aerobic overflow metabolism

traitmech:000705 · CLASS · PROPOSED

A physiological phenotype in which microbial cells divert part of their catabolic carbon flux to excreted, incompletely oxidized products with lower ATP yield per substrate than complete respiration, despite possessing respiratory capacity and sufficient oxygen for respiration.

Trait evidence (3)

DOI:10.1038/msb.2009.82
S. cerevisiae and E. coli fully oxidize glucose at low concentrations and shift to overflow metabolism at high glucose concentrations.

Molenaar et al. 2009, PMID:19888218, PMC2795476; Current growth models and their limitations, not the abstract. The surrounding paragraph supplies the fully aerobic, incomplete-oxidation and retained respiratory-capacity differentia. This Perspective contains original modeling, not new experimental replication of the cited organisms. The terminology discussion also includes mixed-acid-to-lactate shifts; the qualified label here does not define every use of unqualified overflow metabolism.
DOI:10.1038/nature15765
cells use fermentation instead of the more efficient respiration to generate energy, despite the availability of oxygen.

Basan et al. 2015, PMID:26632588, PMC4843128; scientific abstract. Relevant Results, growth Methods, model scope, Extended Data Table 1, actual Figure 1 and Extended Data Figure 2 were inspected through public XML and figure assets. Acetate excretion depends on growth conditions; the fitted threshold is not universal. The oxidative-fermentation accounting includes oxygen-dependent NADH oxidation. Net excretion does not exclude acetate reuptake. Proteome allocation is a tested model in this system, not a necessary mechanism for every member of the trait. Complete supplements, equations and referenced batch-culture methods were not independently reanalyzed. Publisher retrieval failed; the public full-text XML was accessible.
DOI:10.1111/febs.13019
All fermenting yeasts exhibited significant ethanol formation within the first 20 min in response to a glucose pulse

Hagman et al. 2014, PMID:25161062, PMC4240471; Results and Discussion / Consumption of glucose and generation of biomass and ethanol, not the abstract. Introduction, relevant Results, Experimental procedures and actual Figures 1-2 were inspected. Glucose pulses into initially respiratory cultures produced ethanol in responsive yeasts while dissolved oxygen was controlled above 30% air saturation. The authors report no first-hour repression of respiration; Figure 2 does not establish monotonic or unchanged oxygen-consumption rates. Replication excludes V. polyspora; E. coryli received supplementation. This short-term Crabtree assay is not an exact synonym for the entire microbial phenotype. Supplemental time series and strain origins were not fully reviewed.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1038/msb.2009.82

Parent traits (1)

phenotype METPO:1000059

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (2)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Retain oxygen-sufficient overflow as a conditional phenotype with an explicit hierarchy boundary.

CURATION TODO OPEN aerobic-overflow-scope-and-parent · raised by codex · 2026-10-12

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

The qualifier aerobic is deliberate. Unqualified overflow, Crabtree effect, respiro-fermentation and industrial aerobic fermentation are not asserted as exact synonyms. The local METPO:1002005 fermentation record is donor/acceptor-defined and excludes external electron acceptors; Basan's oxidative branch uses different accounting. https://github.com/berkeleybop/metpo/issues/468 discusses fermentation hierarchy, and the pinned ontology already differs from the retained local parent/definition. Neither that process nor METPO:1000060 metabolism is adopted as an is-a parent of this organismal phenotype. METPO:1000059 phenotype is used pending upstream hierarchy review. Product-specific ethanol/butanediol fermentation, aerotolerance, facultative anaerobiosis, copiotrophy and diauxic growth are not equivalent. Product detection or oxygen presence alone is insufficient: oxygen limitation must be excluded. No universal substrate, product, concentration, growth-rate threshold, complete respiratory shutdown or fixed molecular mechanism is required.

Resolve natural strain provenance and taxon-specific mechanisms before adding canonical examples or a graph.

KNOWLEDGE GAP OPEN aerobic-overflow-examples-and-mechanism · raised by codex · 2026-10-12

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

Laboratory reference strains and engineered perturbations are qualified evidence, not proof that every member of a species has this phenotype under all conditions. Canonical taxa require primary strain provenance and authority-resolved identities. No common protein-resolved causal graph is established here; bacterial and yeast mechanisms must retain their experimental scope. Gene presence and predicted flux alone do not demonstrate overflow. Canonical examples, causal graphs and external xrefs are therefore unasserted. Qualified MED and Crossref records for all three citations exposed no linked correction or retraction on 2026-10-12; this bounded check is not a guarantee that no notice exists. Basan's publisher access remains unavailable.

Curation history

2026-10-12T01:03:22Z · MINTED_TRAITMECH_ID · codex
Added aerobic overflow metabolism with three DOI-backed sources and directly checked snippets. Reserved 000705, v581 and 1065800-1065899 after ignored/hidden worktree and pending-PR checks. Oxygen-sufficient scope, hierarchy and inference limits are explicit. Existing traits unchanged; timestamp is the observed UTC curation decision.
2026-10-12T01:08:15Z · CLARIFIED_EVIDENCE_SCOPE · codex
Address #1881: distinguish the authors' reported lack of early respiratory repression from a claim that individual oxygen-consumption rates never decrease. Retain the original curation event unchanged.
2026-10-12T01:53:37Z · REPLACED_UNSUPPORTIVE_SNIPPET · codex
Address #1883: replace the yeast data-collection quotation with an 18-word Results span that reports significant ethanol formation after a glucose pulse. Retain oxygen-controlled assay context, the 25-word bound and both earlier curation events unchanged.

Recorded curation sessions

2026-10-12T01:06:48Z · codex
- CREATE — Add DOI-backed aerobic overflow metabolism phenotype
  Created traitmech:000705 as a PROPOSED PHYSIOLOGY class under METPO:1000059 with three directly checked DOI-backed snippets, explicit oxygen and hierarchy scope, and provenance/mechanism gaps. Reserved v581 and METPO:1065800-1065899 after current-main, ignored/hidden worktree and pending-PR checks. Added a guarded writer and focused tests; existing traits are unchanged. Broad QC, generated products and adversarial review follow this curation event.
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2026-10-12T01:08:51Z · codex
- EDIT — Clarify respiratory-repression interpretation
  Addressed issue 1881 by attributing the no-early-repression result to Hagman et al. and explicitly excluding a monotonic or unchanged oxygen-consumption interpretation of Figure 2. The guarded writer accepts only the exact original draft or corrected output, appends CLARIFIED_EVIDENCE_SCOPE, and retains the initial event and CREATE history unchanged. Added an exact-preimage upgrade test; source snippets and trait scope are unchanged.
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2026-10-12T01:54:55Z · codex
- EDIT — Replace yeast measurement snippet with a positive result
  Addressed issue 1883 from external review 5485934905 on PR 1882. Replaced the generic data-collection quote with an exact 18-word Results span reporting significant ethanol formation after a glucose pulse. Corrected the source-section note, retained oxygen-control and respiration qualifiers, and appended REPLACED_UNSUPPORTIVE_SNIPPET without altering either prior event or history record. Added a guarded two-event preimage upgrade regression, clarified claim-bearing snippet selection in add-trait, and updated the proposal narrative. Existing review bundles remain unchanged; regenerated-product validation and a linked resolved review follow.
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