Gut microbiome profiles and associated metabolic pathways in HIV-infected treatment-naïve patients

Abstract

The normal composition of the intestinal microbiota is a key factor for maintaining health homeostasis and, accordingly, dysbiosis is well known to be present in HIV-1 patients. Here, we investigate the gut microbiota profile of HIV-1 positive patients without antiretroviral therapy and healthy donors living in Latin America. We enrolled 13 HIV positive patients (six elite controllers, EC and seven non-controllers, NC) and nine healthy donors (HD). Microbiota compositions in stool samples were determined by sequencing the V3-V4 region of the bacterial 16S rRNA and functional prediction was inferred using PICRUSt. Several taxa were enriched in EC compared to NC or HD groups, including Acidaminococcus, Clostridium methylpentosum, Barnesiella, Eubacterium coprostanoligenes and Lachnospiraceae UCG-004. Importantly, we confirmed that the route of infection is a strong factor associated with changes in gut microbiome composition and we extended these results by identifying several metabolic pathways associated with each route of infection. Moreover, we observed several bacterial taxa associated with different viral subtypes such as Succinivibrio which were more abundant in patients infected by HIV subtype B, and Streptococcus enrichment in patients infected by subtype C. In conclusion, our data brings a significant contribution to our understanding of dysbiosis-associated changes in HIV infection and describes, for the first time, differences in microbiota composition according to HIV subtypes.

A specific structure and high richness characterize intestinal microbiota of HIV-exposed seronegative individuals

“…In fact, there were no significant differences between both groups in alpha and beta diversity analyses of fecal microbiota. Remarkably, microbiota composition in HIV-infected individuals stands out by increased numbers of Proteobacteria Succinivibrio and Klebsiella; Veillonellaceae pathobionts such as Dialister , Allisonella , and Veillonella , as well as by enrichment of Prevotella and Alloprevotella , as previously described worldwide [ 10 – 12 ].…”