Update data/rag/knowledge_base/Acidaminococcus/genus.json

data/rag/knowledge_base/Acidaminococcus/genus.json

@@ -1,76 +1,131 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Acidaminococcus",
-  "taxonomy": {
-    "family": "Acidaminococcaceae",
-    "order": "Veillonellales",
-    "class": "Negativicutes",
-    "phylum": "Firmicutes"
+
+  "overview": {
+    "short": "Acidaminococcus species are Gram-negative, anaerobic cocci belonging to the class Negativicutes, characterized by amino acid fermentation rather than carbohydrate metabolism.",
+    "clinical_context": "Part of the normal gastrointestinal flora and occasionally isolated from polymicrobial anaerobic infections."
   },
-  "overview": "Acidaminococcus is a genus of Gram-negative staining anaerobic cocci belonging to the Firmicutes phylum. Despite being Firmicutes, they stain Gram-negative due to their atypical cell wall structure. They are obligate anaerobes that primarily ferment amino acids—especially glutamate—rather than carbohydrates. They are part of the normal intestinal microbiota.",
-  "key_traits": [
-    "Gram-negative cocci (rare phenotype within Firmicutes)",
-    "Obligate anaerobes",
-    "Ferment amino acids but do not ferment carbohydrates",
-    "Non-motile",
-    "Catalase negative",
-    "Indole negative",
-    "Grow poorly on carbohydrate-rich media",
-    "Colonies small, translucent, often difficult to recover"
-  ],
-  "ecology": "Acidaminococcus species reside predominantly in the human gastrointestinal tract. They are adapted to amino acid–rich environments and play a role in amino acid metabolism within the microbiome.",
-  "pathogenicity": "Generally low virulence. Rarely implicated in intra-abdominal infections, bacteremia, pelvic abscesses, and polymicrobial infections. Clinical relevance usually arises when gut integrity is compromised.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Amino acid fermentation, especially glutamate and ornithine.",
-      "Carbohydrates not fermented (key differentiator).",
-      "ONPG negative.",
-      "No growth in 6.5% NaCl.",
-      "Produce volatile fatty acids including acetate and butyrate."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Cocci",
+    "Motility": "Negative",
+    "Capsule": "Unknown",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "non_definitive_tests": [
-      "Carbohydrate acid production should not be used for genus-level identification.",
-      "Gram stain may appear variable; morphology alone is insufficient."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Veillonella ferments lactate to propionate; Acidaminococcus does not utilize lactate and instead ferments amino acids.",
-      "Megasphaera is larger, often Gram-variable, and ferments different substrates including some carbohydrates.",
-      "Negativicoccus shows slightly different fermentation patterns and may produce propionate from lactate.",
-      "Unlike true Gram-negative cocci (e.g., Neisseria), Acidaminococcus is strictly anaerobic and does not oxidize carbohydrates."
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Convex"
     ],
-    "key_rag_filters": [
-      "Gram-negative cocci + anaerobic → strong push toward Acidaminococcus / Veillonella / Megasphaera.",
-      "Amino acid fermentation without carbohydrate utilization → strongly supports Acidaminococcus.",
-      "Failure to metabolize lactate → rules out Veillonella.",
-      "Strict anaerobic growth → rules out Neisseria, Moraxella, and all aerobic Gram-negative cocci."
-    ]
+    "Oxygen Requirement": "Obligate Anaerobe",
+    "Growth Temperature": "35//37",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Negative",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Negative",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Negative",
+    "Maltose Fermentation": "Negative",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Negative",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Negative",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Negative",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "K/K",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "None"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Gram-negative cocci in pairs or clusters",
-      "Strict anaerobe",
-      "No carbohydrate fermentation",
-      "Ferments amino acids such as glutamate",
-      "Small, slow-growing colonies on anaerobic media"
-    ],
-    "important_tests": [
-      "Amino acid fermentation panel (glutamate utilization)",
-      "Gas chromatography of metabolic acids",
-      "16S rRNA sequencing",
-      "MALDI-TOF MS"
-    ],
-    "confirmation_methods": [
-      "16S rRNA sequencing (most reliable)",
-      "MALDI-TOF MS",
-      "Differentiation based on amino acid fermentation vs. lactate fermentation",
-      "Strict anaerobiosis with Gram-negative cocci morphology"
-    ]
+
+  "field_notes": {
+    "Gram Stain": "Despite being Gram-negative, Acidaminococcus belongs to a lineage phylogenetically related to Gram-positive bacteria.",
+    "Glucose Fermentation": "Species do not ferment carbohydrates and instead utilize amino acids for energy.",
+    "Oxygen Requirement": "Strict anaerobiosis is a defining characteristic."
   },
-  "notes": "Members of the genus may be misidentified as Veillonella unless amino acid fermentation is noted. Their atypical Gram-negative staining despite being Firmicutes can lead to confusion in routine workflow.",
-  "references": [
-    "Jorgensen et al. Manual of Clinical Microbiology, 12th Edition.",
-    "Winn et al. Koneman’s Diagnostic Microbiology.",
-    "Recent publications on Negativicutes taxonomy and metabolism."
+
+  "key_differentiators": [
+    {
+      "field": "Oxygen Requirement",
+      "expected": "Obligate Anaerobe",
+      "distinguishes_from": ["Neisseria", "Veillonella"],
+      "notes": "Strict anaerobic growth separates Acidaminococcus from aerobic Gram-negative cocci."
+    },
+    {
+      "field": "Shape",
+      "expected": "Cocci",
+      "distinguishes_from": ["Bacteroides", "Fusobacterium"],
+      "notes": "Coccoid morphology helps differentiate from anaerobic Gram-negative rods."
+    },
+    {
+      "field": "Glucose Fermentation",
+      "expected": "Negative",
+      "distinguishes_from": ["Veillonella"],
+      "notes": "Lack of carbohydrate fermentation supports Acidaminococcus."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Veillonella",
+      "reason": "Both are anaerobic Gram-negative cocci isolated from similar clinical contexts."
+    },
+    {
+      "genus": "Megasphaera",
+      "reason": "Phylogenetic relatedness within Negativicutes."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Aerobic or facultative growth argues against Acidaminococcus.",
+    "Carbohydrate fermentation suggests Veillonella.",
+    "Rod-shaped morphology excludes this genus."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Anaerobic growth confirmation",
+      "reason": "Essential for correct genus assignment."
+    },
+    {
+      "test": "Amino acid fermentation profiling",
+      "reason": "Characteristic metabolic feature of Acidaminococcus."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Recommended due to biochemical inertness and rarity."
+    }
+  ],
+
+  "supported_species": [
+    "fermentans",
+    "intestini"
   ]
-}
+}