This study aims to investigate the effects of adding 2‰ Lithospermum erythrorhizon (LE) extract to the high soybean meal diet on the growth, intestinal antioxidant capacity, intestinal microbes, and metabolism of pearl gentian grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂). Three diets included FM, SBM, and SBMLE, in which FM was the whole fish meal diet, SBM was the soybean meal replacing 50% fish meal protein, and SBMLE was the SBM diet supplemented with 2‰ LE extract. After a 56-day feeding trial, the results showed the weight gain rate (WGR), specific growth rate (SGR), and feed efficiency rate (FER) of pearl gentian grouper in FM and SBMLE group was significantly higher than that of SBM (P < 0.05). Furthermore, high soybean meal dietary added LE extract inclusion significantly increased the SOD, CAT, and GSH-Px activity while significantly decreasing the MDA level (P < 0.05). Significant differences were in the gene expression of cytokines il1-β, il8, tnf-α, il10, and tgf-β between the SBMLE and SBM groups (P < 0.05). In addition, Microbiomics results revealed increased ASVs and alterations in gut microbiota composition, characterized by a decrease in Bacteroidota and an increase in Proteobacteria, Nautella, and lactococcus after adding LE extract. Furthermore, the substantial reduction in Firmicutes and Acidobacterota induced by high soybean meal feed was reversed by LE extract. Metabolic pathway enrichment analysis showed that LE extract mitigated soybean-induced enteritis (SBMIE) by affecting two critical metabolic pathways: arachidonic acid metabolism and histidine metabolism. In conclusion, adding LE extract to a high soybean meal diet can improve the growth performance and immunity of the pearl gentian grouper, and LE can play a mitigating role in SBMIE by regulating lipid metabolism, amino acid metabolism, and intestinal flora balance.
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