data/rag/knowledge_base/Acidaminococcus/genus.json

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

  "overview": {
    "short": "Acidaminococcus species are Gram-negative, anaerobic cocci belonging to the class Negativicutes, characterized by amino acid fermentation rather than carbohydrate metabolism.",
    "clinical_context": "Part of the normal gastrointestinal flora and occasionally isolated 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"
  },

  "field_notes": {
    "Gram Stain": "Despite being Gram-negative, Acidaminococcus belongs to a lineage phylogenetically related to Gram-positive bacteria.",
    "Glucose Fermentation": "Species do not ferment carbohydrates and instead utilize amino acids for energy.",
    "Oxygen Requirement": "Strict anaerobiosis is a defining characteristic."
  },

  "key_differentiators": [
    {
      "field": "Oxygen Requirement",
      "expected": "Obligate Anaerobe",
      "distinguishes_from": ["Neisseria", "Veillonella"],
      "notes": "Strict anaerobic growth separates Acidaminococcus from aerobic Gram-negative cocci."
    },
    {
      "field": "Shape",
      "expected": "Cocci",
      "distinguishes_from": ["Bacteroides", "Fusobacterium"],
      "notes": "Coccoid morphology helps differentiate from anaerobic Gram-negative rods."
    },
    {
      "field": "Glucose Fermentation",
      "expected": "Negative",
      "distinguishes_from": ["Veillonella"],
      "notes": "Lack of carbohydrate fermentation supports Acidaminococcus."
    }
  ],

  "common_confusions": [
    {
      "genus": "Veillonella",
      "reason": "Both are anaerobic Gram-negative cocci isolated from similar clinical contexts."
    },
    {
      "genus": "Megasphaera",
      "reason": "Phylogenetic relatedness within Negativicutes."
    }
  ],

  "when_to_question_identification": [
    "Aerobic or facultative growth argues against Acidaminococcus.",
    "Carbohydrate fermentation suggests Veillonella.",
    "Rod-shaped morphology excludes this genus."
  ],

  "recommended_next_tests": [
    {
      "test": "Anaerobic growth confirmation",
      "reason": "Essential for correct genus assignment."
    },
    {
      "test": "Amino acid fermentation profiling",
      "reason": "Characteristic metabolic feature of Acidaminococcus."
    },
    {
      "test": "MALDI-TOF MS",
      "reason": "Recommended due to biochemical inertness and rarity."
    }
  ],

  "supported_species": [
    "fermentans",
    "intestini"
  ]
}