Distinct gut microbiota composition in gay men. MSM-Microbiome

The human intestinal microbiota is essential for human health and well-being and is driven by genetic1, lifestyle2–4 and environmental factors5,6. It forms, at least in resource-rich countries, a composition landscape with density peaks that can stratify the human population into enterotypes dominated by Bacteroides, Prevotella and Ruminococcus, respectively7,8. Many diseases have been linked to perturbations of this landscape9–11 including HIV-1 infection12–15, although the precise effects of HIV-1 on the human microbiome are not well defined. HIV-1 exerts a rapid and severe damage of the gut-associated lymphoid tissue and epithelial barrier, creating a “leaky gut” that allows translocation of commensal gut bacterial products into systemic circulation16,17. Initial cross-sectional studies in humans provided contradictory associations between microbial richness and HIV status12,14,15 and suggested shifts from Bacteroides to Prevotella predominance following HIV-1 infection12,15. Such shifts, however, have not been found in animal models18 or in studies matched for HIV-1 risk groups19, nor have the cohorts been analyzed for potential confounding factors. Here, we demonstrate in two independent cohorts of HIV-1-infected subjects and HIV-1-negative controls in Barcelona and Stockholm that men who have sex with men (MSM) predominantly belong to the Prevotella-rich enterotype whereas most non-MSM subjects are enriched in Bacteroides, independently of HIV-1 status, and with only a limited contribution of diet effects. Moreover, MSM have a significantly richer and more diverse fecal microbiota than non-MSM individuals. After accounting for sexual practice, HIV-1 infection does lead to significantly reduced bacterial richness, which provides a target for novel interventions to improve HIV-associated immune dysfunction