HIV positive patients on antiretroviral therapy have an altered mucosal intestinal but not oral microbiome

Abstract

This study characterized compositional and functional shifts in the intestinal and oral microbiome in HIV-positive patients compared to uninfected individuals. 79 specimens were collected from 5 HIV-positive and 12 control subjects from five locations (colon brush, colon wash, TI brush, TI wash and saliva) during colonoscopy and at patient visits. Microbiome composition was characterized using 16S rRNA sequencing and microbiome function was predicted using bioinformatics tools (PICRUSt and Bugbase). Our analysis indicated that the β diversity of all intestinal samples (colon brush, colon wash, TI brush, TI wash) from patients with HIV was significantly different from patients without HIV, as measured by weighted UniFrac distances. Specifically, bacteria from genera Prevotella, Fusobacterium, Eubacterium, Megasphaera, Mogibacterium and Mitsuokella were more abundant in samples from HIV-positive patients. On the other hand, bacteria from genera Ruminococus, Blautia, and Clostridium were more abundant in samples from HIV-negative patients. Additionally, HIV-positive patients had higher abundances of biofilm-forming and pathogenic bacteria. Furthermore, pathways related to translation and nucleotide metabolism were elevated in HIV-positive patients whereas pathways related to lipid and carbohydrates metabolism and membrane transport were positively correlated with samples from HIV-negative patients. Our analyses further showed variations in microbiome composition in HIV-positive and negative patients by sampling site, with samples from colon wash, colon brush and TI wash significant between groups while samples from TI brush and saliva were not significant. Taken together, here we report altered intestinal microbiome composition and function in patients with HIV compared to uninfected patients, though we found no changes in the oral microbiome.