HIV infection is associated with compositional and functional shifts in the rectal mucosal microbiota
Open accessAbstract
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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Decreased Lachnospira abundance has been reported in the gut microbiota of subjects with cholesterol gallstones and in the rectal mucosa of patients with HIV.
“Decrease in Lachnospira abundance was recently highlighted in the gut microbiota of subjects with cholesterol gallstones 62 as well as in the rectal mucosa of patients with HIV, 63”
From High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome (2016) · cites this paper as [63]
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- Authors
- McHardy, I. H., Li, X., Tong, M., Ruegger, P., Jacobs, J., Borneman, J., Anton, P., & Braun, J.
- Affiliations
- University of California, Los Angeles (US)
- Cedars-Sinai Medical Center (US)
- University of California, Riverside (US)
- Corresponding author
- Braun, Jonathan
- Venue
- Microbiome
- Published
- 2013-10-12
- Volume
- 1
- Issue
- 1
- Pages
- 26-26
- ISSN
- 2049-2618 (ISSN-L)
- PMC
- PMC3971626
- OpenAlex
- W2122354899
- Cited by
- 234
- References
- 69
- Citations by year
- 2026: 9 · 2025: 12 · 2024: 13 · 2023: 17 · 2022: 14 · 2021: 24 · 2020: 20 · 2019: 29 · 2018: 23 · 2017: 25 · 2016: 19 · 2015: 14 · 2014: 12 · 2012: 1
- FWCI
- 6.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Microbiome (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- University of California, Los Angeles (AI 28697, P30 DK041301, UL1 TR000124)
- Center for AIDS Research, University of Washington (AI28697)
- National Institute of Diabetes and Digestive and Kidney Diseases (P01DK046763, T32DK007180)
- Clinical and Translational Science Institute, University of California, Los Angeles (UL1TR000124)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Health Sciences › Medicine › Emergency Medicine › HIV-related health complications and treatments
- Keywords
- HIV infection, rectal mucosa, gut microbiota, commensal microbiota, antiretroviral therapy, microbial community composition, opportunistic pathogens, anaerobic bacteria, amino acid metabolism, vitamin biosynthesis, siderophore biosynthesis, HIV reservoir
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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