Soybean meal (SBM) and soy protein concentrate (SPC) are essential components in salmonid diets as a sustainable alternative to fishmeal (FM). Optimizing the SBM-to-SPC ratio is crucial for reducing feed costs while improving performance. This study aimed to optimize the SBM-to-SPC ratio across two strains of rainbow trout (Oncorhynchus mykiss) to study strain-specific responses through performance, microbiome-gut-liver axis, and mechanistic statistical modeling.
1500 fish (4.2 g) were randomly distributed into 10 treatments (triplicates, 50 fish/tank) following a 2 × 5 factorial design. Two strains (ARS Hagerman vs. Commercial) were fed five diets with varying SBM/SPC ratios: FM (control)- 0% SBM/SPC; 13% SBM/19.5% SPC (M13/C19.5); 23% SBM/13% SPC (M23/C13); 34% SBM/6.5% SPC (M34/C6.5); and 45% SBM/0% SPC (M45/C0); at apparent satiation twice daily for eight weeks. Growth performance showed a significant (p < 0.05) ‘Strain × Diet’ interaction, with M34/C6.5 diet matching FM, and M45/C0 diet reducing performance. The Commercial strain had superior feed utilization, but the Hagerman strain showed higher feed intake. The FM diet exhibited higher whole-body lipid and energy content. Distal intestinal histology indicated that high-SBM extreme (M45/C0) affected the gut barrier and increased goblet cell density. SBM/SPC ratios reshaped the gut microbiome and functions. High SBM shifted communities away from Bacillota and downshifted central carbohydrate pathways (glycolysis/TCA/PPP), whereas M34/C6.5 diet preserved an FM-like response. A strong correlation exists between gut microbial composition, gut histology, and the gut-liver axis genes. The mechanistic modeling, ordinary least squares (OLS), integrated multiple responses within the microbiome-gut-liver axis, supporting a ‘diet → intestinal barrier → performance’ pathway (Figure 1). Conclusively, the OLS modeling suggests that a stronger gut barrier status is associated with better fish performance. Reducing SPC from 19.5% to 6.5% with an SBM increment from 13% to 34% showed similar performance to the FM-based diet.