The experiment was carried out to evaluate the effects of double-layer-coated Enterococcus faecium on the growth performance, liver biochemical indices, digestive enzyme activity, intestinal morphometry, immunity gene expression, and microbiota of crucian carps (Carassius auratus gibelio). A total of 320 fish (mean weight 11.0 ± 0.04 g) were randomly distributed into 3 treatment groups of 4 replicates per treatment (20 fish/replicate). Three different experimental diets were designed: dietary C without double-layer-coated E. faecalis, dietary LP supplemented with 1.0 × 107 CFU/g, and dietary HP supplemented with 1.0 × 108 CFU/g double-layer-coated E. faecalis. The fish was fed for 70 days with different diets, followed by a challenge with lipopolysaccharide (LPS). The results showed that the weight gain and specific growth rate increased and the feed conversion rate decreased in the dietary HP (P < 0.05). The dietary LP had higher lipase and protease activities, and amylase activity increased in the dietary LP and HP after the LPS challenge (P < 0.05). The dietary HP had higher villi height (VH), thicker muscular thickness (MT), and higher VH/MT (VCR) in the intestine (P < 0.05). The intestines were damaged by the LPS challenge; the damage to the dietary HP was alleviated, showing a higher VH, thicker MT, and higher VCR (P < 0.05). The glutathione peroxidase activity of the liver was increased in the dietary HP (P < 0.05). There was no significant difference in liver antioxidant capacity with the LPS challenge among all diets. There was no significant difference in the expression level of the Occludin and Claudin-12 genes among all diets that was up-regulated in dietary HP after LPS challenge (P < 0.05). High-throughput sequencing revealed that the supplementation of double-layer-coated E. faecium increased the species diversity of the intestinal. In conclusion, double-layer-coated E. faecium can improve the absorption of nutrients, enhance immunity, maintain balance in the intestine microbiota, and promote the growth of crucian carp. The supplementation of double-layer-coated E. faecium in the diet can alleviate the intestinal damage caused by LPS challenge.
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