title: Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.
abstract: BACKGROUND
  Improved understanding of the lung microbiome in HIV-infected individuals could lead to better strategies for diagnosis, therapy, and prophylaxis of HIV-associated pneumonias. Differences in the oral and lung microbiomes in HIV-infected and HIV-uninfected individuals are not well defined. Whether highly active antiretroviral therapy influences these microbiomes is unclear.
  
  
  OBJECTIVE
  We determined whether oral and lung microbiomes differed in clinically healthy groups of HIV-infected and HIV-uninfected subjects.
  
  
  METHODS
  Participating sites in the Lung HIV Microbiome Project contributed bacterial 16S rRNA sequencing data from oral washes and bronchoalveolar lavages (BALs) obtained from HIV-uninfected individuals (n = 86), HIV-infected individuals who were treatment naive (n = 18), and HIV-infected individuals receiving antiretroviral therapy (n = 38).
  
  
  RESULTS
  Microbial populations differed in the oral washes among the subject groups (Streptococcus, Actinomyces, Rothia, and Atopobium), but there were no individual taxa that differed among the BALs. Comparison of oral washes and BALs demonstrated similar patterns from HIV-uninfected individuals and HIV-infected individuals receiving antiretroviral therapy, with multiple taxa differing in abundance. The pattern observed from HIV-infected individuals who were treatment naive differed from the other two groups, with differences limited to Veillonella, Rothia, and Granulicatella. CD4 cell counts did not influence the oral or BAL microbiome in these relatively healthy, HIV-infected subjects.
  
  
  CONCLUSIONS
  The overall similarity of the microbiomes in participants with and without HIV infection was unexpected, because HIV-infected individuals with relatively preserved CD4 cell counts are at higher risk for lower respiratory tract infections, indicating impaired local immune function.
authors.affiliation: 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado.|2 Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado.
authors.forename: James M
authors.initials: JM
authors.lastname: Beck
authors.affiliation: 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
authors.forename: Patrick D
authors.initials: PD
authors.lastname: Schloss
authors.affiliation: 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
authors.forename: Arvind
authors.initials: A
authors.lastname: Venkataraman
authors.affiliation: 4 Department of Medicine, Indiana University, Indianapolis, Indiana.
authors.forename: Homer
authors.initials: H
authors.lastname: Twigg
authors.affiliation: 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia.
authors.forename: Kathleen A
authors.initials: KA
authors.lastname: Jablonski
authors.affiliation: 6 Department of Microbiology and.
authors.forename: Frederic D
authors.initials: FD
authors.lastname: Bushman
authors.affiliation: 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado.
authors.forename: Thomas B
authors.initials: TB
authors.lastname: Campbell
authors.affiliation: 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
authors.forename: Emily S
authors.initials: ES
authors.lastname: Charlson
authors.affiliation: 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
authors.forename: Ronald G
authors.initials: RG
authors.lastname: Collman
authors.affiliation: 8 Department of Medicine, University of Washington, Seattle, Washington.
authors.forename: Kristina
authors.initials: K
authors.lastname: Crothers
authors.affiliation: 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.|9 Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan.
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Curtis
authors.affiliation: 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia.
authors.forename: Kimberly L
authors.initials: KL
authors.lastname: Drews
authors.affiliation: 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado.
authors.forename: Sonia C
authors.initials: SC
authors.lastname: Flores
authors.affiliation: 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Fontenot
authors.affiliation: 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia.
authors.forename: Mary A
authors.initials: MA
authors.lastname: Foulkes
authors.affiliation: 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
authors.forename: Ian
authors.initials: I
authors.lastname: Frank
authors.affiliation: 10 Department of Computational and Systems Biology and.
authors.forename: Elodie
authors.initials: E
authors.lastname: Ghedin
authors.affiliation: 11 Department of Medicine, University of California San Francisco, San Francisco, California; and.
authors.forename: Laurence
authors.initials: L
authors.lastname: Huang
authors.affiliation: 11 Department of Medicine, University of California San Francisco, San Francisco, California; and.
authors.forename: Susan V
authors.initials: SV
authors.lastname: Lynch
authors.affiliation: 12 Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.
authors.forename: Alison
authors.initials: A
authors.lastname: Morris
authors.affiliation: 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado.
authors.forename: Brent E
authors.initials: BE
authors.lastname: Palmer
authors.affiliation: 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Schmidt
authors.affiliation: 13 The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.
authors.forename: Erica
authors.initials: E
authors.lastname: Sodergren
authors.affiliation: 13 The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.affiliation: 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
authors.forename: Vincent B
authors.initials: VB
authors.lastname: Young
mesh_terms: D000328:Adult; D023241:Antiretroviral Therapy, Highly Active; D001992:Bronchoalveolar Lavage Fluid / Q000382:microbiology*; D015331:Cohort Studies; D005260:Female; D015658:HIV Infections / Q000188:drug therapy / Q000382:microbiology*; D006801:Humans; D008168:Lung / Q000382:microbiology*; D008297:Male; D064307:Microbiota; D008875:Middle Aged; D009055:Mouth / Q000382:microbiology*; D011446:Prospective Studies
keywords: HIV infection; bronchoalveolar lavage; bronchoscopy; lung; microbiome