identifier: METPO:1000607
label: obligately anaerobic
definition: An oxygen preference in which molecular oxygen (O₂) inhibits or prevents
  growth.
definition_source: https://www.ncbi.nlm.nih.gov/books/NBK482349/
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000601
synonyms:
- synonym_text: obligate anaerobe
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: obligate anaerobic
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: https://www.ncbi.nlm.nih.gov/books/NBK482349/
  snippet: Oxygen is toxic to anaerobes
  notes: Supports oxygen inhibition/toxicity for obligately anaerobic organisms.
- reference: PMID:22778399
  snippet: obligate anaerobe Bacteroides fragilis
  notes: 'Organism example: Bacteroides fragilis is described as an obligate anaerobe.'
canonical_examples:
- taxon_id: NCBITaxon:1488
  taxon_label: Clostridium acetobutylicum
  note: "Model obligate anaerobe (ABE fermentation; oxygen-sensitive)."
  reference: PMID:11466286
causal_graphs:
- graph_id: obligate_anaerobe_oxygen_toxicity
  title: Obligate anaerobe oxygen-toxicity mechanism
  description: Evidence-backed causal sketch linking obligate anaerobiosis to oxygen-blocked
    growth and oxygen-sensitive metabolic chemistry.
  nodes:
  - node_id: obligate_anaerobic_trait
    label: obligately anaerobic
    node_type: TRAIT
    grounding: METPO:1000607
    description: Molecular oxygen inhibits or prevents growth.
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Dioxygen exposure that blocks obligate anaerobe growth.
  - node_id: reactive_oxygen_species
    label: reactive oxygen species
    node_type: CHEMICAL
    grounding: CHEBI:26523
    description: Oxygen-derived oxidants such as superoxide and hydrogen peroxide.
  - node_id: low_potential_metal_centres
    label: low-potential metal centres
    node_type: MOLECULAR_FUNCTION
    description: Oxygen-sensitive catalytic centers used in anaerobic metabolism.
  - node_id: anaerobic_metabolism
    label: anaerobic metabolism
    node_type: BIOLOGICAL_PROCESS
    description: Energy metabolism optimized for anoxic conditions.
  - node_id: oxygen_exposure
    label: oxygen exposure
    node_type: ENVIRONMENTAL_FACTOR
    description: Exposure of anaerobic cells to molecular oxygen, triggering oxidative
      stress.
  - node_id: oxidative_damage_biomolecules
    label: oxidative damage to biomolecules
    node_type: BIOLOGICAL_PROCESS
    description: ROS-mediated oxidative damage to proteins and nucleic acids.
  - node_id: hydrogen_peroxide
    label: hydrogen peroxide
    node_type: CHEMICAL
    description: Reactive oxygen species; substrate for Fenton chemistry.
    grounding: CHEBI:16240
  - node_id: ferrous_iron
    label: ferrous iron (Fe(II))
    node_type: CHEMICAL
    description: Fe(II) reactant driving hydroxyl-radical generation via Fenton reaction.
  - node_id: hydroxyl_radical
    label: hydroxyl radical
    node_type: CHEMICAL
    description: Highly damaging ROS produced via Fenton chemistry.
    grounding: CHEBI:29191
  - node_id: dna_damage
    label: DNA damage
    node_type: BIOLOGICAL_PROCESS
    description: Irreparable lesions blocking replication caused by hydroxyl radicals.
  - node_id: pyruvate_formate_lyase
    label: pyruvate formate-lyase (PFL)
    node_type: GENE_OR_PROTEIN
    description: Glycyl-radical enzyme rapidly inactivated by O2.
  - node_id: pyruvate_ferredoxin_oxidoreductase
    label: pyruvate:ferredoxin oxidoreductase (PFOR)
    node_type: GENE_OR_PROTEIN
    description: O2-sensitive anaerobic metalloenzyme.
  - node_id: fefe_hydrogenase
    label: '[FeFe]-hydrogenase'
    node_type: GENE_OR_PROTEIN
    description: Oxygen-sensitive low-potential redox enzyme.
  edges:
  - subject: molecular_oxygen
    predicate: inhibits
    object: obligate_anaerobic_trait
    description: Oxygen blocks growth of obligate anaerobes.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: oxygen blocks their growth
      notes: Review identifies blocked growth as the defining trait of obligate anaerobes.
    predicate_id: RO:0002212
  - subject: anaerobic_metabolism
    predicate: depends on
    object: low_potential_metal_centres
    description: Obligate anaerobic metabolism often relies on oxygen-sensitive radical
      chemistry and low-potential metal centers.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: radical chemistry and low-potential metal centres
      notes: Supports low-potential metal centers as anaerobic metabolic features.
    predicate_id: RO:0002502
  - subject: molecular_oxygen
    predicate: poisons
    object: low_potential_metal_centres
    description: Dioxygen can directly poison catalytic sites central to anaerobic
      metabolism.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: direct poisoning by molecular oxygen and ROS
      notes: Supports oxygen-sensitive catalytic sites as a mechanism of growth inhibition.
  - subject: reactive_oxygen_species
    predicate: damages
    object: low_potential_metal_centres
    description: ROS provide an additional route for damage to oxygen-sensitive anaerobic
      enzymes.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: direct poisoning by molecular oxygen and ROS
      notes: Supports ROS-mediated impairment of anaerobic catalytic sites.
  - subject: oxygen_exposure
    predicate: causes
    object: reactive_oxygen_species
    description: O2 exposure generates ROS such as superoxide, peroxides, and hydroxyl
      radicals.
    evidence:
    - reference: DOI:10.1186/s40168-024-01909-7
      notes: As a consequence of oxygenation, reactive oxygen species like superoxide,
        peroxides, and hydroxyl radicals are produced.
    predicate_id: biolink:causes
  - subject: oxygen_exposure
    predicate: causes
    object: oxidative_damage_biomolecules
    description: O2 exposure causes oxidative stress damaging biomolecules.
    evidence:
    - reference: DOI:10.1186/s40168-024-01909-7
      notes: ROS cause oxidative stress due to damage to biomolecules like proteins
        and nucleic acids.
    predicate_id: biolink:causes
  - subject: hydrogen_peroxide
    predicate: causes
    object: hydroxyl_radical
    description: H2O2 reacts with Fe(II) to produce hydroxyl radicals (Fenton chemistry).
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      notes: Fe(II)+H2O2 produces hydroxyl radicals.
    predicate_id: biolink:causes
  - subject: ferrous_iron
    predicate: causes
    object: hydroxyl_radical
    description: Fe(II) drives hydroxyl-radical generation via the Fenton reaction.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      notes: Fe(II)+H2O2 produces hydroxyl radicals.
    predicate_id: biolink:causes
  - subject: hydroxyl_radical
    predicate: causes
    object: dna_damage
    description: Hydroxyl radicals create irreparable lesions and block replication.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      notes: hydroxyl radicals create irreparable lesions and block replication.
    predicate_id: biolink:causes
  - subject: molecular_oxygen
    predicate: inactivates
    object: pyruvate_formate_lyase
    description: O2 rapidly inactivates the glycyl-radical enzyme PFL.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      notes: PFL is rapidly inactivated by O2; even low O2 levels can inactivate PFL
        within seconds.
  - subject: molecular_oxygen
    predicate: inactivates
    object: pyruvate_ferredoxin_oxidoreductase
    description: O2 directly inactivates the metalloenzyme PFOR.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      notes: O2 directly inactivates diverse metalloenzymes (e.g., PFOR).
  - subject: molecular_oxygen
    predicate: inactivates
    object: fefe_hydrogenase
    description: O2 directly inactivates oxygen-sensitive [FeFe]-hydrogenases.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      notes: O2 directly inactivates diverse metalloenzymes... hydrogenases.
curation_history:
- timestamp: '2026-05-05T01:35:46.852690+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: Added definition source and evidence for oxygen-sensitive anaerobic growth.
  llm_assisted: true
- timestamp: '2026-05-05T18:39:46-07:00'
  curator: codex
  action: ADDED_ORGANISM_EXAMPLE
  changes: Added Bacteroides fragilis 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 oxygen toxicity in obligate anaerobes.
  llm_assisted: true
- timestamp: '2026-05-23T08:21:49Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002502×1).
  llm_assisted: true
- timestamp: '2026-06-13T21:03:25Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002212×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 8 evidence-backed generic edges (9 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:10Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:causes×5).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:31Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:16240×1, CHEBI:29191×1).
  llm_assisted: true