data/rag/knowledge_base/Bacteroides/fragilis.json

{
  "schema_version": "1.0",
  "level": "species",
  "genus": "Bacteroides",
  "species": "fragilis",

  "overview": {
    "short": "Bacteroides fragilis is a bile-resistant, encapsulated anaerobic Gram-negative rod.",
    "clinical_context": "Most clinically significant Bacteroides species; commonly causes intra-abdominal abscesses and bacteraemia."
  },

  "expected_fields": {
    "Gram Stain": "Negative",
    "Shape": "Rods",
    "Motility": "Negative",
    "Capsule": "Positive",
    "Spore Formation": "Negative",
    "Haemolysis": "Negative",
    "Haemolysis Type": "None",
    "Media Grown On": [
      "Anaerobic Blood Agar",
      "Bacteroides Bile Esculin Agar"
    ],
    "Colony Morphology": [
      "Grey",
      "Smooth",
      "Convex"
    ],
    "Oxygen Requirement": "Obligate Anaerobe",
    "Growth Temperature": "20//45",
    "Catalase": "Positive",
    "Oxidase": "Negative",
    "Indole": "Negative",
    "Urease": "Negative",
    "Citrate": "Negative",
    "Methyl Red": "Variable",
    "VP": "Negative",
    "H2S": "Negative",
    "DNase": "Variable",
    "ONPG": "Positive",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Negative",
    "Esculin Hydrolysis": "Positive",
    "Nitrate Reduction": "Variable",
    "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": "Positive",
    "Maltose Fermentation": "Positive",
    "Mannitol Fermentation": "Positive",
    "Sorbitol Fermentation": "Negative",
    "Xylose Fermentation": "Positive",
    "Rhamnose Fermentation": "Negative",
    "Arabinose Fermentation": "Positive",
    "Raffinose Fermentation": "Negative",
    "Trehalose Fermentation": "Positive",
    "Inositol Fermentation": "Negative",
    "Gas Production": "Variable",
    "TSI Pattern": "Unknown",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "None"
  },

  "species_markers": [
    {
      "field": "Capsule",
      "value": "Positive",
      "importance": "critical",
      "notes": "Major virulence factor unique within the genus."
    },
    {
      "field": "Bile resistance",
      "value": "Positive",
      "importance": "high",
      "notes": "Growth on bile-containing media is characteristic."
    }
  ],

  "recommended_next_tests": [
    {
      "test": "API 20A",
      "reason": "Species-level anaerobe identification.",
      "api_kit": "API 20A"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Rapid and accurate species identification."
    }
  ]
}