Update data/rag/knowledge_base/Bacteroides/thetaiotaomicron.json

data/rag/knowledge_base/Bacteroides/thetaiotaomicron.json

@@ -1,46 +1,107 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Bacteroides",
   "species": "thetaiotaomicron",
-  "full_name": "Bacteroides thetaiotaomicron",
-  "clinical_significance": "A dominant gut commensal with extensive polysaccharide-degrading capacity. A frequent isolate in peritoneal infections, intra-abdominal abscesses, and polymicrobial bacteremia. Less virulent than B. fragilis but clinically significant.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative rods; pleomorphic.",
-    "culture": "Non-pigmented; somewhat more fastidious than B. fragilis; bile resistant.",
-    "biochemical": [
-      "Catalase negative",
-      "Indole positive (common distinguishing trait)",
-      "ONPG negative",
-      "Non-motile",
-      "Bile resistant",
-      "Strong polysaccharide utilization capabilities"
-    ]
+
+  "overview": {
+    "short": "Bacteroides thetaiotaomicron is an obligately anaerobic Gram-negative rod notable for extensive carbohydrate metabolism.",
+    "clinical_context": "Primarily a gut commensal; rarely isolated from clinical infections."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Indole positive differentiates B. thetaiotaomicron from B. fragilis and B. vulgatus.",
-      "More fastidious growth and smaller colonies than B. fragilis.",
-      "Associated with extensive glycan metabolism in gut ecology."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Negative",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Anaerobic Blood Agar"
     ],
-    "from_other_genera": [
-      "Indole positivity with bile resistance is uncommon outside Bacteroides.",
-      "Morphology and SCFA profile differ from Parabacteroides."
-    ]
+    "Colony Morphology": [
+      "Grey",
+      "Smooth",
+      "Convex"
+    ],
+    "Oxygen Requirement": "Obligate Anaerobe",
+    "Growth Temperature": "20//45",
+    "Catalase": "Variable",
+    "Oxidase": "Negative",
+    "Indole": "Positive",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Variable",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Positive",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Positive",
+    "Nitrate Reduction": "Variable",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Positive",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Positive",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Positive",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Positive",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Positive",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "None"
   },
-  "virulence_factors": [
-    "Polysaccharide utilization loci (PUL systems)",
-    "Capsular variability enabling immune evasion",
-    "SCFA production influencing host metabolism"
+
+  "species_markers": [
+    {
+      "field": "Indole",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Key differentiator from B. vulgatus and most non-fragilis species."
+    },
+    {
+      "field": "ONPG",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Reflects enhanced carbohydrate metabolism."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Bacteroides fragilis",
+      "reason": "Shared bile tolerance and esculin hydrolysis."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "Indole positivity",
-    "16S rRNA sequencing",
-    "Bile resistance + anaerobic rod morphology"
+
+  "when_to_question_identification": [
+    "Indole negativity suggests B. vulgatus.",
+    "Capsule positivity with high virulence suggests B. fragilis."
   ],
-  "treatment_notes": "Susceptibility similar to B. vulgatus. Metronidazole effective. Resistance lower than B. fragilis.",
-  "notes": "A key model species in microbiome research due to vast carbohydrate-active enzyme repertoire.",
-  "references": [
-    "Human microbiome (HMP) literature",
-    "Bacteroides glycan metabolism research"
+
+  "recommended_next_tests": [
+    {
+      "test": "API 20A",
+      "reason": "Supports anaerobe species differentiation.",
+      "api_kit": "API 20A"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Most reliable method for species-level identification."
+    }
   ]
-}
+}