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Fermentation

METPO:1002005 · CLASS · REVIEWED

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.

Trait evidence (2)

  • DOI:10.3389/fmicb.2021.703525
    substrate of a fermentation has to serve as electron donor as well as acceptor

    Supports donor/acceptor definition of anaerobic bacterial fermentation.

  • DOI:10.1111/1751-7915.13746
    Substrate-level phosphorylation is one of the main sources of energy

    Supports substrate-level phosphorylation as a major fermentative energy-conservation mechanism.

Fermentation redox and substrate-level phosphorylation

Evidence-backed causal sketch linking organic substrate redox balancing to fermentative ATP generation.

MECHANISTIC · This composite graph combines substrate-level phosphorylation with ferredoxin-linked and ion-gradient modules found in subsets of fermenters. The C. acetobutylicum ATCC 824 PFOR example supports the pyruvate-to-reduced-ferredoxin branch and is not a universal fermentation marker.

Fermentation redox and substrate-level phosphorylation Interactive directed graph showing evidence-backed causal relationships for Fermentation.

Edge evidence

  • Fermentation uses organic substrate

    Fermentation uses an organic substrate as both electron donor and acceptor source.

    • DOI:10.3389/fmicb.2021.703525 substrate of a fermentation has to serve as electron donor as well as acceptor Supports organic substrate donor/acceptor role.
  • organic substrate oxidation reduces reduced redox cofactors

    Substrate oxidation generates reduced redox cofactors.

    • DOI:10.1111/1751-7915.13746 a substrate is oxidized to an intermediate Review describes substrate oxidation with cofactor reduction in fermentation.
  • reduced redox cofactors reoxidized by fermentation products

    Product-forming reductions regenerate oxidized cofactors.

  • Fermentation conserves energy by substrate-level phosphorylation

    Substrate-level phosphorylation is a major fermentative energy-conservation route.

  • substrate-level phosphorylation has output ATP RO:0002234

    Substrate-level phosphorylation directly forms ATP.

    • DOI:10.1111/1751-7915.13746 energy-rich bonds (for example via substrate-level phosphorylation) Supports SLP as ATP-linked energy conservation.
  • Fermentation excludes external inorganic terminal electron acceptor

    Fermentation excludes use of external inorganic terminal electron acceptors, distinguishing it from anaerobic respiration.

    • DOI:10.1093/femsre/fuae016 Excludes processes that use external inorganic terminal acceptors, explicitly naming nitrate and sulfur respiration.
  • glycolysis (Embden-Meyerhof-Parnas pathway) feeds into pyruvate

    Glycolysis (EMP) feeds carbon flux to pyruvate, the entry point for fermentation branches.

  • pyruvate:ferredoxin oxidoreductase produces reduced ferredoxin METPO:2007800

    Pyruvate:ferredoxin oxidoreductase oxidizes pyruvate and produces reduced ferredoxin.

  • ferredoxin:NAD+ oxidoreductase transfers electrons from reduced ferredoxin to NAD+

    Ferredoxin:NAD+ oxidoreductase reoxidizes reduced ferredoxin by transferring electrons to NAD+.

    • DOI:10.1093/femsre/fuae016 Ferredoxin-NAD+ reductase transfers electrons from reduced ferredoxin to NAD+; strong redox-balancing edge.
  • flavin-based electron bifurcation reduces reduced ferredoxin METPO:2007802

    Flavin-based electron bifurcation couples exergonic and endergonic redox reactions, reducing low-potential ferredoxin.

    • DOI:10.1038/s41467-023-41212-x Couples an exergonic and an endergonic redox reaction within a single soluble enzyme complex, typically reducing low-potential ferredoxin.
  • ion-motive force drives ATP synthase

    Ion-motive force generated during fermentation drives ATP synthase-mediated ATP formation.

    • DOI:10.1093/femsre/fuae016 Ion gradients drive ATP synthesis via ATP synthases; links fermentation to chemiosmotic ATP conservation.
  • ATP synthase produces ATP METPO:2007800

    ATP synthase forms ATP using the ion-motive force.

  • glycolysis (Embden-Meyerhof-Parnas pathway) contributes to Fermentation RO:0002326

    EMP glycolysis supplies pyruvate to downstream fermentation branches.

    • DOI:10.1093/femsre/fuae016 Glycolysis (EMP) and the pentose phosphate pathway feed to pyruvate. Verified against the free public article text.
  • pyruvate:ferredoxin oxidoreductase oxidizes pyruvate METPO:2007803

    Pyruvate:ferredoxin oxidoreductase oxidizes pyruvate while reducing ferredoxin.

    • DOI:10.1093/femsre/fuae016 Pyruvate:ferredoxin oxidoreductase produces reduced ferredoxin; central to redox balancing. Verified against the free public article text.
  • ferredoxin:NAD+ oxidoreductase oxidizes reduced ferredoxin METPO:2007803

    Ferredoxin-NAD+ reductase oxidizes reduced ferredoxin while reducing NAD+.

    • DOI:10.1093/femsre/fuae016 Ferredoxin-NAD+ reductase transfers electrons from reduced ferredoxin to NAD+; strong redox-balancing edge. Verified against the free public article text.

Protein and taxon examples

Graph nodeProteinTaxonUniProt statusRole and evidence
pyruvate:ferredoxin oxidoreductase UniProtKB:Q97GY6
Pyruvate:ferredoxin oxidoreductase 		Clostridium acetobutylicum ATCC 824
NCBITaxon:272562 		UNREVIEWED
retrieved 2026-08-24 · entry v152 · sequence v1

PFOR encoded by locus CA_C2229, the expressed enzyme linking pyruvate oxidation to reduced ferredoxin in fermentative C. acetobutylicum ATCC 824.

  • DOI:10.1128/mbio.01808-15 Under all conditions, only CA_C2229 was transcribed and translated. The primary fluxomic, transcriptomic, and proteomic study identifies CA_C2229 as the expressed PFOR locus and describes production of reduced ferredoxin, CO2, and acetyl-CoA. UniProtKB Q97GY6 is its exact unreviewed entry in reference proteome UP000000814.

Provenance

Identifier source
METPO (2026-06-12)
Author
Luke Wang
Definition source
DOI:10.3389/fmicb.2021.703525

Parent traits (1)

Children (9)

Cross-references

  • GO:0006113

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1002005 [-0.758, -6.428, +3.551, +10.454, …]

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/fermentation-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 fermentation

## Executive scope

**Target trait:** Fermentation
**Identifier:** **“METPO:1002005”**
**Category/kind/status:** METABOLISM / CLASS / REVIEWED
**Parent:** METPO:1000800

For TraitMech, the defensible core meaning is a **bioenergetic phenotype**: an organism can conserve energy by oxidizing an organic substrate without an external terminal electron acceptor, while reducing substrate-derived organic intermediates/products to close redox balance. Buckel states that, because oxygen and other inorganic acceptors are absent, the substrate must serve as both electron donor and acceptor; nitrate, sulfate, or Fe(III) use would instead make the process respiration. A 2023 microbiology reference similarly says that no terminal acceptor is available and electrons are relocated to organic catabolic products. (weissbrodt2023basicmicrobiologyand pages 16-18, buckel2021energyconservationin pages 1-2)

This scope is narrower than the bioprocess use of *fermentation*. In biotechnology, “fermentation” may mean any microbial cultivation used to manufacture a product, including aerobic lysine production or recombinant-protein production. Precision fermentation likewise denotes optimized engineered cell factories and may be fully aerobic; it is therefore an application/process descriptor, not sufficient evidence for the phenotype **“METPO:1002005”**. (knychala2024precisionfermentationas pages 1-2, buckel2021energyconservationin pages 1-2)

## 1. Trait boundaries

### Include

- Anaerobic redox conversion of carbohydrates, amino acids, or other organic substrates into incompletely oxidized products.
- Internal redox balancing in which substrate-derived intermediates receive reducing equivalents.
- ATP conservation through substrate-level phosphorylation (SLP).
- In taxa that possess them, additional energy conservation through Rnf-linked ion gradients, biotin-dependent ion-pumping decarboxylases, ATP synthase, or flavin-based electron bifurcation. These are important extensions to the older view that fermentation conserves energy exclusively through SLP. (buckel2021energyconservationin pages 1-2)
- Product branches including lactate, ethanol, acetate, butyrate, volatile fatty acids, CO₂, and H₂, provided the complete reaction is redox-balanced. (weissbrodt2023basicmicrobiologyand pages 16-18, buckel2021energyconservationin pages 1-2)

### Exclude or model separately

1. **Anaerobic respiration.** Nitrate, sulfate, Fe(III), fumarate, DMSO, or another externally supplied terminal acceptor indicates respiration, even when oxygen is absent. “Anaerobic” alone is therefore not diagnostic. (weissbrodt2023basicmicrobiologyand pages 16-18, buckel2021energyconservationin pages 1-2)
2. **Aerobic overflow metabolism.** Ethanol or lactate formation in oxygenated cultures can resemble fermentation biochemically, but oxygen availability and respiratory activity must be recorded; do not infer the strict trait solely from product detection.
3. **Methanogenesis.** Methane production uses specialized archaeal energy metabolism and should not automatically be treated as fermentation. Fermenters can instead supply acetate, H₂, and CO₂ to methanogens.
4. **Malolactic conversion.** Malate-to-lactate/CO₂ may alter acidity but does not necessarily provide the core ATP-generating fermentation phenotype; curate as a separate module unless growth/energy conservation is demonstrated.
5. **Industrial or precision fermentation.** Recombinant proteins, enzymes, lipids, and metabolites can be produced in aerated bioreactors. The term describes manufacturing, not necessarily the strict causal trait. (knychala2024precisionfermentationas pages 1-2)
6. **Genomic prediction alone.** Presence of enzymes or an incomplete pathway supports potential, not demonstrated phenotype. Growth, substrate consumption, redox-balanced products, ATP conservation, or flux evidence is preferable.

## 2. Candidate graph nodes

### Trait and process nodes

- Fermentation — **“METPO:1002005”**
- Glycolysis — **GO:0006096**
- Substrate-level phosphorylation — **GO:0006757**
- NAD⁺ regeneration / cellular redox balancing — label-only pending ontology verification
- Alcoholic fermentation — label-only or a verified GO/MetaCyc pathway identifier
- Homolactic fermentation — label-only or verified pathway identifier
- Mixed-acid fermentation — label-only
- Glutamate fermentation through the 3-methylaspartate pathway — label-only; Firmicutes-specific
- Glutamate fermentation through the 2-hydroxyglutarate pathway — label-only; strict-anaerobe-specific
- Flavin-based electron bifurcation — label-only pending verified GO term
- Rnf-dependent ion-gradient generation — label-only

### Chemicals and redox carriers

- Glucose — **CHEBI:17234**
- Pyruvate — **CHEBI:15361**
- ATP — **CHEBI:15422**
- ADP — **CHEBI:16761**
- NAD⁺ — **CHEBI:57540**
- NADH — **CHEBI:57945**
- Ethanol — **CHEBI:16236**
- Acetaldehyde — **CHEBI:15343**
- Carbon dioxide — **CHEBI:16526**
- Lactate — **CHEBI:24996**

Showing the first 60 of 223 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 (4)

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

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

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

  2. · ADDED_CAUSAL_GRAPH · codex

    Added DOI-backed causal graph for fermentation redox balancing and substrate-level phosphorylation.

  3. · GROUND_CAUSAL_PREDICATES · claude

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

  4. · REMOVE_REDUNDANT_SYNONYM · claude

    Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).

  5. · ENRICH_CAUSAL_GRAPH · claude

    Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.

  6. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×2, METPO:2000017×1).

  7. · GROUND_CAUSAL_NODES · claude

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

  8. · GROUND_CAUSAL_NODES · claude

    Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15361×1, CHEBI:17513×1, CHEBI:15846×1).

  9. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A075WCC3×1, UniProtKB:I3R731×1).

  10. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)

  11. · 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.

  12. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

    Re-grounded 3 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (2 to produces, 1 to reduces), 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.

  13. · REVIEW_UNIPROT_INSTANCE_GROUNDINGS · codex

    Reviewed 1 organism-specific UniProtKB grounding(s): replaced 0 with taxon-agnostic GO/InterPro terms and retracted 1 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).

  14. · CURATE_PROTEIN_TAXON_EXAMPLE · codex

    Added a DOI-backed C. acetobutylicum ATCC 824 PFOR example from the experimentally expressed CA_C2229 locus, grounded PFOR and ATP synthase to current semantic terms, retained unresolved FNOR as explicitly reviewed label-only, and documented the graph's branch-specific scope.

  15. · ADD_EXACT_ONTOLOGY_MATCH · codex

    Ontology exact-match review (2026-08-25): approved exact xref(s): GO:0006113. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.

  16. · 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.