The AMKAJ 2 Study: Microbiome and Mucosal Immunology Among MSM Couples in Kenya

The Anza Mapema kwa Afya Jamii Mbili (AMKAJ 2) Study was a pilot investigation built on findings from the earlier AMKAJ 1 project to further investigate the biological factors contributing to HIV and STI vulnerability among men who have sex with men (MSM) in Kenya. This pilot study focused specifically on MSM couples, examining the composition of the penile and rectal microbiomes and how these microbial communities related to mucosal immune responses. It was also conducted in Kisumu, Western Kenya, and enrolled 50 MSM and their 50 male sexual partners to explore whether similarities in microbiota and immune activation existed within sexual pairs.
MSM in sub-Saharan Africa have continued to experience a significantly higher burden of HIV compared to the general population. In Kisumu, nearly 30% of MSM were living with HIV by the age of 30. While prior research had demonstrated that genital microbiomes could be shared between heterosexual couples and linked to STI risk, similar studies among MSM couples remained scarce. This knowledge gap was particularly important given the growing evidence that both penile and rectal microbiomes, through their influence on local inflammation, play a key role in determining susceptibility to HIV and other STIs.
The AMKAJ 2 Study pursued three primary aims. First, it aimed to characterize the penile and rectal microbiomes of MSM and their male sexual partners, identifying both microbial similarities and differences within couples. The study also investigated behavioral, biological, and demographic factors that contributed to variation in microbiome composition. Second, it mapped these microbiome profiles to mucosal immune responses, using urinary and rectal cytokine measurements to assess inflammation at each site. Third, it explored whether patterns of mucosal inflammation were correlated within sexual pairs and whether this correlation was associated with shared microbial characteristics.
Earlier studies among heterosexual populations had shown that certain BV-associated bacteria could be transmitted between partners and were linked to an increased risk of HIV acquisition. In men, particularly those who were uncircumcised, the presence of these bacteria was associated with greater odds of HIV seroconversion. However, data on how such microbial communities were shared or differed within MSM couples had been limited. Additionally, while non-human primate studies had suggested that rectal microbiome composition could influence immune cell activity and vaccine response, research in human MSM populations was still emerging. These findings highlighted the need to better understand rectal microbiota in the context of HIV prevention.
By addressing this gap, the AMKAJ 2 Study became one of the first to evaluate both microbiome similarity and immune correlation within MSM sexual partnerships. Its findings contributed important insights into how biological factors beyond sexual behavior alone can influence STI and HIV risk in key populations. The study offered valuable evidence to inform future research and intervention design, laying a foundation for the development of more personalized, biologically informed HIV prevention strategies tailored to the needs of MSM communities in Kenya and similar settings.