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mixed-acid fermentation

traitmech:000027 · CLASS · REVIEWED

A fermentation in which sugars are converted via the glycolytic pathway to a mixture of acids (lactic, acetic, formic, succinic) plus ethanol, CO2 and H2. Characteristic of enteric bacteria such as Escherichia coli.

Mixed-acid fermentation yields a spectrum of acids plus ethanol and gases

Evidence-backed causal sketch linking glycolytic sugar catabolism to mixed acid + ethanol + CO2 + H2 production in enterobacteria.

Mixed-acid fermentation yields a spectrum of acids plus ethanol and gases Interactive directed graph showing evidence-backed causal relationships for mixed-acid fermentation.

Edge evidence

  • mixed-acid fermentation participates in fermentation biolink:participates_in

    Mixed-acid fermentation is a class of fermentation metabolism.

    • DOI:10.3389/fmicb.2021.703525 Energy-conservation review lists the mixed-acid product spectrum.
  • mixed-acid fermentation produces mixed acid + ethanol + CO2/H2 products METPO:2007800

    The pathway yields the characteristic acid + ethanol + gas spectrum.

    • DOI:10.3390/molecules31020333 Classical-fermentation review describes mixed-acid fermentation by enterobacteria.
  • mixed-acid fermentation has output pyruvate

    Glycolysis upstream of mixed-acid fermentation produces pyruvate.

    • DOI:10.35812/cellulosechemtechnol.2024.58.90 Pyruvate, ATP, and NADH are produced when glucose or other carbon sources reach the primary glycolytic pathway.
  • pyruvate formate lyase (PflB) catalyzes conversion of pyruvate

    PflB cleaves pyruvate into formate and acetyl-CoA.

    • DOI:10.1128/iai.00176-23 Pyruvate formate lyase (PflB) catalyzes the conversion of pyruvate into formate and acetyl-CoA.
  • pyruvate formate lyase (PflB) produces formate METPO:2007800

    PflB cleavage of pyruvate yields formate.

    • DOI:10.1128/iai.00176-23 Pyruvate formate lyase (PflB) catalyzes the conversion of pyruvate into formate and acetyl-CoA.
  • phosphotransacetylase / acetate kinase (Pta/AckA) converts acetate

    Pta and AckA convert acetyl-CoA to acetate (with ATP generation).

    • DOI:10.1128/iai.00176-23 Acetyl-CoA is further metabolized by Pta and AckA to generate acetate.
  • formate induces synthesis of formate hydrogenlyase complex (FHL)

    Formate induces synthesis of the membrane-bound FHL complex.

    • DOI:10.1128/aem.01472-24 Formate induces the synthesis of the membrane-bound FHL complex that catalyzes formate disproportionation into CO2 and H2.
  • formate hydrogenlyase complex (FHL) produces molecular hydrogen METPO:2007800

    FHL disproportionates formate into CO2 and H2.

    • DOI:10.1128/aem.01472-24 Formate is disproportionated into CO2 and H2 by the formate hydrogenlyase complex via FdhF and hydrogenase 3 (HycE).
  • formate hydrogenlyase complex (FHL) produces carbon dioxide METPO:2007800

    FHL disproportionates formate into CO2 and H2.

    • DOI:10.1128/aem.01472-24 Formate is disproportionated into CO2 and H2 by the formate hydrogenlyase complex.
  • acidic conditions positively regulates formate hydrogenlyase complex (FHL) RO:0002213

    Acidic conditions favor FHL-mediated formate cleavage.

    • DOI:10.35812/cellulosechemtechnol.2024.58.90 The enzyme complex formate:hydrogen lyase (FHL) cleaves formate under acidic conditions into H2 and CO2.
  • ambient molecular oxygen inhibits molecular hydrogen RO:0002212

    Oxygen prevents fermentative hydrogen generation.

    • DOI:10.35812/cellulosechemtechnol.2024.58.90 The presence of oxygen prevents the generation of hydrogen.
  • mixed-acid fermentation lowers cytoplasmic pH

    Acid generation by MAF lowers cytoplasmic pH.

    • DOI:10.1128/iai.00176-23 MAF results in the generation of acid, which subsequently lowers the pH of the cytoplasm.
  • pyruvate formate lyase (PflB) produces acetyl-CoA METPO:2007800

    Pyruvate formate-lyase cleaves pyruvate into acetyl-CoA and formate.

    • DOI:10.3389/fmicb.2021.703525 Connecting edge wiring the enrichment node into the graph.

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.3389/fmicb.2021.703525

Parent traits (1)

kg-microbe context

Matched 1 kg-microbe node via parent_proxy.

  • 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/mixed_acid_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: mixed-acid fermentation

## Trait record and scope

- **Trait:** mixed-acid fermentation
- **Identifier:** `traitmech:000027`
- **Category / kind / status:** METABOLISM / CLASS / REVIEWED
- **Parent:** `METPO:1002005`

Mixed-acid fermentation is best modeled as an **anaerobic fermentative capacity**, rather than the production of any single acid. In the canonical enterobacterial implementation represented by *Escherichia coli*, glycolysis supplies pyruvate, ATP, and reducing equivalents; carbon then partitions among formate, acetate, ethanol, lactate, and succinate, while formate may subsequently be converted to H₂ and CO₂. The parallel branches jointly conserve ATP and restore redox balance when oxygen or another usable terminal electron acceptor is unavailable. (fa¶rster2014metabolicengineeringof pages 1-2, taggar2024hydrogenproductionvia pages 5-7)

The phenotype is therefore supported most strongly by a **product spectrum plus anaerobic pathway activity**, not merely by detecting acetate, lactate, or formate. In one anaerobic glucose experiment, *E. coli* produced approximately 35 mM acetate and 15 mM formate, together with lactate and succinate; the exact ratios are medium-, strain-, pH-, and growth-phase-dependent and should not be made definitional. (metcalfe2020onlineanalysisand pages 9-10)

### Boundaries and nearby traits

1. **Homolactic fermentation:** predominantly reduces pyruvate to lactate. Lactate production alone is insufficient to establish mixed-acid fermentation.
2. **2,3-Butanediol fermentation:** common in some enterobacteria but channels pyruvate through acetoin/2,3-butanediol. It should remain a neighboring trait unless the organism demonstrably produces the mixed-acid spectrum.
3. **Alcoholic or solvent fermentation:** ethanol can be one mixed-acid product, but ethanol-dominant engineered strains are not necessarily performing the native mixed-acid phenotype.
4. **Aerobic acetate overflow:** acetate secretion during rapid aerobic growth is not mixed-acid fermentation, despite sharing Pta–AckA chemistry.
5. **Anaerobic respiration:** growth using nitrate, fumarate, or another external terminal electron acceptor is respiration, not fermentation, even if fermentation products coexist.
6. **Formate-hydrogenlyase activity:** H₂/CO₂ production is an important enterobacterial submodule, but it is not universally present in every organism described phenotypically as a mixed-acid fermenter.
7. **Methyl-red phenotype:** sustained acidification is a useful assay proxy, but a positive indicator test is not by itself a complete mechanistic definition.

## Candidate causal-graph nodes

### Trait and process nodes

- `traitmech:000027` — mixed-acid fermentation
- `METPO:1002005` — supplied parent trait
- Glycolysis — `GO:0006096`
- Fermentation — `GO:0006113`
- Anaerobic cellular respiration — `GO:0045333` (**boundary/exclusion node**, not part of the core trait)
- Redox balancing — label-only candidate
- Substrate-level phosphorylation — label-only candidate pending exact ontology review
- Reductive C4-dicarboxylate/succinate branch — label-only candidate
- Formate-hydrogenlyase pathway — label-only candidate

### Environmental and experimental nodes

- Anaerobiosis / oxygen limitation — label-only or ENVO grounding to be checked against the intended graph schema
- Fermentable sugar availability
- Glucose-fed anaerobic culture
- Acidic extracellular pH
- Stationary versus exponential growth phase
- Closed anaerobic bioreactor
- Exogenous formate addition
- FTIR headspace monitoring
- Raman liquid-phase monitoring

Anaerobiosis should be modeled as a **contextual enabling factor**, not as an absolute universal trigger: facultative enterobacteria can use alternative anaerobic respiratory pathways when suitable electron acceptors are present. FNR and ArcAB coordinate the aerobic-to-anaerobic transition, but the available evidence supports a broad regulatory edge more strongly than individual promoter-level edges. (fa¶rster2014metabolicengineeringof pages 1-2)

### Organisms

- *Escherichia coli* — `NCBITaxon:562`
- Enterobacterales/enteric bacteria — use a taxon-level node only after confirming the desired NCBI rank and identifier
- *Citrobacter*, *Enterobacter*, *Salmonella*, and related taxa — candidate examples, not interchangeable mechanistic evidence

The proposed core graph should be explicitly labeled **enterobacterial/*E. coli*-centric**. Gene-level conservation and product ratios must not be generalized automatically to all organisms called mixed-acid fermenters.

### Genes, proteins, enzymes, and complexes

Showing the first 60 of 224 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Curation history

  1. · PROPOSED_FROM_RESEARCH · claude

    Proposed candidate METABOLISM trait (mixed-acid fermentation); product-specific sub-variant of the existing Fermentation class (METPO:1002005).

  2. · CURATED_CAUSAL_GRAPH · claude

    Added evidence-backed causal graph (mixed-acid fermentation) with GO node grounding and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.

  3. · ENRICH_CAUSAL_GRAPH · claude

    Added 10 evidence-backed generic edges (12 new nodes) from the deep-research report.

  4. · FIX_ORPHAN_NODE · claude

    Connected orphaned node 'acetyl_coa' via pyruvate_formate_lyase -[produces]-> acetyl_coa.

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×4, RO:0002212×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16526×1, CHEBI:18276×1).

  7. · GROUND_CAUSAL_NODES · claude

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

  8. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×1).

  9. · MIGRATE_MICROBE_DOMAIN_EDGES_PART2 · claude

    Re-grounded 5 causal edge(s) off microbe-domain METPO predicates onto their causal-graph counterparts (5 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.

  10. · NORMALISE_NODE_SENSE · claude

    One node_id per SENSE (issues 356, 384): ambient_oxygen is the chemical sense here. Already the ambient sense. Listed so a re-run still normalises the label and still retracts ENVO:01001495 if it has been re-applied — the grounder keys on (label, node_type), so an un-normalised label is what lets the retracted CURIE come back.