Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss)

Authors: BROWN, RYAN - University Of New Mexico; Wiens, Gregory - Greg; SALINAS, IRENE - University Of New Mexico

Submitted to: Fish and Shellfish Immunology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2018
Publication Date: 12/1/2018
Citation: Brown, R., Wiens, G.D., Salinas, I. 2018. Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss). Fish and Shellfish Immunology. 86:497-506. https://doi.org/10.1016/j.fsi.2018.11.079.
DOI: https://doi.org/10.1016/j.fsi.2018.11.079

Interpretive Summary: Animals have microbes associated with mucosal surfaces and these microbes are collectively referred to as the host-associated microbiome. It is not clear in fish, whether host genetics influence the gut and gill microbiomes. For these studies, we used two genetic lines of rainbow trout that differ in their resistance to challenge with bacterial cold water disease agent, Flavobacterium psychrophilum. In fish reared under similar conditions, gill tissue and mid-gut tissue were sampled, and associated microbes were identified by sequencing the bacterial 16S gene. The resistant line exhibited fewer bacterial species and lacked potentially disease-associated microorganisms Brevinema sp. and Enterobacteriaceae members. The gill microbiomes did not differ between genetic lines. These data suggest that host genetics as well as rearing condition may influence the fish gut associated microbiome.

Technical Abstract: Commensal microorganisms present at mucosal surfaces play a vital role in protecting the host organism from bacterial infection. There are multiple factors that contribute to selecting for the microbiome, key of which are host genetics. Flavobacterium psychrophillum, the causative agent of Bacterial Cold Water Disease in salmonids, accounts for acute losses in wild and farmed Rainbow Trout (Oncorhynchus mykiss). The U.S. National Center for Cool and Cold Water Aquaculture has used family-based selective breeding to generate a line of rainbow trout with enhanced resistance to F. psychrophilum. The goal of this study is to determine whether selective breeding impacts the gut and gill microbiome of the F. psychrophilum-resistant as compared to a background matched susceptible trout line. Mid-gut and gill samples were collected from juvenile fish (mean bwt 118g) and microbial diversity assessed by 16S rDNA amplicon sequencing. Results indicate that alpha diversity was significantly higher in the mid-gut of the susceptible line compared to the resistant line, while no significant differences in alpha diversity were observed in the gills. Mycoplasma sp. was the dominant taxon in the mid-gut of both groups, although it was present at a decreased abundance in the susceptible line. We also observed an increased abundance of taxa that could potentially be pathogenic in the susceptible line, including Brevinema sp. and Enterobacteriaceae members. Within the gills, both lines exhibited similar microbial profiles, with Candidatus Branchiomonas being the dominant taxon. Together, these results suggest that selectively bred Flavobacterium psychrophillum-resistant trout may harness a more resilient gut microbiome, attributing to the disease resistant phenotype, providing a framework for future experiments.