identifier: METPO:1000605
label: facultatively anaerobic
definition: An oxygen preference in which growth can occur with or without molecular
  oxygen (O₂).
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: facultative
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: facultative anaerobe
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: https://www.ncbi.nlm.nih.gov/books/NBK482349/
  snippet: can grow in the presence or absence of oxygen
  notes: Supports facultative anaerobiosis as growth under oxic or anoxic conditions.
- reference: DOI:10.1093/femsre/fuac008
  snippet: Escherichia coli is a facultative anaerobe
  notes: 'Organism example: Escherichia coli is described as facultatively anaerobic.'
canonical_examples:
- taxon_id: NCBITaxon:562
  taxon_label: Escherichia coli
  note: "grows aerobically or by fermentation/anaerobic respiration"
  reference: PMID:7747938
- taxon_id: NCBITaxon:1280
  taxon_label: Staphylococcus aureus
  note: "facultative anaerobe"
  reference: PMID:24628867
causal_graphs:
- graph_id: facultative_anaerobe_oxygen_switch
  title: Facultative anaerobe oxygen-responsive metabolism
  description: Evidence-backed causal sketch linking facultative anaerobiosis to oxygen-responsive
    switching between aerobic and anaerobic metabolism.
  nodes:
  - node_id: facultative_anaerobic_trait
    label: facultatively anaerobic
    node_type: TRAIT
    grounding: METPO:1000605
    description: Growth can occur with or without molecular oxygen.
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Dioxygen acts as a respiratory substrate and regulatory signal.
  - node_id: aerobic_respiration
    label: aerobic respiration
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0009060
    description: Oxygen-dependent respiratory energy metabolism.
  - node_id: anaerobic_respiration
    label: anaerobic respiration
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0009061
    description: Respiratory energy metabolism using non-oxygen electron acceptors.
  - node_id: fnr_regulator
    label: FNR oxygen-responsive regulator
    node_type: GENE_OR_PROTEIN
    description: Oxygen-dependent transcriptional regulator of anaerobic respiration
      genes in E. coli.
  - node_id: arca_regulator
    label: ArcA/ArcAB two-component regulator
    node_type: GENE_OR_PROTEIN
    description: Two-component regulatory system that represses the aerobic respiration
      program during the aerobic-to-anaerobic transition.
  - node_id: alternative_electron_acceptors
    label: alternative terminal electron acceptors
    node_type: CHEMICAL
    description: Non-oxygen terminal electron acceptors (e.g. nitrate, fumarate, DMSO,
      TMAO) used for anaerobic electron transport.
  - node_id: anaerobic_etc
    label: anaerobic electron transport chain operation
    node_type: BIOLOGICAL_PROCESS
    description: Operation of the electron transport chain using non-oxygen terminal
      electron acceptors when O2 is absent.
  edges:
  - subject: molecular_oxygen
    predicate: enables
    object: aerobic_respiration
    description: In facultative anaerobes, oxygen availability permits aerobic respiration.
    evidence:
    - reference: DOI:10.1111/cmi.13338
      snippet: cope with changing oxygen levels
      notes: Review frames facultative anaerobe fitness around changing oxygen availability;
        exact pathways vary by organism.
    predicate_id: RO:0002327
  - subject: molecular_oxygen
    predicate: regulates
    object: fnr_regulator
    description: FNR senses oxygen status and changes respiratory gene expression.
    evidence:
    - reference: DOI:10.1007/BF00445650
      snippet: molecular oxygen is an important regulatory signal
      notes: Review describes oxygen-dependent regulation by FNR.
    predicate_id: RO:0002211
  - subject: fnr_regulator
    predicate: activates in absence of oxygen
    object: anaerobic_respiration
    description: FNR activates anaerobic respiratory gene expression under anoxic
      conditions.
    evidence:
    - reference: DOI:10.1007/BF00445650
      snippet: activates transcription in the absence of O2
      notes: Supports FNR activation of anaerobic respiration genes without oxygen.
  - subject: facultative_anaerobic_trait
    predicate: has alternative process
    object: anaerobic_respiration
    description: Facultative anaerobiosis includes the capacity to grow using anaerobic
      respiration when oxygen is absent.
    evidence:
    - reference: DOI:10.1007/BF00445650
      snippet: expression of anaerobic respiration
      notes: E. coli-focused evidence for anaerobic respiratory programs in a facultative
        anaerobe.
  - subject: molecular_oxygen
    predicate: oxidizes/inactivates
    object: fnr_regulator
    description: Oxygen oxidizes the FNR [4Fe-4S] cluster, inactivating FNR and preventing
      transcription of anaerobic respiration genes.
    evidence:
    - reference: DOI:10.1101/2025.01.08.631794
      notes: In the presence of oxygen, FNR is inactivated through oxidation of its
        FeS cluster, preventing transcription of anaerobic respiration genes.
  - subject: arca_regulator
    predicate: represses
    object: aerobic_respiration
    description: ArcAB represses the aerobic respiration program, mediating metabolic
      adaptation to lower oxygen.
    evidence:
    - reference: DOI:10.1128/mbio.01448-23
      notes: ArcAB, a two-component regulatory system that represses aerobic respiration,
        is a key mediator of metabolic adaptation.
  - subject: alternative_electron_acceptors
    predicate: enable
    object: anaerobic_etc
    description: Alternative terminal electron acceptors enable anaerobic electron
      transport chain operation when oxygen is absent.
    evidence:
    - reference: DOI:10.1038/s41467-024-51029-x
      notes: Alternative terminal electron acceptors (nitrate, fumarate, DMSO, TMAO)
        allow anaerobic ETC operation when O2 is absent.
  - subject: anaerobic_etc
    predicate: is part of
    object: anaerobic_respiration
    description: Anaerobic ETC operation constitutes the respiratory energy metabolism
      used in the absence of oxygen.
    evidence:
    - reference: DOI:10.1038/s41467-024-51029-x
      notes: Anaerobic ETC operation with alternative terminal electron acceptors
        underlies anaerobic respiration in facultative anaerobes.
curation_history:
- timestamp: '2026-05-05T01:35:46.851077+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 facultative anaerobic growth.
  llm_assisted: true
- timestamp: '2026-05-05T18:39:46-07:00'
  curator: codex
  action: ADDED_ORGANISM_EXAMPLE
  changes: Added Escherichia coli organism example with DOI-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-responsive facultative anaerobic
    metabolism.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:29Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1, RO:0002211×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 4 evidence-backed generic edges (3 new nodes) from the deep-research
    report.
  llm_assisted: true