Agricultural intensification drives the evolution of host specialism in the ecological generalist bacterium Campylobacter jejuni

Modern agriculture has dramatically changed the distribution of animal species on earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the time-scale and genomic adaptations that promote proliferation of the most common food-born bacterial pathogen (C. jejuni) in the most extensively farmed agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist C. jejuni lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20^th century. Cattle adaptation was facilitated by horizontal gene transfer and significant gene gain and loss, related to differences in host diet, anatomy and histology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.