Pathogen Transmission and Gut Microbiomes at the Human, Animal, and Environmental Interface in Uganda

ABSTRACT
Gut microbiomes are shaped by diet, environment, and interspecies interactions, with implications for pathogen transmission across humans, domestic animals, and wildlife. We investigated human–animal contact networks and health in communities surrounding Bwindi Impenetrable National Park (BINP), Uganda, using integrated ethnographic, epidemiological, and metagenomic approaches. Surveys of 100 participants collected demographic data, health diaries, and stool samples, alongside contact network data spanning humans, domestic, peri-domestic, and wild animals. Over 2,400 bacterial genomes from ~600 human, livestock, and mountain gorilla microbiomes were analysed to assess microbial sharing.
Participants frequently reported illness, with human–human and livestock contacts most common, alongside occasional direct wildlife interactions, including with gorillas. Shared bacteria, including antimicrobial resistance genes, were detected across species, and novel Campylobacter strains were identified in asymptomatic individuals. Despite evidence of microbial sharing, microbiomes remained largely host-specific. These findings highlight an environment conducive to pathogen transmission and underscore the importance of One Health approaches to address interconnected health risks and inequities in under-researched tropical regions.