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In the study, the effects of selenium on intestinal tissue morphology, antioxidant-related genes, and intestinal flora of grass carp (Ctenopharyngodon idella) were studied. For this purpose, 180 healthy grass carps (20.0±2.0 g) were randomly divided into three groups with three replicates each: the corresponding amount of anhydrous sodium selenite was added to make experimental water solutions of different concentrations, including 0 μg/L Se4+ (control group), 200 μg/L Se4+ group and 300 μg/L Se4+ group. The experiment was carried out for 42 days. The obtained results showed that: at the end of the experiment, the 200 μg/L Se4+ adaptation can have beneficial effects on the intestinal villi height and goblet cells. The CuZnSOD and CAT genes mRNA levels of grass carp intestine were strongly upregulated in the 200ug/L Se4+ group. 200ug/L selenium could increase the expression level of the Hsp70 gene in the intestinal tract of grass carp after 42 days of adaptation. At the genus level, the most abundant sequence in the gut of Se-treated grass carp was Pseudomonas, while Aeromon, Flavobacterium, and Defluviimonas were more abundant in the control group. In conclusion, this study demonstrates that 200ug/L Se4+ selenium adaptation can positively affect gut morphology and antioxidant responses and can alter the gut microbiota structure of grass carp. The results will provide a theoretical basis for further research on the effect of selenium on aquatic animals. [ABSTRACT FROM AUTHOR]