Pulmonary complications are a principal cause of morbidity and mortality in untreated HIV/AIDS, but infectious and noninfectious respiratory illnesses remain major problems even in effectively treated patients. In addition, chronic lung diseases are now emerging in importance, including accelerated COPD. While immune dysfunction clearly plays a central role in lung infections, the emergence of a pathogen results from complex relationships among microbial inhabitants within a niche that interact with each other and the host immune system. Also, while the lower respiratory tract is normally sterile, many conditions such as smoking, COPD and chronic illness enable colonization, which contribute to lung inflammation and injury. Despite the overlap of immune deficiency, pulmonary infections and chronic lung disease, little is knov/n about respiratory microbiome changes in HIV/AIDS, its relationship to infectious complications, and role in chronic pulmonary diseases. Recent advances in molecular technology have led to unprecedented ability to analyze complex microbial populations, revealing extensive communities of often unculturable or previously unidentified organisms. Our group pioneered the use of high density pyrosequencing and, in the SIV/macaque gut model, carried out one of the few studies of immunodeficiency virus effects on the microbiome. How HIV alters the human microbiome has not been examined, and it is unknown if effects on respiratory microbiota contribute to lung complications of HIV infection or accelerated COPD when smoking is combined with HIV infection. We hypothesize that HIV leads to progressive changes in the respiratory tract microbiome. and these changes will be modulated by ART-induced immune reconstitution: that alterations in lov^er respiratory tract microbiota contribute to chronic inflammation and accelerated development of COPD in HIV infection: and that the microbiome is modified by smokina and diet. To address these hypotheses we will employ high density deep sequencing to: (1) Define the lower and upper respiratory tract microbiome in HIV-infected and uninfected individuals;(2) Determine the effects of progressive immune deficiency and ART-induced immune reconstitution;(3) Define the respiratory microbiome in HIV-infected and uninfected individuals with COPD;(4) Determine the effects of smoking and diet on the respiratory microbiome, and relationship between respiratory tract and gut;(5) Develop new methods to identify novel microbiome constituents not identifiable using 16S sequencing;(6) Establish collaborative projects with other HIV/Lung Microbiome centers.

Public Health Relevance

The human body lives in balance with microbes that inhabit surfaces and body cavities, and it is increasingly recognized that the relationship between these microbes and the host contribute to health and disease. Immune deficiency is a central component of HIV/AIDS so it is likely that the normal balance is altered, but this has not been studied. We will study how the microbes of the respiratory system are altered in HIV infection, and how this contributes to lung complications that remain among the most serious problems for people with HIV/AIDS.

National Institute of Health (NIH)
National Heart, Lung, and Blood Institute (NHLBI)
Research Project--Cooperative Agreements (U01)
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Special Emphasis Panel (ZHL1-CSR-Z (S1))
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Colombini-Hatch, Sandra
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University of Pennsylvania
Internal Medicine/Medicine
Schools of Medicine
United States
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Segal, Leopoldo N; Clemente, Jose C; Tsay, Jun-Chieh J et al. (2016) Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat Microbiol 1:16031
Williams, Brett; Mirmonsef, Paria; Boucher, Charles A B et al. (2016) A Summary of the First HIV Microbiome Workshop 2015. AIDS Res Hum Retroviruses 32:935-941
Kelly, Brendan J; Imai, Ize; Bittinger, Kyle et al. (2016) Composition and dynamics of the respiratory tract microbiome in intubated patients. Microbiome 4:7
Kelly, Brendan J; Gross, Robert; Bittinger, Kyle et al. (2015) Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. Bioinformatics 31:2461-8
Beck, James M; Schloss, Patrick D; Venkataraman, Arvind et al. (2015) Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Am J Respir Crit Care Med 192:1335-44
Bisson, Gregory P; Zetola, Nicola; Collman, Ronald G (2015) Persistent high mortality in advanced HIV/TB despite appropriate antiretroviral and antitubercular therapy: an emerging challenge. Curr HIV/AIDS Rep 12:107-16
Young, J C; Chehoud, C; Bittinger, K et al. (2015) Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. Am J Transplant 15:200-9
Elliott, Sarah T C; Wetzel, Katherine S; Francella, Nicholas et al. (2015) Dualtropic CXCR6/CCR5 Simian Immunodeficiency Virus (SIV) Infection of Sooty Mangabey Primary Lymphocytes: Distinct Coreceptor Use in Natural versus Pathogenic Hosts of SIV. J Virol 89:9252-61
Morris, Alison; Gibson, Kevin; Collman, Ronald G (2014) The lung microbiome in idiopathic pulmonary fibrosis. What does it mean and what should we do about it? Am J Respir Crit Care Med 190:850-2
Bittinger, Kyle; Charlson, Emily S; Loy, Elizabeth et al. (2014) Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing. Genome Biol 15:487

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