identifier: METPO:1000525
label: microbe
definition: A material entity that is too small to be viewed by the unaided eye,
  typically requiring microscopy for observation. Used as the domain class for
  METPO organism-to-X object properties so that organism-level assertions can
  be expressed as `<microbe-instance> <METPO predicate> <object-class>`.
definition_source: PMID:21413255
trait_category: UPPER
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000186
evidence:
- reference: PMID:21413255
  snippet: microorganisms
  notes: Medical Microbiology chapter supports 'microbe' (microorganism) as
    the standard high-level class for the bacteria, archaea, and microbial
    eukaryotes covered by this knowledge base.
- reference: DOI:10.3233/AO-220262
  snippet: BFO is a genuine top-level ontology
  notes: Supports METPO:1000186 (material entity) as the BFO-aligned parent.
curation_history:
- timestamp: '2026-05-16T09:30:00-07:00'
  curator: claude
  action: CREATED_UPPER_CLASS_RECORD
  changes: 'Created upper-ontology CLASS record for METPO:1000525 (microbe)
    so that the domain of un-deprecated metabolism OBJECT_PROPERTYs (which
    all declare domain https://w3id.org/metpo/1000525) resolves to a curated
    TraitMech record.'
  llm_assisted: true
- timestamp: '2026-05-16T09:45:00-07:00'
  curator: claude
  action: REMOVED_NON_EQUIVALENT_XREF
  changes: 'Removed xref to OBI:0100026 (organism) per Copilot review of PR
    #55. The schema documents xrefs as ontology *equivalents*; OBI:0100026
    "organism" is broader than "microbe" (it covers macro-organisms too),
    so treating it as an equivalence mapping would mis-align downstream
    consumers. No clean NCBITaxon, OBI, or ENVO equivalent for "microbe"
    exists because the concept cuts across bacteria, archaea, and microbial
    eukaryotes; left without xrefs.'
  llm_assisted: true