The Cloacal Microbiome Changes with the Breeding Season in a Wild Bird

The symbiotic microbial communities, or “microbiomes,” that reside on animals are dynamic, and can be affected by the behavior and physiology of the host. These communities provide many critical beneficial functions for their hosts, but they can also include potential pathogens. In birds, bacteria residing in the cloaca form a complex community, including both gut and sexually-transmitted bacteria. Transmission of cloacal bacteria among individuals is likely during the breeding season, when there is direct cloacal contact between individuals. In addition, the major energetic investment in reproduction can draw resources away from immune responses that might otherwise prevent the successful establishment of microbes. We assessed dynamic variation in the cloacal microbiome of free-living rufous-collared sparrows (Zonotrichia capensis) through sequential breeding and non-breeding seasons. We found that the cloacal bacterial communities differed between the sexes when they were in breeding condition. Further, in males, but not in females, the bacterial community became more diverse with the onset of reproduction, and then decreased in diversity as males transitioned to non-breeding condition. Individuals sampled across sequential breeding seasons did not accumulate more bacterial taxa over seasons, but bacterial community composition did change. Our results suggest that the cloacal microbiome in birds is dynamic and, especially in males, responsive to breeding condition.