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swimming motility

traitmech:000702 · CLASS · PROPOSED

A motile phenotype in which an organism propels itself through a liquid medium.

Trait evidence (2)

  • DOI:10.1038/s41467-020-18253-7
    Their swimming direction is stabilised by their flagella (archaella)

    Thornton et al. 2020, PMID:32901025, PMC7478972, scientific abstract. Qualified MED identity, title and DOI checked. Results, Swimming behaviour in three dimensions, and Methods on culture and holographic reconstruction directly support liquid swimming by environmental Haloferax sp. Boulby Mine and Haloarcula sp. Great Salt Lake isolates. Mean-squared displacement separated swimming from diffusion. Figure 2 was visually inspected; Supplementary Note 1 describes sampling locations. Methods explicitly leave exact species unresolved. Cultures were grown in 25% dissolved-salt MGM to early exponential phase. The measured trajectories, not merely genes or simulations, support the phenotype. Chemotactic efficiency simulations do not define swimming or establish a universal speed optimum. Raw movies were not reanalyzed. MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the check. Source: https://www.nature.com/articles/s41467-020-18253-7.

  • DOI:10.1038/s41467-018-07802-w
    However, the free-swimming capability of the different strains did not correlate well to the spreading capability in soft agar.

    Kuhn et al. 2018, PMID:30560868, PMC6299084, Results, Filament composition affects flagella-mediated swimming; quote checked directly in full-text XML, not the abstract. Qualified MED identity and DOI checked. Figure 3 and Supplementary Table 1 (printed p. 10, PDF p. 11) were visually inspected. Main Results describe a delta-flaA2B2 background, called wild type for the polar system. Supplementary Figure 11 (printed p. 7, PDF p. 8) instead retains both lateral flagellins for a separate soft-agar assay. Preserve this discrepancy; do not apply the main-text claim to every experiment. Methods distinguish three-dimensional cell tracking in regular or Ficoll-supplemented liquid from soft-agar spreading, and reject Brownian-only tracks. Thus liquid swimming is observed in engineered material; it is not inferred from agar halos or a sequence feature. Filament simulations are separate model evidence. Raw movies were not reanalyzed. MED, Crossref and the retrieved publisher page exposed no linked correction or retraction at the check. Source: https://www.nature.com/articles/s41467-018-07802-w.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1038/s41467-020-18253-7

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.

Keep liquid propulsion distinct from surface movement and passive displacement.

CURATION TODO OPEN swimming-motility-scope-and-assays · raised by codex · 2026-10-11

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.

Motile METPO:1000702 is the broader energy-dependent locomotion phenotype. Swimming concerns propulsion through liquid, including near a boundary, not locomotion across a supporting substrate. Swarming traitmech:000062, twitching traitmech:000061 and gliding METPO:1000706 are not exact synonyms. Passive advection, settling, Brownian motion, colony growth and appendage possession alone are insufficient. Neither a particular speed, solitary behavior, chemotaxis nor a specified propulsion apparatus is required. Bacterial flagella and archaeal archaella must not be conflated. An organism can exhibit swimming and surface motility in different conditions; no organism-level disjointness is asserted. Existing flagellar-motility process nodes, swimming-velocity capacities and taxis discussions are not exact ungrounded instances of this trait. Upstream METPO issue 271 requests this gap; it does not supply an accepted identifier. External phenotype equivalences and lexical variants remain unasserted pending authority checks.

Resolve taxon-specific examples and mechanisms without inferring motion from sequence.

KNOWLEDGE GAP OPEN swimming-motility-examples-and-mechanisms · raised by codex · 2026-10-11

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.

No canonical examples are assigned in this first pass: the haloarchaeal isolates lack resolved species identities in the study, and exact taxon anchors for the bacterial experimental background have not been independently verified here. Engineered material remains valid qualified phenotype evidence, not an unmodified natural exemplar. A causal graph is deferred pending source-bounded branches and eligible taxon-paired protein examples. Do not impose one lineage's motor or chemotaxis machinery on all swimming organisms, or use a NONMECHANISTIC graph to bypass grounding requirements. A flagellin, archaellin, motor gene or predicted motility system alone does not establish liquid propulsion under a tested condition. The present evidence covers bacterial and archaeal cases, not a systematic survey of eukaryotic propulsion or every swimming mechanism.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added liquid swimming motility beneath motile with two DOI-backed primary studies and checked verbatim abstract/full-text snippets. Ignored/hidden worktree, live ontology and pending-PR checks support 000702 and v578 block 1065500-1065599. Existing records unchanged. Assay, strain and sequence-inference limits are explicit. Timestamp records the observed UTC curation decision.

  2. · CURATED_WITH_LITERATURE · codex

    Corrected the unqualified bacterial strain-background statement after visually checking Supplementary Figure 11. Attributed the main-text deletion claim and retained the supplementary lateral-flagellin exception without conflating soft-agar and liquid assays. Addresses issue #1872; prior curation event preserved.

Recorded curation sessions

  • · codex
    • CREATE — Add evidence-backed swimming motility

      Added traitmech:000702 below METPO:1000702 with two DOI-backed primary studies, scientific-abstract and full-text snippets, and explicit liquid-propulsion, assay, strain and sequence-inference limits. Reserved v578 block METPO:1065500-1065599 after ignored/hidden worktree, upstream and pending-PR audits. Canonical examples and graphs remain deferred; prior trait YAMLs are unchanged.

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  • · codex
    • EDIT — Qualify swimming experiment strain backgrounds

      Addressed issue #1872: the draft generalized a main-text lateral-flagellin-deletion statement to all studied strains. After visual inspection of Supplementary Figure 11 (printed p. 7, PDF p. 8), attributed the main-text claim and retained its separate lateral-flagellin-bearing soft-agar experiment. Liquid-tracking evidence, identity, parent, citations and snippets are unchanged. Preserved the initial event and appended a literature-curation event through the guarded writer.

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