identifier: METPO:1000611
label: strictly anaerobic
definition: An obligately anaerobic oxygen preference in which a microorganism does
  not grow in the presence of oxygen gas (O₂).
definition_source: https://www.ncbi.nlm.nih.gov/books/NBK482349/
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000607
synonyms:
- synonym_text: strict obligate anaerobe
  synonym_type: RELATED_SYNONYM
  source: https://www.ncbi.nlm.nih.gov/books/NBK482349/
evidence:
- reference: https://www.ncbi.nlm.nih.gov/books/NBK482349/
  snippet: will not survive if there is more than half a percent oxygen
  notes: Supports strict anaerobiosis as a highly oxygen-sensitive subtype.
- reference: PMID:39189748
  snippet: Clostridioides difficile is a strict anaerobic, sporulating Firmicutes
  notes: 'Organism example: Clostridioides difficile is described as strictly anaerobic.'
canonical_examples:
- taxon_id: NCBITaxon:817
  taxon_label: Bacteroides fragilis
  note: "Aerotolerant obligate anaerobe; abundant gut anaerobe model. Clostridium spp. are alternative strict-anaerobe exemplars."
  reference: PMID:14749831
causal_graphs:
- graph_id: strict_anaerobe_oxygen_sensitivity
  title: Strict anaerobe oxygen-sensitivity mechanism
  description: Evidence-backed causal sketch linking strict anaerobic growth to anoxic
    environments and oxygen-sensitive cellular chemistry.
  nodes:
  - node_id: strictly_anaerobic_trait
    label: strictly anaerobic
    node_type: TRAIT
    grounding: METPO:1000611
    description: Does not grow in the presence of oxygen gas.
  - node_id: anoxic_condition
    label: anoxic condition
    node_type: ENVIRONMENTAL_FACTOR
    description: Oxygen-excluding environment required for strict anaerobic growth.
    grounding: PATO:0001456
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Dioxygen exposure that prevents strict anaerobe growth.
  - node_id: reactive_oxygen_species
    label: reactive oxygen species
    node_type: CHEMICAL
    grounding: CHEBI:26523
    description: Oxygen-derived oxidants.
  - node_id: oxygen_sensitive_enzymes
    label: oxygen-sensitive enzymes
    node_type: GENE_OR_PROTEIN
    description: Anaerobic enzymes vulnerable to oxygen or ROS.
  - node_id: iron_sulfur_cluster_enzymes
    label: iron-sulfur cluster enzymes
    node_type: GENE_OR_PROTEIN
    description: Mononuclear iron enzymes and solvent-exposed iron-sulfur cluster
      enzymes that are directly oxidized by oxygen.
  - node_id: glycyl_radical_enzymes
    label: glycyl radical enzymes
    node_type: GENE_OR_PROTEIN
    description: Enzyme class inherently incompatible with molecular oxygen.
  - node_id: low_potential_metabolic_enzymes
    label: low-potential energy-metabolism enzymes (PFOR/PFL)
    node_type: GENE_OR_PROTEIN
    description: Oxygen-sensitive anaerobic energy-metabolism enzymes such as pyruvate:ferredoxin
      oxidoreductase (PFOR) and pyruvate formate lyase (PFL).
  edges:
  - subject: anoxic_condition
    predicate: enables
    object: strictly_anaerobic_trait
    description: Strict anaerobes require oxygen-excluding conditions for growth.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: hypoxic or anoxic conditions
      notes: Review supports anoxic environments as the ecological context for anaerobe
        growth.
    predicate_id: RO:0002327
  - subject: molecular_oxygen
    predicate: inhibits
    object: strictly_anaerobic_trait
    description: Oxygen exposure blocks strict anaerobic growth.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: oxygen blocks their growth
      notes: Supports oxygen as an inhibitory exposure for obligate anaerobes.
    predicate_id: RO:0002212
  - subject: molecular_oxygen
    predicate: causes formation of
    object: reactive_oxygen_species
    description: Oxygen exposure can generate reactive oxygen stress.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: molecular oxygen and ROS
      notes: Review links oxygen exposure to ROS stress in anaerobes.
    predicate_id: biolink:produces
  - subject: reactive_oxygen_species
    predicate: damages
    object: oxygen_sensitive_enzymes
    description: ROS can impair oxygen-sensitive anaerobic enzyme systems.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: poisoning by molecular oxygen and ROS
      notes: Supports enzyme vulnerability as a mechanism of oxygen toxicity.
  - subject: molecular_oxygen
    predicate: oxidizes/inactivates
    object: iron_sulfur_cluster_enzymes
    description: Oxygen directly oxidizes mononuclear iron enzymes and solvent-exposed
      iron-sulfur clusters.
    evidence:
    - reference: DOI:10.1128/iai.00502-24
      notes: '"oxygen directly oxidizes mononuclear iron enzymes and solvent-exposed
        iron-sulfur clusters" - general oxygen toxicity mechanism across anaerobes.'
  - subject: molecular_oxygen
    predicate: inactivates
    object: glycyl_radical_enzymes
    description: Glycyl radical enzymes are inherently incompatible with molecular
      oxygen.
    evidence:
    - reference: DOI:10.1128/iai.00502-24
      notes: '"Certain enzyme classes (e.g., glycyl radical enzymes) are inherently
        incompatible with molecular oxygen" - broad across taxa.'
  - subject: molecular_oxygen
    predicate: inactivates
    object: low_potential_metabolic_enzymes
    description: Key anaerobic energy-metabolism enzymes (PFOR, PFL) with low-potential
      Fe-S clusters are oxygen sensitive.
    evidence:
    - reference: DOI:10.1038/s43705-023-00251-7
      notes: '"key enzymes involved in energy metabolism in anaerobes such as pyruvate
        ferrodoxin oxidoreductase (PFOR), pyruvate formate lyase (PFL)... are known
        to be O2 sensitive" - general anaerobe biology.'
curation_history:
- timestamp: '2026-05-05T01:35:46.855051+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-05T01:09:05-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Clarified wording, added definition source, synonym, and evidence.
  llm_assisted: true
- timestamp: '2026-05-05T18:39:46-07:00'
  curator: codex
  action: ADDED_ORGANISM_EXAMPLE
  changes: Added Clostridioides difficile organism example with PMID-backed evidence.
  llm_assisted: true
- timestamp: '2026-05-10T00:00:00-07:00'
  curator: codex
  action: ADDED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph for strict anaerobe oxygen sensitivity.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:30Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:38:00Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (ENVO:01001057×1).
  llm_assisted: true
- timestamp: '2026-06-13T21:03:25Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002212×1, biolink:produces×1).
  llm_assisted: true
- timestamp: '2026-06-15T07:19:08Z'
  curator: claude
  action: FIX_NODE_GROUNDING_CURIE
  changes: Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label
    fix; verified vs OAK).
  llm_assisted: true
- timestamp: '2026-06-17T04:09:43Z'
  curator: claude
  action: REMOVE_REDUNDANT_SYNONYM
  changes: Removed 1 synonym(s) whose text duplicated the label (seeder redundancy;
    no information lost).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 3 evidence-backed generic edges (3 new nodes) from the deep-research
    report.
  llm_assisted: true