data/rag/knowledge_base/Bacillus/subtilis.json

{
  "schema_version": "1.0",
  "level": "species",
  "genus": "Bacillus",
  "species": "subtilis",

  "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."
  },

  "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"
    ],
    "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"
  },

  "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."
  ],

  "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."
    }
  ]
}