Dynamic Structural Adaptation and Molecular Response of the Digestive Organs During Feed Domestication in Coilia nasus

Coilia nasus, a nutritionally and economically valuable migratory fish, has long relied on natural bait for its cultivation. However, the inherent instability of natural bait supplies poses a major bottleneck for large-scale aquaculture, necessitating a transition to formulated diets. To elucidate the adaptive response mechanisms underlying this dietary transition, we conducted sampling at three critical stages of feed domestication. This research revealed that while dietary shifts led to moderate alterations in muscle lipid and protein content, overall growth performance remained largely unaffected. During domestication, we observed significant structural remodeling of the stomach, intestine, and liver, along with increased activities of trypsin and lipase. The intestinal microbiota shifted, with Firmicutes abundance increasing notably during the domestication process, although the natural bait group exhibited even higher Firmicutes abundance than the formulated-feed group. Multi-omics analysis of intestinal samples from key domestication stages revealed significant enrichment of lipid metabolism pathways. It suggests that changes in genes and metabolites may be associated with the adaptive response to formulated-feed, including alterations in membrane stability, lipid metabolism and inflammatory state. This study provides the first comprehensive characterization of the structural and molecular adaptations of the digestive system of C. nasus during formulated-feed domestication. These findings offer a theoretical foundation for optimizing feeding protocols and supporting the sustainable aquaculture of this species.