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HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota

BACKGROUND: Regardless of infection route, the intestine is the primary site for HIV-1 infection establishment and results in significant mucosal CD4+ T lymphocyte depletion, induces an inflammatory state that propagates viral dissemination, facilitates microbial translocation, and fosters establish...

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Autores principales: McHardy, Ian H, Li, Xiaoxiao, Tong, Maomeng, Ruegger, Paul, Jacobs, Jonathan, Borneman, James, Anton, Peter, Braun, Jonathan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971626/
https://www.ncbi.nlm.nih.gov/pubmed/24451087
http://dx.doi.org/10.1186/2049-2618-1-26
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author McHardy, Ian H
Li, Xiaoxiao
Tong, Maomeng
Ruegger, Paul
Jacobs, Jonathan
Borneman, James
Anton, Peter
Braun, Jonathan
author_facet McHardy, Ian H
Li, Xiaoxiao
Tong, Maomeng
Ruegger, Paul
Jacobs, Jonathan
Borneman, James
Anton, Peter
Braun, Jonathan
author_sort McHardy, Ian H
collection PubMed
description BACKGROUND: Regardless of infection route, the intestine is the primary site for HIV-1 infection establishment and results in significant mucosal CD4+ T lymphocyte depletion, induces an inflammatory state that propagates viral dissemination, facilitates microbial translocation, and fosters establishment of one of the largest HIV reservoirs. Here we test the prediction that HIV infection modifies the composition and function of the mucosal commensal microbiota. RESULTS: Rectal mucosal microbiota were collected from human subjects using a sponge-based sampling methodology. Samples were collected from 20 HIV-positive men not receiving combination anti-retroviral therapy (cART), 20 HIV-positive men on cART and 20 healthy, HIV-negative men. Microbial composition of samples was analyzed using barcoded 16S Illumina deep sequencing (85,900 reads per sample after processing). Microbial metagenomic information for the samples was imputed using the bioinformatic tools PICRUST and HUMAnN. Microbial composition and imputed function in HIV-positive individuals not receiving cART was significantly different from HIV-negative individuals. Genera including Roseburia, Coprococcus, Ruminococcus, Eubacterium, Alistipes and Lachnospira were depleted in HIV-infected subjects not receiving cART, while Fusobacteria, Anaerococcus, Peptostreptococcus and Porphyromonas were significantly enriched. HIV-positive subjects receiving cART exhibited similar depletion and enrichment for these genera, but were of intermediate magnitude and did not achieve statistical significance. Imputed metagenomic functions, including amino acid metabolism, vitamin biosynthesis, and siderophore biosynthesis differed significantly between healthy controls and HIV-infected subjects not receiving cART. CONCLUSIONS: HIV infection was associated with rectal mucosal changes in microbiota composition and imputed function that cART failed to completely reverse. HIV infection was associated with depletion of some commensal species and enrichment of a few opportunistic pathogens. Many imputed metagenomic functions differed between samples from HIV-negative and HIV-positive subjects not receiving cART, possibly reflecting mucosal metabolic changes associated with HIV infection. Such functional pathways may represent novel interventional targets for HIV therapy if normalizing the microbial composition or functional activity of the microbiota proves therapeutically useful.
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spelling pubmed-39716262014-04-02 HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota McHardy, Ian H Li, Xiaoxiao Tong, Maomeng Ruegger, Paul Jacobs, Jonathan Borneman, James Anton, Peter Braun, Jonathan Microbiome Research BACKGROUND: Regardless of infection route, the intestine is the primary site for HIV-1 infection establishment and results in significant mucosal CD4+ T lymphocyte depletion, induces an inflammatory state that propagates viral dissemination, facilitates microbial translocation, and fosters establishment of one of the largest HIV reservoirs. Here we test the prediction that HIV infection modifies the composition and function of the mucosal commensal microbiota. RESULTS: Rectal mucosal microbiota were collected from human subjects using a sponge-based sampling methodology. Samples were collected from 20 HIV-positive men not receiving combination anti-retroviral therapy (cART), 20 HIV-positive men on cART and 20 healthy, HIV-negative men. Microbial composition of samples was analyzed using barcoded 16S Illumina deep sequencing (85,900 reads per sample after processing). Microbial metagenomic information for the samples was imputed using the bioinformatic tools PICRUST and HUMAnN. Microbial composition and imputed function in HIV-positive individuals not receiving cART was significantly different from HIV-negative individuals. Genera including Roseburia, Coprococcus, Ruminococcus, Eubacterium, Alistipes and Lachnospira were depleted in HIV-infected subjects not receiving cART, while Fusobacteria, Anaerococcus, Peptostreptococcus and Porphyromonas were significantly enriched. HIV-positive subjects receiving cART exhibited similar depletion and enrichment for these genera, but were of intermediate magnitude and did not achieve statistical significance. Imputed metagenomic functions, including amino acid metabolism, vitamin biosynthesis, and siderophore biosynthesis differed significantly between healthy controls and HIV-infected subjects not receiving cART. CONCLUSIONS: HIV infection was associated with rectal mucosal changes in microbiota composition and imputed function that cART failed to completely reverse. HIV infection was associated with depletion of some commensal species and enrichment of a few opportunistic pathogens. Many imputed metagenomic functions differed between samples from HIV-negative and HIV-positive subjects not receiving cART, possibly reflecting mucosal metabolic changes associated with HIV infection. Such functional pathways may represent novel interventional targets for HIV therapy if normalizing the microbial composition or functional activity of the microbiota proves therapeutically useful. BioMed Central 2013-10-12 /pmc/articles/PMC3971626/ /pubmed/24451087 http://dx.doi.org/10.1186/2049-2618-1-26 Text en Copyright © 2013 McHardy et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
McHardy, Ian H
Li, Xiaoxiao
Tong, Maomeng
Ruegger, Paul
Jacobs, Jonathan
Borneman, James
Anton, Peter
Braun, Jonathan
HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota
title HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota
title_full HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota
title_fullStr HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota
title_full_unstemmed HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota
title_short HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota
title_sort hiv infection is associated with compositional and functional shifts in the rectal mucosal microbiota
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971626/
https://www.ncbi.nlm.nih.gov/pubmed/24451087
http://dx.doi.org/10.1186/2049-2618-1-26
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