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

data/rag/knowledge_base/Azotobacter/beijerinckii.json

@@ -1,41 +1,115 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Azotobacter",
   "species": "beijerinckii",
-  "full_name": "Azotobacter beijerinckii",
-  "clinical_significance": "Not a human pathogen. Found in soil, compost, and rhizosphere environments. Named after the Dutch microbiologist Martinus Beijerinck.",
-  "phenotype_profile": {
-    "morphology": "Large Gram-negative ovoid rods; form cysts under nutrient limitation.",
-    "culture": "Grows aerobically on nitrogen-free media. Colonies non-pigmented to lightly brown. Produces abundant polysaccharide slime.",
-    "biochemical": [
-      "Catalase positive",
-      "Oxidase positive",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Nitrogen fixation positive",
-      "Cyst formation present"
-    ]
+
+  "overview": {
+    "short": "Azotobacter beijerinckii is a free-living, nitrogen-fixing, aerobic Gram-negative rod commonly isolated from soil and freshwater environments.",
+    "clinical_context": "Not considered a human pathogen; isolates are environmental or incidental laboratory findings."
   },
-  "differentiation": {
-    "from_close_species": [
-      "A. beijerinckii typically forms less intense pigment than A. vinelandii.",
-      "Cyst morphology differs slightly from A. chroococcum (less laminated).",
-      "Colonies more mucoid compared to A. vinelandii."
+
+  "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": [
-      "Ability to grow on nitrogen-free medium distinguishes Azotobacter from most aerobes.",
-      "Cyst formation differentiates from Pseudomonas or Alcaligenes."
-    ]
+    "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": "Variable",
+    "Motility Type": "Peritrichous"
   },
-  "confirmation_methods": [
-    "16S rRNA sequencing",
-    "Cyst morphology",
-    "Nitrogenase activity test (acetylene reduction assay)",
-    "Pigment absence/weak pigmentation"
+
+  "species_markers": [
+    {
+      "field": "Pigment",
+      "value": "Variable",
+      "importance": "low",
+      "notes": "Pigmentation may range from none to light brown depending on growth conditions."
+    },
+    {
+      "field": "Nitrate Reduction",
+      "value": "Variable",
+      "importance": "low",
+      "notes": "Less consistent nitrate reduction compared to A. vinelandii."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Azotobacter chroococcum",
+      "reason": "Overlapping colony morphology, capsule production, and nitrogen fixation."
+    },
+    {
+      "species": "Azotobacter vinelandii",
+      "reason": "Very similar aerobic metabolism and biochemical profile."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Pigment production alone is insufficient for species-level differentiation.",
+    "Clinical pathogenicity suggests misidentification.",
+    "Fermentative metabolism is inconsistent with Azotobacter species."
   ],
-  "treatment_notes": "Not clinically relevant.",
-  "notes": "Frequently used in studies of cyst development and nitrogen fixation.",
-  "references": [
-    "Environmental microbiology studies",
-    "Nitrogen fixation literature"
+
+  "recommended_next_tests": [
+    {
+      "test": "Nitrogen fixation assay",
+      "reason": "Confirms defining metabolic trait of the genus."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Most reliable method for differentiating Azotobacter species."
+    },
+    {
+      "test": "Whole-genome sequencing",
+      "reason": "Required for definitive species-level resolution within Azotobacter."
+    }
   ]
-}
+}