Comprehensive Analysis of miRNAs, mRNAs, and lncRNAs in Intestines of Breast- and Formula-Fed Pigs

Breast-fed (BF) and formula-fed (FF) pigs have different intestinal morphologies and physiologies. However, how molecular expression affects intestinal morphology is imperfectly known. We compare expression profiles and functions of miRNA, mRNA, and lncRNA in the intestines of 210-d-old BF and FF pigs. Jejunum and duodenum villus height and mucosal thickness were significantly higher in BF pigs than FF pigs (p < 0.05). Of 88 identified differentially expressed (DE) miRNAs in BF pigs, 39 were up- and 49 were down-regulated; of 117 lncRNAs, 53 were up- and 64 were down-regulated; and of 387 mRNAs, 242 were up- and 145 were down-regulated. GO and KEGG analysis revealed overlapping DE mRNA corresponding genes and target genes of DE miRNA and lncRNA to be associated with pathways involved in cold-induced thermogenesis, digestion, and xenobiotics metabolism. Gene families (e.g., UGT, ABC, AHCY and SLC) potentially involved in intestinal morphological development are identified. Further analysis indicates that the CYP1A1-LOC100515741/LOC100622246/LOC100739163 and AHCYL2-miR-145-3p network may regulate the development of intestinal morphology in pigs. Collectively, these results improve our understanding of the possible long-term health effects of specific alterable early-life risk factors and exposures.