identifier: METPO:1000604
label: microaerophilic
definition: An oxygen preference that requires molecular oxygen (O₂) at concentrations
  lower than atmospheric.
definition_source: https://www.ncbi.nlm.nih.gov/books/NBK154539/
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000601
synonyms:
- synonym_text: Ox_microerophile
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: microaerophile
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: https://www.ncbi.nlm.nih.gov/books/NBK154539/
  snippet: require oxygen to survive but require its presence in lower concentrations
  notes: Supports microaerophily as oxygen requirement below atmospheric concentration.
- reference: PMID:26284041
  snippet: C. jejuni is a microaerophilic, fastidious bacterium
  notes: 'Organism example: Campylobacter jejuni is described as microaerophilic.'
canonical_examples:
- taxon_id: NCBITaxon:197
  taxon_label: Campylobacter jejuni
  note: "Canonical microaerophile (requires reduced O2, ~5-10%)."
  reference: PMID:26284041
causal_graphs:
- graph_id: microaerophile_low_oxygen_respiration
  title: Microaerophilic low-oxygen respiration mechanism
  description: Evidence-backed causal sketch linking microaerophily to microoxic environments
    and high-affinity terminal oxidases.
  nodes:
  - node_id: microaerophilic_trait
    label: microaerophilic
    node_type: TRAIT
    grounding: METPO:1000604
    description: Growth requires oxygen below atmospheric concentration.
  - node_id: microoxic_environment
    label: microoxic environment
    node_type: ENVIRONMENTAL_FACTOR
    description: Low-oxygen zone that supports microaerobic respiration.
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Dioxygen present at low concentration.
  - node_id: high_affinity_terminal_oxidase
    label: high-affinity terminal oxidase
    node_type: GENE_OR_PROTEIN
    description: Respiratory oxidase enabling oxygen use at low concentration.
  - node_id: cbb3_oxidase
    label: cytochrome cbb3 oxidase
    node_type: GENE_OR_PROTEIN
    description: High-affinity cytochrome oxidase associated with microaerobic metabolism.
  - node_id: cytochrome_bd_oxidase
    label: cytochrome bd ubiquinol oxidase
    node_type: GENE_OR_PROTEIN
    description: High-affinity quinol oxidase widespread in low-oxygen-adapted bacteria.
    grounding: UniProtKB:A0A0N0XA94
  - node_id: low_oxygen_respiration
    label: respiration under low oxygen
    node_type: BIOLOGICAL_PROCESS
    description: Aerobic respiratory electron transport carried out at low O2 concentrations.
  - node_id: branched_respiratory_chain
    label: branched respiratory chain
    node_type: PATHWAY
    description: Respiratory chain with multiple terminal oxidase branches.
  - node_id: oxygen_adaptation
    label: adaptation to fluctuating oxygen
    node_type: BIOLOGICAL_PROCESS
    description: Physiological adjustment to changing environmental O2 levels.
  - node_id: catalase_kata
    label: catalase (KatA)
    node_type: GENE_OR_PROTEIN
    description: Enzyme that detoxifies hydrogen peroxide.
  - node_id: hydrogen_peroxide
    label: hydrogen peroxide
    node_type: CHEMICAL
    description: Reactive oxygen species byproduct.
    grounding: CHEBI:16240
  - node_id: superoxide_dismutase_sodb
    label: superoxide dismutase (SodB)
    node_type: GENE_OR_PROTEIN
    description: Enzyme protecting against reactive oxygen species.
  - node_id: reactive_oxygen_species
    label: reactive oxygen species
    node_type: CHEMICAL
    description: ROS generated by oxygen exposure.
    grounding: CHEBI:26523
  - node_id: ahpc
    label: alkyl hydroperoxide reductase (AhpC)
    node_type: GENE_OR_PROTEIN
    description: Predominant H2O2 scavenger at low oxygen.
  edges:
  - subject: microoxic_environment
    predicate: enables
    object: microaerophilic_trait
    description: Microaerophiles grow optimally in microoxic conditions.
    evidence:
    - reference: DOI:10.1038/nrmicro2970
      snippet: microaerophiles grow optimally under microoxic conditions
      notes: Nature Reviews Microbiology analysis defines the microoxic context.
    predicate_id: RO:0002327
  - subject: high_affinity_terminal_oxidase
    predicate: enables use of
    object: molecular_oxygen
    description: High-affinity terminal oxidases enable respiration at scarce oxygen
      concentrations.
    evidence:
    - reference: DOI:10.1038/nrmicro2970
      snippet: harvest O2 present at low, even nanomolar, concentrations
      notes: Supports the low-oxygen respiratory role of high-affinity oxidases.
  - subject: high_affinity_terminal_oxidase
    predicate: contributes to
    object: microaerophilic_trait
    description: High-affinity terminal oxidases are mechanistic contributors to microaerophilic
      growth.
    evidence:
    - reference: DOI:10.1038/nrmicro2970
      snippet: provide microaerobes with access to scarce supplies of O2
      notes: Supports terminal oxidases as causal entities for low-oxygen growth.
    predicate_id: RO:0002326
  - subject: cbb3_oxidase
    predicate: has function
    object: high_affinity_terminal_oxidase
    description: The cbb3 oxidase is an example high-affinity oxidase for microaerobic
      metabolism.
    evidence:
    - reference: DOI:10.1042/BST0300653
      snippet: characterized by its high oxygen affinity
      notes: Supports cbb3 oxidase as a high-affinity oxygen-reducing enzyme.
    predicate_id: RO:0000085
  - subject: cbb3_oxidase
    predicate: enables
    object: low_oxygen_respiration
    description: cbb3-type cytochrome c oxidases are common in microaerophilic Proteobacteria
      and enable respiration under low O2.
    evidence:
    - reference: DOI:10.3390/ijms24076428
      notes: cbb3-type cytochrome c oxidases are common in microaerophilic Proteobacteria.
    predicate_id: RO:0002327
  - subject: cytochrome_bd_oxidase
    predicate: enables
    object: low_oxygen_respiration
    description: Cytochrome bd quinol oxidases are widespread in low-oxygen-adapted
      organisms and enable respiration under low O2.
    evidence:
    - reference: DOI:10.3390/ijms24076428
      notes: bd-type quinol oxidases are widespread in bacteria and archaea that live
        under low-oxygen conditions.
    predicate_id: RO:0002327
  - subject: branched_respiratory_chain
    predicate: enables
    object: oxygen_adaptation
    description: Branched respiratory chains enable microbes to adapt to fluctuating
      oxygen.
    evidence:
    - reference: DOI:10.3389/fmicb.2024.1468929
      notes: Branched respiratory chains enable microbes to adapt to fluctuating oxygen.
    predicate_id: RO:0002327
  - subject: catalase_kata
    predicate: detoxifies
    object: hydrogen_peroxide
    description: Catalase prevents hydrogen peroxide accumulation.
    evidence:
    - reference: DOI:10.3390/pathogens13100842
      notes: katA encodes catalase that prevents H2O2 accumulation.
  - subject: superoxide_dismutase_sodb
    predicate: protects against
    object: reactive_oxygen_species
    description: Superoxide dismutase protects against reactive oxygen species.
    evidence:
    - reference: DOI:10.3390/pathogens13100842
      notes: sodB encodes superoxide dismutase (SOD); it protects against ROS.
  - subject: ahpc
    predicate: scavenges
    object: hydrogen_peroxide
    description: AhpC is the predominant hydrogen peroxide scavenger at low oxygen.
    evidence:
    - reference: DOI:10.1186/s12866-024-03201-y
      notes: AhpC is considered the predominant H2O2 scavenger at low oxygen.
curation_history:
- timestamp: '2026-05-05T01:35:46.850463+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 low-oxygen growth requirement.
  llm_assisted: true
- timestamp: '2026-05-05T18:39:46-07:00'
  curator: codex
  action: ADDED_ORGANISM_EXAMPLE
  changes: Added Campylobacter jejuni 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 microoxic respiration via high-affinity
    terminal oxidases.
  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:0002326×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:13:18Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    supports → enables ×1.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:21Z'
  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: '2026-06-13T21:03:25Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0000085×1).
  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 6 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 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×3).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:30Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:16240×1, CHEBI:26523×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:17Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A0N0XA94×1).
  llm_assisted: true