Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss)

Authors: CHAPAGAIN, PRATIMA - Middle Tennessee State University; WALKER, DONALD - Middle Tennessee State University; Leeds, Timothy - Tim; Cleveland, Beth; SALEM, MOHAMED - University Of Maryland

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2020
Publication Date: 10/29/2020
Citation: Chapagain, P., Walker, D., Leeds, T.D., Cleveland, B.M., Salem, M. 2020. Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss). Biomed Central (BMC) Genomics. 20:788. https://doi.org/10.1186/s12864-019-6175-2.
DOI: https://doi.org/10.1186/s12864-019-6175-2

Interpretive Summary: High fillet yield is a performance trait desired by US rainbow trout producers that can positively affect production efficiency and profitability. This trait can be improved by genetic selection but the physiological and metabolic differences between fish with high and low fillet yield are not well understood. To expand knowledge of the fillet yield trait, the gut microbial profile was characterized in genetic lines of rainbow trout characterized by high and low fillet yield. Findings indicate a unique microbial profile associated with each line, indicating that the gut microbiome responds to genetic selection for fillet yield. Microbial differences likely contribute to unique metabolite and enzyme profiles in the gut that affect nutrient metabolism and muscle growth in the host. These findings provide a more extensive understanding of the mechanisms associated with high fillet yield; this knowledge is central for identifying production strategies that further improve this trait.

Technical Abstract: 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 and 13 fish representing an F1 low-muscle yield genetic line 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. Tukey’s transformed inverse Simpson indices indicated that high-muscle yield genetic line samples have higher microbial diversity compared to those of the low-muscle yield genetic line.. The fecal samples showed distinct clusters with significant differences in microbial assemblages between the high- and low- muscle yield genetic lines. Further, Tax4Fun analyses predicted characteristic functional capabilities of microbial communities in the high- and low-muscle yield genetic line samples. The significant differences of the microbial assemblages between high- and low- muscle yield genetic lines 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 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.