Microbial communities impact a variety of processes including a host’s ability to access nutrients and maintain health, but can also include pathogens with a detrimental impact. Since the spread of anatomically modern humans across the planet, we have drastically changed the way we live (e.g. agriculture, antibiotic usage). These changes presumably affected our microbial communities. To examine the microbial communities of our ancestors, researchers use two approaches: first, the study of present-day hunter-gatherer societies, suggesting modern humans lost much of their microbial diversity; second, comparative analyses of our closest relatives in their natural environment. We review studies of the microorganisms in the chimpanzees of Taï National Park (particularly bacteria and retroviruses). We discuss how microorganisms are transmitted between chimpanzees, which microorganisms coevolved with their hosts and which were transmitted between chimpanzees and their prey. We examine how the close evolutionary relationship of primates and humans facilitates the zoonotic transmission of microorganisms and how disease ecology informs assessments of human disease risk.