Update data/rag/knowledge_base/Bacillus/mycoides.json

data/rag/knowledge_base/Bacillus/mycoides.json

@@ -1,39 +1,101 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Bacillus",
   "species": "mycoides",
-  "full_name": "Bacillus mycoides",
-  "clinical_significance": "Primarily an environmental organism associated with soil and plant roots. Rare cause of human infection, usually considered a contaminant.",
-  "phenotype_profile": {
-    "morphology": "Large Gram-positive rods; spore-forming; motile.",
-    "culture": "Distinctive rhizoid ('mycelium-like') spreading colonies. β-hemolytic on blood agar.",
-    "biochemical": [
-      "Motile",
-      "β-hemolytic",
-      "Catalase positive",
-      "ONPG negative",
-      "Grows in 6.5% NaCl variably",
-      "Nitrate reduction positive"
-    ]
+
+  "overview": {
+    "short": "Bacillus mycoides is a Gram-positive, aerobic, spore-forming rod characterized by distinctive rhizoid colony morphology.",
+    "clinical_context": "Primarily environmental; rarely implicated in human disease."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Rhizoid colony morphology is strongly characteristic.",
-      "More spreading and filamentous colonies than B. cereus.",
-      "Genetically close to B. cereus group but phenotypically distinct."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Rods",
+    "Motility": "Variable",
+    "Capsule": "Negative",
+    "Spore Formation": "Positive",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Variable",
+    "Media Grown On": [
+      "Blood Agar",
+      "Nutrient Agar"
     ],
-    "from_other_genera": [
-      "Spore-forming and rhizoid growth exclude Enterobacterales.",
-      "Motility differentiates from B. anthracis."
-    ]
+    "Colony Morphology": [
+      "Rhizoid",
+      "Spreading",
+      "Filamentous"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "10//40",
+    "Catalase": "Positive",
+    "Oxidase": "Variable",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Variable",
+    "Methyl Red": "Variable",
+    "VP": "Variable",
+    "H2S": "Negative",
+    "DNase": "Variable",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Positive",
+    "Esculin Hydrolysis": "Variable",
+    "Nitrate Reduction": "Variable",
+    "NaCl Tolerant (>=6%)": "Variable",
+    "Lipase Test": "Variable",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Variable",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Variable",
+    "Mannitol Fermentation": "Variable",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Variable",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Variable",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Variable",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Variable",
+    "TSI Pattern": "Variable",
+    "Colony Pattern": "Rhizoid",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "Rhizoid colony morphology",
-    "16S rRNA sequencing"
+
+  "species_markers": [
+    {
+      "field": "Colony Morphology",
+      "value": "Rhizoid",
+      "importance": "critical",
+      "notes": "Highly characteristic spreading rhizoid colonies."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Bacillus cereus",
+      "reason": "Shared genetic background but distinct colony morphology."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Absence of rhizoid growth argues against B. mycoides.",
+    "Strong haemolysis suggests B. cereus group."
   ],
-  "treatment_notes": "Not medically significant; treat only if recovered from sterile site with supporting clinical signs.",
-  "notes": "Member of the B. cereus group with distinctive colony morphology.",
-  "references": [
-    "Environmental Bacillus research"
+
+  "recommended_next_tests": [
+    {
+      "test": "Colony morphology assessment",
+      "reason": "Primary discriminator for B. mycoides."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Confirms species within Bacillus group."
+    }
   ]
-}
+}