Integrated Omics Analysis of the Effects of Nano-Antimicrobial Peptides on the Intestinal Microbiota and Metabolome of Tibetan Sheep

This study investigated the effects of dietary nano-antimicrobial peptides (NAPs) on the microbial communities and metabolic profiles in Tibetan sheep. Using 16S rRNA gene high-throughput sequencing and non-targeted metabolomics, the contents of the small intestine, rumen, and rectum were systematically analyzed in a control group (Group A) and a NAP-supplemented group (Group B). Multi-omics integration methods, including O2PLS and Pearson correlation analysis, were employed to explore the association between microbial communities and metabolites. Alpha and beta diversity analyses revealed significant differences (P < 0.05) in the microbial community structure of the small intestine between the two groups. In contrast, the rumen and rectal microbiota remained relatively stable, indicating that the regulatory effects of NAPs on the intestinal microecology are site-specific. In the small intestine, NAPs altered the composition of dominant functional microbiota and the abundance of taxa related to energy metabolism. Metabolomic analysis identified significant shifts in metabolic profiles, specifically within the bile acid, fatty acid, and phospholipid pathways (P < 0.05). Group A exhibited baseline steady-state characteristics (e.g., cholic acids and phospholipids), whereas Group B showed activation of unsaturated fatty acids and related metabolites. Multi-omics integration revealed a stable systematic association between intestinal microbial genera and metabolites. Specifically, bile acid and prostaglandin metabolites were negatively correlated with Firmicutes-related taxa, suggesting a potential role for bile acid metabolism in regulating intestinal microecology and host immunity. These findings suggest that NAP supplementation may contribute to maintaining host energy metabolism and intestinal homeostasis by regulating intestinal microecology.