Effect of advanced HIV infection on the respiratory microbiome

Homer Twigg, Kenneth S. Knox, Jin Zhou, Kristina A. Crothers, David E. Nelson, Evelyn Toh, Richard B. Day, Huaiying Lin, Xiang Gao, Qunfeng Dong, Deming Mi, Barry Katz, Erica Sodergren, George M. Weinstock

Research output: Contribution to journalArticle

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Abstract

Rationale: Previous work found the lung microbiome in healthy subjects infected with HIV was similar to that in uninfected subjects. We hypothesized the lung microbiome from subjects infected with HIV with more advanced disease would differ from that of an uninfected control population. Objectives: To measure the lung microbiome in an HIV-infected population with advanced disease. Methods: 16s RNA gene sequencing was performed on acellular bronchoalveolar lavage (BAL) fluid from30subjects infectedwithHIV with advanced disease (baseline mean CD4 count, 262 cells/mm3) before and up to 3 years after starting highly active antiretroviral therapy (HAART) and compared with 22 uninfected control subjects. Measurements and Main Results: The lung microbiome in subjects infected with HIV with advanced disease demonstrated decreased alpha diversity (richness and diversity) and greater beta diversity compared with uninfected BAL. Differences improved with HAART, but still persisted up to 3 years after starting therapy. Population dispersion in the group infected with HIV was significantly greater than in the uninfected cohort and declined after treatment. There were differences in the relativeabundanceofsomebacteria between the two groupsat baseline and after 1 year of therapy. After 1 year on HAART, HIV BAL contained an increased abundance of Prevotella and Veillonella, bacteria previously associated with lung inflammation. Conclusions: The lung microbiome in subjects infected with HIV with advanced disease is altered compared with an uninfected population both in diversity and bacterial composition. Differences remain up to 3 years after starting HAART. We speculate an altered lung microbiome in HIV infection may contribute to chronic inflammation and lung complications seen in the HAART era.

Original languageEnglish (US)
Pages (from-to)226-235
Number of pages10
JournalAmerican Journal of Respiratory and Critical Care Medicine
Volume194
Issue number2
DOIs
StatePublished - Jul 15 2016

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Microbiota
HIV Infections
Highly Active Antiretroviral Therapy
HIV
Lung
Bronchoalveolar Lavage
Population
Pneumonia
Veillonella
Prevotella
RNA Sequence Analysis
Bronchoalveolar Lavage Fluid
CD4 Lymphocyte Count
Healthy Volunteers
Therapeutics
Bacteria
Genes

Keywords

  • Advanced disease
  • HIV infection
  • Lung microbiome
  • Microbial diversity

ASJC Scopus subject areas

  • Medicine(all)
  • Pulmonary and Respiratory Medicine
  • Critical Care and Intensive Care Medicine

Cite this

Twigg, H., Knox, K. S., Zhou, J., Crothers, K. A., Nelson, D. E., Toh, E., ... Weinstock, G. M. (2016). Effect of advanced HIV infection on the respiratory microbiome. American Journal of Respiratory and Critical Care Medicine, 194(2), 226-235. https://doi.org/10.1164/rccm.201509-1875OC

Effect of advanced HIV infection on the respiratory microbiome. / Twigg, Homer; Knox, Kenneth S.; Zhou, Jin; Crothers, Kristina A.; Nelson, David E.; Toh, Evelyn; Day, Richard B.; Lin, Huaiying; Gao, Xiang; Dong, Qunfeng; Mi, Deming; Katz, Barry; Sodergren, Erica; Weinstock, George M.

In: American Journal of Respiratory and Critical Care Medicine, Vol. 194, No. 2, 15.07.2016, p. 226-235.

Research output: Contribution to journalArticle

Twigg, H, Knox, KS, Zhou, J, Crothers, KA, Nelson, DE, Toh, E, Day, RB, Lin, H, Gao, X, Dong, Q, Mi, D, Katz, B, Sodergren, E & Weinstock, GM 2016, 'Effect of advanced HIV infection on the respiratory microbiome', American Journal of Respiratory and Critical Care Medicine, vol. 194, no. 2, pp. 226-235. https://doi.org/10.1164/rccm.201509-1875OC
Twigg, Homer ; Knox, Kenneth S. ; Zhou, Jin ; Crothers, Kristina A. ; Nelson, David E. ; Toh, Evelyn ; Day, Richard B. ; Lin, Huaiying ; Gao, Xiang ; Dong, Qunfeng ; Mi, Deming ; Katz, Barry ; Sodergren, Erica ; Weinstock, George M. / Effect of advanced HIV infection on the respiratory microbiome. In: American Journal of Respiratory and Critical Care Medicine. 2016 ; Vol. 194, No. 2. pp. 226-235.
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AU - Day, Richard B.

AU - Lin, Huaiying

AU - Gao, Xiang

AU - Dong, Qunfeng

AU - Mi, Deming

AU - Katz, Barry

AU - Sodergren, Erica

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N2 - Rationale: Previous work found the lung microbiome in healthy subjects infected with HIV was similar to that in uninfected subjects. We hypothesized the lung microbiome from subjects infected with HIV with more advanced disease would differ from that of an uninfected control population. Objectives: To measure the lung microbiome in an HIV-infected population with advanced disease. Methods: 16s RNA gene sequencing was performed on acellular bronchoalveolar lavage (BAL) fluid from30subjects infectedwithHIV with advanced disease (baseline mean CD4 count, 262 cells/mm3) before and up to 3 years after starting highly active antiretroviral therapy (HAART) and compared with 22 uninfected control subjects. Measurements and Main Results: The lung microbiome in subjects infected with HIV with advanced disease demonstrated decreased alpha diversity (richness and diversity) and greater beta diversity compared with uninfected BAL. Differences improved with HAART, but still persisted up to 3 years after starting therapy. Population dispersion in the group infected with HIV was significantly greater than in the uninfected cohort and declined after treatment. There were differences in the relativeabundanceofsomebacteria between the two groupsat baseline and after 1 year of therapy. After 1 year on HAART, HIV BAL contained an increased abundance of Prevotella and Veillonella, bacteria previously associated with lung inflammation. Conclusions: The lung microbiome in subjects infected with HIV with advanced disease is altered compared with an uninfected population both in diversity and bacterial composition. Differences remain up to 3 years after starting HAART. We speculate an altered lung microbiome in HIV infection may contribute to chronic inflammation and lung complications seen in the HAART era.

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