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 20th 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.