Journal
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
Volume 187, Issue 10, Pages 1067-1075Publisher
AMER THORACIC SOC
DOI: 10.1164/rccm.201210-1913OC
Keywords
lung; microbiome; bronchoscopy; metagenome
Categories
Funding
- U.S. Public Health Service [U01HL098962, R01HL090339, U01HL98961, R01HG005975, U01HL098996, R01HL090342, U01HL098964, R01HL090335, K24HL087713, U01HL098958, U01HL098960]
- NIH/HMP [RO100417746]
- University of Pittsburgh Clinical Translational Science Institute by the National Institutes of Healt [UL1 RR024153, UL1TR000005]
- University of California San Francisco Clinical and Translational Science Institute [UL1TR000004]
- Colorado CTSI [UL1 TR000154]
- National Institute of Allergy and Infectious Diseases
- National Cancer Institute [UO1-AI-35042, UL1-RR025005, UO1-AI-35043, UO1-AI-35039, UO1-AI-35040, UO1-AI-35041]
- National Institute of Allergy and Infectious Diseases [UO1-AI-35004, UO1-AI-31834, UO1-AI-34994, UO1-AI-34989, UO1-AI-34993, UO1-AI-42590]
- Eunice Kennedy Shriver National Institute of Child Health and Human Development [UO1-HD-32632]
- National Cancer Institute
- National Institute on Drug Abuse
- National Institute on Deafness and Other Communication Disorders
- National Center for Research Resources (UCSF-CTSI) [UL1 RR024131).]
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Rationale: Results from 16S rDNA-encoding gene sequence-based, culture-independent techniques have led to conflicting conclusions about the composition of the lower respiratory tract microbiome. Objectives: To compare the microbiome of the upper and lower respiratory tract in healthy HIV-uninfected nonsmokers and smokers in a multicenter cohort. Methods: Participants were nonsmokers and smokers without significant comorbidities. Oral washes and bronchoscopic alveolar lavages were collected in a standardized manner. Sequence analysis of bacterial 16S rRNA-encoding genes was performed, and the neutral model in community ecology was used to identify bacteria that were the most plausible members of a lung microbiome. Measurements and Main Results: Sixty-four participants were enrolled. Most bacteria identified in the lung were also in the mouth, but specific bacteria such as Enterobacteriaceae, Haemophilus, Methylobacterium, and Ralstonia species were disproportionally represented in the lungs compared with values predicted by the neutral model. Tropheryma was also in the lung, but not the mouth. Mouth communities differed between nonsmokers and smokers in species such as Porphyromonas, Neisseria, and Gemella, but lung bacterial populations did not. Conclusions: This study is the largest to examine composition of the lower respiratory tract microbiome in healthy individuals and the first to use the neutral model to compare the lung to the mouth. Specific bacteria appear insignificantly higher abundance in the lungs than would be expected if they originated from the mouth, demonstrating that the lung microbiome does not derive entirely from the mouth. The mouth microbiome differs in nonsmokers and smokers, but lung communities were not significantly altered by smoking.
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