here we conducted a metatranscriptomics analysis on biofilm and effluent samples obtained from a chemostat with an anaerobic benzene-degrading and nitrate-reducing culture that has been running for more than 14 years. The transcripts associated with strict anaerobic Firmicutes dominated all samples with 36.2-58.7% relative abundance. Among Firmicutes, members of Peptococcaceae comprised 21.5-36.3% relative abundance of the samples. A gene cluster containing genes encoding the proposed anaerobic benzene carboxylase (abcA and abcD) and a benzoate-coenzyme A ligase (bzlA) was found in the metatranscriptomic dataset that showed extraordinary similarity (> 96% at the amino acid level) and gene synteny to the proposed cluster encoding putative enzymes for direct benzene carboxylation to benzoate. Moreover, compared to the genes involved in downstream benzoyl-CoA degradation, the abcA and abcD and bzlA were among the highest transcripts with the abcA as the most transcribed gene. These results provide compelling evidence that benzene is directly carboxylated to benzoate by the products of abcAD genes and then ligated with CoA by the product of bzlA gene.	root:Environmental:Terrestrial:Soil:Oil-contaminated
MGYS00001761	NGEE Arctic Microbial Communities of Polygonal Grounds	Arctic soils contain an estimated 12-42% of the global soil C and much of this carbon is trapped in permafrost. With increasing global temperatures, thawing permafrost is becoming a potential source of greenhouse gas (GHG) emissions. On the Alaskan North Slope the collapse and rise of soil due to formation of ice wedges and permafrost thaw create distinct features called polygons. As part of the U.S. Department of Energy (DOE) Next Generation Ecosystem Experiment (NGEE) in the Arctic, we collected seasonally thawed active layer soils across a transect of polygon features at the Barrow Environmental Observatory (BEO). We used Illumina HiSeq technology to sequence metagenomes. The sequence data was accompanied by GHG flux measurements, geophysical and geochemical soil characteristics.	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00001760	Effects of Western diets based on lean seafood or lean meat on energy intake, diet-induced obesity and gut microbiota in C57BL/6J mice	Male C57BL/6J mice were fed a casein-based low fat (LF) diet or Western diets (WDs) containing a mixture of lean seafood (seafood WD) or lean meat (meat WD). Glucose and insulin tolerance tests were performed after 10 and 11 weeks, respectively. After 12 weeks, mice were euthanized. Blood and tissues were sampled, and cecum content was collected. We tested meal preference and performed meal response tests to evaluate changes in postprandial glucose and C-peptide levels. We measured energy metabolism by indirect calorimetry, and spontaneous locomotor activity was recorded.	root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
MGYS00001758	Environmental samples from Yellowstone Lake	"DNA was extracted from various water and streamer sites in Yellowstone Lake.
"	root:Environmental:Aquatic:Lentic
MGYS00001756	Bacterial diversity in home and personal care products	Bacterial contamination of home and personal care products is not well documented in scientific literature despite it being a major cause of product recalls and a health risk to consumers. This study aimed to survey the types and relative abundances of bacterial genera responsible for the contamination of selected home and personal care products.	root:Engineered
MGYS00001753	Effects of Leuconostoc mesenteroides starter culture on microbial communities and metabolites during kimchi fermentation	Kimchi fermentations usually rely upon the growth of naturally occurring various heterofermentative lactic acid bacteria (LAB), which sometimes makes difficult to produce kimchi with uniform quality. The use of Leuconostoc mesenteroides as a starter has been considered to produce commercial fermented kimchi with uniform and good quality in Korea. In this study, a combination of a barcoded pyrosequencing strategy and a 1H-NMR technique was used to investigate the effects of Leu. mesenteroides strain B1 as a starter culture on kimchi fermentation. Baechu (Chinese cabbage) and Chonggak (radish) kimchi with/without Leu. mesenteroides inoculation were prepared, respectively, and their characteristics including pH, cell numbers, bacterial community, and metabolites were monitored periodically for 40 days. The barcoded pyrosequencing analysis showed that numbers of bacterial operational taxonomic unit (OTU) in starter kimchi decreased more quickly than non-starter kimchi. Members of the genera, Leuconostoc, Lactobacillus, and Weissella were dominant LAB regardless of kimchi type and starter inoculation. Among three the genus Leuconostoc was most abundant, followed by Lactobacillus and Weissella. The use of Leu. mesenteroides as a starter increased Leuconsotoc proportions and decreased Lactobacillus proportions in both kimchi over the kimchi fermentations. However, interestingly, the use of the kimchi starter maintained Weissella proportions of starter kimchi more highly than non-starter kimchi until fermentations finished. The metabolite analysis using the 1H-NMR technique showed that both Baechu and Chonggak kimchi with the starter culture consumed more free sugars more rapidly with more productions of lactic and acetic acids and mannitol, which were well in accordance with the decreases of pH values and the increase of bacterial cell numbers. The PCA strategy using all kimchi componemts including carbohydrates, amino acids, and organic acids also showed that starter kimchi was fermented faster and more. In conclusion, this study showed that kimchi fermentations with the use of Leu. mesenteroides as a starter were completed more rapidly with the more production of kimchi metabolites, which may contribute to produce commercial kimchi with more uniformity and functional properties. And the combination of the barcoded pyrosequencing strategy and the 1H-NMR technique used in this study can monitor microbial succession and their metabolites effectively and will help to understand the relationships between microbial community and metabolite production (taste and function) in diverse fermented foods including kimchi.	root:Engineered:Food production:Fermented vegetables
MGYS00001752	Biomass-Adapted Thermophilic Consortia	Microbial consortia adapted to biomass at elevated temperature were enriched from compost inocula. These adapted consortia were simplified bacterial communities that secreted glycoside hydrolase enzymes with significant activity on purified substrates and pretreated biomass.	root:Engineered:Solid waste:Composting
MGYS00001750	16S rDNA analysis of antibiotic-treated mice mutant for interferon-lambda pathway genes	Wild-type (B6) mice or mice mutant for Stat1, Irf3, or Ifnlr1 were left untreated or treated for 14 days with an antibiotic cocktail of vancomycin, neomycin, ampicillin, and metronidazole in their drinking water. Stool was collected after the treatment and DNA was extracted and purified. Amplification of the V4 region of 16S rDNA was performed with individual barcodes for each sample, followed by pooling and sequencing on an Illumina MiSeq.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001749	Identification of microbial differences between IgA-High and IgA-Low wild-type mice in two facilities	Wild-type mice from specific-pathogen-free facilities were distinguished phenotypically by fecal IgA levels. Fecal samples were collected from IgA-High and IgA-Low mice from two separate facilities. Amplification of the V4 region of 16S rDNA was performed with individual barcodes for each sample, followed by pooling and sequencing on an Illumina MiSeq.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001748	Effects of cholera on the human gut microbiota, and interactions between human gut microbes and Vibrio cholerae.	Given the global burden of diarrheal diseases, it is important to understand how members of the gut microbiota affect the risk for, the course of, and recovery from disease.  This is true for young children when the gut microbiota is being assembled, as well as for adults.  Recent culture-independent analyses of the fecal microbiota of healthy Bangladeshi infants and children, sampled monthly from birth through the second year of life, have identified a group of age-discriminatory bacterial taxa that together define a normal program of postnatal development (maturation) of the gut microbiota. The acute voluminous diarrhea caused by Vibrio cholerae represents a dramatic example of enteropathogen invasion and gut microbial community disruption.  We have conducted a detailed time-series metagenomic study of the fecal microbiota during the acute diarrheal and recovery phases of cholera in a cohort of Bangladeshi adults living in an area with a very high burden of disease. Recovery is characterized by a pattern of accumulation of bacterial taxa that mirrors the normal pattern of assembly/maturation of the microbiota in healthy Bangladeshi children. To define underlying mechanisms, we created an artificial community of 14 sequenced human gut bacterial species in gnotobiotic mice, composed of taxa that directly correlate with recovery from cholera and that are indicative of normal microbiota maturation in healthy Bangladeshi children. One of these age-discriminatory species, Ruminococcus obeum, exhibited consistent increases in its relative abundance upon V. cholerae infection of the mice. Follow-up mono- and bi-colonization studies established that R. obeum restricts V. cholerae colonization. RNA-Seq of the community's meta-transcriptome, combined with assays of autoinducer-2 (AI-2) production and function, revealed that expression of R. obeum luxS (AI-2 synthase) and AI-2 production increase significantly with V. cholerae invasion, and that R. obeum AI-2 causes quorum-sensing mediated repression of toxin co-regulated pilus, a primary V. cholerae colonization factor. Co-colonization experiments in gnotobiotic mice established that R. obeum AI-2 reduces Vibrio colonization/pathogenicity through a novel pathway that does not depend on the canonical V. cholerae AI-2 sensor, LuxP.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001746	impact of diet on gene expression in bovine rumen microbiomes	impact of diet on gene expression in bovine rumen microbiomes	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001745	Ventilator-associated pneumonia	We explored bacterial community diversity of supraglottic secretions, endotracheal apirate and broncho-alveolar lavage from intubated patients hospitalised in the intensive care unit.	root:Host-associated:Human:Respiratory system:Pulmonary system
MGYS00001743	The microbiota of developing cod larvae	The submitted dataset consists of pyrosequenced barcoded v4 16S rDNA amplicons representing bacterial communities associated with developing cod larvae, rearing water, and live feed samples. Cod larvae were reared with two different feeding regimes (copepods or rotifers).  Sampling of larvae and rearing water was carried out at 8, 17, 32, and 61 dph for two rearing tanks; one for each feeding regime. Each live feed culture was sampled once; the copepods at 8 dph, the rotifers at 17 dph, and Artemia culture at 32 dph. Total DNA from individual larvae, water and live feed samples were used as templates in PCR reactions. The V4 region of the 16S rRNA gene was amplified using a nested PCR protocol as described in Bakke et al. 2013, Environmental Microbiology Reports 5(4), 537-548. Two pooled amplicon libraries were generated (one for each rearing tank/feeding regime) and each of them was sequenced on one half of a 454 plate with a GS FLX instrument at the Norwegian Sequencing Centre.	root:Host-associated:Fish
MGYS00001741	mucosal microbiota	Changes in mucosal microbiota during healing.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00001736	River Sediment metagenomes of textile dye degrading communities collected from Ankleshwar, India	Samples were collected from Indian (Ankleshwar) river sediment heavily polluted with textile dyes. A control site was also used. 1-2 g of river sediment was inoculated (in triplicate) in to Bushnell Hass Broth either supplemented with or without various textile dyes. 1-2 g of sediment form the control site was also inoculate (in triplicate) into Bushnell Hass Broth without addition of textiles dyes. Cultures were incubated at 37oC  until decolourisation of the dyes occurred (usually within 24-48 hours). Two rounds of subculturing occurred where 1-2 ml of culture medium was inoculated into fresh Bushnell Hass Medium with or without dye. After these round of subculturing, all 9 cultures were sampled for metagenomics and metaproteomics.	root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
MGYS00001735	Analysis of variations in the microbiota of chickens fed diets supplemented with different feed additives	Conventional rearing of broiler chickens is based on routine supplementation of the feed with anticoccidials which are approved for use against intestinal coccidiosis. A sub-group of anticoccidials, which functions as ionophores, is also effective against some gram-positive bacteria, including Clostridium perfringens. This is an intestinal bacterium associated with growth depression and important gastrointestinal health problems such as necrotic enteritis and the gizzard erosion syndrome. The dual function of ionophores is part of the explanation to their widespread use in broiler feeds. The ionophore narasin has been the predominant anticoccidial used in broiler rearing in the Nordic countries. Research suggests that although narasin is not used in human medicine, its  use in broiler rearing might promote persistence of vancomycin resistant enterococci. This has led to an expressed concern that use of narasin may stimulate occurrence and spread of bacteria resistant to clinically relevant antibiotics. Dissemination of antibiotic resistant bacteria is a world-wide problem, and there is an increasing pressure to reduce the use of antimicrobial agents in animal production. The purpose of this project was to test non-antibiotic feed additives and identify characteristics of the intestinal microbiota in chickens fed diets supplemented with these alternatives to in-feed anticoccidials.The samples originate from four different feeding trials with Ross 308 broiler chickens reared under similar conditions. The chickens were divided into 6 groups, which were fed similar commercial pelleted diets formulated to meet the Ross 308 nutrition specifications with group specific supplements.Trial 1: group 1, narasin; group 2, no additive; group 3, acid product-A; group 4, acid product-B; group 5, acid product-C; group 6, acid product-D.Trial 2: group 1, narasin; group 2, no additive; group 3, acid product-E; group 4, acid product-F, group 5; yeast product-A, group 6; plant/acid product-A.Trial 3: group 1, narasin; group 2, no additive; group 3; yeast product-B + synbiotic-A, group 4; yeast product-B + plant product-A; group 5, yeast product-A + acid product-B; group 6, yeast product-A + acid product-D.Trial 4: group 1, narasin; group 2, no additive	root:Host-associated:Birds:Digestive system:Fecal
MGYS00001733	Surveillance for prevalence of drug resistance bacteria in Ugandan animal agriculture	Surveillance for prevalence of drug resistance bacteria in Ugandan animal agriculture	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001732	Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli	A longituinal study looking at changes in the colon and cecum microbiota of parasite infected male C57BL/6 mice. 16s rDNA sequencing was used.	root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
MGYS00001731	16S pyrosequencing of the microbiota in Anopheles gambiae mosquitoes after bloodfeeding on blood treated or not with penicillin-streptomycin antibiotic cocktail.	16S pyrosequencing of the microbiota in Anopheles gambiae mosquitoes after bloodfeeding on blood treated or not with therapeutic concentrations of penicillin-streptomycin antibiotic cocktail.	root:Host-associated:Insecta
MGYS00001729	Computational integration of genomic traits into 16S rDNA microbiota sequencing studies	Molecular sequencing techniques help to understand microbial biodiversity with regard to species richness, assembly structure and function. In this context, available methods are barcoding, metabarcoding, genomics and metagenomics. The first two are restricted to taxonomic assignments, while genomics only refers to functional capabilities of a single organism. Metagenomics by contrast yields information about organismal and functional diversity of a community. However currently it is very demanding regarding labour and costs and thus not applicable to most laboratories. Here, we show in a proof-of-concept that computational approaches are able to retain functional information about microbial communities assessed through 16S rDNA (meta)barcoding by referring to reference genomes. We developed an automatic pipeline to show that such integration may infer preliminary or supplementary genomic content of a community. We applied it to two biological data sets and delineate significantly overrepresented protein families between communities. The script alongside supporting data is available at http://bioapps.biozentrum.uni-wuerzburg.de.	root:Host-associated:Plants
MGYS00001728	A case of hepatic brucelloma studied by next generation sequencing	A clinical examination of a patient pointed to a hepatic brucelloma. However, the presence of Brucella was not confirmed by culture and PCR experiments. We aimed at identifying the bacterium by whole metagenome shotgun sequencing of DNA extracted from the hepatic biopsy.	root:Host-associated:Human:Digestive system
MGYS00001727	In-depth diversity analysis of the bacterial community resident in camel rumen	We applied amplicon barcoded pyrosequencing to study bacterial community resident in the camel rumen. we generated 145043 raw reads with average read length of 382.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001726	Bombus terrestris gut microbiome	TODO	root:Host-associated:Insecta
MGYS00001725	pigs gut microbiota	diet divers for analysis of pigs gut section microbiota	root:Host-associated:Mammals:Excretory system
MGYS00001723	Metagenomic analysis of chicken cecal feces	Metagenomic analysis of chicken cecal feces obtained from chicken farm in Japan were carried out to know microbiota composition.	root:Host-associated:Birds:Digestive system:Fecal
MGYS00001722	Bacterial composition and survival on Sahara dust particles transported to the European Alps	The Sahara Desert is the primary source of wind-blown biological and mineral particles (aerosols) on Earth, 10% of which arrive to Europe. Aerosols that are deposited on high alpine snowfields in freezing conditions are well preserved and facilitate downstream biological analyses. As little is known about the structure and viability of bacteria transported during Saharan dust events (SDEs), the goal of this study was to characterize SDE-associated bacteria in snow using an interdisciplinary approach. We collected samples from a snow profile at the Jungfraujoch (Swiss Alps; 3621 m asl), where the presence of distinct ochre Sahara dust layers (SD-layers) could be ascribed to two SDEs reported in February and May 2014. Backward trajectories, physicochemical analyses of the snow, and dust particle concentrations of distinct geochemical compositions permitted us to determine the origin of the SDEs. Bacterial community structures were assessed using high throughput sequencing; distinct differences in bacterial community structures and metabolic activity associated with SD-layers as compared to clean snow layers were observed. Most striking was the exclusive presence in the SD-layers of bacteria that are adapted to hostile environments, and are hence well suited to survive the harsh conditions of long-distance airborne transport.	root:Environmental:Aquatic:Freshwater:Ice
MGYS00001721	Expression of the blood-group-related gene B4galnt2 alters susceptibility to Salmonella infection	Glycans play important roles in host-microbe interactions. Tissue-specific expression patterns of the blood group glycosyltransferase β-1,4-N-acetylgalactosaminyltransferase 2 (B4galnt2) are variable in wild mouse populations, and loss of B4galnt2 expression is associated with altered intestinal microbiota. We hypothesized that variation in B4galnt2 expression alters susceptibility to intestinal pathogens. To test this, we challenged mice genetically engineered to express different B4galnt2 tissue-specific patterns with a Salmonella Typhimurium infection model. We found B4galnt2 intestinal expression was strongly associated with bacterial community composition and increased Salmonella susceptibility as evidenced by increased intestinal inflammatory cytokines and infiltrating immune cells. Fecal transfer experiments demonstrated a crucial role of the B4galnt2-dependent microbiota in conferring susceptibility to intestinal inflammation, while epithelial B4galnt2 expression facilitated epithelial invasion of S. Typhimurium. These data support a critical role for B4galnt2 in gastrointestinal infections. We speculate that B4galnt2-specific differences in host susceptibility to intestinal pathogens underlie the strong signatures of balancing selection observed at the B4galnt2 locus in wild mouse populations.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001719	Biogeography of tropical riverine bacterioplankton communities determined by deep sequencing of 16S rRNA gene	Riverine systems are intimately coupled with and shaped by the characteristics of their watershed, yet we know little about the effect of these connections to bacterioplankton communities. Here, we characterise water samples collected on the basis of dominant watershed land-use types observed along the tropical riverine system using 16S rRNA gene Illumina MiSeq sequencing. Three types of samples were analysed with different land-use types: pristine, urban and agricultural. Bacterioplankton communities were greatly discriminated by watershed land-use types rather than environmental or climate characteristics. Watershed land-use promoted allochtonous bacterial sequences, eutrophication-linked bacterial sequences, extinction and stress to indigenous bacterioplankton taxa. Despite the considerable variation across watershed land-use types, total bacterioplankton richness was greatly contributed by among-site richness than within-site richness. Bacterioplankton taxa showed a remarkable stability over time irrespective of climatic perturbations emphasizing the possibility of being temporally predictable.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001718	Long-term monitoring of structures of microbial communities along a vegetation gradient from alpine meadows to a glacier forefield	In a 14-months monitoring campaign, we assessed seasonal changes in soil properties and in microbial community structures at 4 locations representing an altitude and vegetation gradient (from alpine meadows at 1980 m a.s.l. to a glacier forefield at 2519 m a.s.l.). Fungal and bacterial community structures and abundances were investigated through T-RFLP profiling and qPCR of the 16S and 18S rRNA genes. In addition, Illumina sequencing was performed to identify key bacterial groups on selected samples. Seasons affected the soils and the soil microbial communities more significantly than sites (plant species, grazing). The physico-chemical properties of the soils changed greatly during the course of the year. Bacterial and fungal community structures changed during the sampling period, but didn't always complete a full seasonal cycle. Our sequence data indicates that under winter snowpack, bacterial communities were dominated by ubiquitous opportunistic groups (i.e. beta-Proteobacteria), while in the snow-free seasons, other groups (i.e. Cyanobacteria) became more abundant.	root:Environmental:Terrestrial:Soil
MGYS00001717	Deep sequencing of 16S rRNA gene reveals discrete series of microbial community succession in tropical drinking water treatment plant	Microbial community dynamics in drinking water treatment plant are remarkably understudied, despite the high demand of microbiologically safe drinking water supplies. In this study, data on coherent dynamics of taxa- and microbial community shifts along the treatment barriers of drinking water treatment plant are reported. By sequencing the 16S rRNA gene amplicon at adequate depth, a high degree of microbial diversity and overrepresentation of typical freshwater genera including Undibacterium, Novosphingobium and Cylindrospermopsis were observed. Undibacterium had a considerable contribution to the abundance of the phylum Proteobacteria and demonstrated a remarkable ability to predict microbial diversity. Shifts in community structure were due to substantial elimination of bacterial taxa by sand filtration, and significant enrichment of rare taxa following chlorination.  Coherent dynamics of taxa across treatment barriers revealed series of discrete microbial secondary successions punctuated by treatment barriers. Based on microbial community succession data, the fate of noxious bacteria  in drinking water treatment plants can be tracked.	root:Environmental:Aquatic:Freshwater:Drinking water
MGYS00001716	Diversity of particle-attached bacteria in the Baltic Sea	To evaluate if changes in salinity affecting diversity of particle-associated (PA) and free-living (FL) bacteria, we sampled both bacterial fractions in two seasons (summer and fall/winter) in surface waters of three selected stations of the Baltic Sea representing marine, mesohaline and oligohaline environments. All samples were PCR amplified with 30 cycles using the primer pair Bakt_341F (CCTACGGGNGGCWGCAG) and Bakt_805R (ACHVGGGTATCTAATCC). Primers were tailed with sample-specific 5 bp barcodes a 454-adptor region, spanning variable regions V3 and V4 of the 16S rRNA gene. PCR products were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter GmbH, Krefeld, Germany), quantified with a Picogreen assay (LifeTechnologies, Carlsbad, USA), diluted and equally pooled. The bidirectional sequencing was performed on a 454 platform with Titanium Flex chemistry (Roche etc.).	root:Environmental:Aquatic:Marine
MGYS00001715	Assessment of community structures along the depth profile of an alpine snowpack in winter and at snowmelt	In this study, we assessed the hypothesis whether microbial communities in an alpine snowpack in Switzerland would change between two seasons (winter and snowmelt). We characterised physical-and chemical changes of the snowpack along the two seasons, and combined it with the assessment of the microbial community structure. Bacterial community composition was investigated through Illumina sequences of the variable regions V3 /V4 of the 16S rRNA gene. Our results showed a pronounced shift of bacterial community structures during the seasons. In winter, less diverse, but more evenly distributed communities were found throughout the entire snowpack. At snowmelt, higher diversity, and richness of bacterial OTUs was detected.  Bacterial taxa inhabiting the snow change from spore forming-psychrophilic organisms (eg. Firmicutes) in winter to a more varied composition of ubiquitous heterotrophy (i.e. Betaproteobacteria) at snowmelt.	root:Environmental:Aquatic:Freshwater:Ice
MGYS00001714	A MEMBRANE AERATED BIOFILM REACTOR (MABR) FOR SULFIDE CONTROL USING A BUBBLELESS MEMBRANE AERATION	A UASB reactor was operated combined to a membrane aerated biofilm reactor (MABR) for sulfate removal and for elemental sulfur reclamation. A commercial silicon tube was use as an oxygen delivery diffuser. The process achieved high rates of sulfide removal from liquid phase (90%). The hydrogen sulfide removal was influenced by the pH value and at pH value of 7.5, 98% of the H2S was removed. The elemental sulfur was observed in inside the membrane, with content in the biomass of 21%. 16S rRNA gene-based high throughput Illumina MiSeq sequencing was used to demonstrate the microbial community diversity and the different layers inside the silicon tube.	root:Engineered:Bioreactor
MGYS00001713	Evaluation of the bioremediation potential of Atlantic Amazon	Samples were collected from coastal area in the Amazonian basin	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001712	Microbial ecology in polar environments	A total of 52,928 pyrosequencing reads were analyzed in order to reveal the bacterial community structures in stream and lake surface water samples from Fuglebekken and Revvatnet basins of the southern Svalbard. Depending on the sample examined, bacterial communities at higher taxonomic level consisted mainly either of Bacteroidetes, Betaproteobacteria and Microgenomates (OP11), or of Planctomycetes, Betaproteobacteria and Bacteroidetes members, whereas in two of them, a notable Microgenomates population was identified. At the lower taxonomic level, bacterial communities comprised mostly of Microgenomates, Comamonadaceae, Flavobacteriaceae, Legionellales, SM2F11, Parcubacteria (OD1) and TM7 members, although at different proportions in each sample. The abundance of OTUs shared in common among samples exceeded 70%, with the exception of samples in which the proliferation of Planctomycetaceae, Phycisphaeraceae and Candidatus Methylacidiphilum spp. lowered their relative abundance. Multi-variable analysis indicated that As, Pb and Sb were the main environmental factors influencing bacterial profiles.	root:Environmental:Aquatic:Freshwater:Ice
MGYS00001708	Analysis of gut microbiota in infants	The human gut microbiome has been demonstrated to play a vital role in health and disease. Dysbiosis may contribute significantly to adverse outcomes in child health. Using metagenomics this project seeks to identify microbiome signatures that might influence health of children.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001706	Natural and Artificial Milk Feeding Promote Different Rumen Microbial Colonization but not Differences in Gene Expression Levels at the Rumen Epithelium of Newborn Goats	The aim of this work was to evaluate the effect of feeding management during the first month of life (natural with the mother, NAT, or artificial with milk replacer, ART) on the rumen microbial colonization and the innate immune response. Thirty pregnant goats carrying two fetuses were selected. At birth one kid was taken immediately away from the doe and fed milk replacer (ART) while the other remained with the mother (NAT). Groups of four kids (from ART and NAT experimental groups) were slaughtered at 1, 3, 7, 14, 21 and 28 days of life. On the sampling day, after slaughtering, the rumen content was sampled and epithelial rumen tissue was collected. Pyrosequencing analyses of the bacterial community structure on samples collected at 3, 7, 14 and 28 days showed that both systems promoted significantly different colonization patterns (P = 0.003). Diversity indices increased with age and were higher in NAT feeding system.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00001705	A method for identifying metagenomic species and variable genetic elements by exhaustive co-abundance binning	The microbial diversity of environments like the human gut extends far beyond what is covered by reference genomes. Here we present a method for exhaustive and unsupervised co-abundance gene binning across a series of highly complex metagenomic samples. As the method does not rely on previously sequenced reference genomes it allows for discovery of new species, viruses and clonal heterogeneity. We demonstrate the method on human gut microbiome data and identify 7,381 co-abundance gene groups (CAGs) ranging in size from 3 to 6,319 genes. The CAGs represent a wide variety of biological entities including microbial genomes, phages and clonal differences. We name the 741 largest of these metagenomic species (MGS), because they correspond to microbial species. In addition, we establish microbial host affiliations by dependency-associations for many small CAGs. Longitudinal sampling in the same individuals indicates that some of these dependency-associations are important for the persistence of their microbial host	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001703	Diet assessment of European eel (Anguilla anguilla) leptocephali in the Sargasso Sea	Diet assessment of European eel (Anguilla anguilla) leptocephali in the Sargasso Sea	root:Host-associated:Fish
MGYS00001702	Geographic and host-associated variations in bacterial communities on the leaf surfaces of field-grown broccoli	This study is the first to describe bacterial community composition and diversity on broccoli leaf surfaces in-depth using 454 pyrosequencing of 16S rRNA genes. This study suggested variability of bacterial communities associated with geography of farming sites, and alterations by host growth and host health conditions. In a global view of fresh produce, this study delineated bacterial community composition specific for broccoli, which is more similar to ground vegetables than tree fruits and vegetables.	root:Host-associated:Plants:Phylloplane
MGYS00001701	The vaginal and urinary microbiota in health, during BV and after treatment	The urinary and vaginal fluid microbiota was analysed using sequencing of the rRNA gene V1-V2 regions. Vaginal fluid and urine samples were taken from women with bacterial vaginosis (BV) and analysed throughout the course of a clinical study that aimed at characterising the effect of a newly developed pessary containing an amphoteric tenside compared to a pessary containing lactic acid. Before participating women received either pessary, theywere first treated with the antibiotic metronidazole. Vaginal fluid samples were taken and analysed at five different time points thoughout the study. Urine samples were taken and analyed before and after metronidazole treatment. As healthy control groups, vaginal fluid samples were taken and analysed from healthy women and urine samples from healthy men and women.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00001700	Characterization of Arabian fermented foods microbiota and interaction with gut microbiome of ‎Bedouin population	More than 2 million of Saudi population live a nomadic life and consume specific types of local ‎fermented foods and dairy products in routine diet. Microbial communities within such fermented ‎foods are often originating from environmental sources and the bacterial species in such type of ‎foods eventually reach the gut where they can interact with intestinal microbiota of the host. This ‎interaction is significant for human health, as local fermented food microbiota is considered ‎important source of probiotics and as well as of other environemtnal microorganisms that can ‎intervene in the gut microbiome composition and homeostasis. The interaction between the ‎microbiota of gut and intake food highlight the importance to investigate the microbiological ‎quality of fermented foods. In this study, we are proposing to analyze the microbiota of locally ‎fermented foods and their impact on the gut microbiome of Bedouin population of Saudi Arabia. ‎We aim to concomitantly analyse the samples via direct observation using Gram staining, electron ‎microscopy and by extensive culturomics analysis. High throughput MALDI-TOF mass ‎spectrometry system will be used for identification of isolated species. In addition, each sample ‎will be studied by 16S rRNA amplicon targeting V6 region pyrosequencing. Comperative analysis ‎will be perfomed to identifiy the impact and specific species richness in Bedouin gut's microbiome ‎due to the consumption of local fermented foods. We propose to apply these techniques on 10 ‎stool samples from Bedouin individuals compare with 7 samples of locally fermented foods ‎commonly use by those peoples.‎	root:Engineered:Food production:Dairy products
MGYS00001698	Host Transcriptomics and gut microbiome analysis in broilers with contrasting Feed Conversion Ratio	World population leading to consequent high pressure placed on animal biotechnologists/ researcher to increase the yield of current food crops and livestock, while identifying new and alternative food sources. In today's economically fast growing world poultry industry is also feeling its pace to be increased. Identification of genes associated with fatness or leanness will help in selection of individuals with better performance and thereby results in profitable poultry farming. In addition, Whole transcriptome shotgun sequencing or RNA-seq is an efficient and reliable technology for transcriptomic analysis so as to reveal genetic architecture, to identify sequence variation, and to quantify gene expression. The ultimate aim is to identify the genes which are associated with feed conversion ratio. The biomarkers identified will be useful for selection of birds with low FCR. The host genetic responses associated with weight gain and feed conversion efficiency have also played a role in changes in the physiology and gut microbial structure of birds. Therefore, shot gun and amplicon sequencing will be carrying out of each metagenomes. The ultimate aim is to detect possible association between FCR and gut microflora. The bacteria identified could be useful for feed formulation for broiler. Successful completion of project will result in identification of novel/ unigene associated with FCR in broiler. Based on identified unique/ novel gene, selection of good feed efficient birds can be done that will result in to economic production of broilers in shorter duration and profitable meat production. Also emergent microbial strains will identified by metagenome analysis and their association with good FCR birds.	root:Host-associated:Birds:Digestive system:Fecal
MGYS00001697	Biodegradable organic carbon amendments enhance attenuation of trace organic contaminants in biochar amended stormwater biofilters	Biochar-amended infiltration systems may significantly improve urban water quality by  enhancing removal of trace organic contaminants (TOrCs) from runoff. As biochar's  sorption capacity will eventually saturate, stimulation of biological TOrC attenuation may  be beneficial. The objective of this study was to determine if biodegradable organic carbon amendments can improve TOrC attenuation in biochar-amended biofilters. It was  hypothesized that microbial growth in response to dissolved organic carbon (DOC)  availability would establish more robust and diverse microbial communities, leading to  enhanced TOrC biodegradation and sorption to biological material. This hypothesis was  evaluated in TOrC-spiked microcosm and column experiments, utilizing a representative  microbial consortium from actual runoff and DOC extracted from straw and compost.  Microcosms with compost DOC exhibited broader TOrC biodegradation potential than  microcosms with raw runoff or straw DOC. 16s rRNA gene sequencing revealed  community clustering according to DOC type, suggesting that DOC availability caused  shifts in community structure that affected TOrC biodegradation. Columns exhibited  enhanced biological TOrC attenuation in presence ofbiofilms established with compost  DOC but not straw DOC. These results reveal that biodegradable organic carbon sources  stimulate biological TOrC attenuation in biochar-amended biofilters, providing insight  into the design of stormwater biofilters for improved water quality.	root:Engineered:Wastewater:Nutrient removal:Dissolved organics (aerobic)
MGYS00001696	Enrichment of anaerobic nitrate-dependent methanotrophic Candidatus Methanoperedens nitroreducens archaea from an Italian paddy field soil	Paddy fields are a significant source of methane and contribute up to 20% of total methane emissions from wetland ecosystems. These inundated, anoxic soils featuring abundant nitrogen compounds and methane are an ideal niche for nitrate-dependent anaerobic methanotrophs. After 2 years of enrichment with a continuous supply of methane and nitrate as the sole electron donor and acceptor, a stable enrichment dominated by 'Candidatus Methanoperedens nitroreducens' archaea and 'Candidatus Methylomirabilis oxyfera' NC10 phylum bacteria was achieved. The results of qPCR quantification of 16S rRNA gene copies, analysis of metagenomic 16S rRNA reads,and fluorescence in situ hybridization (FISH) correlated well and showed that, after two years, 'Candidatus Methanoperedens nitroreducens' had the highest (2.2±0.4*108) 16S rRNA copies per mL and constituted approximately 22% of the total microbial community.Metagenomic sequencing by Ion Torrent Technology was carried out after one and two years of enrichment. Phylogenetic analysis showed that the 16S rRNA genes of the dominant microorganisms clustered with previously described 'Candidatus Methanoperedens nitroreducens ANME2D' (96% identity) and 'Candidatus Methylomirabilis oxyfera' (99% identity) strains. The pooled metagenomic sequences resulted in a high-quality draft genome assembly of 'Candidatus Methanoperedens nitroreducens Vercelli' that contained all key functional genes for the reverse methanogenesis pathway and nitrate reduction. The diagnostic mcrA gene was 96% similar to 'Candidatus Methanoperedens nitroreducens ANME2D' (WP_048089615.1) at the protein level.The 'Candidatus Methylomirabilis oxyfera' draft genome contained the marker genes pmoCAB, mdh, and nirS and putative NO dismutase genes. Whole-reactor anaerobic activity measurements with methane and nitrate revealed an average methane oxidation rate of 0.012 mmol h-1 L-1, with cell-specific methane oxidation rates up to 0.57 fmol cell-1 day-1 for 'Candidatus Methanoperedens nitroreducens'. In summary, this study describes the first enrichment and draft genome of methanotrophic archaea from paddy field soil, where these organisms can contribute significantly to the mitigation of methane emissions.	root:Environmental:Aquatic:Freshwater:Wetlands
MGYS00001695	Metagenomic analysis of the upper bronchial tract microbiome in patients with chronic obstructive pulmonary disease and 'healthy' smoker controls	Chronic Obstructive Pulmonary Disease (COPD) may worsen with microbial changes in the respiratory tract but studies into taxonomic structure of the COPD lung microbiome have yielded equivocal results. This may reflect the poor resolving power of taxonomic classification when only based 16S rRNA amplicon sequencing. We here report the metagenomic characterisation of COPD microbiome to more accurately reveal its species-level structure and functional capacity. The bacterial metagenomes within sputum samples from eight COPD patients and ten ?healthy? smokers (Controls) were sequenced and suggested increases in the abundance of bacterial species, particularly within Streptococcus in COPD. The functional capacity of the COPD lung microbiome indicated an increased capacity for bacterial growth, which could be an important feature in bacterial-associated acute exacerbations. Regression analyses correlated COPD severity (FEV1 % of predicted) with differences in the abundance of Streptococcus pneumonia and functional classifications related to a reduced capacity for bacterial sialic acid metabolism. Neither of these lung microbiome characteristics correlated with patient age or smoking pack history, further suggesting an association with COPD pathology. This study suggests that the COPD lung microbiome could be used in patient risk stratification and in identifying novel monitoring and treatment methods.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00001694	Prokaryotic responses to ammonium and organic carbon reveal alternative CO2 fixation pathways and importance of alkaline phosphatase in the mesopelagic North Atlantic	To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryoticabundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, communitycomposition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments withwater from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organicmatter (i.e. pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organicmatter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DICfixation rates —assumed to be related to autotrophic metabolisms— were equally stimulated as all the other heterotrophic-relatedparameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation viaanaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be relatedto cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balanceduring catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into themesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic andautotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudiedmicrobial processes of potential importance in mesopelagic waters that require future attention.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00001693	Hot stream metagenomic analysis	The examination of microbial diversity and distribution is one of the key concern in environmental microbiology. Identification of the microorganism exist in a particular environment is critical for understanding the function of organisms in that environment and the processes influencing the diversity of those organisms.  The hot springs are one of the most unique and diverse geothermal ecosystems on Earth, that host a collection of deeply-rooted and under studied prokaryotes. The combination of stringent chemical condition and extreme temperature encountered in geothermal system offers a vital opportunity for studying the diversity and function of indigenous microbiota. The unique microbial ecosystems of the hot springs from Saudi Arabia have never been studied in detail before. The purpose of this project is to examine the chemical and metabolic profile and to identify the bacterial and archaeal communities of the hot springs located at the southwestern region of the Saudi Arabia. This study will be conducted at five terrestrial hot springs for a period of two years. Culture-dependent and culture-independent metagenomic microbiological techniques will be used to investigate the microbial community composition and metabolic properties of the hot-springs microbial ecosystem.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00001692	Bioelectrochemical phenol degradation	The use of bielectrochemical technologies for the remediation of hydrocarbon contaminated environments is gaining interest as an innovative approach for the stimulation of the microbial metabolism in anaerobic conditions. A lab-scale bieoelectrochemical reactor for groundwater treatment was operated under continuous flow conditions with phenol (25 mg/L) as a model contaminant. When the anode was poised at +200 mV (vs SHE) phenol was removed with a rate of 77±4 mg/(L d) and a current of 5.3±0.2 mA was produced. At the end of the experiment the bacterial and archaeal communities in the microbial inoculum (i.e. refinery wastewater), on the anode (i.e. graphite granules) and in the effluent were characterized by Next Generation Sequencing (NGS) of the 16S rRNA gene. NGS results showed the enrichment of the genus Geobacter on the graphite, suggesting its potential role in the bioelectrochemical removal of phenol.	root:Engineered:Bioreactor:Continuous culture
MGYS00001691	Temporal dynamics and diversity of Legionella community in cooling tower water	The persistence and abundance of Legionella species in man-made freshwater systems constitutes a public health concern. Cooling towers are the main source of legionellosis outbreaks. These outbreaks are mostly associated with L. pneumophila and its monitoring in freshwater environments is of high relevance. In this study, a developed Legionella genus-specific Illumina-based approach targeting the 16S rRNA gene was applied to a set of cooling tower water samples monthly sampled from January 2013 to December 2014 in order to provide accurate identification and precise detection and quantification of Legionella species, including the most clinically relevant L. pneumophila	root:Environmental:Aquatic
MGYS00001690	By taking three metagenomic approaches to reveal the microplankton communities from composition to functional properties in this study.	The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function.	root:Environmental:Aquatic:Freshwater:Lentic
MGYS00001689	BACTERIAL DIVERSITY AND SULFIDE REMOVAL IN AN INTERNAL SILICON MEMBRANE REACTOR	The objective of this study was to assess the feasibility of using an Internal Silicon Membrane Reactor (ISMR) to treat dissolved sulfide and to characterize its microbial community. The Internal Silicon Membrane Reactor (ISMR) has shown to be an effective system to eliminate sulfide produced in anaerobic reactors. Removal efficiencies of sulfide reached 96% in a combined anaerobic/micro-aerobic reactor and significant sulfate production did not occur. The oxygen transfer was strongly influenced by air pressure and flow. Pirosequencing analysis indicated different sulfide-oxidizing bacteria attached on to the membrane. The results also indicates a high similarity between the biomass deposited in the membrane wall and the biomass drawn from of the material support, that demonstrate the development of sulfide oxidizing bacteria in an anaerobic sludge under micro aerobic condition.	root:Engineered:Bioremediation:Persistent organic pollutants (POP)
MGYS00001688	Set Anode Potentials Affect the Electron Fluxes and Microbial Community Structure in Propionate-Fed Microbial Electrolysis Cells	The anode potentials in microbial electrolysis cells (MECs) influence the energy availability for the microbial growth, the microbial community structure and also the reactor performance. However, the stimulus of set anode potentials (SAPs) on the performances of MECs fed with a high concentration of propionate have not been demonstrated. Here, we examined the impact of various SAPs (-0.25, 0, and 0.25 V vs. SHE) on the reactors performance, electrons flux to various sinks, and the microbial community structure in a double chamber MECs fed with propionate (36mM). Electron balances and microbial fingerprinting showed that SAPs modulate the electron fluxes between the electrical current and CH4 and also affected the microbial community structure of a propionate fed MECs. Electrical current (49-71%) and CH4 (22.9-41%) was the largest electron sinks regardless of the potentials tested. However, 0 V indicated that higher electron fluxes to the electrical current (71±5%) and lower fraction to CH4 (22.9±1.2%). In contrast, more negative SAP (-0.25 V) had a lower percentage of the electrical current and there was a greater fraction of electron loss to CH4 (41.1±2%). Furthermore, open circuit (O.C) reactors had significantly higher CH4 (73±4%) than the SAP-MECs. A complete degradation of propionate (36mM) with no accumulation of it intermediates was observed in all the tested SAPs. Analysis of 16S r RNA gene indicated that more negative SAP (-0.25 V) showed a highly diverse communities the other potentials tested. Interestingly, in all the anode of SAPs dominated by G. sulfurreducens followed by Smithella spp. and Syntrophobacter sulfatereducens. While, the suspensions were predominated by the classic propionate fermenters namely S. sulfatereducens, Smithella spp. and Methanobacterium formicicum. Overall, these results provide new insights on the influence of SAPs of MECs fed with a high concentration of propionate.	root:Engineered:Bioreactor:Continuous culture
MGYS00001687	Daily cycle of bacterial active community structure	Microbial communities at high altitude ecosystem spring sites, are subjected along the day to extreme changes in irradiation and temperature. Herein, we determined the composition of actively transcribing bacteria from spring waters through 16S rRNA gene tag pyrosequencing (cDNA) experimentally exposed along the day (morning, noon and afternoon) to variable solar radiation and light quality, and evaluated their influence on nutrients recycling. Irradiation, temperature and nutrients rates of change were associated with changes in the active bacterial community structure, predominantly conformed by Cyanobacteria, Verrucomicrobia, Proteobacteria, and other 35 Phyla including also the recently described Candidate Phyla Radiation (e.g., Parcubacteria, Gracilibacteria, OP3, TM6, SR1). An increase of diversity was observed at noon when the highest irradiances were measured (3.3 -3.9 H', 1125 W m-2) compared to morning and afternoon (0.6-2.8 H'). These increase was associated with a decrease of Cyanobacteria and an enhancement of Proteobacteria and initially low frequently and rare bacteria phyla (<0.5% sequences contribution). UV radiation compared to full sun radiation indicates the presence of a higher number of stimulatory compared to inhibitory effects, including contrasting responses of some Orders, e.g., positive effects were found for Cyanobacteria, Rhodobacterales, Rhodospirillales, Bacteroidales; whereas negative effects for the orders Oceanospirillales, Fibrobacterales, Alteromonadales and Sphingobacteriales. Nutrient recycling was influenced by microbial composition changes, particularly for Cyanobacteria, nitrifying bacteria and Chlorobi. In total, our results indicate that phototrophic bacteria from high altitude aquatic ecosystems were affected but potentially resilient to the negative effect of high solar radiation influencing nutrient recycling in these ecosystems.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001686	Molecular diversity patterns among various phytoplankton size-fractions in West Greenland in late summer	Arctic regions to date experience the most pronounced transformations due to global change. Current hypotheses propose an elevated impact of those environmental changes on the biodiversity, community composition and metabolic processes of species. Influence on ecosystem function and services, particular when invasive or toxigenic harmful species become dominant, can alter processes on smaller and larger scales. Our study focused on the comparison of molecular biodiversity of three planktonic size-fractions (micro-, nano-, picoplankton) in coastal waters of West Greenland and the correlation with environmental parameters. Molecular diversity was assessed via sequencing the 28S rRNA hypervariable D1/D2 region by parallel amplicon sequencing. We showed that biodiversity distribution within the area of Uummannaq Fjord, Vaigat Strait and Disko Bay differed markedly within and among size-fractions. In general, we observed a higher diversity within the picoplankton size fraction compared to the nano- and microplankton. Community composition of all three size fractions correlated to size, silicate and phosphate, chlorophyll a (chl a) and dinophysistoxin (DTX), but each size fraction community also correlated with other and different environmental parameters. We observed a more homogeneous community of the picoplankton across all stations compared to the bigger size classes, despite different environmental conditions of the sampling areas. This might suggest habitat occupation for larger organisms over plasticity, while smaller organisms compensate a lower potential plasticity with higher diversity. The presence of potential harmful algal bloom (HAB) species (such as Alexandrium fundyense, A. ostenfeldii) in the area points out the risk for this vulnerable ecosystem in a changing world.	root:Environmental:Aquatic:Marine:Coastal
MGYS00001685	Microbialite and microbial mats systems in lagoons, salt flats and Volcanoes of Andean South America Altiplane	High Andean Mountain lakes are a unique extreme environment all over the world since their locations are in high altitude saline deserts, largely influenced by volcanic activity. UV radiation, arsenic content, high salinity, and low dissolved oxygen content, together with extreme daily temperature fluctuations and oligotrophic conditions, shape up an environment that recreates the early earth and, even more, the extraterrestrial conditions. The discovery of living microbialites and microbial mats in 2009 has increased the interest in this area as an early earth counterpart. Since then, and up to now, we have started a prospection for this kind of environments in Argentina, Chile and Bolivia. In this study, we report our metagenomic WGS results from several of these unique environments	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Saline:Microbial mats
MGYS00001682	Comparison between metagenome sequencing using 16S spiking or MDA amplification	Bioinformatical research on viruses is still limited because of the low amounts of viral DNA that can be obtained for analysis. To overcome this limitation, DNA is often amplified with multiple displacement amplification (MDA), which causes an unavoidable bias. Here, we describe a DNA-spiking method to avoid the bias that is created when using amplification of DNA before metagenome sequencing. To obtain sufficient DNA for sequencing, a bacterial 16S rRNA gene was amplified and the obtained DNA was spiked to a DNA sample containing DNA from a bacteriophage population before sequencing using Ion Torrent technology. After sequencing, the 16S rRNA gene reads DNA was removed by mapping to the Silva database. The new DNA-spiking method was compared with the MDA technique.The new method provides a simple and inexpensive protocol with very low bias in sequencing of metagenomes for which low amounts of DNA are available.	root:Engineered:Modeled:Simulated communities (DNA mixture)
MGYS00001679	Genetic determinants of the gut microbiome in the TwinsUK cohort	Recent genetic studies in mice and humans have revealed intriguing genetic associations with the gut microbiome. Here we report a 16S rRNA-based analysis of the gut microbiome in 1,126 twin pairs, a subset of which we previously analyzed. Tripling the sample reduced the confidence intervals around heritability estimates and uncovered newly heritable taxa, many of which are validated in other studies. Repeat sampling of subjects showed heritable taxa to be temporally stable. A candidate gene approach uncovered associations between heritable taxa and genes related to diet, metabolism and olfaction. We replicate an association between Bifidobacterium and the lactase (LCT) gene region and identify an association between ALDH1L1 and SHA-98, suggesting a link between formate production and blood pressure. Additional genes detected are involved in barrier defense and self/non-self recognition. Our results indicate that diet sensing, metabolism, and immune defense are important drivers of human-microbiome co-evolution.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001677	Bacterial Communiy Structures are Unique and Resilient in Full-Scale Bioenergy Systems	Anaerobic digestion is the most successful bioenergy technology worldwide with, at its core, undefined microbial communities that have poorly understood dynamics. Here, we investigated the relationships of bacterial community structure (>400,000 16S rRNA gene sequences for 112 samples) with function (i.e., bioreactor performance) and environment (i.e., operating conditions) in a yearlong monthly time series of nine full-scale bioreactor facilities treating brewery wastewater (>20,000 measurements). Each of the nine facilities had a unique community structure with an unprecedented level of stability. Using machine learning, we identified a small subset of operational taxonomic units (OTUs; 145 out of 4,962), which predicted the location of the facility of origin for almost every sample (96.4% accuracy). Of these 145 OTUs, syntrophic bacteria were systematically overrepresented, demonstrating that syntrophs rebounded following disturbances. This indicates that resilience, rather than dynamic competition, played an important role in maintaining the necessary syntrophic populations. In addition, we explained the observed phylogenetic differences between all samples based on a subset of environmental gradients (using constrained ordination), and found stronger relationships between community structure and its function rather than its environment. These relationships were strongest for two performance variables - methanogenic activity and substrate removal efficiency - both of which were also affected by microbial ecology because these variables were correlated with community evenness (at any given time) and variability in phylogenetic structure (over time), respectively. Thus, we quantified relationships between community structure and function, which opens the door to engineer communities with superior functions.	root:Engineered:Bioreactor:Continuous culture
MGYS00001674	Detection and quantification of Pseudomonas species, including P. aeruginosa, in cooling tower water using a genus-specific Illumina-based approach	Pseudomonas species are frequent inhabitants of freshwater environments and often colonisers of water supply networks via bioadhesion and biofilm formation. P. aeruginosa is the most characterized species of the genus and the most commonly associated to human disease, causing a wide variety of infections that have causality links with their presence in freshwater systems. Though several other Pseudomonas species are of ecological and health importance, little knowledge regarding environmental Pseudomonas species still exists. In the present study, an Illumina-based approach using Pseudomonas genus-specific primers and targeting the 16S rRNA gene was validated and applied to a set of freshwater samples, collected from a cooling tower system during two years.	root:Environmental:Aquatic:Freshwater
MGYS00001673	Bacterial community characterisation and pathogen profiling in a cooling tower system using an Illumina-based approach	The increasing level of human exposure to freshwater systems requires effective water quality monitoring and surveillance to reduce health risks linked to contaminated environments with pathogenic waterborne and water-based bacteria. Despite the considerable advantages of sequence-based molecular techniques, the usefulness and potential for implementation of next-generation sequencing in environmental research and routine environmental diagnostics has not be thoroughly evaluated and assessed. In this study, a Illumina MiSeq-based approach, targeting the 16S rRNA gene V4-V5 regions was applied to cooling tower water samples monthly collected from January 2013 to December 2014, in order to characterise the temporal dynamics and structure of the bacterial community as well as to detect the main potentially pathogenic bacterial genera.	root:Environmental:Aquatic:Freshwater
MGYS00001671	Bacterial Diversity of Activated Sludge from 14 Sewage Treatment Plants Revealed by 454 Pyrosequencing	Massively parallel 454 sequencing of hypervariable regions in rRNA genes was used to profile microbial communities from 15 activated sludge samples of 14 wastewater treatment plants (WWTP) from 4 countries.  Totally, 355641 effective reads were generated from these 15 samples. These reads were assigned into different taxonomies by using RDP classifier. Besides, Cluster analysis, PCA, colinearity analysis was also used to assess the beta-diversity among all these sludge samples.	root:Engineered:Wastewater:Activated Sludge
MGYS00001670	metagenome of the anaerobic digested sludge before and after long-term oxytetracycline exposure	Metagenome of the anaerobic digested sludge before and after long-term oxytetracycline exposure was revealed by high throughput illumina sequenceing. And, the mobilome of the anaerobic digested sludge before antibiotic exposure was compared with that after exposure.	root:Engineered:Wastewater:Water and sludge
MGYS00001669	Biogeography of bacterioplankton communities in freshwater boreal ecosystems	Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Illumina sequencing of the 16S rRNA gene, we investigate the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Qu?bec. We show that both hydrology and local water chemistry (mostly pH) interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams towards larger rivers and lakes dominated by fewer taxa. Increases in water residence time along the hydrologic continuum were accompanied by major losses of bacterial richness and by an increased differentiation of communities driven by local conditions (pH and other related variables). This suggests that hydrology and network position modulate the relative role of environmental sorting and mass effects on community assembly by determining both the time frame for bacterial growth and the composition of the immigrant pool. The apparent low dispersal limitation (i.e., the lack of influence of geographic distance on the spatial patterns observed at the taxonomic resolution used) suggests that these boreal bacterioplankton communities derive from a shared bacterial pool that enters the networks through the smallest streams, largely dominated by mass effects, and that is increasingly subjected to local sorting of species during transit along the hydrologic continuum.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001668	metagenome of thermophilic anaerobic sludge before and after antibiotic exposure	metagenome of thermophilic anaerobic digested sludge before and after oxytetracycline exposure was sequenced using Illumina Hiseq. And, the mobilomes of both sludge were analyzed.	root:Engineered:Wastewater:Water and sludge
MGYS00001667	Performance and microbial community composition in a long-term operated sequential anaerobic-aerobic bioreactors treating coking wastewater	The anaerobic and aerobic combined biosystem is assumed to consume less energy for the treatment of high strength industrial wastewater. In this study, the pollutant removal performance and microbial diversity were revealed in a long run (over 300 days) bench scale sequential anaerobic-aerobic biosystem treating coking wastewater. Anaerobic treatment could remove one third of COD and more than half of phenols at a hydraulic retention time of 42 hours, while the combined system with a total HRT of 114 hours removed COD, TOC, total phenols, thiocyanate and cyanide by 81.6?3.3%, 85.2?4.2%, 99.9?0.02%, 98.2?0.3, 87.2?3.9% respectively. Comprehensive two dimensional gas chromatography with time-of-flight mass spectrometric analysis revealed almost complete removal of phenol derivatives and nitrogenous heterocyclic compounds (NHCs) by the combination in which anaerobic process alone contributed in average 58.4% and 59.1% removal, respectively. In order to appraise microbial activity in bioreactors, the bacterial, archaeal and fungal communities were analyzed by 454 pyrosequencing. Proteobacteria (relative abundance 61.2 - 93.4%), particularly Betaproteobacteria (34.4-70.1%) were the most predominant bacterial group. Phenol degrading and hydrolytic bacteria like Ottowia (14.1-46.7%), Soehngenia (3.0-8.2%) and Corynebacterium (0.9-12.0%) were most abundant genera in anaerobic sludge, whereas in aerobic sludge Thiobacillus (6.6- 43.6%), Diaphorobacter (5.1-13.1%) and Comamonas (0.2-11.1%)were speculated as major degraders of phenol, thiocyanate and NHCs, respectively. Despite of low density of fungi, oleaginous yeast Trichosporon which degrades phenolic compounds was found abundant in aerobic sludge. The results revealed that the removal of pollutants was related with phylogenetic abundance of microbial diversity. This study revealed the feasibility of less energy intensive optimization for the removal of organic pollutants from coking wastewater, and the potential association between some important bacterial groups and key pollutants.	root:Engineered:Wastewater:Industrial wastewater
MGYS00001666	High habitat-specificity in fungal communities of an oligo-mesotrophic, temperate lake	Freshwater fungi are a poorly studied paraphyletic group that include a high diversity of phyla. Most studies of aquatic fungal diversity have focussed on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in meso-oligotrophic, temperate Lake Stechlin in northern Germany, including the pelagic and littoral water column, sediments, and biotic substrates. We pyrosequenced a universal eukaryotic marker within the ribosomal large subunit (LSU) in order to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1024 fungal OTUs (97% criterion). Diversity was highest in the sediment, biofilms, and benthic samples (293-428 OTUs), intermediate in water and reed samples (36-64 OTUs), and lowest in plankton (8 OTUs) samples. NMDS clustering clearly grouped the eight studied habitats into six clusters, indicating that total diversity was strongly influenced by turnover among habitats. Fungal communities exhibited pronounced changes at the levels of phylum and order along a gradient from littoral to pelagic habitats. The large majority of OTUs could not be classified below the order level due to the lack of aquatic fungal entries in taxonomic databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat-specificity to total fungal diversity. This remarkable diversity is probably an underestimate, because most lakes undergo seasonal changes and previous studies have uncovered differences in fungal communities among lakes.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001665	Metatranscriptomes from Blanes Bay, Barcelona, mesocosm experiments	Water from Blanes Bay was incubated for nine days in mesocosms. The water was treated with nutrients (NO3, PO4, SiO4; NA and NB samples) and acidified using CO2 (KA and KB samples). RNA after stable RNA depletion and poly-T depletion was Illumina sequenced.	root:Environmental:Aquatic:Marine:Intertidal zone
MGYS00001664	Ammonia oxidizing microorganisms are an important source of nitrous oxide (N2O) in aquatic environments	Ammonia oxidizing microorganisms are an important source of nitrous oxide (N2O) in aquatic environments, , but the impact that acidification has on the rate and mechanism of N2O production by these organisms is not well understood. Here we present evidence from 15N-tracer incubations that acidification (from pH 7.54 to 7.20) significantly enhances N2O production by the ammonia oxidizer community in the shallow hypolimnion (17 m) of Lake Lugano in southern Switzerland. This community is dominated by the ammonia oxidizing bacteria of the genus Nitrosospira. Although ammonia oxidation rates were not significantly different among the pH treatments, the pH reduction did enhance the yield, or the ratio of N2O relative to NOx- (nitrite + nitrate) produced by ammonia oxidizers, from 2.6 × 10-5 to 8.8 × 10-5 mol N-N2O/mol N-NOx- at an O2 concentration of 290 μM, and from 5.7 × 10-5 to 12.1 × 10-5 mol N-N2O/mol N-NOx- at an O2 concentration of 70 μM. The increases were due at least in part to enhanced incorporation of N derived from exogenous NO2- into N2O. Incorporation of N from this exogenous NO2- is consistent with hybrid N2O formation, where the N2O produced contains one ammonia- (NH3-) derived N atom and one nitrite- (NO2-) derived N atom but it is not consistent with nitrifier denitrification (enzymatic reduction of 2 NO2- to N2O). In all incubations, most of the N incorporated into N2O appears to have been derived from NH3 rather than exogenous NO2-. We also present evidence of hybrid N2O formation during similar incubations of seawater (at its unaltered pH) from 200 m depth off the coast of Namibia, a coastal upwelling zone and known hotspot of N2O production whose ammonia oxidizer community is dominated by archaea.	root:Environmental:Aquatic
MGYS00001663	Acidification and warming affect prominent bacteria during two seasonal phytoplankton bloom mesocosms	In contrast to clear stimulatory effects of rising temperature, recent studies reported conflicting results of CO2 effects on planktonic bacteria. To obtain a better understanding of the impact of future climate scenarios on the development of bacterial communities, we performed bifactorial mesocosm experiments (pCO2 and temperature) with Baltic Sea water, during a diatom bloom in autumn and during a summer bloom. The development of bacterial community composition BCC followed well-known bloom dynamics with Alphaproteobacteria dominating during the bloom peak and Bacteroidetes dominating during bloom decay. A principle coordinate analysis (PCoA) of bacterial OTUs (operational taxonomic units) revealed that phytoplankton succession and temperature were the major bacterial community structuring variables whereas only a weak impact of pCO2 was found. This was corroborated by the trends in bacterial bulk parameters. However, significant and potentially direct effects of pCO2 on the relative abundance of several dominant OTUs occurred and were in some cases accompanied by an antagonistic temperature effect. Our results suggest the necessity of high-resolution BCC analyses and statistical analyses on OTU level to observe strong effects of CO2 on specific bacterial groups, which in turn might influence also particular organic matter degradation processes.	root:Environmental:Aquatic:Marine
MGYS00001660	Four metagenomes and four metatranscriptomes sampled along a transect in the plume of the Sarno River in the Gulf of Naples (Italy).	The study aimed to investigate closely related samples under the influence from the Sarno River, the most polluted river in Europe, to inform about differences within the taxonomical and functional diversity along a transect from the rivers mouth to the open Gulf of Naples.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001659	Fecal microbiome transplantation between chow-fed and high fat diet-fed rats	Obesity, insulin resistance and the metabolic syndrome are associated with changes to the gut microbiota; however, the mechanism by which modifications to the gut microbiota might lead to these conditions is unknown. Here we show that increased production of acetate by an altered gut microbiota leads to activation of the parasympathetic nervous system which in turn promotes increased glucose-stimulated insulin secretion (GSIS), increased ghrelin secretion, hyperphagia, obesity and its related sequelae. Taken together, these data identify increased acetate production by a nutrient-gut microbiota interaction and subsequent parasympathetic activation as possible therapeutic targets for obesity.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001657	Minimum Effective Concentration of Streptomycin in Inducing Antibiotic Resistance	It has been demonstrated that antibioticresistancecould be selected for and enrichedunder high antibiotic concentrations in biological wastewater treatment systems. However, limit knowledge is known about the antibiotic concentrations in influents that exert selection for antibiotic resistance in biological wastewater treatment systems.Herein, this study investigated the long-term effects of different streptomycin concentrations on selection of antibiotic resistance in an aerobic biofilm reactor treating simulated antibiotic production wastewater(606 days)by using multiple culture-independent andculture-dependent methods. qPCR, high-throughput quantitative PCR and metagenomic sequencing were used to detected ARGs and MGEs.Although the efficient COD removal from 88.52% to 92.83%was observed across all six stages (streptomycin: 0, 0.1, 1, 5, 25, 50 mg/L), increasing streptomycin concentration caused proliferation of ARB, ARGs and MGEs.And the Minimum effectiveconcentration of streptomycin causing a significant increase of relative abundance of ARGs and MGEs was at the levels ranging from 1 to 5 mg•L-1. This work proposed an experimental significant effect concentration which can guide implementation of antibiotic emission limits into biological treatment systems.	root:Engineered:Wastewater:Water and sludge
MGYS00001655	Changes of resistome, mobilome and potential hosts of antibiotic resistance genes during the transformation of anaerobic digestion from mesophilic to thermophilic	This study aimed to reveal how antibiotic resistance genes (ARGs) and their horizontal and vertical transfer-related items (mobilome and bacterial hosts) respond to the transformation of anaerobic digestion (AD) from mesophilic to thermophilic using the strategy of one-step temperature increase. The resistomes and mobilomes of mesophilic and thermophilic sludge were investigated using metagenome sequencing, and the changes in twenty-four representative ARGs belonging to three categories, class 1 integron and bacterial genera during the transition period were further followed using qPCR and 454-pyrosequencing. After temperature increase, the abundance of the resistome of digested sludge decreased from 125.97 ppm (day 0, mesophilic) to 50.65 ppm (day 57, thermophilic) with the reduction of most ARG types except for the aminoglycoside resistance genes. Thermophilic sludge also had a smaller mobilome, including plasmids, insertion sequences and integrons, than that of mesophilic sludge, suggesting the lower horizontal transfer potential of ARGs under the thermophilic condition. On the other hand, the total abundance of 18 bacterial genera, which were suggested as the possible hosts for 13 ARGs through network analysis, was decreased from 23.27% in mesophilic sludge to 11.92% in thermophilic sludge, indicating less hosts for the vertical expansion of ARGs after the hike of temperature. The results highlighted that the better reduction of resistome abundance by thermophilic AD might be associated with the decrease of both the horizontal and vertical transferabilities of ARGs.	root:Engineered:Wastewater:Water and sludge
MGYS00001654	A metaproteomic analysis of the response of a freshwater microbial community under nutrient enrichment	Eutrophication can lead to an uncontrollable increase in algal biomass, which has repercussions for the entire microbial and pelagic community. Studies have shown how nutrient enrichment affects microbial species succession, however details regarding the impact on community functionality are rare. Here, we applied a metaproteomic approach to investigate the functional changes to algal and bacterial communities, over time, in oligotrophic and eutrophic conditions, in freshwater microcosms. Samples were taken early during algal and cyanobacterial dominance and later under bacterial dominance. 1048 proteins, from the two treatments and two timepoints, were identified and quantified by their exponentially modified protein abundance index. In oligotrophic conditions, Bacteroidetes express extracellular hydrolases and Ton-B dependent receptors to degrade and transport high molecular weight compounds captured while attached to the phycosphere. Alpha- and Beta-proteobacteria were found to capture different substrates from algal exudate (carbohydrates and amino acids, respectively) suggesting resource partitioning to avoid direct competition. In eutrophic conditions, environmental adaptation proteins from cyanobacteria suggested better resilience compared to algae in a low carbon nutrient enriched environment. This study provides insight into differences in functional microbial processes between oligo- and eutrophic conditions at different timepoints and highlights how primary producers control bacterial resources in freshwater environments	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001653	anaerobic digestion	anaerobic digestion	root:Engineered:Wastewater:Water and sludge
MGYS00001652	Organic micropollutants in aerobic and anaerobic membrane bioreactors (MBR): changes in microbial communities and gene expression	The effect of organic micro-pollutants (OMPs) in wastewater on the microbial populations essential to the aerobic activated sludge and anaerobic digestion processes is not well understood. The purpose of this study was to examine the effect of OMPs on microbial population dynamics associated with both aerobic and anaerobic wastewater treatment. It was also desired to determine what OMPs show better biodegradability in aerobic compared to anaerobic membrane bioreactor (MBR) systems while monitoring biodegradation-related and antibiotic resistance-related gene expression levels in both reactors. To achieve this, two MBR systems (aerobic and anaerobic) were operated under the same conditions, treating wastewater spiked with a cocktail of 27 OMPs. Next-generation sequencing platforms were used to monitor changes in the microbial populations in the MBRs and their gene expression levels. Results show that spiking of OMPs in the wastewater feed had a clear effect on predominant and keystone bacterial populations in both MBRs while also significantly impacting gene expression levels associated with biodegradation. Finally, multiple antibiotic-type OMPs were found to have higher removal rates in the anaerobic MBR, while also ultimately impacting the presence of associated antibiotic resistance genes in both systems.	root:Engineered:Wastewater:Water and sludge
MGYS00001651	Metagenomic analysis of microbes attached to fuel cell electrodes	Whole genome shotgun metagenomics of microbes attached to closed circuit and open circuit fuel cells.	root:Engineered
MGYS00001650	Alterations of the Fecal Microbiome in Parkinson's Disease	In the course of Parkinson's disease (PD), the enteric nervous system is probably the first structure being affected by alpha-synuclein pathology. Recent research has shown that there is an intense bidirectional interaction between gut microbiota and the brain via diverse pathways. We speculated that intestinal microbiota may be implicated in PD. We compared the fecal microbiomes of 72 PD patients and 72 control subjects by pyrosequencing the bacterial 16S rRNA gene.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001649	Influence of carbon sources and concrete on microbially induced corrosion of carbon steel in subterranean groundwater environment	Microbially induced corrosion of carbon steel was assessed in environment simulating deep geological repository of radioactive waste. A dense and diverse biofilm was formed on surfaces of steel in biotic systems without concrete. Addition of nutrients changed the bacterial communities forming biofilm, increased corrosion rate and changed the properties of corrosion products i.e. composition and resistance. Presence of concrete altered the corrosion behaviour of steel and hindered the biofilm formation on steel. The corrosion rate was consistently radically decreased, as the properties of the corrosion product, were different from those in the other systems.	root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
MGYS00001646	Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing DS10	High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and alpha-diversity assessment for microbial communities. We demonstrate that high-quality read length and abundance are the primary factors differentiating correct from erroneous reads produced by Illumina GAIIx, HiSeq and MiSeq instruments. We present guidelines for user-defined quality-filtering strategies, enabling efficient extraction of high-quality data and facilitating interpretation of Illumina sequencing results.	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00001645	Microbial biogeography of grapes predicts regional metabolite patterns in wine	Microbial activity is an inherent feature of wine production. The microbial communities of grapes present regionally defined patterns, influenced by vineyard and climatic conditions. However, the degree to which these microbial patterns associate with the chemico-sensory qualities of wine is unclear. We demonstrate that both grape microbiota and wine metabolite profiles distinguish growing sub-regions and individual vineyards within Napa and Sonoma County, California. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate closely with the chemical composition of the finished wines. Grape must microbiota serve as highly accurate biomarkers for predicting metabolite abundance in finished wines using machine-learning models. The use of pre-harvest microbiota as an early predictor of wine qualities is unprecedented and poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is a definable feature that quantitatively contributes to wine terroir.	root:Host-associated:Plants
MGYS00001643	Thermophilic two-phase anaerobic digestion using innovative fixed-bed reactor for enhanced organic matter removal and bioenergy recovery from sugarcane vinasse	Thermophilic two-phase anaerobic digestion using innovative fixed-bed reactor for enhanced organic matter removal and bioenergy recovery from sugarcane vinasse	root:Engineered:Biotransformation:Mixed alcohol bioreactor
MGYS00001642	Nitrification at different salinities: biofilm community composition and physiological plasticity	The submitted dataset consists of pyrosequenced barcoded v4 16S rDNA amplicons representing bacterial communities in nitrifying moving bed bioreactors operated at different salinities; freshwater, brackish (20 ‰) and seawater. The microbial communities from the biofilm carriers were profiled using 454-pyrosequencing of 16S rRNA gene amplicons. The nitrifying fraction of the communities were identified and compared between the reactors operated at distinct salinities.	root:Engineered:Bioreactor
MGYS00001641	Inhibition factors in biofilm N removal systems treating wastes generated by amine based CO2 capture	The submitted dataset consists of pyrosequenced barcoded v4 16S rDNA amplicons representing bacterial communities associated with bioreactors for biological nitrogen removal for treating wastes generated by amine based CO2 capture. In order to identify limiting factors for successful up-scaling, we compared the nitrifying activity of moving bed biofilm reactors (MBBR) with or without chronic exposure to organic loading in the form of acetate. Three moving bed biofilm reactors (MBBR) were operated for 48 days in continuous mode. Reactor 1 was run as a control to confirm process stability, while chronic exposure to organic loading was tested in duplicate (Reactor 2 and 3) in order to verify reproducibility. To study inhibition and the effect on the relative abundance of nitrifying bacteria within the nitrifying biofilm over time, the bacterial communities were characterized by pyrosequencing of 16S rDNA amplicons. The sequence data were used for determining the relative abundance of ammonia and nitrite oxidizing bacteria.	root:Engineered:Bioreactor:Continuous culture
MGYS00001640	Role of salt and storage packaging conditions defining the spoilage microbial diversity of raw pork sausages	Both salt concentration and packaging type can modify the nature and the dynamic of microbial ecosystems in meat products. The purpose of this work was to investigate the influence of these two parameters on the bacterial communities of raw pork sausages using a metagenomic approach and to correlate these data with sensory analysis.  Two concentrations of sodium chloride were tested: normal content (2 % w/w) vs. a 25 % reduction (1.5 % w/w) and for each, packaging was either vacuum or modified atmosphere (N2%-CO2%). Sausages were stored at 8 °C during 21 days until their use-by date. Spoilage assessment was performed by sensory and physicochemical analyses. To characterize the bacterial diversity, the 16S rDNA of five replicates per condition tested was amplified for pyrosequencing at a scale of 15,000 reads per library. Reads were then clustered into Operational Taxonomic Units (OTU).  Spoilage was characterized by an important greying of the products and a production of gas and off-odours defined as rancid, sulphurous and sour. It was more pronounced for samples under modified atmosphere and easier to be ascertained with the lowest salt content. The 20 samples taken altogether,provided 387,111 bacterial 16S rRNA sequences which were analyzed and binned into 78 OTUs (97% threshold).. Packaging atmosphere influenced the average bacterial richness with 69 OTUs (+/-?) identified in vacuum-packed meat and a lower diversity of 46 OTUs (+/-?)in modified atmosphere-packed meat. The richness was influenced mainly in the sub-dominant population whereas the core dominant bacterial species were similar in all samples and composed of Lactobacillus sakei, Lactococcus piscium, Carnobacterium divergens, Serratia proteamaculans and Brochothrix thermosphacta. However, salt reduction turned out to induce a significant drop in species diversity evenness among the core dominant species and thus led to a faster spoilage event..   This knowledge will help in defining strategies to offset salt reduction meanwhile keeping the safety of meat products.	root:Engineered:Food production
MGYS00001639	The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types (USDA recommended, vegan, and “typical American”)	We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: 1) the Average American (AMERICAN): focused on convenience foods, 2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and 3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis.	root:Engineered:Food production
MGYS00001637	Thermus thermophilus is responsible for the pink discolouration defect in cheese	High-throughput, culture-independent DNA sequencing-based strategies have revolutionised our understanding of the composition of microbial populations, including those in foods. While many are descriptive studies, there are studies linking particular microorganisms with specific desirable/undesirable impacts being revealed. Here we apply such a strategy to study pink discolouration of cheese, a spoilage defect that affects the associated industry worldwide. Despite efforts over many decades, the basis for this phenomenon has remained elusive with traditional approaches having failed to reveal a microbial basis for this problem.  The bacterial composition problematic cheeses were assessed by DNA sequencing. This revealed the presence of bacteria from the genus Thermus, at higher levels in defect, relative to control, cheeses. This observation was particularly notable in light of the fact that, Thermus, which are non-pathogenic, thermophilic bacteria which do not readily grow on the media employed to culture dairy microorganisms, have previously been associated with pink discolouration problems in the paper industry.  Prompted by this finding, a target-specific culture-based approach was employed and Thermus thermophilus was successfully cultured from defect cheeses. Furthermore, qPCR revealed the species to be present at 103 cfu g-1 in the aforementioned defect-containing cheeses but to be absent or present at low levels only (101 cfu g-1) in the equivalent control cheeses. The link between Thermus and the pinking phenomenon was further investigated through the production and analysis of cheeses into which Thermus was spiked and of control cheeses. Crucially, the defect was reconstructed only in test cheeses containing the cheese-derived T. thermophilus.	root:Engineered:Food production:Dairy products
MGYS00001636	Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage.	This study is a large comprehensive survey of meat and seafood spoilage microbiota using 454-GS-FLX Titanium amplicon sequencing of the 16S rRNA gene V1-V3 fragment. Primer EBP-27F was used as a forward primer and EBP-534R as a reverse primer. Eight different products were analyzed including four meat products : Ground Beef (code sample = GB), Ground Veal (code sample = GV); Poultry Sausages (code sample = PS); Bacon Dices (code sample =  BD), and four seafood products : Salmon Fillets (code sample = SF); Smoked salmon (code sample = SS); Cod fillets (code sample = CF); Cooked Peeled Shrimps (code sample = CS). Ten samples were analyzed per food product (coded 01 to 10) and at two time of storage (T0 for the freshly produced food product; TS for the spoiled product obtained after a certain period of storage time at refrigerated temperature). Overall, 160 samples were analyzed (80 samples at each storage time of analysis). All samples were subject to pyrosequencing replication, one from the 27F primer A-side (EBP-XXXX-XX-F.fastQ files, where XXXX-XX denotes the sample's code) and the second from the 534R primer B-side (EBP-XXXX-XX-R.fastQ files). All samples from a given product at a given storage time and their associated replicates were pooled in a 1/4 lane of a 454 GS-FLX Titanium run yielding an average sequencing depth of 15,000 reads per sample (~7,500 reads/replicate). All FastQ files are corresponding to Quality-filtered reads (length > 250 bp).	root:Engineered:Food production
MGYS00001635	nifH defined community samples used for analysis testing	To test the pyrosequencing technology and analysis pipeline under specific conditions, we use a nifH defined community with genomic DNAs from Desulfitobacterium hafniense DCB-2,  Nostoc sp. PCC 7120 and Burkholderia xenovorans LB400 amplified separately using the same barcode.	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00001634	Phylogenetic identification of GO-reducing bacteria enriched from a coast	This project conducted the phylogenetic identification of bacteria capable of respiration with an extracellular electron acceptor, graphene oxide (GO). GO is the oxidized form of graphene, a 2D honeycomb lattice of carbon. GO can be reduced to the reduced GO (rGO) by bacteria via extracellular electron transferring. Ant the rGO can facilitate the recovering electricity from bacteria. A variety of microorganisms potentially ability to reduce GO, while the reduction of GO was demonstrated by only Schewanella spp. This study enriched GO respiring bacteria from a coast, and identified the enriched GO respiring bacteria by pyrosequencing targeting V4 region of 16SrRNA gene.	root:Environmental:Terrestrial:Soil:Sand
MGYS00001633	microbial community of traditional Korean alcoholic beverages	Makgeolli is a traditional Korean alcoholic beverage manufactured with a natural starter, called nuruk, and grains. Nuruk is a starchy disk or tablet formed from wheat or grist containing various fungal and bacterial strains from the surrounding environment that are allowed to incorporate naturally into the starter, each of which simultaneously participates in the makgeolli fermentation process. In the current study, changes in microbial dynamics during laboratory-scale fermentation of makgeolli inoculated with six different kinds of nuruk were evaluated by barcoded pyrosequencing using fungal- and bacterial-specific primers targeting the internal transcribed spacer 2 region and hypervariable regions V1 to V3 of the 16S rRNA gene, respectively. A total of 61,571 fungal and 68,513 bacterial sequences were used for the analysis of microbial diversity in ferment samples. During fermentation, the proportion of fungal microorganisms belonging to the family Saccharomycetaceae increased significantly, and the major bacterial phylum of the samples shifted from ?-Proteobacteria to Firmicutes. The results of quantitative PCR indicated that the bacterial content in the final ferments was higher than in commercial rice beers, while total fungi appeared similar. This is the first report of a comparative analysis of microbial dynamics during the fermentation of alcoholic beverage using barcoded pyrosequencing of bacterial and fungal rRNA genes.	root:Engineered:Food production:Fermented beverages
MGYS00001632	The Usefulness and Reproducibility of Pyrosequencing for the Analysis of a Microbial Community of a Methane-Oxidizing Biofilm	The usefulness of pyrosequencing for uncovering a methane-oxidizing biofilm community was determined in this study. Four individual DNA samples were prepared from a methanotrophic biofilm, and a multiplex pyrosequencing was performed. A complete library (sum of the 4 libraries) contained 33,639 sequences with an average length of 415 bp. It was interesting that methanotrophs were not dominant when grouped by functionality, making up only 23% of the community. Methylosinus, Methylomonas and Methylosarcina were the dominant methanotrophs. Type II methanotrophs were more abundant than type I (56 vs. 44%), but diversity and species richness of the type II community were lower. Dominant non-methanotrophic genera included Hydrogenophaga, Flavobacterium and Hyphomicrobium. For evaluation of the reproducibility, the complete library was de-multiplexed into 4 libraries, with different sequencing efforts, ranging from 3,915 to 20,133 sequences. Sørrenson abundance similarity results showed that the four libraries were almost identical (the indices > 0.97), and phylogenetic comparisons using UniFrac and P-tests revealed the same results. The 4 libraries had the same taxonomical composition, with similar relative abundances after taxonomic classification.	root:Engineered:Bioreactor
MGYS00001628	Microbial Community in High Arsenic Shallow Aquifers in Hetao Basin of Inner Mongolia, China by 454 Pyrosequencing	A comprehensive survey of microbial community with 454 Pyrosequencing was carried out in 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic boreholes and one low arsenic borehole) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia by. A total of 233,704 reads and 12-267 species-level OTUs were detected. Richness and diversity of microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low arsenic and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four predominant populations in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter were distinctly dominated in high arsenic sediments. Acinetobacter was distinctly dominated in groundwater with the markedly high relative abundance (average 62.41%), and Thiobacillus was significantly abundant (average abundance 24.62%) in sediments. Archaeal sequences of high arsenic groundwater were mostly related to methanogens. Groundwater and sediment samples were divided into low and high arsenic groups based on geochemical parameters and microbial communities by hierarchical clustering and PCoA analyses. This suggested that arsenic is a critical environmental factor that contributes to the difference microbial community structure. BIO-ENV and co-inertia analyses showed that some other geochemical parameters including TOC, SO42-, SO42-/TS and Fe2+ were also the important factors causing the difference of the microbial community. The results of this study expand our current understanding of microbial ecology in high arsenic aquifers and emphasize the potential importance of microbes in arsenic mobilization in the shallow aquifers of Hetao Basin, Inner Mongolia.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001627	The effect of different loading rates of biochar on soil microbes	Biochar and its applications in soil is involved in many aspects related to soil health and quality, for instance, chemical and physical changes in soil. However, the major aspect, which is still far from being understood and has so far received less attention than any other aspects, is the impact of biochar applications on soil microbes and how microorganisms in soil interact and adjust with biochar-modified soil environments.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001626	16S rRNA gene sequencing of Extremelly low birth weight infant	16S rRNA gene sequencing of Extremelly low birth weight infant using primers 926F-1394R	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001625	Fungi associated with Rhamnus cathartica in Southwestern Ontario	Common buckthorn (Rhamnus cathartica) is a competitive Eurasian woody shrub currently invading North America. Buckthorn thickets reduce native diversity and may reduce mycorrhizal diversity through the release of allelochemicals. Two aspects of buckthorn's invasional biology are explored: 1) determining buckthorn's allelochemical impacts on arbuscular mycorrhizae in mature sugar maple (Acer saccharum) stands, and 2) assessing possible changes in mycorrhizal communities in sugar maple soils in an open-greenhouse experiment. Data from invaded and uninvaded sugar maple soils revealed that arbuscular mycorrhizal fungi (AMF) diversity fluctuated as a function of season, sampling site or potting disturbance, but the presence of buckthorn had little effect on AMF development in maple roots. Buckthorn may be a mycorrhizal generalist, and changes in AMF abundance may be more influenced by underlying stochastic soil processes and aboveground plant composition than by buckthorn and its allelochemicals.	root:Host-associated:Plants
MGYS00001623	This dataset contains the output from shotgun metagenomic and genomic sequencing of the microbiota of faecal samples collected from infants prior to developing necrotising enterocolitis (NEC).	This study describes the use of shotgun metagenomic sequencing  to characterise the microbiota of faecal samples collected from infants prior to developing necrotising enterocolitis (NEC) and from matched controls. Additional genomic sequencing of select enterobacteriaceal isolates cultured from these samples was also performed.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001622	Integrated 'omics', targeted metabolite and single-cell analyses of Arctic snow algae functionality and adaptability	Snow algae are poly-extremophilic microalgae and important primary colonisers and producers on glaciers and snow fields. Depending on their pigmentation they cause green or red mass blooms during the melt season. This decreases surface albedo and thus further enhances snow and ice melting. Although the phenomenon of snow algal blooms has been known for a long time, large aspects of their physiology and ecology sill remain cryptic. This study provides the first in-depth and multi-omics investigation of two very striking adjacent green and red snow fields on a glacier in Svalbard. We have assessed the algal community composition of green and red snow including their associated microbiota, i.e., bacteria and archaea, their metabolic profiles (targeted and non-targeted metabolites) on the bulk and single-cell level, and assessed the feedbacks between the algae and their physico-chemical environment including liquid water content, pH, albedo and nutrient availability. We demonstrate that green and red snow clearly vary in their physico-chemical environment, their microbial community composition and their metabolic profiles. For the algae this likely reflects both different stages of their life cycles and their adaptation strategies. Green snow represents a wet, carbon and nutrient rich environment and is dominated by the algae Microglena sp. with a metabolic profile that is characterized by key metabolites involved in growth and proliferation. In contrast, the dry and nutrient poor red snow habitat is colonised by various Chloromonas species with a high abundance of storage and reserve metabolites likely to face upcoming severe conditions. Combining a multitude of techniques we demonstrate the power of such complementary approaches in elucidating the function and ecology of extremophiles such as green and red snow algal blooms, which play crucial roles in glacial ecosystems.	root:Environmental:Aquatic:Freshwater:Ice:Glacier
MGYS00001621	Characterization of the bacterioplankton communities from the Ebro River	Water samples from the River Ebro (Spain) were collected in 2011 in three occasions and the bacterioplankton communities inhabiting the reaches separated by the reservoirs were characterized by 454 pyrosequencing of the 16S rRNA gene	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001620	study of the Ancona harbor microbial community using 16S rRNA pyrosequencing.	The sediments of the Ancona harbor (Italy) are polluted by crude oil, hence co-contaminated by different classes of molecules like hydrocarbons and heavy metals. In our study, we aimed to investigate the bacterial community composition of highly contaminated sediments and the deriving enrichment cultures established using different hydrocarbon pollutants. To depict the assemblage of bacteria populations we used 16S rRNA pyrosequencing data.	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
MGYS00001619	Sulfate reducing and methanogenic microbial community structure in Outokumpu deep bedrock fracture zones	Sulfate reducing bacterial communities and methanogenic archaeal communities were characterized by amplicon sequencing the marker gene for sulfate reduction and methanogenesis, dsrB and mcrA, respectively. Study was conducted in Outokumpu Deep Drill Hole, Finland in a depth range of 180-2300 m.	root:Environmental:Terrestrial:Rock-dwelling (subaerial biofilm)
MGYS00001603	Reduced membrane fouling in an anaerobic electrochemical membrane bioreactors using graphene-coated hollow fiber membranes as the cathode	Electrically conductive, graphene-coated hollow-fiber porous membranes were used as cathodes in anaerobic electrochemical membrane bioreactors (AnEMBRs) operated at different applied voltages (0.7 V and 0.9 V) using a new rectangular reactor configuration, compared to a previous tubular design (0.7 V). The onset of biofouling was delayed and minimized in rectangular reactors operated at 0.9 V, compared to those at 0.7 V due to higher rates of hydrogen production. Maximum transmembrane pressures for the rectangular reactor were only 0.10 bar (0.7 V) or 0.05 bar (0.9 V) after 56 days of operation, compared to 0.46 bar (0.7 V) for the tubular reactor after 52 days. The thickness of the membrane biofouling layer was approximately 0.4 ?m for rectangular reactors and 4 ?m for the tubular reactor. Pyrosequencing of 16S rRNA gene and qPCR analysis revealed that the predominant bacteria were Desulfovibrio sp., and methanogenic archaea were mainly Methanobacteriaceae in both the tubular and the rectangular AnEMBRs. The ratio of archaea-to-bacteria varied depending on applied voltage and reactor configuration with higher ratio (>0.6) at 0.7 V than at 0.9 V (~0.1).  Higher permeate quality (TSS = 0.05 mg/L) was achieved in the rectangular AnEMBR than the tubular AnEMBR (TSS = 17 mg/L), likely due to higher current densities that minimized the accumulation of cells in suspension. These results show that the new rectangular reactor design, which had increased rates of hydrogen production, successfully delayed the onset of cathode biofouling and improved reactor performance.	root:Engineered:Bioreactor
MGYS00001605	Exploring the brine pool in the Red Sea as a source of exoelectrogenic communities	One of the challenges for using microbial electrochemical technologies (METs) with highly saline or thermophilic solutions is the lack of microbes capable of forming a biofilm and generating electrical current under these conditions. Three different locations at different depths of brine pools in the Red Sea were investigated as inocula sources for exoelectrogenic biofilms that could grow at 70oC in highly saline medium: Valdivia, Atlantis II, and Kebrit. Of these, only the inoculum from the Valdivia brine pool produced high and consistent current 6.8 ? 2.1 A/m2-anode (over 60 days) in microbial electrolysis cells (MECs) operated at a set anode potential of +0.2 V vs Ag/AgCl (+0.405 V vs. SHE), with 10 mM acetate as the electron donor. Analysis of the microbial communities with the Valdivia inoculum using 16S rRNA gene pyrosequencing showed at the genus level that sequences most similar to Bacteroides were the predominant microorganisms at the anode. These results show that microorganisms capable of producing electrical current are present in at least one of these extreme environments in the Red Sea. Enriching for efficient exoelectrogenic communities from extreme environments will provide new opportunities for niche-specific applications of METs.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00001606	Comparative analysis of twelve viromes from fen and bog peat pore water	Using pyrosequencing,12 peatland metaviromes have been produced for both fen and bog at 4 different dates. Using shotgun metagenomics we observed a shift in viral diversity between winter/spring and summer/autumn, indicating a seasonal succession of viral communities, mainly driven by weather-related environmental changes.	root:Environmental:Terrestrial:Soil:Wetlands
MGYS00001607	Natural variation of Pacific oyster hemolymph microbiota at two sites in the Wadden Sea (Texel, Netherlands, & Sylt, Germany) throughout the summer season 2012	Pacific oysters (Crassostrea gigas) from two genetically differentiated populations from the Wadden Sea - one from Texel, the other from Sylt - were reciprocally translocated between the sites at the beginning of June 2012. Half of the oysters were additionally pretreated with antibiotics to remove resident microbiota. Local controls were included as well, resulting in four groups at each site: antibiotic treated local or translocated, and control local or translocated oysters.Hemolymph samples were taken immediately after the pretreatment in the lab and then on 3 (monthly, Texel) and 5 (biweekly, Sylt) occasions in the field. Exact position of each oyster in the field was recorded, so that the data allow for study of spatial patterns of oyster hemolymph microbiota. One seawater sample is included for reference for each sampling point.	root:Host-associated:Mollusca:Digestive system
MGYS00001608	Subseafloor microbes at Mid-Cayman Rise	Two new vent-systems on the Mid-Cayman Rise each exhibit novel geologic settings and distinctively hydrogen-rich vent fluid compositions.  We have determined and compared the chemistry, energy landscape, abundance, community composition, diversity, and function of microbes in venting fluids from both sites: Piccard, the world?s deepest vent site-site, hosted in mafic rocks, and Von Damm, an adjacent, ultramafic-influenced system.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00001609	Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2013	This projects explores the functional diversity and activity of rocky subseafloor microbial communities in hydrothermal vent systems. Samples were collected in 2013 from a number of low temperature diffuse fluid vents at Axial seamount, located in the northeast Pacific Ocean. Shotgun metagenomics and metatranscriptomics were performed on four diffuse vent samples.  Previous work at this site determined the taxonomic structure and distribution of microbial communities in venting fluids, but the contribution and mechanisms of the different redox driven metabolisms and the impact these reactions have on vent chemical signatures have not been fully characterized. This study helps to determine the genetic potential and expression patterns of the largely uncharacterized subseafloor microbial community and shows how these patterns change across the complicated biogeochemical gradients of hydrothermal vent systems.	root:Environmental:Aquatic:Marine:Hydrothermal vents:Diffuse flow
MGYS00001610	biogas	biogas from swine manure	root:Engineered:Wastewater:Water and sludge
MGYS00001611	Microbial community structure in six deep crystalline bedrock fracture zones	Bacterial and archaeal communities from six fracture zones from 180-2300 m depths in Outokumpu crystalline bedrock were characterized using high-throughput amplicon sequencing.	root:Environmental:Terrestrial:Rock-dwelling (subaerial biofilm)
MGYS00001612	Metabarcoding-based fungal diversity on coarse and fine particulate organic matter in a first-order stream in Nova Scotia, Canada	Most streams receive substantial inputs of allochthonous organic material in the form of leaves and twigs (CPOM, coarse particulate organic matter). Mechanical and biological processing converts this into fine particulate organic matter (FPOM). Other sources of particles include flocculated dissolved matter and soil particles. Fungi are known to play a role in the CPOM conversion process, but the taxonomic affiliations of these fungi remain poorly studied. The present study seeks to shed light on the composition of fungal communities on FPOM and CPOM as assessed in a natural stream in Nova Scotia, Canada. Maple leaves were exposed in a stream for four weeks and their fungal community evaluated through pyrosequencing. Over the same period, four FPOM size fractions were collected by filtration and assessed. Particles had much lower ergosterol contents than leaves, suggesting major differences in the extent of fungal colonization. Pyrosequencing documented a total of 821 fungal operational taxonomic units (OTU), of which 726 were exclusive to particles and 47 to leaf samples. Most fungal phyla were represented, including yeast lineages (e.g., Taphrinaceae and Saccharomycotina), Basidiomycota, Chytridiomycota and Cryptomycota, but several classes of Pezizomycontina (Ascomycota) dominated. Cluster dendrograms clearly separated fungal communities from leaves and from particles. Characterizing fungal communities may shed some light on the processing pathways of fine particles in streams and broadens our view of the phylogenetic composition of fungi in freshwater ecosystems.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001601	Assessing the groundwater quality at a Saudi Arabian agricultural site and the occurrence of antibiotic-resistant opportunistic pathogens on irrigated food produce	This study monitors the groundwater in wells situated near to agricultural fields of Saudi Arabia. Vegetables irrigated with the groundwater were also assessed for their microbial safety. The amount of total nitrogen exceeded the 15 mg/L permissible for agricultural irrigation in most of the sampled groundwater. Fecal coliforms in density >12 MPN/100 mL were detected in some of the groundwater wells of close proximity to a chicken farm. Coupled with qPCR-based fecal source tracking, monitoring effort showed that groundwater in two of the wells nearest to the chicken farm were relatively more perturbed than the other wells. Anthropogenic contamination resulted in a shift of predominant bacterial phylum within the groundwater microbial communities. Specifically, there was an elevated presence of Proteobacteria but a lower microbial richness in the groundwater perturbed by anthropogenic contamination. Acinetobacter was detected at high relative abundance of up to 48.6% in the total microbial community of groundwater but culture-based analysis did not recover any antibiotic-resistant bacteria and opportunistic pathogens from the groundwater. Although Enterococcus faecalis and Pseudomonas aeruginosa were isolated from the vegetables irrigated with the groundwater, quantitative microbial risk assessment suggests that the annual risk incurred from consumption of these vegetables are within the acceptable limits of 10-4. Our findings highlighted that the groundwater quality at this agricultural site in the western Saudi Arabia was not as pristine as commonly perceived. Despite the poor groundwater quality, there was no significant impairment of food quality arising from the groundwater.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001600	Bioremediation and metal resistant bacteria in a closed, cold northern mine	Closed, water filled mined produce heavy metal rich acid mine draining that affects the environment in many ways. In this study we have characterized the bacterial community on the water of closed Kotalahti mine by 16S rRNA gene targeted 454 amplicon sequencing as well as by heavy metal resistance gene targeting clone libraries combined with Sanger sequencing.	root:Environmental:Aquatic:Freshwater:Groundwater:Mine drainage
MGYS00001599	Microbial and geochemical sampling in high pressure, low biomass terrestrial subsurface Pyhäsalmi mine.	Microbial and geochemical sampling in high pressure, low biomass terrestrial subsurface Pyh?salmi mine. Pyrosequencing of bacterial and archaeal 16S rDNA and rRNA and fungal ITS DNA and cDNA fractions.	root:Environmental:Terrestrial:Soil:Mine
MGYS00001598	Probing the texture of the rare biosphere	Probing the texture of the rare biosphere: We have bracketed the dimensions of the rare biosphere in two marine bacterial samples by comparing a deep (1 million sequences per sample) pyrosequencing analysis of the two samples and the cultures isolated from one of them.	root:Environmental:Aquatic:Marine
MGYS00001597	Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland	In this study we investigated fungal communities in packer-isolated bedrock fractures in Olkiluoto, Finland at depths ranging from 296 m to 798 m below surface level. DNA- and cDNA-based high-throughput amplicon sequencing analysis of the fungal internal transcribed spacer (ITS) gene markers was used to examine the total fungal diversity and to identify the active members in deep fracture zones at different depths.	root:Environmental:Terrestrial:Geologic
MGYS00001596	Canonical correlation methods for exploring microbe-environment interactions in deep subsurface	The active and general sulphate reducing bacterial popilation of crystalline bedrock fracture fluids from Olkiluoto Island, Finland, were investigated by dsrB gene and transcript trageted 454 amplicon sequencing. The effect of geochemical parameters on the SRB community was tested by canonical correlation methods.	root:Environmental:Terrestrial:Geologic
MGYS00001595	Microbial communities and nutrient dynamics in experimental microcosms are altered after the application of a high dose of Bti	Bacillus thuringiensis subsp. israelensis (Bti) is the most widely used biopesticide against mosquitoes and blackflies, with a history of high specificity and efficacy. However, interactions of Bti with native microfauna in the environment are poorly understood. High and low Bti (VectoBac G) applications, in addition to an untreated control, were assigned to replicate ?1 m^2? mesocosms in a completely randomized design under field conditions. The abundance of Culex spp., phytoplankton, sestonic particulates, nutrients and other water quality parameters were assessed throughout this large-scale 82-day field study. Bacterial communities present in the water column were assessed by next generation sequencing of 16S rRNA genes, comparing treatments and sampling dates. The high Bti application rate significantly reduced mosquito abundance, phytoplankton biomass, sestonic particulates, nutrients, and other physicochemical variables in the water, and was also associated with higher bacterial diversity. Beta diversity analysis revealed that bacterial communities in the water column were influenced significantly by the high Bti treatment. Together, our results demonstrate significant dose-dependent changes to aquatic ecosystem chemistry and bacterial community composition associated with Bti application.	root:Engineered:Modeled
MGYS00001593	Microbiota, microbiome, and virome of an aquaculture sample	This study aims to characterize the microbial ecology of a water sample collected from a salmonid aquaculture plant.	root:Environmental:Aquatic:Aquaculture
MGYS00001592	Uncultured archaeal communities in anoxic, saline groundwater were characterized using 16S rRNA and rDNA targeted 454 amplicon sequencing.	Uncultured archaeal communities in anoxic, saline groundwater were characterized using 16S rRNA and rDNA targeted 454 amplicon sequencing.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001591	Bacterial diversity in groundwater of three hard-rock aquifers in the Armorican massif (Brittany, France)	Hard-rock aquifers are widespread subsurface habitats that are readily colonized by microorganisms. These environments are characterized by heterogeneous hydrologic circulation, which strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. However, little is known about the effects of hydrologic circulation on microbial communities. Groundwater of different ages (residence time) was sampled along hydrogeologic flow paths in three contrasting hard-rock aquifers in Brittany (France). Residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by community RNA extraction and 454 sequencing of 16S rRNA amplicons.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001590	Zonation of bacterioplankton communities along aging upwelled water in the northern Benguela upwelling	"Upwelling areas are shaped by enhanced primary production in surface waters, accompanied by a well-investigated planktonic succession. Although bacteria play an important role in biogeochemical cycles of upwelling systems, little is known about bacterial community composition and its development during upwelling events. The aim of this study was to investigate the succession of bacterial assemblages in aging upwelled water of the Benguela upwelling from coastal to offshore sites. Water from the upper mixed layer at 12 stations was sampled along two transects from the origin of the upwelling to a distance of 220 km. 16S rRNA gene amplicon sequencing was then used in a bacterial diversity analysis and major bacterial taxa were quantified by catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Additionally, bacterial cell numbers and bacterial production were assessed . Community statistical analysis revealed a reproducible zonation along the two transects, with four clusters of significantly different microbial assemblages. Clustering was mainly driven by phytoplankton composition and abundance. Similar to the temporal succession that occurs during phytoplankton blooms in temperate coastal waters, operational taxonomic units (OTUs) affiliated with Bacteroidetes and Gammaproteobacteria were dominant during algal blooming whereas ""Pelagibacterales"" were highly abundant in regions with low algal abundance. The most dominant heterotrophic OTU (9% of all reads) was affiliated with ""Pelagibacterales"" and showed a strong negative correlation with phytoplankton. By contrast, the second most abundant heterotrophic OTU (6% of all reads) was affiliated with the phylum Verrucomicrobia and correlated positively with phytoplankton. Together with the close relation of bacterial production and phytoplankton abundance, our results showed that bacterial community dynamics is strongly driven by the development and composition of the phytoplankton community."	root:Environmental:Aquatic:Marine:Oceanic:Photic zone
MGYS00001589	The microbial community of aquatic sediments influenced by heavy metals	Microbial communities within sediments regulate biogeochemical cycling throughout aquatic ecosystems.  However, microbial community structure can become influenced through heavy metal toxicity, often caused by anthropogenic disturbance.  Toxicity of heavy metals can become reduced over time through mineralization and/or sorption of previously bioavailable metal ions.  As consequence, it is anticipated that microbial communities should exhibit a more pronounced observable response to available metal concentrations within the local environment.  In this study, lake sediments collected from two heavy metal impacted geographical regions (Poyang Lake, China and sites adjacent to the Muskegon Watershed, MI, USA) were analyzed for microbial community structure using high-throughput sequencing technology.  Total and available metal concentrations were also investigated in order to elucidate the relative strengths each fraction exerted on local sediment microbial communities.  Results indicate a weak relationship of metal influence on microbial community diversity, but strong positive and negative correlations of available heavy metals with specific taxonomic groups and OTUs of bacteria and archaea.  This shows the importance of analyzing available metals when examining the impact of this disturbance on microbial community structure within aquatic sediments.	root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
MGYS00001588	Bacterial diversity assessment of Tulshi shyam hot spring using metagenomic appraoch	A taxonomic description of bacteria was deduced from 5.78 MB metagenomic sequence retrived from Tulshi shyam Hot spring, India using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). Metagenome sequences represented the 98.2% bacteria origin, 1.5% of eukaryotic and 0.3% were unidentified. A total of 16 bacterial phyla demonstrating 97 families and 287 species were revealed in the hot spring metagenome.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00001587	Changeability of bacterial community composition caused by seawater exposure to crude oil at low temperature	A crude oil contamination at sea causes changes in marine bacterial abundance and composition. Microorganisms that are initially undetectable in a pristine environment become prevalent following an exposure to petroleum compounds. The overarching goal of the study were examine through laboratory experiments changes in abundance and composition of bacteria. Here we present laboratory data obtained with crude oil in the range 30ppb ? 2000ppb (nominal concentration) during an 11 days exposure. Changes in chemical composition coincided with major changes in total number of bacteria as well as in bacterial composition.	root:Engineered:Biotransformation:Microbial enhanced oil recovery
MGYS00001586	"Microbial diversity and the implications of sulfide levels in an anaerobic
reactor used to remove an anionic surfactant from laundry wastewater"	The objective of this study was to evaluate the removal of linear alkylbenzene sulfonate (LAS) from commercial laundry wastewater using an expanded granular sludge bed (EGSB) reactor with two specific LAS\nloading rates (SLLRs), 1.0 and 2.7 mg LAS gVS ?1 d ?1. The biomass was characterized using denaturing gradient gel electrophoresis (DGGE) and 16S Ion Tag sequencing. Higher LAS removal (92.9%) was observed\nin association with an SLLR of 1.0 mg LAS gVS ?1 d ?1 than with an SLLR of 2.7 mg LAS gVS ?1 d ?1 (58.6%). A\nrelationship between the S ?2 concentration in the effluent and the surfactant removal efficiency was\nobserved. This result is indicative of the inhibition of LAS-removing microbiota at S ?2 concentrations\ngreater than 20 mg S L?1. By using DGGE, microbial stratification was observed in the reactor in association with granule size, even though the reactor is considered to be a completely mixed regime. The\nRDP-classifier identified 175 genera, 33 of which were related to LAS degradation.	root:Engineered:Wastewater:Industrial wastewater
MGYS00001585	A flow-through rolling tank allows to conduct experiments on particulate organic matter at near in-situ conditions.	Downward fluxes of particulate organic matter (POM) are the major sink of atmospheric CO2 into aquatic sediments, remaining there for thousands of years. Budget calculations of the biological carbon pump are greatly based on the ratio between carbon export (sedimentation) and remineralization (release to the atmosphere). Current methodologies determine microbial dynamics on POM using closed vessels, thus, strongly biased towards heterotrophy due to rapidly changing water chemistry (Bottle Effect). We developed a flow-through rolling tank for long term studies that continuously maintains POM at near in-situ conditions. There, bacterial communities follow those in-situ, contrary to rapidly changing ones in closed rolling tanks. The active particle-associated community in the flow-through system is stable over several days contrary to several hours previously reported. Decrease in particles photosynthetic rates is much slower in our system than in traditional ones. These results call for reevaluating experimentally-derived carbon fluxes, using our new experimental tool.	root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum
MGYS00001584	Functional redundant and similar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage	Numerous observations indicate a high flexibility of microbial communities in different biogas reactors during anaerobic digestion. Here we describe our findings regarding the functional redundancy and similarity of involved microorganisms in four continuously-stirred tank lab-scale biogas reactors (CSTRs, 39 ?C, 12 L volume) supplied with different mixtures of sugar beet silage (SBS) and maize silage (MS) resulting in similar biogas yields in all reactors. CSTRs were set-up with inoculum from a full-scale biogas plant, fed with mixtures of MS and SBS in the ratios of 1:0 (CF1), 6:1 (CF2), 3:1 (CF3), 1:3 (CF4) with equal organic loading rates (OLR 1.25 kg VS m-3 d-1) and operated for 140 d. The compositions of bacterial and archaeal communities degrading the different substrate mixtures were analyzed by 454 amplicon sequencing approach based on 16S rRNA genes. Both bacterial and archaeal communities shifted with increasing amounts of SBS. As the compositional shifts within the microbial communities did not influence the respective biogas production, similar process dynamics indicate functional redundant archaeal and functional similar bacterial communities in each individual CSTR.	root:Engineered:Biogas plant:Wet fermentation
MGYS00001583	Mid- and hind-gut of rainbow trout gastrointestinal tract (GIT) fed alternative protein diet	Feeding alternative diet to replace the conventional fishmeal diet has been the focus in aquaculture nutrition. This study investigates the effect of two alternative diets on the GIT of rainbow trout raised in a cultured environment.	root:Host-associated:Fish:Digestive system
MGYS00001582	Removal of bacterial contaminants and antibiotic resistance genes by conventional wastewater treatment processes in Saudi Arabia: Is the treated wastewater safe to reuse for agricultural irrigation?	This study aims to assess the removal efficiency of microbial contaminants in a local wastewater treatment plant over the duration of one year, and to assess the microbial risk associated with reusing treated wastewater in agricultural irrigation. The treatment process achieved 3.5 logs removal of heterotrophic bacteria and up to 3.5 logs removal of fecal coliforms. The final chlorinated effluent had 1.8 x 102 MPN/100 mL of fecal coliforms and fulfils the required quality for restricted irrigation. 16S rRNA gene-based high-throughput sequencing showed that several genera associated with opportunistic pathogens (e.g. Acinetobacter, Aeromonas, Arcobacter, Legionella, Mycobacterium, Neisseria, Pseudomonas and Streptococcus) were detected at relative abundance ranging from 0.014 to 21 % of the total microbial community in the influent. Among them, Pseudomonas spp. had the highest approximated cell number in the influent but decreased to less than 30 cells/100 mL in both types of effluent. A culture-based approach further revealed that Pseudomonas aeruginosa was mainly found in the influent and non-chlorinated effluent but was replaced by other Pseudomonas spp. in the chlorinated effluent. Aeromonas hydrophila could still be recovered in the chlorinated effluent. Quantitative microbial risk assessment (QMRA) determined that only chlorinated effluent should be permitted for use in agricultural irrigation as it achieved an acceptable annual microbial risk lower than 10-4 arising from both P. aeruginosa and A. hydrophila. However, the proportion of bacterial isolates resistant to  6 types of antibiotics increased from 3.8% in the influent to 6.9% in the chlorinated effluent. Examples of these antibiotic-resistant isolates in the chlorinated effluent include Enterococcus and Enterobacter spp. Besides the presence of antibiotic-resistant bacterial isolates, tetracycline resistance genes tetO, tetQ, tetW, tetH, tetZ were also present at an average 2.5 x 102, 1.6 x 102, 4.4 x 102, 1.6 x 101 and 5.5 x 103 copies per mL of chlorinated effluent. Our study highlighted that potential risks associated with the reuse of treated wastewater arise not only from conventional fecal indicators or known pathogens, but also from antibiotic-resistant bacteria and genes.	root:Engineered:Wastewater:Water and sludge
MGYS00001581	Impact of the diet on the intestinal microbiota in African children moving from rural to urban areas	We studied the intestinal microbial changes in groups of African children belonging to the same ethnicity in which transition from a rural environment to urban areas, together with improvement of socio-economic conditions, results in exposure to a ?globalized? western type diet. Introduction of foods from animal origin and rich in fat and simple sugar into a traditional African diet, composed by cereals, legumes and vegetables, causes gut microbiota shift, leading to progressive loss of biochemical functions associated to production of Short Chain Fatty Acids. Key microbial profiles are lost in the course of urbanization and improvement of economic conditions independently from geography and ethnicity, resulting in a marked shift in bacterial communities, typical of western populations.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001580	Metagenomics of the mid- and hind-gut of rainbow trout gastrointestinal tract (GIT) fed alternative protein diets	Rainbow trout is an important aquaculture species. Feeding alternative diet to replace the conventional fishmeal diet has been the focus in aquaculture nutrition. This study investigates the effect of two alternative diets on the GIT of rainbow trout raised in a cultured environment.	root:Host-associated:Fish:Digestive system
MGYS00001579	Relationship between co-substrate and microbial composition in the degradation of anionic surfactant	Different carbon sources were used as co-substrate to evaluate the removal of linear alkylbenzene sulfonate (LAS) from laundry wastewater, as well as the related microbial community. An anaerobic fluidized bed reactor (AFBR) was operated in three stages, after the biomass adaptation without LAS (stage I). Those stages were differentiated by the co-substrate supplementation: stage II, sucrose plus ethanol, stage III, only ethanol, stage IV, no co-substrate. Laundry wastewater was diluted to obtain approximately 20 mg.L-1 of LAS in the AFBR influent. The replacement of sucrose plus ethanol in the substrate composition with only ethanol favored the removal efficiency of LAS, and that removal remained high after the co-substrate was removed (Stage II: 52%; Stage III: 73%; Stage IV: 77%). Those results suggest that the microbial community favored by only ethanol was more capable of degrading LAS than the community favored by sucrose plus ethanol. The presence of sucrose favored the Comamonadaceae family (stage II). After the sucrose was removed (stage III), the Comamonadaceae family decreased and the Rhodocyclaceae family increased. Some genera from the Rhodocyclaceae family are possibly related to LAS degradation. The relative abundance of these genera increased in stage IV in the absence of the co-substrate. Therefore, only ethanol is suggested as a more suitable co-substrate than sucrose plus ethanol in the co-metabolic process of LAS removal.	root:Engineered:Wastewater:Industrial wastewater
MGYS00001578	RNA and DNA based biodiversity of sea ice protists over the central Arctic Ocean	Sea ice is a large ecosystem contributing significantly to Polar primary productivity. Especially in the northern hemisphere sea ice consists of often several meters thick multi-year ice (MYI) and thinner first-year ice (FYI). Current global warming is most severe in Arctic regions and as a consequence sea ice cover, especially for MYI is decreasing. Despite its apparent hostile nature sea ice interior is inhabited by a microbial community of bacteria and protists, many of which are photosynthetic. The composition of these communities is yet not known in detail and the relation between active cells versus those just entrapped has not been studied. Here we present data on eukaryotic biodiversity in MYI and FYI from the Central Arctic Ocean using high-throughput sequencing of 18S rRNA and rDNA amplicons. By analyzing datasets from environmental DNA versus RNA we compare the DNA-based total biodiversity to that from RNA amplicons representing the more active part of the community. We found differences between these two in that Bacillariophyceae OTUs are over-represented in the active part of the community. The important arctic diatom Melosira arctica seems to be more abundant in MYI.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00001576	Bacterial communities in thermophilic H2-producing reactors investigated using 16S rRNA 454 pyrosequencing	In this study, the composition and diversity of the bacterial community in thermophilic H2-producing reactors fed with glucose were investigated using pyrosequencing. The H2-producing experiments in batch were conducted using 0.5 and 2.0 g.l-1 glucose at 55o C. Under the two conditions, the H2 production and yield were 1.3 and 1.6 mol H2/mol glucose, respectively. Acetic, butyric, iso-butyric, lactic and propionic acids were detected in the two reactors. The increase in substrate concentration favored a high H2 yield. In this reactor, a predominance of acetic and iso-butyric acids, 27.7% and 40%, were measured, respectively. By means of pyrosequencing, a total of 323 and 247 operational taxonomic units were obtained, with a predominance of the phylum Firmicutes (68.73 ? 67.61%) for reactors with 0.5 and 2.0 g.l-1glucose, respectively. Approximately 40.55% and 62.34% of sequences were affiliated with Thermoanaerobacterium and Thermohydrogenium, microorganisms that produce H2 under thermophilic conditions.	root:Engineered:Bioreactor:Continuous culture
MGYS00001575	Picoplankton diversity in the South Adriatic Sea during a strong deep winter convection year	The South Adriatic is a key area for the Adriatic and the deep Eastern Mediterranean mainly because it is a dense water source and a driving engine of the Eastern Mediterranean deep circulation cell. In addition, the South Adriatic is an entry point for water masses in the Adriatic. It is the place where Ionian saltier and warmer waters are mixing with Adriatic fresher waters through the process of open-ocean winter convection. The biodiversity and seasonality of bacterial picoplankton before, during and after deep winter convection in the oligotrophic South Adriatic waters were assessed combining comparative 16S rRNA sequence analysis and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The picoplankton communities reached their maximum abundance in the euphotic zone in spring when the maximum value of chlorophyll a was recorded in response to deep winter convection. The communities were dominated by Bacteria while Archaea were a minor constituent. A seasonality of bacterial richness and diversity was observed, with minimum values in the winter convection and spring post-convection period, and maximum values during summer stratified conditions. SAR11 was the main constituent of the bacterial communities and reached the maximum abundance in the euphotic zone in spring after the convection episode. Cyanobacteria were the second most abundant group strongly depending on the convection event when minimal cyanobacterial abundance was observed. Euphotic zone in spring and autumn were characterized by Bacteroidetes and Gammaproteobacteria. The Bacteroidetes clades NS2b, NS4 and NS5 and the gammaproteobacterial SAR86 clade were detected to co-occur with phytoplankton blooms. SAR324, SAR202 and SAR406 were present in the deep layer exhibiting different seasonal variations in abundance. Overall, our data demonstrate that the abundances of particular bacterial clades and the overall bacterial richness and diversity are strongly impacted by strong winter convection.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001574	Using Illumina MiSeq platform to sequence the partial 16S rRNA library of the hot spring sample	A comprehensive investigation of the microbial community composition and taxonomy of Sungai Klah, which is located in Perak, Malaysia. It is the second hottest geothermal springs in Malaysia. The hot spring is a streamer-like and several spring heads with boiling temperature (100-110 ?C) are presence. Other parts of the streaming water exhibit the temperature ranging from 50?100 ?C. Little knowledge on the types of hyper- and thermophilic within this hot spring is known. Furthermore, this high temperature environment condition serves as a source for understanding the genetic diversity, population structure, and ecological roles of these boiling point-tolerant microorganisms.	root:Environmental:Aquatic:Thermal springs:Near-boiling (>90C)
MGYS00001573	Exploring the River Continuum Concept for Bacterioplankton	Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared to macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water column samples collected from the river channel across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel, were characterised using pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from Bacteroidetes dominated in the headwaters to an Actinobacteria dominated community downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature above other measures of position such as Euclidian distance between sites and site catchment area; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid (LNA) bacteria relative to high nucleic acid (HNA) bacteria were found to correspond with these downstream changes in community structure, indicating that functional changes correspond with the taxonomic succession. Our findings suggest that bacterial communities across the Thames basin exhibit a marked ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physiochemical status of the river.	root:Environmental:Aquatic:Freshwater:Lotic
MGYS00001572	Microbial communities in deep crystalline bedrock aquifers of Olkiluoto, Finkand	The deep subsurface microbial communities in the crystalline bedrock aquifers of Olkiluoto, Finland, were studied. The actively transcribing community was examined by targeting the archaeal and bacterial 16S rRNA and the mRNA transcripts of the mcrA genes of the  methanogens and the dsrB gene transcripts of the sulphate reducers using 454 amplicon sequencing.	root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00001571	Growth of heterotrophic aquatic bacteria in winter is controlled by organic matter availability rather than temperature	In winter 2009/10, a sudden under-ice bloom of heterotrophic bacteria occurred in the seasonally ice-covered, temperate, deep, oligotrophic Lake Stechlin (NE Germany). Extraordinary high bacterial abundance and biomass were fueled by the breakdown of a massive bloom of Aphanizomenon flos-aquae. The ice-cover was blanketed by snow leading to a significant reduction of the incident light. This exerted a pronounced physiological stress on the cyanobacteria. These were rapidly colonized by heterotrophic bacteria resulting in a sudden proliferation of associated and subsequently of free-living bacteria. Total bacterial protein production reached 201 ?g C l-1 d-1 - ca. five times higher than previously measured values that year. Fluorescence in situ hybridization and denaturing gradient gel electrophoresis at high temporal resolution showed a sharp change in bacterial community structure coinciding with changes in cyanobacteria physiology. Pyrosequencing of 16S rRNA genes revealed that during cyanobacteria breakdown diversity of cyanobacteria-associated and free-living bacteria communities were reduced to a few dominant families. Some of these families were not detectable during the early stages of the cyanobacterial bloom indicating that senescent cells of cyanobacteria select for specific and well adapted bacterial communities. This massive bacterial bloom was rapidly terminated by heterotrophic nanoflagellates shortly before ice-off. Our case study suggests that in winter, unlike commonly postulated, carbon rather than temperature is the limiting factor for bacterial growth. This highlights the need for year-round studies of aquatic ecosystems including the winter season to correctly understand and model element and energy cycling through aquatic food webs, particularly the microbial loop.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001570	Through the pyrosequencing analysis of samples from support mateial and phase separator from the anaerobic fluidized bed reactor total of 83 genera was found, which 18 are involved to the nonionic surfactant degradation.	Through the pyrosequencing analysis of samples from support mateial and phase separator from the anaerobic fluidized bed reactor total of 83 genera was found, which 18 are involved to the nonionic surfactant degradation as well as its byproducts. The genera with the highest relative abundance were Sporomusa, Geobacter, Desulfobulbus, Synergistes, Sedimentibacter, Holophaga, Serpens and Azonexus. All samples showed high phylogenetic diversity in which found genera are somehow related to the degradation of LAE and were favored by the configuration of the anaerobic fluidized bed reactor.	root:Engineered:Biotransformation:Mixed alcohol bioreactor
MGYS00001569	Assessing polychlorinated biphenyl degradation by an anaerobic microbial consortium in batch reactors with biofilm	Anaerobic biomass was used as inoculum in batch reactors undergoing fermentative-methanogenic conditions aiming to removal PCBs congeners (0.7 mg mL-1). Ethanol (460 mg L-1) and sodium formate (680 mg L-1) was used as co-substrate and polyurethane foam (PF) as support for biomass immobilization. Control reactors (RWCS, RCS and RCS-PF) did not contain PCBs, and biomass received a heat-treatment (RCS-PCB-HT). Ethanol and sodium formate stimulate the metabolism of biomass, since there was an increased methane production in reactors RCS and RCS-PF. The low yield of methane in reactors RCS-PCB and RCS-PCB-PF suggests an inhibitory effect of PCB over the methanogenic community. Reactors RCS-PCB presented a substantial reduction of the initial concentration of PCBs from 0.7 to 0.2 mg mL-1 after 60 days. For domain Bacteria, the reactors with PCBs (RCS-PCB and RCS-PCB-PF) were grouped with 86% similarity and only 55% with free-PCBs reactors (RWCS, RCS and RCS-PF) suggesting a selection of specific population in the presence of PCBs. For Archaea domain the reactors RCS-PCB and RCS-PCB-PF were grouped with 94% similarity and those without PCBs (RWCS, RCS and RCS-PF) with 86%. However, between these groups the similarity was 59% indicating that besides the selection of specific populations induced by PCBs the variation was not as evident as observed for the Bacteria domain. Reactors containing PCBs (RCS-PCB and RCS-PCB-PF) had an increased prevalence of Firmicutes and Chloroflexi phyla and, a pronounced relative abundance of Sedimentibacter, (7.4 and 12.4, respectively) a bacterium correlated with reductive dechlorination of PCBs.	root:Engineered:Bioreactor
MGYS00001568	Targeted population genomics of marine Synechococcus cyanobacteria	Large-scale sequencing of nucleic acids extracted from diverse sources is now widely used to study the structure and function of bacterial communities. However, the biological complexity of natural environments, combined with both technical and practical difficulties in analysing large datasets often means the full potential of this technique is rarely achieved. In this respect, we present a targeted metagenomic pipeline, focusing on extracting one component of a complex bacterial community. We used a 3 step process: flow cytometric sorting, followed by direct whole genome amplification on purified cells, then high throughput sequencing. We selected Synechococcus, a ubiquitous marine picophytoplankton, as a target and tested our methods on defined mixtures of cultivated isolates before applying the approach on environmental samples. We show that this targeted approach can provide precise and in-depth assessment of the genomic potential of a selected group where low environmental abundance would limit the return of metagenomic information from community-wide DNA surveys. This approach will help to explore fine-scale population structure and biogeography in a genomic context and therefore the underlying mechanisms that allow specific keystone populations, e.g., marine Synechococcus, to cohabit and contribute to nutrient cycling across a range of habitats.	root:Host-associated:Plants
MGYS00001567	Metatranscriptome of a marine bacterioplankton in the North Sea assessed by total RNA sequencing	Marine metatranscriptome data was generated as part of a more detailed study investigating the bacterioplankton communities towards the end of a diatom-dominated spring phytoplankton bloom. This genomic resource article reports a metatranscriptomic dataset from amidst the winter time prior the occurrence of the spring diatom bloom. Up to 58% of all sequences could be assigned onto ORFs and taxonomic analysis based on expressed 16S rDNA revealed identified Gammaproteobacteria, Alphaproteobacteria and to a lesser extend Flavobacteria as the most active community members.	root:Environmental:Aquatic:Marine
MGYS00001566	Black Water Project	Bacterial community characterization from a sewage system	root:Engineered:Wastewater
MGYS00001565	PCR-amplified 16S rRNA gene tag sequencing from Banyoles karstic area (Catalonia, Spain).	16S rRNA gene was sequenced using the primers set 341F-907R covering the hypervariable regions V3?V5. Amplicons were pyrosequenced using the 454 FLX system (454 Life Sciences, Branford, CT, USA) at the Research and Testing Laboratory (Lubbock, TX). Lakes Cis?, Vilar, and Lake Banyoles-basin III (C-III) are in the Banyoles karstic area northeastern Spain (42?8''N, 2?45''E), samples from the metalimnion and hypolimnion of these lakes are explored in this study. These stratified aquatic ecosystems have incoming sulfate-rich water seeping in through bottom springs resulting in deep waters rich in sulfur-reduced compounds. An oxic-anoxic interface, or redoxcline, is established in the water column where light and sulfide usually coexist.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001564	Diversity of Haptophytes in two years (2009-2011) of monthly samples of subsurface water in the Skagerrak revealed by 454 pyrosequencing.	At station OF2 (59.186668 N, 10.691667 E) in the Skagerrak, samples of the subsurface (1m) pico- and nanoplankton were collected monthly for two years (September 2009-June 2011). 20L were prefiltered through 45 micron, and size-fractionated into 0.8-3 micron and 3-45 micron size fractions. The haptophytes were targeted by amplification of cDNA with haptophyte-specific SSU rDNA V4 primers Hap454 described in Egge et al. 2013 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0074371).	root:Environmental:Aquatic:Marine
MGYS00001562	Metagenomic Study of North East Lakes and Ponds	Conditions that favor cyanobacterial dominance in algal blooms, and thus facilitate microcystin production, are not well understood (2). To address this issue we designed an experiment to measure taxonomic diversity during different stages of algal blooms across a geographic region. Microcystin levels and bulk algal counts are reported over a fourteen week period from samples taken once weekly at five different locations in four northeastern states. In addition, we conducted a 16S survey and metagenomic sequencing of directly sampled blooms at three different time points from each of the five sites.  Water samples were collected from five lakes and ponds in the northeast United States over a fourteen-week period from July 20 to October 21, 2010 by investigators at partner institutions across the North East Cyberinfrastructure Consortium (NECC) (Table 1). Samples were collected in triplicate once weekly from Lake Champlain at Highgate Springs, VT, Lake Winnipesaukee, NH, Sebasticook Lake, Maine and Trustum and Yawgoo Ponds in Rhode Island (Figure 1). Whole water was shipped overnight to the University of Vermont DNA Sequencing Facility where all further processing was carried out. A total of 204 samples were collected and processed. Microcystin levels and raw algae counts were measured for all samples. Total flourescent particle counts from flow cytometry analysis were used to select three time points representing the beginng, midpoint and end of the blooms at each location. These selected time points were further processed for DNA sequencing.   Whole DNA was extracted from each of the three selected time points for all locations and subjected to 16S rRNA amplicon sequencing. Samples were barcoded, multiplexed and sequenced on a single plate of a 454 Life Sciences Genome Sequencer FLX at the Genetic Analysis Genomics Core Facility,?Huck Institutes for Life Sciences, Penn State University producing 1.1M sequence reads.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001556	Dysbiosis of gut microbiota contributes to the pathogenesis of hypertension	Hypertension is one of the most prevalent cardiovascular diseases worldwide. Recent findings have identified a link between gut microbiota and blood pressure, yet the contributions of gut microbes and bacterial metabolites towards hypertension remain largely uncharacterized. We carried out metagenomic and metabonomics analyses, in combination with faecal microbiota transplantation, and elucidate that dysbiosis of gut microbiome triggers the pathogenesis of hypertension through altering the metabolic effects.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001555	454-pyrosequencing technology was employed to investigate the microbial communities from anaerobic fluidized bed reactor treating laundry wastewater.	In this study, 454-pyrosequencing technology was employed to investigate the microbial communities from anaerobic fluidized bed reactor treating laundry wastewater. Biomass from the support material (S) and phase separator (PS) were analysed in two stages, with (S-I and PS-I) and without sucrose (S-II and PS-II) as co-substrate. The pyrosequencing generated in total 18,523 sequences of the 16S rRNA representing from 4 samples that widely represented the diversity of the microbial communities. Among them 17 phyla, 30 classes, 49 orders, 64 families and 92 genera of Bacteria. While Proteobacteria followed by Bacteroidetes was found to be the dominant  phylum in the samples from the stage I (with sucrose), in samples from the stage II (without sucrose) were Proteobacteria and Gemmatimonadetes. The absence of sucrose in the last stage did not affect the Shannon-Weiner and Simpson indices. Regarding the Pielou index the most heterogeneous samples in terms of microbial distribution was PS-I, followed by S-I. The differences found between the samples indicated that the treatment process likely had effects on the microbial structure. Gemmatimonas, Desulfobulbus and Zoogloea were the most abundante genus related with surfactants degradation.	root:Engineered:Wastewater:Industrial wastewater
MGYS00001554	Metagenomics of the Respiratory disease complex in Broilers	To collect the respiratory fluid for the poultry for the diagnosis of the Respiratory disease complex.	root:Host-associated:Birds:Respiratory system
MGYS00001553	Analysis of plant derived alkaloids on rumen microbiota using an in vitro Rusitec system	Rumen microbiota have important metabolic functions for the host animal. This study aimed at characterizing changes in rumen microbial abundances and predicted metabolic pathways using an in vitro model, and to evaluate a potential modulatory role of plant derived alkaloids (PDA) using MiSeq paired ends sequencing and PICRUSt predicitve metabolic pathway analysis. The measurement of community diversity  showed an exponential increase and eventual plateau for all samples. Beta diversity analysis showed high levels of variation between individual fermenters, resulting in high variation within treatments.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00001552	Microbial diversity associated with Sphagnum mosses	Bryophytes belong to the phylogenetically oldest land plants. The bryophyte genus Sphagnum is the dominant component of the mire and bog vegetation, which are of high importance for our world climate. Recently, it was shown that Sphagnum mosses are colonized in high abundances with special microbial communities, which fulfil important functions for the moss plantlets as well as for the whole bog ecosystem. However, data obtained resulted in a lot of new scientific questions; which are the objective of the current project. The major aim of this project was to illuminate the biodiversity and ecological characteristics of the Sphagnum-associated microbiome as a bio-resource.	root:Host-associated:Plants
MGYS00001551	Four samples were collected from biological reactors treating wastewater containing an anionic surfactant (linear alklybenzene sulfonate - LAS)	Four samples were collected from biological reactors treating wastewater containing an anionic surfactant (linear alklybenzene sulfonate - LAS), aiming to analyze the microbial structure. Two reactors were fed with wastewater containing LAS (~10 mg/L), at a hydraulic retention time (HRT) of 35 h. Reactor R1L was fed with a synthetic wastewater containing LAS and reactor RL1 was fed with a laundry wastewater diluted (1:25). LAS degradation rate was 82?9% and 45?16% in the reactors RL1 and RS1, respectively. The samples were collected from the biomass in the sludge-blanket (SB) and phase-separator (PS) from reactors RL1 and RS1. These samples were named as SB-RL1, PS-RL1, SB-RS1 and PS-RS1. The samples were sequenced in a 454 platform. The four samples were sequenced in a run using barcodes (SBRL1: CGACGTGACT; PS-RL1: TACACACACT; SB-RS1: TACACGTGAT; PS-RS1: TACAGATCGT).	root:Engineered:Wastewater:Water and sludge
MGYS00001550	Microbial community response during the iron fertilization experiment LOHAFEX	Iron fertilization experiments in high-nutrient, low-chlorophyll areas are known to induce phytoplankton blooms. However, little is known about the response of the microbial community upon iron fertilization. As part of the LOHAFEX experiment in the southern Atlantic Ocean, Bacteria and Archaea were monitored within and outside an induced bloom, dominated by Phae- ocystis-like nanoplankton, during the 38 days of the experiment. The microbial production increased 1.6-fold (thymidine up- take) and 2.1-fold (leucine uptake), while total cell numbers increased only slightly over the course of the experiment. 454 tag pyrosequencing of partial 16S rRNA genes and catalyzed reporter deposition ???uorescence in situ hybridization (CARD FISH) showed that the composition and abundance of the bacterial and archaeal community in the iron-fertilized water body were re- markably constant without development of typical bloom-related succession patterns. Members of groups usually found in phy- toplankton blooms, such as Roseobacter and Gammaproteobacteria, showed no response or only a minor response to the bloom. However, sequence numbers and total cell numbers of the SAR11 and SAR86 clades increased slightly but signi???cantly toward the end of the experiment. It seems that although microbial productivity was enhanced within the fertilized area, a succession- like response of the microbial community upon the algal bloom was averted by highly effective grazing. Only small-celled mem- bers like the SAR11 and SAR86 clades could possibly escape the grazing pressure, explaining a net increase of those clades in numbers.	root:Environmental:Aquatic:Marine:Oceanic:Photic zone
MGYS00001546	The dynamic bacterial communities of a melting High Arctic glacier snowpack	Snow environments can occupy over a third of land surface area, but little is known about the dynamics of snowpack bacteria. The effect of snow melt on bacterial community structure and diversity of surface environments of a Svalbard glacier was examined using analyses of 16S rRNA genes via T-RFLP, qPCR and 454 pyrosequencing. Distinct community structures were found in different habitat types, with changes over 1 week apparent, in particular for the dominant bacterial class present, Betaproteobacteria. The differences observed were consistent with influences from depositional mode (snowfall vs aeolian dusts), contrasting snow with dust-rich snow layers and near-surface ice. Contrary to that, slush as the decompositional product of snow harboured distinct lineages of bacteria, further implying post-depositional changes in community structure. Taxa affiliated to the betaproteobacterial genus Polaromonas were particularly dynamic, and evidence for the presence of betaproteobacterial ammonia-oxidizing bacteria was uncovered, inviting the prospect that the dynamic bacterial communities associated with snowpacks may be active in supraglacial nitrogen cycling and capable of rapid responses to changes induced by snowmelt. Furthermore the potential of supraglacial snowpack ecosystems to respond to transient yet spatially extensive melting episodes such as that observed across most of Greenland?s ice sheet in 2012 merits further investigation.	root:Environmental:Aquatic:Freshwater:Ice
MGYS00001545	Salmo intestinal mucus microbes	Pilot study to determine if it was possible to isolate DNA from the commensal microbiota present on healthy Atlantic salmon and sepparate fecal amd omtestinal mucus content to be used for metagenomics	root:Host-associated:Fish:Digestive system:Foregut
MGYS00001544	Micromes on salmon skin and surrounding sea water	Pilot study to investigate if sampled Atlantic salmon skin mucus surrounding sea water could prodce quality metagenome sequence reads.	root:Host-associated:Fish:Skin
MGYS00001543	study of microbial communities of a lake during winter	three different depth points, sediment and water(2 levels)	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001542	Metagenomes of Danish EBPR WWTPs	Metagenome sequencing of activated sludge from Danish enhanced biological phosphorus removal wastewater treatment plants.	root:Engineered:Wastewater:Nutrient removal:Biological phosphorus removal:Activated sludge
MGYS00001540	metagenomics of medieval human remains from Sardinaia, Italy	Medieval skeletons from Sardinia in which Lesions indicative of pathologies were present were sampled and DNA extracted and sequenced by shotgun metagenomics  in order to find evidence of a bacterial cause to the pathologies observed.	root:Host-associated:Human
MGYS00001537	Analysis of stool samples from sickle cell disease patients and healthy controls	Analysis of stool samples from sickle cell disease patients and healthy controls	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001528	Sedimentary ancient DNA over a period of last ~14,500 years	Biodiversity of Eukaryotes was described using universal phylogenetic marker gene with a well-preserved sediment core over last post-glacial period - a period of last ~14,500 years in North-Eastern Europe. Sedimentary ancient DNA (sedaDNA) was extracted from the minuscule sediment samples with ~150 year intervals step and amplified at a low amplification level from each sub-sample.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00001527	Bacterial, archaeal and eukaryotic diversity associated with hydrothermal sediments retrieved from the Menez Gwen, Lucky Strike, and Rainbow vent fields was assessed by rRNA gene tag pyrosequencing.	Menez Gwen, Lucky Strike, and Rainbow are the three most visited and well-known deep-sea hydrothermal vent fields in the Azores region, located in the Mid-Atlantic Ridge. Their distinct geological and ecological features allow them to support a diversity of vent communities, which are largely dependent on Bacteria and Archaea capable of anaerobic or microaerophilic metabolism. These communities play important ecological roles through autotrophy, feeding, and in establishing symbiotic associations. However, the occurrence and distribution of these microbes remain poorly understood, especially in deep-sea sediments. Here we provide the first comparative survey of the sediment-associated microbial communities from these three neighboring vent fields. The taxonomic profiles of bacterial, archaeal and eukaryotic representatives were assessed by rRNA gene tag pyrosequencing. The Menez Gwen, Lucky Strike, and Rainbow studied sites presented distinct microbiomes. The occurrence of anaerobic methanogens and microaerobic Epsilonproteobacteria, particularly at the Menez Gwen site, suggest that the sediment communities are potentially enriched in subseafloor microbes, rather than from pelagic microbial taxa. Cosmopolitan OTUs were also detected mostly at Lucky Strike and Rainbow sites and affiliated with the bacterial clades JTB255, Sh765B-TzT-29, Rhodospirillaceae and OCS155 marine group and with the archaeal Marine Group I. Some variations in the community composition along the sediment depth were revealed. Trace metal contents and hydrothermal influence are suggested as being reflected in the composition of the microbial assemblages in the sediments of the three vent fields. Altogether, these findings represent valuable information for the understanding of the microbial distribution and potential ecological roles in deep-sea hydrothermal fields.	root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
MGYS00001526	Oil spill impacted sediments	Offshore spilled oils can cause long-term ecological effects in the marine environment. Environmental DNA metasystematics (EDMS) was applied to characterize the ecological effects of the Hebei Spirit oil spill on micro- and macro-biomes of sediments. Alterations on diversities and structures of micro- and macro-biomes were observed in the contaminated area with elevated concentration of total polycyclic aromatic hydrocarbons (?PAHs; sum of concentrations of parent- and alkyl-PAHs). EDMS potentially provides a powerful tool for ecological assessment of multiple communities in ecosystems affected by oil spills.	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated sediments
MGYS00001525	Viral metagenome study of Han River body	Viral metagenomic study was performed on the Han River body, one of the major river in South Korea. Surface samples were collected from upstream to downstream of the waterbody.	root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems
MGYS00001524	Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill	The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00001522	Metagenomic analysis of microbial CpG methylation in Delaware estuarine riverbank sediment	Marine sediments harbor a vast amount of Earth?s microbial biomass, yet little is understood regarding how cells subsist in these low-energy environments without forming endospores. DNA methylation, a reversible process that involves the addition of a methyl group to a nucleotide base via a methyltransferase, exists as a possible epigenetic mechanism for non-sporulated cells in low-energy sediment environments to regulate gene expression and potentially lower cellular activity. To investigate the presence and scope of this phenomenon in estuarine sediment microbial communities, we sequenced three metagenomic and 16S rRNA gene amplicon libraries extracted from a sediment core collected from the banks of the Oyster Rocks site of the Broadkill River, Milton, Delaware, USA. We targeted 5-methylcytosine at CpG sites by digesting metagenomic libraries with the methylation-sensitive restriction endonuclease HpaII. By quantitatively distinguishing ?mixed? methylation states for populations of CpG site copies, we identified dynamic, non-binary shifts in CpG methylation for community taxa and function.	root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
MGYS00001521	Ammonium influences microbial community composition in anaerobic digestion of swine manure	Objectives?To reveal the shift of microbial communities along ammonium gradients, and to examine the relationship between microbial community composition and the AD performance.Results: The CH4 production declined with increasing ammonium concentration, and was inhibited when ammonium exceeded 4000 mg/L. The VFAs especially acetate accumulated with elevated ammonium. The prokaryotic community composition and structure varied along the ammonium gradients. In particular, genera Clostridium, Tepidimicrobium, Sporanaerobacter, Peptostreptococcus, Sarcina and Peptoniphilus showed good tolerance to ammonium. However, Syntrophomonas with poor tolerance to ammonium may be inhibited during anaerobic digestion. Methanosarcina was the dominant methanogen. Conclusions: Excessive ammonium would decouple the linkage between acidification and methanogenesis. The shift of specific taxa under ammonium gradients may reflect their adaptations to different niches, which finally results in different efficiency in anaerobic digestion.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001520	"Metagenome of ""hand-picked"" Achromatium cells from Lake Stechlin, NE, Germany"	Polyploid bacteria are more common than previously believed; however, little is known about the genetic and functional diversity incurred by having multiple chromosomes. We show, using the largest known freshwater bacterium, Achomatium sp., that single cells can host a genetic diversity equal to that of entire populations. No correlation was found between genetic diversity and functional role.  The cells contain an excessive number of transposable elements and we hypothesize that these are involved in, intracellular, inter- and intra-chromosome gene re-arrangements; however, the integrity of operons is maintained. We further hypothesize that gene convergence is strongly reduced in these cells as suggested by the high diversity of the usually conserved 16S rRNA gene. Imaging the 16S rRNA distribution inside the cells points to the potentially spatial-differential expression of genes. Thus, intracellular gene transfer (iGT) leads to a large genetic diversity and potentially accelerated evolution. Polyploidy, multiple alleles, and localized gene expression, suggests Achromatium (and perhaps other polyploid bacteria) uses a genetic machinery similar to multicellular eukaryotes.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001519	Bioprospecting for genes encoding hydrocarbon-degrading enzymes from metagenomic samples isolated from northern Adriatic Sea sediments	Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been selected using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (http://redpet.bioinfo.pbf.hr/REDPET), which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM-profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. The use of this system for bioprospecting was exemplified using potential alkB and almA genes from this library.	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00001518	microbial diversity and function	studyed microbial diversity and function which is in the sediment polluted by antimony	root:Environmental:Aquatic:Marine:Sediment
MGYS00001517	Sequencing the bacterial metatranscriptome associated with the marine sponge Crambe crambe	Crambe crambe was sampled from the Western Mediterranean and immediately presserved in RNA later. Total RNA was extracted en rRNA and eukaryotic mRNA were removed and the remaining bacterial mRNA (and unremoved rRNAs and eukaryotic mRNAs) were sequenced with the Illumina HiSeq using paired end sequencing.	root:Host-associated:Porifera
MGYS00001516	Changes in the microbial community of an anammox consortium during adaptation to marine conditions revealed by 454 pyrosequencing	The submitted dataset consists of pyrosequenced barcoded v4 16S rDNA amplicons representing freshwater anammox consortia that were adapted to salinities of 3 and 30 g/L NaCl. While adaption from 0 to 3 g/L salinity took 153 days, adaption from 3 to 30 g/L salinity took only 40 days, and no inhibition was observed. A major succession in the anammox community wasobserved at 3 g L-1 where the dominating population shifted from Ca. Brocadia fulgida to Ca. Kuenenia stuttgartiensis. The latter dominated at high salinity and seemed to be essential for the high (? 96%)ammonium and nitrite removal efficiencies achieved.	root:Environmental:Aquatic:Marine
MGYS00001515	Plasmidomes of aerobic biofilm under long-term oxytetracycline exposure	Aerobic biofilm was exposed to oxytetracycline with gradually increased concentration from 0mg/L to 5mg/L and 25mg/L. Plasmid of the aerobic biofim bacteria from different exposure stages was extracted and sequenced by using illumina Hiseq sequencing.	root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
MGYS00001512	Postglacial viability and colonization in North America's ice-free corridor	During the Last Glacial Maximum (LGM) continental ice sheets isolated Beringia (northeast Siberia and northwest North America) from unglaciated North America. By ~15-14 thousand years ago (cal. kyr BP), glacial retreat opened a 1,500-km-long corridor between the ice sheets. It remains unclear when plants and animals colonized this corridor and it became biologically viable for human migration. We obtained radiocarbon dates, pollen, macrofossils and metagenomic DNA from lake sediment cores in a bottleneck portion of the corridor. We find evidence of steppe vegetation, bison and mammoth by ~12.6 cal. kyr BP, followed by open forest, with evidence of moose and elk at ~11.5 cal. kyr BP, and boreal forest ~10 cal. kyr BP. Our findings reveal that the first Americans, whether Clovis or earlier groups in unglaciated North America before 12.6 cal. kyr BP, are unlikely to have travelled this route into the Americas. However, later groups may have used this north-south passageway.	root:Environmental:Aquatic:Marine:Sediment
MGYS00001508	Evaluating the diversity and activity of marine archaea via 16S rRNA gene and transcript sequencing	This study evaluates the diversity and activity of marine archaea via 16S rRNA gene and transcript sequencing. This method is complementary to evaluation of the activity of these organisms by evaluating the differential uptake of isotope labeled bicarbonate and amino acids with nano-scale secondary ion mass spectrometry and isotope ratio mass spectrometry.	root:Environmental:Aquatic:Marine
MGYS00001507	Comparison of samples and mock communities amplified with single-base variations in 515-Forward universal primer	This study is a comparison of marine environmental and marine mock community samples amplified with different versions of a commonly used universal forward primer 515.  A mismatch in the 4th position in the 515F primer to the Thaumarchaea was corrected by replacing the (C) in that position with an ambiguity (N).	root:Environmental:Aquatic:Marine
MGYS00001506	Monthly time-series analysis of the marine microbial community from surface to seafloor at the San Pedro Ocean Time-series station	This study primarily evaluates the monthly dynamics of the marine microbial community at the San Pedro Ocean Time-series station (SPOT; near Los Angeles, CA, USA). Other marine samples from two different locations in the San Pedro Channel (Pacific Ocean) have also been analyzed to compare the microbial communities to the SPOT station.	root:Environmental:Aquatic:Marine
MGYS00001505	Studying the metagenomic diversity of tiger gut	Tiger gut metagenome is studied in order to asses the diversity of microbes residing in gut of tigers occupying different territories.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001504	Environmental alkali multi-extreme Diamante Lake Red Biofilm WGS	Diamante Lake is a multi-extreme environment located in Catamarca province, Argentina. Developing on the bottom of calcareous rocks we found Red Biofilms (DLRB). The taxonomic composition metabolic potential was determined by shotgun sequencing.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001501	18S rRNA genes from benthic Antarctic sediments	We sampled surface sediment from 24 sites across a 5,500 km region of western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities (both 16S and 18S) and sediment geochemistry.	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00001500	VARIATIONS IN MICROBIAL COMMUNITY COMPOSITION IN DEEP SUBSURFACE PIEZOMETER INSTALLATIONS	The Boom Clay layer is presently investigated as a potential host rock for geodisposal of nuclear waste in Belgium. The HADES underground research facility (EIG Euridice c/o SCK?CEN), located at 230 m depth under the site of SCK?CEN (Mol, Belgium), provides access to this clay layer for in situ geological, geochemical and geomicrobiological testing.  In order to predict how microbiology will affect the biogeochemical processes in a disposal scenario, the resident microbial communities of Boom Clay and the man-made structures within this clay are being characterised.    \tIn this study, water samples were collected from Boom Clay via various existing HADES piezometers. Microbial cells from these samples were concentrated on a 0.45 ?m filter membrane, followed by DNA extraction, PCR amplification of the V1-V3 region of bacterial 16S rDNA, automated sequencing and an in-house developed bio-informatics pipeline. The aim was to assess differences or shared features of the microbial communities residing in piezometer boreholes, supplementary to the previous screening of a single, vertical piezometer [1],  and to correlate variations to geochemical analyses.  While the boreholes of two piezometers seem highly enriched in one family of Betaproteobacteria (Rhodocyclaceae), the other piezometers seem to balance dominance between members of the Chloroflexi, Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Chlorobi, although in different ratios and with variations in overall diversity. Along the five piezometers, bacterial communities of the filters within one piezometer seem more similar to each other compared to those in other piezometers, despite a variety of filter materials or Boom Clay layers sampled within one piezometer.   \tThe observed variability in bacterial community composition suggests enrichment of certain members of the community according to the engineering properties of the piezometer installation. Although such locally enriched microbial community might not be representative for the total (engineered) clay environment, it shows that technical installations (such as piezometers) can introduce and promote local variations in the  otherwise oligotrophic clay environment and the associated bioprocesses.   \tFurther studies of other piezometers and of clay samples are needed, to pinpoint the source bacterial community underlying in situ enrichment, to unravel the mechanism that shapes such microbial community in different repository conditions and to outline the relevance of the (dominant) microbial classes in defining borehole water (and gas) chemistry.  [1]\tWouters K, Moors H, Boven P & Leys N (2013) Evidence and characteristics of a diverse and metabolically active microbial community in deep subsurface clay borehole water. FEMS Microbiol Ecol. 86: 458-473.	root:Environmental:Aquatic:Marine:Intertidal zone
MGYS00001498	Calcium induced alteration of gut microbiome in a murine model of colon cancer	Calcium supplementation correlated with distinctly segregating gut microbial communities as defined by 16S rRNA gene sequencing from both fecal and cecal samples	root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
MGYS00001493	Metagenomic analysis of infant stool sample	Stool sample from a premature human infant (UC1).  This study used metagenomic methods (community genomic analysis and sequencing of amplified 16S rRNA genes) to document microbial colonization of the gut of a premature infant born at 28 weeks gestation. Analysis of 16S rRNA gene sequences collected approximately daily revealed three compositional phases during colonization. We reconstructed genomes of the dominant organisms and intensively curated population genomic datasets from the third phase. In the third phase, the communities were dominated by a nearly clonal Serratia population, two Citrobacter strains sharing >99% nucleotide identity, and contained a lower abundance Enterococcus population, multiple plasmids and bacteriophage. The relative abundance of the Citrobacter strains changed significantly over time. Modeling of Citrobacter strain abundances suggests differences in growth rates and/or host colonization patterns. We identified genotypic variation potentially responsible for divergent strain ecologies, including hotspots of sequence variation in regulatory genes and intergenic regions, and in genes involved in transport, flagellar biosynthesis, substrate metabolism, and host colonization, as well as differences in the complements of these genes. Our results demonstrate that a community genomic approach can elucidate gut microbial colonization at the resolution required to discern medically relevant strain and species population dynamics, and hence improve our ability to diagnose and treat microbial community-mediated disorders.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001491	Metagenomic profiling of bacterial communities associated with Tyrian Purple production in a marine gastropod	Dicathais orbita is a marine mollusc well known for the production of anticancer compounds that are precursors to Tyrian purple. This study aimed to assess the full diversity of bacteria associated with the Tyrian purple producing hypobranchial gland and to identify bacteria specifically associated with the purple producing gland by comparing with the foot tissues using a high-throughput sequencing approach. The total genomic DNA was extracted from the hypobranchial gland and foot of D. orbita for high-throughput sequencing targeting the variable region V1-V3 of 16S rRNA bacterial gene. 16S rRNA bacterial sequences were processed by using combinations of QIIME and MEGAN software. The metagenome analysis revealed highly diverse bacterial assemblage associated with the hypobranchial gland and foot tissues of D. orbita. The most dominant bacteria phylum in the metagenome data set was Proteobacteria followed by Tenericutes, Spirochaetes and Bacteroidetes. Our result has also provided that larger numbers of bacterial taxa were present in the foot than the hypobranchial gland of D. orbita. This study also revealed the high abundance of Vibrio spp. in the Tyrian purple producing gland of a muricid mollusc. It also reports the presence of unique bacterial communities which shows indole production, bromoperoxidase and brominated secondary metabolites in the biosynthetic gland. This study reveals the full diversity of bacteria associated with the Tyrian purple producing gland of a marine muricids and also helped in establishing the potential role of bacteria in the biosynthesis of Tyrian purple.	root:Host-associated:Mollusca:Digestive system:Glands
MGYS00001489	16S rRNA genes from benthic Antarctic sediments	We sampled surface sediment from 24 sites across a 5,500 km region of western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities (16S and 18S rRNA) and sediment geochemistry.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00001488	Metagenomic study on the Iron-containing microbial mats of the Jan Mayen hydrothermal vent fields	Five iron mat communities were sampled with a hydraulic biosyringe suction pump in the Jan Mayen hydrothermal vent fields (71?N 6?W). The sampling method led to two phases; a solid bottom fraction (raw, R) and a liquid (top, T) part, that were both sampled separately. Two different hydrothermal conditions were considered; high-flux hydrothermal venting (warm, W) as opposed to diffuse fluid flows (cold, C).	root:Environmental:Aquatic:Marine:Hydrothermal vents:Microbial mats
MGYS00001487	Microbial diversity in deep-sea sediments from the Menez Gwen hydrothermal vent system of the Mid-Atlantic Ridge	Deep-sea hydrothermal sediments are known to support remarkably diverse microbial consortia. Culture-independent sequence-based technologies have extensively been used to disclose the associated microbial diversity as most of the microorganisms inhabiting these ecosystems remain uncultured.  Here we provide the first description of the microbial community diversity found on sediments from Menez Gwen vent system. We compared hydrothermally influenced sediments, retrieved from an active vent chimney at 812 m depth, with non-hydrothermally influenced sediments, from a 1400 m depth bathyal plain. Considering the enriched methane and sulfur composition of Menez Gwen vent fluids, and the sediments physicochemical properties in each sampled area, we hypothesized that the site-associated microbes would be different. To address this question, taxonomic profiles of bacterial, archaeal and micro-eukaryotic representatives were studied by rRNA gene tag pyrosequencing. Communities were shown to be significantly different and segregated by sediment geographical area. Specific mesophilic, thermophilic and hyperthermophilic archaeal (e.g., Archaeoglobus, ANME-1) and bacterial (e.g., Caldithrix, Thermodesulfobacteria) taxa were highly abundant near the vent chimney. In contrast, bathyal-associated members affiliated to more ubiquitous phylogroups from deep-ocean sediments (e.g., Thaumarchaeota MGI, Gamma- and Alphaproteobacteria).\nThis study provides a broader picture of the biological diversity and microbial biogeography, and represents a preliminary approach to the microbial ecology associated with the deep-sea sediments from the Menez Gwen hydrothermal vent field.	root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
MGYS00001486	Growth and activity of ANME clades with different sulfate and sulfide concentrations in presence of methane	Extensive geochemical data showed that significant methane oxidation activity exists in marine sediments. The organisms responsible for this activity are anaerobic methane-oxidizing archaea (ANME) that occur in consortia with sulfate-reducing bacteria. A distinct zonation of different clades of ANME (ANME-1, ANME-2a/b and ANME-2c) exists in marine sediments, which could be related to the localized concentrations of methane, sulfate and sulfide. In order to test this hypothesis we performed long-term incubation of marine sediments under defined conditions with methane as a headspace gas: low or high sulfate (?4 and ?21 mM, respectively) in combination with low or high sulfide (?0.1 and ?4 mM, respectively) concentrations. Control incubations were also performed, with only methane, high sulfate or high sulfide. Methane oxidation was monitored and growth of subtypes ANME-1, ANME-2a/b, and ANME-2c assessed using qPCR analysis. A preliminary archaeal community analysis was performed to gain insight into the ecological and taxonomic diversity. Almost all of the incubations with methane had methane oxidation activity, with the exception of the incubations with combined low sulfate and high sulfide concentrations. Sulfide inhibition occurred only with low sulfate concentrations, which could be due to the lower Gibbs free energy available as well as sulfide toxicity. ANME-2a/b appear to mainly grow in incubations which had high sulfate levels and methane oxidation activity, whereas ANME-1 did not show this distinction. ANME-2c only grew in incubations with only sulfate addition. These findings are consistent with previously published in situ profiling analysis of ANME subclusters in different marine sediments. Interestingly, since all ANME subtypes also grew in incubations with only methane or sulfate addition, ANME may also be able to perform anaerobic methane oxidation under substrate limited conditions or alternatively perform additional metabolic processes.	root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum
MGYS00001485	Microbial community composition in acidic and pH neutral sediments from two hypersaline lakes in Western Australia	Hypersaline environments, especially salt lakes, are extreme habitats for microbial life. The water bodies and sediments of salt lakes in Western Australia show a wide range of geochemical conditions. However, little is known about the composition and potential functions of the native microbial communities in these ecosystems. Here we compared microbial communities in the sediments of two salt lakes in Western Australia, slightly acidic Lake Orr and slightly alkaline Lake Strawbridge. Community composition was determined by 454 pyrosequencing of bacterial and archaeal 16S rRNA genes. The diversity and richness within the slightly acidic sediments of Lake Orr were lower compared to the pH neutral to alkaline sediments of Lake Strawbridge. Furthermore both salt lakes strongly differed regarding their geochemistry and microbial community composition. The archaeal community in both lakes was dominated by the Halobacteriacea, whereas Proteobacteria, Firmicutes and Bacteroidetes dominated the bacterial community. Inferred from the 16S rRNA gene based microbial community composition we found a high metabolic diversity including heterotrophic organisms, phototrophs, methanogens, fermenters, autotrophic organisms, sulfate reducers, sulfur oxidizers and metal reducers. The high phylogenetic and metabolic diversity in the salt lakes suggests that hypersaline lakes are important ecosystems with an active contribution to various biogeochemical element cycles.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
MGYS00001483	Sources and dynamics of microbial communities in cryoconite on an Alpine glacier	Cryoconite holes, i.e. small ponds that form on glacier surface, are considered the most biologically active environments on glaciers. Ecology of cryoconite holes in polar regions has been widely investigated, while that of cryoconite holes on mountain glaciers has been neglected. In this study we investigated the temporal dynamics of the microbial communities in cryoconite holes on the Forni Glacier (Italian Alps) along the ablation season and the contribution of eolian transport from periglacial environments to the microbial communities of cryoconite holes. We used Next-Generation Sequencing to assess the structure of bacterial communities, and estimated also photosynthesis and respiration rates of cryoconite holes with field measurements. We found a seasonal succession of bacterial communities, with autotrophic populations dominating communities after snow melting, and heterotrophic populations increasing in abundance later in the season. However, communities in cryoconite holes were mainly heterotrophic. Surprisingly, we also observed similarity between communities in cryoconite holes within few tens of meters to one another. Conversely, none of the periglacial environments we investigated (moraines, proglacial plain, and the debris of probable endoglacial origin) hosted bacterial communities similar to those found in the cryoconite holes in any season. Hence, periglacial environments seem not to be the source of bacteria living in the cryoconite, but may provide inputs of organic matter to cryoconite necessary to sustain the heterotrophic communities of cryoconite holes even without affecting the structure of their microbial communities.	root:Environmental:Aquatic:Freshwater:Ice:Glacier
MGYS00001482	Metatranscriptome sequencing of Tara Oceans DNA samples corresponding to size fractions for  prokaryotes.	Metatranscriptome sequencing from  different depths to retain small cell size (Bacteria Organisms). The RNA was extracted and submitted to high throughput sequencing.	root:Environmental:Aquatic:Marine
MGYS00001481	The oral metagenome in health and disease	The oral cavity of humans is inhabited by hundreds of bacterial species and some of them have a key role in the development of oral diseases, mainly dental caries and periodontitis. We describe for the first time the metagenome of the human oral cavity under health and diseased conditions, with a focus on supragingival dental plaque and cavities. Direct pyrosequencing of eight samples with different oral-health status produced 1 Gbp of sequence without the biases imposed by PCR or cloning. These data show that cavities are not dominated by Streptococcus mutans (the species originally identified as the ethiological agent of dental caries) but are in fact a complex community formed by tens of bacterial species, in agreement with the view that caries is a polymicrobial disease. The analysis of the reads indicated that the oral cavity is functionally a different environment from the gut, with many functional categories enriched in one of the two environments and depleted in the other. Individuals who had never suffered from dental caries showed an over-representation of several functional categories, like genes for antimicrobial peptides and quorum sensing. In addition, they did not have mutans streptococci but displayed high recruitment of other species. Several isolates belonging to these dominant bacteria in healthy individuals were cultured and shown to inhibit the growth of cariogenic bacteria, suggesting the use of these commensal bacterial strains as probiotics to promote oral health and prevent dental caries.	root:Host-associated:Human:Digestive system:Oral
MGYS00001477	Bacterial diversity of polluted surface sediments in northern Adriatic Sea determined by pyrosequencing	Samples were collected from surface sea sediments at seven sites in the northern Adriatic Sea; there were six sites in proximity of industrial complexes and one from a tourist site (recreational beach). The samples were assayed for alkanes and polycyclic aromatic hydrocarbons. The composition of the hydrocarbon samples suggested that industrial pollution was present in most cases. A sample from one site was also grown aerobically under crude oil enrichment in order to evaluate the response of indigenous bacterial populations to crude oil exposure. Analysis of 16S rRNA gene sequences showed varying microbial biodiversity depending on the level of pollution - ranging from low (200 detected genera) to high biodiversity (1000+ genera), with lowest biodiversity observed in polluted samples. This showed a considerable biodiversity in all the sediment samples, which was severely restricted after selection on crude oil. Phylogenetic analysis of putative alkB genes showed a high evolutionary diversity of the enzymes in the samples and suggested considerable potential for bioremediation and bioprospecting. We present the first systematic analysis of bacterial communities from sediments of northern Adriatic sea that will provide a baseline assessment that may serve as a reference point for the eco - system changes and hydrocarbon degrading potential - a potential that could soon gain importance due to plans for oil exploitation in the area.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00001475	Capturing early changes in the marine bacterial community as a result of crude oil pollution in a mesocosm experiment	Shifts in marine bacterial communities resulting from crude oil contamination were characterized by 16S rDNA PCR ? DGGE and 454 high-throughput sequencing with the aims to 1) reveal short-term changes in the structure of the marine bacterial community 2) identify the blooming bacteria resulting from oil occurrence by DNA analysis. A longer-term vision of this study is to use a selection of bacterial genes markers in combination with monitoring technology to sense and warn for oil contamination. Here, we present results obtained from seawater incubations with North Sea oil in absence (O) or presence (OD) of dispersant, carried out at low temperature (4 ?C) and in the presence of zooplankton. Despite the dispersant treatment, chemistry in O and OD was very similar possibly due to the setup with low mixing energy. Both O and OD treatments induced rapid (1 day) re-arrangement of bacterial community and enrichment of Pseudoalteromonas, Pseudomonas, Glaciecola, known as biosurfactant producers, as well as bacteria assigned to Sulfitobacter, Piscirickettsiaceae (Marine Methylotrophic Group 3), Neptunomonas and Vibrio. Pseudofulvibacter genus was enriched by oil in the treatment without dispersant. The oil- contaminated seawater contained bacterial genera of Polaribacter and Marinomonas identical in 98 -99 % to those found in the North Sea crude oil itself. This suggests that bacteria blooming in oil-contaminated seawater can also stem from the bacterial community in oil itself and contribute to the structural community shift observed.	root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
MGYS00001474	Novel subsurface lineages dominate fumarolic microbial communities at Tramway Ridge, Mt. Erebus, Antarctica	Using 16S rRNA gene amplicons and whole genome shotgun sequencing, we identified and enumerated members of the subsurface-associated microbial community in the high-elevation fumarolic sediments of Tramway Ridge.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00001473	Investigation of the protein synthesis potential in bacterial communities from Landsort Deep sediment	Numerous investigations of microbial communities using  sequencing of total DNA have revealed an extensive diversity of microbial taxa in an array of different environments. Community analysis based on total DNA solely, however, does not reveal whether community members are alive (i.e. in a growing, active, dormant state) or dead. This dilemma is of particular concern at the seafloor of the Baltic Sea?s deepest point, the Landsort Deep, where the anoxic bottom sediment is below half a kilometer of highly stratified water column with distinct differences in community structure and functions at different depths. Our previous metagenomics results showed that these anoxic sediments hold a taxonomically diverse community rich in functional capacities, but whether the diversity reflected living organisms was not evident. In this study, we sought to provide improved insight into the physiological state of the Landsort Deep sediment bacterial community members through complementary sequencing of 16S rDNA amplicons, total DNA and total RNA. Ratios of 16S rRNA OTUs in total RNA and rDNA amplicons were used to estimate protein synthesis potential among the sediment community members. Results show surprisingly high protein synthesis potential for sediment Cyanobacteria that are abundant seasonally in surface water. Furthermore, Mycobacteria, which are comparatively abundant in the Landsort Deep sediment metagenome to that of other marine sediment metagenomes, show levels of protein synthesis potential indicating they are alive and contribute to the sediment community functioning. In conclusion, our approach provides a new window of insight into the complexities of sediment microbial communities, and highlights both expected and unexpected members of the living community in the anoxic sediment of Landsort Deep.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00001472	Metagenomics of magnetotactic bacteria from Dianchi Lake	We used metagenomics to probe the community structure, magnetosome biomineralization mechanisms and potential ecological roles of magnetotactic bacteria from Dianchi Lake in southwestern China.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001471	Bioelectrochemical toluene degradation in marine environments	Accidental oil spills can lead to considerable release of toxic petroleum hydrocarbons in marine environments. Due to their recalcitrance under anoxic conditions in the sediment, oxidative bioremediation strategies have been developed. Here we investigated an alternative strategy to remove monoaromatic hydrocarbons from marine environments by stimulating the biodegradation with an electrode as solid electron acceptor. Using toluene as a model compound, degradation was accomplished in BES with simultaneous current production. Glass BES reactors were set up using sediment collected from an hydrocarbon contaminated marine site as microbial inoculum, and artificial ocean water as growth medium. Anode potentials of 0 mV and +300 mV (vs Ag/AgCl) were tested in order to check their influence on current production, enrichment of electrocatalytically active microorganisms and hydrocarbon degradation rate. At the end of the experiment microbial characterization of the communities attached to the electrodes and in the bulk of each reactor was performed by Illumina sequencing of the 16S rRNA. Degradation of toluene was directly linked to current generation up to 431 mA/m, but over time decreasing peak currents were obtained upon renewed toluene spiking. In both the conditions a degradation rate of 1 mg/(L d) was observed. Monitoring of sulfate/sulfide concentrations during bioelectrochemical experiments suggested that sulfur metabolism might play an important role in toluene degradation on a bio-anode, potentially leading to passivation over time. The microbial communities were dominated by sulfate reducing microorganisms, particularly the family Desulfobulbaceae appeared to be linked both with current production and toluene degradation.	root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum
MGYS00001469	Spatio-temporal survey of bacterial and archaeal diversity and community composition in four contrasting sediments of the Western English Channel Observatory	Sediment samples were taken from four sites in the Western English Channel as part of the Plymouth Marine Laboratory Benthic Survey. The four sites were chosen due to their contrasting combinations of depth, sediment type and level of exposure. Jennycliff (50? 20.91 N, 04? 07.71 W) and Cawsand (50? 19.81 N, 04? 11.50 W) represent shallow habitats (approximately 10 m deep), are sheltered from the prevailing south westerly winds but have different sediments types (Jennycliff is coarse silt whereas Cawsand is very fine sand). Rame Head (50? 17.75 N, 04? 16.00 W) and L4 (50? 13.30 N, 04? 11.40 W) are exposed sites with a depth of approximately 50 m, again with contrasting sediment type, Rame Head being medium silt and L4 fine sand. Samples used in this study were taken approximately bimonthly from July 2009 to May 2010. However, samples could not be taken at L4 in November 2009 due to adverse weather conditions at this site. DNA was extracted and bacterial and archaeal abundance, diversity and community composition assessed using both quantitative PCR and 454 pyrosequencing of the V4-V5 region of archaeal 16S rRNA genes. DNA libraries were prepared for sequencing using the Roche emPCR Method Manual Lib-L MV and the Roche Sequencing Method Manual for the GS FLX Titanium Series at PML. Picotitre plates were used with an 8 lane gasket.	root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00001467	The studies presented here aim to gain evaluate the potential of an anaerobic microbial consortium to biologically translate Cr(VI) from sediments amended with NPs (i.e., Fe2O3 and Fe3O4).	Chromium has been listed as one of the top 20 contaminants on the superfund priority list of hazardous substances for the past few years due to its tremendous toxicity. In general, chromium mainly exists in trivalent (Cr(III)) and hexavalent (Cr(VI)) species. Carbon sources and electron shuttles compounds, some novel materials, like nanoparticls (NPs), would play an important role in Cr(VI) reduction in anaerobic condition. Thus, the studies presented here aim to gain evaluate the potential of an anaerobic microbial consortium to biologically translate Cr(VI) from sediments amended with NPs (i.e., Fe2O3 and Fe3O4).	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00001466	Response of the sediment bacterial community to a spring phytoplankton bloom at the Western English Channel Observatory site L4	The impact of the seasonal deposition of phytoplankton and phytodetritus on surface sediment bacterial abundance and community composition was investigated at the Western English Channel site L4. Sediment and water samples were collected from January to September in 2012, increasing in frequency during periods of high water column phytoplankton abundance. Compared to the past two decades, the spring bloom in 2012 was both unusually long in duration and contained higher than average biomass. Within spring months, the phytoplankton bloom was well mixed through the water column and showed accumulations near the sea bed, as evidenced by flow cytometry measurements of nanoeukaryotes, water column chlorophyll and the appearance of pelagic phytoplankton at the sediment. Measurements of chlorophyll and chlorophyll degradation products indicated phytoplankton material was heavily degraded only when it reached the sediment surface: the nature of the chlorophyll degradation products was indicative of grazing activity. The abundance of bacterial 16S rRNA genes per gram sediment (used as a proxy for bacterial biomass) increased markedly with the onset of the phytoplankton bloom, and correlated with measurements of chlorophyll at the sediment surface. Together, this suggests that bacteria may have responded to nutrients released via grazing activity. In depth sequencing of 16S rRNA genes was also performed on four replicate samples from eight sampling point throughout the duration of the spring bloom. This indicated that the composition of the bacterial community shifted rapidly through-out the prolonged spring bloom period; primarily due to an increase in the abundance of members of the Flavobacteria.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00001465	Investigation of the response of the active microbial community to CO2 exposure from a controlled sub-seabed CO2 leak in Ardmucknish Bay (Oban, Scotland)	The impact of a controlled sub-seabed CO2 leak on the composition of the active community of benthic bacteria was assessed before, during and after CO2 release. A total of 4.2 tonnes of CO2 was injected into the overlying unconsolidated sediments, over a 37 day period, during which flow was increased from 10 to 210 kg per day. Five replicate sediment samples were taken from the epicentre and 450m distant during 4 time points (7 days before CO2 exposure, after 14 and 36 days of CO2 release, and 6 after the CO2 release had ended). RNA was extracted from the top 1 cm sediment and possible changes to the composition of the active benthic bacterial community assessed by in depth sequencing of 16S rRNA. CO2 related changes were detected to the relative abundance of both major and minor bacterial taxa: most notably an increase in the relative abundance of the Planctomycetacia after 14 days of CO2 release.	root:Environmental:Aquatic:Marine:Cold seeps
MGYS00001464	Shotgun metagenomic study of sedimentary ancient DNA (sedaDNA), from four strata of sediment core taken from an Bouldner Cliff, a submarine archaeological site in the Solent. Dates of	The Mesolithic to Neolithic transition in Europe marked the transition of humans from hunter-gathers to agriculturalists. This event coincided with rising sea levels in the area and submergence of numerous paleosols, obscuring the earliest evidence of the transition from the archaeological record. A combination of archaeological and molecular approaches of sediment cores dating from 8030-7980 cal BP show the presence of domesticated plant species, suggesting neolithicisation of the area 2,000 years earlier than expected. The submitted raw sequence data here correspond to four strata of a core sample within this time range. Using a shotgun metagenomic approach we identified sequences of domesticated plant species amongst background ecology of the early Neolithic, around 8,000 cal BP.	root:Environmental:Aquatic:Marine:Intertidal zone:Sediment
MGYS00001463	Trying to sew with a needle from a haystack: cautionary tales of assembly and taxonomy assignment from a White Oak River sediment metagenome	We analyzed a short read metagenome dataset from estuarine sediment in the White Oak River, NC to examine microbial community composition and functional potential. The dataset was assembled through multiple methods into longer reads, which were analyzed for functional and taxonomic content. While different assemblies yielded somewhat similar functional calls showing anaerobic metabolic pathways, the taxonomic calls varied depending on the pipeline applied. Homology-based assignment for taxonomy was most consistent with direct ribosomal RNA amplicon analysis, yet wide variations were seen between amplicon and metagenome identifications. Deep branching organisms may result in misidentification of genes through pipelines. We questioned whether assembly was creating chimeras and if fragment recruitment could assist in assembly. We show that close relatives may assist in assembly refinement, but that many relatives are missing for this environment in the databases. In total, we have a cautionary tale of the potential for bias and misidentification in metagenomic annotation, depending on analysis method	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00001462	Linking DNRA community structure and activity in a shallow lagoonal estuarine system	Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are two nitrate respiration pathways in the microbial nitrogen cycle. Diversity and abundance of denitrifying bacteria have been extensively examined in various ecosystems. However, studies on DNRA bacterial diversity are limited, and the linkage between structure and activity of DNRA communities has yet to be discovered. We examined the composition, abundance and activities of DNRA communities at five sites along salinity gradients in the New River Estuary, North Carolina, USA, a shallow eutrophic system. Sediment slurry incubation experiments with 15N-nitrate were conducted to measure potential DNRA rates while abundance of DNRA communities was estimated using quantitative PCR of nrfA genes encoding cytochrome C nitrite reductase, which is unique to DNRA.  A pyrosequencing method targeting nrfA genes was developed using an Ion Torrent sequencer to examine diversity and composition of DNRA communities within the estuarine sediment communities. We found a positive correlation between nrfA gene abundance and DNRA rates. Among the environmental variables, %organic and sulfide in sediments might support higher activities of DNRA communities. Pyrosequencing analysis of nrfA genes revealed spatial variation of DNRA communities along the saline gradient of New River Estuary. Relative abundance of dominant populations was found to have significant influences on overall activities and abundance of DNRA communities. Thus, we found that abundance of dominant DNRA bacteria was an important regulator of DNRA activities in the eutrophic New River Estuary.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00001461	Anthropogenic contamination in Red Sea and their potential impact on marine water microbial community	Good water quality in the Red Sea is imperative for the continued sustenance of key industries like desalination and aquaculture, as well as to ensure minimal public health impact. Through the use of next-generation sequencing, this study aims to evaluate the impact anthropogenic contamination has on seawater microbiota at four sampling zones of near-shore water (<1.5km from the coast) and from two swash zones of local beaches. Conventional water quality parameters relating to nutrient content and enterococci numbers were also monitored. Occasional breaches in the enterococci numbers (> 35 MPN/100ml) and significantly higher abundance of genera associated with opportunistic pathogens were detected in the water samples collected from swash zones of beaches. Total organic carbon (1.48-2.18 mg/L) and nitrogen (0.15-0.27 mg/L) content in these water samples were also significantly higher than that detected in the near-shore waters (1.13 mg/L for organic carbon and 0.09 mg/L for total nitrogen). The abundance of certain genera, for example Clostridia group, was observed to correlate with the nutrient content (Spearman?s rank > 0.503). Furthermore, Enterococcus faecalis and E. faecium isolated from the beach sands showed resistance to up to 5 types of antibiotics (i.e., kanamycin, erythromycin, chloramphenicol, ceftazidime and meropenem). OTUs associated with cyanobacteria, Prochlorococcus and Ostreococcus were more prevalent in the near-shore waters collected in closest proximity to a sewage outfall. Microbial richness at these sites was on average 702 OTUs, and was significantly lower than the average 1062 OTUs determined from all other samples. Our findings suggest that anthropogenic contamination arising from sewage discharge and recreational activities resulted in different extent of perturbations on marine water community in near-shore and swash zones of the Red Sea.	root:Environmental:Aquatic:Non-marine Saline and Alkaline
MGYS00001458	This study utilizes a metagenome-based approach to elucidate the phylogenetic and functional gene diversity of fecal microbiome in Galapagos land and marine iguanas.	While much has been known about the fecal microbiome of mammalian herbivorous, little is known about the fecal microbiome of reptilian herbivores. To elucidate the functional gene diversity of reptilian herbivores, we performed a metagenome-based analysis of the fecal samples from the algae-consuming marine iguana (Amblyrhynchus cristatus) and terrestrial flora-consuming land iguanas (genus Conolophus) that are indigenous on the Gal?pagos Archipelago. Further comparison was made against the mammalian herbivorous hosts, and our findings suggested that the phylogenetic affiliations of both land iguanas (LI) and marine iguanas (MI) fecal microbiota clustered apart, and shared low similarity with the mammalian herbivorous hosts. Furthermore, functional gene diversities in both iguana hosts showed differentiation based on the diet, in which the MI fecal microbiota had a functional diversity that clustered apart from the other terrestrial-flora consuming LI iguana and herbivorous mammalian hosts. The differentiation in the functional gene diversity of MI fecal microbiota is likely attributed to a distinctly unique diet that is based on marine algae. A further examination of the carbohydrate-degrading genes revealed that several of the prevalent glycosyl hydrolases (GH), glycosyl transferases (GT), carbohydrate binding modules (CBM) and carbohydrate esterases (CE) gene classes were conserved among all examined herbivorous mammalian and reptilian hosts, reiterating the important roles these genes have in the breakdown and metabolism of herbivorous diet. However, some classes of carbohydrates-degrading families like GH2, GH13, GT2, GT4, CBM50, CBM48, CE4 and CE11, as well as genes associated with sulfur metabolism and dehalogenation were highly expressed or unique to the MI fecal microbiota. In contrast, gene sequences that relate to archaeal methanogenesis were detected only in LI fecal microbiome, and carbohydrate-degrading families like GH13, GH66, GT2, GT4, CBM50, CBM13, CE4 and CE8 were highly abundant in the LI. Certain bacterial populations were enriched over ten generations in various substrates (e.g. glucose, arabinose, xylose), and the enriched populations exhibited differences based on the iguana host and the type of enrichment substrate. Majority of the enriched bacterial populations belong to genera Clostridium spp. and Enterococcus spp. that likely accounted for the high prevalence of GH13 and GH2, as well as the GT families (e.g. GT2, GT4, GT28, GT35 and GT51) that were ubiquitously present in the fecal microbiota of all herbivorous hosts.	root:Host-associated:Reptile
MGYS00001455	Multiple approaches detect the presence of fungi in human breast milk samples.	BackgroundHuman breast milk contains a variety of bacteria, which is transmitted to the infant and contributes to microbiota development and immune maturation. The description of fungal organisms in breastmilk from healthy mothers is uncovered although the presence of fungal species has been reported in the human gut and in other mammalians? milk.  Methods  Breast milk samples from healthy lactating mothers (n=65) within 1 month after birth were analyzed. Fungal presence was confirmed by microscopy using fungal-specific fluorescent probes (FISH), isolation in culture media and isolates identification by specific ITS and 18S PCR and Sanger-sequencing.  Total fungal load was estimated by qPCR using fungal-specific primers, and the fungal composition was determined by 28S high-throughput rDNA sequencing. In addition, milk macronutrients and human somatic cells were also quantified by spectrophotometry and cytometry. ResultsUsing different culture media, we isolated 18 strains, whose ITS and 18S rDNA genes sequencing led to confirm the presence of viable fungal species. The qPCR data showed that 89% of the samples had detectable levels of fungal DNA, at an estimated median load of 4,1x105 cells/ml in colostrum, 4,5x105 cells/ml in transition milk and 2,8x105 cells/ml in mature milk samples. Pyrosequencing of the PCR-amplified 28S rDNA gene showed that the most common genera detected were Malassezia (44%), followed by Candida (19%) and Saccharomyces (12%). Nutrient analysis of the milk samples showed significant positive correlations of Malassezia presence with lactose content, and Candida presence with protein content. We also found a significant negative correlation between Lodderomyces genus and human somatic cells, as well as positive correlations of Cladosporium and Alternaria with bacterial load. ConclusionsIn this study we have detected the presence of viable fungal species in human breast milk.  Interaction between fungi and milk?s components and bacteria present may have a relevant role for infant?s health development. However, further research should be performed to understand the origin and role of these microorganisms and their potential transmission to the developing infant.	root:Host-associated:Human:Milk
MGYS00001453	Metagenomic analysis of anaerobic reactors for wastewater treatment	Differently seeded but functionally identical anaerobic sequencing batch reactors were analysed using metagenomic and metaproteomic analyses	root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
MGYS00001452	A Metagenomic Anlaysis of a Winogradsky Column Supplemented with Molybdate	Two Winogradsky Columns were constructed from the University of Strathclyde burn. A control column and a column supplemented with Molybdate were created. The columns were homogenised and metagenomic analysis was carried out using WGS sequencing on an Ion Torrent PGM Sequencer. It was hypothesised that the column containing Molybdate should be enriched with nitrate reducing bacteria.	root:Engineered:Bioremediation:Hydrocarbon
MGYS00001450	Citrate addition enhanced anaerobic hydrocarbon degrader activity	Citrate addition can increase phosphorus and hydrocarbon bioavailability to enhance hydrocarbon bioremediation, but the overall microbial community response is poorly understood. In order to elucidate the potential mechanisms of citrate addition for hydrocarbon biostimulation, the structure and function of microbial communities were investigated in a gasoline-contaminated site in calcareous cold region soil.There are three treatments (no amendment, phosphate amendment, phosphate and citrate amendment) for the biostimulation deliveries. DNA was extracted from soils for different biostimulation treatments. 16S metagenomics sequencing library was constructed with primers 926F and 1392R and was sequenced on an Illumina Miseq sequencer.	root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
MGYS00001449	Microbes present in feed to Atlantic salmon	THe samples are to investigate the type of microbes that Atlantic salmon are feed through feed	root:Engineered:Food production
MGYS00001448	Disentangling facilitation drivers in arid environments: the role of soil microorganisms	1.\tNurse plants promote establishment of other plant species by buffering climate extremes and improving soil properties. Soil biota plays an important role, but an analysis to disentangle the effects of soil microorganisms, soil properties and microclimate on facilitation is lacking. \n2.\tIn three microhabitats (gaps, small and large Retama shrubs), we placed 6 microcosms with sterilized soil, two per soil origin (i.e., from each microhabitat). One in every pair received an alive, and the other a sterile, inoculum from its own soil. Seeds of annual plants were sown into the microcosms. Germination, survival and biomass were monitored. Soil bacterial communities were characterized by pyrosequencing. \n3.\tGermination in living Retama inoculum was nearly double that of germination in sterile inoculum. Germination was greater under Retama canopies than in gaps. Biomass was up to three times higher in nurse than in gap soils. Soil microorganisms, soil properties and microclimate showed a range of positive to negative effects on understory plants depending on species identity and life stage.\n4.\tNurse soil microorganisms promoted germination, but the effect was smaller than the positive effects of soil properties and microclimate under nurses. Nurse belowground environment (soil properties and microorganisms) promoted plant growth and survival more than nurse microhabitat.	root:Environmental:Terrestrial:Soil:Desert
MGYS00001447	Samples from salt marshes in the south of England	Samples were collected from natural and realigned sites, and during Summer and Winter.	root:Environmental:Terrestrial:Soil
MGYS00001446	Citrate may stimulate the anaerobic hydrocarbon degraders in the groundwater	Citrate addition can increase phosphorus and hydrocarbon bioavailability to enhance hydrocarbon bioremediation, but the overall microbial community response is poorly understood. In order to elucidate the potential mechanisms of citrate addition for hydrocarbon biostimulation, the structure and function of microbial communities were investigated in a gasoline-contaminated site in calcareous cold region soil.There are three treatments (no amendment, phosphate amendment, phosphate and citrate amendment) for the biostimulation deliveries. DNA was extracted from Tenax beads incubated in two infiltrators for different biostimulation treatments. 16S metagenomics sequencing library was constructed with primers 926F and 1392R and was sequenced on an Illumina Miseq sequencer.	root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
MGYS00001445	Atlantic salmon Microbiota	Pilot study to determine if it was possible to isolate DNA from the commensal microbiota present on healthy Atlantic salmon skin-mucus and intestinal content to be used for PacBio sequencing	root:Host-associated:Fish
MGYS00001444	Gut microbiome from patients obtained by 16s rRNA sequencing.	Advento study is a research about chronic diseases that are frequent in adult population, specially diabetes and cardiovascular conditions.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001443	Comparison between samples obtained from Curua Una reservoir	Three samples were collected from Curua Una reservoir to compare metagenomic features between samples.	root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems
MGYS00001442	Potential and active functions in the gut microbiota of a healthy human cohort	Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001437	Fecal microbiota of fur animal	In this study, the fecal microbiota of the fox and raccoon dog were analyzed. Total DNA was extracted from fecal samples, and the v4 16S rRNA amplicons were characterized on an Illumina MiSeq platform.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001432	Metagenomic, Metatranscriptomic and Metviriomic analysis of samples collected at four time points during a single day at the Gulf of Aqaba in the Red Sea.	To gain knowledge about the abundance of phage-harbored metabolic genes and the extent to which they are expressed in the marine environment, and to detect changes in viral and host populations as well as variations in gene expression, four samples were collected from the Gulf of Aqaba in the Rea Sea. gDNA, vDNA and RNA was collected in 2012 at four different time points over 24 hours. Using a unique approach, no amplification or enrichment methods were applied to any of the fractions prior to sequencing in order to limit sample-specific biases.	root:Environmental:Aquatic:Marine
MGYS00001430	Metagenomic investigation of the coastal region of south Gujarat using soil sample - Nargol, Umargam and Dandi	metagenomic investigation of the coastal region of south Gujarat. Soil and water samples were collected and pooled from three different location; dandi, umargam and nargol. From the pooled sample, environmental metagenomic DNA was isolated followed by WGS using  Illumina Miseq platform.	root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00001426	Citrate may stimulate the anaerobic hydrocarbon degraders	Citrate may stimulate the anaerobic hydrocarbon degraders	root:Environmental:Terrestrial:Soil:Clay:Oil-contaminated
MGYS00001425	Nitrogen  fertilization  directly  affects  soil  bacterial  diversity  and  indirectly  affects  bacterial community composition through soil acidification and plant community changes in grassland	Nitrogen  (N)  deposition  influences  both  above-  and  belowground  communities  and  influences  ecosystem  functioning.  However  the  mechanisms  underlying  alternations  in  bacterial  communities  following  N  enrichment  remain  elusive,  as  does  an  integrated  understanding  of  plant-soil-microbe interactions. In this study, the responses of soil bacterial community composition and diversity to N enrichment  were  investigated  at  surface  (0-10 cm)  and  sub-surface  (10-20 cm)  soils  in a  temperate  steppe  ecosystem.  N  addition  (>120  kg  N  ha -1   yr -1 )  resulted  in  a  significant  shift  in  bacterial community  composition  and  a  decrease  in  bacterial  diversity  in  surface  soil,  but  the  effect  on  the sub-surface  layer  was  far  less  pronounced,  even  at  the  highest  addition  rate  (240  kg  N  ha -1   yr -1 ). Bacterial  community  composition  was  significantly  correlated  with  soil  and  plant  characteristics. Hierarchical structural equation modeling showed that soil ammonium availability was responsible for the shift in bacterial richness, whereas alternation in soil pH and plant composition contributed to the change in bacterial communities. Our results suggest that N fertilization directly affects soil bacterial richness  and  indirectly  affects  bacterial  communities  via  soil  acidification  and  changes  in  plant composition. This indicates that N addition in a temperate steppe ecosystem influences soil bacterial diversity and community composition in an inconsistent manner.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00001424	Towards the core microbiome for a thermophilic biogas plant applying metagenome and metatranscriptome analyses complemented by cultivation and characterization if isolates for major functional groups.	Towards the core microbiome for a thermophilic biogas plant applying metagenome and metatranscriptome analyses complemented by cultivation and characterization if isolates for major functional groups.	root:Engineered:Biogas plant
MGYS00001423	Towards the core microbiome for a thermophilic biogas plant applying metagenome and metatranscriptome analyses complemented by cultivation and characterization of isolates for major functional groups.	Towards the core microbiome for a thermophilic biogas plant applying metagenome and metatranscriptome analyses complemented by cultivation and characterization of isolates for major functional groups.	root:Engineered:Biogas plant
MGYS00001422	Amplicon sequencing of four biogas plants	Amplicon sequencing of four biogas plants	root:Engineered:Biogas plant
MGYS00001421	Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health	BACKGROUND: To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. METHODOLOGY/PRINCIPAL FINDINGS: We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. CONCLUSIONS/SIGNIFICANCE: After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems.	root:Environmental:Terrestrial:Soil:Desert
MGYS00001420	Impact of faecal microbiota transplantation on the intestinal microbiome in metabolic syndrome patients	Ten individuals with metabolic syndrome underwent a single faecal microbiota transplantation (FMT): 5 of which were allogenic, the other 5 autologous. Stool samples were collected before FMT (day 0) and days 2, 14, 42 and 84 after FMT; and from the donor before FMT. Metagenomic shotgun sequencing was performed on all samples.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001419	Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity	Diazotrophs provide the only biological source of fixed atmospheric nitrogen in the biosphere. Although they are the key player for plant-available nitrogen, less is known about their diversity and potential importance in arid ecosystems. We investigated the nitrogenase gene diversity in native and agricultural desert soil as well as within root-associated microbiota of medicinal plants grown in Egypt through the combination of nifH-specific qPCR, fingerprints, amplicon pyrosequencing, and FISH-CLSM. Although the diazotrophic microbiota were characterized by generally high abundances and diversity, statistically significant differences were found between both soils, the different microhabitats, and between the investigated plants (Matricaria chamomilla L., Calendula officinalis L., and Solanum distichum Schumach. and Thonn.). We observed a considerable community shift from desert to agriculturally used soil that demonstrated a higher abundance and diversity in the agro-ecosystem. The endorhiza was characterized by lower abundances and only a subset of species when compared to the rhizosphere. While the microbiomes of the Asteraceae were similar and dominated by potential root-nodulating rhizobia acquired primarily from soil, the perennial S. distichum generally formed associations with free-living nitrogen fixers. These results underline the importance of diazotrophs in desert ecosystems and additionally identify plants as important drivers in functional gene pool diversity.	root:Host-associated:Plants:Rhizosphere
MGYS00001418	Retrieval of Commamox genomes using metagenomics	Retrieval of Commamox genomes using metagenomics.	root:Engineered:Wastewater:Industrial wastewater:Petrochemical
MGYS00001417	Extradiol dioxygenase pyrosequencing- Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid Poplar	It is envisaged that a detailed understanding of rhizospheric microbial populations will greatly contribute to a better design and implementation of rhizoremediation. In order to investigate the long-term succession of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula x tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at 7 different time-points during the course of 2 years and sampling time-points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing whereas catabolic communities were monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late phase communities.	root:Host-associated:Plants:Rhizosphere
MGYS00001416	16S rRNA gene pyrosequnecing- Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid Poplar	It is envisaged that a detailed understanding of rhizospheric microbial populations will greatly contribute to a better design and implementation of rhizoremediation. In order to investigate the long-term succession of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula x tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at 7 different time-points during the course of 2 years and sampling time-points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing whereas catabolic communities were monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late phase communities.	root:Host-associated:Plants:Rhizosphere
MGYS00001415	Alk B pyrosequencing -Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid Poplar	It is envisaged that a detailed understanding of rhizospheric microbial populations will greatly contribute to a better design and implementation of rhizoremediation. In order to investigate the long-term succession of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula x tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at 7 different time-points during the course of 2 years and sampling time-points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing whereas catabolic communities were monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late phase communities.	root:Host-associated:Plants:Rhizosphere
MGYS00001414	Diversity of Clostridium cluster I community in a biogas plant	A two stage biogas production plant was analyzed for the diversity of bacteria from Clostridium cluster I and presence of its pathogenic members. A group specific approach was used to amplify 16S rRNA genes of Clostridium cluster I. Amplicons were sequences by 454 technology. Samples include substrates used for anaerobe digestion, i.e. maize silage, whole plant silage and cattle manure, and material from main and secondary digester. The biogas plant consisted of two parallel digesters one operated with cattle manure, the other without.	root:Engineered:Biogas plant
MGYS00001413	The sapro-rhizosphere concept: Energy flow from plant roots via saprotrophic fungi to bacteria	Two common saprotrophic, rhizosphere-inhabiting fungi, Trichoderma harzianum and Mucor hiemalis, were confronted in a microcosm system with bacterial communities extracted from two plant rhizospheres (Carex arenaria and Festuca rubra).	root:Host-associated:Plants:Rhizosphere
MGYS00001400	Community structure and diversity of the root-associated microbiome of Ilex paraguariensis St. Hil (Yerba Mate) after bio-inoculation with Kosakonia radicincitans YD4	Using ITS amplicon sequencing, structure and diversity of the root-associated fungal community of Ilex paraguariensis St. Hil (Yerba Mate) was investigated in a pot experiment in Argentina.	root:Host-associated:Plants:Root
MGYS00001399	Community structure and diversity of the root-associated microbiome of Ilex paraguariensis St. Hil (Yerba Mate)	Using ITS amplicon sequencing, structure and diversity of the root-associated fungal communities of Ilex paraguariensis St. Hil (Yerba Mate) was investigated in different plantations from Argentina.	root:Host-associated:Plants:Root
MGYS00001396	Microbial diversity on Icelandic glaciers and ice caps	Algae are important primary colonizers of snow and glacial ice, but hitherto little is known about their ecology on Iceland?s glaciers and ice caps. Due do the close proximity of active volcanoes delivering large amounts of ash and dust, they are special ecosystems. This study provides the first investigation of the presence and diversity of microbial communities on all major Icelandic glaciers and ice caps over a three year period. Using high-throughput sequencing of the small subunit ribosomal RNA genes (16S and 18S), we assessed the snow community structure and complemented these analyses with a comprehensive suite of physical-, geo- and biochemical characterizations of the aqueous and solid components contained in snow and ice samples. Our data reveal that a limited number of snow algal taxa (Chloromonas polyptera, Raphidonema sempervirens and two uncultured Chlamydomonadaceae) support a rich community comprising of other micro-eukaryotes, bacteria and archaea. Proteobacteria and Bacteroidetes were the dominant bacterial phyla. Archaea were also detected in sites where snow algae dominated and they mainly belong to the Nitrososphaerales, which are known as important ammonia oxidizers. Multivariate analyses indicated no relationships between nutrient data and microbial community structure. However, the aqueous geochemical simulations suggest that the microbial communities were not nutrient limited because of the equilibrium of snow with the nutrient-rich and fast dissolving volcanic ash. Increasing algal secondary carotenoid contents in the last stages of the melt seasons have previously been associated with a decrease in surface albedo, which in turn could potentially have an impact on the melt rates of Icelandic glaciers.	root:Environmental:Aquatic:Freshwater:Ice:Glacier
MGYS00001395	The plant is crucial: specific composition and function of the phyllosphere microbiome of indoor ornamentals	The indigenous phyllosphere microbiome was identified as a key component for plant growth and health, and for positive effects on microbial diversity within a built environment. Nevertheless, there is still limited understanding of the phyllosphere microbiota and its driving factors. To study the variability of the microbiome in relation to plant genotype and climate, we investigated 14 phylogenetically diverse plant species grown under different controlled conditions in the greenhouses of the Botanical Garden in Graz (Austria). All investigated plants showed highly specific bacterial abundances of up to 106 CFU cm-2 on their leaves. Bacterial diversity (Shannon index H?: 4.1 ? 6.8) and number of putative OTUs (Chao 1: 501 ? 1,097) were strongly plant species-dependent, but comprised similar dominant phyla: Firmicutes, Proteobacteria and Actinobacteria. Non-metric multidimensional scaling and BIO-ENV analysis showed a higher correlation of community composition to plant genotype rather than the ambient climatic variables. The antagonistic potential of the phyllosphere microbiome towards the plant pathogen Botrytis cinerea measured by production of antifungal volatile organic compounds (VOCs) differed in a range of 2 up to 58% of the isolates. Frequently isolated VOCs produces were represented by Bacillus ssp., Stenotrophomonas rhizophila and Kocuria ssp. Surprisingly, the applied biopesticide B. thuringiensis Bt407 was found well-established in all phyllospheres. This study indicates that indoor ornamentals feature a distinct, stable microbiota with a high proportion of antifungal VOC-producers on leaves irrespective of the indoor climate. Hence, the microbiome of phyllospheres stabilize microbial diversity indoors, and can lead to beneficial effects on human health inside buildings.	root:Host-associated:Plants
MGYS00001393	Sedimentary DNA reveals cyanobacterial community diversity over 200 years in two perialpine lakes	We present a method for reconstructing past cyanobacterial communities using a temporally high resolved genetic approach on sedimentary DNA (sedDNA) from two stratified peri-alpine lakes in Switzerland (Lake Greifensee and Lake Zurich). We successfully sequenced a 400 nucleotides-long amplicon in the 16S rRNA gene using high-throughput sequencing. The amplicons were used to build a phylogeny summarizing the diversity over the past 200 years in the two lakes. Sequencing revealed a high diversity of cyanobacteria in both lakes. Operational taxonomic units (OTUs) spanned the whole phylum Cyanobacteria and included representatives of a newly described line of bacteria termed Malainabacteria which share common ancestry with cyanobacteria, and have not been previously reported in lakes. The sequencing data was validated using a dataset comprising of 40 years of pelagic phytoplankton microscopic identification from each lake. Common taxa identified in the pelagic samples were also recovered from the sediments. The linear model confirmed a strong and significant relationship (R2=0.86) between pelagic species richness estimated by microscopy and OTU richness from the sediments. The slope for each lake was close to the 1:1 line, but the diversity derived from the sedDNA had a higher baseline compared to microscopy. The water-sediments richness relationship differed among cyanobacterial orders, revealing that diversity of Chroococcales and Synechococcales was widely underestimated by microscopy. Our results demonstrate the feasibility of this approach for the reconstruction of past cyanobacterial pelagic communities using lake sedDNA, and its potential for exploring variation in phylogenetic diversity and community structure over long-term lake historical changes.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001392	Retrieval of Commamox genomes using metagenomics	Retrieval of Commamox genomes using metagenomics.	root:Engineered:Wastewater:Industrial wastewater:Petrochemical
MGYS00001391	Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge	Overgrowth of filamentous bacteria in activated sludge wastewater treatment plants (WWTPs) leads to impaired sludge settleability, a condition known as bulking, which is a common operational problem worldwide. Filaments with the Eikelboom 0092 morphotype are commonly associated with such bulking episodes. Members of the uncultured B45 phylotype, which is embraced within the phylum Chloroflexi, were recently shown to exhibit this morphology. Although these organisms are among the most abundant populations recorded in activated sludge processes, nothing is known about their metabolic characteristics. In this study, a genome sequence, representing the phylotype, was retrieved from a metagenome generated from an activated sludge WWTP plant. The genome consisted of two chromosomes and one plasmid, which were 4.0, 1.0, and 0.04 Mbps in size, respectively. A metabolic model was constructed for this organism, based on annotation of its genome, showing its ability to generate energy by aerobic respiration, utilizing oxygen, nitrite, or nitrous oxide as electron acceptors, or by fermentation of sugars. This model was validated partially in situ. The provisional name of Candidatus ?Promineofilum breve? is proposed for this species. This study represents the first detailed information on an uncultured genus of filamentous organisms from activated sludge.	root:Engineered:Wastewater:Activated Sludge
MGYS00001390	Bacterial diversity across a strong vertical contrast ecosystem; a salt wedge karstic estuary	Highly stratified karstic estuaries (salt-wedge estuaries) are characterized by a strong gradient of salinity and other environmental parameters. The bacterial diversity in many estuaries has been documented but no information is available about the diversity of bacteria in Mediterranean karstic estuaries. A combination of 454 pyrosequencing of the 16S rRNA gene and catalyzed reporter deposition-fluorescence in situ hybridization techniques were used to estimate the bacterial diversity across the karstic Krka River Estuary in February and July 2013. The bacterial community at the OTU level showed stronger seasonal, rather than spatial, variation that is caused by the phytoplankton bloom in February. The alphaproteobacterial SAR11 clade was an important group whose abundance showed a decrease toward the low salinity riverine water. Higher relative abundance of the SAR11 clade was detected in July when more oligotrophic conditions were observed. Roseobacter responded to the phytoplankton bloom in February increasing its abundance in the water layer with higher phytoplankton biomass. Cyanobacteria showed substantial seasonal change being an important primary producer in July during lower nutrient conditions. Actinobacteria and Betaproteobacteria were characteristic for the freshwaters layer of the estuary with Actinobacteria showing strong seasonal change and higher abundance in July. Bacteroidetes and Gammaproteobacteria also showed seasonal differences with higher abundances in February during the phytoplankton bloom in the inner part of the estuary. The bacterial community in the Krka River Estuary showed pronounced seasonal changes, due to the phytoplankton bloom observed in February, and vertical changes, as a result of a stable, sharp halocline that is characterizing this type of estuaries.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00001389	Metagenomic study of the microbial genes abundance in treated palm oil mill effluent	Metagenomic study of the microbial genes abundance in treated palm oil mill effluent	root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
MGYS00001388	Ribosomal tag pyrosequencing of DNA and RNA reveals  'rare' taxa with high protein synthesis potential in the sediment of a hypersaline lake in Western Australia	Ribosomal tag pyrosequencing of DNA and RNA reveals  'rare' taxa with high protein synthesis potential in the sediment of a hypersaline lake in Western Australia	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
MGYS00001387	DRY AND RAINY SEASONS REFLECT DIFFERENT SCENARIOS IN THE BACTERIAL COMMUNITY OF THE RHIZOSPHERE OF ENDEMIC CACTACEAE	We applied multiplexed barcoded 16S ribosomal RNA gene pyrosequencing to survey the diversity and distribution of bacteria of the rizhosphere of endemic cactaceae	root:Host-associated:Plants:Rhizosphere
MGYS00001386	Pyrosequencing of biofilm 16S ribosomal RNA (rRNA) supported on various materials with a wastewater inoculum.	The aim of this study was to provide new knowledge of bacterial community structure and composition found on various types of synthetic and natural support media used in the previous study. This was achieved by applying PCR based 454 pyrosequencing to bio?lm samples obtained from the media surfaces from laboratory scale, temperature-controlled experimental facility of the aerobic reactors. Then analyzed the sequences using bioinformatics tools. In particular we sought new understanding of the in?uence of different temperature conditions and media types on the bio?lm composition responsible for wastewater treatment. To the best of our knowledge, this study is the first application of pyrosequencing to characterize and compare biofilm samples on different types of media. Such information is important for the best operation and management of the FBRs in the future. It will prove very helpful in the selection of proper media having tendency of carrying diverse biofilm for respective wastewater treatment in the areas with extreme temperature conditions.	root:Engineered:Bioreactor:Continuous culture
MGYS00001385	Microbial diversity and community respiration in freshwater sediments influenced by artificial light at night	An increasing proportion of the Earth?s surface is illuminated at night. In aquatic ecosystems, artificial light at night (ALAN) may influence microbial communities living in the sediments. These communities are highly diverse and play an important role in the global carbon cycle. We combined field and laboratory experiments using sediments from an agricultural drainage system to examine how ALAN affects communities and alters carbon mineral- ization. Two identical light infrastructures were installed parallel to a drainage ditch before the start of the experiment. DNA metabarcoding indicated that both sediment communities were similar. After one was lit for five months (July?December 2012), we observed an increase in photoautotroph abundance (diatoms, Cyanobacteria) in ALAN-exposed sediments. In laboratory incubations mimicking summer and winter (six weeks each), communities in sediments that were exposed to ALAN for 1 year (July 2012?June 2013) showed less overall seasonal change compared with ALAN-naive sediments. Nocturnal community respiration was reduced in ALAN-exposed sedi- ments. In long-term exposed summer-sediments, we observed a shift from negative to positive net ecosystem production. Our results indicate ALAN may alter sediment communities over time, with implications for ecosystem- level functions. It may thus have the potential to transform inland waters to nocturnal carbon sinks.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00001384	Microbial dynamics and biofouling in suspended and attached growth anaerobic membrane bioreactors treating low-strength synthetic wastewater	Two lab-scale anaerobic membrane bioreactors (AnMBRs), one up-flow attached-growth (UA) and another continuously stirred (CSTR), were operated under mesophilic conditions (35 ?C) while treating low-strength synthetic wastewater (800 mg/L COD). Each reactor was attached to both polyvinylidene fluoride (PVDF) and polyethersulfone (PES) microfiltration (MF) membranes concurrently in external cross-flow configuration. Both reactors were upstarted and run under the same operating conditions for multiple biofouling experiments. COD removal rates were similar for both reactors (90-96%). During the first fouling experiment conducted for the CSTR reactor, the PES membrane experienced an increase in transmembrane pressure (TMP) to above 60 kPa within the first 20 days of operation while all other membranes in both reactors experienced more gradual fouling rates. High performance liquid chromatography (HPLC) protein analysis of the soluble extracellular polymeric substances (EPS) of all biofilm samples showed a peak at retention time of 6 min that dominated in size when premature fouling was observed. This peak was also seen consistently in the soluble microbial products (SMP) of the retentate for both reactors. Microbial dynamics in reactor biomasses and in membrane biofilms were monitored using Ion Torrent sequencing targeting 16S rRNA genes. Results showed that presence of syntrophic bacteria and methanogens were higher in attached biomass as compared to suspended biomass while several dominant OTUs closest related to fermentative bacteria were dominant in the suspended biomass of the CSTR. Despite the UA reactors? inherent affinity for attached biomass, methane production rates were roughly 15% higher in the CSTR AnMBR than the UA. Furthermore, several groups of bacteria associates with the phylum Firmicutes were present in the CSTR suspended sludge at high relative abundances only in samples taken close to increases in TMP across the PES membrane, suggesting a possible connection with premature fouling.	root:Engineered:Bioreactor
MGYS00001383	MiDAS DNA Extraction and primer choice	Evaluation of the impact of DNA extraction and primer choice on the observed microbial community in activated sludge using 16S rRNA amplicon sequencing.	root:Engineered:Wastewater:Activated Sludge
MGYS00001382	MiDAS DNA Extraction metagenomics and metatranscriptomics	Evaluation of the impact of DNA extraction and primer choice on the observed microbial community in activated sludge using metagenomics and metatranscriptomics.	root:Engineered:Wastewater:Activated Sludge
MGYS00001381	Metaproteomics of aquatic microbial communities in a deep and stratified estuary	Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in Eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific ?nepheloid? taxa that may contribute significantly to coastal ocean nutrient cycling.	root:Environmental:Aquatic:Estuary
MGYS00001380	Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice	Antibiotics have long-lasting consequences on the gut microbiota with the potential to impact host physiology and health. However, little is known about the transgenerational impact of an antibiotic-perturbed microbiota. Here we demonstrated that adult pregnant female mice inoculated with a gut microbial community shaped by antibiotic exposure passed on their dysbiotic microbiota to their offspring. This dysbiotic microbiota remained distinct from controls for at least 5 months in the offspring without any continued exposure to antibiotics. By using IL-10 deficient mice, which are genetically susceptible to colitis, we showed mice that received an antibiotic-perturbed gut microbiota from their mothers had increased risk of colitis. Taken together, our findings indicate that the consequences of antibiotic exposure affecting the gut microbiota can extend to a second generation.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001379	GD_MGS_title	GD_MGS_describe	root:Environmental:Air
MGYS00001378	Molecular study on haloarchaea producing industerially important enzymes	Samples collected from soda lakes  in wadi al natrun ,egypt to study microbial diversity  and isolated DNA directly from environment to study molecular compositionof haloalkilophilic archaea producing important enzymes.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline
MGYS00001377	The first report of arbuscular mycorrhizal fungi in a New Zealand coastal dune reveals a diverse community	Arbuscular mycorrhizal fungi (AMF) are components of coastal dune ecosystems around the globe where they provide a range of benefits to plants. The diversity and structure of AMF communities within these ecosystems, however, are poorly known. This study presents the first report of an AMF community in a New Zealand dune. Root samples were collected from the grass Spinifex sericeus R. Br., which dominates dunes of the North Island of New Zealand, along a 90m transect. Spores were also collected. The AMF community within the roots was surveyed using 454 sequencing of the SSU gene region. The 22 operational taxonomic units recognised formed a phylogenetically diverse community, including at least 8 genera across the Glomerales and Diversisporales, with an additional genus detected by the spore investigation. Some root and spore derived sequences generated close BLAST matches to AMF from distant countries while others represent previously unknown biodiversity. Spore morphology also suggests undescribed AMF are present. The community was heavily dominated by the genera Rhizophagus and Racocetra, together with AMF from a clade with no matches to a described genus. Spatial heterogeneity was observed, with taxonomic composition changing over distances of only 30 m.	root:Host-associated:Plants:Rhizosphere
MGYS00001374	Ectomycorrhizal and fine root foraging across European forests: the concept of complementarity within 'root-mycorrhiza-bacteria' continuum	Ectomycorrhizal and fine root foraging across European forests: the concept of complementarity within 'root-mycorrhiza-bacteria' continuum	root:Host-associated:Plants:Rhizosphere:Forest soil
MGYS00001373	characterization of cervico-vaginal microbiota associated with HPV infection	Persistent high risk (HR)-HPV infection is a necessary condition for cervical cancer development. Lactobacillus depletion and increased bacterial diversity in vaginal microbiota facilitate HPV infection and persistence.Cervico-vaginal samples were obtained from samples collected within HPV screening programs for cervical cancer. One-year follow-up data were used to differentiate samples from patients developing persistent infection. Pyrosequencing of 16S rRNA was used to characterize the vaginal microbiota and to define community state type (CST) in each sample. Linear discriminant analysis effect size (LEfSe) was used to identify enriched taxa during HPV infection and persistence.	root:Host-associated:Human:Reproductive system:Female
MGYS00001372	Plants Assemble Species Specific Bacterial Communities From Common Core Taxa in Three Arcto-Alpine Climate Zones	Evidence for the pivotal role of plant-associated bacteria to plant health and productivity has accumulated rapidly in the last years. However, several key questions remain unanswered, among which is the impact of climate zones on the plant-associated microbiota. Importantly, plant-bacterial interactions in wild plants and in arcto-alpine biomes have not been well studied as compared to those in tropical and temperate biomes. We hypothesized that the bacterial communities associated with pioneer plants in the former regions have major roles in plant health support, and this would be reflected in the formation of climate and host plant specific endophytic communities. We also hypothesized that these endophytes would have a tight association with their respective host plants. To examine the drivers of the plant-associated bacterial communities, we compared the latter in the perennial plants Oxyria digyna and Saxifraga oppositifolia - naturally growing in three arcto-alpine regions [Mayrhofen, Austria - alpine, Kilpisj?rvi, Finland - low Arctic and Ny-?lesund, Svalbard -highArctic] - with those in the corresponding bulk soils. As expected, the bulk soil bacterial communities in the three regions were significantly different. The relative abundances of Proteobacteria decreased progressively from the alpine to the high-arctic soils, whereas those of Actinobacteria increased. The candidate division AD3 and Acidobacteria abounded in the low Arctic. With respect to the endophytic bacterial communities, plant species and geographic region were the major determinants of the community structures. The plants in the alpine region had higher relative abundances of Proteobacteria, as compared to the plants from the low- and high-arctic regions which were dominated by Firmicutes. A highly conserved shared set of omnipresent bacterial taxa was found to occur in the two plant species, here denoted as the ?tight? core bacteriome. Burkholderiales, Actinomycetales and Rhizobiales were common members of this core, and these taxa were the main contributors to the differences in the endophytic bacterial community structures across compartments as well as regions. We postulate that this tight core is due to selection by the two plants, concomitant with a highly efficient adaptation of such ?core bacteriome? to the plant-associated habitats.	root:Host-associated:Plants
MGYS00001370	Kelp forest microbial diversity	Kelp forest ecosystems are biodiversity hotspots, providing habitat for dense assemblages of marine organisms and an important source of energy and nutrients for both marine and terrestrial food webs. The surfaces of kelps support diverse microbial communities that are essential for the growth and development of their hosts, and for facilitating the transfer of carbon from algal primary production to higher trophic levels. We quantified the diversity and distribution of bacterial communities present on the surfaces of eight sympatric species of kelp from four sites on the central coast of British Columbia. Patterns of host-asscoiated microbial diversity were compared with samples collected from seawater and rocky substrate. This study is among the first to quantify the distribution of microbial diversity across sympatric species within kelp forests, providing an additional level of data towards a more comprehensive understanding of these ecologically important habitats.	root:Host-associated:Plants
MGYS00001369	System-level response to long-term irrigation in a drought-stressed pine forest	The impact of climate change on the soil microbiome potentially alters the biogeochemical cycle of terrestrial ecosystems. In semi-arid environments, water availability is a major constraint on biogeochemical cycles due to the combination of high summer temperatures and low rainfall. Here, we explored how ten years of irrigation of a water-limited pine forest in the central European Alps altered the soil microbiome and associated ecosystem functioning. A decade of irrigation stimulated tree growth, resulting in higher crown cover, larger yearly increments of tree biomass, increased litter fall, and greater root biomass. Greater amounts of plant-derived inputs associated with increased primary production in the irrigated forest stands stimulated soil microbial activity coupled to pronounced shifts in the microbiome from largely oligotrophic to more copiotrophic lifestyles. Microbial groups benefitting from increased resource availabilities (litter, rhizodeposits) thrived under irrigation, leading to enhanced soil organic matter mineralization. This unique long-term study provides new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest ecosystem and improves our understanding of the persistency of long-term soil carbon stocks in a changing climate.	root:Host-associated:Plants:Rhizosphere:Forest soil
MGYS00001366	Effects of wood ash on forest soil microbial communities	Varying levels of wood ash were added to two Ontario forests and the effects of the organic layer soil microbial communities were assessed.	root:Host-associated:Plants:Rhizosphere:Forest soil
MGYS00001365	Transgenic banana plants expressing Xanthomonas wilt resistance genes revealed a stable non-target bacterial colonization structure	Africa is among the continents where the battle over genetically modified crops is currently being played out. The impact of GM in Africa could potentially be very positive. In Uganda, researchers have developed transgenic banana lines resistant to banana Xanthomonas wilt. The transgenic lines expressing hrap and pflp can provide a timely solution to the pandemic. However, the impact of the transgenes expression on non-target microorganisms has not yet been investigated. To study this effect, transgenic and control lines were grown under field conditions and their associated microbiome was investigated by 16S rRNA gene profiling combining amplicon sequencing and molecular fingerprinting. Three years after sucker planting, no statistically significant differences between transgenic lines and their non-modified predecessors were detected for their associated bacterial communities. The overall gammaproteobacterial rhizosphere microbiome was highly dominated by Xanthomonadales, while Pseudomonadales and Enterobacteriales were accumulated in the pseudostem. Shannon indices revealed much higher diversity in the rhizosphere than in the pseudostem endosphere. However, the expression of the transgenes did not result in changes in the diversity of Gammaproteobacteria, the closest relatives of the target pathogen. In this field experiment, the expression of the resistance genes appears to have no consequences for non-target rhizobacteria and endophytes.	root:Host-associated:Plants
MGYS00001364	Microbial diversity analysis of silage grass	Methane production via anaerobic fermentation of silaged energy grass, semiliquid, or solid municipal waste of complex composition by methanogenic microbial communities is a multistage process involving at least four groups of microorganisms. These are hydrolytic bacteria (polysaccharolytic, proteolytic, and lipolytic), fermentative bacteria, acetogenic bacteria (syntrophic, proton-reducing), and methanogenic archaea; complex trophic interactions exist between these groups.	root:Engineered:Food production:Silage fermentation
MGYS00001363	Analysing core microbiome of the Alpine bog vegetation	The current study address microbial diversity of Alpine bog vegetation using deep-sequencing of microbial 16S rRNA genes. Higher plant, bryophyte and lichen species were sampled from plots (1m2) in two Austrian bogs, Rotmoos and P?rgschachen Moor. The plots were dominated by Sphagnum magellanicum or Sphagnum angustifolium. Altogether, 46 plant and lichen samples of 24 species were collected. Amplicons were generated using 515F/806R (Caporaso et al. 2010 PNAS) and were sequenced using Illumina MiSeq v2 platform.	root:Environmental:Aquatic:Freshwater:Wetlands:Bog
MGYS00001360	Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America	Bananas (Musa spp.) belong to the most important global food commodities, and their cultivation represents the world''s largest monoculture. Although the plant-associated microbiome has substantial influence on plant growth and health, there is a lack of knowledge of the banana microbiome and its influencing factors. We studied the impact of (i) biogeography, and (ii) agroforestry on the banana-associated gammaproteobacterial microbiome analyzing plants grown in smallholder farms in Nicaragua and Costa Rica. Profiles of 16S rRNA genes revealed high abundances of Pseudomonadales, Enterobacteriales, Xanthomonadales, and Legionellales. An extraordinary high diversity of the gammaproteobacterial microbiota was observed within the endophytic microenvironments (endorhiza and pseudostem), which was similar in both countries. Enterobacteria were identified as dominant group of above-ground plant parts (pseudostem and leaves). Neither biogeography nor agroforestry showed a statistically significant impact on the gammaproteobacterial banana microbiome in general. However, indicator species for each microenvironment and country, as well as for plants grown in Coffea intercropping systems with and without agri-silvicultural production of different Fabaceae trees (Inga spp. in Nicaragua and Erythrina poeppigiana in Costa Rica) could be identified. For example, banana plants grown in agroforestry systems were characterized by an increase of potential plant-beneficial bacteria, like Pseudomonas and Stenotrophomonas, and on the other side by a decrease of Erwinia. Hence, this study could show that as a result of legume-based agroforestry the indigenous banana-associated gammaproteobacterial community noticeably shifted.	root:Host-associated:Plants:Phylloplane:Endophytes
MGYS00001359	Meterosideros Flower Microbiota	Eukaryote-associated microbiomes interact with their hosts in multiple manners, thereby affecting the hosts? phenotype, physical condition and behaviour. In plants, bacteria have numerous functions, with variable net effects, both in natural and agricultural systems. However, information about the composition and diversity of the bacterial communities associated with different aboveground plant organs, particularly flowers, is lacking. In addition, the relative effects of microhabitat and environmental conditions on community establishment require further attention. Here, using culture-independent methods, we determine that leaves and three floral microhabitats of Metrosideros polymorpha (Myrtaceae), a tree endemic to Hawai?i, host unique indicator communities composed of relatively abundant bacterial taxa. These indicator communities are accompanied by a large number of ubiquitous or rare bacteria with lower abundances. In our study system, the strong effect of microhabitat filtering on plant-associated community composition and bacterial richness and diversity strongly exceeds the influence of environmental effects such as precipitation, altitude, substrate age and geographic distance. Thus, the bacterial richness of aboveground plant organs is strongly underestimated when only one microhabitat, e.g., leaves, is considered. Our study represents a first step towards a comprehensive characterisation of the distribution, composition, and underlying factors, of plant bacterial communities, with implications for future basic and applied research on plant health, pollination and reproduction.	root:Host-associated:Plants:Phylloplane
MGYS00001358	Response of plant-associated bacterial community to simulated climate changes	The microorganisms inhabiting plant, such as leaf and root play important roles in plant growth. However, the microbial community structure and their response to climate changes are poorly understood. The objective was to survey the composition of microbial communities from root and clarify the response of bacterial communities to elevated CO2 and/or soil temperature.	root:Host-associated:Plants
MGYS00001357	The bacteria and fungi associated with the leaves of Arabidopsis thaliana	Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses, and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host''s genotype influences the structure of its microbial community is lacking. We conducted a field experiment using Arabidopsis thaliana to determine if host-genetic variation shapes the composition of its leaf bacterial and fungal community.	root:Host-associated:Plants:Phylloplane
MGYS00001355	Microbiome and metagenome of forest biochar	We analyzed taxonomic marker gene amplicons from microbial communities in four-year-old biochar particles and in adjacent soils across three forest environments.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00001354	Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils	Forest ecosystems need to be sustainably managed, as they are major reservoirs of biodiversity, provide important economic resources and modulate global climate. We have a poor knowledge of populations responsible for key biomass degradation processes in forest soils and the effects of forest harvesting on these populations. Here we investigated the effects of three timber harvesting methods, varying in the degree of organic matter removal, on hemicellulolytic bacterial and fungal populations ten to sixteen years after harvesting and replanting. We used stable-isotope probing to identify populations that incorporated 13C-labeled hemicellulose, analyzing 13C-enriched phospholipid fatty acids, bacterial 16S rRNA genes and fungal ITS regions. In soil microcosms, we identified 104 bacterial and 52 fungal hemicellulolytic operational taxonomic units (OTUs). Several of these OTUs are affiliated with taxa not previously reported to degrade hemicellulose, including the bacterial genera Methylibium, Pelomonas and Rhodoferax, and the fungal genera Cladosporium, Pseudeurotiaceae, Capronia, Xenopolyscytalum and Venturia. The effect of harvesting on hemicellulolytic populations was evaluated based on in situ bacterial and fungal OTUs. Harvesting treatments had significant but modest long-term effects on relative abundances of hemicellulolytic populations, which differed in strength between two ecozones and between soil layers. For soils incubated in microcosms, prior harvesting treatments did not affect the rate of incorporation of hemicellulose carbon into microbial biomass. In six ecozones across North America, distributions of the bacterial hemicellulolytic OTUs were similar, while distributions of fungal ones differed. Our work demonstrates that diverse taxa in soil are hemicellulolytic, many of which are differentially affected by the impact of harvesting on environmental conditions. However, the hemicellulolytic capacity of soil communities appears resilient.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00001353	Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils	Forest ecosystems need to be sustainably managed, as they are major reservoirs of biodiversity, provide important economic resources and modulate global climate. We have a poor knowledge of populations responsible for key biomass degradation processes in forest soils and the effects of forest harvesting on these populations. Here we investigated the effects of three timber harvesting methods, varying in the degree of organic matter removal, on hemicellulolytic bacterial and fungal populations ten to sixteen years after harvesting and replanting. We used stable-isotope probing to identify populations that incorporated 13C-labeled hemicellulose, analyzing 13C-enriched phospholipid fatty acids, bacterial 16S rRNA genes and fungal ITS regions. In soil microcosms, we identified 104 bacterial and 52 fungal hemicellulolytic operational taxonomic units (OTUs). Several of these OTUs are affiliated with taxa not previously reported to degrade hemicellulose, including the bacterial genera Methylibium, Pelomonas and Rhodoferax, and the fungal genera Cladosporium, Pseudeurotiaceae, Capronia, Xenopolyscytalum and Venturia. The effect of harvesting on hemicellulolytic populations was evaluated based on in situ bacterial and fungal OTUs. Harvesting treatments had significant but modest long-term effects on relative abundances of hemicellulolytic populations, which differed in strength between two ecozones and between soil layers. For soils incubated in microcosms, prior harvesting treatments did not affect the rate of incorporation of hemicellulose carbon into microbial biomass. In six ecozones across North America, distributions of the bacterial hemicellulolytic OTUs were similar, while distributions of fungal ones differed. Our work demonstrates that diverse taxa in soil are hemicellulolytic, many of which are differentially affected by the impact of harvesting on environmental conditions. However, the hemicellulolytic capacity of soil communities appears resilient.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00001352	Soil microbiome responses to the short-term effects of Amazonian deforestation	Slash-and-burning forest clearing is a common practice in the Amazon region. In order to understand to what extent this may change the basic mechanisms of soil fertility, we analyzed the structure of the microbial community in forest and deforested soils and relate these to changes in soil chemical factors. Deforestation decreased soil organic matter (OM) content and factors linked to soil acidity, and raised soil pH, base saturation, and the concentration of exchangeable bases. Concomitantly to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundance of putative copiotrophic microbes such as Actinobacteria, and a decrease in the relative abundance of bacteria such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils; however we did observe changes in community functions, which included increases in DNA repair, protein processing, modification, degradation and folding functions. In addition there were changes in composition of the bacterial groups associated with metabolism-related functions. Co-occurrence microbial network structures identified distinct phylogenetic pattern for forest and deforested soils and opened the possibilities to investigate relationships between Planctomycetes and Al content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomical and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash-and-burning deforestation in the Amazon region.	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00001351	Rhizosphere microbial community composition affects cadmium and zinc uptake of the metal-hyperaccumulating plant Arabidopsis halleri	The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants by either directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step towards the application and optimization of phytoremediation. We studied the effect of a ?native? compared to a strongly disturbed (gamma-irradiated) soil microbial community on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated compared to the gamma-irradiated soil. Gamma-irradiation did not affect soil metal bioavailability or plant growth. However, it strongly altered soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri revealed distinct differences in microbial community richness and evenness between the untreated and gamma-irradiated soil. Classification and comparative sequence analysis allowed the identification of microbial taxa (Lysobacter, Streptomyces, and Agromyces) that might have enhanced the accumulation of Cd and Zn by A. halleri in the microcosms with the untreated soil. We discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interplay between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction strategies as efficient and sustainable remediation procedure.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00001350	Analysis of microbial communities in leafy greens using Illumina MiSeq	Our work provides the first microbial profiling of leafy green phyllosphere in Europe and contributes to the questions on how the community structure changes on different types of leafy greens and at different time points within one planting.	root:Host-associated:Plants:Phylloplane
MGYS00001348	Arabidopsis thaliana culture collections of leaf- and root-associated bacteria  (Synthetic Communities 16S rRNA data)	Roots and leaves of healthy plants host taxonomically structured bacterial assemblies, and members of these communities contribute to plant growth and health. We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing. We found an extensive taxonomic overlap between the leaf and root microbiotas. Genome drafts of 400 isolates revealed a large overlap of genome-encoded functional capabilities between leaf and root-derived bacteria with few significant differences at the level of individual functional categories. Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiotas on their cognate host organs, but are also capable of ectopic leaf or root colonization. Whilst this raises the possibility of reciprocal relocation between root and leaf microbiota members, genome information and recolonization experiments also provide evidence for microbiota specialization to their respective niche.	root:Host-associated:Plants
MGYS00001346	Metagenome of the culturable bacterial endophytes of Palm Oil Fruit	The bacterial endophytes within the palm oil fruit (Elaeis guineensis) were cultured using a palm-oil enriched medium and the bacterial cells present in the microcosm were separated by filtration through a 14 micrometer pore filter. The DNA obltained by these cells was then sequenced using 454 pyrosequencing technology on the 454 GS FLX platform. A single fragment (shotgun) library was sequenced in two separate runs.	root:Host-associated:Plants:Rhizoplane:Endophytes
MGYS00001345	Ileum content of female broilers belonging to different genetics	Ileum content of female broilers belonging to different genetics	root:Host-associated:Birds:Digestive system:Digestive tube
MGYS00001344	Total metagenomic analysis	Comparison between samples obtained from tucurui reservoir	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001343	Taxonomic and functional diversity of the virus community from a South African thermal spring	The virus community composition and functional gene content from a South African hot spring (Brandvlei)was analyzed through a shotgun metagenomics approach.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00001342	Estimation of variability in the gut microbiota resistome of the Russian citizens aimed at identification of pathways for transmission and spread of antibiotic resistance.	A problem of antibiotic resistance emergence in microbiome will be investigated in the research. To date, gut microbiome (as well as soil microbiome) is considered to be antibiotic resistance reservoir. The resistance can accumulate in the microbiome after antibiotic treatment against infectious agents, and it can be passed to pathogenic bacteria during further infections, even though absence of the target infection is checked after each therapy. Moreover, use of antibiotics in agriculture and every day life (without doctor’s recommendations) creates an environment for antibiotic resistance transfer between microbiomes, as there is always a selective pressure for it. That is a quite dangerous situation, as there is a permanent ubiquitous antibiotic resistance (AR) background. In the framework of the research available data on Russian and worldwide microbiomes (more than 2000 by 2015 year) will be analyzed and groups of patients who passed antibiotic treatment will be studied. Using obtained results a map of antibiotic resistance expansion will be created, dominating mechanisms of the resistance transfer and AR genes hosts will be revealed. Additionally, laboratory methods and mathematical analysis for genes’ and mechanisms’ screening will be developed. The developed models AR transfer will make possible modeling of various methods for AR transfer prevention, or, alternatively, modeling of consequences of different antibiotics’ use. Concluding, basic mechanisms of AR emergence will be described (6-1-3) and new methods of screening will be proposed. Furthermore, principle of the screening operation will be demonstrated on available data on AR, as well as on chosen clinical groups.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001341	Root microbiome in phytohormone mutants.	The root bacterial microbiome of Arabidopsis thaliana was profiled, via 16S rRNA gene sequencing. Roots of wild-type plants and isogenic mutants in biosynthesis/signaling of salicylic acid, jasmonic acid and ethylene were profiled. Endophytic compartment and rhizosphere were independently profiled from each plant, as well as bulk soil controls.	root:Host-associated:Plants:Rhizosphere
MGYS00001340	Extensive overlap of tropical rainforest bacterial endophytes between soil, plant parts and plant species.	The extent to which distinct bacterial endophyte communities occur between different plant organs and species is unclear, and has implications for bioprospecting efforts. Using V3 region of bacterial 16S rRNA gene, we investigated the diversity patterns in total, uncultured bacterial endophyte communities of three rainforest plant species, comparing leaf, stem, and root endophytes, plus rhizosphere soil community employing MiSeq. There was extensive overlap in bacterial communities between plant organs, between replicate plants of the same species, between plant species, and between plant organ and rhizosphere soil, with no consistent clustering by compartment or host plant species. Both the lack of clustering in an NMDS ordination and an NMTD analysis suggested that bacterial endophyte OTUs were stochastically distributed amongst plant species and organs, and rhizosphere soil. Percentage turnover of OTUs samples was similar for plant individuals of the same species and of different species, at around 80-90%. Our results suggest that sampling of extra individuals, extra plant organs, extra species, or use of rhizosphere soil, might be about equally effective for obtaining new OTUs for culture. Our observations suggest that the plant endophyte community may be much more diverse, but less predictable, than would be expected from culturing efforts alone.	root:Host-associated:Plants:Rhizosphere:Epiphytes
MGYS00001339	Root microbiome of phytohormone mutants in synthetic recolonization experiments.	The root bacterial microbiome of Arabidopsis thaliana was profiled, via 16S rRNA gene sequencing. Plants were grown in a sterilized calcined clay substrate inoculated with 37 root isolates plus E. coli. Root endophytic comparment of wild-type plants and isogenic mutants in biosynthesis/signaling of salicylic acid, jasmonic acid and ethylene were profiled. A subset of the plants revceived exogenous aplication of salicylic acid on the leaves.	root:Host-associated:Plants:Rhizome
MGYS00001338	Community profile of winery wastewater treatment plant	Here we investigated the community profile of a winery wastewater treatment plant dominated by glycogen accumulating organisms.	root:Engineered:Wastewater:Industrial wastewater
MGYS00001337	Effects of crown gall disease on natural microbiota of Vitis vinifera	The crown gall disease in grapevine is mediated by Agrobacterium vitis and results in tumorous growth. The tumor offers an ecological niche for the pathogen and eventually for other bacteria as well. We wanted to know if the crown gall disease affects the bacterial community of the grapevine plant. Using next generation sequencing of the V4 region of 16S rDNA amplicons we recorded the microbiota from galled and non-galled grapevine plants as well as of the soil at three seasons of the year. The root, trunk, one-year-old cane and the soil hosted distinct microbiota, which differed according to spring, summer, and autumn. However, the crown gall disease influenced the structure of the microbiota only in grapevine trunks. There the bacterial richness was higher and comprised for example exclusively the plant pathogens Xanthomonas sp., Sodalis sp., and an unknown Gammaproteobacterium. The seasons additionally affected the microbiota in the trunks with and without a crown gall differently. A. vitis, Pseudomonas sp. and Enterobacteriaceae sp. were the most abundant sequences in crown galls at each season. In contrast, in healthy trunks (=non-galled) the microbial composition changed from season to season. Altogether, twenty-two operational taxonomic units, representing bacterial species, were significantly enriched in crown galls and only three in healthy trunks. Our results support the idea that other bacteria than the pathogen A. vitis can adapt to the crown gall environment. How these profit from the new environment and if they influence crown gall development will be the subject of future work.	root:Host-associated:Plants
MGYS00001336	Effects of organic matter manipulation on bacterial community diversity and function	Lake ecosystems provide important services including their ability to support complex food webs, and their connection to the global carbon cycle. These services are dependent on how microorganisms interact with available organic matter (OM), both dissolved and particulate. Therefore, in order to manage these important ecosystems and their services successfully, it is necessary to understand how the quality and quantity of DOM affects microbial communities. Linking DOM quality and quantity to microbial community complexity and function are crucial steps toward a mechanistic understanding of freshwater ecosystems. Understanding these relationships at the microbial scale will enable us to make predictions about landscape-scale environmental change and its effect on aquatic carbon cycling and food web processes. In this study, I aim to investigate the effect of organic matter manipulation on the molecular structure of DOM and the microbial community composition and function in freshwater boreal lakes.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00001335	A diverse array of bacteria that inhabit the rhizosphere and different plant organs play a crucial role in plant health and growth.	This study addressed two fundamental questions: (1)How does the bacterial community structure differ between the different organs of Lepidium perfoliatum L.?(2) Do different tissues have thepotential to influence the structure of bacterial communities?	root:Host-associated:Plants
MGYS00001333	Accessing and Identification of Novel Environmental Alleles of the ACC Deaminase Domain Region through a Competition Assay	Rhizosphere soil samples from four Maize inbred lines (Oh43, MS71, M37W, and NC358) were collected from a field in Missouri, USA, in 2010. PCR reactions, pooled DNA extracted from all four lines, used custom primers a2F 5'- GSAACAAGACGCGCAAG-3' and a2R 5'-CACSAGCACGCACTTCATG-3', to amplify a 37 amino acid region from the full-length accD gene. These degenerate primers were designed using an alignment of bacterial accD genes obtained from public databases.	root:Host-associated:Plants:Rhizosphere
MGYS00001332	tes	test 2	root:Host-associated:Plants:Phylloplane
MGYS00001331	Class project on metagenomics using samples from soil.	Class project to get a hand on exercise on metagenomics. Samples were collected from soil and sequenced in Ion torrent PGM.	root:Environmental:Terrestrial:Soil
MGYS00001330	Soils collected from a petroleum hydrocarbon contaminated site in Greenland.	Soils collected from a petroleum hydrocarbon contaminated site in Greenland.	root:Environmental:Terrestrial:Soil:Oil-contaminated
MGYS00001329	Root microbiome of Arabidopsis plants with altered phosphate starvation response	The root bacterial microbiome of Arabidopsis thaliana was profiled, via 16S rRNA gene sequencing. Plants were grown in either a previouly characterizes wiled soil or in gnotobiotic plate conditions with a 35 bacteria synthetic community. Root endophytic comparment of wild-type plants and isogenic mutants was charachterized. For the synthetic community experiments, different phosphate levels in the media were used.	root:Host-associated:Plants:Rhizosphere
MGYS00001328	Environmental soil samples from a gasoline contaminated site in Meadow Lake, Saskatchewan, Canada.	A gasoline contaminated site in Meadow Lake, Saskatchewan was monitored for hydrocarbon degradation. Different types of biochar and forms of phosphate were tested to track optimal degradation of gasoline at the site.	root:Environmental:Terrestrial:Soil:Oil-contaminated
MGYS00001327	Yeast diversity during the fermentation of Andean chicha: a comparison between high-throughput sequencing and culture-dependent approaches.	The diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beverage chicha was investigated. Samples taken at different stages from two chicha productions were analyzed by culture-dependent and culture-independent methods. Classical microbiological methods allowed isolation of five hundred eighty-two yeasts identified into 16 species by RFLPs and sequencing of D1/D2 26S rRNA gene. Genetic typing of isolates from the dominant species, Saccharomyces cerevisiae, by PCR of delta elements revealed up to 42 different patterns. High-throughput sequencing of D1/D2 26S rRNA gene amplicons from chicha samples allowed detection of more than one hundred yeast species and almost fifty filamentous fungi taxa. Analysis of the data revealed that yeasts dominated the fermentation, although, a significant percentage of filamentous fungi appeared in the first step of the process. Statistical examination of results showed that very few taxa were represented by more than 1% of the reads per sample at any step of the process. S. cerevisiae represented more than 90% of the reads in the fermentative samples. Other yeast species, different from S. cerevisiae, dominated the pre-fermentative steps and abounded in fermentative samples when S. cerevisiae was in percentages below 90%. Most yeasts species detected by pyrosequencing were not recovered by cultivation. In contrast, the cultivation-based methodology detected very few yeast taxa, and most of them corresponded with none or very few reads in the pyrosequencing analysis.	root:Engineered:Food production:Fermented beverages
MGYS00001326	Impact of air pollution and urbanization on the bacterial phyllosphere of Ivy (Hedera sp.)	The surface of plant leaves, also termed the phyllosphere, is a selective habitat for microbes. From this phyllosphere microbiome, the bacterial composition seems to depend on plant host species, leaf characteristics, season, climate, and geographic distance between the plant hosts. In this study, we investigated the effect of an urban environment and air pollution on the bacterial composition of phyllosphere communities. We performed a passive biomonitoring experiment in which leaves were sampled from Ivy (Hedera sp.), a common evergreen climber species in the area under study. The bacterial community composition was determined using 16S rRNA gene sequencing on the Illumina MiSeq platform. In addition, exposure to anthropogenic particulate matter was estimated using leaf biomagnetic analyses. We found that the phyllosphere microbial communities of Ivy were greatly different between urban and more rural locations, as we observed a shift in several of the dominant taxa Beijerinckia, Hymenobacter, Methylocystaceae and Methylobacterium. Interestingly, the communities also showed greater variability in the urban area than at the less urbanized locations where we measured lower levels of air pollution. These results indicate that an urban environment and local air pollution   can greatly affect the local phyllosphere community composition.	root:Host-associated:Plants:Phylloplane
MGYS00001325	Microbial community dynamics and response to plant growth-promoting organisms in the rhizosphere of four common food crops cultivated in hydroponics	As part of the European Space Agency MELiSSA project, the effects of Myco Madness, a commercial combination of plant growth-promoting organisms, on the microbial communities of four common four crops (durum wheat, bread wheat, potato, soybean) cultivated in hydroponics was assessed. Small relative amounts (<0.5%) of successful infestation of plant root zone microbiome by Myco Madness PGPOs resulted in important changes in the composition of these communities. The dynamics of root zone communities were also followed over time. These results suggest that the microbial communities associated with hydroponic nutrient solutions are affected by plant developmental stage-associated changes in root exudation patterns.	root:Host-associated:Plants:Root
MGYS00001324	Identification of the oak microbiome	Metabarcoding was used to study bacteria in oak samples. Samples were taken from oaks showing signs of acute oak decline. A general 16S rRNA gene primer was used followed by pyrosequencing.	root:Host-associated:Plants
MGYS00001323	Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes	Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes	root:Host-associated:Plants
MGYS00001322	effect of IFNg and Akkermansia muciniphila on mouse gut microbiome composition	16s rRNA V4 region is sequenced to measure the composition of gut microbiome for IFNg knockout mice, wild type mice and germ free mice that colonized with Akkermansia muciniphila then treated with IgG or Anti-IFNg	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001321	Metagenomic analysis of an Iranian Hypersaline Lake microbial ecosystem	We studied microbial communities in three different stations of an Iranian Hypersaline Lake (Lake Meyghan). These stations are characterized by a salinity ranging from 5%, 20% to over 30% total salt and a slightly alkaline Ph range (from 7.7 to 8.8). The microbial communities are dominated by Archaea at higher salinity and by Bacteria at lower salinity.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline
MGYS00001320	construction of minimal coastal microbial mats	"Minimal coastal microbial mats were created with diluted coastal mat samples obtained from the Dutch barrier island of Schiermonnikoog. The MM""s were inoculated in fresh sterilized sand in glass containers contained in a MicroBox. The MicroBox has a transparent lid (allowing photosynthetic growth) and a gas exchange filter. The MM""s are propagated under laboratory conditions at a 16h light / 8h dark regime and at a constant 23 C. Serial dilutions used for this data-set are 0, 3 and 5-fold."	root:Environmental:Aquatic:Marine:Coastal
MGYS00001318	Global Rivers	Metagenomic analysis provides knowledge of the diversity and ecological function of the biota inhabiting rivers, whether or not they can be seen or cultured.  Using MinION rapid sequencing and real time analysis of DNAs obtained from rivers, we demonstrate the utility and potential of this approach for monitoring for agricultural and industrial effects on the river biota, detecting pathogen diversity and progression through river systems, judging risk associated with water uses, and ultimately enhancing water quality.	root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems
MGYS00001316	A metagenomics study of two north sea communities.	A metagenomics study of two north sea communities.	root:Environmental:Aquatic:Marine
MGYS00001315	Analysis of gut microbiota in infants	The human gut microbiome has been demonstrated to play a vital role in health and disease. Dysbiosis may contribute significantly to adverse outcomes in child health. Using metagenomics this project seeks to identify microbiome signatures that might influence health of children.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001314	Marine sediment from Gulf of Mexico	After the Deepwater Horizon oil spill in the Gulf of Mexico changes were detected in the microbial communities. There’s a little information about the microbial communities from southern regions of the Gulf of Mexico and it important to know its structure in case of future ecological disasters. In this study we take samples from marine sediments and analyzed it using shotgun sequencing.	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00001313	16S rRNA gene sequencing of the extremelly birth weight infant gut	16S rRNA gene sequencing of the extremelly birth weight infant gut primers 530F-926R	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001312	Global surveillance of infectious diseases and antimicrobial resistance from sewage	Adequately monitoring of large populations and their environments is essential if we want to monitor pathogens and antimicrobial resistance around the globe. Recent developments in high‐throughput sequencing allow to rapidly identify nucleic acids from various organisms in clinical and environmental samples. Sewage systems are recognized as an important source of human pathogens, especially in crowded settings with poor infrastructure. A point‐prevalence metagenomic analysis is applied to sewage samples collected globally from the main sewage system of major cities prior to treatment plants inlet. The project is a proof‐of‐concept study for applying metagenomic approaches that could initiate a global surveillance of human infectious diseases including antimicrobial resistance from sewage collected in major cities around the world to detect, control, prevent and predict human infectious diseases.	root:Engineered:Wastewater:Water and sludge
MGYS00001311	Impact of LAB supplementation in drinking water on chicken crop and ceca	Impact of LAB supplementation in drinking water on chicken crop and ceca tested at 14 and 35 days	root:Host-associated:Birds:Digestive system:Ceca
MGYS00001310	Before and after a geosequestration experiment, volumes of reservoir water were filtered in order to infer on taxonomy, structure of the underlying microbial communities.	Before and after a geosequestration experiment, volumes of reservoir water were filtered in order to infer on taxonomy, structure of the underlying microbial communities.	root:Environmental:Aquatic:Freshwater:Drinking water:Delivery networks
MGYS00001308	16S rRNA gene sequencing in extremely low birth weight infant gut	16S rRNA gene sequencing in extremely low birth weight infant gut. Primers used for amplifying 16S rRNA were 27F and 519R	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001307	Small sub-sample	This is only a very small subsample of metagenomic data	root:Host-associated:Plants:Rhizosphere
MGYS00001306	Diplonemids are the most diverse planktonic eukaryotes in the world ocean	Diplonemids sequence data corresponding to the V9 loop of the 18S rDNA in 850 size-fractionnated plankton communities sampled at 123 location including samples from the mesopelagic zone.	root:Environmental:Aquatic:Marine
MGYS00001305	LAB in feed	Metagenomic study of cecum contents of chickens fed with LAB	root:Host-associated:Birds:Digestive system:Ceca
MGYS00001304	Can insecticide resistance alter behaviour and fitness by modifying the gut microbiome?	Resistance to a range of insecticides is conferred by upregulation of the cytrochrome P450 gene Cyp6g1 in Drosophila melanogaster, and has been associated with sex-specific pleiotropic effects on behaviour and fitness. Cyp6g1 is primarily overexpressed in the gut in insecticide resistant individuals and metabolises a large range of molecules, and thus upregulation may alter the gut environment and the community composition of the gut microbiota. The community composition of gut microbiota can have profound effects on behaviour and fitness, and if Cyp6g1 expression can explain differences in gut microbiota then it may help explain its observed fitness effects. Comparing microbial community composition between the guts of insecticide resistant and susceptible individuals (high and low Cyp6g1 expression, respectively) via 16s rRNA sequencing would be the first necessary experiment to demonstrate that insecticide resistance can alter behaviour and fitness by modifying the gut microbiome.	root:Host-associated:Insecta:Digestive system
MGYS00001303	A plaque on both your houses. Exploring the history of urbanisation and infectious diseases through the study of archaeological dental tartar	Human health experiences throughout much of (pre-)history remain clouded by a lack of reliable data on disease exposure and transmission. Archaeological dental tartar (mineralized plaque) entraps and preserves DNA and proteins from multiple oral and systemic infectious disease pathogens. This project aims to develop pilot data on oral microbial profiles and disease exposure within the historic period through the metagenomic analysis of archaeological dental calculus.	root:Host-associated:Human:Digestive system:Oral
MGYS00001298	Experimental Metagenome on MinION	This is an artificial metagenome created by pooling various proportions of DNA from four microbe cultures to simulate a simple metagenome for analysis by Oxford nanopore MinION.  Single-species cultures of Escherichia coli, Pseudomonas fluorescens, Microcystis aeruginosa, and Synechococcus elongatus were grown to log phase then harvested for DNA extraction.  Following mechanical shearing, templates were prepared using either equimolar amounts of each species or combinations of DNAs where one species was rare (0.05%). Libraries were created using his-tag bead purification according to MinION specifications and libraries were sequenced using MinION R7.x flow cells.  For validation, a final library was prepared using a mock microbial community with 20 species included in “staggered” proportions (obtained from ATCC, the mixture had 1,000 to 1,000,000 16S rRNA operon copies per organism per μL of material supplied).  This latter library, as it was supplied at a low concentration, required pre-amplification with Phi29 prior to library preparation.	root:Engineered:Modeled:Simulated communities (DNA mixture)
MGYS00001297	Assembled contigs from rhizosphere metatranscriptome	RNA was extracted from the rhizopheres of three crop plants and unplanted soil.  rRNA was removed using Ribo-Zero and any remaining rRNA reads removed using SortMeRNA.  Remaining high quality reads were assembled using Trinity	root:Host-associated:Plants:Rhizosphere
MGYS00001296	Metagenomic recovery of phage assemblage from Manikaran hot springs	Phages are the most dominant predators of prokaryotic community at thermal springs characterized by restricted eukaryotic grazing pressures yet understanding of the phage ecology remains limited at hydrothermal environments. This study examines the metagenomic profiles of phages across Himalayan hot springs (1760 m) at Manikaran by employing the environmental data from sediment (n = 4, 78°C-98°C) and microbial mat (n = 2, 57°C) deposited around thermal discharges that led to de novo reconstruction of 65 phages (24-200 Kbp). 91% (60/65) of the phages belonged to the order Caudovirales including members from Myoviridae, Siphoviridae, Podoviridae and Inoviridae with distinguishing enrichment of Siphoviridae and Myoviridae across sediment and microbial mats, respectively highlighting the temperature driven shaping of phage community. Whole genome based analysis of the phages demonstrated well-conserved phages across sediments in contrast to the microbial mat owing to moderately mesophilic microbial mats (57°C) compared to the thermophillic sediments (78°C-98°C). A minimal phage genome (28 orthologous proteins) was maintained across both sediment and microbial mats including proteins like histidine kinase, integrase, and Clp protease suggesting a common origin over an inter-habitat distance of 500 m. In an attempt to reconstruct potential hosts for phages from the metagenome data, genomes for Ralstonia (5 Mbp), Pseudoxanthomonas (3.5 Mbp), Dechloromonas (1.9 Mbp), Herbaspirillum (1.5 Mbp) were assembled with integrated phages and unique CRISPR arrays suggesting prior phage infections and rapidly acquired immunity against future phage attacks at these hot springs. This study provides detailed insights into the genetic give-and-take between hosts and their phages in specific ecological niches of Manikaran thermal springs.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00001293	Biological soil crusts, Southern Spain	Biological soil crusts play vital roles in dryland regions that cover over 35% of the Earth´s land mass, including 24% of Europe. They provide important ecosystem services such as limitation of soil erosion, retention of water,  improving soil fertility and nitrogen and carbon fixation.	root:Environmental:Terrestrial:Soil:Desert
MGYS00001292	Diversity and assembling processes of bacterial communities in cryoconite holes of a Karakoram glacier	Cryoconite holes are small ponds that form on the surface of glaciers that contain a dark debris, the cryoconite, at the bottom and host active ecological communities. Differences in the structure of bacterial communities have been documented among Arctic and mountain glaciers, and among glaciers in different areas of the world. In this study we investigate the structure of bacterial communities of cryoconite holes of Baltoro Glacier, a large (62 km in length and 524 km2 of surface) glacier of the Karakoram, by high throughput sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene. We found that Betaproteobacteria, dominated bacterial communities, with large abundance of genera Polaromonas, probably thanks to the highly versatile metabolism of this genus, and Limnohabitans, which may have been favoured by the presence of supraglacial lakes in the area where we sampled cryoconites. In addition, cryoconites that occurred in separate areas on the surface of the glacier hosted different bacterial communities, while no spatial pattern of variation in community structure was observed within each area. This probably occurred because of variation in environmental conditions, mainly pH, of cryoconite holes in different areas of the glacier surface.	root:Environmental:Aquatic:Freshwater:Ice:Glacier
MGYS00001291	Oyster and water samples from Texas bays.	Oyster and water samples from Texas bays.	root:Environmental:Aquatic:Marine:Coastal
MGYS00001289	Lipases from Metagenomic Sources	Soil samples were collected from restaurant grease-deposit-site. An enriching step was carried out by inoculating minimal medium with soil and grown at 20°C. Olive oil was added to the medium as the only carbon source. This was done to enrich the samples for organisms having the ability to grow by metabolising oil. DNA was extracted. The acquired metagenome was sequenced at GATC (Constance, Germany). The DNA was sequenced in 300 bp paired end reads using the MiSeq platform.	root:Environmental:Terrestrial:Soil:Oil-contaminated
MGYS00001287	scs diatom	"Bacteria attached to a diatom host cell are thought to operate as potential symbionts, functioning as mutualistic, parasitic, or commensal epibionts. This study investigates if similar relationships can be found at the level of the individual diatom host cell by analyzing the metagenomes of six representative Thalassiosira host cells with dissimilar associated bacteria. Diatoms were collected from the deep chlorophyll maximum in the oligotrophic waters of Station ALOHA (22° 45""N, 158° 00""W), isolated using fluorescently activated cell sorting, and DNA amplified using multiple displacement amplification. Preliminary analysis of the 16S rDNA of 32 host cells found that the composition of bacterial associations could be divided into three distinct groups; six cells from the two most common groupings were selected for further analysis. This initial metagenomic analysis explores nutrient pathways, antibiotic production, quorum sensing, motility, and other genes that may be essential to the diatom-bacterial symbiotic interaction. This work surveys the potential genetic contribution of bacteria, diatoms, as well as community-level interactions that determine the health of the diatom host cell and their bacterial consortia."	root:Host-associated:Algae:Brown Algae
MGYS00001285	Regional heterogeneity and seasonal succession in proteorhodopsin containing marine microbial assemblages	A significant proportion of the marine prokaryote community is comprised of microbes that utilise proteorhodopsin (PR), a retinal based photoreceptor used for generating ATP from light. Using an amplicon sequencing approach, we examined spatial and temporal patterns in the diversity of PR containing Bacteria and Archaea (PRBA) along the east coast of Australia, during a period of 12 month from surface samples collected at 3 oceanographic time-series sites spanning 15° of latitude. Coastal PRBA assemblages were dynamic in both space and time, with diversity linked to several environmental factors, with positive correlations to temperature, Secchi depth and Prochlorococcus cell abundance and negative correlations to phosphate concentration observed. Shifts in the taxonomic composition of the PRBA assemblage were best explained by temperature and day length. Seasonality in taxonomic structure was accompanied by temporal variability in proteorhodopsin spectral tuning characteristics. The ratio of blue absorbing proteorhodopsin proteins (BPR) to green absorbing proteorhodopsin proteins (GPR) was strongly linearly correlated with day length, with levels of GPR increasing with day length. These observations highlight the dynamic nature of proteorhodopsin containing marine assemblages, which exhibit substantial shifts in both taxonomy and spectral tuning properties in response to seasonal and spatial variability in environmental conditions.	root:Environmental:Aquatic:Marine
MGYS00001284	Metagenome of the soil from hot spring is to be studied to get better ubderstanding of its biome.	Soil is rich in microbes. Metagenomics of soil sample from extreme environment will be helpful for discovery of a new novel bacterial stain.	root:Environmental:Terrestrial:Soil
MGYS00001282	Subseafloor microbes at Mid-Cayman Rise	The Mid-Cayman Rise hosts two geochemically distinct vent fields: Von Damm, situated in ultramafic rock, and Piccard, a mafic vent field that is the deepest known vent site in the world. We have analyzed and compared taxonomic and metabolic diversity as well as strain-level variation from 11 metagenomes from Von Damm and 4 metagenomes from Piccard.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00001281	Metagenome from microbial community of plankton and sediment	"In this work, we have characterized the microbial diversity in mesopelagic and bathypelagic zones of the water column (500, 1000 m and 1250 m depth) and bottom sediment from the Marmara Sea by amplifying, cloning and sequencing archaeal, bacterial and eukaryotic small-subunit rRNA (SSU rRNA) genes and by direct pyrosequencing of environmental DNA from 1000 m-deep plankton and sediment (approximately 35 Mbp, respectively).  The plankton sample was recovered from the water column in the Central Basin of the Marmara Sea (40° 50.3'N 28°1.4' E) at 1000m depth.  The sediment sample was recovered from the Central Basin of the Marmara Sea at 1,300 m depth (40° 46.8'N and 29°6.1' E).  A comparative metagenomics analysis of these data with that of previous studies of deep-sea and surface plankton, subsurface deep-sea sediment, whale carcasses and soil reveals interesting trends.  <a href=""http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=Nucleotide&cmd=search&term=HM103388:HM103902[accn]"">HM103388-HM103902 </a> are ribosomal RNA sequences associated with this study."	root:Environmental:Aquatic:Marine
MGYS00001280	Reduced diversity and altered composition of the gut microbiome in individuals with Myalgic Encephalomyelitis/ChronicFatigue Syndrome	Gastrointestinal disturbances are among the cluster of symptoms commonly reported by individuals diagnosed with ME/CFS (Myalgic Encephalomyelitis/Chronic Fatigue Syndrome), who are also often reported to exhibit altered plasma cytokine profiles. In plasma of ME/CFS patients (n=48) and healthy controls (n=39), we examined a set of inflammatory markers: C-reactive protein (CRP), Intestinal Fatty Acid Binding Protein (I-FABP), lipopolysaccharide (LPS), LPS binding protein (LBP), and soluble CD14 (sCD14).  Levels of LPS, LBP, and sCD14 were elevated in ME/CFS subjects.  Levels of LBP were correlated with LPS and sCD14 and LPS levels correlated with sCD14. We examined the gut microbiota by 16S rRNA sequencing. We observed that bacterial diversity was decreased in the ME/CFS specimens compared to controls, in particular a reduction in the relative abundance and diversity of Firmicutes.  The ME/CFS samples also exhibited an increase in the pro-inflammatory family Enterobacteriaceae and decrease in the anti-inflammatory Ruminococcaceae, including Faecalibacterium, and reduced amounts of beneficial Bifidobacterium species.  Using a machine learning approach, individuals were classified correctly as ME/CFS with an average success rate of 0.8928.  Our results indicate dysbiosis of the gut microbiota in this disease and further suggest an increased incidence of microbial translocation, which may play a role in inflammatory symptoms.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001279	Microbiota composition in Anorexia Nervosa patients before and after weight gain as compared to healthy controls	The aim of this study was to study i) to what extend the microbiota of AN is perturbed in comparison to NW and ii) whether these perturbations are recovered after weight gain and/or normalisation of eating behaviour. In this study we have comprehensively analysed the gut microbiota (by sequencing of the V4 region of the 16S rRNA gene using MiSeq PE250) and short-chain fatty-acids (SCFA) profile in stool samples of AN patients ahead (n=55) and after weight gain (n=44) in comparison to normal-weight participants matched for age and gender (NW, n=55).	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001271	metataxonomics analysis of fungal populations in Vitis vinifera L. cv. Corvina grapes and musts	"The fungal populations present in Vitis vinifera L. cv. Corvina grapes and musts were compared in two different years vintages. The comparison was carried out through ITS1-5.8S-ITS2 454-pyrosequencing. Grapes were collected from a recent vineyard located in the Italian winery region called ""Valpolicella"" (Sant""Ambrogio, Verona, Italy). After the harvesting, grapes were subjected to withering in a dedicated warehouse located a few kilometers far from the vineyars (<5Km). The warehouse is supplemented with automatic systems able to control and modify the internal temperature and humidity. The duration of grape withering was defined according to the regional rules for Amarone production (Paronetto and Dellaglio, 2011), which define the time in which the grapes for Amarone vinification can be mashed. The comparison of the fungal populations present in these samples sheds lights on the Amarone production, allowing the identification of the persistent fungal genera and on genera varying as suffering from seasonal environmental changes."	root:Host-associated:Plants
MGYS00001267	16s rRNA gene amplicon sequencing of 50 week-old mouse gut microbiota as performed on Illumina MiSeq and Oxford Nanopore MinION sequencer.	Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-generation sequencing technologies have facilitated the elucidation of the microbial community composition with higher accuracy and greater throughput than was previously achievable; however, the short sequencing reads often limit the microbial composition analysis at the species level due to the high similarity of 16S rRNA amplicon sequences. To overcome this limitation, we used the nanopore sequencing platform to sequence full-length 16S rRNA amplicon libraries prepared from the mouse gut microbiota. A comparison of the nanopore and short-read sequencing data showed that there were no significant differences in major taxonomic units (89%) except one phylotype and three taxonomic units. Moreover, both sequencing data were highly similar at all taxonomic resolutions except the species level. At the species level, nanopore sequencing allowed identification of more species than short-read sequencing, facilitating the accurate classification of the bacterial community composition. Therefore, this method of full-length 16S rRNA amplicon sequencing will be useful for rapid, accurate and efficient detection of microbial diversity in various biological and clinical samples. Sci Rep. 2016 Jul 14;6:29681. doi: 10.1038/srep29681.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001263	Soil microcosms amended with 13C wheat Targeted Locus	To identify soil bacteria assimilating carbon from whole plants, we incubated soil from (cattle) pasture and natural beech forest with 13C-labelled wheat roots in microcosms for 72 hours. The degradation of the plant material was followed by measuring total CO2 and 13CO2. Pyrosequencing of density-resolved 16S rRNA identified soil bacteria involved in the assimilation of carbon from wheat residues.	root:Environmental:Terrestrial:Soil:Crop:Agricultural land
MGYS00001261	16S rRNA amplicons for dugout DNA samples - primers removed.	Three methods to profile a microbial community are compared.  These samples are 16S rRNA amplicons from a single DNA sample	root:Environmental:Aquatic:Freshwater
MGYS00001256	Modulation of the infant gut microbiota by a starter infant formula containing a synbiotic of bovine milk-derived oligosaccharides and Bifidobacterium animalis subsp. lactis CNCM I-3446	NCT01983072	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001254	The Effect of High Oxalate Exposure on the Gut Microbiota of Neotoma albigula	The mammalian gut microbiota is a complex ecosystem with hundreds to thousands of interacting species and numerous ecological niches, in a nearly closed off system primarily shaped by host physiology and diet.  Given the complexity of this system, it is difficult to elucidate specific interactions that shape the gut microbiota and its response to a dietary challenge. Oxalate, a simple organic acid widely distributed among plants, is a carbon and energy source for some gut bacteria that cannot be metabolized by mammalian enzymes.  Therefore, this compound can be used to identify fundamental ecological interactions between diet and the gut microbiota without confounding factors associated with other dietary components or host physiology.  We examined interactions between oxalate and the gut microbiota of the mammalian herbivore Neotoma albigula, which consumes a high oxalate diet in the wild.   By comparing the relative abundance of genes and metabolic pathways in the gut microbiota after exposure to 0.2% oxalate or 6% oxalate, we will elucidate those pathways that are enriched or inhibited by high oxalate exposure.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001253	Soil samples collected for whole-genome shotgun sequencing.	Soil samples collected for whole-genome shotgun sequencing.	root:Environmental:Terrestrial:Soil
MGYS00001252	Managing human microbiomes: Explaining heterogeneous responses in butyrate to dietary supplementation with resistant starch	Colonic bacteria produce the health-promoting metabolite butyrate. We sought to influence butyrate production in 20 healthy adults by supplementing their diet with resistant starch (RS). While average fecal butyrate increased from 8 to 12 mmol/kg wet feces, responses varied widely between individuals. Three types of responses were categorized: enhanced, high, and low (n = 11, 3, and 6 respectively). Fecal butyrate increased by 87% in the enhanced group, while it remained =12 mmol/kg in the high group and =8 mmol/kg in the low group. Microbiome analyses revealed that RS-degrading organisms increased from ~ 2 to 10% in the enhanced and high groups, but remained at ~ 2% in the low group. This lack of increase in RS-degrading microbes is likely why individuals in the low group do not benefit in butyrate with RS. This study underscores the importance of understanding inter-individual variability in managing ecosystem services from microbiomes.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001251	Phage therapy in Bangladeshi children hospitalized with acute bacterial diarrhea	NCT00937274	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001247	Metagenomics of laying hens	To study the effect on the microbiota of laying hens, dietary treatments were established supplementing a basal diet with prebiotic whey at 6% and probiotic Pediococcus acidilactici. Metagenomic sequences were obtained after DNA isolation from caecal samples	root:Host-associated:Birds:Digestive system:Ceca
MGYS00001246	Viral metagenome of Lake Soyang	This is a viral metagenome study of an oligotrophic freshwater lake, Lake Soyang, located in South Korea. The samples were collected from the surface of the lake.	N/A
MGYS00001244	Microbiomes from different citrus rootstock genotypes	This project is devote to study the citrus microbiome of two rootstock genotypes grown in different environments.	root:Host-associated:Plants:Rhizosphere
MGYS00001242	Plastic Metagenome Study	Plastic associated metagenomes from LMFS.	root:Engineered
MGYS00001241	The rumen microbial network is key to understanding how the mode of action of yeast and bicarbonate differs.	The rumen microbiota plays an essential role in maintaining an optimal fermentation pattern to satisfy the energy and protein requirement of the host. In this study, the effect of 2 additives (live yeast: YD and sodium bicarbonate: SBD) on the rumen microbial network structure was investigated in dairy cattle fed highly fermentable diets. Both YD and SBD were able to restore rumen fermentation, probably mediated through a stabilisation of the pH, however there seemed to be differences in the way this was actually achieved. Lactate concentration decreased and higher NDF digestibility was recorded with YD compared to either SBD or control. These changes were associated with different shifts in the bacterial population: higher bacterial richness in the solid fraction, decrease in Ruminobacter and increase in Megasphaera with YD, increase in Fibrobacter and Ruminococcus and decrease in Prevotella with both YD and SBD. Bacterial network and canonical correspondence analysis revealed the presence of 2 major bacterial consortiums (mutualistic groups composed of 6 and 4 genera respectively) negatively correlated with each other and having an opposite effects on VFA and acetate production. The use of network and interaction plots has shed new light on the mode of action, of apparently similar additives, on the rumen microbiota.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00001240	Faecal microbiome of Simmental calves determined by 16S rRNA gene amplicon sequencing	Calves undergo several changes of basic nutrition during early development from birth to weaning accompanied by pivotal changes of anatomy and physiology of the gastrointestinal tract. These changes go along with concomitant changes of the gastrointestinal tract microbiota. Therefore the aim of our study was to examine the fecal microbiota of six Simmental dairy calves during early development in a longitudinal study by using 16S rRNA gene amplicon pyrosequencing. Animals were followed up from birth to the time after weaning - calves were sampled six times according to critical timepoints during physiologic development. Overall, after quality control 253,528 reads (from 35 samples) were obtained. Reads were classified into 5,410 operational taxonomic units based on 0.03 16S rRNA distance with Bacteroidetes, Firmicutes and Proteobacteria being the most abundant phyla. The calves showed a high inter-individual variation in the composition of their fecal microbiota, although some tendencies could be seen: (i) an increasing diversity and species richness of the fecal bacterial community with increasing age and (ii) an increasing within-age-group similarity and distinct bacterial communities in early timepoints (from birth to the middle of the milk feeding period) compared to the timepoints around weaning.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001239	The influence of chitin addition on the lettuce rhizosphere microbiome	Within this study we used chitin as a soil amendment to influence plant growth, disease resistance and the rhizosphere microbiome. Lettuce plants were grown in potting soil for eight weeks or in potting soil amended with 2% chitin. The effect of the chitin addition was observed at the end of the experiment. Using amplicon sequencing, we already reported some first results, which can be found in: Debode et al. (2016) Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology. Frontiers in Microbiology 7.	root:Host-associated:Plants:Rhizosphere
MGYS00001238	Biofilm sloughing in integrated fixed-film activated sludge (IFAS) systems	Biofilm sloughing is an integral aspect, and a dynamic activity of biofilm development. This study focused on biofilm sloughing on carriers in integrated fixed-film activated sludge (IFAS) systems in both laboratory (LS; synthetic feed) and full-scale (FS; municipal) systems. During biofilm development in the LS system the relative hydrophobicity of flocs and biofilm increased with an increase in carrier bound biomass. There was a decline in relative hydrophobicity of the flocs and attached biomass upon sloughing. The protein to polysaccharide ratio in the extracted EPS of the suspended biomass (flocs and sloughed biomass) and biofilms decreased and increased, respectively, which corresponds to confocal imaging showing that micro-colonies with polysaccharide rich content sloughing from the biofilms. Sloughed biomass rapidly associated with flocs to form large and compact structures that led to a decrease in SVI from 60-70 ml/L to 34 ml/L. The α and β diversities determined by 16S rRNA gene sequencing (Illumina) of FS samples revealed greater diversity of the biofilm community compared to flocs. The α diversity of biofilms and suspended solids decreased and increased, respectively, during sloughing. The shift in community structure was in part due to the loss of Comamonadacae from the biofilm. At the class level, after biofilm sloughing, Alphaproteobacteria, Gammaproteobacteria, Flavobacteria, and Acidobacteria-6 dominated on the remaining biofilm. The relative abundance of Rhodocyclacae decreased in biofilms and flocs, after biofilm sloughing. Live-dead staining revealed areas of the biofilm where viability of biomass is an additional factor in sloughing.	root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
MGYS00001234	Novel immunomodulatory flagellin-like protein FlaC in Campylobacter jejuni and other Campylobacterales	The human diarrheal pathogens Campylobacter jejuni and Campylobacter coli interfere with host innate immune signalling by different means, and their flagellins, FlaA and FlaB, have a low intrinsic property to activate the innate immune receptor TLR5. We have investigated here the hypothesis that the unusual secreted, flagellin-like molecule FlaC present in C. jejuni, C. coli and other Campylobacterales might activate cells via TLR5 and interact with TLR5. FlaC shows a striking sequence identity in its D1 domains to TLR5-activating flagellins of other bacteria such as Salmonella, in contrast to non-stimulating Campylobacter flagellins. We overexpressed and purified FlaC, and tested its immunostimulatory properties on cells of human and chicken origin. Treatment of cells with highly purified FlaC resulted in p38 activation. FlaC directly interacted with TLR5. Preincubation with FlaC decreased the responsiveness of chicken and human macrophages towards the bacterial TLR4 agonist LPS, suggesting that FlaC mediates crosstolerance. C. jejuni flaC mutants induced an increase of cell responses in comparison to the wild type, which was suppressed by genetic complementation. Supplementing excess purified FlaC likewise reduced the cellular response to C. jejuni. In vivo, the administration of ultapure FlaC led to a decrease in caecal IL-1beta expression and a significant change of the caecal microbiota in chickens. We propose that Campylobacter spp. have evolved a novel type of immunostimulatory flagellin-like secreted effector in order to specifically modulate host responses, for example towards other PRR ligands such as LPS.	root:Host-associated:Birds:Digestive system:Fecal
MGYS00001233	Intestinal microbiota composition of interleukin-10 deficient C57BL/6J mice and susceptibility to Helicobacter hepaticus-induced colitis	The mouse pathobiont, Helicobacter hepaticus, can induce typhlocolitis in interleukin-10 deficient mice, and H. hepaticus infection of immunodeficient mice is widely used as a model to study the role of pathogens and commensal bacteria in the pathogenesis of inflammatory bowel disease. C57BL/6J Il10-/- mice kept under specific pathogen-free conditions in two different facilities (MHH and MIT), displayed strong differences with respect to their susceptibilities to H. hepaticus-induced intestinal pathology. Mice at MIT developed robust typhlocolitis after infection with H. hepaticus, while mice at MHH developed no significant pathology after infection with the same H. hepaticus strain. We hypothesized that the intestinal microbiota might be responsible for these differences and therefore performed high resolution analysis of the intestinal microbiota composition in uninfected mice from the two facilities by deep sequencing of partial 16S rRNA amplicons. The microbiota composition differed markedly between mice from both facilities. Significant differences were also detected between two groups of MHH mice born in different years. Of the 119 operational taxonomic units (OTUs) that occurred in at least half the cecum or colon samples of at least one mouse group, 24 were only found in MIT mice, and another 13 OTUs could only be found in MHH samples. While most of the MHH-specific OTUs could only be identified to class or family level, the MIT-specific set contained OTUs identified to genus or species level, including the opportunistic pathogen, Bilophila wadsworthia. The susceptibility to H. hepaticus-induced colitis differed considerably between Il10-/- mice originating from the two institutions. This was associated with significant differences in microbiota composition, highlighting the importance of characterizing the intestinal microbiome when studying murine models of IBD.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001232	Ontogeny of the gut microbiota in the cockroach Blattella germanica	Bacterial symbionts of insects have many metabolic activities that are absent in their hosts, and vice versa.  Blattabacterium lives inside the fat body cells of most of the cockroaches and plays an important role in nitrogen recycling. These insects also carry a variety of exosymbionts attached to the gastrointestinal walls, which collaborate in digestion and act as a barrier against colonization by pathogens, among other functions. For this work, the cockroach Blattella germanica was chosen in part by its importance as an indoor pest and also, because of its experimental convenience due to its short life cycle. The mode of acquisition of the gut exosymbionts is unknown, as well as the dynamics of their ecological succession across the life cycle of the insect. We have characterized the intestinal flora by different approaches. First, electron scanning microscopy confirmed the presence of a bacterial biofilm exclusively in the hindgut. qPCR revealed that the bacterial load in the gut increases with age. Pyrosequencing the hyper-variable regions V1-V3 of the 16S rRNA genes present in the guts of all the nymphal instars and adults of B. germanica revealed that the microbial composition is stage-specific through the development of the insect. Last, analysis of the embryos demonstrated that Blattabacterium is the only symbiont inherited maternally via the eggs, running out to elucidate the mode of adquisition of the intestinal microbiota.	root:Host-associated:Insecta:Digestive system
MGYS00001231	Interactions between gut microbiota, host genetics and diet in the development of metabolic syndrome	Obesity, diabetes and metabolic syndrome are the results of complex interactions between genetic and environmental factors, including the gut microbiota. To dissect interactions between the gut microbiota, diet and genetic background, we utilized three inbred strains of mice, which differ in development of obesity and metabolic syndrome, plus three derivative lines generated by breeding these strains in a common environment. Analysis of metabolic parameters and gut microbiota in the inbred strains and their environmentally normalized derivatives revealed strong interactions between the microbiota, diet, environmental history and metabolic phenotypes. Some phenotypes could be transferred to germ-free recipient animals by fecal transplant. Strong strain-dependent and strain-independent correlations were found between specific microbes and metabolic phenotypes. Environmental reprogramming of the microbiota resulted in one obesity-prone strain becoming obesity-resistant. Thus, in mice, development of obesity/metabolic syndrome is the result of strong interactions between the gut microbiota, host genetics and diet. In permissive genetic backgrounds, environmental reprograming of the microbiota can ameliorate development of metabolic syndrome.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001230	Fecal transplants modulate a high-fat diet-related alterations of gut microbiota in mice	"Background. The intestinal microbiota is altered in obese human subjects and in animal models of obesity. Transplantation of feces from lean, healthy donors to obese recipients has been shown to improve peripheral insulin sensitivity in subjects with metabolic syndrome.
Aim. We examined the gut microbiota in mice after administering a long-term, high-fat diet (HFD) supplemented with feces from lean mice
Methods. Forty-eight C57BL6/W mice were allowed to adapt to a non-specific pathogen free (SFP) environment for 2 weeks before being divided into three groups of 16 animals. Animals in each group were fed for 28 weeks with a normal diet (ND), HFD, or HFD supplemented  with feces from ND-fed mice (HFDS). The composition of colonizing bacteria was evaluated in mice droppings collected under SPF conditions at the beginning of the study (week 0) and at 12 and 28 weeks using an Ion 16S Metagenomics Kit on an Ion Torrent PGM"	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001229	All 16S rRNA amplicon sequences for dugout DNA samples	Three methods to profile microbial community are compared. These samples are 16S rRNA amplicon sequencing of a single DNA sample.	root:Environmental:Aquatic:Freshwater
MGYS00001227	Hellbender cutaneous microbiomes	Characterization of microbial communities has become useful in studying the ties between organismal health and the host microbiome. Pathogens currently threaten the existence of many amphibian species, and some studies have characterized the amphibian cutaneous microbiome. Hellbender salamanders (Cryptobranchus alleganiensis) provide an ideal system to explore the relationship between microbiome and disease due to differences in health between the two hellbender subspecies. The Ozark hellbender subspecies (C. a. bishopi) currently exhibits chronic wounds believed to be caused by bacterial infections, whereas the eastern hellbender (C. a. alleganiensis) does not. Through bacterial 16s rRNA amplicon sequencing, we detected more than 8,000 distinct operational taxonomic units in the cutaneous and environmental microbiome. We found differences in the bacterial communities between the two subspecies, while but there were no differences between the Ozark wound and healthy samples nor between respective subspecies environment samples. Several opportunistic pathogens were found to have an association with Ozark hellbenders. These findings suggest that wounds present only in the Ozark hellbenders may be due to a reduced immunocompetence relative to eastern hellbenders. Using next generation sequencing allowed for an in-depth exploration of the distribution and abundance of bacteria between two threatened amphibian subspecies.	root:Host-associated:Amphibia
MGYS00001226	pig microbiota	pig gut microbiota	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001225	The Pig's other genome: a reference gene catalogue of the gut microbiome	Pig is a main species for livestock and biomedicine. The pig genome sequence was recently reported. To boost research, we established a catalogue of the genes of the gut microbiome based on faecal samples of 287 pigs from France, Denmark and China. More than 7.6 million non-redundant genes representing 719 metagenomic species were identified by deep metagenome sequencing, highlighting more similarities with the human than with the mouse catalogue. The pig and human catalogues share only 12.6 and 9.3 % of their genes, respectively, but 70 and 95% of their functional pathways. The pig gut microbiota is influenced by gender, age and breed. Analysis of the prevalence of antibiotics resistance genes (ARGs) reflected antibiotics supplementation in each farm system, and revealed that non-antibiotics-fed animals still harbour ARGs. The pig catalogue creates a resource for whole metagenomics-based studies, highly valuable for research in biomedicine and for sustainable knowledge-based pig farming.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001222	Amplicon study from BBSRC-DBT project	Metagenomic analysis of caecum in Global Commercial Broilers and Kadaknath using 16sRNA V3-V4 primers.	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00001217	Long-term effect of the administration of two doses of formic acid on the intestinal microbiota profile of growing pigs	Thirty-four post-weaned pigs (35 day of age, of an average body weight of 7081.78 ± 956.23 g) were individually reared in cages. Based on litter and body weight, pigs were assigned to one of the three experimental diets. The diets were based on the same basal diet (C), without antibiotic supplementation, and supplemented with 1.4 kg/ton (L) and 6.4 kg/ton (H) of Ca-formate respectively. Pigs were fed with the experimental diets for 6 week and then slaughtered. Samples composed on scraped mucosa and digesta content was obtained from mid-jejunum and immediately frozen in liquid nitrogen. Total bacterial DNA was extracted using Qiamp Stool Mini Kit (Qiagen). The library formation and sequencing of 16S rRNA gene were performed with MiSeq® Reagent Kit V3-V4 on MiSeq-Illumina® platform. The letters “C”, “L” and ”H” in samples name indicate the three different diets, respectively.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00001214	Comparison between mouse caecal contents and faeces	Comparison between shotgun metagenomic results obtained from paired mouse caecal contents and faeces	root:Host-associated:Mammals:Digestive system
MGYS00001209	Radcliffe dental calculus	Ancient dental calculus from skeletons from the Radcliffe Hospital burial ground	root:Host-associated:Human:Digestive system:Oral
MGYS00001208	The antibiotic resistance potential of the preterm infant gut microbiome measured using shotgun metagenomics.	These samples were generated to quantify and interrogate the antibiotic resistome within a cohort of premature infants, using shotgun metagenomic sequencing.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00001207	Metagenomic samples from soil	Soil consist of wide range of microbes that can be applied for various processes. This study aims to do meta-genomics analysis of the given soil sample.	root:Environmental:Terrestrial:Soil
MGYS00001206	De novo transcriptome of a novel Graphium fungal species derived from a mixed microbial composting community enriched with wheat-straw, further grown on wheat straw	A simplified mixed microbial composting community was grown under laboratory conditions. A novel fungal isolate was found to be highly abundant and culturable.  This species was further grown singly on wheat-straw as a sole carbon source.  Its transcriptome was de novo assembled and used in transcriptome informed proteomics.	root:Engineered:Solid waste:Composting
MGYS00001205	Using metagenomic approach to study the microbial community structures in drinking water system.	The tap filters (Torayvino, Toray Industries Inc., Japan) were installed at the tap ends of a residential area, and continuously filtered 2000 L drinking water within ~2 days. After that, the filters were immersed into 50% ethanol solution to fix the microorganisms collected on the surface of hollow filter membrane in the filter. Then, extract the biomass on the membrane filter and extract DNA for metagenomic sequencing.	root:Environmental:Aquatic:Freshwater:Drinking water:Delivery networks
MGYS00001204	Wheat straw mixed microbial community metatranscriptome	Metatranscriptome of a mixed microbial composting community grown on wheat straw for 1 week.	root:Engineered:Solid waste:Composting:Grass
MGYS00001203	Multiple mycorrhizal fungi connect the roots of orchid and ash in a Newfoundland fen	The observation made by naturalists in Newfoundland that Cypripedium reginae, the showy lady slipper orchid, and Fraxinus nigra, the black ash tree, regularly co-occur, and that the orchid is not seen without the ash, has led to the suggestion of a fungal connection between the two plants. A DNA sequencing analysis was done to find shared fungi between both plants. Fungal DNA was sequenced using the Ion Torrent and Illumina Next Generation sequencing systems. Several fungal associates were found shared between C. reginae and F. nigra, and differences were observed between the OTU outputs between Ion Torrent and Illumina NGS.	root:Host-associated:Plants:Rhizosphere
MGYS00001202	"16S amplicon data from soils in ""Soil Service"" sites."	Using these 16S data as a complementary study for the captured metagenomes targeted using Sequence Capture probes.	root:Environmental:Terrestrial:Soil
MGYS00001201	Sequencing of Ammonia oxidising bacteria from FISH enriched samples	Fluorescence In-Situ Hybridization was used to label Ammonia Oxidising bacteria, which were subsequently sorted with flow cytommetry and sequenced. Two conditions (aerobic and anaerobic) are compared, with two replicates each.	root:Engineered
MGYS00001200	Metagenomic study of the eukaryotic microorganisms diversity of a pond based on an environmental DNA (eDNA) sample.	Usually, to determine the biological quality of a body of water, micro fauna and especially macroinvertebrates are determined using a binocular microscope. This study aims to compare this traditional method of species census with the analysis by metagenomic of environmental DNA (eDNA) from the same pond sample.	root:Environmental:Aquatic:Freshwater:Pond
MGYS00001199	Amplicon-based metagenomics analysis of Vitis vinifera L. cv. Corvina grapes and fresh musts	"The fungal populations present in Vitis vinifera L. cv. Corvina grapes and musts were compared in two different years vintages. The comparison was carried out through ITS1-5.8S-ITS2 454-pyrosequencing. Grapes were collected from a recent vineyard located in the Italian winery region called ""Valpolicella"" (Sant""Ambrogio, Verona, Italy). After the harvesting, grapes were subjected to withering in a dedicated warehouse located a few kilometers far from the vineyars (<5Km). The warehouse is supplemented with automatic systems able to control and modify the internal temperature and humidity. The duration of grape withering was defined according to the regional rules for Amarone production (Paronetto and Dellaglio, 2011), which define the time in which the grapes for Amarone vinification can be mashed. The comparison of the fungal populations present in these samples sheds lights on the Amarone production, allowing the identification of the persistent fungal genera and on genera varying as suffering from seasonal environmental changes."	root:Host-associated:Plants
MGYS00001198	Metagenomic analysis of soil samples from an oil contaminated military base	Samples were taken from 3 contaminated and 1 non contaminated sites of the military base in 3 depth (1m, 5.5-5.8m and 7.5-7.8m). After DNA extraction whole metagenome sequencing was performed on Illumina MiSeq platform.	root:Environmental:Terrestrial:Soil:Sand:Oil-contaminated
MGYS00001196	Metagenomes from the marine sponge Ianthella Basta	We applied differential coverage binning of multiple metagenomes from two different microbial cell enrichments derived from the marine sponge Ianthella basta.	root:Host-associated:Invertebrates
MGYS00001195	Microbial community diversity in reactors digesting chicken manure	Microbial community diversity in reactors digesting chicken manure	root:Engineered:Bioreactor
MGYS00001193	A Catalogue of the Mouse Gut Metagenome	The importance of the gut microbiota for regulation of whole body metabolism, energy homeostasis, development of the immune system and even complex behavioural traits is well documented. The acquisition of comprehensive gene catalogues of the human gut metagenome using “next generation sequencing” has immensely advanced our insight into the complex metagenome-host genome interaction and the connection between common human diseases and the gut microbiota. Causal links are difficult to establish in humans, and therefore, mice still serve as important models for functional studies. We used HiSeq2000-based whole metagenome sequencing to establish a catalogue of 2.6 million non-redundant microbial genes from faecal samples of 184 mice representing different strains, fed different diets, obtained from different providers, and kept in different housing laboratories to secure high diversity and representation. Similar to the human gut microbiome, more than 99% of the genes in the catalogue were bacterial, suggesting that the mouse microbiota overall comprises between 800 and 900 bacterial species. A core mouse gut microbiome was defined at the genus level comprising 60 genera, 25 of which were shared with the core genera in the human gut microbiome. Although the mouse gut microbiome was functionally similar to its human counterpart, sharing 79.9% of its KEGG orthologous groups, only 4.0% of the mouse gut microbial genes were shared with those identified in human gut microbiome, emphasising the need for a specific mouse catalogue. We observed marked differences regarding provider, housing laboratory, strains, gender and feed, emphasizing the need for carefully controlled experimental conditions and caution comparing data from different laboratories.   As we have accounted for these factors in creating the catalogue, it provides a useful reference for future studies, including studies using short reads for comprehensive analyses of the mouse gut microbiome.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001192	Bioelectrochemical BTEX removal at different voltages: assessment of the degradation and characterization of the microbial communities	BTEX compounds (Benzene, Toluene, Ethylbenzene and Xylenes) are toxic hydrocarbons that can be found in groundwater due to accidental spills. Bioelectrochemical systems (BES) are an innovative technology to stimulate the anaerobic degradation of hydrocarbons. In this work, single chamber BESs were used to assess the degradation of a BTEX mixture at different applied voltages (0.8 V, 1.0 V, 1.2 V) between the electrodes. At the end of the experiment the microbial communities were characterized by high throughput sequencing of the 16S rRNA gene. Hydrocarbon degradation was linked to current production and to sulfate reduction, at all the tested potentials. The highest current densities applied (about 200 mA/m2 with a maximum peak at 480 mA/m2) were observed when 0.8 V were. The application of an external voltage increased the removal of toluene, m-xylene and p-xylene. The highest removal rate constants at 0.8 V, calculated for toluene, m-xylene and p-xylene, were: 0.4 ± 0.1 days-1, 0.34 ± 0.09 days-1 and 0.16 ± 0.02 days-1, respectively).At the end of the experiment, the microbial communities were characterized by high throughput sequencing of the 16S rRNA gene. Microorganisms belonging to the families Desulfobulbaceae, Desulfuromonadaceae and Geobacteraceae were enriched on the anodes suggesting that both direct electron transfer and sulfur cycling occurred. The cathodic communities were dominated by the family Desulfomicrobiaceae that may be involved in hydrogen production.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00001191	Technical biases and variations on species abundances for a repetitively sequenced fecal sample 16S rRNA library.	The high throughput sequencing powered by next generation sequencing offered unprecedented resolution in delineating the composition of microbial profiles. To best evaluate the biases and artifacts entangled within the sequencing output we had repeatedly sequenced an amplicon library from the same fecal sample 10 times in 4 distinct Illumina MiSeq sequencing runs. Analysis of the observed Operational Taxonomic Units (OTUs) showed as expected a strong correlation of relative abundance with the coefficient of variation. The results are used to argue about the appropriate relative abundance exclusion cutoff used in the Rhea pipeline for the analysis of microbial profiles.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001187	Microbiome samples derived from Buruli ulcer wounds and non-Buruli ulcer skin ulcerations	Background: Buruli ulcer (BU) is an infectious disease caused by Mycobacterium ulcerans and considered the third most prevalent mycobacterial disease in humans. This skin disease can affect the entire body surface, but primarily the lower extremities, with symptoms varying from nodules to ulcers. Secondary bacterial infections in open BU lesions are the main cause of pain, delayed healing and systemic illness, resulting in prolonged hospital stay. Thus understanding the diversity of bacteria in these open lesions is important for proper treatment. The normal skin flora is known to protect the host through commensal relationships, however, certain factors such as ulceration can shift the skin flora from being primarily commensal to potentially pathogenic. Therefore, the objective of this study was to characterize and compare the skin bacteria from BU ulcers, non-BU ulcers, and similar locations on the skin of healthy individuals. Results: Using 16S rRNA sequencing, we determined the microbial composition of 5 BU lesions, 3 non-BU lesions and 3 healthy skin samples, and compared these using a data analysis pipeline. Our results showed a lower bacterial diversity in both the BU and non-BU lesions compared to the healthy skin. However, no significant differences were found between BU and non-BU lesions. The BU lesions were characterized by an increase of Bacteroidetes compared to the non-BU wounds, which contained more (Gamma)Proteobacteria. Furthermore, the BU lesions also contained significantly more obligate anaerobes. All lesions contained a mixture of gram-positive and gram-negative bacteria, with more gram-negatives present in the BU and non-BU lesions than in healthy skin samples. With this molecular-based study, we were also able to detect bacteria, which were missed by culture-based methods in previous BU studies.Conclusions: Our study suggests that BU leads to changes in the bacterial community within the lesions. These changes are potentially detrimental and may cause a delay in the healing process. In order to determine if the alterations in Bacteroidetes were due to a specific wound environment, underlying pathophysiological conditions created by M. ulcerans, or associated with wound location on the body, further microbiome studies are necessary.	root:Host-associated:Human:Skin
MGYS00001185	Complicated Sputum Microbial Composition in the Patients of Pulmonary Tuberculosis	Background. Amount of studies have suggested the relationship between the microbiota and the onset of diseases, especially some chronic diseases. An understanding of bacterial community in the sputum from patients has deeply recognized the pulmonary tuberculosis.   Methods. We enrolled 31 patients suffering from pulmonary tuberculosis and 24 healthy persons as the normal control, and then extracted the total DNA of sputum samples of pulmonary tuberculosis patients and respiratory secretions of normal person. 16S rDNA V3 hyper-variable regions were amplified using bar-coded primiers and pyro-sequenced using  Roche 454 FLX .   Results. All the sequences we get were analysed by tools in the Ribosomal Database Project. the amplicons were classified into 24 main phyla, there are 24 phylum in the pulmonary tuberculosis samples and 17 phylum in normal person. Microbiota changed in the sputum of pulmonary tuberculosis patients, and we can separate pulmonary tuberculosis patients from normal person through the respiratory microbial community. The microbial composition in the sputum of pulmonary tuberculosis patients is much more diversity than that in normal person(p<0.05). Furthermore, lots of foreign bacteria such as Stenotrophomonas, Cupriavidus, Pseudomonas, Thermus, Sphingomonas, Methylobacterium, Diaphorobacter, Comamonas and Mobilicoccus uniquely distributed in the pulmonary tuberculosis patients.   Conclusions. The study concludes that the respiratory tract microbial composition  in pulmonary tuberculosis become much more complicated than that in normal person. Besides, amount of foreign bacteria exist in the sputum of pulmonary tuberculosis patients. The role these foreign bacteria played in the onset or processing of pulmonary tuberculosis may need pay much more attention to.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00001184	Term and preterm shotgun samples	This study was approved by the University of East Anglia (UEA) Faculty of Medical and Health Sciences Ethics Committee, and sample collection was in accordance with protocols laid out by the NRES approved UEA Biorepository (Licence no: 11208). Infants were born at the Neonatal Intensive Care Unit (NICU) of the Norfolk and Norwich University Hospital (NNUH, Norwich, UK) and The Rosie Hospital (Cambridge, UK) were recruited by doctors or nurses with informed and written consent obtained from parents.  Both NICUs have similar protocols for feeding, prescription of antibiotics, and antifungal drugs with the exception that NNUH administered a probiotic treatment containing Bifidobacterium bifidum and Lactobacillus acidophilus (i.e. Infloran®) to their infants from birth.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001183	Metagenome analysis of oil drilling waste at a oil drilling waste recycling plant	The 1 % weight emission-limit of drill waste set by the authorities has set an end to disposal of waste containing oil-based drilling fluids into the sea. The waste mud is instead shipped on shore for cleansing and re-cycling. Several waste plants have been built along the coast of Norway for this purpose. The business of handling and recycling oil drill waste is relatively new, and there is limited documentation of any possible negative health effects for workers handling drilling mud at these plants. The on-site occupational health services report of ailments such as of odors, fatigue, headaches and sickness. These are vague descriptions that may have several causes, but exposure on the work place cannot be ruled out. It is therefore desirable to survey the risk of exposure and possible negative health effects at these work places. For this purpose the chemical and biological agents in the air generated by recycling of the oil drilling waste was characterized and the community biodiversity and function of the drilling waste was analyzed by shotgun sequencing.	root:Environmental:Aquatic:Marine:Oil-contaminated sediment
MGYS00001182	Metagenomic analysis of sediment (MNS3) of Manikaran hot springs	Bacteriophages are the most dominant predators of prokaryotic communities in thermal springs yet understanding of the phage ecology remains limited in these hydrothermal environments. Here we examine the metagenomic phage profile from hot spring sediments (n = 4, 78°C-98°C) and microbial mats (n = 2, 57°C).  Caudovirales comprised 91% of the 65 reconstructed phage genotypes, including members of the Myoviridae, Siphoviridae, Podoviridae, and Inoviridae. Siphoviridae were predominant in the sediment and Myoviridae in the microbial mats. Phage genomes were often more well-conserved across sediments compared with microbial mats, which could suggest that there are fewer hosts in the sediments, which represent an extreme environment (78°C-98°C).  A minimal phage genome (28 orthologous proteins) was maintained across both sediment and microbial mats including proteins like histidine kinase, integrase, and Clp protease suggesting a common origin over an inter-habitat distance of 500 m, which are part of survival strategy of bacterial communities at thermophillic environments. We reconstructed bacterial genomes, including Ralstonia (5 Mbp), Pseudoxanthomonas (3.5 Mbp), Dechloromonas (1.9 Mbp), Herbaspirillum (1.5 Mbp), which were predicted to be hosts based on integrated phage DNA and unique CRISPR arrays, suggesting prior phage infections. This study provides detailed insight into the genetic give-and-take between hosts and phages in the ecological niches of thermal springs.	root:Environmental:Aquatic:Thermal springs:Sediment
MGYS00001181	Artificial mix of real bacterial sequences	Artificial mix of real bacterial sequences. 15 genomes, even representation. 10X coverage	root:Engineered:Modeled:Simulated communities (sequence read mixture)
MGYS00001180	Metagenomic analysis of sediment (MNS2) of Manikaran hot springs	Bacteriophages are the most dominant predators of prokaryotic communities in thermal springs yet understanding of the phage ecology remains limited in these hydrothermal environments. Here we examine the metagenomic phage profile from hot spring sediments (n = 4, 78°C-98°C) and microbial mats (n = 2, 57°C).  Caudovirales comprised 91% of the 65 reconstructed phage genotypes, including members of the Myoviridae, Siphoviridae, Podoviridae, and Inoviridae. Siphoviridae were predominant in the sediment and Myoviridae in the microbial mats. Phage genomes were often more well-conserved across sediments compared with microbial mats, which could suggest that there are fewer hosts in the sediments, which represent an extreme environment (78°C-98°C).  A minimal phage genome (28 orthologous proteins) was maintained across both sediment and microbial mats including proteins like histidine kinase, integrase, and Clp protease suggesting a common origin over an inter-habitat distance of 500 m, which are part of survival strategy of bacterial communities at thermophillic environments. We reconstructed bacterial genomes, including Ralstonia (5 Mbp), Pseudoxanthomonas (3.5 Mbp), Dechloromonas (1.9 Mbp), Herbaspirillum (1.5 Mbp), which were predicted to be hosts based on integrated phage DNA and unique CRISPR arrays, suggesting prior phage infections. This study provides detailed insight into the genetic give-and-take between hosts and phages in the ecological niches of thermal springs.	root:Environmental:Aquatic:Thermal springs:Sediment
MGYS00001179	Freshwater shotgun metagenome from the surface of Nakdong River during algal bloom, Busan, South Korea	We monitored seasonal variation of shotgun metagenome during occurrence of algal bloom	root:Environmental:Aquatic:Freshwater
MGYS00001178	metagenomic Shotgun analysis of cecum microbiome of poultry	metagenomic Shotgun analysis of cecum microbiome of poultry from Indian sub Continent	root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
MGYS00001177	Study of the changes in the metagenome of the groundwater community at	During the 1960s, assorted radioactive waste was disposed at the Little Forest Legacy Site near Sydney (Australia). Trenches were dug and filled with waste. It has been observed that after rainfall events, water overflows. The study aims to evaluate the potential community changes and relate them with expected fluctuating redox conditions.	root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
MGYS00001175	The initial state of the human gut microbiome determines its reshaping by antibiotics	The human gut microbiota is affected by antibiotics, but the heterogeneous response between individuals remains unexplored. To specifically address this question and examine the effect of antibiotics on selection of resistance genes, we administered the second-generation cephalosporin cefprozil to healthy volunteers. Stool samples gathered before antibiotic exposure, at the end of the treatment and three months later were analyzed using shotgun metagenomic sequencing. We show that normal antibiotic treatment can alter the gut microbiome in a specific, reproducible and predictable fashion. Strikingly, we identified a subgroup of participants that were enriched in opportunistic pathogen Enterobacter cloacae after exposure to the antibiotic, an effect linked to lower initial microbiome diversity and to the Bacteroides enterotype. Resistance genes that were not detectable before the treatment were observed after a 7-day course of antibiotic. Knowledge of the initial composition of the microbiome could assist in the prevention of the adverse effects of antibiotics.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001173	Functional and taxonomic profiling of microbial communities in caves of the Algarve, Southern Portugal.	This project is designed to deliver dense genetic data sets and sharply improve our understanding of microbial diversity, functioning and biogeography across cave ecosystems. The distinct Algarve karst region (southern Portugal) will be used as a model system in an unprecedented metagenomics quest for the hidden microbial taxa, genes and metabolic pathways present in pristine/undisturbed cave sediments. By overcoming the typical hurdles of traditional microbial cultivation approaches, and targeting cave microbial communities in a DNA-based, cultivation-independent fashion instead, this project will shed new light on the metabolic potential and life-style of hitherto “unculturable” microorganisms that inhabit these unique settings. Extensive data acquisition on key functional genes will ultimately permit future design of novel microbial cultivation platforms based on the predicted metabolism of cave sediment microorganisms. Furthermore, this analysis as a whole will considerably augment our current, limited knowledge of microbial diversity and function in these distinct ecosystems, which remain under-appreciated despite their relevance for global biogeochemistry.	root:Environmental:Terrestrial:Soil
MGYS00001172	Metagenomic study of composts produced onfarm	In order to characterize the microbial biodiversity of two composts produced “on-farm”, that have showed different suppressive activity against Rhizoctonia solani and Sclerotinia minor, a metagenomic approach by sequencing 16S r-DNA, for to study bacterial diversity and 18S r-DNA, for to study fungi diversity, both amplified from total DNA extracted from the two composts, will be perform.	root:Engineered:Solid waste:Composting
MGYS00001168	Cervical microbiota analysis	The human cervical microbiome may affect natural history of various sexually transmitted infections, including human papillomavirus (HPV). Persistent oncognic HPV infection is a necessary cause of cervical carcinoma. Subjects in this study consisted of 120 women, and they have visited three or more times to study hospital. Subjects enrolled with HPV infection were followed for about 18~24 months. Hybrid capture method was used for detection of oncogenic HPV. Metagenomic DNA was extracted from cervical swab samples of subjects, and bacterial 16S rRNA gene was amplified for microbial community analysis. The compositions of bacterial community were sequenced by pyrosequencing and analyzed.The composition of bacterial community was unique by disease status in each subject. The most predominant phyla were Firmicutes, Proteobacteria, and Actinobacteria. Relatively lower diversity values obtained from bacterial community in vaginal samples than other body sites were observed (41-117 OTUs and lower than 2.35 of Shannon diversity index). These results indicate that the composition of bacterial community in cervical sample of each subject is unique and the composition could be related to the disease status. Further studies of additional subjects will provide a significant difference of cervical bacterial communities among disease status, and this difference help to understand the correlation between microbiome and HPV infection.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00001167	Forest harvesting reduces the soil metagenomic potential for biomass decomposition	Soil is the key resource that must be managed to ensure sustainable forest productivity. Soil microbial communities mediate numerous essential ecosystem functions, and recent studies show that forest harvesting alters soil community composition. From a long-term soil productivity study site in a temperate coniferous forest in British Columbia, 21 forest soil shotgun metagenomes were generated, totaling 187 Gb. A method to analyze unassembled metagenome reads from the complex community was optimized and validated. The subsequent metagenome analysis revealed that, 12 years after forest harvesting, there were 16% and 8% reductions in relative abundances of biomass decomposition genes in the organic and mineral soil layers, respectively. Organic and mineral soil layers differed markedly in genetic potential for biomass degradation, with the organic layer having greater potential and being more strongly impacted by harvesting. Gene families were disproportionately affected, and we identified 41 gene families consistently affected by harvesting, including families involved in lignin, cellulose, hemicellulose, and pectin degradation. The results strongly suggest that harvesting profoundly altered below-ground cycling of carbon and other nutrients at this site, with potentially important consequences for forest regeneration. Thus, it is important to determine whether these changes foreshadow long-term changes in forest productivity or resilience and whether these changes are broadly characteristic of harvested forests.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00001163	Diet determines bacterial diversity and community structure in Bornean pitcher plants	Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their primary nutrient source, sequestering nitrogen from arthropod prey and bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial diversity and community structure was comparable across plant species and most tissues, except digestive fluids. These showed opposing trends with N. hemsleyana harbouring a more diverse bacterial community. In N. rafflesiana fluid, high levels of Acidocella spp. implied a close association with the plant. In N. hemsleyana fluid, vertebrate gut symbionts as well as saprophytic taxa could be detected, the latter of which might act as competitors for nutrients. Generally, digestive fluid communities were highly variable in structure, which might be applicable to a difference in digestion status. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and rare encounters with bats, respectively.	root:Host-associated:Plants
MGYS00001162	Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of cheese microbiota	Microbial communities of cheeses, in particular traditional ones are very diverse, questioning their origin, safety and functional role in cheese making. Metagenomic analysis of these communities by Very High Throughput Sequencing Technology (VHTST) with short read shotgun sequencing is a promising approach for their microbial profiling and functional study. However, VHTST requires an adequate genome sequence database to assign the short reads.  The objective of the present study was to constitute a reference genome catalogue suitable for short read metagenomic analysis. Bacteria isolated from dairy products, and belonging to 137 different species and 67 genera were selected, including isolates from the genera Alkalibacterium, Brochotrix, Kluyvera, Luteococcus, Marinilactibacillus and Vagococcus, for which no genome sequences were available. Draft genomes sequences were produced, and 117 among 142 were suitable for public databases and submitted, mainly at high quality level. As a proof of concept for the use of VHTST profiling, the microbial composition of the surfaces of two smear cheeses and one blue-veined cheese was analyzed with the use of these new genomes. A significant part of the cheese microbiota was composed of microorganisms that were not deliberately inoculated, including Gram-negative genera such as Pseudoalteromonas, Halomonas, Vibrio, Marinilactibacillus and Psychrobacter.  The depth of this metagenomic analysis revealed the presence of strains sharing almost complete gene set with over 99.9% identity with newly sequenced strains. They may correspond to 'terroir' strains that add typical values to traditional productions. The availability of the genomes sequenced in the present study and particularly those which are not deliberately inoculated, and the broaden use of VHTST will considerably extend our understanding of cheese microbiota, and of genetic determinants involved in the generation of desirable or undesirable properties.	root:Engineered:Food production:Dairy products
MGYS00001161	Kansas, Cultivated corn soil metagenome reference core Project	none provided	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00001155	Bacterial diversity in various environments such as cultivated soil, alpine soil,  semi-arid soil	For cultivated soil, alpine soil,  semi-arid soil, samples were taken in the field in 2012 and 2013. They were soil micro-samples as they all weighed between 70 and 150 mg.Samples labelled xb or a (69 samples) come from an alpine soil. They were taken along a 80-m long transect in La Vanoise Park (France). The transect was sampled twice in 2012 and 2013. Samples labelled GMV1 to GMV23 come from a 10-m long transect in Widou (Senegal) were the soil is semi-arid. Samples labelled LD1 to LD22 come from a 2-m long transect in a cultivated soil near Lyon.	root:Environmental:Terrestrial:Soil
MGYS00001143	Oral microbiome samples from the Philippines	Metagenomic sequencing of saliva samples from individuals with hunter-gatherer or agriculturalist lifestyles from locations in the Philippines.	root:Host-associated:Human:Digestive system:Oral:Saliva
MGYS00001137	Metagenome and metatranscriptome profiling of moderate and severe COPD sputum in Taiwanese Han males	Metagenome and metatranscriptome profiling of moderate and severe COPD sputum in Taiwanese Han males	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00001135	Local surveillance of infectious diseases and antimicrobial resistance from sewage	Adequately monitoring of large populations and their environments is essential if we want to monitor pathogens and antimicrobial resistance around the globe. Recent developments in high‐throughput sequencing allow to rapidly identify nucleic acids from various organisms in clinical and environmental samples. Sewage systems are recognized as an important source of human pathogens, especially in crowded settings with poor infrastructure. A temporal metagenomic analysis is applied to sewage samples collected from sewage system of Copenhagen (capital of Denmark) at three sewage plants prior to treatment plants inlet. The project is a proof‐of‐concept study for applying metagenomic approaches that could initiate a the local surveillance of human infectious diseases including antimicrobial resistance from sewage to detect, control, prevent and predict human infectious diseases.	root:Engineered:Wastewater:Water and sludge
MGYS00001118	Bacteria and yeast involved in red-browning defect in smear cheese	This study is focused on the characterisation of microbiota in red-spoiled (n=6) and not-spoiled cheeses (n=6), and onto the wooden shelves (12) used for ripenning.	root:Engineered:Food production:Dairy products
MGYS00001112	Cheese Processing Targeted Locus	Grana Trentino is a hard Parmesan-like cheese made from raw milk with a traditional technology. Microbiota development from raw milk to aged Grana Trentino cheese during production and maturation processes is the object of this study. This evaluation is important to understand the role of bacteria in determining cheese flavor and sensorial traits. The microbial composition and spatial distribution within Grana Trentino from raw milk to 18 month ripened cheese was characterised on two cheese-making days using partial 16S rRNA pyroseqeuncing 454 analysis of tagged amplicons.  <p> Milk, whey and cheese were collected at different times ripening and in different locations.	root:Engineered:Food production:Dairy products
MGYS00001111	Effects of different stages of lactation on the microbial evolution during cheese fermentation: from milk to DPO Fontina Cheese by 454 -pyrosequencing	The bacterial populations of raw milk and Fontina cheeses produced in two cheese factories were investigated by 454 - high-throughput sequencing. Total microbial DNA was isolated from milk and cheeses sampled at 24h and after 7, 28 and 84 day of ripening. In each cheese factory nine cheese-making days were followed in a four months long period: three in the first 40 days after partum (S1), three in the following 40 days when the cows had their estrus cycle (S2) and three in the last 40 days (P3) when cows were pregnant. DNA was used as template in Polymerase Chain Reaction (PCR) to study the hypervariable V1, V2 and V3 regions of the bacterial 16S rRNA gene and analysed by 454-pyrosequencing. A total of 2,518,829 sequence reads were generated by the pyrosequencing of 18 milk and 72 cheese samples	root:Engineered:Food production:Dairy products
MGYS00001110	Metagenomic characterization of three Swedish sewage treatment plants	Sewage treatment plants (STPs) have repeatedly been suggested as “hotspots” for the emergence and dissemination of antibiotic-resistant pathogens. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed.	root:Engineered:Wastewater:Activated Sludge
MGYS00001109	Dietary silver nanoparticles can disturb the gut microbiota in mice	Humans are increasingly exposed via the diet to Ag nanoparticles (NP)used in the food industry. Because of their anti-bacterial activity, ingested Ag NP might disturb the gut microbiota that is essential for local and systemic homeostasis. We explored here the possible impact of dietary Ag NP on the gut microbiota in mice at doses relevant for currently estimated human intakeMice were orally exposed to food (pellets) supplemented with increasingdoses of Ag NP (0, 46, 460 or 4600 ppb) during 28 d. Body weight, systemicinflammation and gut integrity were investigated to determine overall toxicity, and feces DNA collected from the gut were analyzed by Next Generation Sequencing (NGS) to assess the effect of Ag NP on the bacterial population. Ag NP were characterized alone and in the supplemented pellets by scanning transmission electron microscopy (STEM) and energy dispersive X-ray analysis (EDX).	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00001108	Effect of phytostimulatory seed-inoculant Azospirillum lipoferum CRT1 on total bacterial comminity (rrs) in the maize rhizosphere	The field trials were run in 2015 in Chatonnay (site P), Cessieu (site BV) and Saint Savin (site FV), which are located in the vicinity of Bourgoin-Jallieu (Isère, France). Maize seeds were inoculated or not by a suspension of  Azospirillum lipoferum CRT1 cells. DNA was extracted from root-adhering soil and nifH gene diversity was sequenced  using 515/806 targeting V4 variable region by Illumina Miseq (2 × 125 bp). Samples 261 to 265 correspond to site BV non-inoculated (NI) formulation F1. Samples 286 to 290 correspond to BV inoculated (I) formulation F1. Samples 311 to 315 correspond to FV-NI-F1. Samples 331 to 335 correspond to FV-I-F1 Samples 351 to 355 correspond to P-NI-F1. Samples 371 to 375 correspond to P-I-F1. Samples 271 to 275 correspond to site BV non-inoculated (NI) formulation F2. Samples 296 to 300 correspond to BV inoculated (I) formulation F2. Samples 321 to 325 correspond to FV-NI-F2. Samples 341 to 345 correspond to FV-I-F2 Samples 361 to 365 correspond to P-NI-F2. Samples 381 to 385 correspond to P-I-F2.	root:Host-associated:Plants:Rhizosphere
MGYS00001107	Human gut bacteria that rescue growth and metabolic defects transmitted by microbiota from undernourished children	Human gut bacteria that rescue growth and metabolic defects transmitted by microbiota from undernourished children	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00001106	To evaluate, using as model the major pest of commodities, Plodia interpunctella, and adopting a culture-independent approach, the impact of different food substrates on the host-associated bacterial communities.	The feeding behavior of insects may influence the associated bacterial community; this possibility and its magnitude are currently a matter of debate. Using as model the major pest of commodities, Plodia interpunctella, and adopting a culture-independent approach, the impact of different food substrates on the host-associated bacterial communities was evaluated. The analysis of similarity confirmed the differences among microbiotas of moths fed with five substrates and the diet is the only tested factor that explains the observed dissimilarity. The few bacteria shared between food and insect, provide evidences for a limited conveyance of bacteria to the host by diet; more likely, diets with different composition indirectly promote changes on the insect’s microbiota. Moth microbiotas were characterized by two enterotypes, associated with insect fed on diet rich in carbohydrates and proteins, respectively. These results were also confirmed by statistical analyses performed on the predicted functional potential. A core microbiota composed of six taxa was shared between eggs and adults, regardless of the population of origin. The finding of possible human and animal pathogens on chili and in the microbiotas of moths fed on it, open to the possibility that P. interpunctella may convey, through frass, potential pathogens to stored products.	root:Host-associated:Insecta:Digestive system
MGYS00001105	Daisy Lake Shotgun Test	Organic matter (OM) derived from terrestrial ecosystems influences both the food webs and biogeochemical cycles of lakes. The boreal ecozone holds an estimated 60% of the world’s fresh water, but lakes in this region tend to be nutrient-poor and less productive, making them especially reliant on carbon subsidies from riparian litterfall. The availability of these carbon subsidies for aquatic food webs depends on microbial communities, but little is known about how the taxonomic and functional diversity of heterotrophic bacteria might influence the rate at which this OM is decomposed in natural systems. Drawing upon biodiversity-ecosystem functioning theory, we predicted that decomposition rates, indicative of both food web production and whole-lake carbon cycling, increase with the taxonomic and functional diversity of bacterial communities. We characterized both bacterial community composition and microbial functional traits in nearshore sediments from 8 catchments along a gradient of terrestrial OM inputs using next-generation sequencing (16S rRNA amplicon sequencing and shotgun metagenomics). We found that both species richness and composition explained variation in rates of OM decomposition among sites. Differences in species composition were largely driven by 17 bacterial families, with abundances of Acidobacteria, Firmicutes and Actinobacteria changing along OM gradients. Ongoing shotgun sequencing will provide more detailed information on the functional traits present in lake sediments. This study highlights the role of microbial communities in the transfer of resources from terrestrial ecosystems, and improves our understanding of how catchment disturbances affect boreal aquatic ecosystems.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00001103	Effect of phytostimulatory seed-inoculant Azospirillum lipoferum CRT1 on functional community of diazotroph (nifH)in the maize rhizosphere	The field trials were run in 2015 in Chatonnay (site P), Cessieu (site BV) and Saint Savin (site FV), which are located in the vicinity of Bourgoin-Jallieu (Isère, France). Maize seeds were inoculated or not by a suspension of  Azospirillum lipoferum CRT1 cells. DNA was extracted from root-adhering soil and nifH gene diversity was sequenced  using polF/polR primers by Illumina Miseq (2 × 300 bp). Samples 261 to 265 correspond to site BV non-inoculated (NI) formulation F1. Samples 286 to 290 correspond to BV inoculated (I) formulation F1. Samples 311 to 315 correspond to FV-NI-F1. Samples 331 to 335 correspond to FV-I-F1 Samples 351 to 355 correspond to P-NI-F1. Samples 371 to 375 correspond to P-I-F1. Samples 271 to 275 correspond to site BV non-inoculated (NI) formulation F2. Samples 296 to 300 correspond to BV inoculated (I) formulation F2. Samples 321 to 325 correspond to FV-NI-F2. Samples 341 to 345 correspond to FV-I-F2 Samples 361 to 365 correspond to P-NI-F2. Samples 381 to 385 correspond to P-I-F2.	root:Host-associated:Plants:Rhizosphere
MGYS00001102	Effect of phytostimulatory seed-inoculant Azospirillum lipoferum CRT1 on functional community of ACC deaminase producers (acdS) in the maize rhizosphere	The field trials were run in 2015 in Chatonnay (site P), Cessieu (site BV) and Saint Savin (site FV), which are located in the vicinity of Bourgoin-Jallieu (Isère, France). Maize seeds were inoculated or not by a suspension of  Azospirillum lipoferum CRT1 cells. DNA was extracted from root-adhering soil and nifH gene diversity was sequenced  using acdSF5/acdSR8 primers by Illumina Miseq (2 × 125 bp). Samples 261 to 265 correspond to site BV non-inoculated (NI) formulation F1. Samples 286 to 290 correspond to BV inoculated (I) formulation F1. Samples 311 to 315 correspond to FV-NI-F1. Samples 331 to 335 correspond to FV-I-F1 Samples 351 to 355 correspond to P-NI-F1. Samples 371 to 375 correspond to P-I-F1. Samples 271 to 275 correspond to site BV non-inoculated (NI) formulation F2. Samples 296 to 300 correspond to BV inoculated (I) formulation F2. Samples 321 to 325 correspond to FV-NI-F2. Samples 341 to 345 correspond to FV-I-F2 Samples 361 to 365 correspond to P-NI-F2. Samples 381 to 385 correspond to P-I-F2.	root:Host-associated:Plants:Rhizosphere
MGYS00001101	CSF	CSF	root:Host-associated:Human
MGYS00001099	The Effect of Probiotics with Antibiotics on Gut Microbiota during the Helicobacter Eradication: Randomized Controlled Trial	The effect of probiotics with antibiotics on gut microbiota during the Helicobacter eradication was analyzed using 16S rRNA gene pyrosequencing. The diversity of microbiota obtained from antibioitcs alone treatment group was more changed than that of probiotics cotreatment group. This study will provide information to treat Helicobacter infected patients.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001079	Transient rapamycin treatment robustly increases lifespan and healthspan in middle-aged mice	The FDA approved drug rapamycin increases lifespan in rodents1 and improves measures of age-related function in rodents2 and humans3; thus, rapamycin has promising translational potential as an intervention to promote both longevity and healthspan. Nevertheless, significant questions remain regarding the optimal dose, treatment regimen, efficacy, and safety of rapamycin administration in the context of healthy ageing4. Here we show that 3 months of rapamycin treatment is sufficient to increase life expectancy by more than 50% and improve measures of healthspan in middle-aged mice. Transient treatment with rapamycin is also associated with a remodelling of the microbiome, including dramatically increased prevalence of segmented filamentous bacteria in the small intestine. We also define a dose in female mice that does not extend lifespan. This higher dose of rapamycin is associated with a striking shift in cancer prevalence toward aggressive haematopoietic cancers and away from non-haematopoietic malignancies in females. These data demonstrate that a single short-term rapamycin treatment late in life can be effective at delaying ageing and suggest that a similar regimen may be applicable to promote healthy ageing in people.	root:Host-associated:Mammals:Digestive system
MGYS00001073	Bacterial 16s Amplicon Sequencing of the Atlantic Ocean	Latitudinal transect of the Atlantic Ocean, depth range from 20-200m, size fractioned by filtering (0.22, 3, 8 µm). Amplicon Sequencing of the V5-V6 region of the bacterial 16s rRNA Gene.	root:Environmental:Aquatic:Marine:Oceanic:Abyssal plane
MGYS00001069	Eco-pathogenomics of chlamydial infection: The role of the vaginal microbiota	Chlamydia trachomatis genital infection is one of the most widespread sexually transmitted infections in the United State and worldwide, its high prevalence speaks volume about the remarkable adaptability to thrive in human and to bear upon, perhaps outcompete against, indigenous vaginal microbiota. However, the roles of vaginal microbiome, particularly its relations to the varied degree of host predisposition to disease upon exposure to pathogens, are largely undetermined. In this study, we investigated vaginal microbial community composition and structure upon active Chlamydial infection and clearance of infection for 9 months after treatment, using a collection of samples from 101 young women. One striking findings is that the hallmark of healthy vagina Lactobacillus is markedly underrepresented in the investigated cohort, particularly L. crispatus, L. jensenii, L. gasseri, while the abundance of L. iners is similar to healthy or asymptomatic cohort. To make the results more comparable between different studies, we also compare 16S gene V1-V3 amplicon with V1-V2 amplicon in their taxonomic assignment. Furthermore, strong association of microbial community compositional profiling and pathological conditions is revealed. Gardnerella vaginalis is identified as the most abundant species in vaginal microbiota with active Chlamydial infection in addition to a group of other low abundant phylotypes, while Lactobacillus iners become the most prevalent species when infection is cleared. Our results provide evidences of the interactive roles of vaginal microbiota during the episode of infection and restoration of health or asymptomatic state, to facilitate further risk assessment and developing strategic plans of diagnostics and personalized treatments to promote health and quality of life.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00001068	Temporal stability of the oral microbiota: A longitudinal study of the dental, tongue, and salivary bacterial consortia	Every individual harbors a distinct oral microbiome that is influenced by environmental changes and shifts dramatically during the transition to disease. Examining baseline variation within and between individuals over time is critical to understanding this disease transition. Here we examined the temporal stability of supragingival plaque, tongue dorsum, and salivary microbial communities of healthy individuals. Ten subjects were sampled over 90 days and oral bacterial communities were profiled by high-throughput 16S rRNA gene sequencing. In all cases, supragingival plaque consortia were distinct from tongue dorsum and salivary communities. Overall, 97% of bacterial operational taxonomic units (OTUs) found in saliva were also detected in tongue samples, whereas only 2% of salivary OTUs were associated with supragingival plaque. Relative to other sites, the tongue dorsum also exhibited the highest relative temporal stability in bacterial composition. Because of the temporal variability in intra-individual microbiota, pooling of data from at least three time-points was required to capture the majority of an individual?s diversity at all time points. Using machine learning, we could also identify each subject by their microbial profiles alone with 95% accuracy, owing to each individual?s distinct oral microbial profiles. We also identified a core set of bacterial OTUs from all samples that classified within six genera: Streptococcus, Fusobacterium, Haemophilus, Neisseria, Prevotella, and Rothia. A set of 14 additional core OTUs were present in the majority of subjects, sites, and time-points, affiliated with the Campylobacter, Bergeyella, and Porphyromonas genera. This study characterizing a baseline and examining temporal shifts of the healthy core microbiota provides an useful prospect to examine dysbiosis during disease. While this knowledge can be harnessed to develop novel prognostics and diagnostics for disease conditions, the intra-individual differences in oral microbiota also highlight the need for an individualized approach to bacterial surveillance in dentistry.	root:Host-associated:Human:Digestive system:Oral
MGYS00001067	New Primers for Discovering Fungal Diversity using Nuclear Large Ribosomal DNA	Identification and classification of a wide variety of organisms using DNA sequences has helped overcome many limitations of traditional morphological approaches. However, the utility of DNA as a tool to catalogue biodiversity, resolve phylogenies, or explore patterns in ecological communities depends strongly on choice or design of primers for selecting the appropriate genetic markers. Unfortunately, no primers have been developed to target the D1 region across a wide diversity of fungi, with a short amplicon suitable for the Illumina MiSeq platform.  Here we introduce and evaluate two primer sets targeting the D1 region of the large subunit of ribosomal DNA to evaluate fungal diversity in 24 environmental subarctic soil and peat samples.	N/A
MGYS00001066	What controls long-term changes in freshwater microbial community composition?	Microbial ecology came to the forefront of biological and ecological science in the 1990s with the development of high-throughput DNA sequencing and other molecular techniques.  Recently this field entered a second age of understanding that microbial diversity was organized into patterns at various scales, consistent with ecological concepts that were once thought applicable only to macro-organisms.  Evidence of these patterns in diversity contradicts the traditional microbial hypothesis from Bass-Becking (1934) that ?Everything is everywhere, but the environment selects,? and indicates that, as with larger organisms, dispersal processes influence microbial diversity even at regional and local scales.  It is clear that both dispersal and environmental conditions are related to patterns of diversity, but to date the mechanistic controls and the relative importance of these factors have not been determined.  This study aims to resolve these controls through a combination of field and lab experiments with monitoring and surveys of the phylogenetic composition and ecosystem function (metabolism) of microbial communities.  This research builds on a long-term record showing consistent spatial and temporal patterns of microbial growth and community composition in ~25 lakes and streams of the Toolik Lake Research Area in Arctic Alaska.  Using experiments coupled with established sampling protocols and routines, this research will answer 3 basic questions, and focus on the long-term aspects of dispersal events and climate change: (1) How does environment influence microbial community composition and rate of function? (2) How are distribution patterns of microbial communities in lakes, streams, and soils influenced by dispersal via down-slope water flow? (3) How are seasonal, inter-annual, and long-term shifts in microbial community composition related to temporal shifts in environmental conditions such as those caused by climate change?  Long-term investigations of microbial communities are critical for understanding patterns of diversity and their controls, especially because the most enduring dispersal events are also most rare.  Moreover, because this work is located in the Arctic it will capture the earliest biological effects of global climate change.	root:Environmental:Aquatic:Freshwater
MGYS00001064	The microbial database of activated sludge - Denmark (MiDAS-DK)	V13 16S rRNA amplicon sequencing of Danish activated sludge wastewater treatment plants.	root:Engineered:Wastewater:Activated Sludge
MGYS00001019	Metacommunity analysis of two protozoan taxa (Amoebozoa) in grassland soils	To contribute to the current understanding of free-living soil protozoan, we examined the diversity of two widespread and common groups of soil amoebae, the genus Acanthamoeba and the Myxomycetes, in the topsoil of grasslands from three German regions (Schorfheide-Chorin, Hainich-D?n, Schw?bische Alb). We choose these two taxa of Amoebozoa because of the converging evidence of their prevalence in soils and because they are overlooked by both traditional and molecular sampling methodologies: they are rarely, if ever, recovered using eukaryote-wide primers. We developed specific primers to target the variable region V2 in the first part of the small subunit of the ribosomal RNA gene, using Roche GS FLX high-throughput sequencing.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000991	Arctic Ocean metagenomes from HLY1502	Arctic Ocean metagenomes sampled aboard CGC Healy during the 2015 GEOTRACES Arctic research cruise	root:Environmental:Aquatic:Marine:Oceanic
MGYS00000990	Minor impacts of reduced pH on bacterial biofilms on settlement tiles along natural pH gradients at two CO2 seeps in Papua New Guinea	To study the effect of reduced pH on bacterial biofilms on tropical coral reefs, settlement tiles were deployed along pH gradients in December 2011 at two reefs in Papua New Guinea which hosted hydrothermal CO2 seeps. This ENA entry contains the sequences from biofilm samples from the lower side of eight settlement tiles (4 per reef) that were sampled 5 and 13 months after deployment. These samples covered pH values between 8.0 and 7.6 and constitute a subset of a larger pool of samples from the settlement tiles that was analyzed with ARISA only. The bacterial biofilm consisted predominantly of Alpha-, Gamma- and Deltaproteobacteria, as well as Cyanobacteria, Flavobacteriia and Cytophaga. Bacterial biofilm composition was heterogeneous with approximately 20% shared operational taxonomic units between samples. Among the observed environmental parameters, pH only had a very weak effect on community composition (R? ~ 1%, based on ARISA) and did not affect community richness and evenness.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00000974	Core genomes of cosmopolitan surface ocean plankton	"The sunlight surface layer of the ocean is the largest
            contiguous biome on the planet.  The photoautotrophic microbial communities
            in the ocean fix roughly equal amounts of CO2 through photosynthesis as all
            terrestrial biomes, despite a widespread paucity of multiple nutrients.
            The accompanying bacterioplankton communities are important in recycling
            nutrients for autotrophs, providing or requiring vitamin cofactors, thereby
            influencing the biogeochemical cycles of important green house gasses
            N2O, CO2, dimethyl sulfide, and methane. The bacterioplankon communities
            contain a high level of diversity , particularly of uncultivated organisms
            with unknown genome contents. Single cell genomics and metagenomic assemblies
            have characterized the genomes of a few uncultivated organisms , yet a
            substantial portion of the community remains uncharacterized.  Here we report
            the collection, assembly, and analysis of 225 metagenomes collected from the
            euphotic zone of every ocean at temperatures from 0?C to 30?C.  A global assembly
            resulted in 3 Gbp of contiguous DNA assemblies, or approximately 100 genomes
            , representing over 80% of all metagenomic reads.  A large majority of the
            assemblies are cosmopolitan, with over 50% being found in 50% of the metagenomic
            sites, indicating a widespread genomic commonality between geographicall
            y separated communities. The emergent genome biogeography illuminates a
            temperature-driven distribution of genomes at multiple taxonomic levels from
            strain to phyla, while protein family level analyses at a global and genus level
            point to nutrient availability dictating finer scale variation.  The assemblies
            provide a genomic characterization of the so-called microbial dark matter in this
            environment at an unprecedented scale and point to lineage specific metabolic
            specialization both in core metabolism and nutrient acquisition, a potential niche
            diversification that leads to metasymbiosis within a complex community."	root:Environmental:Aquatic:Marine:Oceanic:Photic zone
MGYS00000402	sequencing of Rubus V-118-13 for virus analysis	Blackberry Loch Ness showing virus like symptoms was analysed using RT-PCR. Further analysis was performed using HGS. Total RNA was extracted from leaves using MagMax 96 Total RNA Isolation Kit (Life Technologies). RiboMinus Plant Kit for RNA-Seq (Life Technologies) was used to eliminate rRNA from the sample. Sample was sequenced on Ion Torrent PGM and Illumina platforms.	root:Host-associated
MGYS00000403	sequencing of Rubus V-067-13 for virus analysis	Wild Rubus showing virus like symptoms was analysed using RT-PCR. Further analysis was performed using NGS. Total RNA was extracted from leaves using MagMax 96 Total RNA Isolation Kit (Life Technologies). RiboMinus Plant Kit for RNA-Seq (Life Technologies) was used to eliminate rRNA from the sample. Sample was sequenced on Ion Torrent PGM and Illumina platforms..	root:Host-associated
MGYS00000985	Bacterial diversity, community composition and potential activity in surface waters of the Gulf of Naples	Bacterioplankton are the key components of the biogeochemical cycles in marine ecosystem. Consequently, their richness and evenness are critical for the way the ecosystem functions, and need regular monitoring in order to have a proper assessment of ecosystem health and functioning. It is also important to estimate the functional potential of each bacterial population so as to understand their individual contribution to the ecosystem processes. Community structure and function of bacterial assemblages are influenced by a number of biotic and abiotic interactions which are highly dynamic in marine ecosystems, especially in the coastal areas. This study aims to investigate the diversity, community composition and functional potential of bacterial communities in a coastal area of the Mediterranean Sea.	root:Environmental:Aquatic:Marine:Coastal
MGYS00000984	16s metagenomics of dam water from 3 sources.	16s metagenomics study of dam water from 3 sources from Bulgaria. 7 samples from Miseq 2x300 PE run. The study aims to explore the natural microbiome of the fresh water from 3 different lakes.	root:Environmental:Aquatic:Lentic
MGYS00000572	Enrichment from groundwater treating sand filters	Samples collected at waterworks sand filters were enriched for specific functional groups e.g. ammonium oxidizers. These enrichment cultures were tested in column experiments. Samples were taken at experimental termination. 16S rRNA amplicon sequencing was done on the original sand filter material, the cultures and the samples.	root:Environmental:Aquatic
MGYS00000973	Bacterial and fungal core microbiomes associated with purple prairie clover during ensiling and aerobic spoilage.	Bacterial and fungal core microbiomes associated with purple prairie clover during ensiling and aerobic spoilage.	root:Environmental:Terrestrial:Agricultural field
MGYS00000969	Ecoli data	Compassion study	root:Host-associated:Human:Circulatory system:Blood
MGYS00000968	the Ecoli fastq file	a compassion study	root:Host-associated:Human:Circulatory system:Blood
MGYS00000956	Soil Genome sequencing	The microdiversity of soil	root:Environmental:Terrestrial:Soil
MGYS00000950	Rice field soil Targeted Locus (Loci)	To study the community structures after the addition of ammonium and nitrate	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000943	Characterization of the vaginal microbiome in women with cervical intraepithelial neoplasia	Background: The healthy vaginal microbiota is typically Lactobacillus spp. dominant and it plays an important role in the prevention of urogenital diseases and infections. Persistent infection with oncogenic HPV subtypes is necessary for the development of invasive cervical cancer. Recent evidence indicates that the vaginal microbiome may play a functional role in the persistence or regression of Human Papillomavirus (HPV) infections. The vaginal microbiome in women with cervical intra-epithelial neoplasia (CIN) has yet to be investigated.  Objectives: To characterize the vaginal microbiome structure and diversity in women with different CIN grades.  Material and Methods:  Population: Reproductive age, non-pregnant women of reproductive age with CIN attending the colposcopy clinic. Setting: Imperial College Healthcare NHS Trust. Interventions: Vaginal swabs were collected from the posterior vaginal fornix and bacterial DNA extracted. The vaginal microbiome was characterised by 16S rRNA gene sequencing using an Illumina MiSeq platform. Women were categorized in to two groups on the basis of histology and cytology; women with low-grade (LSIL) and high-grade squamous intra-epithelial lesions (HSIL). Analysis: Supervised, and unsupervised multivariate modeling of sequence data was used to examine bacterial species classification data, and correlated these to the disease severity. Richness and diversity indices were calculated for patient population groups.   Results: We analysed 39 women with CIN, which were divided in to LSIL (n=11) and HSIL (n=28) grades. Hierarchical clustering analysis of bacterial species data revealed 3 distinct community state types (CST I: Lactobacillus crispatus; CST III: Lactobacillus iners; CST IV: mixed diverse Lactobacillus-depleted microbiome) in women with CIN. 26% of our predominantly Caucasian population had a high-diversity, non-Lactobacillus dominated microbiome (CST IV), which is approximately 3 times greater than the rate documented for Caucasian women without CIN in previous reports. None of the women with CIN had a Lactobacillus gasseri-dominated (CST II). The proportion of women with CST IV vaginal microbiome was similar for women with LSIL (n=3 out of 11; 27%) versus women with HSIL (8 out of 28; 28%).  Conclusions: One third of women with CIN have a more diverse Lactobacillus-depleted vaginal microbiome, higher than the rates previously reported in normal populations. This high rate of microbiome diversity may reflect lesions that are likely to progress and warrants further investigation. A Lactobacillus gasseri-dominated microbiome was not observed in this population of women with CIN. This supports previous reports indicating that Lactobacillus gasseri is correlated with rapid HPV clearance. Future therapeutic strategies may allow modulation of the vaginal microbiome toward a vaginal community structure that promotes HPV clearance.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00000942	The vaginal microbiome during pregnancy and the postpartum period in a European population.	Determining the composition and structure of the vaginal microbiome during pregnancy is critical to understanding its role in maintaining reproductive health outcomes. Historically, studies on the pregnant vaginal microbiome have been limited to Northern American populations. Using MiSeq sequencing of 16S rRNA gene amplicons, we characterised the vaginal microbiota of a mixed British ethnic cohort of women (n=42) who experienced normal, uncomplicated term delivery and whom were sampled longitudinally throughout pregnancy (8-12, 20-22, 28-30 and 34-36 weeks gestation) and the postpartum period (6 weeks) in. We show that the composition of the vaginal microbiome dramatically changes postpartum to become less Lactobacillus spp. dominant with greater alpha-diversity (CST IV) irrespective of the community structure for that individual during pregnancy and independent of their ethnic background. As observed in North American populations, a British population is characterised by a vaginal microbiome during pregnancy that is dominated by Lactobacillus spp. and low alpha-diversity (community state types CST I, II and III). However, significant numbers of women in this British cohort have an L. jensenii (CST V) dominated microbiome that is characterised by low levels of alpha-diversity. CST V was predominantly observed in women with Asian and Caucasian ethnic backgrounds whereas CST II (L. gasseri) was absent in samples collected from Black women. This study reveals new insights into biogeographical and ethnic effects upon the microbial communities in the vaginal microbiome during pregnancy and in the postpartum period and has important implications for future studies designed to explore relationships between the vaginal microbiome, host health and pregnancy outcomes.	root:Host-associated:Human:Reproductive system:Vagina
MGYS00000941	We analysed the gut microbiota of rats kept in the same cage	Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, potentially leading to false conclusions. With obesity at pandemic levels animal systems of this disease have been developed; we investigated the role of experimental design on one such rodent model.  We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6) and lean (homozygous n= 6; heterozygous n= 6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance. Importantly, the obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?	root:Host-associated:Mammals:Digestive system
MGYS00000939	Chinese Poyang Lake resistant genes from soil metagenome	Chinese Poyang Lake resistant genes from soil metagenome	root:Environmental:Terrestrial:Soil
MGYS00000897	Puerto Morelos summer	Metagenome of coral rubble in Puerto Morelos, Quintana Roo. Mexico.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00000866	Bacillus anthracis DNA in environmental metagenome	This study examined the efficacy of sequence analysis for detection of B. anthracis in an environmental background. Whole-genome sequencing was applied to titrated genome copy numbers of B. anthracis in the presence of background nucleic acid extracted from aerosol and soil samples.	root:Environmental:Terrestrial:Soil
MGYS00000865	Drivers of Diversity for Microbial Communities Inhabiting Halites from the Hyper-arid Zone of the Atacama Desert	The Atacama Desert is one of the oldest and driest deserts in the world and its hyper-arid core is described as ?the most barren region imaginable?. Under these extreme moisture, thermal, and solar radiation stress, habitats inside halite pinnacles harbour flourishing microbial communities. We use a combination of high-throughput sequencing and microscopy methods to characterize the microbial assemblages of halites collected in several areas of the desert. We found communities dominated by Archaea and relying on a single phylotype of Halothece cyanobacteria for primary production. A few other phylotypes of salt-adapted bacteria and archaea, including Salinibacter, Halorhabdus, and Halococcus were major components of the halite communities indicating specific adaptations to the unique halite environments. Multivariate statistical analyses of diversity metrics clearly separated the halite communities from that of the surrounding soil and revealed a distribution patterns of halite communities strongly correlated to atmospheric moisture. Communities from halites exposed to costal fogs were more diverse than halites from the Yungay area, in both their archaeal and bacterial assemblages, and were colonized by a novel algae related to oceanic picoplankton of the Mamiellales. In contrast, we did not find any algae in the Yungay pinnacles suggesting that the environmental conditions in this habitat might be at the limit for eukaryotic life.	root:Environmental:Terrestrial:Soil:Desert
MGYS00000864	Methane inhibition alters the microbial community, hydrogen flow and fermentation response in the rumen of cattle.	The effects of the anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology and H2 /CH4 production were investigated in vivo. Eight rumen fistulated Brahman steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate diet (60:40) with increasing levels (low, mid and high) of chloroform in a cylcodextrin matrix. The increasing levels of chloroform resulted in an increase in H2 expelled as CH4 production decreased with no effect on dry matter intakes. The amount of expelled H2 per mole of decreased methane, was lower for the roughage hay diet suggesting a more efficient redirection of hydrogen into other microbial products compared with concentrate diet. A shift in rumen fermentation towards propionate and branched-chain fatty acids was observed for both diets. Animals fed with the hay:concentrate diet had both higher formate concentration and H2 expelled than those  fed only roughage hay.  Metabolomic analyses revealed an increase in amino acids, organic and nucleic acids for both diets when methanogenesis was inhibited. These changes in the rumen metabolism were accompanied by a shift in the microbiota with an increase in Bacteroidetes:Firmicutes ratio and a decrease in archaea and Synergistetes for both diets. Within the Bacteroidetes family, some OTUs assigned to Prevotella were promoted under choloroform treatment. These bacteria may be partly responsible for the increase in amino acids and propionic acid in the rumen. No significant changes were observed for abundance of fibrolytic bacteria, protozoa and fungi, which suggests that fibre degradation was not impaired. The observed 30% decrease in methanogenesis did not adversely affect rumen metabolism and the rumen microbiota was able to adapt and redirect metabolic H2 into microbial end-products for both diets. However, dietary supplements or microbial treatments may also be required to capture any additional H2 expelled by the animal to further improve rumen efficiency.	root:Host-associated:Mammals:Digestive system:Foregut:Rumen
MGYS00000632	Experimental trial using phytase in the diet for broiler	The aim is to verify the impact of the phytase added in the broiler diet on microbial profile of caecum and broiler meat	root:Host-associated:Birds
MGYS00000629	An integrated multi-omics approach reveals the effects of supplementing grass or grass hay with vitamin E on the rumen microbiome and its function	Rumen function is generally sub-optimal leading to losses in the form of methane and nitrogen. Analysis of the rumen microbiome is thus important to understand underlying microbial activity under different feeding strategies. This study investigated the effect of forage conservation method and vitamin E supplementation on rumen function using the rumen simulation technique (Rusitec). Dietary treatments consisted of ryegrass (GRA) or ryegrass hay (HAY) supplemented with 20% concentrate containing zero or 50 IU/d vitamin E, as ?-tocopheryl acetate, according to a 2?2 factorial design. Forage conservation method did not substantially change the nutrient composition but had a profound impact on the structure and diversity of the main rumen microbial communities. HAY diets promoted a more complex bacterial community (+38 OTUs) dominated by Firmicutes. This adaptation, together with increased rumen protozoa levels and greater diversity in the bacterial and methanogen communities, led to greater fibre degradation (+12%) in HAY diets, but also to greater proteolysis (+15%) than observed with GRA diets. Inter-species H transfer between fibrolytic bacteria, protozoa and methanogens was greater in HAY diets, which resulted in higher metabolic H recovery and ultimately higher methane emissions (+35%). On the contrary, GRA diets promoted more simplified methanogen and bacterial communities. This bacterial community was dominated by Bacteroidetes and Lactobacillus, thus lactate formation may have acted as an alternative H sink in GRA diets. Moreover the structure of the bacterial community with GRA diets was highly correlated with N utilization, and GRA diets promoted greater bacterial growth and microbial protein synthesis (+16%), as well as a more efficient microbial protein synthesis (+22%). A dose-response experiment using batch cultures revealed that ?-tocopheryl acetate was more effective than ?-tocopherol in improving rumen fermentation, moreover a high vitamin E dose (500 IU/L) had a negative impact on rumen function. This improvement consisted of a small increase in feed degradability (+8%), possibly as a result of the antioxidant properties of vitamin E which led to higher bacterial and protozoal levels. Moreover, vitamin E supplementation promoted substantial changes in the methanogen community suggesting that some methanogen species are particularly sensitive to oxidative stresses. Our findings suggested that when possible  grass should be fed instead of grass hay, in order to improve rumen function and to decrease the environmental impact of livestock agriculture.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000863	Testing 602	First attempt to figure this out	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000862	FVB F Partial Co2	Diet effects on FVB microbiome	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000861	FVB Partial Co1	Examining effect of diet on microbiome in cohort1	root:Host-associated:Mammals:Digestive system:Midgut
MGYS00000851	Bacterial Communities Associated with Atherosclerotic Plaques from Patients with Atherosclerosis	16S rRNA amplicon sequencing	root:Host-associated:Human:Circulatory system
MGYS00000823	Studying the presence and selection of antibiotic resistance genes	Antibiotic resistance genes can directly enter WWTPs, pass through the WWTPs, and enter receiving waters, thus potentially spreading resistance and posing a growing concern to the public. My goals here are two-fold. First, I want to test if specific operating metrics, such as temperature, pH, BOD concentration, and N concentration, have an influence on the presence and persistence of antibiotic resistance genes in sludge communities. Second, I want to determine whether antibiotic resistance genes are under active selection within WWTPs. To accomplish this second goal, I will evaluate whether antibiotic resistance genes are actively transcribed, which would suggest potential direct selection. I will also test whether antibiotic resistance genes correlate with biodiversity, where I expect that a negative relationship between biodiversity and antibiotic resistance genes is indicative of active selection. I will use a metagenomics and metatranscriptomics approach to test for the presence and expression of target genes. This will help identify potential selection pressures that enable antibiotic resistance genes to pass through WWTPs and be released into receiving waters.	root:Engineered:Wastewater:Activated Sludge
MGYS00000802	Diversity and rehabilitation of prokaryotic communities of European biological soil crusts	Biological soil crusts (biocrusts) play vital roles in dryland regions that cover over 35% of the Earth?s land mass, including 24% of Europe. They provide important ecosystem services such as limitation of soil erosion, retention of water, improving soil fertility, and nitrogen and carbon fixation. Here, we present a characterization of the prokaryotic components of European biocrusts, particularly in light of the fact that biocrusts are very susceptible to land use change, long-term farming and chronic physical disturbance. Knowledge of soil microorganisms is rarely considered within the context of biodiversity management, although the diversity and services provided by soil biota are of decisive importance for intact ecosystem function. Secondly, a rehabilitation study was carried out in order to investigate the recovery processes of biocrusts in response to anthropogenic perturbation. The successional pattern of recovery was assessed in the form of returning organisms including bacteria, fungi, algae, lichens, bryophytes and higher plants.	root:Environmental:Terrestrial:Soil:Desert
MGYS00000795	Glacial snow and soil Targeted Locus (Loci)	This study was to investigate the dominant bacterial community from glacial snow and how they changed when they were exposed to glacial soil.	root:Environmental
MGYS00000581	Virus diversity in Namib Desert soils	The taxonomic composition of soil viruses along the Namib Desert aridity gradient was assessed using deep sequencing of metavirome libraries extracted from surface soils. Soil physicochemical data were used to determine influences, if any, on the observed soil-specific taxonomic compositions of virus communities.	root:Environmental:Terrestrial:Soil:Sand:Desert
MGYS00000777	Influence of biodiversity on the functionality of activated sludge communities	We are addressing a critical and unresolved ecological question: When are community composition and biodiversity important for the provision of a particular ecosystem function and when are they not? We hypothesize that community composition and biodiversity are more important for rare ecosystem functions than for common ecosystem functions. If an ecosystem function is rare, then differences or changes in community composition could have profound effects on the biotransformation rate of that function. In contrast, if an ecosystem function is common, then differences or changes in community composition are unlikely to have an effect on that function.	root:Engineered:Wastewater:Industrial wastewater
MGYS00000616	Mock Community Sample	Mock Community Sample	root:Engineered:Modeled
MGYS00000776	Comparison of two soil microbiomes with different organic matter content	"Comparison of two microbiomes of two adjacents environments in Florianopolis (Brasil): a rich organic matter/high plant diversity env. (""Forest"") and a poor sand-like dune env. with sea influence (""Dune"")."	root:Environmental:Terrestrial:Soil
MGYS00000764	Wisconsin, Switchgrass soil metagenome reference core Project	none provided	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000377	Microbial biodiversity and structure in soil affects the composition of pyrrolizidine alkaloids in Jacobaea vulgaris	Secondary metabolites like pyrrolizidine alkaloids (PAs) act as defense compounds against aboveground and belowground attackers. We studied to get a better understanding of relevance of microbial diversity in the rhizosphere for plant growth and behavior, specifically related to secondary metabolites production. We made soil dilution to compare the composition of soil microbial communities of soil suspension, incubation and rhizosphere soil by 16s rRNA high throughput pyrosequencing, as a consequence, to determine the effects on plant behaviors. The dilution procedure leads to reduction of the diversity of bacteria at the phylum level. After regrown, the structure of microbial community in the rhizosphere changed significantly as compared to the composition in the incubated soil. Jacobeae vulgaris as model plants growing in the soil where microbial diversity were decreased, had a higher biomass and higher amount of free base form of PAs? production, which indicates the reduction of soil microbial community in the rhizosphere shows significant feedback. Our study adds evidence that soil microbes may play a role in the evolution of plant secondary metabolites in plants.	root:Environmental:Terrestrial:Soil
MGYS00000759	Agricultural soils from the East China	To understand AOA and AOB distribution in different kind of soils in the East China.	root:Environmental:Terrestrial:Soil
MGYS00000740	Compartmentalization of the microbial community structure in submerged aerobic membrane bioreactors treating wastewater	This study examines the distribution of biomass within submerged membrane bioreactor (MBR) systems, and how, from an engineering and ecological perspective, this may be important to the function, design and operation of submerged MBRs for wastewater treatment.  The microbial-membrane interface, particularly with respect to biofouling, can be a defining feature of the MBR process in biological wastewater treatment. Submerged aerobic MBRs are revealed to be a series of compartments: mixed liquor suspended biomass (MLSB); extra-membrane loosely bound biofilm (EMLB); extra-membrane tightly bound biofilm (EMTB);  and intra-membrane core biofilm (IMCB; formed in voids 20 - 100 ?m in diameter) with both flat sheet and hollow-fibre membranes. Microscopy and 16S rRNA gene sequencing were used to characterize the biomass from these compartments within a laboratory scale aerobic MBR feed with synthetic wastewater. Although there were similarities distinct differences in the predominant populations between compartments were observed,  Dysgonomonas, a facultative anaerobe, Acetobacterium, a gram-positive anaerobe, and Blastobacter, capable of nitrogen-fixation, were predominant in the IMCB. Xanthobacter, a denitrifier , and Subtercola, a floc-forming bacteria were present in the MLSB. Rhodocista, known to be a phototroph or aerobic chemoheterotroph was found in the MLSB as well as the EMTB and EMLB. Mycoplana and Caldimonas, aerobic chemoorganoheterotrophs, were unique to EMLB and EMTB, respectively. Changes in substrate availability, including dissolved oxygen concentration, and microenviornmental conditions across the compartments, are likely important factors shaping these communities within these compartments.	root:Engineered:Bioremediation:Terephthalate:Wastewater:Bioreactor
MGYS00000720	Diversity and Abundance of Ammonia Oxidizing Archaea in the Coastal Sea Surface Microlayer	This is a part of a project targeting the distribution and diversity of ammonia oxidizing archaea in the sea surface microlayer (SML). Previous reports have reported the high abundance of Thaumarcheota in the SML in lake environments but the distribution of archaea in the SML of marine environments have yet to be investigated. Using 16S rRNA gene pyrosequencing and qualitative PCR techniques, we found that the relative abundance of phylum Thaumarchaeota can also be high in the SML and their abundances were weakly co-related to the chlorophyll-a and transparent exopolymer particles concentrations in the SML. Additionally, archaeal groups originating from soil or terrestrial were also found in higher proportions in the SML compared to the underlying water (20cm).	root:Environmental:Aquatic:Marine:Coastal
MGYS00000615	454Titanium barcoded pyrosequencing of the 16S rRNA and proteorhodopsin-containing photoheterotrophs genes was used to characterize the structure and microbial diversity across a seasonal change (August to March), in waters off Maria Island.	Observational and modelling studies have shown that currents along the east coast boundary of Tasmania are influenced by the strength of a residual East Australian current (EAC), experiencing distinctive seasonal and interannual variation in water properties. In this study we investigated whether the influence of the EAC changes the microbial community structure, including photoheterotrophic proteorhodopsin-containing bacteria (PRB), a key component of the microbial community. Seawater samples were collected from August 2011 to March 2012 from surface waters at the National Reference Station Maria Island Mooring. The microbial communities were characterized by 454 pyrosequencing of the 16S rRNA and proteorhodopsin genes. Our data show marked changes in microbial assemblages over the season, in particular in February and March. The maximal effect of the EAC was observed by the increased abundance of Prochlorococcus spp., associated with warm and highly oligotrophic open ocean waters. PRB sequence diversity indicated that Alphaproteobacteria related clades SAR116 and SAR11 predominated at most times while Archaea marine group II predominated mostly in winter. Quantitative PCR demonstrated that SAR 11 PRB populations were more abundant during the last months of summer and were positively correlated with pigments (i.e. divinyl chlorophyll a and zeaxanthin), and inversely correlated to nutrient (NO2-/NO3- and PO43-) concentrations. Overall, these findings indicate that further increases in the influence of the EAC could alter the bacterioplankton community structure towards that of typical of open ocean systems.	root:Environmental:Aquatic:Marine
MGYS00000425	Metagenomic Characterisation of Opaque Beer Industry Wastewater, Zvishavane	The availability of clean portable water has been a challenge for many Zimbabwean municipalities over the years. Currently, several towns and cities are facing water quality problems generally caused by pollution due to inadequate maintenance of waste water treatment plants, expensive waste water treatment technologies and poor institutional framework. In this study the waste water treatment efficiencies of 15 opaque beer brewery waste water treatment plants were determining by measuring how each plant altered known physico-chemical indicators of waste water quality. It was assumed that the observed degree of alteration in waste water physico-chemical properties was due a number of factors, with the plant?s microbial diversity and load being a key factor. The thinking behind this assumption is that where you have more microorganisms of many different types, you are likely to find more efficient degradation of wastewater than in the opposite scenario. As a consequence, the study also sought to determine the microbial diversity in the two extremes, i.e. in the plant with the highest and lowest degree of alteration of wastewater physico-chemical parameters.	root:Engineered:Wastewater:Water and sludge
MGYS00000423	Metagenomic Characterisation of Opaque Beer Industry Wastewater, Fairbridge	The availability of clean portable water has been a challenge for many Zimbabwean municipalities over the years. Currently, several towns and cities are facing water quality problems generally caused by pollution due to inadequate maintenance of waste water treatment plants, expensive waste water treatment technologies and poor institutional framework. In this study the waste water treatment efficiencies of 15 opaque beer brewery waste water treatment plants were determining by measuring how each plant altered known physico-chemical indicators of waste water quality. It was assumed that the observed degree of alteration in waste water physico-chemical properties was due a number of factors, with the plant?s microbial diversity and load being a key factor. The thinking behind this assumption is that where you have more microorganisms of many different types, you are likely to find more efficient degradation of wastewater than in the opposite scenario. As a consequence, the study also sought to determine the microbial diversity in the two extremes, i.e. in the plant with the highest and lowest degree of alteration of wastewater physico-chemical parameters.	root:Engineered:Wastewater:Water and sludge
MGYS00000718	Structure and functions of the bacterial root microbiota in wild and domesticated barley and signatures of positive selection in the rhizosphere metagenome	We have profiled the rhizosphere and the root bacterial communities retrieved from soil-grown, wild, landrace and modern accessions of barley using a 16S rRNA gene amplicon pyrosequencing approach. Phylogenetic assignment of the generated sequencing reads revealed that the microbial communities thriving at the barley root-soil interface appears to be gated, as indicated by a narrow phylogenetic composition, largely dominated by members of the families Flavobacteriaceae, Rhizobiaceae and Comamonadaceae Interestingly, constrained ordinations and linear model analysis revealed that host microhabitats (i.e. root and rhizosphere) are the major determinants of the barley microbiota, while the host genotype determines its ribotype profiles to a limited extent, suggesting that the structure of the barley microbiota is a conserved trait in the tested accessions.  To gain insights on the molecular cues underlying microbial recruitment at the root-soil interface, we reconstructed 20Gbp of the barley rhizosphere metagenome. Interestingly, we observed that ~10% of the protein families encoded by the barley microbiome display a ratio between non-synonymous and synonymous substitutions (w) significantly higher than the mean of the sequenced metagenome. Intriguingly, these data might indicate an evolutionary pressure on proteins required for the microbial colonisation of the rhizosphere. Remarkably, proteins previously reported in host-microbe interactions studies (e.g. putative bacterial effectors) showed a w significantly different across genotypes, suggesting that host genetic traits contribute, at least in part, to bacterial functional diversification in the rhizosphere.  Our work provides a foundation for future studies aiming at the characterisation of the genetic bases of plant-microbiota interactions and, in the long term, the introgression of the microbiota metabolic potential into plant breeding	root:Host-associated:Plants:Rhizosphere
MGYS00000489	Gut microbial metabolism shifts towards a more toxic profile with supplementary iron in a kinetic model of the human large intestine	Safety of oral iron administration in African children has been questioned as it is associated with an increased burden of infectious disease. However, it remains unclear to which extent oral iron administration affects the intestinal microbiome. Therefore, we here investigated the impact of multiple iron preparations and doses on the growth and metabolism of a human gut microbiota in a well-controlled in vitro model of the large intestine. Microbiome analysis showed clear iron-induced changes and prominent shifts included a decrease of Bifidobacteriaceae and Lactobacillaceae under iron-rich conditions, paralleled by an increase of  Roseburia and Prevotella. Metagenomic analyses showed a general enrichment of bacterial motility-chemotaxis systems under iron-rich conditions. Metabolome profiling showed that gut microbial activity markedly shifted from a saccharolytic to a proteolytic profile in response to iron. Levels of branched chain fatty acids and ammonia increased significantly, in particular under ferrous sulfate-rich conditions. Importantly, cell viability tests showed increased cytotoxicity of metabolite-containing effluent from iron-rich conditions. We also identified microbial metabolites with siderophoric activity that were specifically produced under low-iron conditions. Our data indicate that in the absence of host influences, iron induces a more hostile intestinal environment characterized by i) reduction of beneficial microbes and increase of certain bacterial species with pathogenic potential, ii) increased levels of bacterial metabolites that can impair the barrier function of the gut wall, and iii) increase of virulence-associated pathways of enteric pathogens. It can be envisaged that these in vitro phenomena also contribute to an increased risk for enteric infections in vivo.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000715	Pilot study of the composition of fecal/gut metagenome of tiger populations in India	Tigers are an endangered species living in shrinking habitat. We aim to understand the impact of proximity to human settlement on gut metagenome of tigers. Here a pilot study has been conducted to designed detailed experiments to trace lineage of pathogens, track microbiome and test the presence of gut parasites.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000714	Wisconsin, Native Prairie soil metagenome reference core Project	none provided	root:Environmental:Terrestrial:Soil
MGYS00000713	Wisconsin, Continuous corn soil metagenome reference core Project	none provided	root:Environmental:Terrestrial:Soil
MGYS00000712	Title : Biological soil crust  microbiota	Desert soil- and rock-surface communities are of crucial importance in the global biogeochemical cycles of carbon and nitrogen. In arid regions, nitrogen inputs depend on biological nitrogen fixation. Biological soil crusts contribute substantially to nitrogen fixation and act as net exporters of ammonium, nitrate and organic nitrogen to the underlying soil layers. Approximately half of the total biological nitrogen fixation on land is attributed to cryptogamic covers. Up to 70% of the fixed nitrogen can be released into the underlying soils and hence is available to other organisms. The N-cycle includes the assimilatory pathways dinitrogen fixation and nitrate assimilation. Some prokaryotes are capable of obtaining metabolic energy from nitrification and denitrification. Here, we studied the nitrogen cycling in biological soil crusts in Southern Spain.	root:Environmental:Terrestrial:Soil:Desert
MGYS00000711	Comparative metagenomics of microbial communities in gorgonian corals, marine sediments and seawater	The sustainability of coral reefs bears fundamental implications to the functioning of coastal ecosystems and the biogeochemistry of our planet. The coral-associated microbiota plays a pivotal role as a fitness-enhancing factor in the survivability and persistence of the coral holobiont in marine biomes. Nevertheless, we currently lack knowledge of the taxonomy and functional traits of the highly complex microbiome that populates most coral species. Conspicuously, symbionts inhabiting soft corals which usually thrive and dominate in temperate waters have been scarcely examined.  In this study, we employ a comparative metagenomics approach to uncover the distinct phylogenetic and functional features of the microbiome of soft corals. To this end, high-throughput, Illumina metagenome sequencing of seawater, sediments and of the symbiotic consortium from the gorgonian corals Eunicella verrucosa, Eunicella gazella and Leptogorgia sarmentosa was performed.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00000704	Soil Targeted Locus (Loci)	Studying the effect of the erosion of microbial genetic diversity on nitrogen-cycling in soil.	root:Environmental:Terrestrial:Soil
MGYS00000702	Methanogen diversity in indigenous and introduced ruminant species on the Tibetan plateau	Host factors are regarded as important in shaping the archaeal community in the rumen but few controlled studies have been performed to demonstrate this across host species under the same environmental conditions. A study was designed to investigate the structure of the methanogen community in the rumen of two indigenous (Yak and Tibetan sheep) and two introduced domestic ruminant (cattle and crossbred sheep) species raised and fed under similar conditions on the high altitude Tibetan plateau. The methylotrophic Methanomassiliicoccaceae was the predominant archaeal group in all animals even though Methanobrevibacter are usually present in greater abundance in ruminants globally. Furthermore, within the Methanomassiliicoccaceae family members from Mmc. Group 10 and Mmc. Group 4 were dominant in Tibetan plateau ruminants compared to Mmc. Group 12 found to be highest in other ruminants studied. Small ruminants presented the highest number of sequences that belonged to Methanomassiliicoccaceae compared to the larger ruminants. Although the methanogen community structure was different among the ruminant species, there were striking similarities between the animals in this environment. This indicates that factors such as the extreme environmental conditions and diet on the Tibetan plateau might have a greater impact on rumen methanogen community than host differences.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000700	Gut metagenomes from culturomics	The study of the human gut microbiota was relaunched by metagenomic studies.	root:Host-associated:Human:Digestive system:Hindgut:Rectum
MGYS00000691	Temperate rainforest nematodes Metagenome	A survey of nematode diversity in a temperate rainforest from soil, litter and canopy habitats - a pooled sampled of 12 MID-tagged temperate forest samples from soil (4), litter (4), and canopy (4) .	root:Environmental:Terrestrial:Soil
MGYS00000689	Mechanistic insights beyond metabolic consequences link into microbial reprogramming to poly-aromatic hydrocarbons	PAH-contaminated soil from Lugones, Asturias, Spain.	root:Environmental:Terrestrial:Soil
MGYS00000687	Soil Metagenome	A study on metagenomic soil was conducted under the long-term managements till and conventional tillage in crop rotation and succession in an experimental area of Embrapa Soja. The objective was to identify the genetic diversity and biotechnological potential of microorganisms and to compare the microbial communities of soils which may thus infer about the sustainability of different management systems.	root:Environmental:Terrestrial:Soil
MGYS00000686	Michigan switchgrass bulk soil replicate #2 soil metagenome	DNA was extracted from agricultural bulk soil for metagenomic comparison.  The goal of this project is to compare bulk and rhizosphere bacterial communities in switchgrass and Miscanthus plant treatments.  This is an ongoing study.	root:Host-associated:Plants:Rhizosphere
MGYS00000684	Rhizotron Metagenome Targeted Locus	Biodiversity Manipulation in Rhizosphere and Soil.  The purpose of this project is to analyze the influence of beech  and ash saplings on litter cycling and soil microbial communities using  rhizotrons planted with beech and ash saplings, as well as control  rhizotrons without any tree plant.	root:Environmental:Terrestrial:Soil
MGYS00000683	Geothermal soil crust Targeted Locus (Loci)	Diatomaceous samples from a geothermal biological soil crust.  Alkaline siliceous geothermal biological soil crust samples from across 1ha and subdivided by photic/depth.   <p> Soil cores were collected across a 1ha geothermal biological crusted        soil system with the goals of describing a novel microbial        environment, and investigating spatial heterogeneity in soil microbial        systems.  Soil cores were further separated into photic/depth levels,        and replicated.  18S universal primers were used for amplifications,        and individual samples were pyrosequenced (454-Ti).  	root:Environmental:Terrestrial:Soil
MGYS00000682	Antarctic Soil Microbiome Targeted Locus	High-throughput pyrosequencing analysis of amplified 16S rRNA genes from soil samples from the most prominent plant communities and soil types collected in ice-free areas of Keller Peninsula, King George Island, Antarctica.   The Antarctic soil metagenome is part of a larger project from the National     Institutes of Science and Technology - Antarctic Environmental Research     (abbreviated as INCT-APA in Brazilian Portuguese). The Institute was     created by the Brazilian Ministry of Science and Technology (Minist rio de     Ci ncia e Tecnologia (MCT) in search of excellence in scientific activities     at an international level in strategic areas defined by the Action Plan     2007-2010 of the Science Programme, Technology and Innovation for     Antarctica, by means of programmes and instruments made operational by CNPq     and by FAPERJ (Research support Foundations at different levels). The     referred initiative has the view to implement a network of atmospheric,     oceanic and cryospheric monitoring, in the Antarctic region. More details     about the Institute and its objectives can be found at     http://www.biologia.ufrj.br/inct-antartico/wp-content/uploads/2011/11/APA.pdf          Specifically, the Antarctic metagenome project aims to obtain a detailed     baseline description of the soil bacterial communities found in the     Antarctic soils against which to compare changes in the Antarctic     microbiome caused by climate changes or human activities. In addition, using     Antarctica as a simple ecosystem model with low or no human influence, to     determine the major factors responsible for the overall patterns of soil     microbial diversity in Antarctica.	root:Environmental:Terrestrial:Soil
MGYS00000681	Core Sample from Deep Subsurface Metagenome	An innovative technology to manage municipal biosolids and recycle this waste into clean energy is proposed and tested by City of Los Angeles. With appropriate geological formation selection, proper design, and monitoring, biosolids slurry can be injected into soft, porous, sand formations below the earth surface at 5000ft or more. The high temperature salinity condition in the subsurface will kill pathogens in the biosolids, and stimulate the growth of methanogens to generate methane. This research will take a metagenomic approach to understand the bacteria community structure and diversity changes following the deep-well inject of biosolids.	root:Environmental:Terrestrial:Soil:Sand
MGYS00000679	Harvard Forest soil microbial gene expression	This project sequenced the metagenome and metatranscriptome of a temperate forest soil microbial community.  Soil was collected from within a transition hardwood-white pine/hemlock forest in the Prospect Hill Tract of Harvard Forest (Massachusetts, USA; 42.54 N 72.18W; elevation: 385 m) on 27 September, 2010.  Two cores were taken from 1-10 cm below the leaf horizon using a 10 mm diameter soil corer.  These cores were homogenized, placed into 50 ml Falcon tubes, flash frozen in liquid nitrogen, and transported to the lab on dry ice.  Visible pieces of plant material were removed from soil subsamples with sterile forceps.  During plant removal, the subsamples were placed on a sterile surface, laid within a bed of dry ice.  Total microbial DNA and RNA was then extracted from these subsamples using PowerSoil Total RNA and DNA isolation kits (MoBio), according to the manufacturer's protocol.  Total DNA was quantified and used directly for pyrosequencing.  Total RNA was further processed to reduce the proportion of ribosomal RNA transcripts via a custom subtractive hybridization procedure.  Remaining total RNA was then linearly amplified, converted to cDNA, and used for pyrosequencing.  Soil DNA and cDNA were sequenced with full plate runs on a Roche Genome Sequencer FLX instrument using Titanium chemistry.	root:Host-associated:Protozoa
MGYS00000680	Vernal Pool Microcosm Soil Samples	These metagenomes were constructed to investigate taxonomic and functional diversity of the microbial community in artificial vernal pools with and without nitrate addition.  The first received nitrate addition and had a high denitrification rate, while the second was a control that received no nitrate addition and had no detectable denitrification.  	root:Environmental:Aquatic:Freshwater
MGYS00000678	Metagenomes isolated from NE Brazil	Mangroves are important and productive ecosystems found in tropical and subtropical environments, providing habitats for a variety of species. These ecosystems have been suffering from impacts through the years and consequently the activity of soil microorganisms, which are directly related to valuable processes in these environments, is affected. Understanding the diversity and function of microbial communities and their response to environmental changes is essential for the maintenance of significant functions in these ecosystems. Currently few studies in Brazil are devoted to the understanding of microbial diversity in mangrove soils. Thus it becomes essential to study the microbial diversity in these environments and to search for genes encoding for enzymes of biotechnological interest. For this reason, the aim of this study was to assess the soil microbial diversity from four mangroves in Ceara state, northeast Brazil, and its response to possible impacts, and search genes of biotechnological interest using metagenomics strategies.  The four studied mangroves are located in the state of Ceara, northeastern Brazil. Two of them are located in the extreme east (Jaguaribe Mangrove) and west (the Mangrove Timonha) coast of the state separated by 530 km and the other two are located in a central region, near the city of Fortaleza, state capital (Coco and Pacoti mangroves). Jaguaribe (JAG) mangrove is located at the largest river of the state, in a sub-urbanized region, and impacted by agriculture run-off and extensive shrimp farming. In contrast, Timonha (TIM) is an undisturbed mangrove, located in an island inside the estuary, with limited access to humans. The Coc? (COC) and Pacoti (PAC) mangroves, located in the metropolitan region of Fortaleza, suffer impacts due to water pollution, deforestation of native vegetation, especially vegetation of dunes and mangroves, extraction of sand, clay, stone and release of industrial effluents. The sampling locations TIM - S 02?56.587? W 041?19.064?; JAG - S 04?26.749? W 37?46.989?; PAC - S 03?49.226? W 038?24.286?; COC - S 03?46.482? W 38?26.552?. Sediment samples were collected in three sites inside the mangroves aiming to cover typical habitats in this ecosystems: near the river, Rhizophora mangle forest and the last one in an area covered by Avicennia schaueriana. In each habitat five sediment cores from 0-10 cm layer in an area of 10 m2, in the low tide of 0.0, were collected. The fifteen samples from each mangrove were pooled to form a single composite sample and DNA metagenomic extraction was carried out using the PowerMaxSoil DNA Extraction kit (MoBio Laboratories, Carlsbad, CA, USA) following the manufacturer's protocol. The extracted DNA was then subjected to 454 pyrosequencing.	root:Environmental:Terrestrial:Soil
MGYS00000677	Alert biopiles	Goal of this project was to identify the microorganisms and functional genes that are associated with a very efficient bioremediation experiment in the Canadian high Arctic. <p>   DNA can be obtained from Etienne Yergeau/Charles Greer at the National Research Council of Canada, Biotechnology Research Institute. 	root:Engineered:Bioremediation
MGYS00000676	WGA	Although high throughput sequencing is a powerful tool to access the composition of different microbial communities, low biomass environments often possess insufficient amounts of DNA for such analyses.  An example of such an environment is airborne dust that is limited in biomass as well as in the quantity of sample available for analysis. The interest in studying microbial population diversity in intercontinental dust from the Chad Republic, Africa, using culture-independent methods led to a search for protocols that enhance the amount of DNA without compromising the robustness of the analysis.  Whole genome amplification (WGA) is a method that has been used to amplify small amounts of DNA from a variety of samples. Little is known about the bias generated by WGA and the implication of bias in the pyrosequencing results.  To answer this question, DNA was extracted from a sandy soil and used as a model to optimize the protocol for DNA extraction and WGA analyses of the microbial communities that might be found in Chad sand samples. Ribosomal intergenic space analysis and 454 pyrosequencing of amplified 16S rRNA fragments showed that DNA submitted to whole genome amplification differed significantly after whole genome amplification. The 16S rRNA microbial community obtained from WGA had a higher Shannon diversity index and higher rarefaction curves compared with the microbial community obtained without amplification of the template DNA.  Changes observed with WGA were both qualitative and quantitative.	root:Environmental:Terrestrial:Soil:Sand
MGYS00000675	Permafrost metagenome	The fate of the carbon stocked in permafrost soils following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but their composition and functional potential in permafrost soils are largely unknown.   <p> A 2m deep permafrost and its overlying active layer soil were subjected to metagenome sequencing, quantitative PCR, and microarray analyses. The active layer soil and 2m permafrost soil microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two soils also possessed a highly similar spectrum of functional genes, especially when compared to other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both soils in the metagenomic libraries and some (e.g. pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2m permafrost soil showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated and showed that the whole community genome amplification technique used caused large representational biases in the metagenomic libraries.   <p> This study described for the first time the detailed functional potential of permafrost-affected soils and detected several genes and microorganisms that could have crucial importance following permafrost thaw. <p> Sequences deposited into the Sequence Read Archive can be found using the Project data link.	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00000674	Microbial Saltern Metagenome HighSalternSDbayMicD0704	Microbial community collected July 1, 2004, from a 'high' salinity saltern (32.599040, -117.107356).  A water sample from the solar saltern of South Bay Salt Works (Chula Vista, CA) was collected in July 2004 from a ponds with high salinity (28-30%), as measured using a hand refractometer. The microbial fraction was isolated from the water sample by passage through a 0.2 mkm tangential flow filter (TFF, Millipore). The retentate was kept and the microbial fraction was collected from the 0.2 mkm TFF retentate by centrifugation at ~ 2000 xg for 10 min. Microbial DNA was extracted using the Ultra Clean Soil DNA Kit (Mo Bio Laboratories, CA). The microbial DNA samples was amplified using the strand-displacement 29 DNA polymerase (GenomiPhi Amersham Biosciences, NJ). The resulting metagenomic DNA was pyrosequenced on the GS20 sequencer (454 Life Sciences, CT). The raw metagenomic sequences were screened to remove duplicate sequences. The metagenome was named HighSalternSDbayMicD200407 and submitted to NCBI.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
MGYS00000672	Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome	RNA-centered meta-transcriptomic approach to simultaneously obtain information on both structure and function of a soil community.	root:Environmental:Terrestrial:Soil
MGYS00000671	Metagenomic analysis of Pinus pinaster's forest soil in southern Spain	This study mainly consist in the analysis of the Pinus pinaster's soil metagenome. Two different soil samples were obtained corresponding totimes with different gene expression patterns in P. pinaster. The first sample was taken in March and the second one in July. The sampling was made in Los Reales de Sierra Bermeja (Estepona, Spain) with the present UTM coordinates North 30S 303095 4034618 and 1245m of altitude.Sierra Bermeja is a mountain range in the southern Spain near the coast and it is the biggest massif of peridotite all over the world. The peridotiteis a dense, coarse-grained igneous rock, consisting mostly of the minerals olivine and pyroxene. The samples were from the soil around three trees (70 cm approx. from the tree stem) and three different samples were taken from each tree(3 trees x 3 samples = 9 samples per each time). Total DNA from the soil samples were extracted by triplicate (9 x 3 = 27 DNA samples per each time) and the resulting DNA was pooled with equivalent amounts from each DNA samples. Each soil DNA pool was processed and sequenced in a Roche 454 Titanium FLX+ sequencer. Half PicoTiterPlete was used for each sample.	root:Environmental:Terrestrial:Soil
MGYS00000664	Mudflat sediments Targeted Locus (Loci)	mcrA genes recovred from a mudflat of the Yangtze estuary.	root:Environmental:Terrestrial:Soil
MGYS00000663	The fecal microbiota of free-ranging brown bears was collected during their active phase (summer) and hibernation (winter). Germfree mice were colonized with the seasonal bear microbiota.	Hibernation is an adaptation that helps many animals to conserve energy during food shortage in winter. Brown bears double their fat depots during summer and use these stored lipids during hibernation. Although bears seasonally become obese, they remain metabolically healthy. We analyzed the microbiota of free-ranging brown bears during their active phase and hibernation. Compared with the active phase, the hibernation microbiota had reduced diversity, reduced levels of Firmicutes and Actinobacteria, and increased levels of Bacteroidetes. Several metabolites involved in lipid metabolism including triglycerides, cholesterol and bile acids were also affected by hibernation. Transplantation of the bear microbiota from summer and winter to germ-free mice transferred some of the seasonal metabolic features and demonstrated that the summer microbiota promoted adiposity without impairing glucose tolerance, suggesting that seasonal variation in the microbiota may contribute to host energy metabolism in the hibernating brown bear.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00000660	Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria	The verrucomicrobial subdivision 2, class Spartobacteria, is one of the most abundant bacterial lineages in soil and has recently also been found ubiquitous in aquatic environments. A 16S rRNA gene study from samples spanning the entire salinity range of the Baltic Sea indicated that, in the pelagic brackish water, a phylotype of the Spartobacteria is one of the dominating bacteria during summer. Phylogenetic analyses of related 16S rRNA genes indicate that a purely aquatic lineage within the Spartobacteria exists. Since no aquatic representative from the Spartobacteria has been cultured or sequenced, the metabolic capacity and ecological role of this lineage are yet unknown. In this study, we reconstructed the genome and metabolic potential of the abundant Baltic Sea Spartobacteria phylotype by metagenomics. Binning of genome fragments by nucleotide composition and a self-organizing map recovered the near complete genome of the organism, the gene content of which suggests an aerobic heterotrophic metabolism. Notably, we found 23 glycoside hydrolases that likely allow the use of a variety of carbohydrates like cellulose, mannan, xylan, chitin, and starch as carbon sources. In addition, a complete pathway for sulfate utilization was found, indicating catabolic processing of sulfated polysaccharides, commonly found in aquatic phytoplankton. The high frequency of glycoside hydrolase genes implies an important role of this organism in the aquatic carbon cycle. Spatiotemporal data of the phylotype???s distribution within the Baltic Sea indicate a connection to Cyanobacteria that may hence be the main source of the polysaccharide substrates.	root:Environmental:Aquatic:Marine
MGYS00000404	Cow dung metagenomics	MiSeq reads from microbial community of cow dung after different treatments.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000659	Rhizosphere-specific bacterial community structure and activity in long-term contaminated soil	In this study, soil contaminated with PCBs was vegetated by different plant species, horseradish (Armoracia rusticana), black nightshade (Solanum nigrum), and tobacco (Nicotiana tabacum). The aim was to investigate the influence of these plants on both phylogenetic and metabolic diversity of rhizosphere populations and associated decrease of PCBs in the rhizospheres. In addition to plants themselves, the influence of fertilizing on the viability of plants, richness of rhizosphere microorganisms, and decrease of PCB content in soil was determined.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000658	Plant secondary metabolites-induced changes in bacterial diversity and activity in contaminated soil	The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and metabolic activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with chlorobiphenyl-degradation effectivity. We have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons amplified from total community metagenome and DNA-stable isotope probing (SIP) as a direct method which links the metabolic process with its microbial originators.	root:Environmental:Terrestrial:Soil
MGYS00000656	Metagenome from Pru Toh Daeng Peat Swamp	"Metagenome samples were collected from the Pru Toh Daeng peat swamp forest in Narathiwat province, Southern Thailand, in 2007.
 <p>
 Community genomic DNA was extracted from the surface peat soil. Sequencing was carried out by 454 Life Sciences on the Genome Sequencer (GS) FLX System.  The aim of this study is to get a snapshot of the microbial community and obtain sequences encoding an interesting enzyme.
 
 <p>
 Data submitted to the Short Read Archive (SRA) is available from the Project Data button.
 
 
 "	root:Environmental:Terrestrial:Soil
MGYS00000655	Microbial genome analysis of tsunami-affected soil	The 2011 Great East Japan Earthquake Tsunami changed terrestrial environment. We perform metagenome analysis of tsunami-affected soil and genome sequencing of four strains of Arthrobacter sp. living in the affected soil.	root:Environmental:Terrestrial:Soil
MGYS00000653	Metatranscriptomic Analysis for Eukaryotic Functional Genes in Forest Soil	For the extraction of environmental RNA after enrichment with wheat bran and avicel, the sample was collected from the forest humic soil in the site of AIST. A forest soil in the site of AIST Tsukuba, Japan (36.06N 140.17E). The extraction of total RNA and the purification of polyadenylated eukaryotic mRNA from the enriched soil sample were used to commercially available kit, respectively.  The synthesized cDNA sample from the purified mRNA was outsourced to Dragon Genomics Center for 454 GS FLX sequencing. The aim of this study is the exploration of the novel eukaryotic functional genes from an environmental sample using metatranscriptomic approach.  This method is widely applicable to the provision of novel eukaryotic enzymes and proteins of potential industrial or medical use.	root:Environmental:Terrestrial:Soil
MGYS00000651	Analysis of Early Microbial Communities on Recent Volcanic Deposits of Mt. Merapi, Indonesia	Due to the 2010 Mt. Merapi eruption, the land around the mountain was covered by pyroclastic materials. For the environmental rehabilitation of the volcanic eruption-affected area, it is important to know the pioneer soil microbial communities. The aim of this study was to characterize the early microbial communities in the Mt. Merapi unvegetated volcanic deposits. This investigation was designed to compare the microbial communities of the volcanic deposits with those of forest soil near the mountain by using molecular genetic approaches targeting bacterial 16S rRNA genes. Two unvegetated sites (BR and BRU) were established together with a forest site (FR) as a reference. The diversity index were 3.11, 2.25, and 2.91 on sites BR, BRU, and FR, respectively, which indicated that the bacterial diversity was relatively higher in site BR than in the other sites. Results of the PCoA analysis showed that all bacterial communities of the volcanic deposit samples clustered away from those of forest soil samples. Microbial communities in recent volcanic deposits of Mt. Merapi were phylogenetically diverse inspite of very low-carbon conditions. Proteobacteria was the most abundant phylum in the bacterial community of volcanic deposits. Inspection underlying families revealed the predominance of the family Caulobacteraceae in Alphaproteobacteria, Oxalobacteraceae in Betaproteobacteria, and Xanthomonadaceae in Gammaproteobacteria in the volcanic deposit communities.	root:Environmental:Terrestrial:Soil
MGYS00000650	Effects of NaCl concentrations on anode microbes in microbial fuel cells	The study investigated that single-chamber microbial fuel cells were inoculated with paddy-field soil and continuously supplied with acetate media containing different concentrations of NaCl (0 M, 0.05 M, 0.1 M, 0.3 M, 0.6 M and 1.8 M).	root:Environmental:Terrestrial:Soil
MGYS00000648	sewage sludge soil samples were subjected to chitosan treatment, the microbiodiversity and gene diversity were unknown.	sewage sludge soil samples were subjected to chitosan treatment, the microbiodiversity and gene diversity were unknown.	root:Engineered:Wastewater:Water and sludge
MGYS00000597	High throughput analysis of class 1 integron gene casettes in wastewater environments	We applied a novel sequencing pipeline that enable characterization of hundreds of thousands integron-associated gene in the WWTP environment	root:Engineered:Wastewater:Water and sludge
MGYS00000610	Ammonia oxidising Bacteria	Study of ammonia oxidising Bacteria in a Sequencing Batch Reactor over time	root:Engineered:Bioreactor
MGYS00000368	metagenomic study targeting N cycling processes	Sugarcane is a crop for bioenergy in Brazil and one of the main concerns in the production of this crop is the impact on the environment, in particular in greenhouse gases (GHG) emissions. Recent studies have shown that the N2O emissions related to sugarcane production are dependent on soil management practices (Carmo et al. 2013). The way to mitigate N2O emissions would be to understanding the conditions and the processes involved in the N2O production and consumption. However, no studies have linked the emissions of GHGs with soil-borne microbial communities, which are the main players in nutrient cycling.	root:Environmental:Terrestrial:Soil
MGYS00000611	WORKSHOP METAGENOMIC RUMEN STUDY	STUDY OF RUMEN MICROBIOME DIVERSITY COMPOSITION	root:Host-associated:Mammals:Digestive system:Foregut:Rumen
MGYS00000563	Microbial metagenome sequencing from marine sponges (Spongia sp.), seawater and sediments	Marine sponges host abundant and diverse associated bacteria, some of which known to produce biologically active natural products. Although much research effort has been applied to cultivate sponge-associated microorganisms, we still lack the ability to capture the full phylogenetic breadth of this symbiotic consortium in the laboratory. This study uses a cultivation-independent, shotgun metagenomics approach to unveil the taxonomic and functional features of the model sponge host Spongia sp. and its environmental surroundings (seawater and sediments). Samples were taken off the coast of Algarve, South Portugal (North-east Atlantic), and subjected to Illumina sequencing after microbial metagenomic DNA extraction. Taxonomic and functional profiles were assessed using MG-RAST with the Genbank and COG databases, respectively. Most abundant phyla in the sponge microbiome were Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Cyanobacteria, Planctomycetes and Acidobacteria, in this order, altogether comprising 84.35% of all the classifiable sequence reads. In contrast, the dominant phyla in seawater were Bacteroidetes and Proteobacteria (89.3% of all classifiable reads), whereas sediments were dominated by Proteobacteria, Bacteroidetes, Planctomycetes, Actinobacteria and Firmicutes (85%). We found significantly higher frequencies of transcription and translation termination factors in sediments and seawater, respectively, than in marine sponge microbial metagenomes. Moreover, higher abundances of motility and chemotaxis gene reads were found in the former microhabitats in comparison with the marine sponge microbiome, where a conspicuously higher frequency of Clustered Regularly Interspaced Palindromic Repeats (CRISPRs), accompanied by much lower viral abundance, was otherwise observed. These results suggest a highly distinct microbiome inhabiting Spongia sp., both in terms of taxonomy and function, characterized by the prevalence of k-strategy prokaryotes which collectively possess a sophisticated, early-branched viral defence system.	root:Mixed
MGYS00000474	Comparison between raw seawater and two-week enrichment with methanesulfonate	Coastal surface seawater from the North Atlantic ocean was filtered and its metagenome was sequenced by Illumina HiSeq 2500. In parallel, half of the sample was filtered and enriched with the addition of methanesulfonate as sole added source of carbon and energy during 16 days following which its metagenome was sequenced by the same method.	root:Environmental:Aquatic:Marine:Coastal
MGYS00000645	Human Microbiome Project (HMP) 16S rRNA Gene Diversity, the diversity of 16S ribosomal RNA genes in the human microbiome: 454 Protocol Validation - Mock	This HMP Centers' Evaluation of the standard 454 SOP represents the pyrosequencing of 16S rRNA genes amplified from HMP even Mock community distributed to each of the four HMP sequencing centers. The goal of the pilot was to test the provisional 454 sequencing protocol (v4.2) and to evaluate accuracy. This protocol does use barcodes, targets two 16S windows (V1-V3 and V3-V5), and sequences in the reverse direction. (Previously referred to as Centers' Evaluation of 454 SOP (CEFoS) Mock Pilot)	root:Engineered:Modeled:Simulated communities (sequence read mixture)
MGYS00000644	Desert varnish metagenome	Our study provides an insight into the microbial community structure associated with desert varnish, a coating found on exposed rock surfaces in arid environments. We characterize samples from the Mojave Desert, California, USA using whole-genome shotgut sequencing with a special focus on manganese-oxidizing species.	root:Environmental:Terrestrial:Soil:Desert
MGYS00000643	The POU/Oct transcription factor Pdm1/nub is necessary for a beneficial gut microbiota and normal lifespan of Drosophila	Maintenance of a stable gut microbial community relies on a delicate balance between immune defense and immune tolerance. We have used Drosophila to study how the microbial gut flora is affected by changes in host genetic factors and immunity. Flies with a constitutively active gut immune system, due to a mutation in the POU transcriptional regulator Pdm1/nubbin (nub) gene, had higher loads of bacteria and a more diverse taxonomic composition than controls. In addition, the microbial composition shifted considerably during the short life-span of the nub1 mutants. This shift was characterized by a loss of relatively few operational taxonomic units (OTUs) and a remarkable increase in a large number of Acetobacter spp. and Leuconostoc spp. Treating nub1 mutant flies with antibiotics prolonged their life-time survival with more than 100%. Immune gene expression was persistently high also in the presence of antibiotics, indicating that the early death was not a direct consequence of an over-active immune defense but rather an indirect consequence of the microbial load and composition. Thus, changes in host genotype and inability to regulate normal growth and composition of the gut microbiota, leads to a shift in the microbial community, dysbiosis and early death.	root:Host-associated:Arthropoda:Digestive system:Gut
MGYS00000641	"Beyster Family Fund and Life Technologies Foundation-funded Global
Ocean Sampling Expedition, 2009-2011"	"Microbial communities in a range of aquatic environments
provide key ecological services while also potentially harboring dangerous
pathogens.  During 2009-2011, microbial communities from aquatic
communities in close contact with humans were collected and characterized
using shotgun metagenomic sequencing.  Sampled environments include
coastal sites in the Pacific and Atlantic Ocean, extensive surveys of the
Mediterranean and Baltic Seas, along with the Black Sea, Lake Constance,
Lake Banyoles, Lake Ciso, and Lake Redon."	root:Environmental:Aquatic:Marine
MGYS00000640	Gut barrier impairment by high-fat diet in mice depends on housing conditions.	SCOPE: Diet-induced obesity (DIO) is proposed to cause impairments in intestinal barrier integrity, but contradictory results have been published and it appears that the outcomes depend on other environmental factors. We therefore assessed whether the hygienic status of animal facilities alters the gut barrier in DIO mice.  METHODS AND RESULTS: Male C57BL/6N mice were housed in a conventional (CV) or a specific pathogen-free (SPF) animal facility and were fed identical diets represented by a high-fat (60kJ% fat) or control diet (11kJ% fat) for 12 weeks. Intestinal barrier function in small and large intestine was evaluated in Ussing chambers by electrical resistance and permeability measurements. Jejunal (p<0.01) and proximal colonic (p<0.05) barrier function was altered in CV DIO mice, but not in SPF DIO mice. Moreover, only CV DIO mice were characterized by metabolic endotoxemia and low-grade inflammation. High-throughput 16S rRNA gene sequencing revealed significant differences in fecal bacterial diversity and composition between the two animal facilities, but only in mice fed the HFD. Moreover, cecal DCA concentrations correlated positively with two yet uncultivated Clostridiales species.  CONCLUSIONS: We demonstrated that housing conditions and associated changes in gut bacterial colonization are pivotal for maintenance of gut barrier integrity in DIO mice.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000602	Rice-straw enriched mixed microbial composting community de novo metatranscriptome	A rice straw enriched mixed microbial composting community was used to inoculate rice straw as sole carbon source under laboratory conditions.  A de novo metatranscriptome was assayed after 1 week of growth and used in transcriptome informed metaproteomics	root:Engineered:Solid waste:Composting
MGYS00000631	Shotgun metagenomics of moose rumen	"The moose (Alces alces) manages to utilize energy from fiber-rich lignocellulose material through enzymes produced by the microbes in its rumen. Some of these specialized enzymes may outperform cellulases and hemicellulases that are used in bio-refinery processes today. Shotgun metagenomics offers a method to study microbial communities in detail and to capture the gene sequences coding for enzymes that can be produced in the laboratory. We applied the technique on rumen material from moose. Through a binning approach, a large number of metagenome-assembled genomes (MAGs) from single species and strains were isolated and characterized based on taxonomy and carbohydrate active enzyme (CAZY) profile. Most of the 99 MAGs were classified to the bacterial phyla Bacteriodetes and Firmicutes, which is in agreement with previous studies of rumen from moose and other herbivores. Phylogenomic analysis of MAGs revealed novel clades within Bacteriodetes with no related previously characterized genome. In addition, new genomes that were closely related to the recently described Melainabacteria, newly proposed candidate divisions SR1 and TM7 and previously uncharacterized Alphaproteobacteria were also retrieved. Putative cellulolytic  functions were observed in several clades of Bacteroidetes and for MAGs of genus Ruminococcus, Fibrobacteres, and Treponema. Cellulosome components were present in MAGs of Ruminococcus but also in certain clades of Bacteroidetes. Cellulosomes are generally described in the Firmicutes family Clostridiales. Multiple putative cellulases were identified within species from several phyla. At a general level, the most frequently occurring polysaccharide-degrading enzymes targeted hemicellulose, starch and pectin. This study describes the first shotgun-metagenomic characterization of moose rumen and the high number of reconstructed genomes provides a valuable link between phylogeny and cellulolytic role.
"	root:Host-associated:Mammals:Digestive system:Foregut:Rumen
MGYS00000630	Dilution methods to manipulate microbial biodiversity	Dilution methods to manipulate microbial biodiversitydilution	root:Engineered:Lab enrichment
MGYS00000369	Microbial Community of Mobilong Acid Sulfate Soil depth profile using Metagenomics	The latter part of the Australian Millenium drought in 2007-2009 caused the acidification of acid sulfate soils in wetland and former floodplain soils, which pose threats to terrestrial and coastal ecosystems even after the recovery of surface flows and ground water levels. Drying and subsequent oxidation of ASS materials caused soil pH to drop to less than 4 (forming sulfuric materials) in some areas, triggering environmental problems such as land degradation, loss of native plants and animals, and release of heavy metals and metalloids into ground water, rivers and wetlands. To understand this microbially-mediated oxidation process, microbial communities were studied within an acidified acid sulfate soil profile, to identify key microorganisms involved in soil acidification. Six soil layers were sampled from a soil profile according to soil morphology at the most acidic locationin the field. Total DNA from soil samples was extracted using MO-BIO PowerMax? Soil DNA Isolation Kit and sequenced by Illumina Miseq (250PE) by The Ramaciotti Centre, NSW, Australia, prepared with a Nextera DNA Sample Preparation Kit. There were five steps of non-specific amplification involved in Nextera-Miseq sequencing for obtaining enough DNA for sequencing.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000628	Metagenome sequencing of DNA-SIP heavy fractions	Soil from the former coking plant in Neuves-Maisons (France) was amended with 13C-phenanthrene, in two conditions, namely bare soil or planted with ryegrass. After ten days, DNA was extracted from soil and separated on cesium chloride gradient. Fractions containing 13C-labeled DNA were sequenced using PE250 MiSeq technology.	root:Environmental:Terrestrial:Soil:Mine
MGYS00000624	Metagenomic analysis of soil microorganisms	Metagenomic analysis of soil microorganisms	root:Environmental:Terrestrial:Soil
MGYS00000599	Light-dependent microbial metabolisms drive carbon fluxes on glacier surfaces	Biological processes on glacier surfaces affect glacier reflectance, influence surface energy budget and glacier response to climate warming, and determine glacier carbon exchange with the atmosphere. Currently, carbon balance of supraglacial environment is assessed as the balance between the activity of oxygenic phototrophs and the respiration rate of heterotrophic organisms. Here we present a metagenomic analysis of tiny wind-blown supraglacial sediment (cryoconite) from Baltoro (Pakistani Karakoram) and Forni (Italian Alps) glaciers providing evidence for the occurrence in these environments of different and previously neglected metabolic pathways. Indeed, we observed high abundance of heterotrophic anoxygenic phototrophs, suggesting that light might directly supplement the energy demand of some bacterial strains allowing them to use as carbon source organic molecules which otherwise would be respired. Furthermore, data suggest that CO2 could be produced also by microbiologically mediated oxidation of CO, which is produced in snow by photodegradation of organic matter.	root:Environmental:Aquatic:Freshwater:Ice:Glacier
MGYS00000619	Mining for novel cellulase genes from different ecosystem metagenomes	The uncultivated microbes are a good resource for identifying potential novel cellulase genes, which are important industrial enzymes.	root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline:Sediment
MGYS00000408	Lake depth metagenomes comparison	We have sampled two depths from lake Redon (2m  (sample 21) and 60m (sample 60) during late september 2013. We plan to study community function and structure in both depths and compare the putative differences we find, regarding lake stratification.	root:Environmental:Aquatic:Freshwater:Lentic
MGYS00000612	Sequences produced using indexed (tagged, barcoded) primers in single and double PCR.	Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversity at all levels, from genetic variation and expression to ecological community assemblage. However, the number of reads produced per sequencing run far exceeds the number required per sample for many applications, compelling researchers to sequence multiple samples per run in order to maximize efficiency. For studies that include a PCR step, this can be accomplished using primers that include an index sequence allowing sample origin to be determined after sequencing. The use of indexed primers assumes they behave no differently than standard primers; however, we found that indexed primers cause substantial template sequence-specific bias, resulting in radically different profiles of the same environmental sample. Likely the outcome of differential amplification efficiency due to primer-template mismatch, two indexed primer sets spuriously change the inferred sequence abundance from the same DNA extraction by up to 77.1\%. We demonstrate that a double PCR approach alleviates these effects in applications where indexed primers are necessary.	root:Environmental:Aquatic:Marine:Intertidal zone
MGYS00000438	Horse Faecal Metagenome-Healthy	In arid parts of Rajasthan, the microbial diversity of the horse faecal metagenome is assessed.	root:Host-associated
MGYS00000440	Mule Faecal Metagenome-Healthy	In arid parts of Rajasthan, the microbial diversity of the mule faecal metagenome was assessed.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000443	Horse Faecal Metagenome-Clinical disorders	Assessing the microbial diversity in GI disorders of horse in the faecal samples	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000444	Donkey Faecal Metagenome	In the arid parts of Rajasthan, the microbial diversity of donkey faecal metagenome is assessed	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000446	Dromedary Faecal Metagenome-GI disorder	In arid parts of Rajasthan, camel is an important source of livelihood for the rural farmers. the present study aimed to study the microbial diversity of faeces in various GI disorders.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000451	Dromedary Faecal Metagenomes-Healthy	In the arid parts of Rajasthan, camel forms an important livestock reared by rural farmers and contributing to the agricultural economy.  Assessing the faecal microbial diversity in various management practices and various districts of Rajasthan was done.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000478	Dromedary C1 Fluid Analysis-Feed Formulations	Microbial diversity of C1 compartmemnt fluid on different feed formulations	root:Host-associated
MGYS00000522	Metagenomes of intestinal samples were obtained from wild type mice to determine the functional and taxonomic coverage by available cultivable bacteria isolated from mouse.	The important role of mice as a model in research of microbe host interactions increased the need for determining the limits of such experiments due to host specificity and adaptation of several microbes. We collected a broad collection of bacteria isolated from mice covering the whole taxonomic range of common gut bacteria. Based on the functional coverage by this collection of several metagenomic samples obtained from mice we can use it to simulate several microbial profiles using minimal consortia of bacteria, facilitating the better understanding of the systems.	root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00000614	DNA barcoding the flora of Kuwait	This project is a combined ecological and molecular investigation into the diversity of the Kuwaiti Flora and the soil seed bank. It is aimed at extracting DNA barcode regions from plant leaves to build a DNA reference library. Also, to investigate the diversity of species present in the soil by DNA extracting soil samples and using tools such as metagenomics and metabarcoding to verify the utility of the database.	root:Host-associated:Plants
MGYS00000340	Circadian rhythms in plant roots	Circadian rhythms in plant roots.	root:Host-associated
MGYS00000461	Reconstructing the ecosystem functions of the active microbial community within Baltic Sea oxygen depleted sediments	In the present study, we sought to establish whether and to what extent the functional capacities were actually expressed in the Landsort Deep anoxic sediment, using a metatranscriptomic approach. Specifically, given the global extension of anoxic ?dead zones? and the global importance of marine sediment as carbon sink, we were interested to investigate if, and how, the sediment community of the anoxic Landsort Deep sediment mineralized the accumulating carbon. Results reveal the extent of what ecosystem functions, and which nutrient recycling processes, the anoxic sediment microbial communities contribute to. This is knowledge which is important to the decision support tools underlying the Helsinki Commission Baltic Sea Action Plan.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00000613	Analysis of metagenomes from oak wood taken from healthy and diseased trees.	The aim is to comparatively analyze the microbiome found in oak trees using metagenomics. Field samples have been taken from healthy oak trees and trees suffering from the disease acute oak decline. Acute oak decline is a spreading disease in Europe and North America, causing wilting and potentially death of oaks.	root:Host-associated:Plants
MGYS00000475	Experimental Metagenome on MinION	This is an artificial metagenome created by pooling various proportions of DNA from four microbe cultures to simulate a simple metagenome for analysis by Oxford nanopore MinION.  Single-species cultures of Escherichia coli, Paracoccus denitrificans, Microcystis aeruginosa, and Synechococcus elongatus were grown to log phase then harvested for DNA extraction.  Following mechanical shearing, templates were prepared using either equimolar amounts of each species or combinations of DNAs where one species was rare (0.05%). Libraries were created using his-tag bead purification according to MinION specifications and libraries were sequenced using MinION R7.x flow cells.	root:Engineered:Modeled:Simulated communities (DNA mixture)
MGYS00000366	Artic fresh water viromes (2)	Recent metagenomic studies have shown that our knowledge about viruses in nature is very scarce. We aimed to augment such knowledge by analyzing newly sequenced polar freshwater viral metagenomes (both arctic and antarctic..)Previously unexplored arctic viromes were dominated by ssDNA viruses with no known relatives in the databases. Arctic and antarctic viromes were shown to differ at the fine grain level, yet we were able to find a circular contig in both environments with very high similarity.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00000609	A Comprehensive survey of Microbial Diversity in Hot Spring of Unai	In the present study, a high-throughput metagenomic sequencing of metagenomic DNA was performed on an Ion Torrent PGM platform for assessment of microbial diversity. Metagenome composed of 688,059 sequences with size 98,567,305 bps with an average length of 182 bps and 45% G+C content. MG-RAST community analysis revealed dominating Bacillus genus in bacterial domain. Remarkably, 20.5% sequences in a poorly characterized group, with versatile presence of commercial enzymes were marked in a functional metagenome analysis.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00000608	Metagenomic analysis of microbial diversity of Tuva hot water spring	Molecular approaches used to analyze the microbial diversity allow the study of uncultivable microorganisms and contribute towards our understanding of the microbial world. In our study, total community DNA was isolated from environmental water sample by manual and kit based methods. Here, we use Ion-torrent PGM platform to sequence metagenome. Analysis of the community DNA revealed that the phyla Firmicutes and Proteobacteria were the most abundant. Moreover, unclassified sequences also found in this metagenome indicate there are possibilities of getting novel organisms.	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00000585	Study of early life microbiota in preterm baby	Study of early life microbiota in preterm baby using 16S rRNA sequencing	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000367	Human faeces Metagenome	Human faeces Metagenome	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000607	Rumen microbiome	Study of rumen microbiome diversity composition	root:Host-associated:Mammals:Digestive system:Foregut:Rumen
MGYS00000606	Nitrifying reactor with FNA treatment	Nitrifying reactor with FNA treatment and varying concentrations	root:Engineered:Wastewater:Nutrient removal:Nitrogen removal
MGYS00000604	Gene-Environment Interactions at the Skin Surface	16S rRNA gene sequences amplified from subjects with eczema and age-matched healthy controls.  Microbes living in and on humans are ten times more numerous than human cells. Culture-based methods have been the primary techniques used to study microbes inhabiting humans; however, many species are not successfully grown in culture. The NIH Roadmap for Medical Research Human Microbiome Project (HMP) aims to investigate the microbes in the gastrointestinal tract, oral cavity, skin, vagina, and nares. The goal of the HMP is to comprehensively characterize the human microbiota and analyze its role in human health and disease.   The skin serves not only as a barrier against invading pathogens and moisture loss, but also as a host to microbial communities. The skin of an adult is an approximately 2 square meter surface with a myriad of microenvironments.  Atopic dermatitis (AD), more commonly known as eczema, is a common skin disorder that is exacerbated by Staphylococcus aureus colonization.  This study aims to investigate the skin microbiota of AD patients at specific timepoints (quiescence, disease flares, and post-treatment) to examine how disease state correlates with changes in the skin microflora.     The 16S small subunit ribosomal (rRNA) gene is present in every bacterial cell, serving as a universal marker. The gene is sufficiently conserved to allow accurate alignment but adequately varied to enable phylogenetic analyses. Sequencing via 16S rRNA-based phylotyping has been used to survey the bacterial microbes on the skin.  Initially, we will examine the bacterial diversity associated with AD using a 16S rRNA survey and later broadening to include fungi, viruses, archaea and mites. In addition, bacteria will be cultured on a wide variety of media and isolates representing both abundant and novel species will be selected for whole genome sequencing.  To characterize fungal diversity, we utilize two phylogenetic markers within the rDNA region: 18S rRNA and the Intervening Internal Transcribed Spacer (ITS) region.  Full microbial diversity will be explored with shotgun metagenomic sequencing.	root:Host-associated:Human:Skin
MGYS00000551	Rumen microbiome	Mocrobiome study of rumen	N/A
MGYS00000552	Metagenomic workshop submission	sequence submission to EBI metagenomics	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000560	Soil metagenome sampled from a chitin-amended agricultural field	Sampling took place on 21 st November 2010. Soil cores were taken from agricultural (pasture) fields located within Northern Ireland amended with Nephrops carapaces. Carapaces were apllied to the field biannually from 2007 (~1.236 kg m-2). Total DNA was extracted using MPBio Fast DNA Kit for soil and sequenced using an Illumina MiSeq platform - paired end reads. The soil is slightly acidic.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000564	NeoM	NeoM	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000565	Kankrej cow metagenome	as   asll anje aklko akkso appks ;kka	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000569	A metagenomics approach to evaluate the impact of Ascophyllum nodosum and Laminaria digitata on the rumen function	There is an increasing need to identify alternative feeds for livestock that do not compete with feeds for human consumption. Seaweed might provide such a resource, but there is limited information available on its value as an animal feed. Here we use a multi-omics approach to investigate the value of two brown seaweeds, Ascophyllum nodosum (ASC) and Laminaria digitata (LAM), as alternative feeds for ruminants. These seaweeds were supplemented at 5% inclusion rate into a control diet (CON) in a rumen simulation fermenter. Seaweeds had no substantial effect on rumen fermentation pattern, feed digestibility or methane emissions in vitro. Concentrations of total bacteria and anaerobic fungi, as well as biodiversity indices, and abundance of the main bacterial and methanogens genera were also unaffected by brown seaweed supplementation. However, specie-specific effects of brown seaweed on the rumen function were noted: ASC promoted a substantial decrease in the N digestibility (-24%) as a result of its high phlorotannins content. Canonical correspondence analysis of the bacterial community revealed that the low N availability led to a change in the structure of the bacterial community. ASC also decreased the concentration of Escherichia coli O157:H7 post-inoculation. On the contrary, LAM which has a much lower phlorotannins content did not cause detrimental effects on N digestibility nor modified the structure of the bacterial community in comparison to CON diets. This adaptation of the microbial community to LAM diets led to a greater microbial ability to digest xylan (+70%) and carboxy-methyl-cellulose (+41%). These differences among brown seaweeds resulted in greater microbial protein synthesis (+15%) and non-ammonia N flow (+11%) in LAM than in ASC diets and thus should led to a greater amino acid supply to the intestine of the animal. In conclusion, it was demonstrated that incorporation of 5% brown seaweed into the diet can be considered as a suitable nutritional strategy for ruminants; however special care must be taken with those seaweeds with high phlorotannins content to prevent detrimental effects on N metabolism. This study demonstrates the value of combining fermentation data with molecular characterisation of the rumen microbiome in evaluating novel feeds for ruminants.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000573	metagenomic amplicon sequensing from soils for novel natural products (16S_PKS)	The final aim of this study is to identify different soil environments potentially rich in novel natural compounds correlating microbial community diversity and biosynthetic genes for polyketide synthesis. The identification of interesting environments for novel natural products will be useful for further drug discovery pipeline development.	root:Environmental:Terrestrial:Soil
MGYS00000576	Haloalkaline thiosulfate reducing bioreactor	Haloalkaline thiosulfate reducing bioreactor community analysis	root:Engineered:Bioremediation:Hydrocarbon:Benzene:Bioreactor
MGYS00000584	Illumina RNA-Seq on Olavius algarvensis worms	Olavius algarvensis is a shallow-water annelid worm that lives in obligate symbiosis with chemosynthetic bacteria. We sequenced batches of o. algarvensis worms incubated under oxic and anoxic conditions, respectively, and performed Illumina transcriptome sequencing on each for host gene discovery.	root:Host-associated:Annelida
MGYS00000588	Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2014	This projects explores the functional diversity and activity of rocky subseafloor microbial communities in hydrothermal vent systems. Samples were collected in 2014 from three low temperature diffuse fluid vents at Axial seamount, located in the northeast Pacific Ocean. We also collected a sample using a CTD within the Axial Caldera, at 1200m depth. Shotgun metagenomics and metatranscriptomics were performed on four diffuse vent samples. This study helps to determine the genetic potential and expression patterns of the largely uncharacterized subseafloor microbial community and shows how these patterns change across the complicated biogeochemical gradients of hydrothermal vent systems.	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00000590	Acropora aspera virome from Heron island, Australia	Previous studies of coral viruses have employed either microscopy or metagenomics, but few have attempted to comprehensively link the presence of a virus-like particle (VLP) to a genomic sequence. We conducted transmission electron microscopy imaging and virome analysis in tandem to characterize the most conspicuous viral types found within the dominant Pacific reef-building coral genus Acropora. Three of the dominant VLPs identified were observed in all tissue layers and budding out from the epidermis, including viruses that were ~70 nm, ~120 nm, and ~165 nm in diameter; these VLPs all contained electron dense cores. These morphological traits are reminiscent of retroviruses, herpesviruses, and nucleocytoplasmic large DNA viruses (NCLDVs), respectively. Some 300-500 nm Megavirus-like VLPs also were observed within and associated with dinoflagellate algal endosymbiont (Symbiodinium) cells. Abundant sequence similarities to a gammaretrovirus, herpesviruses, and members of the NCLDVs corroborated these morphology-based identifications. Additionally sequence similarities to two diagnostic genes, a MutS and a DNA polymerase B gene, were recovered and most closely resembled Pyramimonas orientalis virus, demonstrating the association of a cosmopolitan Megavirus with Symbiodinium. We also identified several other viral particles in host tissues, along with sequences phylogenetically similar to circoviruses, phages, and filamentous viruses. Given that all corals in this study had high titers of viral particles and that aerial exposure of coral colonies during extreme low tides induced bleaching on the reef flat in the weeks during this work, we hypothesize that our collections and experiment coincided with a natural outbreak of viral infection.	root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
MGYS00000591	Microbial diversity in a cave ecosystem	Characterisation of microbial communities in microbial mat and sediment from Movile Cave, Romania	root:Environmental:Aquatic:Freshwater:Groundwater:Cave water
MGYS00000593	Antimicrobial resistance gene monitoring in aquatic environments (Metatranscriptomes).	This dissertation documents the development of an environmental framework for monitoring antimicrobial resistance gene (ARG) dissemination in the aquatic environment. The work opens with a review of the relevant literature and outlines the importance of an environmental framework for monitoring ARG dissemination as part of antimicrobial resistance risk assessments.  The ability to interrogate sequencing data quickly and easily for the presence of ARGs is crucial in order to facilitate their monitoring in the environment. As current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria in the environment were limited in their effectiveness and scope, the dissertation begins by describing the design and implementation of a Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally-acquired ARGs in raw sequencing data. The suitability of metagenomic methods for monitoring the ARG content of effluents from faecal sources was then assessed via a pilot study of a river catchment. Novel metagenomes generated from effluents entering the catchment were interrogated for ARGs. The relative abundance of ARGs in effluents were determined to be higher relative to the background environment, as were sequences relating to human and animal pathogens and mobile genetic elements. Thus, effluents were implicated in the dissemination of ARGs throughout the aquatic environment. To determine if ARGs were potentially in use in the environment, the expression of ARGs within effluents was then evaluated across a series of longitudinal samples through the use of metatranscriptomics, and the presence of potential environmental antimicrobial selection pressures was examined. This demonstrated that the abundance of ARGs, as well as antimicrobial usage at the effluent source, was correlated with the transcription of ARGs in aquatic environments.  The work described in this dissertation has also found that horizontally transmitted ARGs were present in pathogenic endospore-forming bacteria commonly found across the aquatic environment, potentially providing a mechanism for ARG persistence in the environment.  Finally, these findings were integrated into a universal framework for monitoring ARG dissemination in aquatic environments and used to highlight the developments required to incorporate this framework into future environmental ARG research and to facilitate antimicrobial resistance risk assessments.	root:Environmental:Aquatic
MGYS00000594	Antimicrobial resistance gene monitoring in aquatic environments	This dissertation documents the development of an environmental framework for monitoring antimicrobial resistance gene (ARG) dissemination in the aquatic environment. The work opens with a review of the relevant literature and outlines the importance of an environmental framework for monitoring ARG dissemination as part of antimicrobial resistance risk assessments.  The ability to interrogate sequencing data quickly and easily for the presence of ARGs is crucial in order to facilitate their monitoring in the environment. As current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria in the environment were limited in their effectiveness and scope, the dissertation begins by describing the design and implementation of a Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally-acquired ARGs in raw sequencing data. The suitability of metagenomic methods for monitoring the ARG content of effluents from faecal sources was then assessed via a pilot study of a river catchment. Novel metagenomes generated from effluents entering the catchment were interrogated for ARGs. The relative abundance of ARGs in effluents were determined to be higher relative to the background environment, as were sequences relating to human and animal pathogens and mobile genetic elements. Thus, effluents were implicated in the dissemination of ARGs throughout the aquatic environment. To determine if ARGs were potentially in use in the environment, the expression of ARGs within effluents was then evaluated across a series of longitudinal samples through the use of metatranscriptomics, and the presence of potential environmental antimicrobial selection pressures was examined. This demonstrated that the abundance of ARGs, as well as antimicrobial usage at the effluent source, was correlated with the transcription of ARGs in aquatic environments.  The work described in this dissertation has also found that horizontally transmitted ARGs were present in pathogenic endospore-forming bacteria commonly found across the aquatic environment, potentially providing a mechanism for ARG persistence in the environment.  Finally, these findings were integrated into a universal framework for monitoring ARG dissemination in aquatic environments and used to highlight the developments required to incorporate this framework into future environmental ARG research and to facilitate antimicrobial resistance risk assessments.	root:Environmental:Aquatic
MGYS00000598	Pekin duck health with water troughs compared to pin-metered water lines using a US management system	Controversy has developed over the last few years as to whether or not water nipple lines or water troughs are more appropriate for Pekin ducks in grow-out commercial barns. We hypothesized that water troughs would show improved duck body conditions and environmental quality compared to pin-metered water lines.   To test this hypothesis, we housed ducks in two barns, one with water lines and one with water troughs.   Water troughs were constructed to meet RSPCA guidelines for number and density of ducks and with recently described verandas.  Ducks were divided into 4 pens per barn (n = 1000 ducks/pen).  The study was then repeated (n = 8 pens per water source). Ducks were scored for physical traits and assessed for microbial cecal content changes through 16S amplicon sequencing. Water samples were assessed for culturable microbial loads and for microbial community through 16S amplicon sequencing.	root:Engineered:Wastewater:Industrial wastewater:Agricultural wastewater
MGYS00000601	Assessment of Bacterial DNA Extraction Procedures for Metagenomic Sequencing Evaluated on Different Environmental Matrices.	Will follow later.	root:Engineered:Modeled
MGYS00000548	16S V3-V4 metagenome from four Danube water samples	Water samples have been collected at four sites in Croatia/Serbia onthe Danube river. Analysis of the samples' 16S metagenomes should provide an indication how the bacterial community changes going from a relatively clean site to more pulluted sites close to industrial areas.	root:Environmental:Aquatic:Freshwater:Lotic
MGYS00000553	Total RNA-Seq on sputum samples from patients with active tuberculosis	Total RNA from sputum collected from patients with active tuberculosis (TB) was analysed by RNA sequencing. The transcription phenotype of Mycobacterium tuberculosis (Mtb) was found to resemble that of actively replicating bacteria in laboratory culture. Transcription profiling of commensal bacteria in the sputum provided further provide details in of the sputum environment. Understanding of the microbiology and microbial ecology of Mtb after release from tuberculous lesions may reveal novel opportunities to modulate the efficiency of disease transmission.	root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
MGYS00000554	Microbial community composition in the sediment at naturally CO2-rich sites and its implications for ocean acidification research	Microbial processes are fundamental in nutrient cycling and remineralization in marine sediments. To understand how ocean acidification (OA) may influence sediment microbial diversity and activity, naturally CO2-rich sites are increasingly being used. However, the characterization of naturally CO2-rich sites is often limited to OA-related variables, neglecting additional variables that may obscure OA effects, especially when the CO2 increase is caused by geological processes. Here, we reevaluated the factors affecting changes in microbial communities at volcanic CO2 seeps in Papua New Guinea based on a comprehensive characterization of the conditions in the sediment. Microbial community composition was assessed using molecular fingerprinting and amplicon sequencing. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. In-situ microprofiles and trace element concentrations further showed a variation in the strength of the hydrothermal signature of the sediment at similar pH allowing the identification of sites which may better represent future OA than others. At these sites, changes in the microbial community may have implications for element cycling in the sediment. We recommend focusing on a detailed environmental characterization in future OA research, to ensure better comparability between studies and a more reliable selection of naturally CO2-rich sites.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00000555	Wastewater metagenomics.	Wastewater metagenomics.	root:Engineered:Wastewater
MGYS00000559	Metagenomics - bat faecal metagenome	Metagenomics - Sierre Leone bat faecal metagenome	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000568	Marine Microbes pilot study	Pilot study for the Australian Marine Microbes project.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00000577	Transcriptome analysis of the Root, rhizosphere and soil of Oilseed rape lines that showed, high or low malate exudation.	RNA was extracted and sequenced from the root, rhizosphere and bulk soil of 7 pooled Oilseed rape genotypes, that showed; high and low malate exudation.	root:Host-associated:Plants:Rhizosphere
MGYS00000578	Annotation of Fusobacterium	Analysis of genome of the strain	root:Host-associated:Mammals:Circulatory system:Blood
MGYS00000586	Microbial Dysbiosis in gut of Acutely and Chronically SIV Infected macaques	Microbial dysbiosis has been linked to systemic immune activation and accelerated disease progression from acute HIV-1 infection to the end stage disease AIDS.  HIV-1 infection leads to a massive depletion of CD4 T cells within the gut associated lymphoid tissue.  As a part of this depletion CD4 Th17 cells are selectively killed and the mechanisms protecting the body against microbial translocation break down.  The loss of immune regulation and systemic immune activation can lead to changes in the gut microbial community.  These changes can manifest themselves as microbial dysbiosis and microbial translocation, which are believed to be key contributors to systemic immune activation and chronic inflammation.  Chronic inflammation persists in patients treated for HIV-1 and likely contributes to the high incidence of age-related diseases seen in these patients.  Using SIV as a model for HIV-1 transmission and pathogenesis; a study was conducted to determine the changes in the gut microbiota composition through cross-sectional samples of infected individuals. Rhesus Macaque fecal samples were collected from the Jejunum and Rectum and characterized by 16S rRNA Illumina Mi-Seq paired-end sequencing.  A longitudinal study was then performed using 6 infected individuals sampled across different time points of infection.  We were able to  draw important conclusions about how SIV induced changes in the immune system can impact the make-up of gut microbiota, and how the changes in microbiota could possibly impact microbial translocation and chronic inflammation.  Specifically we were able to observe increases in inflammation tolerant taxa, increases in motile taxa, and the loss of taxa important for metabolism related to immune regulation.  The data obtained could be beneficial in providing alternative or complementary treatment options and a better understanding of HIV-1 transmission and pathogenesis.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000600	Effect of DNA extraction methods on the determination of the structure of microbial communities in the phosphogypsum waste heap soil	The aim of this project is to compare the structure of bacterial communities, created by using different DNA extraction protocols, from soil samples of the phosphogypsum waste heap in Wislinka, (Poland, Pomeranian district). The selection of proper methods is of a high importance in every research, due to its influence on the obtained results and theirs interpretation. Therefore, in this project we want to verify, whether the DNA extraction methods have a significant impact on the proper recognition of the final structure of bacterial communities. During this study, we want to determine whether the results are strongly influenced by choice of DNA extraction protocols or significant changes in experimentally estimated structure of community cannot be observed. Several evaluation studies have been performed in order to compare DNA extraction methods from soil samples. However, these studies have never compared the diversity of obtained sequences by high-throughput sequencing. In this project we want to compare not only yield and purity of extracted DNA using different isolation protocols, but also the results of the sequencing, and their impact on recognized complexity of microbial community structure estimated on their basis.  In this study we collected soil samples from the phosphogypsum waste heap in Wislinka, (Pomerania district). The heap was created from production wastes, mainly phosphogypsum and due to that fact it may be attractive place to study biodiversity of microorganisms. This study can be a valuable source of rare and unique types of bacteria living in very unique environmental conditions.	root:Environmental:Terrestrial:Soil:Mine
MGYS00000603	A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds	Reliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring. Here, we present a workflow, from sampling to interpretation, showing how resistance monitoring can be carried out in swine herds using a metagenomic approach. We show that metagenomics outperform traditional MIC and CFU counting in terms of predicting expected resistance based on antimicrobial consumption and demonstrate that composite pen floor samples are suited to approximate the in-animal resistomes. Finally, we show the method is sensitive enough to detect subtle differences in antimicrobial-induced resistome changes and can identify genes whose abundances are affected by antimicrobial usage. We propose metagenomic sequencing should be part of routine livestock resistance monitoring programs and potentially of integrated One Health monitoring in all reservoirs.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000520	Whole genome sequencing of metagenomes extracted from palms of two individuals	Whole genome sequencing of metagenomes extracted from palms of two individuals	root:Host-associated:Human:Skin
MGYS00000543	Study of the abundance of bacteria from human samples	this study contains 12 samples for the analysis of abundance of bacterial communities on human residues farm derived samples	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000530	Dysbiosis of the fecal microbiota in the TNBS-induced Crohn?s disease mouse model	Crohn?s disease (CD) is characterized by chronic transmural inflammation. The symptom of the mice model induced by 2, 4, 6-Trinitrobenzenesulfonic acid (TNBS) is closed to human under CD condition, so this kind of animal is widely used in the related researches. Although the dysbiosis of the fecal microbiota have been proved to play an important role in the patients with CD, the composition of the gastrointestinal microbiota in the mouse model under disease condition is still unclear. In the current study, male seven-weeks BALB/c mice were anesthetized and intrarectal administrated by ethanol (ET group), TNBS in ethanol (TN group) and phosphate buffered saline (PBS) (CK group) as control. The symptoms of individuals under the CD condition were observed, and the changes of the bacterial taxonomic structure and functional composition were revealed by NGS 16S sequencing. The BALB/c mice in TN group demonstrated CD-like symptoms and the damages in the intestinal tract. The NGS 16S results exhibited that the diversity and microbial composition under CD condition are significantly different with those in ET group. The KO profile were generated from PICRUSt, and function modules such as methanogenesis (M00347) and microcin C transport system (M00349) were found enriched in the individuals in the TN group. This study proved that mouse model induced by TNBS could develop the similar symptom to CD patient, and we firstly showed the significant intestinal microbes changes both on taxonomic structure and functional composition in this mouse model.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000379	Artic fresh water viromes (1)	Recent metagenomic studies have shown that our knowledge about viruses in nature is very scarce. We aimed to augment such knowledge by analyzing newly sequenced polar freshwater viral metagenomes (both arctic and antarctic). Previously unexplored arctic viromes were dominated by ssDNA viruses with no known relatives in the databases. Arctic and antarctic viromes were shown to differ at the fine grain level, yet we were able to find a circular contig in both environments with very high similarity.	root:Environmental:Aquatic:Freshwater
MGYS00000256	Rainforest Soil	Many natural ecosystems are efficiently degrading lignocellulose and harbor enzymes that could potentially be harnessed for the production of next generation biofuels from plant biomass. We have used shotgun metagenome sequencing to provide a survey of the microbial community and potential metabolic pathways present in the tropical rain forest soil of Puerto Rico. Wet tropical forest soils are some of the most productive and diverse terrestrial ecosystems on earth. These soils are characterized by high iron concentrations and regular fluctuations between oxic and anoxic conditions on a scale of days to weeks. These dynamic conditions suggest that bacterial and archaeal processes are more important in this type of environment than in other ecosystems.	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00000257	Western English Channel diurnal study	Here we present a multi-omic study of the Bacterial and Archaeal diversity found at the L4 long-term marine observatory.  We have previously generated a six year time series from L4 that showed that the bacterial community shows strong seasonal structuring and diversity peaks every year on the winter solstice.  Here we further confirm this pattern by extending this study to include genes and transcripts generated for eight additional time points in 2008.  This data includes further 16S datasets as well as eight metagenomes (1.2 GB) and eight metatranscriptomes (157MB).  These time points cover three seasons (Jan, April and August) and include day and night (diel) publicSamples.  In addition, the August publicSamples (4) include 4 consecutive samplings within 24 hours at six hour intervals.  Using these data we test whether Archaea also show the same observed seasonal patterns and whether these patterns hold true at the gene (functional) level. Analysis of this combined data set allows five main conclusions to be drawn.  First, Archaea show evidence of following the same seasonal patterns as Bacteria, but have ~6% the richness.  Second, for both Bacteria and Archaea, we confirm that higher 16S diversity reflects higher diversity at the gene-level (including expressed genes) and this diversity also peaks at the winter solstice. Third, interestingly, detectable diversity appears to be higher at night, and this is of special potential relevance as there is more diversity in winter when nights are longer.  Fourth, despite the diversity of these communities, night and day publicSamples taken using Lagrangian (drift) sampling were successful in isolating the same community suggesting communities are more structured than is commonly believed. Finally, this data, as expected, contains a large proportion of orphan genes without known homologues.  When compared to the housekeeping genes identified through SEED subsystem classification, these unknown genes appear to be driving the differences between publicSamples across seasons.  This underscores the importance of determining the functions of more of these sequences in the future. In summary, this study further confirms the strong seasonal patterns characterizing both the bacterial and archaeal communities at this important marine site.  The finding that, despite the huge diversity of these communities, there are evident signs of predictable patterns and detectable stability over time provides compelling evidence that renewed efforts should be focused on finding deterministic patterns in even the most complex microbial communities. The Western Channel Observatory maintains more than 100 years of continual environmental monitoring, including oceanographic and biological measures. At PML we are committed to developing this outstanding time series to include the most up to date techniques available. Our aim is to provide an holistic ecologically relevant dataset that can be used to inform environmental models and help with prediction of the impact that climate change will have on the coastal seas of the United Kingdom. With further development and comparative publicStudies this information can help to inform on global marine environments. To this end we have been employing the latest in high-throughput sequencing technology to investigate the microbial diversity and community function in this ecosystem. The technologies applied include 16S rDNA tag-pyrosequencing to deep sequence microbial diversity, as well as total community metagenomics and metatranscriptomics. This initial study includes 16S rDNA tag sequencing data for bacteria and archaeal groups as well as metagenomics and metatranscriptomics all performed on the GS-flx titanium platform using techniques outlined in Gilbert et al (2009 – Environmental Microbiology) and Gilbert et al (2008 – PloS One.) We will continue to add to this repository to maintain the temporal analysis of this community.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00000258	A core gut microbiome in obese and lean twins	We have characterized the fecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers. The results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiologic states (obese versus lean)	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000259	Glacier Metagenome	The largest part of the Earth's microbial biomass is stored in cold environments, which represent almost untapped reservoirs of novel species, processes, and genes. In this study, the first metagenomic survey of the metabolic potential and phylogenetic diversity of a microbial assemblage present in glacial ice is presented. DNA was isolated from glacial ice of the Northern Schneeferner, Germany. Pyrosequencing of this DNA yielded 1,076,539 reads (239.7 Mbp). The phylogenetic composition of the prokaryotic community was assessed by evaluation of a pyrosequencing-derived data set and sequencing of 16S rRNA genes. The Proteobacteria (mainly Betaproteobacteria), Bacteroidetes, and Actinobacteria  were the predominant phylogenetic groups. In addition, isolation  of psychrophilic microorganisms was performed, and 13 different  bacterial isolates were recovered. Analysis of the 16S rRNA gene sequences of the isolates revealed that all were affiliated to the predominant groups. As expected for microorganisms residing in a low-nutrient environment, a high metabolic versatility with respect to degradation of organic substrates was detected by analysis of the pyrosequencing-derived data set. The presence of autotrophic microorganisms was indicated by identification of genes typical for different ways of carbon fixation. In accordance  with the results of the phylogenetic samples, in which mainly  aerobic and facultative aerobic bacteria were detected, genes  typical for central metabolism of aerobes were found. Nevertheless, the capability of growth under anaerobic conditions was indicated by genes involved in dissimilatory nitrate/nitrite reduction. Numerous characteristics for metabolic adaptations associated with a psychrophilic lifestyle, such as formation of cryoprotectants and maintenance of membrane fluidity by the incorporation of unsaturated fatty acids, were detected. Thus, analysis of the glacial metagenome provided insights into the microbial life in frozen habitats on Earth, thereby possibly shedding light onto microbial life in analogous extraterrestrial environments.	root:Environmental:Aquatic:Freshwater:Ice:Glacier
MGYS00000260	Wheat Rhizosphere, John Innes Centre	The interaction between microbes and plants in the region around plant roots (rhizosphere) is a key determinant of plant productivity. Here we use meta-transcriptomic sequences of mRNA extracted from 4 pooled 1g wheat rhizosphere soil samples to map metabolic interactions in the rhizosphere.	root:Environmental:Terrestrial:Soil
MGYS00000274	Windshield splatter	"How many species inhabit our immediate surrounding? A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds. The windshield of a moving vehicle is subjected to numerous insect strikes and can be used as a collection device for representative sampling. Combined with next-generation sequencing this approach allows for species identification. Here we describe an application of this methodology to two geographic locations within the Northeastern United States. We identified 61 arthropod and 39 plant species, seven of which showed significant difference in the relative abundance between the two localities. Importantly, we developed a novel robust computational framework for the comparison of relative species abundances between geographic locations, which can be used in other read-count-based applications of next-generation sequencing, such as comparison of expression levels. 
The main aim of our study was to contrast eukaryotic species differences between two distinct geographical location in northeastern United States. DNA, isolated from the material stuck to the tapped front bumper of a car driven in these locations, was sequenced using 454 (Roche) FLX pyrosequencing technology."	root:Environmental:Air
MGYS00000275	The Metagenome of the deep chlorophyll maximum in the Mediterranean studied by direct and fosmid library 454 pyrosequencing	"The Deep Chlorophyll Maximum (DCM) is a zone of maximal photosynthetic activity, generally located towards the base of the photic zone in lakes and oceans. The DCM in the Mediterranean is a seasonal phenomenon. The metagenome from a single sample of a mature Mediterranean DCM community has been 454 pyrosequenced both directly and after cloning in fosmids. The comparison between the two approaches revealed a bias in the fosmid libraries against low GC DNA and specifically against the two most dominant members of the community, Candidatus Pelagibacter and Prochlorococcus marinus subsp. pastoris, thus unexpectedly providing a feasible method to obtain large genomic fragments from other less prevalent members of this community. This study is the first to be carried out at this sequencing depth (ca. 600 Mbp combining direct and fosmid sequencing) at any DCM. Our results indicate a microbial community massively dominated by the high-light adapted P. marinus subsp. pastoris, Synechococcus sp. and the heterotroph Candidatus Pelagibacter. The sequences retrieved were remarkably similar to the existing genome of P. marinus subsp. pastoris with a nucleotide identity over 98%. Besides, we found a large number of cyanophages that could prey on this microbe although sequence conservation was much lower. The high abundance of phage sequences in the cellular size fraction indicated a remarkably high proportion of cells suffering phage lytic attack. In addition, several fosmids clearly belonging to Group II Euryarchaeota were retrieved and recruited many fragments from the total DNA sequencing suggesting that this group might be quite abundant in this habitat.
We have extracted metagenomic DNA from the pico-planktonic 5-0.2 μm size fraction (mostly prokaryotic cells) from a single sample obtained in mid October at 50 m depth and analyzed the DNA from this sample (without cloning or amplification) by 454 pyrosequencing (hereafter referred to as Direct Sequencing, DS). We also used 454 to sequence ca. 1152 randomly selected fosmid clones from a metagenomic fosmid library constructed from the same DNA sample. Here we compare the output from both methods and the picture of the microbial community that they provide."	root:Environmental:Aquatic:Marine:Oceanic
MGYS00000276	Kimchi metagenome	"Kimchi, the Korean culture's traditional food, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation. Metagenomic DNA was extracted from kimchi samples obtained periodically and followed by sequencing using a 454 GS-FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera; Leuconostoc, Lactobacillus, and Weissella. Assignment of metagenomic sequences to SEED categories of MG-RAST revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, the Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Lactobacillus sakei subsp. sakei 23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity to Leuconostoc mesenteroides and Lactobacillus genes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophage during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.
We have extracted metagenomic DNA from fermented food kimchi and sequenced the DNA from this sample by 454 GS-FLX titanium without cloning or amplification. Here we analyze changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation using metagenomic approaches."	root:Engineered:Food production:Fermented vegetables
MGYS00000277	Human Gut Microbiome in Crohn's Disease	"Inflammatory bowel diseases (IBD), such as Crohn’s disease, are chronic, immunologically mediated disorders that have severe medical consequences. The current hypothesis is that these diseases are due to an overly aggressive immune response to a subset of commensal enteric bacteria. Studies to date on IBD have suggested that the disorder may be caused by a combination of bacteria and host susceptibility; however the etiologies of these diseases remain an enigma. 
In this application, we propose to develop and demonstrate the ability to profile Crohn’s disease at an unprecedented molecular level by elucidation of specific biomarkers (bacterial strains, genes, or proteins) that correlate to disease symptoms. To achieve this goal, we will employ a multidisciplinary approach based on metagenomic and metaproteomic molecular tools to elucidate the composition of the commensal microbiota in monozygotic twins that are either healthy or exhibit Crohn’s disease (for concordant, both are diseased; for discordant, one is healthy and one is diseased). 
The central hypotheses of this proposal are (1) that specific members and/or functional activities of the gastrointestinal (GI) microbiota differ in patients with Crohn’s disease as compared to healthy individuals, and (2) that it will be possible to elucidate microbial signatures which correlate with the occurrence and progression of this disease by integration of data obtained from 16S rRNA-based molecular fingerprinting, metagenomics, and metaproteomics approaches. To address these hypotheses, three specific aims are proposed: 1) Obtain data on community gene content (metagenome) in a subset of healthy twins and twins with Crohn’s Disease to assess potential differences in the metabolic capabilities of the gut microbiota associated with CD, 2) Obtain data on community protein content (metaproteome) in a subset of healthy twins and twins with Crohn’s Disease to assess the state of expressed proteins associated with CD, 3) Apply various statistical clustering and classification methods to correlate/associate microbial community composition, gene and protein content with patient metadata, including metabolite profiles and clinical phenotype. 
The ultimate goal of these efforts is to identify novel biomarkers for non-invasive diagnostics of CD and to eventually identify drug targets (i.e. bacterial strains) for cure or suppression of disease symptoms. 
PUBLIC HEALTH RELEVANCE: This study aims to unravel the contribution of the bacteria that normally inhabit the human gastrointestinal tract to Crohn’s disease by using a multidisciplinary approach to study changes in the structure and function of gut microbial communities in three sets of patient cohorts who have Crohn’s disease. These results will be compared with those obtained from the study of healthy individuals and have the potential to identify new biomarkers of disease severity, location, and progression."	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000278	Developing infant gut microbiome	The colonization process of the infant gut microbiome has been called chaotic, but this view could reflect insufficient documentation of the factors affecting the microbiome. We performed a 2.5-year case study of the assembly of the human infant gut microbiome to relate life events to microbiome composition and function. Sixty fecal samples were collected from a healthy infant along with a diary of diet and health status. Analysis of >300,000 16S rRNA genes indicated that the phylogenetic diversity of the microbiome increased gradually over time and that changes in community composition conformed to a smooth temporal gradient. In contrast, major taxonomic groups showed abrupt shifts in abundance corresponding to changes in diet or health. Community assembly was nonrandom: we observed discrete steps of bacterial succession punctuated by life events. Furthermore, analysis of ~500,000 DNA metagenomic reads from 12 fecal samples revealed that the earliest microbiome was enriched in genes facilitating lactate utilization, and that functional genes involved in plant polysaccharide metabolism were present prior to the introduction of solid food, priming the infant gut for an adult diet. However, ingestion of table foods caused a sustained increase in the abundance of Bacteroidetes, elevated fecal short chain fatty acid levels, enrichment of genes associated with carbohydrate utilization, vitamin biosynthesis and xenobiotic degradation, and a more stable community composition, all of which are characteristic of the adult microbiome. This study revealed that seemingly chaotic shifts in the microbiome could be attributed to life events.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000282	Antarctica Aquatic Microbial Metagenome	"Microbial metagenome from a lake in Antarctica.
Microbial community isolated from an aquatic lake in Antarctica. "	root:Environmental:Aquatic:Marine
MGYS00000283	MetaSoil	The soil ecosystem is critical for human health, affecting aspects of the environment from key agricultural and edaphic parameters to critical influence on climate change. Soil has more unknown biodiversity than any other ecosystem. We have applied diverse DNA extraction methods coupled with high throughput pyrosequencing to explore 4.88 x 10^9 bp of metagenomic sequence data from the longest continually studied soil environment (Park Grass experiment at Rothamsted Research in the UK). Results emphasize important DNA extraction biases and unexpectedly low seasonal and vertical soil metagenomic functional class variations. Clustering-based subsystems and carbohydrate metabolism had the largest quantity of annotated reads assigned although o50% of reads were assigned at an E value cutoff of 10^-5. In addition, with the more detailed subsystems, cAMP signaling in bacteria (3.24±0.27% of the annotated reads) and the Ton and Tol transport systems (1.69±0.11%) were relatively highly represented. The most highly represented genome from the database was that for a Bradyrhizobium species. The metagenomic variance created by integrating natural and methodological fluctuations represents a global picture of the Rothamsted soil metagenome that can be used for specific questions and future inter-environmental metagenomic comparisons. However, only 1% of annotated sequences correspond to already sequenced genomes at 96% similarity and E values of 10^-5, thus, considerable genomic reconstructions efforts still have to be performed. See http://www.genomenviron.org/Projects/METASOIL.html for additional details.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000288	Brazos-Trinity Basin Sediment Metagenome: IODP Site 1320	This project describes a population genomic study focused on determining the evolutionary rates in natural populations, and to correlate human disturbance to major evolutionary divergence events. Biofilm samples from acid mine drainage were taken in the period 2006-2010 at four locations in the Richmond Mine (Iron Mt., CA). Community genomic DNA was extracted and sequenced by either 454 or Illumina sequencing.	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00000289	Peru Margin Subseafloor Biosphere	"The subseafloor marine biosphere may be one of the largest reserviors of microbial biomass on Earth and has recently been the subject of debate in terms of the composition of its microbial inhabitants, particularly on sediments from the Peru Margin. A metagenomic analysis was made using whole genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment. A total of 61.9 Megabases of genetic material was sequenced from sediments at horizons 1, 16, 32 and 50 meters below seafloor. These depths include sediments from both primarily sulfate-reducing and also methane-generating regions of the sediment column. Many genes of the annotated genes, including those encoding ribosomal proteins, corresponded to those from the Chloroflexi and Euryarchaeota. However, analysis of the 16S small subunit ribosomal genes suggests that Crenarchaeota are the abundant microbial member. Quantitative PCR confirms that uncultivated Crenarchaeota are indeed a major microbial group in these subsurface samples. These findings show that the marine subsurface is a distinct microbial habitat and is different than environments previously studied by metagenomics, especially due to the predominance of uncultivated archaeal groups.

A metagenomic analysis was made using whole genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment."	root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00000291	Viral metagenomic study of two freshwater Lakes	"Viruses are known to be the most abundant biological entities in
    aquatic environment, where they are (i) important top-down regulation factors for
    microbial communities, (ii) known to interfere in major biogeochemical cycles, and
    (iii) thought to be an important source of genetic diversity. Yet, diversity and
    distribution of these viruses is still far from being understood, especially in
    freshwater ecosystems. Metagenomic analysis of two different temperate freshwater
    viral communities showed that most of the viral sequences were not similar to those
    in the current databases. A deep sequencing (1.5 billion sequences) associated to a
    large read size (400 bp) allowed us to assess, for the first time, the diversity in
    the main viral families through direct phylogenetic analysis of specific marker
    genes. The analysis of the major viral groups found in the two lakes shed light on a
    great diversity, and retrieved previously unknown clades among single-stranded DNA
    viruses (Microviridae, Circoviridae, Nanoviridae) and among Caudovirales. The
    absence of lake-specific clade indicated that the new viruses identified were
    ubiquitous, at least on a regional freshwater lake scale. Compared to the previously
    published viromes, a significant genetic similarity between viral communities of
    related environments was highlighted for the first time, despite the great
    geographical distances separating these different communities. Thus, viruses appear
    to be distributed worldwide, and are likely selected by the presence or absence of
    their hosts. Gene richness analysis assessed through rarefaction curves showed an
    extraordinary genetic diversity of viruses in each of the two lakes under study.
    Such diversity was never retrieved previously, even in the last generation of
    published viromes. The global virome is thereby a fantastic pool of unknown genes,
    which remains partially sampled and understood."	root:Environmental:Aquatic:Freshwater:Lake
MGYS00000293	Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics	We investigated the effect of marination on microbiota in modified athmosphere packaged broiler meat using metagenomics. To be able to see the differences in lactic acid bacteria communities on a strain level and to evaluate congruence between the methods, we characterized the lactic acid bacteria communities also by identification of isolates. Most raw poultry sold in Finland at the retail level is mixed with marinades containing oil, sugar, spices and acetic acid and packaged under modified atmosphere. Growth of Leuconostoc spp. has been observed to cause premature spoilage  of marinated broiler meat packages. In this study we investigated whether marinating enriched Leuconostoc spp. in meat microbiota. To obtain a complete view of the microbiota, we sequenced total DNA and 16S rRNA gene amplicons from the microbial communities. In addition, the lactic acid bacterial communities were characterized by identification of colonies. The results showed that marinade increased the proportions of the spoilage-associated Leuconostoc gasicomitatum in the communities as well as the proportions of L. gelidum and Lactobacillus spp.. The proportions of Carnobacterium, Vagococcus, Brochothrix thrermosphacta, Clostridium, Enterobacteriaceae and Vibrio were diminished. Analysis of 16S rRNA gene amplicons resulted in 312 and 284 operational taxonomical units (dissimilarity 0.03) in unmarinated and marinated meat, respectively, indicating that the meat communities were more diverse than hitherto shown. A number of bacterial taxa that have not been associated with late shelf-life meat before were detected, including Vagococcus and Vibrio that belonged to the predominating part of the microbial community in unmarinated meat. According to the functional analysis of the metagenomes, both communities were characterized by high proportions (15.6% or 17.9%) of genes involved in carbohydrate metabolism.	root:Engineered:Food production
MGYS00000294	Mutualism between gut microbiota and the host as revealed in a comparative study of breast-fed versus formula-fed infants	"Ongoing efforts are directed at understanding the mutualism between the
                gut microbiota and the host in breast-fed versus formula-fed infants. Due to the
                lack of tissue biopsies, no investigators have performed a global transcriptional
                analysis of the developing intestine in healthy infants. As a result, the crosstalk
                between the microbiome and the host transcriptome in the developing
                mucosal-commensal environment has not been determined. In this study, we examined
                the host intestinal mRNA gene expression and microbial DNA profiles in full term 3
                month-old infants exclusively formula fed (FF; n=6) or breast fed (BF; n=6) from
                birth to 3 months. Host mRNA microarray measurements were performed on intact
                sloughed epithelial cells in stool samples collected at 3 months. Microbial
                composition from the same stool samples was assessed by metagenomic pyrosequencing.
                Both host mRNA expression and bacterial microbiome phylogenetic profiles provided
                strong feature sets that classified the two groups of babies (FF and BF). To
                determine the relationship between epithelial cell gene expression and the bacterial
                colony profiles, the host transcriptome and functionally profiled microbiome data
                were analyzed in a multivariate manner. From a functional perspective, analysis of
                the gut microbiota's metagenome revealed that virulence characteristics differed
                between the FF and BF babies. Using canonical correlation analysis, evidence of
                multivariate structure relating eleven host immunity/mucosal defense-related genes
                and microbiome virulence characteristics was observed. These results, for the first
                time, provide insight into the integrated responses of the host and microbiome to
                dietary substrates in the early neonatal period.In this study, we examined the host intestinal mRNA gene expression
                and microbial DNA profiles in full term 3 month-old infants exclusively formula fed
                (FF; n=6) or breast fed (BF; n=6) from birth to 3 months. Host mRNA microarray
                measurements were performed on intact sloughed epithelial cells in stool samples
                collected at 3 months. Microbial composition from the same stool samples was
                assessed by metagenomic pyrosequencing. Both host mRNA expression and bacterial
                microbiome phylogenetic profiles provided strong feature sets that classified the
                two groups of babies (FF and BF). To determine the relationship between epithelial
                cell gene expression and the bacterial colony profiles, the host transcriptome and
                functionally profiled microbiome data were analyzed in a multivariate manner. From a
                functional perspective, analysis of the gut microbiota's metagenome revealed that
                virulence characteristics differed between the FF and BF babies. Using canonical
                correlation analysis, evidence of multivariate structure relating eleven host
                immunity/mucosal defense-related genes and microbiome virulence characteristics was
                observed. These results, for the first time, provide insight into the integrated
                responses of the host and microbiome to dietary substrates in the early neonatal
                period."	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000295	Functional diversity of soil microbes across environmental gradients	"Numerous globally distributed 16S rRNA surveys of soil bacterial communities are
    now revealing consistent trends in the main environmental drivers of
    biodiversity. Soil pH is consistently revealed as the predominant correlate of
    taxonomic diversity, with low pH soils comprising less diversity and being
    dominated by a few broad taxonomic groups such as the oligotrophic acidobacteria
    phylum. What is less clear is what these broad differences in patterns of
    taxonomic diversity mean for the functional genetic potential of soils. The low
    culturability of many taxa from low pH soils means that they are significantly
    underrepresented in genome sequence databases. Therefore, this study aims to
    provide a metagenomic comparison of geographically isolated soils of low pH with
    neutral pH soils to identify any broad functional differences between soils of
    similar taxonomic composition."	root:Environmental:Terrestrial:Soil
MGYS00000296	Global Ocean Sampling Expedition	Collection of metagenomes obtained during the Global Ocean Sampling Expedition	root:Environmental:Aquatic:Marine
MGYS00000297	Arctic Winter marine ecosystem	Polar winter waters are one of the least studied marine ecosystems with regard to microbial life and Thaumarchaeota are key microorganisms in this environment. We collected data on abundance and metabolic activity of Thaumarchaeota in Arctic and Antarctic waters in different seasons, including the wintertime. As previously observed, Arctic Thaumarchaeota grew throughout the winter, increasing their abundances one order of magnitude from January to March 2008. Yet, paradoxically, in situ single-cell measurements revealed an unexpected low metabolic activity for this group in both polar systems, i.e., less than 5% of archaeal cells taking up leucine or bicarbonate, inconsistent with known heterotrophic or autotrophic archaeal lifestyles. To resolve how archaea obtain energy and carbon for growth, we analyzed a metagenome collected during the Arctic winter, when the Thaumarchaeota population was at its maximum of abundance (18% of cell counts). Metagenomics and quantitative PCR showed that archaeal amoA genes were abundant in Arctic and Antarctic waters, indicating that polar Thaumarchaeota have the potential for ammonia oxidation.  The presence of a large number of archaeal genes involved in urea transport and degradation together with detectable uptake of 14C-labeled urea by the prokaryotic assemblage, suggest that the products of urea hydrolysis (NH3 and CO2) may be sources of both energy and carbon for polar ammonia oxidizing archaea. This hypothesis, consistent with the idea of polar archaea growing as nitrifiers but with apparent low incorporation of bicarbonate, would provide the molecular basis for the recurrent archaeal growth in polar winter waters.	root:Environmental:Aquatic:Marine
MGYS00000298	Substrate-controlled succession of distinct marine bacterioplankton populations induced by a spring phytoplankton bloom	Phytoplankton blooms characterize temperate ocean margin zones in spring and contribute substantially to their high productivity. We investigated the bacterioplankton response to a diatom bloom in the North Sea and observed an as yet unseen dynamic succession of thriving populations at genus level resolution. Taxonomically distinct expressions of carbohydrate-active enzymes, transporters (in particular TonB-dependent transporters) and phosphate acquisition systems were found, indicating that distinct populations of Bacteroidetes, Gammaproteobacteria and Alphaproteobacteria acted like guilds specialized for successive algal-derived organic matter decomposition. Our results suggest that algal substrate availability and bacterial ecological niches determined the succession. A better understanding of such couplings between bacterioplankton and phytoplankton is needed to pave the way for predictive models of bacterioplankton bloom dynamics and thus more accurate global carbon turnover balances.	root:Environmental:Aquatic:Marine
MGYS00000299	Metatranscriptomics of the marine sponge Geodia barretti: Tackling phylogeny and function of its microbial community.	Geodia barretti is a marine cold-water sponge harbouring high numbers of microorganisms. Significant rates of nitrification have been observed in this sponge, indicating a substantial contribution to nitrogen turnover in marine environments with high sponge cover. In order to get closer insights into the phylogeny and function of the active microbial community and the interaction with its host G. barretti, a metatranscriptomic approach was employed, using the simultaneous analysis of rRNA and mRNA. Of the 262,298 RNA-tags obtained by pyrosequencing, 92% were assigned to ribosomal RNA (ribo-tags). A total of 109 325 SSU rRNA ribo-tags revealed a detailed picture of the community, dominated by group SAR202 of Chloroflexi, candidate phylum Poribacteria and Acidobacteria, which was different in its composition from that obtained in clone libraries prepared form the same samples. Optimized assembly strategies allowed the reconstruction of full-length rRNA sequences from the short ribo-tags for more detailed phylogenetic studies of the dominant taxa. Cells of several phyla were visualized by FISH analyses for confirmation. Of the remaining 21,325 RNA-tags, 10,023 were assigned to mRNA-tags, based on similarities to genes in the databases. A wide range of putative functional gene transcripts from over 10 different phyla were identified among the bacterial mRNA-tags. The most abundant mRNAs were those encoding key metabolic enzymes of nitrification from ammonia-oxidizing archaea as well as candidate genes involved in related processes. Our analysis demonstrates the potential and limits of using a combined rRNA and mRNAapproach to explore the microbial community profile, phylogenetic assignments and metabolic activities of a complex, but little explored microbial community.	root:Host-associated:Porifera
MGYS00000300	HMP Mock Community samples	The HMP metagenomes mock pilot represents the shotgun sequencing of HMP even and staggered Mock communities, distributed to each of the four HMP sequencing centers. The goal of the pilot was to test the sequencing protocol and to evaluate accuracy and consistency between centers.	root:Engineered:Modeled:Simulated communities (DNA mixture)
MGYS00000303	Metagenomics of the gill chamber epibiosis of deep-sea shrimp Rimicaris exoculata and discovery of zetaproteobacterial epibionts	The shrimp Rimicaris exoculata flourishes on deep-sea hydrothermal chimneys along the Mid-Atlantic Ridge (MAR). This species harbors dense community of chemoautotrophic epibiotic bacteria associated with mineral oxide deposits in its enlarged gill chamber. We used metagenomics on specimens from the Rainbow hydrothermal vent site, to investigate the metabolism of the two main sulfur-oxidizing epibionts affiliated to the Epsilonproteobacteria and Gammaproteobacteria. Both epibionts had genes of the Sox pathway for sulfur oxidation and hydrogenases. In the epsilonproteobacterial epibiont, two distinct denitrification systems (Nas/Nir and Nap/Nrf) as well as a complete rTCA cycle for carbon dioxide fixation were found, while the gammaproteobacterial epibiont was found to fix carbon dioxide via the CBB cycle with RuBisCo form II. The shrimp gill chamber metagenome provided information on host-epibiont interactions, like on virulence gene homologues and genes for surface attachment. Likewise, genes were found that might play a role in host nutritional and detoxification processes, and thus are of major importance for the survival of the shrimp and its adaptation to the hydrothermal vent environment. Interestingly, analysis of the metagenome revealed sequences affiliated to the iron-oxidizing class Zetaproteobacteria, which would explain gill chamber iron oxyhydroxide deposits. Presence of Zetaproteobacteria was confirmed by fluorescence in situ hybridizations and thereby provided first evidence for a Zetaproteobacteria-invertebrate.	root:Host-associated:Arthropoda:Respiratory system:Gills
MGYS00000304	Beta Lactam Antibiotics and Human Gut Microbiota	Recent research has disclosed a tight connection between beta-lactam antibiotics, microbial gut metabolism and health but obtaining a complete understanding of this process remains a major goal. Here, we conducted, to the best of our knowledge, the first global comparative OMIC investigation of gut microbial communities in samples of an individual subjected to β-lactam antibiotic therapy at different time frames. Results indicated a drastic change of the total community at response to AB at the day 11thwhich correlated with changes at the level of metabolites, mRNA transcripts and production of proteins. By contrast, AB-resistant active microbiota remains constant, showing a relevant decrease three days later, which indicate an AB time-delay between total and active bacteria. Forty days after AB therapy, the total community is restored but, surprisingly, the low abundant bacteria (Proteobacteria) become the most active members. This is in agreement with unique metabolomic signatures which indicate that human-gut microbe interactions seem to be restored (or improved) as a consequence of AB therapy. It is worth to mention that as a consequence of AB a drastic under-expression of protein production and an attenuation of the metabolic status occurred irreversibly, in agreement with the biodiversity and richness decreased of the total microbiota. Most likely, at the initial stages, AB-resistant bacteria may become, albeit at lower numbers, the most active bacterial members, but their consequent instability as response to AB therapy produced a re-establishment of the overall community containing new active members that has a connection with the host. A complete reprogramming of the bacterial structure and metabolic status seems to occur most likely at day 11th. Taken together, this study suggests a tighter, more coordinated and complex evolutionary and AB ecology scenario of human gut microbial communities than has been previously assumed.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000305	Detoxification of arsenic mediated by microbial sulphate reduction in Mediterranean marine sediments	"Micro-organisms which dwell in sediments have a crucial role in biogeochemical cycles and are thus expected to have a strong influence on the cycle of arsenic, a metalloid responsible for severe water pollution and presenting a major health risk for the populations. Nowadays, environmental genomics techniques allow to study the adaptive and cooperative strategies of microbial communities thriving in polluted environments.
We sequenced the sediment metagenomes from l'Estaque marina (Marseille, France), close to a former metallurgic industrial site highly polluted with arsenic, and from St Mandrier marina, near Toulon (France). The functional and taxonomic profiles of both metagenomes, along with those from four publicly available metagenomes used as control data sets, were obtained using the RAMMCAP workflow.
The biodiversity was higher in both harbour sediment communities in comparison to the controls. The order of Desulfobacterales represented 54.7% of the observed orders in l'Estaque and 31.7% in St Mandrier. Other orders were evenly distributed though the diversity was lower in the highly polluted site of l'Estaque than in St Mandrier.  
The Gene Ontology (GO) entries describing the functional profiles were compared with the controls in order to highlight the over-represented categories in the metagenomes of interest. We observed that categories related to arsenic resistance and oxidative stress were over-represented in l'Estaque. More importantly, the integration of metagenomic and physico-chemical data showed that in l'Estaque, dissimilatory sulphate reduction in the upper layer of sediment could increase arsenic diffusion to the water column and deeper layers, resulting in local detoxification of the sediment. "	root:Environmental:Aquatic:Marine
MGYS00000306	Long insert human faecal metagenomic library.	"Metagenomics allow us to screen the genic content from, virtually, any type of environment with biological content and rendering the possibility of discovering products of interest. Here we propose a method to obtain medium-insert-size (7-15 Kb) metagenomic libraries that are sequenced through a hybrid approach based on pyrosequencing of clone pools and later Sanger-end sequencing of individual clones. Sequences are then assembled and the open reading frames annotated.
We have applied this methodology to study human gut microbiota. From the 358 analysed clones from the library obtained from a faecal sample we found various ORFs annotated as enzymes with already reported industrial or medical application. Finally, forty-three ORFs were annotated as proteins of still unknown function.
This method represents a new approach to explore microbial ecosystems, particularly the human gut microbiome, providing a scalable access to clones with potentially biotechnological and biomedical applications. Thus, previous sequence knowledge will drive the choice of the correct functional screening approach."	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000307	Crohn's Disease viral and microbial metagenome	Healthy adult controls and patients affected by ileocolic Crohn’s disease from Valencia (Spain) were examined for their viral and microbial communities from feces and, in one additional case, present in the intestinal tissue. The taxonomical and functional analyses on unassembled and assembled sequence reads, following two different approaches allows as to compare the viral and microbial communities between both groups in study in several ways. For example we compared by group (controls vs patients), by entity (viruses vs bacteria), by reads assembly (assembled vs unassembled reads) and by methodology (our approach vs an existing pipeline). 	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000308	Follow-up of faecal microbiota in IBS patients	"Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder in western countries. The definition and treatment of IBS is challenging due to its largely unknown aetiology and the variety of symptoms it can present. Previous studies on IBS suggest subtle alterations in the composition of intestinal microbiota. However, no consensus has been reached regarding the association between specific bacteria and IBS. To overcome the confusion introduced by inter-subject variability and heterogeneity within IBS that is problematic in cross-sectional studies, we undertook a longitudinal study that allowed us to compare samples from single patients at moments with different type and/or severity of symptoms. We present results for two IBS patients with diarrhoea subtype and the healthy relative of one of them. Faecal samples collected every two days the first week and then weekly over two months were analysed through metagenomic and metatranscriptomic approaches. Overall, we detect a greater instability of faecal microbiota in IBS patients when compared to the control, and even larger instability
 associated with acute diarrheoa.
 Bacterial composition and encoded functions were fairly stable throughout. On the contrary, the fraction of active bacteria varied markedly in time. Strong and quick compositional shifts were associated with relapse, although with low reproducibility between and within patients. Similarly, changes in the global pattern of gene expression characterized days of worsening, but we could not identify genes or functions associated with relapse. Our results confirm that the association of microbiota with IBS is rather weak."	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000310	Buffalo rumen metagenomics	Rumen metagenomics feed trial shotgun sequencing	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000311	Metagenomic analysis of Ruminal Microbes	Studying effect of various ration on functional and community profile of fiber adherent and liquid associated rumen microbes in buffalo	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000312	"Metatranscriptomes from mesocosm experiments with added organic carbon (OM[ab] samples) and controls (C[ab] samples).
"	Microcosm experiments was done with water from the oxygen minimum zone (around 300-500 m depth) of the subtropical North Atlantic (latitude 17.71 , longitude -41.05) to study the response of mesopelagic prokaryotic communities to pulses of nutrients. Three different treatments and a control were established after prefiltering the seawater through 0.8 µm polycarbonate filters. Microcosms were amended either with thiosulfate (Na2S2O3), ammonium (NH4Cl) or pyruvate plus acetate (C3H3NaO3 and C2H3NaO3) and the control was not supplemented with any organic or inorganic compound. The treatments and the control were established in duplicate in 20 l carboys and held in the dark at in situ temperature for 110-140 h. At the end of the incubation the remaining water was collected through 0.22 µm polycarbonate filters for metatranscriptomic analysis	root:Environmental:Aquatic:Marine
MGYS00000314	BGI Type 2 Diabetes study	A Metagenome-Wide Association Study of gut microbiota identifies markers associated with Type 2 Diabetes based on next generation sequencing technology.	root:Host-associated:Human:Digestive system:Large intestine
MGYS00000316	French Guiana forest soil metagenomic sequencing study	Soil samples have been collected at Trois-Sauts, an isolated settlement in Amazonian National Park. In order to assess anthropogenic impact on microbial communities, a 3km transect has been sampled every 600m in order to generate anthropization gradient, from the village to the forest. Each soil samples DNA has been extracted with MoBio Power Soil Max extraction kit and directly sequenced without any prior amplification with Roche 454 Titanium chemistey	root:Environmental:Terrestrial:Soil:Tropical rainforest
MGYS00000317	Rhizosphere metatranscriptomics	Plant-microbe interactions in the rhizosphere play key roles in biogeochemical cycling, and maintenance of plant health and productivity, yet remain poorly understood. Using RNA based metatranscriptomics, the global active microbiomes were analysed in soil and rhizospheres of wheat, oat, pea, and an oat mutant (sad1) deficient in production of antifungal avenacins.  Rhizosphere microbiomes differed from bulk soil and between plant species. Pea (a legume) had a much stronger effect on the rhizosphere than wheat and oat (cereals), resulting in a dramatically different rhizosphere community. The relative abundance of eukaryotes in the oat and pea rhizospheres was more than five-fold higher than in the wheat rhizosphere or bulk soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, while the pea rhizosphere was highly enriched for fungi. Metabolic capabilities for rhizosphere colonisation were selected, including cellulose degradation (cereals), H2-oxidation (pea) and methylotrophy (all plants). Avenacins had little effect on the prokaryotic community of oat, but the eukaryotic community was strongly altered in the sad1 mutant, suggesting that avenacins have a broader role than protecting from fungal pathogens. Profiling microbial communities with metatranscriptomics allows comparison of relative abundance, from multiple samples, across all domains of life, without PCR bias. This revealed profound differences in the rhizosphere microbiome particularly at the kingdom level between plants.	root:Environmental:Terrestrial:Soil:Agricultural
MGYS00000318	Neandertal bone Vi33.16 metagenome	The Neandertal genome was recently sequenced using DNA extracted from a 38,000-year-old fossil. At the start of the project, the fraction of mammalian and bacterial DNA in the sample was estimated to < 6% and 9%, respectively. Treatment with restriction enzymes prior to sequencing increased the relative proportion of mammalian DNA to 15%, but the large majority of sequences remain uncharacterized. PRINCIPAL FINDINGS: Our taxonomic profiling based on the analyses of 3.95 Gb of Neandertal DNA isolated from the Vindija Neandertal Vi33.16 fossil showed that 90% of about 50,000 rRNA sequence reads were of bacterial origin and that actinobacteria accounted more than 75% of the bacterial rRNA sequences. Likewise, actinobacteria represented more than 80% of the PCR-amplified 16S rRNA sequences from a cave sediment sample taken from the same G layer as the Neandertal bone. We assembled all 16S rRNA sequence read assigned to Streptomycetales, and analysed the patterns of nucleotide differences in the individual sequence reads compared to assembled consensus sequences. The typical ancient nucleotide substitution pattern with a majority of C to T changes indicative of DNA damage was observed for the Neandertal rRNA sequences, but not for the Streptomyces-like rRNA sequences. SIGNIFICANCE: Our analyses suggest that actinobacteria, and especially members of the Streptomycetales, contribute the majority of sequences in the DNA extracted from the Neandertal fossil Vi33.16. The bacterial DNA showed no signs of damage, and we hypothesize that it was derived from cave sediment bacteria that have been enriched inside the bone. The bioinformatic approach used here paves the way for future studies of microbial communities and patterns of DNA damage in bacteria from archaeological bones. Such studies can help identify targeted measures, such as selective degradation of bacterial DNA with particular base composition patterns, to increase the relative amount of ancient DNA in the sample.	root:Host-associated:Human
MGYS00000319	Shifts in Human Intestinal Microbiota after Smoking Cessation	The human intestinal microbiota is a crucial factor in the pathogenesis of various diseases, such as metabolic syndrome or inflammatory bowel disease (IBD). Yet, knowledge about the role of environmental factors such as smoking (which is known to influence theses aforementioned disease states) on the complex microbial composition is sparse. We aimed to investigate the role of smoking cessation on intestinal microbial composition in 10 healthy smoking subjects undergoing controlled smoking cessation. Methods: During the observational period of 9 weeks repetitive stool samples were collected. Based on abundance of 16S rRNA genes bacterial composition was analysed and compared to 10 control subjects (5 continuing smokers and 5 non-smokers) by means of Terminal Restriction Fragment Length Polymorphism analysis and high-throughput sequencing. Results: Profound shifts in the microbial composition after smoking cessation were observed with an increase of Firmicutes and Actinobacteria and a lower proportion of Bacteroidetes and Proteobacteria on the phylum level. In addition, after smoking cessation there was an increase in microbial diversity Conclusions: These results indicate that smoking is an environmental factor modulating the composition of human gut microbiota. The observed changes after smoking cessation revealed to be similar to the previously reported differences in obese compared to lean humans and mice respectively, suggesting a potential pathogenetic link between weight gain and smoking cessation. In addition they give rise to a potential association of smoking status and the course of IBD.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000320	Making and breaking DMS by salt marsh microbes (Illumina HiSeq 100bp)	Study of microbial populations that cycle the globally significant organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS) in coastal intertidal sediments.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00000321	Making and breaking DMS by salt marsh microbes (Illumina MiSeq 250bp)	Study of microbial populations that cycle the globally significant organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethylsulfide (DMS) in coastal intertidal sediments.	root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00000322	Gut metagenome in European women with normal, impaired and diabetic glucose control	Type 2 diabetes (T2D) is a result of complex gene-environment interactions, and several risk factors have been identified, including age, family history, diet, sedentary lifestyle and obesity. Statistical models that combine known risk factors for T2D can partly identify individuals at high risk of developing the disease. However, these studies have so far indicated that human genetics contributes little to the models, whereas socio-demographic and environmental factors have greater influence. Recent evidence suggests the importance of the gut microbiota as an environmental factor, and an altered gut microbiota has been linked to metabolic diseases including obesity, diabetes and cardiovascular disease. Here we use shotgun sequencing to characterize the faecal metagenome of 145 European women with normal, impaired or diabetic glucose control. We observe compositional and functional alterations in the metagenomes of women with T2D, and develop a mathematical model based on metagenomic profiles that identified T2D with high accuracy. We applied this model to women with impaired glucose tolerance, and show that it can identify women who have a diabetes-like metabolism. Furthermore, glucose control and medication were unlikely to have major confounding effects. We also applied our model to a recently described Chinese cohort and show that the discriminant metagenomic markers for T2D differ between the European and Chinese cohorts. Therefore, metagenomic predictive tools for T2D should be specific for the age and geographical location of the populations studied.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000323	Metagenomic study of the virome of African straw-colored fruit bats	Viral emergence as a result of zoonotic transmission constitutes a continuous public health threat. Emerging viruses such as SARS Coronavirus, Hantaviruses and Henipaviruses have a wildlife animal reservoir. Characterizing the viral flora of candidate reservoir species in geographical areas identified as hot spots for viral emergence is a sensible approach to develop tools to predict, prevent or contain emergence events. Here, we explored the viral flora of Eidolon helvum, an Old World fruit bat species widely distributed in Africa that lives in close proximity to humans. We identified a great abundance and diversity of novel herpes and papillomaviruses, described the isolation of a novel adenovirus, and detected, for the first time, sequences of a chiropteran poxvirus that are closely related to a human contagion. In sum, E. helvum display a wide variety of mammalian viruses, some of them genetically similar to known human pathogens, highlighting the possibility of zoonotic transmission.	root:Host-associated
MGYS00000324	A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities	The Baltic Sea is characterized by hyposaline surface waters, hypoxic and anoxic deep waters and sediments. These conditions, which in turn lead to a steep oxygen gradient, are particularly evident at Landsort Deep in the Baltic Proper. Given these substantial differences in environmental parameters at Landsort Deep, we performed a metagenomic census spanning surface to sediment to establish whether the microbial communities at this site are as stratified as the physical environment. We report strong stratification across a depth transect for both functional capacity and taxonomic affiliation, with functional capacity corresponding most closely to key environmental parameters of oxygen, salinity and temperature. We report similarities in functional capacity between the hypoxic community and hadal zone communities, underscoring the substantial degree of eutrophication in the Baltic Proper. Reconstruction of the nitrogen cycle at Landsort deep shows potential for syntrophy between archaeal ammonium oxidizers and bacterial denitrification at anoxic depths, while anaerobic ammonium oxidation genes are absent, despite substantial ammonium levels below the chemocline. Our census also reveals enrichment in genetic prerequisites for a copiotrophic lifestyle and resistance mechanisms reflecting adaptation to prevalent eutrophic conditions and the accumulation of environmental pollutants resulting from ongoing anthropogenic pressures in the Baltic Sea.	root:Environmental:Aquatic:Marine
MGYS00000325	Sand scarab gut transcriptome	We hypothesized that scarab insect guts function as miniature bioreactors and are, thus, a useful model to obtain fundamental insights into the digestion of complex plant material. More than 100 Gbp of RNA-Seq (Illumina HiSeq, paired-end, 100bp, 400bp insert) were generated.	root:Host-associated:Arthropoda:Digestive system:Gut
MGYS00000327	Microbial life in snake and spider venoms	Envenomation typically involves transdermal insertion of an appendage such as a tooth into prey and venom ejection through the appendage canal. Given the lack of sterility and infrequency of envenomation events in the wild, we hypothesise that the venom glands of animals such as snakes, spiders and scorpions might be niche environments for microorganisms such as bacteria and fungi acquired during envenomation. To explore this hypothesis we have generated 16S amplicon libraries from venoms and envenomation appendage swabs of various snakes, spiders and scorpions from captivity and the wild. We have also obtained two separate envenomation samples were possible, reasoning that the second might be a truer representative of the venom gland population as opposed to e.g. an oral cavity bacterial plug forming at the tip of the tooth between envenomation events. We wish to examine if the bacterial signatures detected differ between host species and sites of sampling.	root:Host-associated
MGYS00000328	Marine microbial indicators in coastal areas: a metagenomic approach	The present project proposes to conduct a thorough investigation of the heterotrophic bacterial communities of different sites of the Gulf of Naples, encompassing different ecological conditions, in order to find microbiological indicators of ecological status.	root:Environmental:Aquatic:Marine
MGYS00000329	Synthetic sequence dataset database metagenome	A metagenomic sequencer dataset built from database sequences to compare the accuracy and performance of various metagenomic sequence dataset analysis pipelines	root:Engineered:Modeled:Simulated communities (DNA mixture)
MGYS00000334	Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States	Although soil microbes play critical roles in terrestrial ecosystems, factors controlling spatial variability in the diversity and functional capabilities of these communities remain poorly understood. Particular knowledge gaps exist for biomes severely impacted by human activities, including the native tallgrass prairie that once covered >65 million ha of the midwestern United States, but has been nearly eradicated by decades of agricultural practices. Here we have reconstructed the microbial biodiversity that once sustained this highly productive ecosystem by analyzing soils from prairie relicts via shotgun metagenomics and targeted sequencing of the 16S rRNA gene. The taxonomic and functional diversity of the microbial communities were well-correlated, demonstrating that these communities are not functionally equivalent as has often been assumed - even small changes in belowground diversity can have important impacts on soil processes. As for many plant and animal communities, we could predict the structure and functional traits of the microbial communities from climatic conditions, allowing us to build predictive maps of soil biodiversity across the historical range of the tallgrass prairie ecosystem. The biogeographical patterns were largely driven by changes in the abundance of Verrucomicrobia, a poorly-studied bacterial phylum that dominated the prairie soils. The shotgun metagenomic data suggest that these spatial patterns were associated with shifts in soil carbon and nitrogen dynamics across the tallgrass prairie ecosystem. We show that we can use metagenomic data to reconstruct the belowground biogeochemical and diversity gradients that once existed, information that could be essential to guiding ongoing efforts to restore the threatened tallgrass prairie ecosystem.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000336	Richmond Mine AMD Biofilm Samples Metagenome	"Richmond Mine acid mine drainage biofilm samples datasets (2006-2010). This project describes a population genomic study focused on determining the evolutionary rates in natural populations, and to correlate human disturbance to major evolutionary divergence events. Biofilm samples from acid mine drainage were taken in the period 2006-2010 at four locations in the Richmond Mine (Iron Mt., CA). Community genomic DNA was extracted and sequenced by either 454 or Illumina sequencing.
"	root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
MGYS00000337	Comparative freshwater metagenomics of Swedish and American lakes	Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared to freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00000338	Metagenome of a microbial consortium obtained from the Tuna oil field in the Gippsland Basin, Australia	In 2011, fluid samples were collected from the A7A oil well in the Tuna oil field (38°10' S, 148°25' E) in the Gippsland Basin, Australia. Chemical analyses of the water revealed the sample was pH 7.2, had a salinity of 2.7%, and contained 270 mg liter–1 calcium, 320 mg liter–1 magnesium, 1,200 mg liter–1 sulfate, and 1,170 mg liter–1 bicarbonate. The temperature in the reservoir was 102°C. One liter of formation water was filtered through a 0.2-M Polyvinylidene difluoride (PVDF) filter disc and subjected to genomic DNA extraction using a Meta-G-Nome DNA isolation kit (Epicenter Biotechnologies). The resultant DNA was sequenced using 100-bp paired-end Illumina HiSeq at the University of Western Sydney.	root:Environmental:Aquatic:Marine:Oil field:bore hole
MGYS00000341	Comparative metagenomic analysis of soil microbial communities varying in disease suppression potential	Microbial communities from wheat rhizosphere samples were analysed through metagenomic sequencing of environmental DNA. Samples from sites varying disease suppression potential were analysed to identify differences in community metagenomic profiles.	root:Environmental
MGYS00000342	Unraveling the stratification of an iron-oxidizing microbial mat by metatranscriptomics	A metatranscriptomic approach was used to study community gene expression in a naturally occurring iron-rich microbial mat. Total microbial community RNA was reversely transcribed and sequenced by pyrosequencing. Characterization of expressed gene sequences provided accurate and detailed information of the composition of the transcriptionally active community and revealed phylogenetic and functional stratifications within the mat. Comparison of 16S rRNA reads and delineation of OTUs showed significantly lower values of metatranscriptomic-based richness and diversity in the upper parts of the mat than in the deeper regions. Taxonomic affiliation of rRNA sequences and mRNA genome recruitments indicated that iron-oxidizing bacteria dominated the community in the upper layers of the mat. Surprisingly, type I methanothrophs contributed to the majority of the sequences in the deep layers of the mat. Analysis of mRNA expression patterns showed that genes encoding the three subunits of the particulate methane monooxygenase (pmoCAB) were the most highly expressed in our dataset. These results provide strong hints that iron-oxidation and methane-oxidation occur simultaneously in microbial mats and that both groups of microorganisms are major players in the functioning of this ecosystem.	root:Environmental:Aquatic:Freshwater
MGYS00000346	Comparative phylogenetic analysis of microbial populations in the mammalian olfactory bulb and nasal cavity	We are examining the hypothesis that white matter microbia originate specifically from the nasal cavities of mammalian species. Perfused tissues from mice, rats and pathogen-free human volunteers are analysed for microbial DNA by 16S phylogenetics.	root:Host-associated:Amphibia
MGYS00000347	Artisanal cheese metagenome 3	Metagenome from artisanal cheeses from Tucuman	root:Engineered:Food production:Dairy products
MGYS00000348	Metagenomic approach to analyze rumen microbiome from Kankrej cows	Kankrej cows were fed with different diet and investigated rumen microbiome using shotgun sequencing on Ion-torrent platform	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000350	Diagnostic Metagenomics: A Culture-Independent Approach to the Investigation of Bacterial Infections	Design, Setting and Patients Forty-five samples were selected from a set of fecal specimens obtained from patients with diarrhea during the 2011 outbreak of STEC O104:H4 in Germany. Samples were chosen to represent STEC-positive patients with a range of clinical conditions and colony counts together with a small number of patients with other infections (Campylobacter jejnuni, Clostridium difficile and Salmonella enterica). Samples were subjected to high-throughput sequencing on the Illumina MiSeq and HiSeq 2500, followed by bioinformatics analysis.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000351	Gut microbiota in chronic kidney disease	gut microbiota in chronic kidney disease	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000352	Human gut microbiota associated to Clostridium difficile infection	We performed a follow-up study of the gut microbiota in patients treated with antibiotic therapy, whom developed Clostridium difficile infection as a consequence. We used the 16s rRNA and metagenomic approaches to gain insights in the effect of the pathogen infection in the structure and functions of the human gut microbiota.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000353	Danube river water sampling at 4 different sites	"Goal is to compare the metagenomes (composition and functional annotation) of the four different sites (clean, town, agricultural area and industrial area) in order to generate specific markers (genes, species ) characteristic for the three different ""pollution phenotypes"""	root:Environmental:Aquatic:Freshwater:Lotic
MGYS00000354	Meta-transcriptomic analysis of rumen microbiome of Mehsani buffalo	Mehsani buffaloes were fed with different proportion of roughages to concentrate ration and investigated for effects of different diet regimes on the meta-transcriptome profile of the rumen microbiome by shotgun sequencing	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000355	Southern Ocean Marine Metagenome	"Microbial communities from a marine environment.
Sequences deposited into the Sequence Read Archive can be found using the Project data link."	root:Environmental:Aquatic:Marine:Oceanic
MGYS00000356	Metagenomic sequencing of coprolites	No abstract provided. See http://rspb.royalsocietypublishing.org/content/279/1739/2825.full.pdf	root:Host-associated:Animal:Digestive system
MGYS00000357	Eukaryotic metatranscriptome from beech litter	Eukaryotic metatranscriptome extracted from Oe litter layer of beech forest Steigerwald.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000358	Coprolithes_Chauvet	No abstract provided. 	root:Host-associated:Animal:Digestive system
MGYS00000360	Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount, 2011-2012	This projects explores the functional diversity and activity of rocky subseafloor microbial communities in hydrothermal vent systems. Samples were collected in 2011 and 2012 from a number of low temperature diffuse fluid vents at Axial seamount, located in the northeast Pacific Ocean. Shotgun metagenomics and metatranscriptomics were performed on four diffuse vent samples.  Previous work at this site determined the taxonomic structure and distribution of microbial communities in venting fluids, but the contribution and mechanisms of the different redox driven metabolisms and the impact these reactions have on vent chemical signatures have not been fully characterized. This study helps to determine the genetic potential and expression patterns of the largely uncharacterized subseafloor microbial community and shows how these patterns change across the complicated biogeochemical gradients of hydrothermal vent systems. 	root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
MGYS00000361	Bacterial community composition of banded-winged whitefly	Facultative bacterial endosymbionts are common, influential associates of arthropods, yet their movement among host species has not been well documented. Plant-mediated transmission of Rickettsia was shown for the whitefly Bemisia tabaci. Bemisia tabaci in USA cotton fields harbors the secondary symbionts Rickettsia, and Hamiltonella, and co-occurs with Trialeurodes sp. nr. abutiloneus whiteflies. To determine whether symbionts may be shared, the microbial diversity of these whiteflies on cotton across the USA was analyzed. Trialeurodes sp. nr. abutiloneus bore Portiera, Pseudomonas, Serratia, Arsenophonus and Wolbachia. No Rickettsia or Hamiltonella were detected. These results provide no evidence for horizontal transmission of symbionts between these whitefly genera.	root:Host-associated:Insecta
MGYS00000362	Comprehensive characterization of plant cell wall degrading enzymes in Cerambycid beetles	Wood-boring beetles from the family Cerambycidae feed exclusively on woody tissues, and to efficiently access the nutrients present in this sub-optimal environment, they depend heavily on the secretion of a range of enzymes, known as plant cell wall degrading enzymes (PCWDEs), to efficiently digest both hemicellulose and cellulose networks.  Here we sequenced the larval gut transcriptome of the Mulberry longhorn beetle, Apriona japonica (Cerambycidae, Lamiinae), in order to investigate the arsenal of putative PCWDEs secreted by this species.  We combined our transcriptome with all available sequencing data derived from other cerambycid beetles in order to analyze and get insight into the evolutionary history of the corresponding gene families.  Finally, we heterologously expressed and functionally characterized the A. japonica PCWDEs we identified from the transcriptome.  Our analyses greatly contribute to a better understanding of the digestion physiology of this important group of insects, many of which are major pests of forestry worldwide.	root:Host-associated:Arthropoda:Digestive system:Gut
MGYS00000363	Soil metagenomes profiling for forensic purposes	Forensic soil analysis has the potential to play a crucial role in criminal investigations. This is particularly the case when a crime occurs outdoors such that soil is transferred to shoes, clothing, vehicles and tools. Owing to the large microbial diversity of soil, DNA profiling of soil microbial communities can serve as a powerful tool for forensic soil examination. This project uses metagenomic approaches to analyse the entire genetic composition of soil samples and use these sequence data for comparison purposes.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000364	Metagenome sequencing of biogas plant operating wet fermentation	Metagenome sequencing of biogas plant operating wet fermentation	root:Engineered:Biogas plant:Wet fermentation
MGYS00000365	Functional metagenomic profiling of Tibetan Plateau soils affected by permafrost or seasonal freezing	Approximately two thirds of the Tibetan Plateau is affected by permafrost and this area reacts particularly sensitively to possible effects of climate change. However, little is known about the functional potential of the microbial communities inhabiting this environment, which is of key importance to predict potential feedback effects, such as increased emissions of greenhouse gas. A metagenomic analysis was performed on soil profiles from two meadow sites on the Tibetan Plateau, either affected by permafrost (site Huashixia [HUA]) or seasonal freezing (Site Haibei Station [HAI]). The goal was to determine how respiratory and fermentative pathways varied with soil depth and across sites.	root:Environmental:Terrestrial:Soil
MGYS00000370	Interactions between anaerobic ammonium and sulfur-oxidizing bacteria in a laboratory scale model system	The recycling of fixed nitrogen from marine systems proceeds via two different nitrogen removal pathways, namely denitrification or anaerobic ammonium oxidation (anammox). Both processes require oxidized N (i.e. nitrate or nitrite) as electron acceptor to ultimately release dinitrogen gas (N2). For a supply with its substrates (ammonium and nitrite) anammox activity depends on the tight coupling with other nitrogen transformations.  The aerobic oxidation of ammonium is one of the routes that have been described recently as a source of nitrite. Another possibility is the linkage of the aforementioned N2-releasing processes, a scenario in which denitrification might be providing substrates for anammox. We were especially interested in coupling sulfide-dependent denitrification to anammox, as sulfide is, besides oxygen, the most important reductant at the chemocline of marine anoxic basins and also abundant within sediments. Although sulfide is toxic at ?M concentrations and has been shown to have a negative effect on anammox activity, we hypothesize that denitrification converts sulfide and nitrate, thereby allowing anammox to stay active despite an influx of sulfide and supply them with nitrite from partial denitrification.	root:Engineered:Bioreactor
MGYS00000371	Illumina and 454-based metatranscriptomic analyses of a diatom-induced bacterioplankton bloom in the North Sea	Planktonic bacteria from marine pelagic coastal zones are much more diverse than in the open ocean and consist of members with distinct ecological niches. In this study we investigated bacterioplankton communities that were sampled during a diatom-dominated spring phytoplankton bloom near the North Sea island Helgoland (about 40?km off the German coast). Sequencing of total community RNA allowed simultaneous detection of the community composition via 16S ribosomal RNA analyses, and the expressed functional genes via messenger RNA analyses. As most prominent community members, Flavobacteria (Ulvibacter, Formosa, Polaribacter), Alphaproteobacteria (SAR11 clade and Rhodobacteraceae) and Gammaproteobacteria (Reinekea spp. and SAR92 clade) could be identified down to genus level, which was confirmed by 16S rRNA gene amplicon ('pyrotag') sequencing of the same samples. These samples were also sequenced in a metagenome approach, assembled and taxonomically classified. Mapping of the transcripts on the metagenomes allowed investigation of the expression profiles of the prominent taxa. Members of the Flavobacteria, Alphaproteobacteria and Gammaproteobacteria exhibited distinct expression profiles of uptake transporters and carbohydrate-active enzymes, indicating a specialization on different nutrients. Members of the flavobacterial genera Formosa and Polaribacter acted as major polymer degraders, whereas members of the alphaproteobacterial Rhodobacteraceae and the gammaproteobacterial Reinekea exhibited a less specialized behavior, enabling them to rapidly adapt to changing nutrient conditions. Complementary sequencing effort using 454 pyrosequencing and Illumina enabled a comprehensive picture of the dominant metabolic processes down to genus level. This helped to identify the strategies of how members of the bacterioplankton evade extinction in a seemingly homogenous habitat.	root:Environmental:Aquatic:Marine
MGYS00000373	ASS lime injection - injection site	Due to very low inflows from the Murray-Darling Basin from 2007-2009, water levels in the Lower Murray River dropped to -1m AHD in April 2009. The low water levels and restricted water allocations during this hydrological drought period caused the acid sulfate soils subsequently acidified and salinized. Given the acidic drainage water presents a potential risk to the water quality and environmental values of the Lower River Murray, a subsoil neutralisation using a limestone slurry and a modified mole drain technique was applied. The aim of this trial is to examine whether the introduction of alkalinity (limestone) at depth in the oxidised and rewet acid sulfate soils, will sufficiently raise the pH to begin the process of sulfate reduction. It is hoped by promoting sulfate reduction, via sulfate reducing bacteria, the soils will begin to remediate, producing less acidic drainage to the salt drains in the irrigation areas.	root:Environmental:Terrestrial:Soil:Clay
MGYS00000374	Saline desert Metagenome	Saline desert Metagenome	root:Environmental:Terrestrial:Soil
MGYS00000375	Xenomicrobiota transplanted into germfree mice	Xenomicrobiota from a variety of different environments were transplanted into germfree mice. Assembly and composition of the gut-selected communities were analyzed by amplicon-sequencing. In a follow-up experiment, mice that harbored gut-selected communities were cohoused with each other.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000376	Vitamin Supplementation by Gut Symbionts Ensures Metabolic Homeostasis in an Insect Host	Many animals are dependent on intestinal microbes for nutrition. However, our understanding of how the host regulates its metabolism in response to beneficial symbionts remains limited. Here we elucidate the functional importance of the African cotton stainer?s (Dysdercus fasciatus) association with two actinobacterial gut symbionts and subsequently examine the insect?s transcriptional response following symbiont elimination. Genomic analyses and bioassays demonstrate the symbionts? contribution towards host fitness through the supplementation of B vitamins. Concordantly, comparative transcriptomic analyses reveal a differential up-regulation of genes involved in import and processing of B vitamins in aposymbiotic bugs; an expression pattern that is indicative of vitamin deficiency in animals. Normal expression levels of these genes, however, can be restored by either artificial supplementation of B vitamins into the insect?s diet or reinfection with actinobacterial symbionts. Furthermore, the functional characterization of the differentially expressed thiamine transporter 2 (THTR2) through heterologous expression in Xenopus laevis oocytes confirms its role in cellular uptake of vitamin B1. Taken together, our findings demonstrate that ? despite an extracellular localization ? beneficial gut microbes can be integral to an insect?s metabolic homeostasis, reminiscent of bacteriome-localized intracellular mutualists.	root:Host-associated:Arthropoda:Digestive system:Gut
MGYS00000380	Metagenome of grass carp intestinal contents and mucosa	Intestinal microbiota is a complex ecosystem and plays an important role in host biology. More and more researches focus on the bacterial community of the host intestine. However, there is still limited information on a better understanding of fish intestinal microbiota. Due to the importance of grass carp in aquaculture of China, it is necessary to pay attention to its intestinal microbiota. In this study, the composition of bacterial communities in intestinal contents and mucosa of grass carp was analyzed by 454 pyrosequencing.	root:Host-associated:Fish:Digestive system:Intestine
MGYS00000382	Amazon Continuum Metagenomes	This project focuses on the Amazon River-to-tropical Atlantic Ocean continuum because of both its immense scale and its apparent sensitivity to climate variability and anthropogenic forcing. The river's effect on the ocean depends not only on the river hydrology, but what the river carries and how those components are modified during transit from their terrestrial or aquatic origins. We brought together limnologists and oceanographers in an integrated project to improve our understanding of carbon exchange between the atmosphere and this tropical river continuum, focusing on the lower reach, nearshore, and offshore tropical Atlantic, with the goal of improving predictive capabilities under differing climate change scenarios.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00000387	Lime was injected to acid sulfate soils with aim to balance the acidity. The indigenous microbial communities before and after injection were investigated.	Due to very low inflows from the Murray-Darling Basin from 2007-2009, water levels in the Lower Murray River dropped to -1m AHD in April 2009. The low water levels and restricted water allocations during this hydrological drought period caused the acid sulfate soils subsequently acidified and salinized. Given the acidic drainage water presents a potential risk to the water quality and environmental values of the Lower River Murray, a subsoil neutralisation using a limestone slurry and a modified mole drain technique was applied. The aim of this trial is to examine whether the introduction of alkalinity (limestone) at depth in the oxidised and rewet acid sulfate soils, will sufficiently raise the pH to begin the process of sulfate reduction. It is hoped by promoting sulfate reduction, via sulfate reducing bacteria, the soils will begin to remediate, producing less acidic drainage to the salt drains in the irrigation areas.	root:Environmental:Terrestrial:Soil
MGYS00000388	Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India	There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics, and compared that to a Swedish lake receiving no input of wastewater from industrial or municipal sources.	root:Environmental:Aquatic:Freshwater:Lake
MGYS00000389	Stable isotope probing/metagenomics of terrestrial dimethylsulfide degrading microorganisms	Dimethylsulfide (DMS), a volatile sulfur compound, plays an important role in the global sulfur cycle and atmospheric chemistry. Microorganisms can use DMS as sole carbon, sulfur or energy source, contributing to the cycling of DMS in a wide variety of ecosystems. The diversity of microbial populations degrading DMS in terrestrial environments is poorly understood. Based on cultivation studies, it has been recognised that a wide range of bacteria isolated from terrestrial ecosystems are able to degrade DMS, yet it remains unknown whether any of these play important roles in situ. In this study we identified bacteria using DMS as a carbon and energy source in terrestrial environments, an agricultural soil and a lake sediment, by DNA stable isotope probing (SIP). Microbial communities involved in DMS degradation were analysed by high-throughput sequencing of SIP gradient fractions and metagenomic sequencing of phi29-amplified community DNA.	root:Environmental:Aquatic:Freshwater:Lentic:Sediment
MGYS00000391	Sydney Harbour metagenomes	Spatial taxonomic and functional diversity in the Sydney Harbour	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00000392	Acid sulfate soil microbial profile - pre-investigation	A pre-investigation of the microbial composition of the acid sulfate soils were carried in Oct 2011 to obtain the microbial information before lime injection	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000393	Southampton Asthma metagenomics	55 subjects underwent detailed clinical and immunological phenotyping,  sputum induction and bronchoscopy during periods of clinical stability. In  addition to 15 healthy controls, 9 mild, 16 moderate and 15 severe ashthmatics  (without bronchiectasis) were included. Protected bronchoalveolar lavage (BAL)  and induced symptoms were analysed by WGS for RNA and DNA from bacterial, viral  and fungal genomes. 88 samples were sequenced using 454 FLX Titanium. Single end  library. Data were provided as fasta files following adapter trimming	root:Host-associated:Human
MGYS00000394	Metagenome fecal microbiota, Illumina seq reads of 12 individuals at 2 timepoints	Two diets, Korean and Western diet. Each 6 individuals, half of which lost a lot of weight and half of which lost little weight. Fecal samples taken before and after diet (3 months).	root:Host-associated:Human:Digestive system
MGYS00000395	Photoheterotrophy in a mesoscale anticyclonic eddy in the Eastern Mediterranean Sea	Mesoscale eddies are semi-closed rotating water bodies with distinct physico-chemical properties and are a widespread phenomenon in the world's oceans. Previous studies found that eddies can affect phytoplankton and bacterioplankton community structure, primary productivity and nitrogen fixation. A considerable fraction of the marine bacterioplankton consists of photoheterhophs. These bacteria can use light to generate biochemical energy for transport and metabolic needs. Unlike photoautotrophs they depend on organic carbon for growth and biomass production. Photoheterotrophy can potentially enhance bacterial growth and/or survival in oligotrophic oceanic conditions. A common group of photoheterotrophs consists of proteorhodopsin (pr) bearing bacteria. The pr gene occurs in diverse microbial taxa including SAR11, a dominant Alphaproteobacteria clade. We hypothesize that anticyclonic eddies, which facilitate nutrient poor conditions by downwelling surface water, favor photoheterhophy. In November 2013 we conducted an oceanographic survey aboard R/V Mediterranean Explorer with the goal to assess the abundance, diversity and expression of photoheterophic genes in an anticyclonic eddy in the ultra-oligotrophic Eastern Mediterranean Sea. The results of this study will shed light on the potential role of physical and chemical gradients created by mesoscale eddies on changes in photoheterotrophic communities, which can have global effects on ocean biogeochemistry and energy flow.	root:Environmental:Aquatic:Marine:Oceanic:Photic zone
MGYS00000399	Transcriptomic analysis of microbial communities isolated from the rhizospheres of wheat, oat and pea, compared to unplanted soil	Rhizosphere microbes are key players in biogeochemical cycles and maintainance of plant health and productivity. Here we used metatranscriptomic analysis of rRNA depleted RNA from the rhizospheres of wheat, oat, pea, and unplanted soil to compare the metabolic functions of microbes in these environments. Using biological replication (n=5) we were able to give statisistical significance to the differences found. Microbes responsed to the rhizosphere environment by increasing metabolic activity in general, and particularly in metabolic pathways involved in sugar, organic acid and aromatics metabolism, oxidative stress, and motility. While general rhizosphere effects on the microbial communities were observed, many specific effects were plant species dependent.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000400	Transcriptome of Lecane inermis for phylogenomic studies of sppiralian relationships	Transcriptome data of Lecane inermis were used alongside other transcriptomic data of spiralian taxa to investigate spiralian relationships in a phylogenomic approach	root:Host-associated:Spiralia
MGYS00000401	Metagenomic sequencing of a Bison priscus bone sample from the Trois-Freres cave (Ariege, France)	The steppe bison (Bison priscus) is an extinct species that was widely distributed in Europe, Central Asia, Beringia and North America during the Pleistocene. It is known from abundant remains, including complete animals found in the permafrost, and from Palaeolithic rock-art pictures. However, the molecular information available for this species is limited to a fragment of the mitochondrial genome control region. In order to obtain a thorough genetic characterization of the steppe bison, we performed high-throughput shotgun sequencing of DNA extracted from a specimen of the Trois-Freres cave (Ariege, France). Analysis of several bone samples from the Salle du Grand Eboulis of this cave enabled identifying a rib from which bison DNA could be reproductively recovered and amplified by PCR. One DNA extract obtained from this rib was converted into an Illumina library, and about 1 billion DNA reads were analysed. Using these sequence data we reconstructed a complete mitochondrial genome of 16,318 bp with an average unique read depth of 10x	root:Host-associated:Animal
MGYS00000406	Metagenomic analysis of sediments along a uranium gradient	Surface sediment from a billabong in the Northern Territory of Australia was collected and spiked with uranyl sulfate at 6 different concentrations (0 - 4,000 mg/ kg). The sediments were then re-deployed at the site and left in these natural environmental conditions for 5 months. DNA was extracted from the sediments and submitted for metagenomic sequencing on the Illumina HiSeq 2500 instrument.	root:Environmental:Aquatic:Freshwater:Sediment
MGYS00000410	Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for  prokaryotes.	Seawater was filtered from different depths to retain small cell sizes (Bacteria Organisms). The DNA was extracted and submitted to high throughput sequencing.	root:Environmental:Aquatic:Marine
MGYS00000412	metagenomic analysis of human gut microbiome	metagenomic analysis of human gut microbiome	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000414	Analysis of sample SRA022105 from Southern Ocean Marine Metagenome ( J. Craig Venter Institute, submitted to NCBI on 28-JUL-2010)	The comparative study of metagenomes arising from oceanic surface waters has attracted great interest in the scientific community. Recent studies have shown the association of microbial communities to environmental factors such as temperature, salinity and latitude. This project's main objectives are: (i) to perform a comparative study between two metagenomes from different environments (cold and warm waters), in order to establish the influence caused by abiotic factors on microbial community present at the collection site, (II) assess the diversity present in each data set (III) Linking genomic each set containing the respective biological pathways, (iv) Undertake comparisons between different sets and identify their commonalities and their differences (V) Expand the information obtained in this study with the literature data. 	root:Environmental:Aquatic:Marine:Oceanic
MGYS00000415	Analysis of sample SRA022106 from Southern Ocean Marine Metagenome ( J. Craig Venter Institute, submitted to NCBI on 28-JUL-2010)	The comparative study of metagenomes arising from oceanic surface waters has attracted great interest in the scientific community. Recent studies have shown the association of microbial communities to environmental factors such as temperature, salinity and latitude. This project's main objectives are: (i) to perform a comparative study between two metagenomes from different environments (cold and warm waters), in order to establish the influence caused by abiotic factors on microbial community present at the collection site, (II) assess the diversity present in each data set (III) Linking genomic each set containing the respective biological pathways, (iv) Undertake comparisons between different sets and identify their commonalities and their differences (V) Expand the information obtained in this study with the literature data. 	root:Environmental:Aquatic:Marine:Oceanic
MGYS00000416	Analysis of sample GS112 take in the Indian Ocean	The comparative study of metagenomas arising from oceanic surface waters has attracted great interest in the scientific community. Recent studies have shown the association of microbial communities to environmental factors such as temperature, salinity and latitude.	root:Environmental:Aquatic:Marine:Oceanic
MGYS00000418	non corroding sheet piles in the soil.	We have investigated the community composition and their metabolic potential of samples from sheet piles in soil. Samples were taken from the soil and soil attached to the sheet piles. The sheet piles were not corroded and showed a mineral coating. The metagenomes were sequenced  by the  Illumina Miseq technique.	root:Environmental:Terrestrial:Soil
MGYS00000419	cattle and buffalo based on roughage based diet	Analysis of rumen microbiome from cattle and buffaloes which were fed with same roughage diet using metatranscriptomics approache	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000421	Sao Paulo Zoo Lake Study	Sao Paulo Zoo Lake Study	root:Environmental:Aquatic:Freshwater:Lake
MGYS00000422	Microbial diversity and isolation of novel hydrolases from the Kudu Rumen	Rumen of various angulates contain a variety of microbes that aid with the digestion of consumed plant material. These microbes have proved to be an important source of hydrolytic enzymes such as cellulases that are of immense importance in the emerging biofuels industry. This study seeks to understand the diversity and function of the Kudu rumen microflora and isolate its novel hydrolases.	root:Host-associated:Mammals
MGYS00000424	Metagenomic analysis of the Binga Hot Springs in Zimbabwe for Microbial Diversity and Hydrolytic Enzymes	Hot springs are an important source novel thermostable industrial enzymes. This study is seeks to use bioinformatics to analyze the metagenome derived from the Binga Hotsprings in Zimbabwe. The analysis will focus on microbial diversity  and function prediction of genes encoding Novel hydrolases of industrial importance	root:Environmental:Aquatic:Thermal springs
MGYS00000427	Gut and Oral Microbiome Dysbiosis in Rheumatoid Arthritis	Bacterial infection has long been implicated with rheumatoid arthritis (RA), but a systematic analysis of the probiotic and pathogenic microbiome in RA has been lacking. It is not clear whether and how the gut or oral microbial community is compositionally and functionally altered in RA, and whether and how the microbiota at different body sites overlap. Here we perform whole-genome shotgun sequencing for fecal, dental and salivary samples from a large cohort of RA patients, analyze metagenomic linkage groups to construct an RA classifier, and assemble a pathogen?s draft genome using SOAPMeta.	root:Host-associated:Human:Digestive system
MGYS00000429	Metagenomics of Spartina anglica phyllosphere	Spartina anglica phyllosphere was investigated using metagenomics and metaproteomics in order to investigate bacterial Dimethylsulphide degradation associated with Spartina anglica in more detail.  DNA from Spartina anglica phyllosphere was extracted and used for metagenomics using the Nextera XT Kit (Illumina). Sequencing was carried out on the Illumina MiSeq. (2 x 301 bp paired end reads)	root:Host-associated:Plants:Phylloplane
MGYS00000432	Evidence for salt tolerance in the human gut mobilome and potential mechanisms.	The human gut microbiome and its associated mobilome is critical to health and wellbeing. It hosts a complex ecosystem comprising a multitude of bacterial species, which contributes functionality that would otherwise be absent from the host. Transient and commensal bacteria in the gut must withstand many stresses. The influence of mobile genetic elements, such as plasmids, in stress adaptation within the ecosystem is relatively unknown. We found evidence for plasmid mediated osmotolerance as a phenotype amongst the Proteobacteria in healthy faecal slurries. A transconjugant carrying multiple plasmids acquired from healthy faecal slurry demonstrated increased osmotolerance in the presence of metal salts, particularly potassium chloride, which was not evident in the recipient. Sequencing and analysis of the total plasmid DNA demonstrated the presence of plasmid-borne osmotolerance systems (including KdpD and H-NS) which may be linked to the observed phenotype.  This is the first report of a transferable osmotolerance phenotype in gut commensals and may have implications for the transfer of osmotolerance in other niches.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000434	BASE - Biomes of Australian Soil Environments	The samples in this study were collected as part of the BASE (Biomes of Australian Soil Environments) project, which is developing a database of Australian soil microbial diversity. The soil ecosystem is critical for ecosystem functioning, affecting human health and food supply, animal and plant health, edaphic factors and climate. The Base project has sampled soils from across a wide range of ecosystem types on the Australian continent and collected both contextual and DNA based data that are publically available and form a base line database of Australian soil microbial biodiversity. More information about BASE can be found at http://www.bioplatforms.com.au/special-initiatives/environment/soil-biodiversity. Collected here is Illumina shotgun sequencing data from these soils.	root:Environmental:Terrestrial:Soil
MGYS00000436	Synthetic community metagenomes study	Sequencing was carried out using Illumina MiSeq 2 x250bp sequencing.	root:Engineered:Modeled
MGYS00000447	Metagenomic sequence data was obtained for multiple sites on three SE Queensland river estuaries looking at the ecological communities.	Metagenomic sequence data was obtained for multiple sites on three SE Queensland river estuaries (Logan, Maroochydoore and Noosa). The study is looking at the ecological communities in each of these systems, and how they are impacted by pollution and environmental conditions.	root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00000448	Elixir marine metagenomics pilot - towards user centric service	"Marine genomics and metagenomics (the study of genetic material recovered directly from marine environmental samples) are still in its infancy, but it is rapidly expanding. To prevent the large-scale implementation of such studies from being disruptive (where the data production is faster than the speed users are able to analyze and interpret it) there is an urgent need to establish dedicated data management e-infrastructure and bioinformatics pipelines specialized for marine research.  The EBI metagenomics portal has for the last year analyzed 3 trillion nucleotides and an increase of 98% over the previous year. To address some of these challenges the Norwegian node suggests establishing a pilot towards marine metagenomics together with EBI and potentially other collaboration partners as a start for marine services. While EBI has developed the EBI-metagenomics portal, a generic pipeline, which aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of the samples, the Norwegian node has developed Meta-pipe in the direction coupled with marine bioprospecting.  Both approaches have their own strengths and weakness, and while there is some overlap in the respective approaches, it is clear that the optimal solution for the community would be harmonization and interoperability between the analysis platforms.  The Norwegian node together with EBI and potentially other partners will harmonize existing pipelines and develop new or improve established components in the pipelines in order to establish long-term sustainable service platforms and not least to start building a ""user community"" for marine metagenomics analysis in ELIXIR"	root:Environmental:Aquatic:Marine
MGYS00000449	Eukaryotic mRNA from 1 year old litter in beech forest of the German Exploratories	Metatranscriptommic study of eukyryotic microbial activity in 1 year old litter in beech forest of the German Exploratories	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000450	Enriched Hetertrophic-Methantrophic Cultures from Different Soils (amplicon)	The project aimed to develop a robust consortia for oxidizing methane from possible emission sources e.g. coal mine and landfills. Different soil/sediments were collected and enriched under 20% methane atmosphere for more than 100 days and DNA were extracted for metagenomic studies. Methane oxidation potentials of each enrichments were analysed and byproducts were screened. Further testings were on-going using the enriched cultures for biofilter applications to treat continuous emissions of methane from point sources.	root:Environmental:Terrestrial:Soil
MGYS00000452	Metagenomics of a freshwater pond in Sheffield, UK.	The microbial community used in the microcosm study was obtained from this pond. The inoculums were subjected to nutrient enrichment studies.	root:Environmental:Aquatic:Freshwater:Lentic
MGYS00000453	Hydrocarbon Metagenomics Project	"Metagenomics for Greener Production and Extraction of Hydrocarbon Energy:
Creating Opportunities for Enhanced Recovery with Reduced Environmental Impact"	root:Environmental:Aquatic:Freshwater
MGYS00000454	Microbial biodiversity and structure in soil affects the composition of pyrrolizidine alkaloids in Jacobaea vulgaris	Secondary metabolites like pyrrolizidine alkaloids (PAs) act as defense compounds against aboveground and belowground attackers. We studied to get a better understanding of relevance of microbial diversity in the rhizosphere for plant growth and behavior, specifically related to secondary metabolites production. We made soil dilution to compare the composition of soil microbial communities of soil suspension, incubation and rhizosphere soil by 16s rRNA high throughput pyrosequencing, as a consequence, to determine the effects on plant behaviors. The dilution procedure leads to reduction of the diversity of bacteria at the phylum level. After regrown, the structure of microbial community in the rhizosphere changed significantly as compared to the composition in the incubated soil. Jacobeae vulgaris as model plants growing in the soil where microbial diversity were decreased, had a higher biomass and higher amount of free base form of PAs? production, which indicates the reduction of soil microbial community in the rhizosphere shows significant feedback. Our study adds evidence that soil microbes may play a role in the evolution of plant secondary metabolites in plants.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000455	Benchmark of metagenome analysis tools	"A set of complex, realistic data sets were simulated based on real Illumina HiSeq 2000 data (100 bp PE reads). Two ""conditions"" consisting of 3 replicates each were used to evaluate the performance of a number of metagenome analysis tools."	root:Engineered:Modeled:Simulated communities (sequence read mixture)
MGYS00000456	Comparison of distal gut microbiota structure and function in US and Egyptian children	Cultural traditions, diet, and lifestyles of ethnic groups living in different geographic locations can serve as a source of variability in human gut microbiota. To examine the differences in gut microbiome of geographically distinct populations, we have carried out phylogenetic, functional, and metabolite analyses of the distal gut microbiota of healthy adolescents from United States and Egypt using next generation high-throughput sequencing.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000464	Denovo test of eDNA sample	In this study we are going to establish the analyses of eDNA from sea water to identify macrofauna species from the North Sea.Instead of targeting single genes of taxa, we aim to sequence total DNA extracts. As a consequence, we expect to catch more diversity and to reduce the loss of information caused by unregularly binding of group specific primers.	root:Environmental:Aquatic:Marine
MGYS00000465	The fecal microbiome was studied in a group of IBD suffers and compared to a control group's fecal microbiome	Ten IBD and 10 healthy individual's fecal microbiomes were determined by NGS sequencing, to identify features that are unique to each group.  This was done using shot-gun metagenomics of DNA extracted from fecal samples and run on a HiSeq 2500.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000466	Metagenomic exploration of Lasundra hot spring	Geothermal areas are the main permanent hot places of the world, and these areas are the major habitats of thermophilic bacteria. In culture independent method, metagenome was isolated using manual and kit based methods. The short gun sequencing of metagenome was performed using Ion torrent PGM platform. The analysis of sequencing data revealed that this spring is dominated by bacterial taxa. MG-RAST based community analysis showed that bacteria were found in dominancy with 99.2% in domain hit distribution. Firmicutes were found to be dominant in domain hit classification followed by proteobacteria. Moreover, unclassified sequences also found in this metagenome indicate there are possibilities of getting novel organisms.	root:Environmental:Aquatic:Thermal springs
MGYS00000467	A human gut microbial gene catalog established by deep metagenomic sequencing (MetaHIT)	A human gut microbial gene catalog established by deep metagenomic sequencing	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000468	Reseq_Jan15 - Eukaryotic mRNA from 1 year old litter in beech forest of the German Exploratories	Reseq_Jan15 - Metatranscriptommic study of eukyryotic microbial activity in 1 year old litter in beech forest of the German Exploratories	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000470	Metagenomes of hydrogen producing, xylan fed termites	Metagenome study with samples from the guts of termites (Nasutitermes exitiosus sp). The termites had xylan as their only carbon source and were raised at temperatures of 33, 40 and 45 degrees respectively while producing highly concentrated hydrogen.	root:Host-associated:Arthropoda:Digestive system:Gut
MGYS00000476	Lacto broiler1d	To study the effect of feed additives on caecum microbiome	root:Host-associated:Birds:Digestive system:Ceca
MGYS00000477	Microbial life in geothermal and volcanic areas	Extreme environments, such as volcanic/geothermal areas, are sites of complex interactions between geosphere and biosphere. Although biotic and abiotic components are strictly related, they were separately studied for long time. , Nowadays, innovative and interdisciplinary approaches are available to explore microbial life thriving in these environments.  Pantelleria island (Italy) hosts a high enthalpy geothermal system characterized by high CH4 and low H2S fluxes. Two selected sites, FAV1 and FAV2, located at the main exhalative area of the island Favara Grande, show similar physical conditions with a surface temperature close to 60?C and a soil gas composition enriched in CH4, H2 and CO2. FAV1 soil is characterized by harsher conditions (pH 3.4 and 12% of H2O content); conversely, milder conditions were recorded at site FAV2 (pH 5.8 and 4% of H2O content). High methanotrophic activity (59.2 nmol g?1 h?1) and wide diversity of methanotrophic bacteria were preliminary  detected at FAV2, while no activity could  be detected at FAV1(1). Our aim was to investigate  how the soil microbial communities of these two close geothermal sites at Pantelleria respond to different geochemical conditions. Bacterial and Archaeal communities of the sites were investigated by MiSeq Illumina sequencing of hypervariable regions of the 16S rRNA gene. More than 33,000 reads were obtained for Bacteria and Archaea from soil samples of the two sites. At FAV1 99% of the bacterial sequences were assigned to four main phyla (Proteobacteria, Firmicutes, Actinobacteria and Chloroflexi). FAV2 sequences were distributed in the same phyla with the exception of Chloroflexi that were represented below 1%. Results indicate a high abundance of thermo-acidophilic chemolithotrophs in site FAV1 dominated by Acidithiobacillus ferrooxidans (25%), Nitrosococcus halophilus (10%), Alicyclobacillus spp. (7%) and the rare species Ktedonobacter racemifer (11%). The bacterial community at FAV2 soil is dominated by the methanotrophs (~40% of the reads) Methylocaldum gracile, Beijerinckia sp. and Methylobacterium sp.. The Archaea assemblages are similar in both sites and dominated by the moderately thermophilic chemolithotrophic ammonia-oxidating candidate species Nitrososphaera gargensis, in the phylum Thaumarchaeota. Volcanic/geothermal activities represent a complex phenomenon, thuis shapeing different and peculiar microbial niches even at adjacent sites. Lower pH, higher water, NH4+ and H2 content are probably the discriminating factors that prevent methanotrophy at FAV1 and favor chemolithotrophy. Site FAV2 hosts an extraordinary diversity of methanotrophs due to large supply of CH4, scarce presence of inhibitors of methanotrophy  (H2S and NH3) and slightly acidic soil pH. This study integrates geochemical and biological information to move a step ahead in the still scarce knowledge on the complex ecology of microbes living in geothermal sites and their interactions with the geosphere. (Oppure: This study integrates geochemical and biological information to move a step forward a more complete knowledge on the complex ecology of microbes living in geothermal sites and their interactions with the geosphere)	root:Environmental:Terrestrial:Volcanic
MGYS00000479	Synthetic community metagenomes	"Library methods comparison across illumina GAII, HiSeq, MiSeq using a synthetic community.
Four libraries methodology Nextera, NexteraXT, TruSeq, Low input have been used in this study"	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00000480	Understanding the carriage dynamics of nasopharyngeal microbiota in Malawian children and adults: a metagenomic analysis.	This study was part of a project investigating the nasopharyngeal carriage of streptococcus pneumoniae in Malawian children and adults by microarray. Because the nasopharynx is colonised by several other microorganisms, we decided to investigate whether pneumococcal carriage dynamics was associated with carriage of particular microbial species. We collected nasopharyngeal swabs from children (n=51) aged 0-15 years and adults (n=55), all carriers of Streptococcus pnumoniae. DNA was extracted directly from the samples, followed by a PCR amplification of the 16S rRNA gene. The 16S amplicons were sequenced by 454 pyrosequencing.	root:Host-associated:Human
MGYS00000482	Elixir marine metagenomics pilot - towards user centric service - Gut samples	"Marine genomics and metagenomics (the study of genetic material recovered directly from marine environmental samples) are still in its infancy, but it is rapidly expanding. To prevent the large-scale implementation of such studies from being disruptive (where the data production is faster than the speed users are able to analyze and interpret it) there is an urgent need to establish dedicated data management e-infrastructure and bioinformatics pipelines specialized for marine research. The EBI metagenomics portal has for the last year analyzed 3 trillion nucleotides and an increase of 98% over the previous year. To address some of these challenges the Norwegian node suggests establishing a pilot towards marine metagenomics together with EBI and potentially other collaboration partners as a start for marine services. While EBI has developed the EBI-metagenomics portal, a generic pipeline, which aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of the samples, the Norwegian node has developed Meta-pipe in the direction coupled with marine bioprospecting. Both approaches have their own strengths and weakness, and while there is some overlap in the respective approaches, it is clear that the optimal solution for the community would be harmonization and interoperability between the analysis platforms. The Norwegian node together with EBI and potentially other partners will harmonize existing pipelines and develop new or improve established components in the pipelines in order to establish long-term sustainable service platforms and not least to start building a ""user community"" for marine metagenomics analysis in ELIXIR"	root:Host-associated
MGYS00000484	Marine metagenomes from 3 sediment samples along a pH gradient in Papua New Guinea	Sediment microbial communities are key players in biogeochemical cycling and the remineralization of organic matter on tropical reefs. To better understand the long-term effects of low pH conditions on sediment microbial communities, microbial diversity and community composition were investigated at naturally CO2-rich tropical coral reefs in Papua New Guinea. Metagenomic and metatranscriptomic analyses will reveal insights into the response of sediment microbial communities and their functions to low pH environments.	root:Environmental:Aquatic:Marine:Sediment
MGYS00000486	Controlling enteric pathogens of poultry	There is rich genetic diversity in India?s native poultry breeds, and the hybrid exotic lines often used in Indian commercial production are distinct from the majority of poultry reared in the UK. The prevalence and dynamics of gastrointestinal infection at farm-level has a direct bearing on economic risk to individual farmers and contributes to overall global concerns of food security and food safety.Changes to diet, use of vaccines or antimicrobials, and flock-level interventions such as ?thinning?, can have profound effects on intestinal health and the evolution and spread of disease-causing microbes and may be amplified by genetic variation in host and microbe populations. Whilst major advances in genomics and genotyping of commercial poultry lines is facilitating the identification of loci linked to susceptibility or resistance, the impact of host and pathogen diversity on disease and production outcomes remains largely unexplored.	root:Host-associated:Birds:Digestive system:Ceca
MGYS00000488	metageomics 16S analysis	A metagenomics analysis and taxonomy 16S RNA	root:Environmental
MGYS00000494	Anopheles_Genome_Variation_Project	For information on this project, contributing investigators and studies, sample details, and data sharing policies please visit http://www.malariagen.net/node/287	root:Host-associated:Insecta
MGYS00000499	The comparison of gut microbiota obtained from centenarian, elderly, and adults living in southwestern longevity belt in Korea	Centenarians have lived for long ages and survived from various death causing factors. Several studies were analyzed the factors of health maintaining in centenarians, while the longevity factors are not completely understood. Recent analyses of gut microbiota have been reported the association of microbiota with health, and some studies were reported the alteration of gut microbiota with aging. In this study, we analyzed the gut microbiota of centenarians in particular regions of Korea to understand their longevity factors. The gut microbiota of centenarians (n=30) was compared with elderly (n=17) and adults (n=9) using pyrosequencing based on 16S rRNA gene. The relative abundance of Bacteroidetes was decreased, while those of Firmicutes and Proteobacteria were increased with aging. However, the proportion of Bacteroidetes was higher in centenarians than elderly subjects. The difference of gut microbiota composition between centenarians and elderly could be generated by diet patterns. Although additional studies such as functional analyses of microbiota between groups were need to understand, this study can provide the information of longevity factors of centenarians.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000500	Changes imposed by Clostridium difficile infection on the human gut microbiome	Clostridium difficile-associated diarrhoea (CDAD) is caused by C. difficile toxins A and B and represents a serious health problem.  In this study, we analyzed the metabolic changes associated to C. difficile infection in the human gut microbiota and its relation with the production or not of toxins A and B. In addition, we sequenced the amplicons of the 16SrDNA gene of the fecal samples to explore the effect of Clostridium difficile infection and toxin production on the intestinal microbial composition.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000502	Gut microbial succession follows acute secretory diarrhea in humans	Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hypotheses for how these communities respond to diarrheal disease and its treatment. Here, we report that after V. cholerae infection, human gut microbiota undergo an orderly and reproducible succession featuring transient reversals in relative levels of enteric Bacteroides and Prevotella. Elements of this succession may be a common feature in microbiota recovery from acute secretory diarrhea, as we observed similar successional dynamics after enterotoxigenic Escherichia coli  (ETEC) infection. Our metagenomic analyses suggest multiple mechanisms driving microbial succession after cholera, including bacterial dispersal properties, changing enteric oxygen and carbohydrate levels, and phage dynamics. Thus, gut microbiota recovery after cholera may be predictable at the level of community structure, but driven by a complex set of temporally varying ecological processes. Our findings suggest opportunities for diagnostics and therapies targeting the gut microbiota in humans recovering from infectious diarrhea.	root:Host-associated:Human:Digestive system
MGYS00000503	Axial Seamount Marker 113 RNA-SIP metatranscriptomes from 2013	Hydrothermal vent systems provide access points to the extensive microbial communities of the rocky subseafloor. These subseafloor communities have the potential to influence ocean biogeochemistry and, in particular, the chemolithoautotrophic populations could potentially provide a large amount of new production to the deep sea. In this study, we used RNA-based stable isotope probing (RNA-SIP) metatranscriptomics to identify the active autotrophic players and genomic pathways present in venting fluids from Axial Seamount, a submarine volcano off the coast of Oregon, USA. Vent fluids for RNA-SIP were collected from a singular vent, Marker 113, and used in shipboard incubations with 13C labeled sodium bicarbonate at 30, 55, and 80?C. Results from RNA-SIP incubations show enrichment of RNA at all three temperatures after 18-36 hours, indicating the presence and activity of subseafloor chemolithoautotrophic microbes in vent fluids. In RNA-SIP experiments across a range of temperatures, both taxonomic and functional diversity was reduced compared to un-manipulated diffuse fluids. At 30?C and 55?C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55?C, and were the only autotrophs present at 80?C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive TCA cycle to the reductive acetyl-CoA pathway with increasing temperature. This study demonstrates the presence of an active autotrophic subseafloor community across geothermal gradients, lending insight into chemolithoautotrophic communities in the subseafloor at deep-sea hydrothermal vents	root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00000504	Metagenome analysis of Amlakhadi canal	Gauging the innate microbial community prevailing in Amlakhadi Canal, Ankleshwar	root:Environmental:Aquatic:Freshwater
MGYS00000505	Defining the core Arabidopsis thaliana root microbiome	Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota  colonizing the rhizosphere (immediately surrounding the root), and the endophytic compartment (within the root), contribute to plant growth, productivity, carbon sequestration, and phytoremediation1,2,3. Colonization of the root occurs despite a sophisticated plant immune system4,5, suggesting finely-tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. We pyrosequenced the bacterial 16S rRNA gene of >600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophyte compartment microbiota of plants grown under controlled conditions in natural soils are (i) sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and (ii) sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils, and in rhizosphere and endophyte compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophyte compartments from either soil feature overlapping low-complexity communities that are markedly enriched for Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stages and genotypes. Our work provides unprecedented rigor to define an endophyte compartment microbiome, facilitating controlled dissection of plant-microbe interactions derived from complex soil communities.	root:Host-associated:Plants
MGYS00000506	Pooled sample of human tongue scrapes from 9 healthy adults.	Human tongue scrapes were taken from 9 healthy adults at University College London, metagenomic DNA extracted and sequenced using 454 technology.	root:Host-associated:Human:Digestive system:Oral:tongue dorsum
MGYS00000507	Tongue metagenome from 9 healthy individuals.	Tongue scrapes were collected from 9 healthy individuals over a period of 3 or 4 weeks, total DNA was extracted, pooled and sequenced.	root:Host-associated:Human:Digestive system:Oral
MGYS00000508	Drain metagenome.	Hair blocking drain was removed from a bathroom shower cubicle. Liquid surrounding the hair and hair were used for the total dna extraction.	root:Environmental:Aquatic:Freshwater:Storm water:Drainage pipe biofilm
MGYS00000509	Soil sample taken from wild flower meadow for metagenome study.	Soil sample taken from wild flower meadow in Danesbury Park, Hertfordshire.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000510	Study of the bacterial and fungal diversity in soil habitats with increased ligninocellulolytic activity	This study aims at the metagenomic analysis of ligninocellulose-degrading microbial communities of Mediterranean forest soils. For this purpose, two soil ecosystems with distinct ecophysiological characteristics were selected, and thorough spatio-seasonal sampling was undertaken. Total DNA was extracted from 48 soil samples, and PCR amplification was performed with both 16S (V3-V4) region- and ITS2-specific universal primers for the analysis of bacterial and fungal diversity, respectively. High-throughput amplicon sequencing was performed with the Illumina MiSeq technology.	root:Environmental:Terrestrial:Soil:Forest soil
MGYS00000511	Coupled metagenomic and metatransciptomic study of the Columbia River coastal margin salinity gradient	Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel shift in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 ?m filters and collected on 0.2 ?m filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, were an average of only 31% similar. We observed shifts from river to ocean in the abundance of genes encoding specific functions, such as catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were highly abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community shifted strongly with salinity, 2) metabolic potential was highly similar across samples, with only small differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.	root:Environmental:Aquatic:Marine:Coastal
MGYS00000512	Rumen Virome metagenome sequencing	The present study was carried out to explore the ruminal viruses and phages from buffalo	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000513	Use of plant growth promoting rhizobacteria on the production of lettuce	Analysis of the effect of different plant growth promoting rhizobacteria on the production of lettuce plants.	root:Host-associated:Plants:Rhizosphere:Soil
MGYS00000514	Metagenomic approach to Analyze Rumen Microbiome from Gir Cows	Gir cows were fed with different diet and investigated rumen microbiome using shotgun sequencing on Ion-torrent platform	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000515	Metagenomic profiling through 16S rRNA deep sequencing of mice strains	Comparative analysis of microbiomes from stools obtained from WT and genetically engineered mice, subjected to normal or high-fat content diet	root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
MGYS00000516	The role of biogeography in shaping diversity of the intestinal microbiota in house mice	The microbial communities inhabiting the mammalian intestinal tract play an important role in diverse aspects of host biology. However, little is known regarding the forces shaping variation in these communities and their influence on host fitness. To shed light on the contributions of host genetics, transmission and geography to diversity in microbial communities between individuals, we performed a survey of intestinal microbial communities in a panel of 121 house mice derived from eight locations across western Europe using pyrosequencing of the bacterial 16S rRNA gene. The host factors studied included population structure estimated by microsatellite loci and mitochondrial DNA, genetic distance and geography. To determine whether host tissue (mucosa)-associated communities display properties distinct from those of the lumen, both the cecal mucosa and contents were examined. We identified Bacteroides, Robinsoniella and Helicobacter as the most abundant genera in both the cecal content and mucosa-associated communities of wild house mice. Overall we found geography to be the most significant factor explaining patterns of diversity in the intestinal microbiota, with a comparatively weaker influence of host population structure and genetic distance. Furthermore, the influence of host genetic distance was limited to the mucosa communities, consistent with this environment being more intimately coupled to the host.	root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
MGYS00000517	Gene-targeted metagenomic analysis of 1-4-?-glucan branching enzyme gene profiles among human and animal fecal microbiota	Organismal and functional aspects of the gut microbiota are of great interest in human microbiome studies. Although 16S rRNA gene sequence-based phylogenetic and whole-genome shotgun (WGS) data analysis are frequently used for assessment of genetic diversity, these techniques pose biological challenges for in-depth understanding of metabolic genes related to the gut microbiota. Phylogenetic analyses of 16S rRNA gene sequences provide limited information on their involvement in metabolic pathways. WGS data provide useful information on metabolic functions; however, this technique generates a large amount of data unrelated to the gene of interest at a high cost. In this study, we employed a metagenomic approach targeting the 1-4-?-glucan branching enzyme (gBE) gene of four host species (chicken, cow, pig, and human). Glycoside hydrolases (GHs) are key enzymes associated with the gut microbiota and its metabolic functions. The gBE gene, belonging to GH family 13, is responsible for glycogen branching and determines its solubility and subsequent catabolic metabolism. In addition to 16S rRNA gene-based phylogenetic analyses, an average of 1,200 reads of gBE were generated from fecal microbiota samples from human (n = 16), chicken (n = 18), cow (n = 15) and pig (n = 20). Each of the hosts showed distinct 16S rRNA and gBE sequence profiles. Human and pig exhibited both unique and common characteristics of operational taxonomic units (OTUs) and gBE profiles. Interestingly, the OTUs identified from the 16S rRNA and gBE gene sequences differed among the host species, suggesting the presence of different gBE genes in the same OTU in 16S rRNA sequences of different vertebrate hosts. Our data suggest that gene-targeted metagenomic analysis is useful for an in-depth understanding of the diversity of a particular gene of interest. Moreover, specific OTUs in the gut may contain metabolic genes the characteristics of which differ according to host genetic background and/or diet.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000518	These samples are selections from a larger cohort that were selected for the participation in the EBI metagenomics training in Sept. 2015	These samples are selections from a larger cohort that were selected for the participation in the EBI metagenomics training in Sept. 2015	root:Host-associated:Human:Skin
MGYS00000519	Study of microbial consortia of withered berries of cv. Corvina using whole metagenome sequencing approach	A whole metagenome sequencing approach was carried out, aiming at the taxonomic identification of the microbial components of berry ecosystem and to unveil whether the variations of environmental withering conditions could lead to significant modifications of microbial consortia and metabolic pathways on grape berries.	root:Host-associated:Plants
MGYS00000521	The Effect of Propidium Monoazide Treatment on Identification of Bacterial Communities of Very Low Birth Weight Preterm Infant Faeces Analysed by 16s rRNA Gene Sequencing	Next-gen sequencing technology had provided a platform for rapid advancement in the field of microbial ecology. The 11 original bacterial phyla, identified by Woese, have been expanded to over 50 following widespread use of NGS techniques. However, NGS is not without it?s flaws. This study will attempt to improve the validity of the NGS protocol by validating the use of propidium monoazide: a dsDNA chelating agent; for non-viable cell exclusion from clinical samples. This will enable researchers and clinicians to identify bacterial phyla actively affecting the biotopes of the preterm infant gut and tailor targeted therapy accordingly.	root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00000523	Metagenomics of TB-associated sputum	Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instru- ment, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110) and single nucleotide polymorphisms (SNPs), we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of ?modern? M. tuberculosis strains. We have provided proof of principle that shotgun metagenomics can be used to detect and characterise M. tuberculosis sequences from sputum samples without culture or target-specific amplification or capture, using an accessible benchtop-sequencing platform, the Illumina MiSeq, and relatively simple DNA extraction, sequencing and bioinformatics protocols. In our hands, sputum metagenomics does not yet deliver sufficient depth of coverage to allow sequence- based sensitivity testing; it remains to be determined whether improvements in DNA extraction protocols alone can deliver this or whether culture, capture or amplifica- tion steps will be required. Nonetheless, we can foresee a tipping point when a unified automated metagenomics-based workflow might start to compete with the plethora of methods currently in use in the diagnostic microbiology laboratory.	root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
MGYS00000525	Influence of soil properties on Archaeal diversity and distribution in the McMurdo Dry Valleys, Antarctica	Archaea are the least studied members of the microbial community in Antarctic soils. Their occurrence in coastal mineral soils has been documented, however, less is known about their distribution in soils across the McMurdo Dry Valleys, Victoria Land. In this study, terminal-restriction fragment length polymorphism (T?RFLP) analysis and 454 pyrosequencing were coupled with a detailed analysis of physicochemical properties to characterize archaeal diversity and identify the environmental factors that might shape and maintain these archaeal communities in soils of the three most southern McMurdo Dry Valleys (Garwood, Marshall, Miers). Archaea were present, although at a low diversity (< 6 operational taxonomic units (OTUs) per sample site) in all mineral soils tested. In total, eighteen archaeal OTUs were detected which showed a predominance of Crenarchaeota belonging to Marine Group 1.1b (>?80% of all archaeal sequences recovered). Less abundant OTUs (2% of all archaeal sequences) were restricted to glacial moraines, including three OTUs (<?0.02% of all archaeal sequences) closely related to members of the phylum Euryarchaeota. Multivariate statistical analysis, ordination of T?RFLP and physicochemical data indicated that differences in moisture, carbon and nitrogen content in the soils have the greatest influence on archaeal community structure. This is the first comprehensive study showing a widespread distribution of Archaea in soils of the McMurdo Dry Valleys and verifies the worldwide distribution of Marine Group 1.1b Crenarchaeota.	root:Environmental:Terrestrial:Soil:Wetlands:Permafrost
MGYS00000528	Soil metagenome.	SoilB soil sample was collected on a rough grass terrain with the trees nearby in Danesbury Park in Hertforshire, UK.	root:Environmental:Terrestrial:Soil:Grasslands
MGYS00000529	Permafrost 454 amplicons	Study of microbial communities in permafrost, active layer and thermokarst bog in Alaska	root:Environmental:Terrestrial:Soil:Permafrost
MGYS00000531	different diet treatments	Mice of 2 genotypes followed 2 different diets.	root:Host-associated:Mammals:Digestive system:Fecal
MGYS00000532	Does dietary mitigation of enteric methane production affect rumen function and animal productivity in dairy cows?	It has been suggested that the rumen microbiome and rumen function might be disrupted if methane production in the rumen is decreased. Furthermore concerns have been voiced that geography and management might influence the underlying microbial population and hence the response of the rumen to mitigation strategies. Here we report the effect of the dietary additives: linseed oil and nitrate on methane emissions, rumen fermentation, and the rumen microbiome in two experiments from New Zealand (Dairy 1) and the UK (Dairy 2). Dairy 1 was a randomized block design with 18 multiparous lactating cows. Dairy 2 was a complete replicated 3 x 3 Latin Square using 6 rumen cannulated, lactating dairy cows. Treatments consisted of a control total mixed ration (TMR), supplementation with linseed oil (4% of feed DM) and supplementation with nitrate (2% of feed DM) in both experiments. Methane emissions were measured in open circuit respiration chambers and rumen samples were analyzed for rumen fermentation parameters and microbial population structure using qPCR and next generation sequencing (NGS). Supplementation with nitrate, but not linseed oil, decreased methane yield (g/kg DMI; P<0.02) and increased hydrogen (P<0.03) emissions in both experiments. Furthermore, the effect of nitrate on gaseous emissions was accompanied by an increased rumen acetate to propionate ratio and consistent changes in the rumen microbial populations including a decreased abundance of the main genus Prevotella and a decrease in archaeal mcrA (log10 copies/ g rumen DM content). These results demonstrate that methane emissions can be significantly decreased with nitrate supplementation with only minor, but consistent, effects on the rumen microbial population and its function, with no evidence that the response to dietary additives differed due to geography and different underlying microbial populations.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000533	Trans-kingdom control of microbiota diurnal oscillations promotes metabolic homeostasis	All domains of life feature diverse molecular clock machineries that synchronize physiological processes to diurnal environmental fluctuations. However, no mechanisms are known to cross-regulate prokaryotic and eukaryotic circadian rhythms in multi-kingdom ecosystems. Here, we show that the intestinal microbiota, in both mice and humans, exhibits diurnal oscillations that are influenced by feeding rhythms, leading to time-specific compositional and functional profiles over the course of a day. Ablation of host molecular clock components or induction of jet lag leads to aberrant microbiota diurnal fluctuations and dysbiosis, driven by impaired feeding rhythmicity. Consequently, jet lag-induced dysbiosis in both mice and humans promotes glucose intolerance and obesity that are transferrable to germ-free mice upon fecal transplantation. Together, these findings provide the first evidence of coordinated meta-organism diurnal rhythmicity, and offer a microbiome-dependent mechanism for common metabolic disturbances in humans with aberrant circadian rhythms, such as those documented in shift workers and frequent flyers.	root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
MGYS00000535	Study on the microbial community of a bioleaching column test	Study on the microbial community related to de bioleaching processes of copper sulfide ore.	root:Engineered:Biotransformation
MGYS00000536	The 2014 and 2015 International Geobiology Courses took place at Little Hot Creek (LHC), California. The data shown here represents an attempt to gather information from a number of sources at LHC.	Samples were collected from a series of hot springs at the headwaters of Little Hot Creek located in the Long Valley Caldera near Mammoth Lake, CA. The springs are supersaturated for carbonate, circumneutral in pH, and range from a temperature of 50? to 80? C. Genomic DNA was isolated from biofilms and water filtered through a PES 0.22?m 13mm filter using the Zymo Xpedition Soil/Fecal kit (Zymo Research Corp., Irvine, CA). Sequencing was conducted using either MiSeq PE250, PE300, or HiSeq Rapid PE250. MiSeq runs were prepared using the Agilent SureSelect kit (Agilent Technologies, Irvine, CA) with an approximate insert size of 400bp, and HiSeq PE250 samples were prepared using the Nextera XT library preparation kit (Illumina, San Diego, CA).	root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
MGYS00000537	In this study we describe some of the challenges of clinical metagenomics through benchtop sequencing of two distinct sample types, designed to highlight current application and opportunities in this field.	Availability of fast, high throughput and low cost whole genome sequencing (WGS) holds great promise within public health microbiology, with applications ranging from outbreak detection and tracking transmission events, to understanding the role played by microbial communities in health and disease. Within clinical metagenomics, identifying microorganisms from a complex and host enriched background remains a central computational challenge. In this study we sequenced two metagenomic samples, a known viral mixture of 25 human pathogens and an unknown complex biological mode using benchtop technology, highlighting the current challenges  and opportunities in this field.	root:Engineered:Modeled:Simulated communities (microbial mixture)
MGYS00000538	Analysis of the goat rumen microbial community following inhibition of methane formation by bromochloromethane (a halogenated methane analogue)	Japanese goats fed a diet of 50% Timothy grass and 50% concentrate with increasing levels of the anti-methanogenic compound, bromochloromethane (BCM) were investigated with respect to the microbial population shifts in the rumen. Microbial ecology methods identified species that exhibited positive and negative responses to the increasing levels of BCM. The methane-inhibited rumen appeared to adapt to the higher H2 levels by shifting fermentation to propionate which was mediated by an increase in the population of hydrogen-consuming Prevotella and Selenomonas spp.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000539	Diesel contamination of Antarctic soils and sediments	Hydrocarbon contamination is a threat resulting from human activity in Antarctica because of the low degradation rate due to the cold climate conditions and the seasonal freezing and thawing of soil in summer ice-free areas like the Antarctic Peninsula. Hydrocarbons can accidentally reach soil and sediments and distribute underground, likely affecting the biota and causing changes in bacterial communities. Monitoring and study of the distribution of hydrocarbons and the consequent response of the microbiota helps in the design of bioremediation strategies and elaboration of contingency plans, both required by the Antarcic Treaty.	root:Environmental:Terrestrial:Soil:Contaminated
MGYS00000540	The RNA metagenomes of Argentine ants (Linepithema humile) collected in New Zealand.	Argentine ants were collected from two nests located in Wellington, New Zealand. RNA was extracted from a pool of 30 ants collected from each of these nests. All RNA was then combined and subjected to de novo metagenomic analysis, using an Illumina MiSeq instrument. Multiple displacement amplification was used to increase the yield of transcribed DNA to meet the minimum input requirements of the Illumina MiSeq. The Illumina TruSeq DNA library preparation was used to prepare libraries, and produce 250 bp paired end reads.	root:Host-associated:Arthropoda
MGYS00000542	Assimilation of C by microbial populations in glacial forefields	Microbial communities and soil carbon (C) have been shown to vary in response to increasing vegetation cover during soil development after deglaciation. However, little is known about the ability of microorganisms to utilize various C sources in glacier forefield soils. We supplied ecologically relevant 13C-labelled C sources (Chlorella, Penicillium and Festuca) to three distinct environments (supraglacial sediments, barren soils and vegetated soils) of the Damma glacier area to monitor 13CO2 production. We identified prokaryotic and fungal populations able to utilize these sources by using DNA-stable isotope probing coupled with Illumina MiSeq sequencing of ribosomal markers. A high initial 13CO2 pulse indicated that 13C-labelled microbial and plant material were consumed. The 13C-enriched DNA results indicated that betaproteobacterial taxa affiliated to the families Oxalobacteraceae and Comamonadaceae were important players in C utilization from different sources and present in all environments. In contrast, different fungal taxa played different roles in C degradation depending on the soil environment. Overall, our findings reveal that C utilization  is driven by similar prokaryotic populations along a glacier forefield, while the distribution of active fungal populations are more influenced by environmental factors.	root:Environmental:Terrestrial:Soil
MGYS00000544	Does dietary mitigation of enteric methane production affect rumen function and animal productivity in dairy cows?	It has been suggested that the rumen microbiome and rumen function might be disrupted if methane production in the rumen is decreased. Furthermore concerns have been voiced that geography and management might influence the underlying microbial population and hence the response of the rumen to mitigation strategies. Here we report the effect of the dietary additives: linseed oil and nitrate on methane emissions, rumen fermentation, and the rumen microbiome in two experiments from New Zealand (Dairy 1) and the UK (Dairy 2). Dairy 1 was a randomized block design with 18 multiparous lactating cows. Dairy 2 was a complete replicated 3 x 3 Latin Square using 6 rumen cannulated, lactating dairy cows. Treatments consisted of a control total mixed ration (TMR), supplementation with linseed oil (4% of feed DM) and supplementation with nitrate (2% of feed DM) in both experiments. Methane emissions were measured in open circuit respiration chambers and rumen samples were analyzed for rumen fermentation parameters and microbial population structure using qPCR and next generation sequencing (NGS). Supplementation with nitrate, but not linseed oil, decreased methane yield (g/kg DMI; P<0.02) and increased hydrogen (P<0.03) emissions in both experiments. Furthermore, the effect of nitrate on gaseous emissions was accompanied by an increased rumen acetate to propionate ratio and consistent changes in the rumen microbial populations including a decreased abundance of the main genus Prevotella and a decrease in archaeal mcrA (log10 copies/ g rumen DM content). These results demonstrate that methane emissions can be significantly decreased with nitrate supplementation with only minor, but consistent, effects on the rumen microbial population and its function, with no evidence that the response to dietary additives differed due to geography and different underlying microbial populations.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000566	Effect and mode of action of chitosan and ivy fruit saponins on the microbiota, fermentation and methanogenesis in the rumen simulation technique	Manipulation of the rumen microbial ecosystem to increase the efficiency of nutrient use by the animal, or to decrease its environmental impact, has long been a goal for nutritionists and gut microbiologist. This paper investigates the effect and mode of action of chitosan (CHI) and ivy fruit saponins (IVY) when used as novel feed additives for ruminants. These compounds were supplemented at 5% inclusion rate into a control diet (CON) in a rumen simulation technique. Both, CHI and IVY had a strong and similar ability to decrease methane emissions in comparison to CON (-42% and -40%, respectively). The mode of action of these feed avidities was however remarkably different: CHI promoted a shift in the fermentation pattern towards more energetically favourable pathways (propionate) which explained about two thirds of the decrease in rumen methanogenesis. This shift was achieved by a simplification and modification of the structure in the bacterial community consisting on an increment of Bacteroidetes and Proteobacteria in detriment of Firmicutes and Fibrobacteres. This substitution of fibrolytic bacteria by amylolitic bacteria induced by CHI resulted on a 2.5-fold increase in the amylase enzymatic activity, lactate concentration (+53%) and microbial protein yield (+14%) with no detrimental effect on feed digestibility. Additionally, CHI decreased the relative abundance of methanogens respect to total bacteria which could also contribute to lower rumen methanogenesis. On the contrary, IVY promoted only minor changes on the fermentation pattern and on the structure of the bacterial community which explained only one third of the observed decrease in rumen methanogenesis. Instead, IVY had a specific effect on the methanogens population. This effect consisted on a change in the structure of the methanogens community and a decrease in its diversity. This specific effect, together with the anti-protozoal activity, can be thus considered the main anti-methanogenic property for IVY. Moreover IVY showed to have some beneficial effect to buffer the post-prandial drop in rumen pH and to decrease rumen ammonia levels (-61%), but its anti-microbial properties had a negative impact on microbial protein synthesis (-10%). Therefore, both CHI and IVY should be further investigated in vivo in order to determine the optimum doses which maintain low rumen methanogenesis but prevent negative effects on the rumen microbial ecosystem.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000567	Effect and mode of action of chitosan and ivy fruit saponins on the microbiota, fermentation and methanogenesis in the rumen simulation technique	Manipulation of the rumen microbial ecosystem to increase the efficiency of nutrient use by the animal, or to decrease its environmental impact, has long been a goal for nutritionists and gut microbiologist. This paper investigates the effect and mode of action of chitosan (CHI) and ivy fruit saponins (IVY) when used as novel feed additives for ruminants. These compounds were supplemented at 5% inclusion rate into a control diet (CON) in a rumen simulation technique. Both, CHI and IVY had a strong and similar ability to decrease methane emissions in comparison to CON (-42% and -40%, respectively). The mode of action of these feed avidities was however remarkably different: CHI promoted a shift in the fermentation pattern towards more energetically favourable pathways (propionate) which explained about two thirds of the decrease in rumen methanogenesis. This shift was achieved by a simplification and modification of the structure in the bacterial community consisting on an increment of Bacteroidetes and Proteobacteria in detriment of Firmicutes and Fibrobacteres. This substitution of fibrolytic bacteria by amylolitic bacteria induced by CHI resulted on a 2.5-fold increase in the amylase enzymatic activity, lactate concentration (+53%) and microbial protein yield (+14%) with no detrimental effect on feed digestibility. Additionally, CHI decreased the relative abundance of methanogens respect to total bacteria which could also contribute to lower rumen methanogenesis. On the contrary, IVY promoted only minor changes on the fermentation pattern and on the structure of the bacterial community which explained only one third of the observed decrease in rumen methanogenesis. Instead, IVY had a specific effect on the methanogens population. This effect consisted on a change in the structure of the methanogens community and a decrease in its diversity. This specific effect, together with the anti-protozoal activity, can be thus considered the main anti-methanogenic property for IVY. Moreover IVY showed to have some beneficial effect to buffer the post-prandial drop in rumen pH and to decrease rumen ammonia levels (-61%), but its anti-microbial properties had a negative impact on microbial protein synthesis (-10%). Therefore, both CHI and IVY should be further investigated in vivo in order to determine the optimum doses which maintain low rumen methanogenesis but prevent negative effects on the rumen microbial ecosystem.	root:Host-associated:Mammals:Digestive system:Stomach:Rumen
MGYS00000579	Brain meta-transcriptomics from harbor seals to infer the role of the microbiome and virome in a stranding event	Marine diseases are becoming more frequent, and tools for identifying pathogens and disease reservoirs are needed to help prevent and mitigate epizootics. Meta-transcriptomics provides insights into disease etiology by cataloguing and comparing sequences from suspected pathogens. This method is a powerful approach to simultaneously evaluate both the viral and bacterial communities, but few studies have?applied this technique in marine systems.?In 2009 seven harbor seals,?Phoca vitulina,?stranded along the California coast from a similar brain disease of?unknown cause of death (UCD). We evaluated the differences between the virome and microbiome of UCDs and harbor seals with known causes of death. Here we determined that UCD stranded animals had no viruses in their brain tissue. However, in the bacterial community, we identified?Burkholderia?and?Coxiella burnetii?as important pathogens associated with this stranding event.?Burkholderia?were 100% prevalent and ~2.8 log2 fold more abundant in the UCD animals. Further, while?C. burnetii?was found in only 35.7% of all samples, it was highly abundant (~94% of the total microbial community) in a single individual. In this harbor seal, C. burnetii?showed high transcription rates of invading and translation genes, implicating it in the pathogenesis of this animal. Based on these data we propose that?Burkholderia?taxa and?C. burnetii?are potentially important opportunistic neurotropic pathogens in UCD stranded harbor seals.	root:Host-associated:Mammals:Nervous system:Brain
MGYS00000583	The oral microbiome in HIV infected individuals	The aim of this project was to compare the oral microbiome of HIV-infected individuals to that of age- and gender-matched HIV-negative individuals. A 16S rRNA gene sequencing approach by means of a Roche GS-FLX+ sequencer was used to characterise the bacterial communities of plaque and saliva from each of the study participants.The oral microbiomes of HIV-positive and -negative individuals were found to be similar overall, although there were minor but significant differences in the composition of the salivary microbiota of the two groups. In addition, the results confirmed that plaque and saliva have a differing bacterial composition.	root:Host-associated:Human:Digestive system:Oral