Update data/rag/knowledge_base/Azotobacter/chroococcum.json

data/rag/knowledge_base/Azotobacter/chroococcum.json

@@ -1,42 +1,106 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Azotobacter",
   "species": "chroococcum",
-  "full_name": "Azotobacter chroococcum",
-  "clinical_significance": "Not a human pathogen. The most commonly encountered Azotobacter species in soil. Widely used in agriculture as a biofertilizer due to strong nitrogen-fixing ability.",
-  "phenotype_profile": {
-    "morphology": "Large Gram-negative rods; cyst-forming; often more spherical in vegetative form compared to A. vinelandii.",
-    "culture": "Grows well on nitrogen-free media. Colonies typically brown to dark brown due to pigment production.",
-    "biochemical": [
-      "Catalase positive",
-      "Oxidase positive",
-      "ONPG negative",
-      "No growth in 6.5% NaCl",
-      "Nitrogen fixation positive",
-      "Produces melanin-like pigments",
-      "Forms thick-walled cysts"
-    ]
+
+  "overview": {
+    "short": "Azotobacter chroococcum is a free-living, nitrogen-fixing aerobic Gram-negative rod commonly isolated from soil.",
+    "clinical_context": "Not considered a human pathogen; usually regarded as an environmental isolate or contaminant."
   },
-  "differentiation": {
-    "from_close_species": [
-      "More spherical cell morphology compared to A. vinelandii.",
-      "Darker pigmentation than A. beijerinckii.",
-      "Commonly dominant species in agriculture-related soils."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Positive",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Nutrient Agar"
     ],
-    "from_other_genera": [
-      "Pigmented nitrogen-fixing aerobe excludes Pseudomonas or Bacillus.",
-      "Cysts differentiate it from Azomonas."
-    ]
+    "Colony Morphology": [
+      "Large",
+      "Mucoid",
+      "Smooth"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "20//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Positive",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Variable",
+    "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": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "Brown",
+    "Motility Type": "Peritrichous"
   },
-  "confirmation_methods": [
-    "MALDI-TOF MS (environmental library required)",
-    "16S rRNA sequencing",
-    "Pigment production",
-    "Cyst formation patterns"
+
+  "species_markers": [
+    {
+      "field": "Pigment",
+      "value": "Brown",
+      "importance": "medium",
+      "notes": "Production of brown-black pigment on aging cultures."
+    },
+    {
+      "field": "Capsule",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Prominent capsule contributes to mucoid colony morphology."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Pseudomonas",
+      "reason": "Both are aerobic Gram-negative rods and oxidase positive."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Clinical pathogenicity suggests misidentification.",
+    "Anaerobic growth excludes A. chroococcum."
   ],
-  "treatment_notes": "Not medically relevant.",
-  "notes": "Most widely studied Azotobacter species for agricultural inoculants.",
-  "references": [
-    "Soil microbiome literature",
-    "Azotobacter biofertilizer studies"
+
+  "recommended_next_tests": [
+    {
+      "test": "Nitrogen fixation assay",
+      "reason": "Characteristic trait of A. chroococcum."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Accurate confirmation of environmental species."
+    }
   ]
-}
+}