Distinct microbiome signatures across the pig gastrointestinal tract link enterotype-like clusters to protein metabolism

This study provides a comprehensive characterization of the entire pig gastrointestinal tract (GIT) microbiome in both mucosa and digesta samples using target amplicon and shotgun metagenomic sequencing approaches. Significant differences in microbial diversity and composition were observed between GIT sections and sample types. The Shannon diversity index and microbial composition at genus and ASV levels varied considerably across the GIT, with Streptococcus being the predominant genus in the digesta and mucosa of the small intestine. Our investigation provided a deeper insight into the gastric microbiota, particularly in the mucosa. Despite similar Shannon diversity index across the three gastric mucosal regions, significant differences were detected in microbial composition at ASV level and relative abundance at the genus level. Shotgun metagenomic analysis of digesta samples revealed functional shifts in microbial communities along the GIT compartments, with the small intestine showing potential anabolic contribution to protein metabolism. Previously identified faecal enterotype-like clusters were reflected in bacterial compositional differences within the digesta of the stomach, ileum and caecum at the species level. The differences observed in the ileum, a major site of nutrient absorption, provide a potential explanation for variations in performance variables such as nitrogen utilization efficiency, that has been associated with enterotypes in pigs. The abundance of Streptococcus alactolyticus in the ileum appears particularly significant in this context. These findings offer a deeper knowledge of the microbial communities different GIT sections and their contribution to nutrient metabolism.