Fermented Rapeseed Meal Mitigates Intestinal and Hepatic Injuries via Gut Microbiota Modulation and Autophagy Activation in Koi Carp ( Cyprinus carpio )

This study assessed whether fermented rapeseed meal (FRSM) could alleviate the negative impacts of rapeseed meal (RSM) on growth, intestinal health, and liver function in koi carp ( Cyprinus carpio ). Eighty‐one koi carp were randomly divided into three dietary groups: a control group receiving a soybean meal (SBM) diet, an unfermented RSM group, and a FRSM group. Growth performance, serum biochemical parameters, tissue histology, gut microbiota, and transcriptomic profiles were assessed. The findings showed that the RSM and FRSM groups had notably lower weight gain, weight gain rate, and specific growth rate (SGR) compared to the SBM group ( p < 0.05). In the RSM and FRSM groups, serum antioxidant enzyme activities (SOD, CAT, and GSH‐PX) significantly decreased, whereas MDA levels and AST activity significantly increased ( p < 0.001). Histological analysis revealed that intestinal villus structures remained intact in all groups, but the FRSM group exhibited a significant reduction in crypt depth ( p = 0.019). Scanning electron microscopy (SEM) showed that the SBM group had a greater microvilli density than the RSM and FRSM groups. Severe hepatic pathological changes were observed in the RSM group, whereas hepatic damage was notably alleviated in the FRSM group. LEfSe analysis identified the Ruminococcus torques group as a distinctive biomarker in the FRSM group, showing significant enrichment relative to both the SBM and RSM groups. RSM induced significant transcriptomic alterations in the intestine and liver, characterized by increased oxidative stress, metabolic dysfunction, and activation of inflammatory pathways. FRSM transformed these responses by enhancing autophagy, lipid metabolism, and cellular repair mechanisms, indicating a protective and regenerative effect. Quantitative PCR analysis validated the expression trends detected in the omics. In conclusion, dietary supplementation with FRSM may alleviate intestinal and hepatic injuries induced by high‐level RSM inclusion, potentially through gut–liver axis modulation, enrichment of Ruminococcus torques group , and activation of autophagy‐related pathways.