identifier: METPO:1000606
label: obligately aerobic
definition: An oxygen preference that requires molecular oxygen (O₂) for 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 aerobe
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: obligate aerobic
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: https://www.ncbi.nlm.nih.gov/books/NBK482349/
  snippet: require oxygen as a terminal electron acceptor
  notes: Supports the requirement for oxygen in obligately aerobic organisms.
- reference: PMID:27203084
  snippet: M. tuberculosis is an obligate aerobe
  notes: 'Organism example: Mycobacterium tuberculosis is described as obligately
    aerobic.'
canonical_examples:
- taxon_id: NCBITaxon:1270
  taxon_label: Micrococcus luteus
  note: "Textbook strict aerobe (respiratory metabolism only)."
  reference: PMID:19948807
causal_graphs:
- graph_id: obligate_aerobe_oxygen_respiration
  title: Obligate aerobe oxygen-dependent respiration mechanism
  description: Evidence-backed causal sketch linking obligate aerobic growth to oxygen-dependent
    terminal oxidase respiration.
  nodes:
  - node_id: obligate_aerobic_trait
    label: obligately aerobic
    node_type: TRAIT
    grounding: METPO:1000606
    description: Growth requires molecular oxygen.
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Dioxygen required for respiratory growth.
  - node_id: electron_transport_chain
    label: electron transport chain
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0022900
    description: Respiratory chain that transfers electrons to terminal acceptors.
  - node_id: terminal_oxidases
    label: terminal respiratory oxidases
    node_type: GENE_OR_PROTEIN
    description: Oxygen-reducing terminal oxidase complexes.
  - node_id: proton_motive_force
    label: proton motive force
    node_type: STATE
    description: Electrochemical gradient powering ATP synthesis.
    grounding: METPO:1007500
  - node_id: aerobic_respiration
    label: aerobic respiration
    node_type: BIOLOGICAL_PROCESS
    description: Oxygen-dependent respiratory metabolism.
    grounding: GO:0009060
  - node_id: anoxia
    label: absence of oxygen (anoxia)
    node_type: ENVIRONMENTAL_FACTOR
    description: Environmental condition lacking molecular oxygen.
  - node_id: superoxide
    label: superoxide
    node_type: CHEMICAL
    description: Reactive oxygen species generated during aerobic metabolism.
    grounding: CHEBI:18421
  - node_id: hydrogen_peroxide
    label: hydrogen peroxide
    node_type: CHEMICAL
    description: Reactive oxygen species generated during aerobic metabolism.
    grounding: CHEBI:16240
  - node_id: superoxide_dismutase
    label: superoxide dismutase activity
    node_type: MOLECULAR_FUNCTION
    description: Enzyme activity that detoxifies superoxide.
    grounding: GO:0004784
  - node_id: catalase
    label: catalase / catalase-peroxidase activity
    node_type: MOLECULAR_FUNCTION
    description: Enzyme activity that detoxifies hydrogen peroxide.
  - node_id: fe_s_cluster_enzymes
    label: Fe-S cluster enzymes
    node_type: GENE_OR_PROTEIN
    description: Enzymes with exposed iron-sulfur clusters vulnerable to ROS.
  edges:
  - subject: obligate_aerobic_trait
    predicate: depends on
    object: molecular_oxygen
    description: Obligate aerobic growth depends on oxygen availability.
    evidence:
    - reference: DOI:10.1016/j.celrep.2023.112444
      snippet: obligate aerobe ... exposed to hypoxia, stops growing
      notes: Mycobacterium tuberculosis example supports oxygen requirement in an
        obligately aerobic bacterium.
    predicate_id: RO:0002502
  - subject: terminal_oxidases
    predicate: reduces
    object: molecular_oxygen
    description: Terminal oxidases use oxygen as the respiratory electron acceptor.
    evidence:
    - reference: DOI:10.1016/j.celrep.2023.112444
      snippet: transfer electrons from the ETC to O2
      notes: Supports oxygen reduction by terminal oxidases in an obligate aerobe.
    predicate_id: METPO:2000017
  - subject: electron_transport_chain
    predicate: includes
    object: terminal_oxidases
    description: Oxygen-dependent respiratory chains terminate in oxygen reductases.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2011.06.016
      snippet: respiratory quinol:O2 oxidoreductase
      notes: Review supports terminal oxygen reductases as respiratory chain enzymes.
    predicate_id: biolink:has_part
  - subject: terminal_oxidases
    predicate: contributes to
    object: proton_motive_force
    description: Oxygen reductases contribute to proton motive force generation.
    evidence:
    - reference: DOI:10.1016/j.bbabio.2011.06.016
      snippet: production of a proton motive force
      notes: Supports bioenergetic coupling by cytochrome bd oxygen reductases.
    predicate_id: RO:0002326
  - subject: molecular_oxygen
    predicate: enables
    object: aerobic_respiration
    description: Molecular oxygen enables aerobic respiration.
    evidence:
    - reference: DOI:10.1111/cmi.13338
      notes: Aerobic respiration is identified as the main cause of bacterial oxygen
        consumption.
    predicate_id: RO:0002327
  - subject: anoxia
    predicate: interrupts flux through
    object: electron_transport_chain
    description: Anoxia interrupts electron flux through the electron transport chain.
    evidence:
    - reference: DOI:10.1128/JB.00797-19
      notes: Interrupted flux through the electron transport chain (ETC) due to the
        absence of oxygen.
  - subject: electron_transport_chain
    predicate: maintains
    object: proton_motive_force
    description: Electron transport chain flux maintains the proton motive force;
      anoxic interruption impairs it.
    evidence:
    - reference: DOI:10.1128/JB.00797-19
      notes: Obligate aerobes must maintain redox balance and the proton motive force
        (PMF) despite interrupted flux through the electron transport chain.
  - subject: superoxide_dismutase
    predicate: mitigates
    object: superoxide
    description: Superoxide dismutase mitigates superoxide stress in aerobes.
    evidence:
    - reference: DOI:10.1016/j.tim.2020.10.001
      notes: Aerobes deploy scavenging enzymes (SOD, catalase, other peroxidases).
    predicate_id: METPO:2007407
  - subject: catalase
    predicate: mitigates
    object: hydrogen_peroxide
    description: Catalase/catalase-peroxidase mitigates hydrogen peroxide stress in
      aerobes.
    evidence:
    - reference: DOI:10.1016/j.tim.2020.10.001
      notes: Aerobes deploy scavenging enzymes (SOD, catalase, other peroxidases).
    predicate_id: METPO:2007407
  - subject: superoxide
    predicate: inactivates
    object: fe_s_cluster_enzymes
    description: Superoxide and H2O2 oxidize and inactivate exposed Fe-S cluster enzymes.
    evidence:
    - reference: DOI:10.1016/j.tim.2020.10.001
      notes: Rate constants for cluster oxidation given (~1e6 M-1 s-1 for superoxide
        and ~1e4 M-1 s-1 for H2O2), explaining ROS-defense need in aerobes.
curation_history:
- timestamp: '2026-05-05T01:35:46.851998+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 obligate oxygen requirement.
  llm_assisted: true
- timestamp: '2026-05-05T18:39:46-07:00'
  curator: codex
  action: ADDED_ORGANISM_EXAMPLE
  changes: Added Mycobacterium tuberculosis 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 obligate aerobic respiration and oxygen-reducing
    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: '2026-05-24T04:41:03Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007500×1).
  llm_assisted: true
- timestamp: '2026-05-26T02:30:12Z'
  curator: claude
  action: RETYPE_CAUSAL_NODES
  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.'
  llm_assisted: true
- timestamp: '2026-05-26T05:00:47Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    requires → depends on ×1.'
  llm_assisted: true
- timestamp: '2026-05-26T05:00:50Z'
  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
    (biolink:has_part×1).
  llm_assisted: true
- timestamp: '2026-06-16T06:30:55Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000017×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 evidence-backed generic edges (7 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
    (METPO:2007407×2, RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:17Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0009060×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:31Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:18421×1, CHEBI:16240×1, GO:0004784×1).
  llm_assisted: true