Topographic diversity of the respiratory tract mycobiome and alteration in HIV and lung disease

Lijia Cui, Lorrie Lucht, Laura Tipton, Matthew B. Rogers, Adam Fitch, Cathy Kessinger, Danielle Camp, Lawrence Kingsley, Nicolas Leo, Ruth M. Greenblatt, Serena Fong, Stephen Stone, John C. Dermand, Eric C. Kleerup, Laurence Huang, Alison Morris, Elodie Ghedin

Research output: Contribution to journalArticlepeer-review


Rationale: Microbiome studies typically focus on bacteria, but fungal species arecommonin 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. Objectives: To characterize the mycobiome at different respiratory tract levels in persons with and without HIV infection and in HIVinfected 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. Measurements and Main 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.

Original languageEnglish (US)
Pages (from-to)932-942
Number of pages11
JournalAmerican Journal of Respiratory and Critical Care Medicine
Issue number8
StatePublished - Apr 15 2015


  • Bronchoalveolar lavage
  • COPD
  • Fungi
  • HIV
  • Microbiome

ASJC Scopus subject areas

  • Pulmonary and Respiratory Medicine
  • Critical Care and Intensive Care Medicine


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