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Abstract
<p class="first" id="P1">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, including host genetics.
<i>Flavobacterium psychrophilum,</i> the causative agent of Bacterial Cold Water Disease
in salmonids, accounts for acute
losses in wild and farmed rainbow trout (
<i>Oncorhynchus mykiss</i>). 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
<i>F. psychrophilum</i>. The goal of this study is to determine whether selective
breeding impacts the gut
and gill microbiome of the
<i>F. psychrophilum</i>-resistant as compared to a background matched susceptible
trout line. Mid-gut and
gill samples were collected from juvenile fish maintained at high or low stocking
densities 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.
<i>Mycoplasma</i> 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 the potential opportunistic pathogen
<i>Brevinema andersonii</i> in the susceptible line. Within the gills, both lines
exhibited similar microbial
profiles, with
<i>Candidatus Branchiomonas</i> being the dominant taxon. Together, these results
suggest that selectively bred
<i>F. psychrophilum</i>-resistant trout may harness a more resilient gut microbiome,
attributing to the disease
resistant phenotype. Importantly, interactions between host genetics and environmental
factors such as stocking density have a significant impact in shaping trout microbial
communities.
</p>