Fish gut health is influenced by various factors, with the environment being a significant one. S. sinensis is a key aquaculture species in China, yet research on the impact of different aquaculture systems on its intestinal health remains limited. This study aims to explore the changes in intestinal morphology and gut microbiota of S. sinensis under two aquaculture systems. The juveniles of S. sinensis were divided into two groups and cultured in traditional ponds (CT) and an in-pond tank culture system (JY), with equal amounts of feed provided daily over a 72-day experimental period. The results showed no significant differences in growth performance metrics, including the specific growth rate, weight gain rate, hepatosomatic index, and viscerosomatic index between the two groups. In terms of intestinal morphology, the JY group villus width was significantly wider than the CT group, and the number of goblet cells in the CT group was significantly higher than that of the JY group (p < 0.05), which suggested that the fish in the JY group may have better intestinal nutrient absorption capacity, while the water quality in the CT group may be worse. The 16S rRNA gene sequencing analysis of the gut microbiota showed that the JY group had a significantly higher Shannon index compared to the CT group (p < 0.05), indicating greater species richness and evenness. Principal Coordinates Analysis (PCoA) revealed a distinct clustering of gut microbiota between the two groups. At the phylum level, the relative abundance of Fusobacteriota was significantly higher in the CT group, whereas Bacteroidota and Proteobacteria were significantly higher in the JY group (p < 0.05). Furthermore, KEGG pathway predictions indicated differences in the potential metabolic capabilities of the gut microbiota between the two groups (p < 0.05). Overall, this study is the first to conduct a comparative analysis of the growth performance, intestinal tissue morphology, and gut microbiota of S. sinensis under two different aquaculture systems, which has valuable implications for the further optimization of aquaculture practices.
