Cited by 556Gut microbiota and healthOral microbiology and periodontitis researchNosocomial Infections in ICU

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Bacterial Topography of the Healthy Human Lower Respiratory Tract

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Dickson, Robert P., Erb-Downward, John R., Freeman, Christine M., McCloskey, Lisa, Falkowski, Nicole R., Huffnagle, Gary B., Curtis, Jeffrey L.·2017·mBio

DOI 10.1128/mbio.02287-16PMC PMC5312084

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Abstract

ABSTRACT Although culture-independent techniques have refuted lung sterility in health, controversy about contamination during bronchoscope passage through the upper respiratory tract (URT) has impeded research progress. We sought to establish whether bronchoscopic sampling accurately reflects the lung microbiome in health and to distinguish between two proposed routes of authentic microbial immigration, (i) dispersion along contiguous respiratory mucosa and (ii) subclinical microaspiration. During bronchoscopy of eight adult volunteers without lung disease, we performed seven protected specimen brushings (PSB) and bilateral bronchoalveolar lavages (BALs) per subject. We amplified, sequenced, and analyzed the bacterial 16S rRNA gene V4 regions by using the Illumina MiSeq platform. Rigorous attention was paid to eliminate potential sources of error or contamination, including a randomized processing order and the inclusion and analysis of exhaustive procedural and sequencing control specimens. Indices of mouth-lung immigration (mouth-lung community similarity, bacterial burden, and community richness) were all significantly greater in airway and alveolar specimens than in bronchoscope contamination control specimens, indicating minimal evidence of pharyngeal contamination. Ecological indices of mouth-lung immigration peaked at or near the carina, as predicted for a primary immigration route of microaspiration. Bacterial burden, diversity, and mouth-lung similarity were greater in BAL than PSB samples, reflecting differences in the sampled surface areas. (This study has been registered at ClinicalTrials.gov under registration no. NCT02392182.) IMPORTANCE This study defines the bacterial topography of the healthy human respiratory tract and provides ecological evidence that bacteria enter the lungs in health primarily by microaspiration, with potential contribution in some subjects by direct dispersal along contiguous mucosa. By demonstrating that contamination contributes negligibly to microbial communities in bronchoscopically acquired specimens, we validate the use of bronchoscopy to investigate the lung microbiome.

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Authors: Dickson, R. P., Erb-Downward, J. R., Freeman, C. M., McCloskey, L., Falkowski, N. R., Huffnagle, G. B., & Curtis, J. L.
Affiliations: Michigan Medicine (US)
Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, Michigan, USA
VA Ann Arbor Healthcare System (US)
University of Michigan (US)
Corresponding author: Curtis, Jeffrey L.
ORCID: Dickson, Robert P.
Freeman, Christine M.
McCloskey, Lisa
Huffnagle, Gary B.
Curtis, Jeffrey L.
Venue: mBio
Publisher: American Society for Microbiology
Published: 2017-03-08
Volume: 8
Issue: 1
ISSN: 2150-7511 (ISSN-L)
2161-2129
DOI: 10.1128/mbio.02287-16
PMC: PMC5312084
OpenAlex: W2588100341
Cited by: 548
References: 45
Citations by year: 2026: 46 · 2025: 60 · 2024: 101 · 2023: 48 · 2022: 68 · 2021: 64 · 2020: 55 · 2019: 40 · 2018: 48 · 2017: 18
FWCI: 17.99
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
journals.asm.org/non-commercial-tdm-license (tdm)
Locations: mBio (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders: HHS | National Institutes of Health (UL1 TR000433, K23 HL130641, U01 HL098961, R01 HL114447)
U.S. Department of Veterans Affairs (I01 BX001389, I01 CX000911)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Health Sciences › Medicine › Critical Care and Intensive Care Medicine › Nosocomial Infections in ICU
Keywords: lung microbiome, lower respiratory tract, bronchoscopic sampling, bronchoalveolar lavage, microaspiration, 16S rRNA gene sequencing
MeSH terms: Adult, Aged, Bacteria, Bronchoalveolar Lavage Fluid, Bronchoscopy, DNA, Bacterial, Female, Humans, Lung, Male, Middle Aged, Mouth, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Bronchoalveolar Lavage, Metagenome, Microbiota, Healthy Volunteers

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Bacterial Topography of the Healthy Human Lower Respiratory Tract

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