data/rag/knowledge_base/Eubacterium/genus.json

{
  "schema_version": "1.0",
  "level": "genus",
  "genus": "Eubacterium",

  "overview": {
    "short": "Eubacterium species are Gram-positive, obligately anaerobic rods commonly found in the human gastrointestinal tract.",
    "clinical_context": "Typically part of normal gut flora but may be isolated from abscesses, bloodstream infections, and polymicrobial anaerobic infections."
  },

  "expected_fields": {
    "Gram Stain": "Positive",
    "Shape": "Rods",
    "Motility": "Variable",
    "Capsule": "Variable",
    "Spore Formation": "Negative",
    "Haemolysis": "Negative",
    "Haemolysis Type": "None",
    "Media Grown On": [
      "Anaerobic Blood Agar"
    ],
    "Colony Morphology": [
      "Small",
      "Grey",
      "Smooth"
    ],
    "Oxygen Requirement": "Anaerobic",
    "Growth Temperature": "30//37",
    "Catalase": "Negative",
    "Oxidase": "Negative",
    "Indole": "Variable",
    "Urease": "Negative",
    "Citrate": "Negative",
    "Methyl Red": "Variable",
    "VP": "Negative",
    "H2S": "Variable",
    "DNase": "Negative",
    "ONPG": "Negative",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Variable",
    "Esculin Hydrolysis": "Variable",
    "Nitrate Reduction": "Variable",
    "NaCl Tolerant (>=6%)": "Negative",
    "Lipase Test": "Negative",
    "Lysine Decarboxylase": "Negative",
    "Ornithine Decarboxylase": "Negative",
    "Ornitihine Decarboxylase": "Negative",
    "Arginine dihydrolase": "Variable",
    "Glucose Fermentation": "Positive",
    "Lactose Fermentation": "Variable",
    "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": "Unknown",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "Unknown"
  },

  "field_notes": {
    "Oxygen Requirement": "Strict anaerobes; growth in aerobic conditions argues against Eubacterium.",
    "Indole": "Highly species-dependent and not genus-defining.",
    "Motility": "Variable across species and strains."
  },

  "key_differentiators": [
    {
      "field": "Catalase",
      "expected": "Negative",
      "distinguishes_from": ["Cutibacterium"],
      "notes": "Catalase negativity helps separate Eubacterium from catalase-positive anaerobes."
    },
    {
      "field": "Oxygen Requirement",
      "expected": "Anaerobic",
      "distinguishes_from": ["Corynebacterium"],
      "notes": "Strict anaerobic growth differentiates from aerotolerant Gram-positive rods."
    }
  ],

  "common_confusions": [
    {
      "genus": "Clostridium",
      "reason": "Shared anaerobic growth and Gram-positive rod morphology."
    },
    {
      "genus": "Actinomyces",
      "reason": "Overlapping anaerobic biochemical profiles."
    }
  ],

  "when_to_question_identification": [
    "Spore formation suggests Clostridium.",
    "Aerobic growth suggests Corynebacterium or related genera.",
    "Strong catalase positivity is inconsistent."
  ],

  "recommended_next_tests": [
    {
      "test": "Anaerobic identification panel",
      "reason": "Supports biochemical profiling under anaerobic conditions.",
      "api_kit": "API Rapid ID 32A"
    },
    {
      "test": "Indole test",
      "reason": "Useful for species-level differentiation.",
      "api_kit": "API Rapid ID 32A"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Most reliable approach for definitive identification.",
      "api_kit": "Not applicable"
    }
  ],

  "supported_species": [
    "limosum",
    "rectale",
    "ventriosum"
  ]
}