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

data/rag/knowledge_base/Acidaminococcus/fermentans.json

@@ -1,44 +1,101 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Acidaminococcus",
   "species": "fermentans",
-  "full_name": "Acidaminococcus fermentans",
-  "clinical_significance": "A commensal anaerobe of the human gut, occasionally isolated from polymicrobial intra-abdominal infections, abscesses, and bacteremia. Typically low virulence but clinically relevant when gut mucosal barriers are compromised.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative cocci in pairs or clusters; may appear Gram-variable.",
-    "culture": "Strict anaerobe. Small, translucent colonies on anaerobic blood agar. No growth in aerobic conditions. Non-pigmented.",
-    "biochemical": [
-      "Amino acid fermenter, especially glutamate (definitive trait)",
-      "Does not ferment carbohydrates",
-      "Catalase negative",
-      "Oxidase negative",
-      "Indole negative",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Produces volatile fatty acids such as acetate and butyrate"
-    ]
+
+  "overview": {
+    "short": "Acidaminococcus fermentans is a Gram-negative, obligately anaerobic coccus that derives energy primarily from amino acid fermentation.",
+    "clinical_context": "Commonly part of the normal gastrointestinal microbiota and occasionally recovered from polymicrobial anaerobic infections."
   },
-  "differentiation": {
-    "from_close_species": [
-      "A. fermentans has strong glutamate fermentation, more robust than A. intestini.",
-      "A. intestini may show slightly different VFA profiles on gas chromatography.",
-      "Both differ from Veillonella by failing to metabolize lactate."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Cocci",
+    "Motility": "Negative",
+    "Capsule": "Unknown",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "from_other_genera": [
-      "Strict amino acid fermentation (not lactate) differentiates from Veillonella.",
-      "Megasphaera is larger and may ferment some carbohydrates.",
-      "Anaerobic Gram-negative cocci exclude Neisseria and Moraxella which are aerobic."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Convex"
+    ],
+    "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"
   },
-  "confirmation_methods": [
-    "16S rRNA sequencing (most definitive)",
-    "MALDI-TOF MS",
-    "Glutamate fermentation profile",
-    "Gas chromatography of fermentation products"
+
+  "species_markers": [
+    {
+      "field": "Amino Acid Fermentation",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Primary metabolic pathway distinguishing Acidaminococcus species."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Veillonella",
+      "reason": "Both are anaerobic Gram-negative cocci isolated from similar sites."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Carbohydrate fermentation suggests Veillonella.",
+    "Aerobic growth is inconsistent with A. fermentans.",
+    "Rod-shaped morphology excludes this species."
   ],
-  "treatment_notes": "Generally susceptible to metronidazole and beta-lactams active against anaerobes. Clinical infections are typically polymicrobial.",
-  "notes": "Most commonly encountered Acidaminococcus species in human samples, though still overall rare.",
-  "references": [
-    "Manual of Clinical Microbiology, 12th Edition.",
-    "Studies on anaerobic Gram-negative cocci metabolism."
+
+  "recommended_next_tests": [
+    {
+      "test": "Anaerobic growth verification",
+      "reason": "Confirms obligate anaerobic metabolism."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable identification due to limited biochemical activity."
+    }
   ]
-}
+}