identifier: METPO:1000887
label: cell width very small
definition: A cell-width phenotype in which the shorter cell dimension is at most
  approximately 0.5 micrometers.
definition_source: DOI:10.1038/ismej.2014.60
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000882
synonyms:
- synonym_text: W_<=0.5
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1038/ismej.2014.60
  snippet: small cells and genomes
  notes: Streamlining review links very narrow cell widths to oligotrophic and streamlined
    lineages.
causal_graphs:
- graph_id: cell_width_very_small_streamlining
  title: Very-narrow cell width by streamlining
  description: DOI-backed graph linking nutrient streamlining to a very-narrow rod
    radius (≤0.5 μm).
  nodes:
  - node_id: cell_width_very_small_trait
    label: cell width very small
    node_type: TRAIT
    grounding: METPO:1000887
    description: Cell width at most ~0.5 μm.
  - node_id: cell_width_trait
    label: cell width
    node_type: TRAIT
    grounding: METPO:1000882
    description: Regulated shorter cellular dimension.
  - node_id: streamlining_selection
    label: streamlining selection
    node_type: BIOLOGICAL_PROCESS
    description: Selection for reduced surface-to-volume ratio under chronic nutrient
      limitation.
  - node_id: oligotrophic_environment
    label: oligotrophic environment
    node_type: ENVIRONMENTAL_FACTOR
    description: Persistent low-nutrient setting that favors miniaturized cells.
  - node_id: high_surface_to_volume_ratio
    label: high surface-to-volume ratio
    node_type: QUALITY
    description: Elevated cell surface area relative to volume, characteristic of
      small/narrow cells.
  - node_id: nutrient_uptake_efficiency
    label: nutrient uptake efficiency
    node_type: CAPACITY
    description: Efficiency of nutrient acquisition from the environment.
  - node_id: small_cell_bacteria
    label: small-cell bacteria
    node_type: STATE
    description: Bacteria with very small cell size, including narrow widths.
  - node_id: oligotrophic_waters
    label: oligotrophic waters
    node_type: ENVIRONMENTAL_FACTOR
    description: Low-nutrient aquatic environments with low organic matter concentrations.
  - node_id: reduced_genome_size
    label: reduced genome size
    node_type: QUALITY
    description: Streamlined small genome characteristic of oligotrophic lineages.
  - node_id: rod_complex
    label: Rod complex
    node_type: GENE_OR_PROTEIN
    description: Elongasome directing organized circumferential peptidoglycan insertion
      that constrains cell width.
  - node_id: apbp_proteins
    label: class A penicillin-binding proteins
    node_type: GENE_OR_PROTEIN
    description: aPBPs mediating isotropic peptidoglycan insertion that enlarges the
      cell cylinder.
  edges:
  - subject: oligotrophic_environment
    predicate: regulates
    object: streamlining_selection
    description: Persistent oligotrophy selects for streamlined narrow cells.
    evidence:
    - reference: DOI:10.1038/ismej.2014.60
      snippet: small cells and genomes
      notes: Supports oligotrophic regimes as drivers of cell-width reduction.
    predicate_id: RO:0002211
  - subject: streamlining_selection
    predicate: produces
    object: cell_width_very_small_trait
    description: Streamlining selection produces very narrow rods.
    evidence:
    - reference: DOI:10.1038/ismej.2014.60
      snippet: small cells
      notes: Supports very narrow width as an outcome of streamlining selection.
    predicate_id: METPO:2000202
  - subject: cell_width_very_small_trait
    predicate: is a
    object: cell_width_trait
    description: Very small cell width is a quantitative bin of the cell-width phenotype.
    evidence:
    - reference: DOI:10.1146/annurev-cellbio-101011-155745
      snippet: MreB-directed peptidoglycan synthesis
      notes: Supports very narrow width as a value within the regulated cell-width
        distribution.
    predicate_id: rdfs:subClassOf
  - subject: high_surface_to_volume_ratio
    predicate: increases
    object: nutrient_uptake_efficiency
    description: High surface-to-volume ratio of narrow cells improves nutrient uptake
      efficiency.
    evidence:
    - reference: DOI:10.31951/2658-3518-2024-a-4-795
      notes: Thanks to their high surface-to-volume ratio, small-cell bacteria absorb
        nutrients most efficiently.
    predicate_id: RO:0002213
  - subject: small_cell_bacteria
    predicate: adapted to
    object: oligotrophic_waters
    description: Small-cell bacteria with very narrow widths are adapted to oligotrophic
      waters.
    evidence:
    - reference: DOI:10.31951/2658-3518-2024-a-4-795
      notes: Especially important in oligotrophic water bodies with low organic matter
        concentrations.
  - subject: reduced_genome_size
    predicate: associated with
    object: streamlining_selection
    description: Reduced genome size is associated with streamlining in oligotrophic
      lineages.
    evidence:
    - reference: DOI:10.1128/mmbr.00124-22
      notes: Many microbial cell lineages in nature share with oligotrophs the property
        of reduced genome size.
    predicate_id: biolink:associated_with
  - subject: rod_complex
    predicate: decreases
    object: cell_width_trait
    description: Rod-complex-mediated organized circumferential PG insertion reduces
      cell width (rod-shaped bacteria).
    evidence:
    - reference: DOI:10.1128/msystems.01017-21
      notes: Rod complex-mediated organized circumferential insertion of PG strands
        reduces cell diameter; may generalize to rod-shaped bacteria.
    predicate_id: RO:0002212
  - subject: apbp_proteins
    predicate: increases
    object: cell_width_trait
    description: aPBP-mediated isotropic PG insertion enlarges the cell cylinder,
      increasing width.
    evidence:
    - reference: DOI:10.1128/msystems.01017-21
      notes: aPBP-mediated isotropic insertion enlarges the cell cylinder; defines
        opposite regulation of width.
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-05-05T01:35:46.921226+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T22:30:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph linking oligotrophic streamlining selection
    to very narrow cell width (≤0.5 μm).
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×1, rdfs:subClassOf×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:13:19Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    drives → regulates ×1.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:21Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (7 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:13Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×2, biolink:associated_with×1, RO:0002212×1).
  llm_assisted: true