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 of weaning pigs.

Methods: : A total of 96 weaning pigs were randomly assigned to 3 groups named the H, M, and L groups. The H, M, and L groups received 20% and 18%, 18% and 16%, and 16% and 14% CP in the early (1-14 days) and late phases (15-28 days), respectively.

Results: : The final body weight and average daily gain were lower in the L group than 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 between the groups. Genes involved in cell proliferation and differentiation and inflammation was downregulated 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 downregulated 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 between the groups. Carbohydrate-fermenting bacteria, such as Megasphaera elsdenii DSM 20460 and Blautia luti DSM 14534, were higher in the M and L groups compared with the H group (p ≤ 0.05). The abundance of Lactobacillus amylovorus DSM 20531 was higher 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 cecal transcriptome and microbiota (p < 0.01).

Conclusion: : Reducing the level of CP modulate cell growth and alleviate inflammation in the cecum. A.