Dynamic picture of the pig gut’s microbiota under normal and pathological conditions

Background: Recent advancements in sequencing technologies and associated bioinformatic tools have eased the analyses of the factors influencing variability in host-associated microbial communities in the gastrointestinal tract (GIT). Although extensive research has focused on fecal microbiota, the small intestine represents a critical, yet less explored, site for understanding the interplay between microbiota, diet, and host health. Study 1 employed CapSa, a non-invasive sampling capsule, to collect microbiota at five distinct administration time points. The aim was to use amplicon sequencing to investigate changes in the small intestine microbiome composition throughout the grower-finisher pig lifespan. Study 2 examined the long-term impact of enterotoxigenic Escherichia coli (ETEC) F4 infections, which cause post-weaning diarrhea (PWD), on small intestine microbiota dynamics. The study provides insights into the long-term responses of microbiota after a short pathological challenge. Results: In both studies, microbiota analysis of the small intestinal content revealed that Firmicutes predominated across all samples, and at weaning, Lactobacillaceae and Lactobacillus were the most abundant. In Study 1, following CapSa administration, Clostridium sensu stricto 1 and Terrisporobacter increased with age/body weight and at slaughter, Streptococcaceae dominated. Significant differences in microbial composition were observed based on sample type and diet, indicating dynamic shifts throughout the pigs’ lives under normal conditions. In Study 2, the abundance of Lactobacillaceae was consistently lower in ETEC-infected pigs. At slaughter, only minimal differences in microbial composition emerged based on the early post-weaning infection status in specific small intestine segments, indicating dynamic infection-induced shifts in the gut microbiota composition. The CapSa sampling method was successful, with a retrieval rate higher than 70% in both studies. Conclusions: This study monitored porcine intestinal microbiota dynamics using an ingestible capsule. In healthy pigs, microbial composition changes occurred from post-weaning to slaughter. In contrast, ETEC infection only minimally altered communities, though small differences at slaughter suggest lasting impacts.