Transcriptome and microbiota analysis reveal differences in the cecum of weaning pigs in response to different dietary crude protein levels

Objective: This study explored the effects of different dietary crude protein (CP) levels on the cecal transcriptome and microbial composition in weaning pigs. Methods: Ninety-six weaning pigs were randomly assigned into three groups designated as H, M, and L groups. The H, M, and L groups were administered 20% and 18%, 18% and 16%, and 16% and 14% CP during the early (1-14 days) and late phases (15-28 days), respectively. Results: The final body weight and average daily gain in the L group were significantly lower than those in the other groups (p = 0.008). The feed conversion ratio was lower in the H and M groups than in the L group (p = 0.01). Cecal transcriptome analysis revealed that heatmap and principal component analysis of differentially expressed genes indicated the presence of distinct clusters among the groups. Genes associated with cell proliferation and differentiation and inflammation were down-regulated in the M and L groups, compared with corresponding genes in the H group (p<0.001). Pathway enrichment analysis suggested that genes related to IL-17 signaling pathway was down-regulated in the M and L groups (p<0.05). Beta diversity analysis and heatmap for microbial composition and function indicated the presence of distinct clusters among the groups. Carbohydrate-fermenting bacteria, such as Megasphaera elsdenii DSM 20460 and Blautia luti DSM 14534, exhibited higher levels in the M and L groups compared with the H group (p≤0.05). The abundance of Lactobacillus amylovorus DSM 20531 was significantly greater in the M group than in the other groups (p≤0.05). The abundance of L. amylovorus DSM 20531 was positively correlated with growth performance. Integrated multi-omics analysis suggested significant similarities between the cecal transcriptome and microbiota (p<0.01). Conclusion: Reducing CP levels modulates cell growth and alleviates inflammation in the cecum. A low CP diet causes cecal microbiota composition shift and promotes the proliferation of carbohydrate-fermenting bacteria. Overall, 18% CP in an early phase and 16% CP in a late phase can substantially improve growth and gut health in weaning pigs.