identifier: METPO:1003024
label: cream pigmented
definition: A pigmentation phenotype in which colony or cell coloration is a pale,
  off-white or cream hue, typically reflecting low-density carotenoid or other light-absorbing
  pigments.
definition_source: DOI:10.1146/annurev.micro.62.081307.162844
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1003021
synonyms:
- synonym_text: Pigment_cream
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1146/annurev.micro.62.081307.162844
  snippet: bacterial carotenoid pigments
  notes: Bacterial-carotenoid review supports low-abundance carotenoids as the basis
    for cream/pale coloration in many bacterial taxa.
causal_graphs:
- graph_id: cream_pigmented_low_carotenoid_density
  title: Cream-pigmentation low carotenoid density
  description: DOI-backed graph linking low-level carotenoid (or analogous light-absorbing
    pigment) biosynthesis and limited pigment accumulation to a cream/pale-colored
    colony phenotype.
  nodes:
  - node_id: cream_pigmented_trait
    label: cream pigmented
    node_type: TRAIT
    grounding: METPO:1003024
    description: Cream/pale colony or cell coloration.
  - node_id: low_carotenoid_biosynthesis
    label: low-level carotenoid biosynthesis
    node_type: BIOLOGICAL_PROCESS
    description: Reduced flux through the bacterial isoprenoid pigment biosynthesis
      pathway compared to brightly pigmented lineages.
    grounding: GO:0016117
  - node_id: low_pigment_accumulation
    label: low pigment accumulation
    node_type: BIOLOGICAL_PROCESS
    description: Reduced steady-state pigment levels relative to brightly pigmented
      lineages.
  - node_id: pale_coloration
    label: pale cream coloration
    node_type: BIOLOGICAL_PROCESS
    description: Optical phenotype of off-white pigmented colonies.
  - node_id: carotenoid_biosynthesis_genes
    label: carotenoid biosynthesis genes (crt locus)
    node_type: GENE_OR_PROTEIN
    description: Core carotenoid-pathway enzymes (e.g. crtE/crtB/crtI-type) required
      for synthesis of colored carotenoids.
  - node_id: carotenoid_gene_disruption
    label: carotenoid biosynthesis gene disruption
    node_type: EXPERIMENTAL_FACTOR
    description: Loss-of-function or repression of core carotenoid-pathway genes.
  - node_id: isoprenoid_precursor_supply
    label: isoprenoid (MEP-pathway) precursor supply
    node_type: BIOLOGICAL_PROCESS
    description: Supply of isoprenoid precursors (IPP/DMAPP/GGPP) via the MEP pathway
      feeding carotenoid biosynthesis.
  edges:
  - subject: low_carotenoid_biosynthesis
    predicate: produces
    object: low_pigment_accumulation
    description: Limited carotenoid (or analogous) pigment biosynthesis produces low
      pigment accumulation.
    evidence:
    - reference: DOI:10.1146/annurev.micro.62.081307.162844
      snippet: bacterial carotenoid pigments
      notes: Supports carotenoid biosynthesis as the source of bacterial pigmentation.
    predicate_id: METPO:2000202
  - subject: low_pigment_accumulation
    predicate: yields
    object: pale_coloration
    description: Low pigment density yields a pale, cream-colored optical phenotype.
    evidence:
    - reference: DOI:10.1146/annurev.micro.62.081307.162844
      snippet: bacterial carotenoid pigments
      notes: Supports pigment density as the determinant of colony color intensity.
    predicate_id: biolink:produces
  - subject: pale_coloration
    predicate: manifests as
    object: cream_pigmented_trait
    description: Pale coloration manifests the cream-pigmented trait.
    evidence:
    - reference: DOI:10.1146/annurev.micro.62.081307.162844
      snippet: bacterial carotenoid pigments
      notes: Supports the trait endpoint.
    predicate_id: METPO:2007400
  - subject: carotenoid_biosynthesis_genes
    predicate: enables
    object: low_carotenoid_biosynthesis
    description: Core crt-locus enzymes are required for carotenoid biosynthesis;
      their activity sets pathway flux.
    evidence:
    - reference: DOI:10.3390/pathogens12010086
      notes: Insertions mapped to crtE, crtI, crtB, crtYc, crtYd involved in synthesis
        of beta-carotene; disrupted mutants retained an off-white appearance.
    predicate_id: RO:0002327
  - subject: carotenoid_gene_disruption
    predicate: decreases
    object: low_carotenoid_biosynthesis
    description: Disruption or repression of core carotenoid-biosynthesis genes lowers
      carotenoid synthesis, leaving colonies pale/off-white.
    evidence:
    - reference: DOI:10.3390/pathogens12010086
      notes: '"Most of these mutants failed to develop pigmentation upon light treatment
        and retained an off-white appearance" with insertions in crt-pathway genes
        (broad but not universal across taxa).'
    predicate_id: RO:0002212
  - subject: isoprenoid_precursor_supply
    predicate: enables
    object: low_carotenoid_biosynthesis
    description: MEP-pathway isoprenoid precursor supply feeds carotenoid biosynthesis;
      reduced precursor supply lowers downstream carotenoid output.
    evidence:
    - reference: DOI:10.3390/microorganisms9040670
      notes: Repression of the MEP-pathway gene ispG significantly lowered cellular
        carotenoid content; repression of MEP/carotenogenesis genes was expected to
        reduce pigmentation.
    predicate_id: RO:0002327
curation_history:
- timestamp: '2026-05-05T01:35:46.944295+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T23:00:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed definition and causal graph linking low-density carotenoid
    biosynthesis to cream/pale colony pigmentation.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×1).
  llm_assisted: true
- timestamp: '2026-05-23T21:30:07Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007400×1).
  llm_assisted: true
- timestamp: '2026-06-13T21:03:26Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 3 evidence-backed generic edges (3 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:13Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×2, RO:0002212×1).
  llm_assisted: true