title: Topographic diversity of the respiratory tract mycobiome and alteration in HIV and lung disease.
abstract: BACKGROUND
  Microbiome studies typically focus on bacteria, but fungal species are common in many body sites and can have profound effects on the host. Wide gaps exist in the understanding of the fungal microbiome (mycobiome) and its relationship to lung disease.
  
  
  OBJECTIVE
  To characterize the mycobiome at different respiratory tract levels in persons with and without HIV infection and in HIV-infected individuals with chronic obstructive pulmonary disease (COPD).
  
  
  METHODS
  Oral washes (OW), induced sputa (IS), and bronchoalveolar lavages (BAL) were collected from 56 participants. We performed 18S and internal transcribed spacer sequencing and used the neutral model to identify fungal species that are likely residents of the lung. We used ubiquity-ubiquity plots, random forest, logistic regression, and metastats to compare fungal communities by HIV status and presence of COPD.
  
  
  RESULTS
  Mycobiomes of OW, IS, and BAL shared common organisms, but each also had distinct members. Candida was dominant in OW and IS, but BAL had 39 fungal species that were disproportionately more abundant than in the OW. Fungal communities in BAL differed significantly by HIV status and by COPD, with Pneumocystis jirovecii significantly overrepresented in both groups. Other fungal species were also identified as differing in HIV and COPD.
  
  
  CONCLUSIONS
  This study systematically examined the respiratory tract mycobiome in a relatively large group. By identifying Pneumocystis and other fungal species as overrepresented in the lung in HIV and in COPD, it is the first to determine alterations in fungal communities associated with lung dysfunction and/or HIV, highlighting the clinical relevance of these findings. Clinical trial registered with www.clinicaltrials.gov (NCT00870857).
authors.affiliation: 1 Center for Vaccine Research.
authors.forename: Lijia
authors.initials: L
authors.lastname: Cui
authors.forename: Lorrie
authors.initials: L
authors.lastname: Lucht
authors.forename: Laura
authors.initials: L
authors.lastname: Tipton
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Rogers
authors.forename: Adam
authors.initials: A
authors.lastname: Fitch
authors.forename: Cathy
authors.initials: C
authors.lastname: Kessinger
authors.forename: Danielle
authors.initials: D
authors.lastname: Camp
authors.forename: Lawrence
authors.initials: L
authors.lastname: Kingsley
authors.forename: Nicolas
authors.initials: N
authors.lastname: Leo
authors.forename: Ruth M
authors.initials: RM
authors.lastname: Greenblatt
authors.forename: Serena
authors.initials: S
authors.lastname: Fong
authors.forename: Stephen
authors.initials: S
authors.lastname: Stone
authors.forename: John C
authors.initials: JC
authors.lastname: Dermand
authors.forename: Eric C
authors.initials: EC
authors.lastname: Kleerup
authors.forename: Laurence
authors.initials: L
authors.lastname: Huang
authors.forename: Alison
authors.initials: A
authors.lastname: Morris
authors.forename: Elodie
authors.initials: E
authors.lastname: Ghedin
mesh_terms: D001992:Bronchoalveolar Lavage Fluid / Q000382:microbiology; D005260:Female; D015658:HIV Infections / Q000150:complications* / Q000382:microbiology*; D006801:Humans; D008168:Lung / Q000382:microbiology; D008297:Male; D054892:Metagenome; D008875:Middle Aged; D029424:Pulmonary Disease, Chronic Obstructive / Q000150:complications* / Q000382:microbiology*; D012137:Respiratory System / Q000382:microbiology*; D013183:Sputum / Q000382:microbiology
keywords: COPD; HIV; bronchoalveolar lavage; fungi; microbiome