identifier: traitmech:000627
label: phagocytosis
definition: A physiological phenotype in which a microbial cell engulfs extracellular
  particles by enclosing them within its membrane and internalizes them into membrane-bound
  compartments.
definition_source: DOI:10.1371/journal.pone.0095577
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000636
evidence:
- reference: DOI:10.1371/journal.pone.0095577
  snippet: remodeling of the collar membrane to engulf the prey, and transport of
    engulfed bacteria into the cell.
  notes: Dayel and King (2014), PMID:24806026, PMC4012994, scientific Abstract directly
    checked in Europe PMC XML and the PLOS article. Results, Discussion and Methods
    were read; actual Figures 1 and 4 were inspected. Live-cell images and SEM/TEM
    support collar-associated engulfment and internalization in Salpingoeca rosetta.
    Mere contact or retention on the collar is not ingestion. Nutrient assimilation
    and the molecular identity of collar links are not established by these images.
    Actual supplements and movies were not inspected. The culture-provenance papers
    cited by the Methods were not followed, so this study is retained as trait evidence
    without a canonical strain assignment.
- reference: DOI:10.1111/nph.20388
  snippet: We found cells ingested proxy (up to 2 μm diameter) and natural (bacteria
    and cyanobacteria) prey particles
  notes: 'Scientific Summary directly checked in Europe PMC full-text XML and PMC11982794;
    PMID:40035416. Results, Discussion and Methods were read, and actual Figures 5,
    6, 9 and 10 were inspected. Scyphosphaera apsteinii RCC1456 cultures internalized
    particles and labeled bacteria into a prominent vacuole. Distinguish pHrodo Escherichia
    coli BioParticles from Acridine Orange-labeled marine bacteria and from inert
    beads. Acidic-organelle staining alone is not prey uptake; some imaging used EGTA
    decalcification. The paper uses phagotrophy for the nutritional interpretation;
    this record asserts particle engulfment, not a measured carbon assimilation rate.
    Figure 10 is a conceptual sequence-based model, not native protein validation:
    its S. apsteinii transcripts come from RCC1455, not the assayed RCC1456, and some
    candidates are from Gephyrocapsa huxleyi. Actual supplements and movies were not
    inspected. No negative comparator-species claim, bead-degrading enzyme assignment
    or inferred nutrient quota is imported.'
canonical_examples:
- taxon_id: NCBITaxon:418940
  taxon_label: Scyphosphaera apsteinii
  reference: DOI:10.1111/nph.20388
  note: 'Strain-qualified example: diploid RCC1456, also AC504, TW15 and NIES-3344.
    Mid- to late-exponential nonaxenic cultures ingested labeled marine bacteria and
    particles under the reported incubation conditions; Figures 5 and 6 were inspected.
    The species taxon ID and scientific name were independently verified at NCBI on
    2026-10-05; this is not a strain-level taxon ID or a claim about every isolate.
    Natural isolation from the Spanish coast of the Balearic Sea by single-cell micropipetting
    on 2001-02-01 was checked directly in the collection record https://www.roscoff-culture-collection.org/rcc-strain-details/1456.
    The transcript-source strain RCC1455 (AC505/TW16) is distinct and is not substituted
    for this exemplar.'
discussions:
- discussion_id: phagocytosis-trait-and-process-scope
  prompt: Keep particle uptake distinct from nutrition and process-level mappings.
  kind: CURATION_TODO
  status: OPEN
  rationale: This class denotes the microbial organism's particle-engulfment phenotype,
    not a host immune cell's response to the microbe. Existing capsule and pathogenic-to-host
    descriptions concern host immune evasion and are not same-scope unresolved trait
    nodes. Phagotrophy denotes a nutritional strategy; the coccolithophore paper uses
    that interpretation, but ingestion of inert particles does not by itself establish
    carbon assimilation. Trophic type METPO:1000631 and heterotrophic METPO:1000644
    require nutritional source use, while predatory bacterium traitmech:000054 is
    bacteria-specific. Endocytosis traitmech:000636 is the direct broader trait because
    the existing particle-enclosure definition entails membrane-bound internalization;
    phenotype METPO:1000059 remains an ancestor. Do not equate phagocytosis with all
    endocytosis, pinocytosis, bacterial predation or phagotrophy. Review external
    process terms separately before asserting any trait-level xref; no synonym or
    ontology equivalence is proposed here.
  posed_by: codex
  posed_date: '2026-10-05'
- discussion_id: phagocytosis-native-mechanism-evidence
  prompt: Require native functional evidence before assigning molecular mechanisms.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: The observed cellular uptake phenotypes do not identify a universal microbial
    protein mechanism. Collar-link composition in S. rosetta remains unresolved. The
    coccolithophore study's KEGG and Swiss-Prot sequence annotations concern RCC1455
    transcripts and G. huxleyi gene models, not direct validation of the RCC1456 uptake
    mechanism. Keep strain provenance, homology, localization, experimental dependence
    and nutrient assimilation as separate evidence requirements. Inspect supplements
    and obtain taxon-paired native protein evidence before adding a causal graph or
    protein accessions.
  posed_by: codex
  posed_date: '2026-10-05'
curation_history:
- timestamp: '2026-10-05T20:40:00Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added phagocytosis as an organism-level particle-engulfment phenotype with
    two DOI-backed snippets, inspected primary figures and a strain-qualified natural
    RCC1456 example. Ignored-and-hidden novelty searches and pinned METPO review found
    no exact record. Reserved METPO:1058000 in v503. Kept nutritional, mapping and
    sequence-based mechanism interpretations separate; no protein graph was inferred.
  llm_assisted: true
- timestamp: '2026-10-06T06:47:04Z'
  curator: codex
  action: REFINE_ENDOCYTOSIS_PARENT
  changes: Refined the direct parent to endocytosis traitmech:000636 by definition-based
    inference. Updated only the parent statement in the scope discussion, which remains
    OPEN for process-mapping review. Preserved definition, evidence, example and prior
    history.
  llm_assisted: true