Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection.

Men who have sex with men (MSM) have differences in immune activation and gut microbiome composition compared with men who have sex with women (MSW), even in the absence of HIV infection. Gut microbiome differences associated with HIV itself when controlling for MSM, as assessed by 16S rRNA sequencing, are relatively subtle. Understanding whether gut microbiome composition impacts immune activation in HIV-negative and HIV-positive MSM has important implications since immune activation has been associated with HIV acquisition risk and disease progression. To investigate the effects of MSM and HIV-associated gut microbiota on immune activation, we transplanted feces from HIV-negative MSW, HIV-negative MSM, and HIV-positive untreated MSM to gnotobiotic mice. Following transplant, 16S rRNA gene sequencing determined that the microbiomes of MSM and MSW maintained distinct compositions in mice and that specific microbial differences between MSM and MSW were replicated. Immunologically, HIV-negative MSM donors had higher frequencies of blood CD38+ HLADR+ and CD103+ T cells and their fecal recipients had higher frequencies of gut CD69+ and CD103+ T cells, compared with HIV-negative MSW donors and recipients, respectively. Significant microbiome differences were not detected between HIV-negative and HIV-positive MSM in this small donor cohort, and immune differences between their recipients were trending but not statistically significant. A larger donor cohort may therefore be needed to detect immune-modulating microbes associated with HIV. To investigate whether our findings in mice could have implications for HIV replication, we infected primary human lamina propria cells stimulated with isolated fecal microbiota, and found that microbiota from MSM stimulated higher frequencies of HIV-infected cells than microbiota from MSW. Finally, we identified several microbes that correlated with immune readouts in both fecal recipients and donors, and with in vitro HIV infection, which suggests a role for gut microbiota in immune activation and potentially HIV acquisition in MSM. Author summary The communities of commensal microbes that colonize the human gut comprise the gut microbiome, which has been shown to play a significant role in shaping the immune system. Recent studies have reported a distinct gut microbiome composition in men who have sex with men (MSM) exhibiting HIV-risk behaviors when compared with low-risk men who have sex with women (MSW), regardless of their HIV infection status. Whether these gut microbiome differences in high-risk MSM directly impact immune activation is important to understand since increased T cell activation is associated with increased HIV transmission risk and more severe disease. To test the immunological effect of the gut microbiome in MSM, we transplanted stool from HIV-negative MSW, HIV-negative high-risk MSM, and HIV-positive MSM to germ-free mice. DNA sequencing showed that specific microbiome differences associated with MSM were successfully engrafted in mice, and that these differences were associated with increased CD4+ and CD8+ T cell activation in the mice. These results provide evidence for a direct link between microbiome composition and immune activation in HIV-negative and HIV-positive MSM, and rationale for investigating the gut microbiome as a risk factor for HIV transmission.