title: Comparison of the respiratory microbiome in healthy nonsmokers and smokers.
abstract: BACKGROUND
  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.
  
  
  OBJECTIVE
  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.
  
  
  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.
authors.affiliation: Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA. morrisa@upmc.edu
authors.forename: Alison
authors.initials: A
authors.lastname: Morris
authors.forename: James M
authors.initials: JM
authors.lastname: Beck
authors.forename: Patrick D
authors.initials: PD
authors.lastname: Schloss
authors.forename: Thomas B
authors.initials: TB
authors.lastname: Campbell
authors.forename: Kristina
authors.initials: K
authors.lastname: Crothers
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Curtis
authors.forename: Sonia C
authors.initials: SC
authors.lastname: Flores
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Fontenot
authors.forename: Elodie
authors.initials: E
authors.lastname: Ghedin
authors.forename: Laurence
authors.initials: L
authors.lastname: Huang
authors.forename: Kathleen
authors.initials: K
authors.lastname: Jablonski
authors.forename: Eric
authors.initials: E
authors.lastname: Kleerup
authors.forename: Susan V
authors.initials: SV
authors.lastname: Lynch
authors.forename: Erica
authors.initials: E
authors.lastname: Sodergren
authors.forename: Homer
authors.initials: H
authors.lastname: Twigg
authors.forename: Vincent B
authors.initials: VB
authors.lastname: Young
authors.forename: Christine M
authors.initials: CM
authors.lastname: Bassis
authors.forename: Arvind
authors.initials: A
authors.lastname: Venkataraman
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Schmidt
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001992:Bronchoalveolar Lavage Fluid / Q000382:microbiology; D015331:Cohort Studies; D005260:Female; D006801:Humans; D008168:Lung / Q000382:microbiology; D008297:Male; D054892:Metagenome; D008875:Middle Aged; D009055:Mouth / Q000382:microbiology; D011446:Prospective Studies; D012016:Reference Values; D012137:Respiratory System / Q000382:microbiology*; D017422:Sequence Analysis, DNA / Q000379:methods; D012907:Smoking; D055815:Young Adult