Integrative transcriptomic and small RNAs sequencing reveals immune mechanism for soybean meal-induced enteritis in hybrid grouper

A 12-week feeding experiment was conducted to reveal the immune mechanism for soybean meal-induced enteritis in hybrid grouper by integrative small RNAs and transcriptomic. Four isonitrogenous and isolipidic diets were formulated by replacing 0%, 10%, 30%, and 50% fish meal protein with soybean meal (namely FM, SBM10, SBM30, and SBM50, respectively). Weight gain and specific growth rates of the SBM50 group were significantly lower than those other groups (P < 0.05), and reduced growth performance was used as the indicator of the SBM stress. The height of the mucosal fold and the muscular layer of the distal intestine in the SBM50 group were extremely lower compared with the FM group (P < 0.01). The intestinal transcriptomic data, including transcriptome and miRNAome, showed that a total of 6,390 differentially expressed (DE) mRNA and 92 DE miRNAs were identified in SBM50 and FM groups. From these, found that immune system-related pathway such as natural killer cell-mediated cytotoxicity, and Fc gamma R-mediated phagocytosis, the intestinal immune network for IgA production were significantly enriched (Q value < 0.0001). KEGG enrichment analysis of DE miRNAs target genes further found that involved in immune system-related natural killer cell-mediated cytotoxicity were enriched. In addition, this pathway was found to have eight mRNA-miRNA interactions. This study reveals that the immune mechanism for SBMIE may be associated with a natural killer cell-mediated cytotoxicity pathway mediated by the miRNA expression. Our findings provide important insights into the immune mechanisms for SBMIE in carnivorous fish by integrative small RNAs and transcriptomic.