Exploring intestinal microbiota in pigs: validation and application of a novel non-invasive sampling device

The study of microbiota's temporal dynamics and individual variability remains challenging. While technological advances have deepened understanding of host-associated microbial communities, progress in non-invasive tools for directly studying small intestine (SI) microbiota has been limited. This Ph.D. research validated a novel non-invasive device, the Capsule for Sampling (CapSa), for collecting gut microbiota samples from pigs. Existing methods for microbiota sampling are invasive and non-repeatable (e.g., ileal cannulation) or non-invasive but imprecise for SI studies (e.g., fecal sampling). CapSa addresses these gaps, enabling accurate, repeatable sampling of SI microbiota. Validation was conducted in postweaning and growing pigs, with a standard operating procedure (SOP) developed for its use. Retrieval was feasible for pigs over 12 kg, as smaller pigs' stomachs impeded recovery. Sampling occurred in the SI's first segment for postweaning pigs and the middle segment for growing pigs, yielding microbiota compositions distinct from the large intestine and feces. CapSa was successfully administered repeatedly throughout pigs’ lifespans, allowing longitudinal microbiota studies without slaughtering. Sampling five times during a pig’s life revealed microbiota evolution under normal conditions and after an ETEC infection, showing persistent impacts detectable at slaughter. These findings demonstrate CapSa's potential for studying SI microbiota and other gut biomarkers in pigs, starting from postweaning age. Although further refinement of the SOP could enhance animal welfare, CapSa represents a significant advancement in non-invasive microbiota research. Its ability to provide precise, longitudinal insights into the gut microbiota establishes it as a valuable tool for advancing our understanding of the SI microbiome and its response to environmental and health-related factors.