The AMKAJ Study 1: Microbiome and Mucosal Immunity Research Among MSM in Kenya

The AMKAJ (Anza Mapema kwa Afya Jamii) Study was a cross-sectional, exploratory research project conducted to investigate the relationship between genital and rectal microbiomes and mucosal immune responses among men who have sex with men (MSM) in Kenya. The study aimed to understand how variations in bacterial communities across penile and rectal sites, alongside levels of local inflammation, might contribute to increased vulnerability to sexually transmitted infections (STIs), including HIV. Given the stark disparities in STI and HIV burden among MSM, this research sought to advance knowledge of the biological mechanisms that drive such risks, thereby informing more targeted and effective prevention strategies.

The AMKAJ Study was nested within the Anza Mapema cohort and involved 40 MSM aged 18 to 35 who had previously participated in the parent study and consented to future research. Each participant attended a single clinic visit during which behavioral data, medical history, and biological specimens, including urine, penile swabs, and rectal swabs, were collected. These samples were subsequently analyzed to characterize microbial communities and measure cytokine profiles, offering insight into local immune activation at mucosal surfaces. This integrated approach allowed for a comprehensive analysis of behavior, biology, and immune function.
The study was guided by two primary aims. The first was to characterize the penile and rectal microbiomes of MSM and to identify the factors shaping their composition, such as circumcision status, HSV-2 serostatus, recent STI diagnoses, sexual behaviors, hygiene practices, and antibiotic use.

Microbiome data from MSM participants were also compared to existing penile microbiome profiles from men who have sex with women (MSW), facilitating a better understanding of population-specific differences.
The second aim focused on exploring how microbiome structure is linked to local mucosal inflammation. By mapping microbial profiles to cytokine expression at penile and rectal sites, the study sought to model potential mechanisms of tissue disruption, including epithelial breakdown and ulcer formation, both of which may heighten susceptibility to HIV and other STIs.
In addition to these core objectives, the AMKAJ Study included exploratory analyses to examine whether associations between microbial community state types (CSTs) and STI/HSV-2 prevalence differed between MSM and MSW populations and whether the factors influencing CSTs varied across these groups. These findings provide critical insight for tailoring public health interventions and developing microbiome-targeted strategies in sexual health programming.
Conducted at the Anza Mapema Centre of Excellence - Tom Mboya and Town Clinics in Kenya, the AMKAJ Study contributed important evidence at the intersection of microbiome research, immunology, and public health. Its findings have added to the growing body of literature on host-microbe interactions and their influence on sexual health and disease vulnerability. Ultimately, the study supports efforts to design more inclusive, biologically informed STI and HIV prevention strategies for populations at heightened risk.