The emergence of zoonotic infectious diseases is a growing concern, with areas where humans come into contact with wildlife and domestic animals being hotspots for this emergence. Why certain microbes switch hosts remains elusive, although factors such as microbe-host contact rates are believed to play a role. To better comprehend the influence of spatiotemporal overlap on microbial sharing, we examined over 500 samples and 2,400 bacterial metagenome-assembled genomes obtained from the gut microbiomes of mountain gorillas, humans, and livestock in Uganda. This study identifies the presence of hundreds of putative novel bacteria addressing a critical gap in our understanding of microbial interactions particularly in high-intensity human-animal interfaces in African settings.