The primate gut teems with bacteria, which play an important role in the health and physiology of their host. Communities of these bacteria are shaped by intrinsic individual characteristics such as sex and age, but also depend on lifestyle factors such as diet, health 62 status, and the social environment. In humans, catalogues of gut microbiome variation are readily available in both industrialized and non-industrialized populations, allowing the identification of factors determining microbial variation. However, such extensive datasets are lacking for other great ape species, although these could help us understand the uniqueness and function of the human gut microbiome. Here, we conducted an extensive analysis of the gut microbiome and its associated factors within the entire European population of zoo-housed bonobos (Pan paniscus) (11 zoos in 5 countries) and in two communities of wild habituated bonobos (LuiKotale, Democratic Republic of the Congo). We collected 707 fresh faecal samples from 212 individuals in a longitudinal fashion. Samples were analysed for microbial content using 16S amplicon sequencing and extensive metadata were collected using observations, questionnaires, and historical records. Preliminary analyses indicate clear-cut differences in gut microbiome composition between wild and zoo-housed bonobos. Regardless of environment, Prevotella was the most abundant and prevalent genus, being found in 98% of the bonobo gut microbial samples. Blautia_A and an unnamed genus in the Lachnospiraceae family were also abundantly found in both wild and zoo-housed bonobos, hinting to the possible existence of a core bonobo microbiome. Further analyses will focus on identifying the factors that determine gut microbiome variation, including sex, age, diet, health status, medicine use, kinship, and social behaviour. This in-depth analysis of the bonobo gut microbiome across ecological conditions will provide further insight into the function and composition of gut microbiome in humans and non-human primates.