identifier: METPO:1000601
label: oxygen preference
definition: A phenotype that is relating to an organism's oxygen requirements or tolerance
  for growth.
definition_source: PMID:21413255
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000059
synonyms:
- synonym_text: Physiology and metabolism.oxygen tolerance.oxygen tolerance
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: metabolism
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: PMID:21413255
  snippet: aerobes require molecular oxygen as a terminal electron acceptor
  notes: Medical Microbiology chapter supports molecular oxygen as the environmental
    axis defining oxygen-preference phenotypes.
- reference: DOI:10.1016/j.bbabio.2011.06.016
  snippet: respiratory quinol:O2 oxidoreductase
  notes: Aerobic respiration review supports terminal oxidases as the enzymatic interface
    between cells and ambient O2.
causal_graphs:
- graph_id: oxygen_preference_o2_availability_axis
  title: Oxygen-preference O2-availability axis
  description: DOI-backed graph linking ambient molecular-oxygen availability to the
    four child oxygen-preference phenotypes (aerobic, anaerobic, microaerophilic,
    facultative) that classify how organisms use or tolerate O2.
  nodes:
  - node_id: oxygen_preference_trait
    label: oxygen preference
    node_type: TRAIT
    grounding: METPO:1000601
    description: Classification of an organism's oxygen requirements or tolerance
      for growth.
  - node_id: ambient_oxygen
    label: ambient molecular oxygen
    node_type: ENVIRONMENTAL_FACTOR
    description: Ambient O2 concentration imposed on the cell.
  - node_id: aerobic_phenotype
    label: aerobic
    node_type: TRAIT
    grounding: METPO:1000602
    description: Growth in the presence of molecular oxygen using O2 as terminal electron
      acceptor.
  - node_id: anaerobic_phenotype
    label: anaerobic
    node_type: TRAIT
    grounding: METPO:1000603
    description: Growth in the absence of molecular oxygen.
  - node_id: microaerophilic_phenotype
    label: microaerophilic
    node_type: TRAIT
    grounding: METPO:1000604
    description: Growth at low molecular-oxygen concentrations.
  - node_id: facultative_phenotype
    label: facultative oxygen preference
    node_type: TRAIT
    grounding: METPO:1000612
    description: Growth across a range of oxygen availabilities, switching between
      aerobic and anaerobic metabolism.
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    description: O2 used as a terminal electron acceptor in aerobic respiration.
    grounding: CHEBI:15379
  - node_id: oxygen_terminal_electron_acceptor
    label: O2 as terminal electron acceptor
    node_type: MOLECULAR_FUNCTION
    description: Use of molecular oxygen as the terminal electron acceptor of the
      respiratory chain.
  - node_id: reactive_oxygen_species_stress
    label: oxygen / reactive oxygen species stress
    node_type: ENVIRONMENTAL_FACTOR
    description: Exposure to O2 and reactive oxygen species such as hydrogen peroxide.
  - node_id: detoxifying_enzyme_expression
    label: detoxifying-enzyme gene expression
    node_type: BIOLOGICAL_PROCESS
    description: Upregulation of genes encoding oxidative-stress detoxifying enzymes.
  - node_id: catalase
    label: catalase
    node_type: GENE_OR_PROTEIN
    description: Enzyme that degrades hydrogen peroxide to water and oxygen.
    grounding: UniProtKB:A0A071MK53
  - node_id: hydrogen_peroxide
    label: hydrogen peroxide
    node_type: CHEMICAL
    description: Reactive oxygen species produced during aerobic metabolism.
    grounding: CHEBI:16240
  - node_id: superoxide_dismutase
    label: superoxide dismutase
    node_type: GENE_OR_PROTEIN
    description: Enzyme that dismutates superoxide; key oxidative-stress defense.
    grounding: UniProtKB:A0A009QPW9
  - node_id: oxygen_tolerance
    label: oxygen tolerance
    node_type: CAPACITY
    description: Capacity of a cell to survive exposure to molecular oxygen.
  edges:
  - subject: ambient_oxygen
    predicate: defines
    object: oxygen_preference_trait
    description: Ambient molecular-oxygen concentration is the quantitative axis defining
      oxygen-preference phenotypes.
    evidence:
    - reference: DOI:10.3389/fmicb.2014.00674
      snippet: various capacities in their utilization of molecular oxygen
      notes: Supports molecular oxygen utilization as the classification axis for
        oxygen-preference phenotypes.
    predicate_id: METPO:2007500
  - subject: aerobic_phenotype
    predicate: is a
    object: oxygen_preference_trait
    description: Aerobic is a child oxygen-preference phenotype.
    evidence:
    - reference: DOI:10.3389/fmicb.2014.00674
      snippet: aerobic ... respiration capacities
      notes: Supports aerobic as an oxygen-use phenotype within oxygen-preference
        classification.
    predicate_id: rdfs:subClassOf
  - subject: anaerobic_phenotype
    predicate: is a
    object: oxygen_preference_trait
    description: Anaerobic is a child oxygen-preference phenotype.
    evidence:
    - reference: DOI:10.3389/fmicb.2014.00674
      snippet: aerobic, microaerobic, and anaerobic reductases
      notes: Supports anaerobic as a distinct oxygen-preference classification.
    predicate_id: rdfs:subClassOf
  - subject: microaerophilic_phenotype
    predicate: is a
    object: oxygen_preference_trait
    description: Microaerophilic is a child oxygen-preference phenotype.
    evidence:
    - reference: DOI:10.3389/fmicb.2014.00674
      snippet: aerophilic, microaerophilic, or anaerobic
      notes: Supports microaerophilic as a low-O2 setting on the oxygen-preference
        axis.
    predicate_id: rdfs:subClassOf
  - subject: facultative_phenotype
    predicate: is a
    object: oxygen_preference_trait
    description: Facultative oxygen preference is a child oxygen-preference phenotype.
    evidence:
    - reference: DOI:10.1111/cmi.13338
      snippet: cope with changing oxygen levels
      notes: Supports facultative organisms as a mixed-O2 setting on the oxygen-preference
        axis, switching between aerobic and anaerobic metabolism.
    predicate_id: rdfs:subClassOf
  - subject: oxygen_terminal_electron_acceptor
    predicate: enables
    object: aerobic_phenotype
    description: Obligate aerobic growth depends on molecular oxygen as terminal electron
      acceptor.
    evidence:
    - reference: DOI:10.1371/journal.ppat.1012084
      notes: Obligate aerobes use only oxygen as the terminal electron acceptor, defining
        aerobic oxygen-preference.
    predicate_id: RO:0002327
  - subject: molecular_oxygen
    predicate: serves as
    object: oxygen_terminal_electron_acceptor
    description: Molecular oxygen functions as the terminal electron acceptor in aerobic
      respiration.
    evidence:
    - reference: DOI:10.1371/journal.ppat.1012084
      notes: Oxygen is used as the terminal electron acceptor of the aerobic respiratory
        chain.
  - subject: reactive_oxygen_species_stress
    predicate: upregulates
    object: detoxifying_enzyme_expression
    description: O2 or H2O2 stress upregulates detoxifying-enzyme genes.
    evidence:
    - reference: DOI:10.1128/aem.00606-23
      notes: Expression of genes encoding detoxifying enzymes was upregulated in response
        to O2 or H2O2 stress.
  - subject: detoxifying_enzyme_expression
    predicate: increases
    object: oxygen_tolerance
    description: A larger detoxifying-enzyme repertoire increases survival under oxygen
      exposure.
    evidence:
    - reference: DOI:10.1128/aem.00606-23
      notes: Cells with more detoxifying genes survived longer than those with few
        scavenging enzymes.
    predicate_id: RO:0002213
  - subject: catalase
    predicate: degrades
    object: hydrogen_peroxide
    description: Catalase rapidly degrades hydrogen peroxide, a reactive oxygen species.
    evidence:
    - reference: DOI:10.1038/s43705-023-00251-7
      notes: Catalase is the most prominent enzyme for H2O2 degradation at higher
        concentrations.
    predicate_id: METPO:2000007
  - subject: superoxide_dismutase
    predicate: increases
    object: oxygen_tolerance
    description: Higher superoxide dismutase activity is associated with higher oxygen
      tolerance.
    evidence:
    - reference: DOI:10.1038/s43705-023-00251-7
      notes: Higher Sod activity corresponded to higher oxygen tolerance.
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-05-05T01:35:46.848644+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-13T11:30:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph framing oxygen preference as the O2-availability
    axis with child aerobic, anaerobic, microaerophilic, and facultative phenotypes.
  llm_assisted: true
- timestamp: '2026-05-13T22:45:00-07:00'
  curator: codex
  action: IMPROVED_CAUSAL_GRAPH_EVIDENCE
  changes: Replaced PMID fallback CausalEdge references with DOI-backed oxygen-utilization
    and facultative oxygen-response citations.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:30Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (rdfs:subClassOf×4).
  llm_assisted: true
- timestamp: '2026-05-24T07:37:39Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007500×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 evidence-backed generic edges (8 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:10Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×2, RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:17Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:15379×1, UniProtKB:A0A071MK53×1, UniProtKB:A0A009QPW9×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:31Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:16240×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:37Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000007×1).
  llm_assisted: true