Oral Vaccination Reduces the Effects of Challenge on the Swine Small and Large Intestine Microbiome.

Porcine proliferative enteropathy remains one of the most prevalent diseases in swine herds worldwide. This disease is caused by , an intracellular bacterial pathogen that primarily colonizes the ileum. In this study, we evaluated changes to the microbiome of the ileal mucosa, ileal digesta, cecal digesta, and feces subsequent to challenge with and to an oral live vaccine against . Given that gut homogenates have been used since 1931 to study this disease, we also characterized the microbial composition of a gut homogenate from swine infected with that was used as challenge material. The challenge led to a dysbiosis of the microbiome of both the small and large intestine marked by an increase of pathobionts including , and . This microbiome response could play a role in favoring colonization and disease as well as potentially predisposing to other diseases. Vaccination altered both small and large intestine microbiome community structure and led to a significant 3.03 log reduction in the amount of shed by the challenged pigs. Vaccination also led to a significant decrease in the abundance of , and among other microbial changes compared with non-vaccinated and challenged animals. These results indicate that infection is associated with broad changes to microbiome composition in both the large and small intestine, many of which can be mitigated by vaccination.