Weaning Influences Epithelial Morphology, Gene Expression and Gut Microbiota Composition in Piglets

Weaning introduces a variety of health-related challenges in piglets, but the relative contributions of the weaning event itself versus biological age at weaning remain unclear. During this period, the gastrointestinal tract has not yet fully developed, adding to the obstacles faced by piglets during this transitory phase in their life, which includes stress from a switch in diet and environment, in addition to potential exposure to pathogens. We investigated the intestinal morphology, expression of genes related to intestinal function and inflammation, and the gut microbiota in 40 piglets weaned at either 3 or 5 weeks of age through complementary analyses: age-matched comparisons (22, 25, 32, 36, and 39 days old) assessed developmental trajectories, while days post-weaning (DPW) comparisons (1 and 4 days post-weaning) isolated acute weaning responses independent of biological age. Animals weaned at 3 weeks of age were divided into five pens of four piglets, while the other group remained with the sow until weaning. At each timepoint, we measured the small intestine length, villus length, crypt depth and mucosal CD3⁺ T-cell infiltration in mid-jejunal tissue. The gene expression of inflammatory markers, tight junction proteins and functional markers was quantified from duodenal and mid-jejunal tissue. The colonic microbiota composition was characterized by 16S rRNA gene sequencing. Both weaning groups showed similar acute morphological responses. However, adaptive gene expression patterns differed significantly. The DPW analysis revealed compensatory mechanisms: at DPW4, the early-weaned piglets exhibited 4-fold higher duodenal IAP than the late-weaned piglets (p < 0.001), while the late-weaned piglets maintained higher antimicrobial defenses (IL-8, p = 0.031; lysozyme, p = 0.027). Additionally, microbiota analysis revealed distinct succession patterns between the two groups. These findings demonstrate that acute physiological responses to weaning are age-independent, but biological maturity fundamentally shapes adaptive mechanisms and recovery trajectories. Early weaning requires compensatory physiological adjustments, while late weaning confers resilience through more stable microbiota and sustained innate defenses.