Multi-omics integrated approach reveals host-microbiome interactions in the adaptive mechanisms of weaning piglets

The weaning transition is a critical phase in piglet development, marked by physiological challenges that influence growth and health. Therefore, this study aims to investigate host-microbiome interactions during the weaning transition using a multi-omics integrated approach. Fecal samples were collected from piglets on the weaning day (W0), 7 days post-weaning (W7), and 14 days post-weaning (W14). Ileal microbiota, microbial-derived metabolites, and tissue samples (ileum, thymus, and mesenteric lymph nodes) were collected at W0 and W14. Fecal microbiota analysis revealed a more stable community at W14 than at W7, with increased presence of fiber-degrading bacteria, including <italic>Prevotella, Treponema, Muribaculaceae,</italic> and <italic>Lachnospiraceae. </italic>The ileal microbiota exhibited an adaptive pattern with increases in <italic>Lactobacillus, Clostridium_sensu stricto_1, and Enterobacteriaceae, </italic>optimized for solid feed digestion and gut stabilization. Morphological analysis of the ileum showed changes in villus architecture between W0 and W14, including increased crypt depth and villus area and decreased villus width, while villus height and goblet cell counts were numerically higher at W14. Transcriptomic profiling revealed the ileum as the primary site of molecular adaptation, with 506 differentially expressed genes involved in immune response pathways, including viral protein interactions with cytokine and cytokine receptor pathways and T cell receptor signaling. The thymus (158 DEGs) and mesenteric lymph nodes (30 DEGs) exhibited modulation of structural pathways linked to systemic immune development, indicating tissue-specific molecular adaptation. Integrated analysis of the host transcriptome and microbial-derived metabolites revealed upregulated glycerophospholipid and glutathione metabolic pathways in piglets 14 days post-weaning, consistent with modulation of membrane structure, barrier function, and antioxidant defense during gut adaptation. Overall, the multi-omics findings provide a comprehensive description of molecular changes associated with weaning adaptation and identify candidate targets for piglet health management during the weaning transition.