identifier: METPO:1000631
label: trophic type
definition: A phenotype that is describing how an organism obtains carbon, energy,
  and electron donors for growth and metabolism.
definition_source: DOI:10.1146/annurev.micro.61.080706.093130
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000059
synonyms:
- synonym_text: Physiology and metabolism.nutrition type.type
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: nutritional type
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: pathways
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Luke Wang
evidence:
- reference: DOI:10.1146/annurev.micro.61.080706.093130
  snippet: carbon source, energy source, and electron donor
  notes: Microbial physiology review frames trophic type as the joint classification
    by carbon, energy, and electron-donor source.
- reference: DOI:10.1073/pnas.0903507106
  snippet: molecular mechanisms of adaptation
  notes: Comparative genomics supports the classification of bacteria by trophic strategy
    from genome-encoded pathways.
causal_graphs:
- graph_id: trophic_type_classification_axes
  title: Trophic type classification axes
  description: DOI-backed graph linking the three classification axes (carbon source,
    energy source, electron donor) to the metabolic pathways an organism encodes,
    which jointly determine its trophic type.
  nodes:
  - node_id: trophic_type_trait
    label: trophic type
    node_type: TRAIT
    grounding: METPO:1000631
    description: Classification of how an organism obtains carbon and energy.
  - node_id: carbon_source_use
    label: carbon source utilization
    node_type: BIOLOGICAL_PROCESS
    description: Use of inorganic (CO2) or organic carbon for biosynthesis.
  - node_id: energy_source_use
    label: energy source utilization
    node_type: BIOLOGICAL_PROCESS
    description: Use of light (phototrophy) or chemical (chemotrophy) energy.
  - node_id: electron_donor_use
    label: electron donor utilization
    node_type: BIOLOGICAL_PROCESS
    description: Use of inorganic (lithotrophy) or organic (organotrophy) electron
      donors.
  - node_id: encoded_metabolic_pathways
    label: encoded metabolic pathways
    node_type: BIOLOGICAL_PROCESS
    description: The set of biosynthetic, energy-conserving, and electron-transfer
      pathways present in the genome.
  - node_id: autotrophic_phenotype
    label: autotrophic
    node_type: TRAIT
    grounding: METPO:1000632
    description: CO2-fixing trophic phenotype.
  - node_id: heterotrophic_phenotype
    label: heterotrophic
    node_type: TRAIT
    grounding: METPO:1000644
    description: Organic-carbon-utilizing trophic phenotype.
  - node_id: phototrophic_phenotype
    label: phototrophic
    node_type: TRAIT
    grounding: METPO:1000660
    description: Light-driven energy-acquisition trophic phenotype.
  - node_id: chemotrophic_phenotype
    label: chemotrophic
    node_type: TRAIT
    grounding: METPO:1000641
    description: Chemical-energy-driven trophic phenotype.
  - node_id: cbb_cycle_rubisco
    label: Calvin-Benson-Bassham cycle (RuBisCO)
    node_type: PATHWAY
    description: CO2-fixation pathway encoded by rbcL/cbbM RuBisCO and full CBB cycle
      genes.
  - node_id: co2_fixation
    label: CO2 fixation
    node_type: BIOLOGICAL_PROCESS
    description: Assimilation of inorganic carbon (CO2) into biomass, the basis of
      autotrophic carbon use.
  - node_id: sox_sulfur_oxidation
    label: SOX sulfur/thiosulfate oxidation
    node_type: PATHWAY
    description: Oxidation of thiosulfate/sulfur species via the soxABXYZ/soxCD system
      as an inorganic electron-donor source.
  - node_id: sugar_uptake_cazyme_catabolism
    label: sugar/polysaccharide uptake and CAZyme catabolism
    node_type: PATHWAY
    description: Heterotrophic uptake (e.g. gtsABC, frcABC) and CAZyme-mediated degradation
      of sugars and polysaccharides for organic-carbon use.
  - node_id: nife_hydrogenase_h2_oxidation
    label: '[NiFe]-hydrogenase H2 oxidation'
    node_type: PATHWAY
    description: Oxidation of molecular hydrogen by [NiFe]-hydrogenases as an inorganic
      electron donor (hydrogen lithotrophy).
  edges:
  - subject: carbon_source_use
    predicate: causes
    object: trophic_type_trait
    description: Carbon-source utilization defines the auto/heterotrophy axis of the
      trophic classification.
    evidence:
    - reference: DOI:10.1146/annurev.micro.61.080706.093130
      snippet: carbon source
      notes: Supports carbon-source utilization as a primary trophic-type axis.
    predicate_id: biolink:causes
  - subject: energy_source_use
    predicate: causes
    object: trophic_type_trait
    description: Energy-source utilization defines the photo/chemotrophy axis of the
      trophic classification.
    evidence:
    - reference: DOI:10.1146/annurev.micro.61.080706.093130
      snippet: energy source
      notes: Supports energy-source utilization as a primary trophic-type axis.
    predicate_id: biolink:causes
  - subject: electron_donor_use
    predicate: causes
    object: trophic_type_trait
    description: Electron-donor utilization defines the litho/organotrophy axis of
      the trophic classification.
    evidence:
    - reference: DOI:10.1146/annurev.micro.61.080706.093130
      snippet: electron donor
      notes: Supports electron-donor utilization as a primary trophic-type axis.
    predicate_id: biolink:causes
  - subject: encoded_metabolic_pathways
    predicate: realizes
    object: trophic_type_trait
    description: The genome-encoded set of carbon-fixation, energy-conserving, and
      electron-transfer pathways realizes the organism's trophic type.
    evidence:
    - reference: DOI:10.1073/pnas.0903507106
      snippet: molecular mechanisms of adaptation
      notes: Supports genome-encoded pathway repertoires as the proximate determinant
        of trophic phenotypes.
  - subject: autotrophic_phenotype
    predicate: is a
    object: trophic_type_trait
    description: Autotrophy is a child phenotype of trophic type.
    evidence:
    - reference: DOI:10.1146/annurev.micro.61.080706.093130
      snippet: carbon source
      notes: Supports autotrophy as one carbon-source-defined trophic phenotype.
    predicate_id: rdfs:subClassOf
  - subject: heterotrophic_phenotype
    predicate: is a
    object: trophic_type_trait
    description: Heterotrophy is a child phenotype of trophic type.
    evidence:
    - reference: DOI:10.1146/annurev.micro.61.080706.093130
      snippet: carbon source
      notes: Supports heterotrophy as one carbon-source-defined trophic phenotype.
    predicate_id: rdfs:subClassOf
  - subject: phototrophic_phenotype
    predicate: is a
    object: trophic_type_trait
    description: Phototrophy is a child phenotype of trophic type.
    evidence:
    - reference: DOI:10.1146/annurev.micro.61.080706.093130
      snippet: energy source
      notes: Supports phototrophy as one energy-source-defined trophic phenotype.
    predicate_id: rdfs:subClassOf
  - subject: chemotrophic_phenotype
    predicate: is a
    object: trophic_type_trait
    description: Chemotrophy is a child phenotype of trophic type.
    evidence:
    - reference: DOI:10.1146/annurev.micro.61.080706.093130
      snippet: energy source
      notes: Supports chemotrophy as one energy-source-defined trophic phenotype.
    predicate_id: rdfs:subClassOf
  - subject: cbb_cycle_rubisco
    predicate: enables
    object: co2_fixation
    description: Form II RuBisCO and a full Calvin-Benson-Bassham cycle enable CO2
      fixation, marking autotrophic carbon-assimilation potential.
    evidence:
    - reference: DOI:10.1128/AEM.00599-24
      notes: All MAGs encode Form II RuBisCO (rbcL/cbbM) and a full CBB cycle, indicating
        CO2 fixation potential.
    predicate_id: RO:0002327
  - subject: co2_fixation
    predicate: causes
    object: carbon_source_use
    description: CO2 fixation establishes inorganic-carbon (autotrophic) use on the
      carbon-source axis of trophic type.
    evidence:
    - reference: DOI:10.1128/AEM.00599-24
      notes: CBB-driven CO2 fixation defines autotrophic carbon assimilation on the
        carbon-source classification axis.
    predicate_id: biolink:causes
  - subject: sox_sulfur_oxidation
    predicate: causes
    object: electron_donor_use
    description: SOX-mediated thiosulfate/sulfur oxidation supplies inorganic electron
      donors, defining lithotrophy on the electron-donor axis.
    evidence:
    - reference: DOI:10.1128/AEM.00599-24
      notes: Presence of soxABXYZ (and soxCD) is tied to thiosulfate oxidation, enabling
        use of sulfur species as electron donors.
    predicate_id: biolink:causes
  - subject: sugar_uptake_cazyme_catabolism
    predicate: causes
    object: carbon_source_use
    description: Sugar transporters and CAZyme catabolism enable heterotrophic/organotrophic
      use of organic carbon on the carbon-source axis.
    evidence:
    - reference: DOI:10.1128/AEM.00599-24
      notes: Sugar transporters (gtsABC, frcABC), maltodextrin import/degradation
        and CAZy enzymes indicate capacity for heterotrophic use of sugars and polysaccharides.
    predicate_id: biolink:causes
  - subject: nife_hydrogenase_h2_oxidation
    predicate: causes
    object: electron_donor_use
    description: '[NiFe]-hydrogenase H2 oxidation supplies an inorganic electron donor,
      contributing hydrogen lithotrophy to the electron-donor axis.'
    evidence:
    - reference: DOI:10.1128/mSystems.00148-24
      notes: Hydrogenase genes link hydrogen-based lithotrophy to chemoautotrophic
        metabolism.
    predicate_id: biolink:causes
curation_history:
- timestamp: '2026-05-05T01:35:46.866871+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T22:00:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph framing trophic type by its three classification
    axes (carbon source, energy source, electron donor) and child phenotypes (autotroph,
    heterotroph, phototroph, chemotroph).
  llm_assisted: true
- timestamp: '2026-05-20T03:35:32Z'
  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: '2026-05-26T05:00:48Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 3 causal-edge predicate label(s) to align with existing groundings:
    determines → causes ×3.'
  llm_assisted: true
- timestamp: '2026-05-26T05:00:51Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:causes×3).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (5 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:15Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:causes×4, RO:0002327×1).
  llm_assisted: true