Distinct Microbial Assemblages Associated with Genetic Selection for High- and Low- Muscle Yield in Rainbow Trout

Abstract

Background Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based genetic selection for muscle yield. To test this hypothesis, fecal samples from 19 fish representing an F2 high-muscle genetic line (ARS-FY-H) and 20 fish representing an F1 low-muscle yield genetic line (ARS-FY-L) were chosen for microbiota profiling using the 16srRNA gene. Significant differences in microbial population between these two genetic lines might represent the effect of host genetic selection in structuring the gut microbiota of the host.Results Tukey’s transformed inverse Simpson indices indicated that ARS-FY-H samples have higher microbial diversity compared to those of the ARS-FY-L (LMM, χ2(1) = 14.11, p < 0.05). The fecal samples showed distinct clusters with significant differences in microbial assemblages between the genetic lines (F1,36= 4.7, p < 0.05, R2 = 11.9%). Further, Tax4Fun analyses predicted characteristic functional capabilities of the microbial communities in the ARS-FY-H and ARS-FY-L samples.Conclusion The significant differences of the microbial assemblages between ARS-FY-H and ARS-FY-L indicate an effect of genetic selection on the microbial diversity of the host. The functional composition of taxa demonstrates correlation of the function in improving the muscle accretion in the host, probably, by producing various metabolites and enzymes that might aid in digestion. Further research is required to elucidate the mechanisms involved in shaping the microbial community through host genetic selection.