Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

TLDR

Lower respiratory tract microbiome composition remains uncertain, with 16S rRNA sequencing studies yielding conflicting results. This study aimed to compare the upper and lower respiratory tract microbiomes of healthy HIV‑uninfected nonsmokers and smokers across multiple centers. Researchers collected standardized oral washes and bronchoscopic alveolar lavages from 64 participants and performed 16S rRNA gene sequencing, applying a neutral ecological model to identify lung‑specific bacterial members. The lung microbiome contains taxa such as Enterobacteriaceae, Haemophilus, Methylobacterium, Ralstonia, and Tropheryma that are disproportionately represented compared to the mouth, indicating a distinct lung community that is not solely derived from oral bacteria, and smoking does not significantly alter lung bacterial populations despite differences in the oral microbiome.

Abstract

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 in significantly 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.