Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices

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.