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 non-smokers and smokers in a multi-center cohort.
METHODS: Participants were non-smokers and smokers without significant co-morbidities. 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 used to identify bacteria that were the most plausible members of a lung microbiome.
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 to values predicted by the neutral model. Trophyrema was also in the lung, but not the mouth. Mouth communities differed between non-smokers 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 non-smokers and smokers, but lung communities were not significantly altered by smoking.