identifier: METPO:1000603
label: anaerobic
definition: An oxygen preference in which growth occurs in the absence of molecular
  oxygen (O₂).
definition_source: PMID:21413255
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000601
synonyms:
- synonym_text: Ox_anaerobic
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: anaerobe
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: PMID:21413255
  snippet: Anaerobes, on the other hand, cannot grow in the presence of oxygen
  notes: Supports anaerobic growth as growth without molecular oxygen.
- reference: PMID:22778399
  snippet: obligate anaerobe Bacteroides fragilis
  notes: 'Organism example: Bacteroides fragilis is described as an anaerobic organism.'
canonical_examples:
- taxon_id: NCBITaxon:1488
  taxon_label: Clostridium acetobutylicum
  note: "obligate anaerobe"
  reference: PMID:18430081
- taxon_id: NCBITaxon:817
  taxon_label: Bacteroides fragilis
  note: "aerotolerant gut anaerobe"
  reference: PMID:22778399
causal_graphs:
- graph_id: anaerobic_trait_oxygen_exclusion
  title: Anaerobic growth oxygen-exclusion mechanism
  description: Evidence-backed causal sketch linking anaerobic growth to absence of
    molecular oxygen and oxygen-derived stress.
  nodes:
  - node_id: anaerobic_trait
    label: anaerobic
    node_type: TRAIT
    grounding: METPO:1000603
    description: Growth occurs without molecular oxygen.
  - node_id: anoxic_condition
    label: anoxic or hypoxic condition
    node_type: ENVIRONMENTAL_FACTOR
    description: Low-oxygen environment that permits anaerobic growth.
  - node_id: molecular_oxygen
    label: molecular oxygen
    node_type: CHEMICAL
    grounding: CHEBI:15379
    description: Dioxygen whose presence can block anaerobic 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: oxygen_sensitive_catalytic_sites
    label: oxygen-sensitive catalytic sites
    node_type: MOLECULAR_FUNCTION
    description: Radical chemistry and low-potential metal centers vulnerable to oxygen
      or ROS.
  - node_id: antioxidant_enzymes
    label: antioxidant enzymes (Sod/Cat/peroxidases)
    node_type: GENE_OR_PROTEIN
    description: Superoxide dismutase, catalase, and peroxidases that detoxify reactive
      oxygen species.
  - node_id: ros_detoxification
    label: ROS detoxification
    node_type: BIOLOGICAL_PROCESS
    description: Enzymatic removal of reactive oxygen species to limit oxidative damage.
  - node_id: respiratory_reductases
    label: respiratory reductases
    node_type: GENE_OR_PROTEIN
    description: Terminal reductases that allow use of non-oxygen molecules as respiratory
      electron acceptors.
  - node_id: alternative_electron_acceptors
    label: alternative anaerobic electron acceptors
    node_type: CHEMICAL
    description: Non-O2 molecules present in anaerobic ecosystems used as terminal
      electron acceptors.
  - node_id: anaerobic_respiration
    label: anaerobic respiration
    node_type: BIOLOGICAL_PROCESS
    description: Energy generation using terminal electron acceptors other than molecular
      oxygen.
    grounding: GO:0009061
  edges:
  - subject: anoxic_condition
    predicate: enables
    object: anaerobic_trait
    description: Anaerobic growth is favored in low-oxygen environments.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: hypoxic environments in which these organisms dwell
      notes: Review links anaerobe ecology to hypoxic environments.
    predicate_id: RO:0002327
  - subject: molecular_oxygen
    predicate: inhibits
    object: anaerobic_trait
    description: Oxygen exposure can block growth of anaerobic organisms.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: oxygen blocks their growth
      notes: Supports oxygen as an inhibitory factor for anaerobic growth.
    predicate_id: RO:0002212
  - subject: molecular_oxygen
    predicate: generates stress via
    object: reactive_oxygen_species
    description: Oxygen exposure can lead to ROS-mediated stress in anaerobes.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: molecular oxygen and ROS
      notes: Review describes oxygen and ROS as linked stressors for anaerobes.
  - subject: reactive_oxygen_species
    predicate: damages
    object: oxygen_sensitive_catalytic_sites
    description: ROS can disrupt oxygen-sensitive radical or metal-center catalysis
      used in anaerobic metabolism.
    evidence:
    - reference: DOI:10.1038/s41579-021-00583-y
      snippet: vulnerable to direct poisoning by molecular oxygen and ROS
      notes: Supports ROS-sensitive catalytic sites as mechanistic vulnerability.
  - subject: antioxidant_enzymes
    predicate: detoxifies
    object: reactive_oxygen_species
    description: Superoxide dismutase, catalase, and peroxidases remove ROS in anaerobes
      exposed to oxygen.
    evidence:
    - reference: DOI:10.1038/s43705-023-00251-7
      notes: organisms use anti-oxidative enzymes - superoxide dismutase (Sod), catalase
        (Cat), and peroxidases - to detoxify ROS.
  - subject: antioxidant_enzymes
    predicate: enables
    object: ros_detoxification
    description: Antioxidant enzyme activity carries out the detoxification of reactive
      oxygen species.
    evidence:
    - reference: DOI:10.1038/s43705-023-00251-7
      notes: Anti-oxidative enzymes (Sod/Cat/peroxidases) detoxify ROS, mediating
        ROS detoxification.
    predicate_id: RO:0002327
  - subject: ros_detoxification
    predicate: protects against
    object: reactive_oxygen_species
    description: ROS detoxification limits oxidative damage from oxygen-derived oxidants
      in anaerobes.
    evidence:
    - reference: DOI:10.1038/s43705-023-00251-7
      notes: Detoxification system removes ROS produced when O2 is reduced, a broad
        protective mechanism.
  - subject: respiratory_reductases
    predicate: enables utilization of
    object: alternative_electron_acceptors
    description: Respiratory reductases let microbes use non-O2 molecules as energy-generating
      electron acceptors.
    evidence:
    - reference: DOI:10.1038/s41564-023-01560-2
      notes: Respiratory reductases enable microbes to utilize molecules present in
        anaerobic ecosystems as energy-generating respiratory electron acceptors.
  - subject: alternative_electron_acceptors
    predicate: enables
    object: anaerobic_respiration
    description: Availability of non-O2 electron acceptors supports anaerobic respiration
      in low-oxygen niches.
    evidence:
    - reference: DOI:10.1038/s41564-023-01560-2
      notes: Molecules in anaerobic ecosystems serve as respiratory electron acceptors
        for anaerobic respiration.
    predicate_id: RO:0002327
  - subject: anaerobic_respiration
    predicate: enables
    object: anaerobic_trait
    description: Use of alternative terminal electron acceptors supports growth without
      molecular oxygen.
    evidence:
    - reference: DOI:10.1038/s41564-023-01560-2
      notes: Diverse gut bacteria use dietary- and host-derived metabolites for anaerobic
        respiration, enabling growth without O2.
    predicate_id: RO:0002327
curation_history:
- timestamp: '2026-05-05T01:35:46.849856+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-excluding 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 exclusion and oxygen-derived stress
    in anaerobic growth.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:29Z'
  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:0002212×1).
  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 (5 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:09Z'
  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: '2026-06-24T17:21:16Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0009061×1).
  llm_assisted: true