data/rag/knowledge_base/Acidaminococcus/fermentans.json

{
  "schema_version": "1.0",
  "level": "species",
  "genus": "Acidaminococcus",
  "species": "fermentans",

  "overview": {
    "short": "Acidaminococcus fermentans is a Gram-negative, obligately anaerobic coccus that derives energy primarily from amino acid fermentation.",
    "clinical_context": "Commonly part of the normal gastrointestinal microbiota and occasionally recovered from polymicrobial anaerobic infections."
  },

  "expected_fields": {
    "Gram Stain": "Negative",
    "Shape": "Cocci",
    "Motility": "Negative",
    "Capsule": "Unknown",
    "Spore Formation": "Negative",
    "Haemolysis": "Negative",
    "Haemolysis Type": "None",
    "Media Grown On": [
      "Blood Agar"
    ],
    "Colony Morphology": [
      "Small",
      "Grey",
      "Convex"
    ],
    "Oxygen Requirement": "Obligate Anaerobe",
    "Growth Temperature": "35//37",
    "Catalase": "Negative",
    "Oxidase": "Negative",
    "Indole": "Negative",
    "Urease": "Negative",
    "Citrate": "Negative",
    "Methyl Red": "Negative",
    "VP": "Negative",
    "H2S": "Negative",
    "DNase": "Negative",
    "ONPG": "Negative",
    "Coagulase": "Negative",
    "Gelatin Hydrolysis": "Negative",
    "Esculin Hydrolysis": "Negative",
    "Nitrate Reduction": "Negative",
    "NaCl Tolerant (>=6%)": "Negative",
    "Lipase Test": "Negative",
    "Lysine Decarboxylase": "Negative",
    "Ornithine Decarboxylase": "Negative",
    "Ornitihine Decarboxylase": "Negative",
    "Arginine dihydrolase": "Negative",
    "Glucose Fermentation": "Negative",
    "Lactose Fermentation": "Negative",
    "Sucrose Fermentation": "Negative",
    "Maltose Fermentation": "Negative",
    "Mannitol Fermentation": "Negative",
    "Sorbitol Fermentation": "Negative",
    "Xylose Fermentation": "Negative",
    "Rhamnose Fermentation": "Negative",
    "Arabinose Fermentation": "Negative",
    "Raffinose Fermentation": "Negative",
    "Trehalose Fermentation": "Negative",
    "Inositol Fermentation": "Negative",
    "Gas Production": "Negative",
    "TSI Pattern": "K/K",
    "Colony Pattern": "Unknown",
    "Pigment": "None",
    "Motility Type": "None"
  },

  "species_markers": [
    {
      "field": "Amino Acid Fermentation",
      "value": "Positive",
      "importance": "high",
      "notes": "Primary metabolic pathway distinguishing Acidaminococcus species."
    }
  ],

  "common_confusions": [
    {
      "genus": "Veillonella",
      "reason": "Both are anaerobic Gram-negative cocci isolated from similar sites."
    }
  ],

  "when_to_question_identification": [
    "Carbohydrate fermentation suggests Veillonella.",
    "Aerobic growth is inconsistent with A. fermentans.",
    "Rod-shaped morphology excludes this species."
  ],

  "recommended_next_tests": [
    {
      "test": "Anaerobic growth verification",
      "reason": "Confirms obligate anaerobic metabolism."
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Reliable identification due to limited biochemical activity."
    }
  ]
}