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Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection

Morris, A and Paulson, JN and Talukder, H and Tipton, L and Kling, H and Cui, L and Fitch, A and Pop, M and Norris, KA and Ghedin, E (2016) Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection. Microbiome, 4.

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Background: Longitudinal studies of the lung microbiome are challenging due to the invasive nature of sample collection. In addition, studies of the lung microbiome in human disease are usually performed after disease onset, limiting the ability to determine early events in the lung. We used a non-human primate model to assess lung microbiome alterations over time in response to an HIV-like immunosuppression and determined impact of the lung microbiome on development of obstructive lung disease. Cynomolgous macaques were infected with the SIV-HIV chimeric virus SHIV89.6P. Bronchoalveolar lavage fluid samples were collected pre-infection and every 4 weeks for 53 weeks post-infection. The microbiota was characterized at each time point by 16S ribosomal RNA (rRNA) sequencing. Results: We observed individual variation in the composition of the lung microbiota with a proportion of the macaques having Tropheryma whipplei as the dominant organism in their lungs. Bacterial communities varied over time both within and between animals, but there did not appear to be a systematic alteration due to SHIV infection. Development of obstructive lung disease in the SHIV-infected animals was characterized by a relative increase in abundance of oral anaerobes. Network analysis further identified a difference in community composition that accompanied the development of obstructive disease with negative correlations between members of the obstructed and non-obstructed groups. This emphasizes how species shifts can impact multiple other species, potentially resulting in disease. Conclusions: This study is the first to investigate the dynamics of the lung microbiota over time and in response to immunosuppression in a non-human primate model. The persistence of oral bacteria in the lung and their association with obstruction suggest a potential role in pathogenesis. The lung microbiome in the non-human primate is a valuable tool for examining the impact of the lung microbiome in human health and disease.


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Item Type: Article
Status: Published
CreatorsEmailPitt UsernameORCID
Morris, A
Paulson, JN
Talukder, H
Tipton, Llat60@pitt.eduLAT60
Kling, H
Cui, L
Fitch, Afitchad@pitt.eduFITCHAD
Pop, M
Norris, KAkan1@pitt.eduKAN1
Ghedin, Eelg21@pitt.eduELG21
Date: 1 January 2016
Date Type: Publication
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Journal or Publication Title: Microbiome
Volume: 4
DOI or Unique Handle: 10.1186/s40168-016-0183-0
Institution: University of Pittsburgh
Schools and Programs: School of Medicine > Computational and Systems Biology
School of Medicine > Critical Care Medicine
School of Medicine > Immunology
Refereed: Yes
Date Deposited: 25 Jul 2016 13:54
Last Modified: 30 Mar 2021 10:55


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