Priority effects and microbial cross-feeding shape zoonotic agent spread in broiler chickens

Abstract Unravelling the colonisation dynamics and physiological effects of zoonotic bacteria such as Campylobacter is imperative to prevent foodborne diseases. We employed a hologenomic approach to jointly analyse metabolic networks and gene expression of the caecal microbiota, with the intestinal gene expression of 613 broiler chickens that did and did not undergo an opportunistic Campylobacter colonisation. We report that an early development of a distinct microbial enterotype enriched with Bacteroides fragilis_A, changed the community to a functional profile that likely benefited Campylobacter through production of key metabolites. The resulting enterotype was not associated with a host immune response, but exhibited an enriched and energetically more demanding functional repertoire compared to the standard enterotype, which could have caused the growth decline observed in Campylobacter-colonised animals. We provide unique insights into microbe-microbe and host-microbe interactions, which point to the early-stage microbiota-development as a relevant factor for later Campylobacter spread in broiler chickens.