Abstract

The Coilia nasus is a valuable fish species native to the Yangtze River in China, but its wild populations have declined sharply due to overfishing and habitat loss. Artificial farming has become essential for protecting this species and meeting market demand. However, farmers currently rely on natural bait such as small shrimp and fish to feed these anchovies, which is expensive, unstable in supply, and can introduce diseases. This study explored whether C. nasus could be trained to eat formulated feed instead. We examined how its digestive organs, gut microbiota, and metabolic processes changed during the transition from natural bait to formulated feed. The results showed that the fish successfully adapted to formulated feed through structural changes in their stomach and intestines, adjustments in digestive enzymes, and shifts in gut microbiota communities. Importantly, C. nasus grew just as well on formulated feed as on natural bait, and their meat even showed improved nutritional quality. These findings provide a scientific basis for farmers to replace natural bait with formulated feed, making anchovy farming more sustainable, cost-effective, and environmentally friendly. 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 s