{
  "abstract": "Rationale: Lung cancer is the leading cause of cancer-related death globally, and rising incidence among traditionally low-risk individuals intensifies the need for improved early-detection methods that the lower-airway microbiome may inform. Objectives: To evaluate how respiratory tract sampling method shapes inferred microbiome structure, and whether bronchial brushing recovers a microbial community ecologically distinct from BAL and oral rinse. Methods: A pilot cohort of 33 participants (8 lung cancer, 25 non-cancer controls) underwent oral rinse, bilateral bronchoalveolar lavage (BAL), and bronchial brushing. Microbiome structure was characterized by small subunit ribosomal rRNA gene amplicon sequence variant (ASV) profiling, with indicator-species analysis and SPIEC-EASI correlation-network mapping used to identify ASVs associated with sample type or cancer status. Measurements and Main Results: Sampling method was the dominant variation axis. BAL communities closely resembled oral rinse (64 jointly indicative ASVs; none shared with brushing), whereas bronchial brushing yielded a distinct but low-biomass signal. After excluding host-derived sequences, a single brush-specific indicator ASV affiliated with Sphingomonadaceae was identified within a 17-node co-occurrence module. Cancer-status effects were not detectable, consistent with limited statistical power. Conclusions: Sampling method is the primary determinant of inferred lower respiratory microbiome structure. Bronchial brushing recovers a distinct but low-biomass signal that is obscured when BAL is used in isolation. However, overlap between this low-biomass signal with host and contaminant sequences indicates that confidently resolving a core microbiome will require deeper sequencing and dedicated contamination controls. These methodological findings directly inform the design of future lung cancer- and disease-association studies.",
  "abstract_shown": true,
  "affiliations": [
    "University of British Columbia"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "name": "A. J. C. Noonan"
    },
    {
      "name": "R. Myers"
    },
    {
      "name": "R. J. McLaughlin"
    },
    {
      "name": "A. Nag"
    },
    {
      "name": "S. Chen"
    },
    {
      "name": "C. Bartolomeu"
    },
    {
      "name": "S. A. Borden"
    },
    {
      "name": "S. Lam"
    },
    {
      "affs": [
        0
      ],
      "name": "S. Hallam"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3y9x5xrcmyaag.bib",
  "cited_by": 1,
  "doi": "10.64898/2026.08.02.742334",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.08.02.742334v2.full",
  "id": "3y9x5xrcmyaag",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.08.02.742334v2",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "microbiology"
    ],
    [
      "openalex",
      "1312|Gut microbiota and health"
    ]
  ],
  "openalex": "W7172286933",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.08.02.742334v2.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-02",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/3y9x5xrcmyaag.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:25:56Z",
      "native_id": "10.64898/2026.08.02.742334",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.08.02.742334v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:microbiology",
      "subfield": "microbiology"
    }
  ],
  "title": "Methodological Impacts on Microbiome Structure and Indicator Status in the Human Lower Respiratory Tract",
  "title_text": "Methodological Impacts on Microbiome Structure and Indicator Status in the Human Lower Respiratory Tract",
  "type": "preprint",
  "updated_at": "2026-10-30T12:25:56Z",
  "url": "https://research.draconitic.com/paper/3y9x5xrcmyaag",
  "venue": "bioRxiv",
  "versions": []
}