identifier: METPO:1005012
label: indole test negative
definition: A phenotype in which an organism tests negative in the indole test, indicating
  it does not produce indole from tryptophan.
trait_category: OTHER
term_kind: CLASS
mapping_status: SEEDED
parent_traits:
- METPO:1005010
curation_history:
- timestamp: '2026-09-12T17:38:53Z'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
- timestamp: '2026-09-12T17:40:50Z'
  curator: codex
  action: ENRICHED_FROM_LITERATURE
  changes: Added the METPO indole-test-negative phenotype with DOI-backed indole-test
    evidence after a repository-wide duplicate review covering ignored and hidden
    files.
  llm_assisted: true
- timestamp: '2026-09-12T17:52:10Z'
  curator: codex
  action: CURATION_REVIEW_REVISION
  changes: 'Tightened Alves Klebsiella wording after local review issue #855 to avoid
    implying Klebsiella pneumoniae is the only indole-negative Klebsiella or Raoultella
    species.'
  llm_assisted: true
- timestamp: '2026-09-12T18:01:45Z'
  curator: codex
  action: CURATION_REVIEW_REVISION
  changes: 'Removed unquoted Klebsiella variicola wording after external review issue
    #856 while preserving the indole-negative Klebsiella pneumoniae interpretation.'
  llm_assisted: true
- timestamp: '2026-09-12T18:09:40Z'
  curator: codex
  action: CURATION_REVIEW_REVISION
  changes: 'Trimmed unsupported Darkoh indole-assay wording after external review
    issue #857.'
  llm_assisted: true
- timestamp: '2026-09-12T18:19:06Z'
  curator: codex
  action: CURATION_REVIEW_REVISION
  changes: 'Replaced a truncated Alves Klebsiella quote after external review issue
    #858.'
  llm_assisted: true
- timestamp: '2026-09-12T21:38:12Z'
  curator: codex
  action: RESOLVED_PARENT_GAP
  changes: Reparented indole test negative below the newly curated METPO:1005010 indole
    test assay parent and marked the temporary assay-parent discussion resolved.
  llm_assisted: true
definition_source: DOI:10.1128/AEM.02787-15
evidence:
- reference: DOI:10.1128/AEM.02787-15
  snippet: Indole, a bacterial product of tryptophan degradation
  notes: Darkoh et al. support indole as a microbial tryptophan-degradation product.
- reference: DOI:10.1128/JCM.00940-06
  snippet: However, K. variicola, R. planticola, and R. terrigena, in addition to
    K. pneumoniae, can show a negative-indole reaction
  notes: Alves et al. describe Klebsiella pneumoniae as an indole-negative Klebsiella
    species in a clinical-isolate biochemical typing context.
- reference: DOI:10.1128/JCM.00940-06
  snippet: A total of 102 (84%) of the 122 isolates were negative for indole production
  notes: Alves et al. reported negative indole-production phenotypes among Klebsiella
    clinical isolates tested biochemically.
canonical_examples:
- taxon_id: NCBITaxon:573
  taxon_label: Klebsiella pneumoniae
  note: Alves et al. describe K. pneumoniae as an indole-negative Klebsiella species
    in a clinical-isolate biochemical typing context.
  reference: DOI:10.1128/JCM.00940-06
discussions:
- discussion_id: indole-test-negative-assay-parent-gap
  prompt: Resolve a non-assay parent for negative indole-test phenotypes before narrowing
    parent_traits below phenotype.
  kind: CURATION_TODO
  status: RESOLVED
  rationale: METPO:1005010 is the seeded superclass of METPO:1005012, but METPO:1005010
    defines an assay rather than a broader microbial trait class, so this record is
    temporarily parented directly to METPO:1000059 phenotype.
  posed_by: codex
  posed_date: '2026-09-12'
  resolved_date: '2026-09-12'
  resolution_note: METPO:1005010 is now represented as the seeded indole-test assay
    parent, so this assay-outcome phenotype can use its exact source superclass instead
    of a temporary direct phenotype parent; this resolves the exact METPO assay-parent
    gap, not the broader non-assay parent question for assay-outcome phenotypes.