A Compositional Look at the Human Gastrointestinal Microbiome and Immune Activation Parameters in HIV Infected Subjects

TLDR

HIV progression involves immune activation and microbial translocation, and gut dysbiosis may contribute to this process. The study hypothesizes that HIV patients have altered GI mucosal microbiomes that correlate with immune activation. The authors collected 121 colonoscopic specimens from HIV‑positive and control subjects, performed 16S rDNA pyrosequencing of lower GI mucosal and luminal microbiomes, and correlated the results with clinical parameters, immune activation, and circulating bacterial products. HIV patients exhibited a less diverse right colon and terminal ileum microbiome with loss of commensal taxa and gain of pathogenic bacteria, marking the first next‑generation sequencing characterization of the terminal ileal and colonic mucosal microbiome in HIV. The study is limited by the use of HIV‑infected subjects on HAART therapy.

Abstract

HIV progression is characterized by immune activation and microbial translocation. One factor that may be contributing to HIV progression could be a dysbiotic microbiome. We therefore hypothesized that the GI mucosal microbiome is altered in HIV patients and this alteration correlates with immune activation in HIV. 121 specimens were collected from 21 HIV positive and 22 control human subjects during colonoscopy. The composition of the lower gastrointestinal tract mucosal and luminal bacterial microbiome was characterized using 16S rDNA pyrosequencing and was correlated to clinical parameters as well as immune activation and circulating bacterial products in HIV patients on ART. The composition of the HIV microbiome was significantly different than that of controls; it was less diverse in the right colon and terminal ileum, and was characterized by loss of bacterial taxa that are typically considered commensals. In HIV samples, there was a gain of some pathogenic bacterial taxa. This is the first report characterizing the terminal ileal and colonic mucosal microbiome in HIV patients with next generation sequencing. Limitations include use of HIV-infected subjects on HAART therapy.