Changes in the ileal, but not faecal, microbiome in response to increased dietary protein level and enterotoxigenic Escherichia coli exposure in pigs

The relationship between porcine gut microbiota composition and animal health is an important area of research, especially due to the need to find alternatives to antimicrobial use to manage disease in livestock production systems. Previous work has indicated that lower crude dietary protein levels can reduce the impacts of post-weaning colibacillosis (PWC), which is a porcine diarrheal disease caused by enterotoxigenic Escherichia coli (ETEC). Here, to explore the complex interactions between the gut microbiota, protein nutrition and ETEC exposure, the microbial compositions of both the ileal digesta and feces were analysed with and without ETEC exposure from pigs fed a low or high protein diet. As ETEC colonisation is mostly localised to the ileum, changes in the small intestinal microbiota were expected in response to ETEC exposure.