Multi-omics reveals soybean meal-induced gut microbiota alterations and metabolic disturbances in largemouth bass (Micropterus salmoides): Implications for aquaculture nutrition

This study employed multi-omics approaches to reveal soybean meal (SBM) -induced alterations in gut microbiota and metabolic disturbances in largemouth bass ( Micropterus salmoides ), providing important insights for aquaculture nutrition. Four isonitrogenous and isolipidic diets, named fishmeal (FM, control), SBM10, SBM30, and SBM50, were formulated by replacing 0%, 10%, 30%, and 50% FM with SBM. A total of 240 healthy largemouth bass (initial weight: 11.00 ± 0.2 g) were randomly assigned into four groups, each in triplicate, with 20 fish per tank. The experiment lasted for 56 days. The results demonstrated an inclusion level-dependent reduction in the final average weight, weight gain rate, and specific growth rate as SBM replacement levels increased, with the SBM50 group showing the lowest values ( P < 0.05). The plica height, plica width, and the number of goblet cells were significantly lower in the SBM50 group compared to the FM group ( P < 0.05). Immunohistochemical results revealed decreased mucin 2 content in the SBM50 group compared to the FM group. Lipopolysaccharide content and fluorescein isothiocyanate-dextran (FITC-dextran) absorbance value in the SBM50 group were significantly higher than those in the FM group ( P < 0.05). The intestinal microbiota analysis showed that, compared to the FM group, the SBM50 group exhibited markedly lower abundances of beneficial genera ( Roseburia and Lactococcus ) but higher levels of potential pathogens ( Salmonella and Enterobacter ; linear discriminant analysis score > 4.0) ( P < 0.05). Metabolomic analysis showed significant differences between FM and SBM50 groups, with decreased levels of indolelactic acid, indole-3-butyric acid, and L-glutamine but elevated soyasaponin i, soyasaponin ii, and linoleic acid levels ( P < 0.05). Transcriptome analysis further revealed significant enrichment of phosphatidylinositol 3-kinase—protein kinase B (PI3K-Akt) and nuclear factor kappa-light-chain-enhancer of activated B cells signaling pathway (NF-κB) signaling pathways in the SBM50 group compared with the FM group ( P < 0.05). Concurrently, key intestinal epithelial barrier genes, including zonula occludens-1 ( zo-1 ), claudin-1 , epithelial cadherin ( E-cadherin ), and myosin heavy chain 10 ( myosin-10 ), were markedly downregulated ( P < 0.05). These results indicate that a substitution level not exceeding 30% did not adversely affect the growth performance of largemouth bass. Higher replacement levels impair growth performance and trigger intestinal inflammation by disrupting gut microbiota homeostasis, altering key metabolites, and compromising intestinal barrier function. These negative effects may be mediated through the downregulation of epithelial barrier-related genes and activation of the PI3K-Akt and NF-κB pathways, necessitating mitigation strategies to maintain gut health.