Update data/rag/knowledge_base/Alicyclobacillus/acidoterrestris.json

data/rag/knowledge_base/Alicyclobacillus/acidoterrestris.json

@@ -1,45 +1,101 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Alicyclobacillus",
   "species": "acidoterrestris",
-  "full_name": "Alicyclobacillus acidoterrestris",
-  "clinical_significance": "Not a human pathogen, but the most economically important Alicyclobacillus species due to its ability to cause spoilage in pasteurized fruit juices. Produces guaiacol and other phenolic compounds responsible for 'smoky' or 'medicinal' off-flavors.",
-  "phenotype_profile": {
-    "morphology": "Gram-positive rods; spore-forming; motile or weakly motile.",
-    "culture": "Grows at 35–55°C (optimal ~45°C). Strong growth at pH 2.5–4.5. Produces taints in acidic media.",
-    "biochemical": [
-      "Strict aerobe",
-      "Catalase positive",
-      "Oxidase negative",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Thermoacidophilic but less extreme than A. acidocaldarius",
-      "Spore-forming",
-      "Produces guaiacol and phenolic metabolites (key trait)"
-    ]
+
+  "overview": {
+    "short": "Alicyclobacillus acidoterrestris is a Gram-positive, aerobic, spore-forming rod best known for spoilage of acidic beverages and heat-resistant spores.",
+    "clinical_context": "Primarily associated with food and beverage spoilage rather than clinical infection."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Produces guaiacol, unlike A. acidocaldarius.",
-      "Grows best at slightly lower temps (40–50°C) compared to the extreme thermophile A. acidocaldarius.",
-      "Primary organism responsible for commercial beverage spoilage."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Rods",
+    "Motility": "Variable",
+    "Capsule": "Negative",
+    "Spore Formation": "Positive",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Nutrient Agar",
+      "Blood Agar"
     ],
-    "from_other_genera": [
-      "No other common beverage spoilage organism forms heat-resistant spores *and* thrives at low pH.",
-      "Distinct from Bacillus due to acid tolerance and ω-alicyclic fatty acids."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Smooth",
+      "Cream"
+    ],
+    "Oxygen Requirement": "Aerobe",
+    "Growth Temperature": "25//55",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Variable",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Negative",
+    "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": "Variable",
+    "Maltose Fermentation": "Variable",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Variable",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Variable",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Variable",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Unknown"
   },
-  "confirmation_methods": [
-    "Guaiacol detection assays (colorimetric or GC-MS)",
-    "16S rRNA sequencing",
-    "Thermoacidophilic growth profile",
-    "MALDI-TOF MS",
-    "Spore heat-resistance testing"
+
+  "species_markers": [
+    {
+      "field": "Growth Temperature",
+      "value": "25//55",
+      "importance": "high",
+      "notes": "Typically less thermophilic than A. acidocaldarius; growth range supports species separation."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Alicyclobacillus acidocaldarius",
+      "reason": "Both are acidophilic spore-formers; separation often relies on growth temperature and application context."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Strong thermophilic growth up to ~70°C suggests A. acidocaldarius rather than A. acidoterrestris.",
+    "Spore formation negativity argues against Alicyclobacillus."
   ],
-  "treatment_notes": "Not medically relevant. In industry, control requires improved sanitation, monitoring of raw fruit, and optimized heat treatments.",
-  "notes": "Principal cause of Alicyclobacillus-related spoilage in fruit juice production.",
-  "references": [
-    "Food microbiology literature on beverage spoilage",
-    "Alicyclobacillus detection and control guidelines",
-    "Manual of Clinical Microbiology (environmental spoilage organisms)"
+
+  "recommended_next_tests": [
+    {
+      "test": "Growth temperature profiling",
+      "reason": "Key discriminator between common Alicyclobacillus species."
+    },
+    {
+      "test": "Molecular identification or MALDI-TOF",
+      "reason": "Recommended when species-level precision matters (e.g., spoilage investigations)."
+    }
   ]
-}
+}