SRA

The human gut microbiota is influenced by various factors, including genetics, health status and environmental conditions, yet, considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men-having-sex-with-men (MSM) is clearly distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family including co-colonization of species from the Prevotella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis clarifying inter-individual differences in MSM linked specific sexual practices to microbiota composition. Moreover, machine learning identified microbial features associated with sexual activities in MSM. Together, this study identifies a previously unrecognized role for sexual activities on gut microbiome diversification in MSM, which may have a large impact on population-based microbiota studies.