Gut Microbiome Changes Associated with HIV Infection and Antiretroviral Therapy

Abstract

Background: The gut microbiome is known to change following HIV infection. However, previous studies have generated inconsistent results regarding the differences in the gut microbiome between HIV positive and negative individuals. Methods: A bioinformatics analysis was performed on nine 16S rRNA gene sequencing data generated from 1082 stool samples (646 from HIV positive individuals and 436 from HIV negative individuals). We compared the differences in the gut microbiome between HIV positive and negative individuals across various factors. Results: The diversity of the gut microbiome differed between HIV positive and negative individuals with respect to age, gender, and whether or not antiretroviral therapy (ART) was initiated. Our analysis showed that ART did not restore the diversity of the gut microbiome. HIV infection changed the dominant genera of the intestine such that the prevalence of Prevotella increased and that of Bacteroides decreased in HIV positive individuals, especially in men who have sex with men (MSMs). Sutterella, Butyricimonas, Lachnospira etc. had significant correlations with the number of CD4+T cells and HIV viral load. In addition, the differentially enriched genera were found to be associated with functional pathways that correlated with ART. Conclusions: This study explored the changes in the gut microbiome in HIV positive individuals and revealed the association between differentially enriched genera and functional pathways involved in ART, which might help to elucidate the effects of HIV infection on the human gut microbiome. Funding Statement: This study was supported by the National Natural Science Foundation of China (NSFC, 81660334), Guangxi Natural Science Foundation (2017GXNSFAA198190, 2018GXNSFAA050099), National Key Science and Technology Project of China (2018ZX10101002-001-006). Declaration of Interests: The authors declare no competing interests. Ethics Approval Statement: The authors stated: Reusable data for our analysis complied with all relevant ethical regulations.