TraitMech

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pH taxis

traitmech:000591 · CLASS · PROPOSED

A motile phenotype in which active locomotion is directionally biased in response to an external pH gradient.

Trait evidence (2)

  • DOI:10.1128/jb.00491-19
    This bacterium was found to perform bidirectional taxis in response to external pH gradients, enabling it to preferentially migrate to neutral environments.

    Abstract, exact-matched at Europe PMC (PMID:31685537). The antecedent is Bacillus subtilis. This observation supports external-gradient-directed movement, including responses from both acidic and alkaline environments in this study. It does not establish neutral pH as a universal preferred destination. Full text was not systematically inspected; receptor-chimera findings in the abstract are not converted into a molecular causal graph or an unqualified natural-strain example.

  • DOI:10.1128/jb.188.7.2656-2665.2006
    Bacteria in more-alkaline regions did not swim toward the acid, suggesting the pH taxis is a form of negative chemotaxis.

    Abstract, exact-matched at Europe PMC (PMID:16547053); full text not inspected. The preceding observation describes Helicobacter pylori moving away from strong acid in a microscope-slide pH gradient. This supports an acid-avoidance response without requiring every pH-tactic organism to show bidirectional attraction to a neutral optimum. Strain-specific mutant, receptor and host-colonization findings are not generalized into the trait definition or mechanism.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1128/jb.00491-19

Parent traits (1)

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.

Preserve directional scope and verify external equivalents.

CURATION TODO OPEN ph-taxis-scope-and-mapping-boundaries · raised by codex · 2026-10-04

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.

Growth pH preference, acid or alkali tolerance, intracellular pH homeostasis and changes in speed alone do not establish pH-directed locomotion. Neither neutral-pH attraction nor bidirectional response is required universally. The local chemotaxis definition specifies flagellar motor switching; motile is the verified broader METPO parent without imposing that apparatus. No external xref or exact synonym is asserted before authority resolution and organismal-scope comparison.

Verify natural strain provenance and protein-resolved mechanisms.

CURATION TODO OPEN ph-taxis-mechanism-and-canonical-strains · raised by codex · 2026-10-04

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 primary abstracts establish pH-tactic behavior, not a single universal receptor mechanism. Before adding canonical examples, verify the unperturbed reference strains against primary strain-provenance sources and resolve their NCBI taxon identities. Before adding a causal graph, inspect the full studies and relevant supplements, distinguish observed perturbation effects from proposed sensing models, and resolve taxon-paired protein accessions. A NONMECHANISTIC graph must not bypass those requirements.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added pH taxis with two primary DOI citations and exact abstract snippets. Ignored-and-hidden searches and structured OWL review found no exact live record or METPO term. Reserved METPO:1054500 in v468. Deferred unverified strain examples, molecular graph grounding and external equivalents; retained directional scope without universal neutral-pH or bidirectionality requirements.