identifier: METPO:1000845 label: Acetogenesis definition: A metabolism that produces acetate as the primary end product through the reduction of carbon dioxide or other carbon compounds using the Wood-Ljungdahl pathway, typically performed by acetogenic bacteria under anaerobic conditions. definition_source: DOI:10.1016/j.bbapap.2008.08.012 trait_category: METABOLISM term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000060 synonyms: - synonym_text: Acetate fermentation synonym_type: RELATED_SYNONYM source: metpo.owl created_by: Jed Dongjin Kim-Ozaeta evidence: - reference: DOI:10.1016/j.bbapap.2008.08.012 snippet: Acetogenesis and the Wood-Ljungdahl Pathway of CO2 Fixation notes: Review supports acetogenesis via the Wood-Ljungdahl CO2-fixation pathway. - reference: DOI:10.1196/annals.1419.015 snippet: convert carbon dioxide and CO into acetyl-CoA notes: Supports acetyl-CoA formation from CO2 and CO in acetogens. canonical_examples: - taxon_id: NCBITaxon:1525 taxon_label: Neomoorella thermoacetica note: "THE model acetogen used to elucidate the Wood-Ljungdahl pathway (formerly Moorella/Clostridium thermoaceticum). Acetobacterium woodii is the modern bioenergetics model." reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC4599090/ causal_graphs: - graph_id: acetogenesis_wood_ljungdahl title: Acetogenesis Wood-Ljungdahl mechanism description: Evidence-backed causal sketch linking anaerobic carbon fixation through the Wood-Ljungdahl pathway to acetate production. nodes: - node_id: acetogenesis_trait label: Acetogenesis node_type: TRAIT grounding: METPO:1000845 description: Acetate-producing anaerobic metabolism. - node_id: anaerobic_condition label: anaerobic condition node_type: ENVIRONMENTAL_FACTOR description: Oxygen-free condition required for many acetogenic enzymes. grounding: PATO:0001456 - node_id: wood_ljungdahl_pathway label: Wood-Ljungdahl pathway node_type: PATHWAY description: Reductive acetyl-CoA pathway used by acetogens. grounding: GO:0030634 - node_id: carbon_dioxide label: carbon dioxide node_type: CHEMICAL grounding: CHEBI:16526 description: Carbon substrate fixed by the Wood-Ljungdahl pathway. - node_id: carbon_monoxide label: carbon monoxide node_type: CHEMICAL grounding: CHEBI:17245 description: Carbon substrate or intermediate in acetyl-CoA synthesis. - node_id: acetyl_coa label: acetyl-CoA node_type: CHEMICAL grounding: CHEBI:15351 description: Central product of Wood-Ljungdahl carbon fixation. - node_id: acetate label: acetate node_type: CHEMICAL grounding: CHEBI:30089 description: Primary end product of acetogenesis. - node_id: formate label: formate node_type: CHEMICAL description: Methyl-branch intermediate from CO2 reduction. - node_id: formyl_thf label: 10-formyl-tetrahydrofolate node_type: CHEMICAL description: Methyl-branch folate-bound formyl intermediate. - node_id: methylene_thf label: 5,10-methylene-tetrahydrofolate node_type: CHEMICAL description: Methyl-branch folate-bound methylene intermediate. - node_id: methyl_thf label: 5-methyl-tetrahydrofolate node_type: CHEMICAL description: Methyl-branch folate-bound methyl carrier feeding methyl transfer. - node_id: acetyl_phosphate label: acetyl phosphate node_type: CHEMICAL description: Activated acetyl intermediate from phosphotransacetylase. grounding: CHEBI:15350 - node_id: atp label: ATP node_type: CHEMICAL description: Energy currency generated by substrate-level phosphorylation at acetate kinase. edges: - subject: acetogenesis_trait predicate: occurs in object: anaerobic_condition description: Acetogenesis is typically an anaerobic metabolism. evidence: - reference: DOI:10.1016/j.bbapap.2008.08.012 snippet: grow organisms and work with enzymes under strictly oxygen-free conditions notes: Review emphasizes oxygen-free handling for acetogenic enzymes and organisms. predicate_id: biolink:occurs_in - subject: acetogenesis_trait predicate: has mechanistic pathway object: wood_ljungdahl_pathway description: The Wood-Ljungdahl pathway is the central acetogenic carbon-fixation route. evidence: - reference: DOI:10.1016/j.bbapap.2008.08.012 snippet: Wood-Ljungdahl Pathway of CO2 Fixation notes: Review title and scope support pathway assignment. - subject: carbon_dioxide predicate: participates in object: wood_ljungdahl_pathway description: Carbon dioxide is fixed through the Wood-Ljungdahl pathway. evidence: - reference: DOI:10.1016/j.bbapap.2008.08.012 snippet: CO2 Fixation notes: Supports CO2 as a pathway substrate. predicate_id: biolink:participates_in - subject: carbon_monoxide predicate: participates in object: wood_ljungdahl_pathway description: Carbon monoxide can be converted through the acetogenic pathway. evidence: - reference: DOI:10.1196/annals.1419.015 snippet: convert carbon dioxide and CO into acetyl-CoA notes: Supports CO as a substrate for acetogenic acetyl-CoA synthesis. predicate_id: biolink:participates_in - subject: wood_ljungdahl_pathway predicate: produces object: acetyl_coa description: The Wood-Ljungdahl pathway synthesizes acetyl-CoA. evidence: - reference: DOI:10.1196/annals.1419.015 snippet: convert carbon dioxide and CO into acetyl-CoA notes: Supports acetyl-CoA as pathway product. predicate_id: METPO:2000202 - subject: acetyl_coa predicate: precursor of object: acetate description: Acetyl-CoA is converted onward to acetate in acetogenesis. evidence: - reference: DOI:10.1016/j.bbapap.2008.08.012 snippet: Energy metabolism associated with acetogenesis notes: Review discusses acetogenic energy metabolism downstream of acetyl-CoA synthesis. - subject: carbon_dioxide predicate: is converted to object: formate description: CO2 is reduced to formate by formate dehydrogenase / HDCR, the first methyl-branch step. evidence: - reference: DOI:10.3389/fbioe.2024.1395540 notes: FDH reduces CO2 to formate; HDCR catalyzes hydrogen-dependent CO2 reduction to formate (methyl-branch core step). - subject: formate predicate: is converted to object: formyl_thf description: Formate is condensed onto tetrahydrofolate by formyl-THF synthetase (Fhs). evidence: - reference: DOI:10.3389/fbioe.2024.1395540 notes: FTS (formyl-THF synthetase) converts formate to formyl-THF consuming 1 ATP; canonical WLP methyl-branch step. - subject: formyl_thf predicate: is converted to object: methylene_thf description: Formyl-THF is processed by cyclohydrolase and methylene-THF dehydrogenase (FolD) to methylene-THF. evidence: - reference: DOI:10.34726/hss.2024.114566 notes: 5,10-methenyl-THF cyclohydrolase and NAD-dependent 5,10-methylene-THF dehydrogenase convert formyl-THF to methylene-THF. - subject: methylene_thf predicate: is converted to object: methyl_thf description: Methylene-THF is reduced to methyl-THF by methylene-THF reductase (MTHFR). evidence: - reference: DOI:10.3389/fbioe.2024.1395540 notes: MTHFR reduces methenyl-THF to methylene-THF to methyl-THF; common acetogen methyl-branch step. - subject: carbon_dioxide predicate: is converted to object: carbon_monoxide description: CO2 is reduced to CO by carbon monoxide dehydrogenase (CODH) in the carbonyl branch. evidence: - reference: DOI:10.34726/hss.2024.114566 notes: In the carbonyl branch CODH reduces CO2 to CO; central carbonyl-branch step. - subject: acetyl_coa predicate: is converted to object: acetyl_phosphate description: Acetyl-CoA is converted to acetyl phosphate by phosphotransacetylase (PTA). evidence: - reference: DOI:10.3389/fbioe.2024.1395540 notes: PTA and ACK convert acetyl-CoA to acetate; PTA yields acetyl phosphate. - subject: acetyl_phosphate predicate: is converted to object: acetate description: Acetyl phosphate is converted to acetate by acetate kinase (ACK), yielding ATP by substrate-level phosphorylation. evidence: - reference: DOI:10.3389/fbioe.2024.1395540 notes: ACK (acetate kinase) converts acetyl-phosphate to acetate, yielding ATP via SLP; trait-defining end-product step. - subject: acetyl_phosphate predicate: produces object: atp description: The acetate kinase step generates ATP via substrate-level phosphorylation. evidence: - reference: DOI:10.3389/fbioe.2024.1395540 notes: ACK convert acetyl-phosphate to acetate, yielding ATP via SLP. predicate_id: METPO:2000202 curation_history: - timestamp: '2026-05-05T01:35:46.915402+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 anaerobic Wood-Ljungdahl carbon fixation and acetate production. 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: '2026-05-24T04:38:00Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (ENVO:01001057×1, GO:0046358×1). llm_assisted: true - timestamp: '2026-05-26T05:00:47Z' curator: claude action: RENAME_PREDICATE_LABELS changes: 'Renamed 3 causal-edge predicate label(s) to align with existing groundings: input to → participates in ×2; occurs under → occurs in ×1.' llm_assisted: true - timestamp: '2026-05-26T05:00:50Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:participates_in×2, biolink:occurs_in×1). llm_assisted: true - timestamp: '2026-06-15T07:19:08Z' curator: claude action: FIX_NODE_GROUNDING_CURIE changes: Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label fix; verified vs OAK). llm_assisted: true - timestamp: '2026-06-15T07:20:37Z' curator: claude action: FIX_NODE_GROUNDING_CURIE changes: Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK). 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 8 evidence-backed generic edges (6 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:11Z' 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: '2026-06-24T17:21:18Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:15350×1). llm_assisted: true