Microbiome-based survey of pathogenic bacteria at the chimpanzee-human-livestock interface, Uganda

Anthropogenic land-use change is intensifying contact among wildlife, humans, and livestock in tropical ecosystems, increasing opportunities for cross-species transmission of infectious agents. Chimpanzees (Pan troglodytes schweinfurthii), owing to their close phylogenetic relationship with humans, are particularly susceptible to pathogen spillover. We performed a microbiome-based screening of potentially pathogenic bacteria in faecal samples from a chimpanzee-human-livestock interface in western Uganda using full-length 16S rRNA gene sequencing. A total of 21 bacterial genera, categorized as potentially pathogenic, were detected across all three studied host groups, from which several taxa of potential zoonotic or health relevance, including Clostridium perfringens, Salmonella enterica, Shigella spp., and Streptococcus suis, were detected in chimpanzees, humans, and goats. Our findings indicate an overlap in bacterial taxa across the interface. The relative abundance of potentially pathogenic bacterial taxa was descriptively lower in chimpanzees than in humans and livestock, but carried both enteric and respiratory bacterial species previously associated with disease outbreaks in captive and wild populations. These findings support integrating bacterial monitoring into conservation-oriented One Health frameworks.