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

data/rag/knowledge_base/Bacillus/subtilis.json

@@ -1,41 +1,102 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Bacillus",
   "species": "subtilis",
-  "full_name": "Bacillus subtilis",
-  "clinical_significance": "A nonpathogenic environmental Bacillus species widely used in biotechnology and molecular biology research. Rare opportunistic infections may occur in immunocompromised patients.",
-  "phenotype_profile": {
-    "morphology": "Large Gram-positive rods; central spores; highly motile.",
-    "culture": "Flat, dry, irregular colonies with dull or matte surface. Typically non-hemolytic or weakly hemolytic.",
-    "biochemical": [
-      "Motile",
-      "Catalase positive",
-      "Usually non-hemolytic",
-      "ONPG negative",
-      "Grows in 6.5% NaCl variably",
-      "Nitrate reduction positive",
-      "Urease negative"
-    ]
+
+  "overview": {
+    "short": "Bacillus subtilis is a motile, aerobic, Gram-positive spore-forming rod commonly found in soil.",
+    "clinical_context": "Usually a contaminant; rare opportunistic infections reported."
   },
-  "differentiation": {
-    "from_close species": [
-      "More matte, dry colonies vs. β-hemolytic B. cereus.",
-      "Highly motile compared to non-motile B. anthracis.",
-      "Lacks parasporal crystals seen in B. thuringiensis."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Negative",
+    "Spore Formation": "Positive",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Variable",
+    "Media Grown On": [
+      "Blood Agar",
+      "Nutrient Agar"
     ],
-    "from_other_genera": [
-      "Spore-forming differentiates from Gram-negative rods.",
-      "Aerobic growth differentiates from Clostridium."
-    ]
+    "Colony Morphology": [
+      "Dry",
+      "Irregular",
+      "Rough"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "10//45",
+    "Catalase": "Positive",
+    "Oxidase": "Variable",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Variable",
+    "Methyl Red": "Variable",
+    "VP": "Positive",
+    "H2S": "Negative",
+    "DNase": "Variable",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Positive",
+    "Esculin Hydrolysis": "Variable",
+    "Nitrate Reduction": "Positive",
+    "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": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "Colony morphology and motility",
-    "16S rRNA sequencing"
+
+  "species_markers": [
+    {
+      "field": "Nitrate Reduction",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Supports B. subtilis over other Bacillus species."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Bacillus licheniformis",
+      "reason": "Overlapping biochemical reactions."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Strong beta-haemolysis suggests B. cereus.",
+    "Capsule production suggests B. anthracis."
   ],
-  "treatment_notes": "Not typically treated; infections are rare.",
-  "notes": "One of the best-studied organisms in microbiology; model for sporulation.",
-  "references": [
-    "Bacillus subtilis genetics research",
-    "Manual of Clinical Microbiology"
+
+  "recommended_next_tests": [
+    {
+      "test": "API 50 CHB",
+      "reason": "Supports species-level carbohydrate differentiation.",
+      "api_kit": "API 50 CHB"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable Bacillus species identification."
+    }
   ]
-}
+}