HabitatMech

upper aerodigestive tract environment

habitatmech:BACDIVE.3974b3f169 ·OTHER ·UNGROUNDED REVIEWED

An anatomical entity environment which is determined by the contiguous air- and saliva-exposed lumen extending from the oral cavity to the lower airways of a vertebrate. — HabitatMech

Source attestations

Each upstream vocabulary's own account of this habitat. Assertion counts are per-source units and are not comparable across sources — GOLD counts organisms, BacDive strains, PREGO taxa.

What each upstream vocabulary says about this habitat
SourceLabel / pathAssertionsUnit
BACDIVE Oral-cavity-and-airways 2102 STRAIN

Broader habitats

Associated taxa

Taxa reported from this habitat, which is weaker than being characteristic of it. rank is out of pool: a high rank in a pool of thousands of near-tied scores is a weak claim. Entries corroborated by a second, independent source are listed first.

Taxa reported from this habitat
TaxonSourceRankPoolCorroborated
Actinomyces viscosus NCBITaxon:1656 BACDIVE 1 881
Bordetella pertussis NCBITaxon:520 BACDIVE 2 881
Schaalia odontolytica NCBITaxon:1660 BACDIVE 3 881
Pseudomonas aeruginosa NCBITaxon:287 BACDIVE 4 881
Streptococcus anginosus NCBITaxon:1328 BACDIVE 5 881
Actinomyces naeslundii NCBITaxon:1655 BACDIVE 6 881
Haemophilus influenzae NCBITaxon:727 BACDIVE 7 881
Klebsiella pneumoniae NCBITaxon:573 BACDIVE 8 881
Streptococcus pneumoniae NCBITaxon:1313 BACDIVE 9 881
Streptococcus sanguinis NCBITaxon:1305 BACDIVE 10 881
Corynebacterium diphtheriae NCBITaxon:1717 BACDIVE 11 881
Streptococcus oralis NCBITaxon:1303 BACDIVE 12 881
Ornithobacterium rhinotracheale NCBITaxon:28251 BACDIVE 13 881
Bacteria NCBITaxon:2 BACDIVE 14 881
Bordetella parapertussis NCBITaxon:519 BACDIVE 15 881
Actinomyces graevenitzii NCBITaxon:55565 BACDIVE 16 881
Elizabethkingia meningoseptica NCBITaxon:238 BACDIVE 17 881
Aggregatibacter aphrophilus NCBITaxon:732 BACDIVE 18 881
Streptococcus gordonii NCBITaxon:1302 BACDIVE 19 881
Streptococcus sp. NCBITaxon:1306 BACDIVE 20 881
Streptococcus pyogenes NCBITaxon:1314 BACDIVE 21 881
Kingella denitrificans NCBITaxon:502 BACDIVE 22 881
Stenotrophomonas sp. NCBITaxon:69392 BACDIVE 23 881
Histophilus somni NCBITaxon:731 BACDIVE 24 881
Staphylococcus aureus NCBITaxon:1280 BACDIVE 25 881

Also called

Curation

What a curator decided about this record, and why. A record built from several source concepts can carry one decision per concept.

  1. CONFIRM_UNGROUNDED 2026-08-14 · claude-opus-5

    Confirmed UNGROUNDED: no ontology term fits this concept. Cohort review (subset/disjoint mapping screen): a composite of two sites. UBERON:0001005 'respiratory airway' covers only the airways half and drops the oral cavity, and it is also the correct target for the separate 'Airways' source — adopting it here would merge the two. No single term covers mouth plus airway; the respiratory-tract terms exclude the oral cavity. (source concept habitatmech:BACDIVE.3974b3f169)

  2. DEFINED 2026-08-17 · claude-opus-5

    Defined as 'upper aerodigestive tract environment' under ENVO:2100000 'anatomical entity environment'. Definition drafted from the record's deep-research report under research/habitats/ and read against it. BacDive's label names two sites and the upstream mapping to UBERON:0001005 'respiratory airway' covered only the airways half, dropping the oral cavity. The definition keeps the contiguous lumen both halves belong to.

Provenance

Generated by scripts/seed_from_sources.py from the committed inventories in data/raw/. View the record.