Dietary bile acid supplementation alters the gut transcriptome and metagenome and contributes to herbivorous diet adaptation in juvenile allodiploid hybrid fish

The aim of this study was to explore the effects of dietary bile acids (BAs) supplementation on herbivorous diet adaptation in allodiploid hybrid fish derived from blunt snout bream (♀) × topmouth culter (♂). Three experimental diets were formulated: a commercial basal diet (CG group), a basal diet supplement with duckweed (H group), and a basal diet supplemented with duckweed and 600 mg kg⁻¹ BA (T group). After 56 days of feeding, the growth parameters increased, and greater intestinal cellulase activity was detected in the T group. Moreover, the T group fish presented a longer and denser small intestinal villi. In general, the characteristics of the H group were intermediate between those of the other two groups (T > H > CG). Compared with CG group fish, 711 specific differentially expressed genes (DEGs) were identified in the intestine of T group fish. The upregulated DEGs were primarily enriched in MAPK signaling pathway, protein digestion and absorption, and mTOR signaling pathway; the downregulated DEGs were predominantly enriched in steroid hormone biosynthesis, fatty acid metabolism and primary bile acid biosynthesis. Besides, several upregulated genes, such as jak, irs, egfr, prss, and cpa which related to cell proliferation and differentiation, digestion, and metabolism, are associated with the changes in intestinal histomorphology. These changes could promote the intestinal adaptation of an herbivorous diet. The metagenome sequencing results revealed that exogenous BAs significantly changed the structure of the gut microbiota; decreased the abundance of potentially pathogenic bacteria or fungi such as Proteobacteria, Mucoromycota, and Pseudomonas; and increased the abundance of probiotics such as the cellulose-producing bacteria Micromonospora. In addition, functional analysis revealed that the abundance of some enzyme families related to cellulose degradation was significantly greater in the T group. These findings suggested that exogenous BAs influences host intestinal gene expression and the structure of the gut microbiota via the gut microbiota-bile acid pathway, which in turn contributes to herbivorous diet adaptation in juvenile allodiploid hybrid fish.