TraitMech

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indole test negative

METPO:1005012 · CLASS · SEEDED

A phenotype in which an organism tests negative in the indole test, indicating it does not produce indole from tryptophan.

Trait evidence (3)

  • DOI:10.1128/AEM.02787-15
    Indole, a bacterial product of tryptophan degradation

    Darkoh et al. support indole as a microbial tryptophan-degradation product.

  • DOI:10.1128/JCM.00940-06
    However, K. variicola, R. planticola, and R. terrigena, in addition to K. pneumoniae, can show a negative-indole reaction

    Alves et al. describe Klebsiella pneumoniae as an indole-negative Klebsiella species in a clinical-isolate biochemical typing context.

  • DOI:10.1128/JCM.00940-06
    A total of 102 (84%) of the 122 isolates were negative for indole production

    Alves et al. reported negative indole-production phenotypes among Klebsiella clinical isolates tested biochemically.

Provenance

Identifier source
METPO (2026-06-12)
Definition source
DOI:10.1128/AEM.02787-15

Parent traits (1)

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Klebsiella pneumoniae NCBITaxon:573 DOI:10.1128/JCM.00940-06 Alves et al. describe K. pneumoniae as an indole-negative Klebsiella species in a clinical-isolate biochemical typing context.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve a non-assay parent for negative indole-test phenotypes before narrowing parent_traits below phenotype.

CURATION TODO RESOLVED indole-test-negative-assay-parent-gap · raised by codex · 2026-09-12

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Resolution: 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.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · ENRICHED_FROM_LITERATURE · codex

    Added the METPO indole-test-negative phenotype with DOI-backed indole-test evidence after a repository-wide duplicate review covering ignored and hidden files.

  3. · CURATION_REVIEW_REVISION · codex

    Tightened Alves Klebsiella wording after local review issue #855 to avoid implying Klebsiella pneumoniae is the only indole-negative Klebsiella or Raoultella species.

  4. · CURATION_REVIEW_REVISION · codex

    Removed unquoted Klebsiella variicola wording after external review issue #856 while preserving the indole-negative Klebsiella pneumoniae interpretation.

  5. · CURATION_REVIEW_REVISION · codex

    Trimmed unsupported Darkoh indole-assay wording after external review issue #857.

  6. · CURATION_REVIEW_REVISION · codex

    Replaced a truncated Alves Klebsiella quote after external review issue #858.

  7. · RESOLVED_PARENT_GAP · codex

    Reparented indole test negative below the newly curated METPO:1005010 indole test assay parent and marked the temporary assay-parent discussion resolved.