Recent studies highlight the significant role of the gut microbiome in modulating fish growth and nutrient metabolism. Herein, we hypothesize that genetic selection influences gut microbial composition. To explore this, fish were obtained from a breeding program for rainbow trout at the National Center for Cool and Cold-Water Aquaculture (NCCCWA), developed in 2002, that initially selected for growth before shifting to muscle yield. Our study investigates gut microbiome dynamics across fish families selected for fillet yield, using samples from the 2020-year class (3rd-generation families from high (ARS-FY-H) or low (ARS-FY-L) fillet yield genetic lines).
Fecal samples from 60 high-yield (ARS-FY-H) and 58 low-yield (ARS-FY-L) fish were analyzed through shotgun metagenomic sequencing to identify microbial taxa linked to fillet yield, body weight, condition factor, omega-3, fillet color, muscle fiber size, and density.
Alpha diversity Shannon index revealed that ARS-FY-L fish had greater microbial diversity (P< 0.05), while beta diversity (nMDS) showed minimal clustering for muscle yield genetic lines. However, muscle fiber size comparisons found significant differences in alpha diversity (Shannon index p-value = 0.00314) and moderately distinct beta diversity (bray-curtis, P = 0.028, R2 = 17%). We identified bacterial taxa showing differential abundance between fish belonging to the divergent phenotypes. For example, bacterial taxa such as Corynebacterium variabile and Jeotgalicoccus halotolerans were differentially abundant between red and white fillet color fish groups, possibly contributing to desired reddish fillet pigmentation through probiotic functions and carotenoid production.
In conclusion, shotgun metagenomics identified microbial taxa associated with different phenotypes, which may serve as biomarkers for fillet yield and quality traits in rainbow trout.