data/rag/knowledge_base/Eubacterium/rectale.json

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

  "overview": {
    "short": "Eubacterium rectale is a Gram-positive, obligately anaerobic rod and a major butyrate-producing bacterium of the human gut microbiota.",
    "clinical_context": "Primarily a commensal organism; rarely implicated in clinical infections but may appear in polymicrobial anaerobic cultures."
  },

  "expected_fields": {
    "Gram Stain": "Positive",
    "Shape": "Rods",
    "Motility": "Negative",
    "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": "Negative",
    "Urease": "Negative",
    "Citrate": "Negative",
    "Methyl Red": "Variable",
    "VP": "Negative",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Negative",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Variable",
    "Esculin Hydrolysis": "Variable",
    "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": "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": "Variable",
    "Inositol Fermentation": "Negative",
    "Gas Production": "Negative",
    "TSI Pattern": "Unknown",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "None"
  },

  "species_markers": [
    {
      "field": "Nitrate Reduction",
      "value": "Negative",
      "importance": "medium",
      "notes": "Helps differentiate E. rectale from nitrate-reducing Eubacterium species."
    },
    {
      "field": "Gas Production",
      "value": "Negative",
      "importance": "low",
      "notes": "Typically does not produce gas during carbohydrate fermentation."
    }
  ],

  "common_confusions": [
    {
      "species": "Eubacterium limosum",
      "reason": "Overlapping anaerobic growth and fermentation profiles."
    },
    {
      "genus": "Clostridium",
      "reason": "Shared anaerobic Gram-positive rod morphology."
    }
  ],

  "when_to_question_identification": [
    "Nitrate reduction positivity suggests Eubacterium limosum or another anaerobe.",
    "Gas production argues against Eubacterium rectale.",
    "Spore formation excludes Eubacterium."
  ],

  "recommended_next_tests": [
    {
      "test": "Nitrate reduction",
      "reason": "Useful discriminator within the genus.",
      "api_kit": "API Rapid ID 32A"
    },
    {
      "test": "Anaerobic biochemical profiling",
      "reason": "Supports species-level differentiation.",
      "api_kit": "API Rapid ID 32A"
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Gold standard for accurate identification.",
      "api_kit": "Not applicable"
    }
  ]
}