Integrated Multi-Omics Analyses Reveal the Effects of Different Diets on Growth, Digestion, and Intestinal Function...

This study aimed to investigate the effects of different diets on the growth performance, digestive capacity, and intestinal health of Megalobrama pellegrini larvae. A 30-day feeding trial was conducted using ten-day-old larvae, which were divided into five dietary groups: microdiet (MD), Tubifex tubifex (Tub), Artemia salina (Art), MD + Tub and MD + Art. Results showed that the Tub group achieved significantly higher final body weight, total length, and survival rate (86.00%) compared to all other dietary groups (p < 0.05). It exhibited the highest activities of trypsin, lipase, and alkaline phosphatase, alongside significantly superior intestinal villus height, width, and muscular thickness compared to other groups (p < 0.05). Gut microbiota analysis not only revealed a higher abundance of beneficial bacterial phyla (e.g., Verrucomicrobia, Bacteroidetes) in the Tub group, but also showed enhanced activity in functional pathways related to lipid metabolism, terpenoid and polyketide synthesis. A total of 1,825 differentially expressed genes (DEGs) and 330 differential metabolites (DMs) were identified between the MD and Tub groups. Transcriptomic analysis showed that DEGs were significantly enriched in pathways related to intestinal digestion and absorption, cell cycle and proliferation, and growth hormone synthesis, secretion, and action. Metabolomic analysis revealed that the primary enriched metabolic pathways in the Tub vs. MD comparison included arginine biosynthesis, the pentose phosphate pathway, and the citric acid cycle. Integrated multi-omics analysis revealed the co-enrichment of glycolysis/gluconeogenesis, nicotinate and nicotinamide metabolism, and arginine and proline metabolism pathways, with genes such as eno1, nmrk1, and oat regulating pyruvate metabolism, NAD⁺ regeneration, and GABA synthesis, respectively. In summary, dietary T. tubifex supplementation improved the growth performance and health status of M. pellegrini larvae by optimizing intestinal morphological structure and gut microbiota composition, as well as activating key metabolic pathways.