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metabolism

METPO:1000060 · CLASS · REVIEWED

A biological process that maintains life in an organism.

Trait evidence (2)

Metabolism substrate-to-growth flow

DOI-backed graph linking substrate uptake, catabolism producing ATP and reducing power, biosynthesis, and growth as the core organization of cellular metabolism.

MECHANISTIC · This upper-level graph is a composite organization of metabolism, not a universal linear pathway. The E. coli AtpD example supports only the respiratory ATP-synthase branch; substrate uptake, biosynthesis, and nonrespiratory energy conservation involve many other proteins.

Metabolism substrate-to-growth flow Interactive directed graph showing evidence-backed causal relationships for metabolism.

Edge evidence

  • substrate uptake feeds catabolism

    Imported substrates feed the catabolic reactions of the cell.

  • catabolism has output ATP and reducing power RO:0002234

    Catabolic reactions generate ATP and reducing equivalents.

  • ATP and reducing power enables biosynthesis RO:0002327

    ATP and reducing power fuel biosynthetic reactions.

  • biosynthesis enables cellular growth RO:0002327

    Biosynthesis supports accumulation of biomass and growth.

  • cellular growth realizes metabolism

    The coordinated substrate-uptake / catabolism / biosynthesis / growth flow realizes the metabolism phenotype.

  • respiratory electron transport chain generates proton motive force biolink:produces

    Electron transfer through respiratory chains translocates protons to create the gradient.

  • ATP synthase uses proton motive force

    ATP synthase consumes the electrochemical proton motive force to drive phosphorylation.

  • ATP synthase produces ATP production METPO:2007800

    ATP synthase phosphorylates ADP to ATP, generating cellular energy currency.

  • respiration energy demand decreases carbon use efficiency RO:0002212

    Diverting more carbon to respiration lowers the fraction converted to biomass.

    • DOI:10.1038/s41467-024-52160-5 CUE declines when more carbon is diverted to respiration to generate energy for uptake, maintenance, and enzyme production.
  • substrate complexity increases energetic cost of metabolism RO:0002213

    Substrates needing enzymatic degradation raise the energetic cost of metabolism.

  • respiratory electron transport chain contributes to catabolism RO:0002326

    Respiratory electron transport is an energy-conserving component of catabolism.

    • DOI:10.1016/j.heliyon.2023.e22459 The transfer of electrons through the respiratory chain is tied to proton movement Verified against the free public article text.
  • carbon use efficiency contributes to cellular growth RO:0002326

    Carbon-use efficiency measures allocation of assimilated carbon to new biomass.

    • DOI:10.1038/s41467-024-52160-5 represents the fraction of C uptake allocated to the production of new microbial biomass Verified against the free public article text.
  • substrate uptake contributes to energetic cost of metabolism RO:0002326

    The accessibility of substrates determines the energetic cost of uptake and processing.

    • DOI:10.1038/s41467-024-52160-5 Polymeric substrates like lignin and cellulose need depolymerization before cellular uptake, whereas smaller substrates readily diffuse across membranes Verified against the free public article text.

Protein and taxon examples

Graph nodeProteinTaxonUniProt statusRole and evidence
ATP synthase UniProtKB:P0ABB4
ATP synthase subunit beta (atpD) 		Escherichia coli K-12
NCBITaxon:83333 		REVIEWED
retrieved 2026-08-24 · entry v155 · sequence v2

Beta component of the F1 catalytic head of the E. coli F1Fo ATP synthase; this accession is not presented as the complete rotary complex.

  • DOI:10.7554/eLife.21598 the potential energy of the proton motive force into rotation of the central stalk that drives conformational changes in the F1 catalytic sites The primary cryo-EM study resolves the E. coli F1Fo complex and its beta-containing catalytic head. UniProtKB P0ABB4 verifies the reviewed AtpD beta component and K-12 taxon.

Provenance

Identifier source
METPO (2026-06-12)
Author
Anthea Guo
Definition source
DOI:10.1126/science.1238842

Parent traits (1)

Children (24)

Cross-references

  • GO:0008152

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000060 [-1.052, -1.766, -1.194, +0.291, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Deep research

Generated by just research-trait; source: research/traits/metabolism/metabolism-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Curation report: microbial metabolism

## Executive scope

**Target trait:** `METPO:1000060` (“metabolism”; category **METABOLISM**, term kind **CLASS**, reviewed; parent `METPO:1000630`). For TraitMech, the most defensible interpretation is the organism-level process/capacity by which a microbe transforms matter and conserves energy through coupled catabolic, anabolic, transport, and bioenergetic reactions. ATP is the principal extant energy currency, while substrate-level phosphorylation and chemiosmotic coupling are the two broadly conserved routes of ATP synthesis. (seto2020howthermodynamicsilluminates pages 4-6, nicholls2023onthepotential pages 1-2)

The graph should not equate metabolism with growth. Growth is a downstream, condition-dependent outcome of metabolic flux plus biomass assembly, maintenance, regulation, and stress costs. Likewise, respiration, fermentation, substrate utilization, trophic mode, metabolite production, and cross-feeding are components or neighboring phenotypes—not synonyms for the broad trait. Metabolism may be observed by substrate disappearance, product formation, ATP or redox changes, isotope incorporation, metabolite profiles, flux estimates, or growth, but no single assay fully defines it.

## Trait boundaries

**Include:** nutrient acquisition; central carbon pathways; oxidation–reduction reactions; electron carriers; respiratory or fermentative energy conservation; ion gradients; ATP formation; precursor/cofactor generation; biosynthesis; waste/product export; and environmental constraints on reaction feasibility.

**Do not automatically include:**

- **Growth rate or biomass yield:** downstream phenotypes influenced by metabolism but also maintenance and regulation.
- **A specific substrate-utilization trait:** narrower than metabolism and conditional on transport plus pathway expression.
- **Aerobicity/anaerobicity:** environmental or respiratory strategy descriptors.
- **Metabolite abundance alone:** a pool-size measurement, not reaction direction or flux. A metabolite can participate in multiple pathways, and increased abundance can reflect increased production or decreased consumption. (go2024integrationofmetabolomics pages 1-3, go2024integrationofmetabolomics pages 3-4)
- **Community co-occurrence:** it does not establish causal metabolic interaction. Reductionist experiments, genetics, isotope tracing, or validated models are needed. (pacheco2023resolvingmetabolicinteraction pages 3-4)
- **Signaling and antimicrobial interactions:** include only when the molecule is explicitly used as an energy/nutrient source or directly changes a curated metabolic mechanism; a recent review treats signaling and antimicrobial roles separately from resource exchange. (pacheco2023resolvingmetabolicinteraction pages 3-4)

## Candidate nodes grouped by type

Identifiers below are conservative suggestions; label-only nodes should remain ungrounded until checked against the project’s ontology release.

### Trait and biological-process nodes

- Metabolism — `METPO:1000060`; broad GO analogue `GO:0008152`.
- Glycolytic process — `GO:0006096`.
- Tricarboxylic acid cycle — `GO:0006099`.
- Oxidative phosphorylation — `GO:0006119`.
- ATP synthesis coupled proton transport — `GO:0015986`.
- Aerobic respiration — `GO:0009060`.
- Substrate-level phosphorylation — label-only candidate.
- Fermentation — use an appropriately specific GO term only after pathway/taxon is known.
- Chemiosmosis, catabolism, anabolism, biomass synthesis, maintenance metabolism, metabolite cross-feeding — label-only or ontology-check candidates.

### Chemicals, nutrients, and physical drivers

- ATP — `CHEBI:15422`; ADP — `CHEBI:16761`; phosphate — `CHEBI:43474`.
- NADH — `CHEBI:16908`; NAD+ — `CHEBI:57540`.
- Ubiquinone — `CHEBI:16389`; ubiquinol — `CHEBI:17976`.
- Proton — `CHEBI:15378`; water — `CHEBI:15377`; dioxygen — `CHEBI:15379`.
- Carbon dioxide — `CHEBI:16526`; dihydrogen — `CHEBI:18276`.
- Acetate — `CHEBI:30089`; ethanol — `CHEBI:16236`.
- Sodium ion — `CHEBI:29101`; potassium ion — `CHEBI:29103`.
- Glucose 6-phosphate — `CHEBI:4170`.
- Electron donor, terminal electron acceptor, carbon source, nitrogen source, trace nutrient, proton-motive force, sodium-motive force, Gibbs free-energy change, and minimum driving force — label-only candidates where a stable ontology mapping has not been verified.

### Proteins, enzymes, transporters, and complexes

- Respiratory complex I / proton-translocating NADH:quinone oxidoreductase; bacterial core usually has 13–14 subunits, including an NADH-oxidizing N module, quinone-associated Q module, and membrane proton-translocating P module. (grivennikova2024protontranslocatingnadh–ubiquinoneoxidoreductase pages 2-4)
- F-type H+-transporting ATP synthase and Na+-coupled F1Fo ATP synthase — ontology/EC mapping should be selected after ion specificity and taxon are known.
- Rnf reduced-ferredoxin:NAD+ oxidoreductase — label-only candidate unless the organism’s characterized complex is specified.
- Electron-bifurcating [FeFe]-hydrogenase; ferredoxin; Nfn transhydrogenase; acetaldehyde:ferredoxin oxidoreductase; acetate kinase; substrate transporters; terminal oxidases/reductases.
- Taxon-specific gene nodes such as bacterial `nuo` genes should be added only with strain-level evidence or a genome annotation accession.

### Cellular locations and environmental nodes

- Cytoplasmic/plasma membrane, cytoplasm, periplasm, extracellular environment, and—only for microbial eukaryotes—mitochondrion or chloroplast.

Showing the first 60 of 209 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Escherichia coli K-12 NCBITaxon:83333 DOI:10.7554/eLife.21598 Strain-level model paired to the reviewed AtpD beta component of the respiratory F-type ATP synthase branch represented in this broad metabolism graph.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · CURATED_CAUSAL_GRAPH · claude

    Added DOI-backed causal graph framing metabolism as the integrated substrate-uptake / catabolism / biosynthesis / growth flow that maintains cellular life.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1).

  4. · RENAME_PREDICATE_LABELS · claude

    Renamed 1 causal-edge predicate label(s) to align with existing groundings: supports → enables ×1.

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1).

  6. · RENAME_PREDICATE_LABELS · claude

    Renamed 1 causal-edge predicate label(s) to align with existing groundings: powers → enables ×1.

  7. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1).

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0016049×1).

  9. · ENRICH_CAUSAL_GRAPH · claude

    Added 5 evidence-backed generic edges (8 new nodes) from the deep-research report.

  10. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces×1, METPO:2000202×1, RO:0002212×1, RO:0002213×1).

  11. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A415TT77×1).

  12. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0022904×1).

  13. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)

  14. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

    Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to has output), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.

  15. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

    Re-grounded 1 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (1 to produces), issue 301 part 2. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Each replacement is a 1:1 mirror of its source predicate that changes only the domain, so the claim each edge makes is unchanged and directions are unchanged. The replacements are proposed in proposals/metpo_traitmech_v9 and are placeholder ids until METPO mints them.

  16. · NORMALISE_NODE_TYPE · claude

    Normalised causal-node type(s) so one node_id means one thing corpus-wide (issue 356): proton_motive_force: CHEMICAL -> STATE. The schema's OWN example of STATE: 'a bioenergetic or molecular state of the cell (e.g. proton motive force ...) ... the state is the gradient / steady-value, not its establishment'. All 35 occurrences describe the gradient -- every description across all four types reads 'electrochemical proton gradient', including the 13 typed BIOLOGICAL_PROCESS ('Transmembrane electrochemical gradient generated by respiration'), which name the gradient and its provenance rather than the generating process. Nothing here means the establishment, so this is a retype and not a rename; records that DO mean the process already use a separate id (proton_motive_force_generation in ph_delta.yaml). Also settles the one edge #356 was filed for: phototrophic.yaml's CAPACITY typing was blocking `powers` (METPO:2007900), which is gated to BIOLOGICAL_PROCESS|STATE.

  17. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500×1).

  18. · CURATE_PROTEIN_TAXON_EXAMPLE · codex

    Retained the upper metabolism graph with an explicit composite-mechanism scope, added a DOI-backed E. coli K-12 AtpD beta-subunit example, and grounded the ATP synthase node to the current GO complex term without treating one component as the whole complex.

  19. · ADD_EXACT_ONTOLOGY_MATCH · codex

    Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0008152. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.

  20. · CONNECT_CAUSAL_GRAPH_COMPONENTS · codex

    Resolved issue #183 graph fragmentation (4 components to 1) with 3 public-source connector(s). No paid research service was called.