Update data/rag/knowledge_base/Exiguobacterium/genus.json

data/rag/knowledge_base/Exiguobacterium/genus.json

@@ -1,75 +1,135 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Exiguobacterium",
-  "taxonomy": {
-    "family": "Bacillaceae",
-    "order": "Bacillales",
-    "class": "Bacilli",
-    "phylum": "Firmicutes"
+
+  "overview": {
+    "short": "Exiguobacterium species are Gram-positive, non-spore-forming rods or short rods, notable for their ability to survive across wide temperature and environmental extremes.",
+    "clinical_context": "Primarily environmental organisms; rarely isolated from clinical specimens, usually as contaminants or opportunistic isolates."
   },
-  "overview": "Exiguobacterium is a genus of Gram-positive to Gram-variable, facultatively anaerobic, non-spore-forming rods with remarkable environmental resilience. Members tolerate a wide temperature range, including cold environments such as glaciers, permafrost, and Antarctic lakes. They are typically environmental organisms but have been occasionally recovered from human clinical specimens.",
-  "key_traits": [
-    "Gram-positive or Gram-variable slender rods",
-    "Non-spore-forming (important discriminator from Bacillus)",
-    "Catalase positive",
-    "Motile or non-motile depending on species",
-    "Facultatively anaerobic",
-    "Growth over wide temperature range (psychrotolerant species common)",
-    "Salt- and pH-tolerant",
-    "Oxidase negative or weak"
-  ],
-  "ecology": "Widely distributed in soil, freshwater, marine environments, glacial ice, permafrost, hot springs, food products, and biofilms on industrial surfaces. Many species exhibit adaptations to extreme temperatures and osmotic stress.",
-  "pathogenicity": "Rare opportunistic pathogens. Documented cases include wound infections, device-associated infections, and rare bacteremia. Most isolates represent environmental contamination or colonization rather than true infection.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Catalase positive, oxidase negative rods.",
-      "Non-spore-forming despite belonging to Bacillales.",
-      "Broad thermal tolerance: some species grow from 4–45 °C.",
-      "Fermentation of sugars yielding lactic and acetic acids.",
-      "Motility variable by species."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Short Rods",
+    "Motility": "Variable",
+    "Capsule": "Unknown",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Nutrient Agar"
     ],
-    "non_definitive_tests": [
-      "Gram stain variable depending on age of culture.",
-      "Metabolic profiles overlap heavily among species; molecular identification preferred."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Bacillus: spore-forming; Exiguobacterium does not form spores.",
-      "Paenibacillus: motile and spore-forming; Exiguobacterium non-spore-forming.",
-      "Corynebacterium: club-shaped rods; Exiguobacterium rods are more uniform.",
-      "Listeria: motile and catalase positive but pathogenic and different biochemical profile.",
-      "Micrococcus: Gram-positive cocci; Exiguobacterium are rods."
+    "Colony Morphology": [
+      "Small",
+      "Smooth",
+      "Cream"
     ],
-    "key_rag_filters": [
-      "Gram-variable rod + catalase positive + non-spore-forming = Exiguobacterium vs Corynebacterium vs Listeria.",
-      "Cold-tolerant environmental isolate strongly suggests Exiguobacterium.",
-      "Motility and broad growth range help differentiate from strictly mesophilic Bacillales."
-    ]
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "-2//50",
+    "Catalase": "Positive",
+    "Oxidase": "Variable",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Variable",
+    "VP": "Variable",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Variable",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Variable",
+    "Nitrate Reduction": "Variable",
+    "NaCl Tolerant (>=6%)": "Positive",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Variable",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Variable",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Variable",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Variable",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Positive",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Variable"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Gram-variable rods",
-      "Catalase positive",
-      "No spores on microscopy",
-      "Yellowish or cream-colored colonies",
-      "Growth across broad temperature ranges (species dependent)"
-    ],
-    "important_tests": [
-      "Catalase",
-      "Spore stain",
-      "Growth range (psychrotolerance)",
-      "Carbohydrate fermentation profiles",
-      "MALDI-TOF MS"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS (excellent accuracy)",
-      "16S rRNA sequencing",
-      "Whole-genome sequencing in research contexts"
-    ]
+
+  "field_notes": {
+    "Growth Temperature": "Members exhibit extreme psychrotolerance and thermotolerance depending on species.",
+    "Motility": "Some species are motile via peritrichous flagella; others are non-motile.",
+    "Oxidase": "Results may vary and are not genus-defining."
   },
-  "notes": "Environmental extremophytes; rarely clinically significant.",
-  "references": [
-    "Extremophile microbiology studies",
-    "Clinical case reports of Exiguobacterium infections"
+
+  "key_differentiators": [
+    {
+      "field": "Growth Temperature",
+      "expected": "-2//50",
+      "distinguishes_from": ["Bacillus", "Paenibacillus"],
+      "notes": "Broad temperature tolerance without spore formation is characteristic."
+    },
+    {
+      "field": "Spore Formation",
+      "expected": "Negative",
+      "distinguishes_from": ["Bacillus"],
+      "notes": "Lack of endospores helps separate Exiguobacterium from spore-forming Gram-positive rods."
+    },
+    {
+      "field": "NaCl Tolerant (>=6%)",
+      "expected": "Positive",
+      "distinguishes_from": ["Listeria"],
+      "notes": "Salt tolerance supports Exiguobacterium identification."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Bacillus",
+      "reason": "Shared Gram-positive rod morphology and catalase positivity."
+    },
+    {
+      "genus": "Listeria",
+      "reason": "Overlap in motility and growth on blood agar."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Spore formation argues against Exiguobacterium.",
+    "Strict anaerobic growth excludes Exiguobacterium.",
+    "Catalase negativity is inconsistent with the genus."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Motility testing",
+      "reason": "Helps refine species-level differentiation.",
+      "api_kit": "API Coryne"
+    },
+    {
+      "test": "Carbohydrate fermentation profiling",
+      "reason": "Useful for separating closely related species.",
+      "api_kit": "API 50 CH"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable confirmation due to biochemical variability.",
+      "api_kit": "Not applicable"
+    }
+  ],
+
+  "supported_species": [
+    "acetylicum",
+    "antarcticum"
   ]
-}
+}