TraitMech

TraitMech › MORPHOLOGY

motility

METPO:1000701 · CLASS · REVIEWED

A phenotype in which an organism has the capability to move independently through its environment, typically by means of flagella, pili, gliding mechanisms, or other locomotory structures.

Bacterial motility machinery

Evidence-backed causal sketch linking motility to flagella, type IV pili, gliding systems, chemotaxis, and energy transduction.

Bacterial motility machinery Interactive directed graph showing evidence-backed causal relationships for motility.

Edge evidence

  • flagellar motor confers motility METPO:2007700

    Rotary flagellar motors enable bacterial swimming and related motility modes.

    • DOI:10.1038/s41579-021-00626-4 allow bacteria to move around Review summarizes flagellar machinery as a major bacterial motility mechanism.
  • type IV pilus confers motility METPO:2007700

    Type IV pili enable twitching motility through extension, adhesion, and retraction.

    • DOI:10.1038/s41579-019-0195-4 Cycles of pilus extension, binding and retraction Supports type IV pili as motility appendages.
  • gliding motility machinery confers motility METPO:2007700

    Gliding machinery allows surface movement without external flagella.

    • DOI:10.1146/annurev.micro.55.1.49 move actively over surfaces Supports gliding as an active bacterial movement mechanism.
  • ion motive force powers flagellar motor METPO:2007900

    Ion motive force powers rotation of many bacterial flagellar motors.

    • DOI:10.3389/fmicb.2021.659464 relationship between the IMF and the functioning Supports ion motive force powering the bacterial flagellar motor.
  • chemotaxis signaling regulates motility RO:0002211

    Chemotaxis signaling regulates the direction and pattern of bacterial movement.

    • DOI:10.3390/biom9070279 chemotactic signaling pathways regulate the direction Supports chemotaxis control of flagella-driven motility.
  • type IV pilus drives twitching motility

    Type IV pili power twitching, a form of bacterial surface translocation.

    • DOI:10.1128/msphere.00390-24 Twitching motility is a form of bacterial surface translocation powered by the type IV pilus (T4P).
  • PilB extension ATPase drives extension of type IV pilus

    PilB ATPase drives extension of the type IV pilus.

    • DOI:10.1128/jb.00359-24 PilB is the homohexameric extension ATPase of the type IV pilus.
  • PilT retraction ATPase drives retraction of type IV pilus

    PilT ATPase drives retraction of the type IV pilus.

    • DOI:10.1128/jb.00359-24 Retraction is carried out by the antagonistic ATPase PilT.
  • type IV pilus retraction generates twitching motility biolink:produces

    Type IV pilus retraction generates the pulling forces underlying twitching motility.

    • DOI:10.1128/jb.00442-23 T4P retraction generates the pulling forces underlying twitching motility.
  • cyclic di-GMP inhibits motility RO:0002212

    Cyclic di-GMP inhibits motility; lowering c-di-GMP relieves this inhibition.

    • DOI:10.1038/s42003-024-07392-y Lower c-di-GMP relieves its inhibition on motility (generic c-di-GMP -> motility edge).
  • archaellum confers motility METPO:2007700

    The archaellum enables swimming motility in archaea, analogous to the bacterial flagellum.

    • DOI:10.1038/s41467-024-50277-1 The archaellum enables cell motility in archaea.

Provenance

Source
METPO (2025-11-25)
Author
Jed Dongjin Kim-Ozaeta
Definition source
DOI:10.1038/s41579-021-00626-4

Parent traits (1)

Children (2)

Synonyms (1)

  • Morphology.cell morphology.motility RELATED_SYNONYM · metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000701 [-1.722, -3.036, -3.705, +0.093, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Deep research

Generated by just research-trait; source: research/traits/morphology/motility-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Curation-focused research report: microbial motility

## Executive summary

**Target:** `METPO:1000701` (“motility”); category MORPHOLOGY; class; parent `METPO:1000059`.

For TraitMech, motility should mean the **intrinsic capacity for active, self-generated translocation**, not merely observed displacement. It includes flagellar swimming, flagellar swarming, type-IV-pilus (T4P) twitching, and independently powered gliding systems. Chemotaxis is a directional-control process layered onto motility; passive advection, rainfall transport, animal-mediated transport, and microbial hitchhiking are movement but not this trait. Growth-driven colony spreading, sliding, appendage presence without demonstrated function, and Brownian displacement should also remain outside the core definition.

The strongest graph backbone is:

1. ion motive force → stator ion flux → flagellar torque/rotation → filament propulsion → motility;
2. ATP hydrolysis by PilB/PilT → T4P extension/retraction → substrate-coupled cell translocation → twitching motility;
3. environmental and regulatory modifiers—including surface hydrophilicity and c-di-GMP-linked regulation—modulate those machines in specific taxa and assays.

## 1. Trait scope and boundaries

### Operational definition

The supplied definition is consistent with current mechanistic understanding: an organism has motility when it can move independently through its environment using a biological propulsion apparatus. Active bacterial movement includes flagellar swimming/swarming and T4P twitching, whereas passive movement can arise from rainfall, protists, nematodes, or hitchhiking on another microbe’s appendage (Alexandre, October 2025; DOI URL: https://doi.org/10.1128/aem.00246-25). (alexandre2025movementofbacteria pages 1-2)

### Included phenotypes

- **Swimming:** individual-cell movement through liquid, usually driven by rotating flagella.
- **Swarming:** coordinated flagellum-dependent surface movement on hydrated semisolid media; it is a composite phenotype influenced by cell density, surfactants, differentiation, chemotaxis, growth, and agar concentration.
- **Twitching:** non-flagellar surface translocation driven by repeated T4P extension, substrate attachment, and retraction.
- **Gliding:** smooth active surface translocation without external flagella; because unrelated gliding machines exist, this should be represented by mechanism-specific child branches rather than one universal machinery edge.
- **Archaeal swimming:** conceptually included when driven by archaella, but bacterial flagellar proteins must not be projected onto archaea.

### Excluded or separately modeled boundary cases

- **Chemotaxis/taxis:** chemotaxis is “the ability to sense chemical gradients and actively direct motility along them,” so it controls direction rather than establishing propulsion capacity. Surface twitching *Pseudomonas aeruginosa* can use spatial sensing, whereas canonical swimming bacteria generally use temporal sensing. These should be regulatory edges, not synonyms for motility (Wheeler et al., published 2 September 2024; https://doi.org/10.1038/s41564-024-01729-3). (wheeler2024individualbacterialcells pages 1-2)
- **Passive transport:** advection, rainfall, sediment movement, vectors, or hitchhiking do not demonstrate independent locomotion. (alexandre2025movementofbacteria pages 1-2)
- **Growth and colony expansion:** increased colony diameter may reflect growth, sliding, wetting, or active motility. A growth control and/or single-cell tracking is required.
- **Biofilm formation and adhesion:** these are associated functions or consequences of motility machines, not motility itself.
- **Appendage presence:** flagella or pili visualized by microscopy support machinery formation, but a functional motility assay is still needed.
- **Magnetotaxis, buoyancy regulation, and passive settling:** these require explicit evidence of energy-dependent self-translocation before inclusion under this term.

## 2. Candidate causal-graph nodes

Identifiers below are limited to mappings that can be stated confidently. Label-only nodes are preferable to unverified CURIEs.

### Trait and biological-process nodes

- Motility — `METPO:1000701`; target node.
- Parent trait — `METPO:1000059`.
- Bacterial-type flagellum-dependent cell motility — `GO:0071973`.
- Bacterial-type flagellum-dependent swarming motility — `GO:0071978`.
- Twitching motility — `GO:0071977`.
- Chemotaxis — `GO:0006935`; regulatory/navigation process, not equivalent to motility.
- Pilus organization — `GO:0043711`.
- Bacterial-type flagellum assembly — `GO:0044780`.
- Gliding motility — retain as a label unless the repository’s ontology release is checked for the exact mechanism-specific term.

### Flagellar machinery and localization nodes

- Flagellar basal body; rotor; stator; hook; filament; hook–filament junction; filament cap.
- MotA, MotB; sodium-driven homologous stators PomA, PomB.
- FliF MS ring; FliG/FliM/FliN C ring; FlgE hook; FliC/FljB flagellin; FliD cap; FlgK/FlgL junction; FliK ruler; FlhA/FlhB export-switch proteins.
- Cytoplasmic membrane — `GO:0005886` is usable as a general cellular-component grounding, though bacterial-envelope-specific ontology terms may be preferable locally.
- Peptidoglycan layer — label or verified GO/ChEBI mapping according to graph conventions.

Showing the first 60 of 276 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · CURATED_WITH_LITERATURE · codex

    Reviewed motility trait and added DOI-backed causal graph for flagellar, pili-mediated, gliding, chemotaxis, and ion-motive-force mechanisms.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×3, RO:0002211×1).

  4. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:R6TBR9×1).

  5. · RENAME_PREDICATE_LABELS · claude

    Renamed 1 causal-edge predicate label(s) to align with existing groundings: powers → enables ×1.

  6. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002327×1).

  7. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0006935×1).

  8. · REMOVE_REDUNDANT_SYNONYM · claude

    Removed 1 synonym(s) whose text duplicated the label (seeder redundancy; no information lost).

  9. · ENRICH_CAUSAL_GRAPH · claude

    Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report.

  10. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces×1, RO:0002212×1, RO:0002327×1).

  11. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:49537×1).

  12. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 1 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)

  13. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0044096×1).

  14. · MIGRATE_ENABLES_TRAIT_EDGES · claude

    Migrated 4 causal edge(s) off enables/RO:0002327 with a TRAIT object (4 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.

  15. · REGROUND_CAUSAL_EDGE · claude

    Re-grounded causal edge(s) off enables/RO:0002327 onto contributes to (RO:0002326), issue 334. biolink declares enables range 'biological process or activity', which only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so an edge pointing at a GENE_OR_PROTEIN entailed a false type. The replacements are chosen per idiom rather than swept: a gene cluster ENCODES its product, a subunit is PART OF the complex it belongs to, and an energy source or acquired repertoire CONTRIBUTES TO the machine it powers or composes. All three declare no rdfs:domain or rdfs:range, so none can reintroduce the class of defect being removed.

  16. · REGROUND_CAUSAL_EDGE · claude

    Reverted the motive-force edge from contributes to back to enables/RO:0002327, issue 334 review. biolink defines contributes to as holding where one entity contributes to the occurrence or GENERATION of the other. A motive force does not generate the motor or machinery - it powers rotation, which is what the edge description says. That is the same energy-powers-a-machine idiom this work deferred for molecular_oxygen and cytoplasmic_na, so deferring it here too is the consistent call. The edge stays baselined under issue 334 until it is modelled as an input to the machine or pointed at the rotation process, either of which is range-correct.

  17. · REGROUND_CAUSAL_EDGE · claude

    Edge ion_motive_force -> flagellar_motor in graph motility_locomotion_machinery: re-grounded it from enables/RO:0002327 to powers/METPO:2007900. Issue 334. biolink declares enables range 'biological process or activity', which of CausalNodeTypeEnum only BIOLOGICAL_PROCESS, PATHWAY and MOLECULAR_FUNCTION satisfy, so this edge entailed a false type on its object. 'Ion motive force POWERS rotation of many bacterial flagellar motors.'