identifier: METPO:1002005 label: Fermentation definition: A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors. definition_source: DOI:10.3389/fmicb.2021.703525 trait_category: METABOLISM term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000800 created_by: Luke Wang evidence: - reference: DOI:10.3389/fmicb.2021.703525 snippet: substrate of a fermentation has to serve as electron donor as well as acceptor notes: Supports donor/acceptor definition of anaerobic bacterial fermentation. - reference: DOI:10.1111/1751-7915.13746 snippet: Substrate-level phosphorylation is one of the main sources of energy notes: Supports substrate-level phosphorylation as a major fermentative energy-conservation mechanism. canonical_examples: - taxon_id: NCBITaxon:562 taxon_label: Escherichia coli note: "mixed-acid fermentation" reference: PMID:25152889 - taxon_id: NCBITaxon:1358 taxon_label: Lactococcus lactis note: "homolactic fermentation" reference: DOI:10.1093/femsre/fuaa033 - taxon_id: NCBITaxon:1488 taxon_label: Clostridium acetobutylicum note: "ABE fermentation" reference: PMID:11466286 causal_graphs: - graph_id: fermentation_redox_energy title: Fermentation redox and substrate-level phosphorylation description: Evidence-backed causal sketch linking organic substrate redox balancing to fermentative ATP generation. nodes: - node_id: fermentation_trait label: Fermentation node_type: TRAIT grounding: METPO:1002005 description: Anaerobic redox metabolism using organic substrates and products. - node_id: organic_substrate label: organic substrate node_type: CHEMICAL description: Fermented carbon and energy source. - node_id: reduced_redox_cofactors label: reduced redox cofactors node_type: CHEMICAL description: Reduced cofactors generated during substrate oxidation. - node_id: fermentation_products label: fermentation products node_type: CHEMICAL description: Reduced products that restore cofactor redox balance. - node_id: substrate_level_phosphorylation label: substrate-level phosphorylation node_type: BIOLOGICAL_PROCESS grounding: METPO:1000804 description: Direct ATP formation by phosphoryl transfer from metabolic intermediates. - node_id: atp label: ATP node_type: CHEMICAL grounding: CHEBI:30616 description: Cellular energy currency generated by fermentation. - node_id: external_inorganic_acceptor label: external inorganic terminal electron acceptor node_type: CHEMICAL description: External inorganic acceptors (e.g. nitrate, sulfur compounds) used in anaerobic respiration but excluded by fermentation. - node_id: glycolysis_emp label: glycolysis (Embden-Meyerhof-Parnas pathway) node_type: PATHWAY description: Central catabolic pathway oxidizing glucose to pyruvate, feeding fermentation branches. - node_id: pyruvate label: pyruvate node_type: CHEMICAL description: Central branch-point metabolite feeding fermentation product pathways. grounding: CHEBI:15361 - node_id: pfor label: pyruvate:ferredoxin oxidoreductase node_type: GENE_OR_PROTEIN description: Enzyme (EC 1.2.7.1) oxidatively decarboxylating pyruvate and reducing ferredoxin. grounding: UniProtKB:A0A075WCC3 - node_id: reduced_ferredoxin label: reduced ferredoxin node_type: CHEMICAL description: Low-potential electron carrier central to anaerobic redox balancing. grounding: CHEBI:17513 - node_id: fnor label: ferredoxin:NAD+ oxidoreductase node_type: GENE_OR_PROTEIN description: Enzyme (EC 1.18.1.3) transferring electrons from reduced ferredoxin to NAD+. grounding: UniProtKB:I3R731 - node_id: nad_plus label: NAD+ node_type: CHEMICAL description: Oxidized nicotinamide cofactor regenerated during fermentative redox balancing. grounding: CHEBI:15846 - node_id: flavin_based_electron_bifurcation label: flavin-based electron bifurcation node_type: BIOLOGICAL_PROCESS description: Mechanism coupling an exergonic and an endergonic redox reaction within a single enzyme complex. - node_id: ion_motive_force label: ion-motive force node_type: BIOLOGICAL_PROCESS description: Transmembrane ion gradient generated by ferredoxin-oxidizing complexes. - node_id: atp_synthase label: ATP synthase node_type: GENE_OR_PROTEIN description: Membrane complex synthesizing ATP from an ion-motive force. grounding: UniProtKB:A0A415TT77 edges: - subject: fermentation_trait predicate: uses object: organic_substrate description: Fermentation uses an organic substrate as both electron donor and acceptor source. evidence: - reference: DOI:10.3389/fmicb.2021.703525 snippet: substrate of a fermentation has to serve as electron donor as well as acceptor notes: Supports organic substrate donor/acceptor role. - subject: organic_substrate predicate: oxidation reduces object: reduced_redox_cofactors description: Substrate oxidation generates reduced redox cofactors. evidence: - reference: DOI:10.1111/1751-7915.13746 snippet: a substrate is oxidized to an intermediate notes: Review describes substrate oxidation with cofactor reduction in fermentation. - subject: reduced_redox_cofactors predicate: reoxidized by object: fermentation_products description: Product-forming reductions regenerate oxidized cofactors. evidence: - reference: DOI:10.1111/1751-7915.13746 snippet: after which the intermediate is reduced notes: Supports product-side reduction and redox cofactor regeneration. - subject: fermentation_trait predicate: conserves energy by object: substrate_level_phosphorylation description: Substrate-level phosphorylation is a major fermentative energy-conservation route. evidence: - reference: DOI:10.1111/1751-7915.13746 snippet: main sources of energy under fermentative conditions notes: Supports SLP as a fermentative energy mechanism. - subject: substrate_level_phosphorylation predicate: produces object: atp description: Substrate-level phosphorylation directly forms ATP. evidence: - reference: DOI:10.1111/1751-7915.13746 snippet: energy-rich bonds (for example via substrate-level phosphorylation) notes: Supports SLP as ATP-linked energy conservation. predicate_id: METPO:2000202 - subject: fermentation_trait predicate: excludes object: external_inorganic_acceptor description: Fermentation excludes use of external inorganic terminal electron acceptors, distinguishing it from anaerobic respiration. evidence: - reference: DOI:10.1093/femsre/fuae016 notes: Excludes processes that use external inorganic terminal acceptors, explicitly naming nitrate and sulfur respiration. - subject: glycolysis_emp predicate: feeds into object: pyruvate description: Glycolysis (EMP) feeds carbon flux to pyruvate, the entry point for fermentation branches. evidence: - reference: DOI:10.1093/femsre/fuae016 notes: Glycolysis (EMP) and the pentose phosphate pathway feed to pyruvate. - subject: pfor predicate: produces object: reduced_ferredoxin description: Pyruvate:ferredoxin oxidoreductase oxidizes pyruvate and produces reduced ferredoxin. evidence: - reference: DOI:10.1093/femsre/fuae016 notes: Pyruvate:ferredoxin oxidoreductase produces reduced ferredoxin; central to redox balancing. predicate_id: METPO:2000202 - subject: fnor predicate: transfers electrons from reduced ferredoxin to object: nad_plus description: Ferredoxin:NAD+ oxidoreductase reoxidizes reduced ferredoxin by transferring electrons to NAD+. evidence: - reference: DOI:10.1093/femsre/fuae016 notes: Ferredoxin-NAD+ reductase transfers electrons from reduced ferredoxin to NAD+; strong redox-balancing edge. - subject: flavin_based_electron_bifurcation predicate: reduces object: reduced_ferredoxin description: Flavin-based electron bifurcation couples exergonic and endergonic redox reactions, reducing low-potential ferredoxin. evidence: - reference: DOI:10.1038/s41467-023-41212-x notes: Couples an exergonic and an endergonic redox reaction within a single soluble enzyme complex, typically reducing low-potential ferredoxin. predicate_id: METPO:2000017 - subject: ion_motive_force predicate: drives object: atp_synthase description: Ion-motive force generated during fermentation drives ATP synthase-mediated ATP formation. evidence: - reference: DOI:10.1093/femsre/fuae016 notes: Ion gradients drive ATP synthesis via ATP synthases; links fermentation to chemiosmotic ATP conservation. - subject: atp_synthase predicate: produces object: atp description: ATP synthase forms ATP using the ion-motive force. evidence: - reference: DOI:10.1093/femsre/fuae016 notes: ATP synthesis via ATP synthases driven by ion gradients during fermentation. predicate_id: METPO:2000202 curation_history: - timestamp: '2026-05-05T01:35:46.935638+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-07T00:00:00-07:00' curator: codex action: ADDED_CAUSAL_GRAPH changes: Added DOI-backed causal graph for fermentation redox balancing and substrate-level phosphorylation. 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 (METPO:2000202×1). llm_assisted: true - timestamp: '2026-06-17T04:09:44Z' 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 7 evidence-backed generic edges (10 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:12Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×2, METPO:2000017×1). llm_assisted: true - timestamp: '2026-06-24T17:21:18Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A415TT77×1). llm_assisted: true - timestamp: '2026-06-24T17:23:32Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15361×1, CHEBI:17513×1, CHEBI:15846×1). llm_assisted: true - timestamp: '2026-06-26T07:15:18Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A075WCC3×1, UniProtKB:I3R731×1). llm_assisted: true