identifier: traitmech:000029
label: propionic acid fermentation
definition: A fermentation that produces propionate (with acetate and CO2) from sugars
  or lactate, typically via the Wood-Werkman (methylmalonyl-CoA) pathway. Characteristic
  of propionibacteria (e.g. Propionibacterium freudenreichii).
definition_source: DOI:10.3390/molecules31020333
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1002005
synonyms:
- synonym_text: propionate fermentation
  synonym_type: RELATED_SYNONYM
  source: DOI:10.3390/molecules31020333
evidence:
- reference: DOI:10.3390/molecules31020333
  notes: Review of classical fermentations describes propionic acid fermentation (acetic
    acid, propionic acid, CO2) and propionibacteria as its agents, including the Wood-Werkman
    route.
- reference: DOI:10.3389/fmicb.2021.703525
  notes: Review of fermentative energy conservation supports propionate formation
    as a redox-balancing, energy-conserving fermentation route.
canonical_examples:
- taxon_id: NCBITaxon:1744
  taxon_label: Propionibacterium freudenreichii
  note: "Canonical propionic-acid fermenter (Swiss-cheese eyes and flavour)."
  reference: PMID:21620505
causal_graphs:
- graph_id: propionic_acid_fermentation_propionate
  title: Propionic acid fermentation produces propionate via the Wood-Werkman pathway
  description: Evidence-backed causal sketch linking methylmalonyl-CoA-pathway catabolism
    of sugars or lactate to propionate, acetate, and CO2.
  nodes:
  - node_id: propionic_acid_fermentation_trait
    label: propionic acid fermentation
    node_type: TRAIT
    grounding: traitmech:000029
    description: Fermentation producing propionate via the Wood-Werkman pathway.
  - node_id: fermentation_process
    label: fermentation
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0006113
    description: ATP-yielding catabolism with organic terminal acceptors.
  - node_id: propionate
    label: propionate
    node_type: CHEMICAL
    description: Reduced end product characteristic of propionibacteria.
    grounding: CHEBI:17272
  - node_id: wood_werkman_cycle
    label: Wood-Werkman cycle
    node_type: PATHWAY
    description: Methylmalonyl-CoA cycle; predominant propionate-forming route in
      propionibacteria.
  - node_id: pyruvate
    label: pyruvate
    node_type: CHEMICAL
    description: Central glycolytic intermediate feeding the Wood-Werkman cycle.
    grounding: CHEBI:15361
  - node_id: oxaloacetate
    label: oxaloacetate
    node_type: CHEMICAL
    description: Formed by biotin-dependent carboxylation of pyruvate.
    grounding: CHEBI:16452
  - node_id: malate
    label: malate
    node_type: CHEMICAL
    description: Reduction product of oxaloacetate in the reductive branch.
  - node_id: fumarate
    label: fumarate
    node_type: CHEMICAL
    description: Dehydration product of malate in the Wood-Werkman route.
    grounding: CHEBI:29806
  - node_id: succinate
    label: succinate
    node_type: CHEMICAL
    description: Reduction product of fumarate en route to propionate.
  - node_id: succinyl_coa
    label: succinyl-CoA
    node_type: CHEMICAL
    description: Intermediate formed from succinate before rearrangement.
  - node_id: methylmalonyl_coa
    label: methylmalonyl-CoA
    node_type: CHEMICAL
    description: Intermediate rearranged toward propionyl-CoA.
  - node_id: propionyl_coa
    label: propionyl-CoA
    node_type: CHEMICAL
    description: Immediate CoA-thioester precursor of propionate.
    grounding: CHEBI:15539
  - node_id: mmc_carboxytransferase
    label: methylmalonyl-CoA carboxytransferase
    node_type: GENE_OR_PROTEIN
    description: Biotin-dependent transcarboxylase converting pyruvate to oxaloacetate.
    grounding: UniProtKB:A0A3S9JES8
  - node_id: biotin
    label: biotin
    node_type: CHEMICAL
    description: Cofactor required by the carboxytransferase step.
  - node_id: acetate
    label: acetate
    node_type: CHEMICAL
    description: Co-product of propionic acid fermentation.
  edges:
  - subject: propionic_acid_fermentation_trait
    predicate: participates in
    object: fermentation_process
    description: Propionic acid fermentation is a class of fermentation metabolism.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.703525
      notes: Energy-conservation review supports propionate formation as a redox-balancing
        fermentation route.
    predicate_id: biolink:participates_in
  - subject: propionic_acid_fermentation_trait
    predicate: produces
    object: propionate
    description: Propionate is the characteristic end product of the pathway.
    evidence:
    - reference: DOI:10.3390/molecules31020333
      notes: Classical-fermentation review describes propionic acid fermentation via
        the Wood-Werkman pathway in propionibacteria.
    predicate_id: METPO:2000202
  - subject: propionic_acid_fermentation_trait
    predicate: has major pathway
    object: wood_werkman_cycle
    description: The Wood-Werkman methylmalonyl-CoA cycle is the predominant propionate-forming
      route.
    evidence:
    - reference: DOI:10.3390/molecules31020333
      notes: Wood-Werkman cycle described as the predominant propionate-forming route
        in Propionibacterium and Acidipropionibacterium.
  - subject: pyruvate
    predicate: causally upstream of
    object: oxaloacetate
    description: Pyruvate is carboxylated to oxaloacetate in a biotin-dependent reaction.
    evidence:
    - reference: DOI:10.3390/molecules31020333
      notes: Pyruvate is carboxylated to oxaloacetate by methylmalonyl-CoA carboxytransferase
        in a biotin-dependent reaction.
  - subject: biotin
    predicate: cofactor for
    object: mmc_carboxytransferase
    description: The transcarboxylation step is biotin-dependent.
    evidence:
    - reference: DOI:10.3390/molecules31020333
      notes: The transcarboxylation converting pyruvate to oxaloacetate is explicitly
        described as biotin-dependent.
  - subject: oxaloacetate
    predicate: causally upstream of
    object: malate
    description: Oxaloacetate is reduced to malate in the reductive branch.
    evidence:
    - reference: DOI:10.3390/molecules31020333
      notes: Oxaloacetate is reduced to malate in the reductive branch leading toward
        succinate.
  - subject: malate
    predicate: causally upstream of
    object: fumarate
    description: Malate is dehydrated to fumarate.
    evidence:
    - reference: DOI:10.3390/molecules31020333
      notes: Malate is dehydrated to fumarate in the Wood-Werkman route.
  - subject: fumarate
    predicate: causally upstream of
    object: succinate
    description: Fumarate is reduced to succinate.
    evidence:
    - reference: DOI:10.3390/molecules31020333
      notes: Fumarate is reduced to succinate en route to propionate formation.
  - subject: succinyl_coa
    predicate: causally upstream of
    object: methylmalonyl_coa
    description: The pathway proceeds through succinyl-CoA and methylmalonyl-CoA intermediates.
    evidence:
    - reference: DOI:10.3390/molecules31020333
      notes: The pathway proceeds through succinyl-CoA and methylmalonyl-CoA intermediates
        during propionate formation.
  - subject: propionyl_coa
    predicate: causally upstream of
    object: propionate
    description: Propionyl-CoA is converted to propionate by a CoA-transferase.
    evidence:
    - reference: DOI:10.3390/molecules31020333
      notes: Propionyl-CoA is finally converted to propionic acid or propionate by
        a CoA-transferase.
  - subject: propionic_acid_fermentation_trait
    predicate: has byproduct
    object: acetate
    description: The fermentation produces propionate with acetate as a co-product.
    evidence:
    - reference: DOI:10.3390/molecules31020333
      notes: The fermentation is defined as producing propionic acid with acetate
        as a co-product.
curation_history:
- timestamp: '2026-05-30T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate METABOLISM trait (propionic acid fermentation); product-specific
    sub-variant of the existing Fermentation class (METPO:1002005).
  llm_assisted: true
- timestamp: '2026-06-10T14:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (propionic acid fermentation) with GO
    node grounding and METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-14T06:55:38Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:17272×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 9 evidence-backed generic edges (12 new nodes) from the deep-research
    report.
  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
    (CHEBI:29806×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:33Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:15361×1, CHEBI:16452×1, CHEBI:15539×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:19Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A3S9JES8×1).
  llm_assisted: true