GENOMICS INSIGHTS INTO HOST- MICROBIAL INTERACTION IN RAINBOW TROUT: POTENTIAL ROLE IN FISH GROWTH, MUSCLE YIELD AND DISEASE RESISTANCE

Abstract

Diverse microbial communities colonizing the intestine of fish contribute to their growth, digestion, nutrition, and immune function. In this study, amplicon-based sequencing was used to study rainbow trout gut microbiota, which are associated with differential growth rates and muscle yield observed in fish breeding programs. For the growth rate study, four full-sibling families were stocked in the same tank and fed an identical diet. Fecal samples from two fast-growing and two slow-growing fish were selected from each family for 16S rRNA microbiota profiling. To determine whether gut microbiota correlated with muscle yield, microbial profiling of fecal samples from 19 fish representing an F2 high-muscle yield genetic line (ARS-FY-H) and 13 fish representing an F1 low-muscle genetic line (ARS-FY-L) were investigated. Beta diversity of the bacterial communities from the growth rate fish samples showed significant variation between breeding families but not between the fast- and slow-growing fish. However, indicator bacteria with functional implications were representative of fast-growth rate. Similarly, microbial assemblages in muscle yield samples indicated that ARS-FY-H fish have higher microbial diversity compared to those of the ARS-FY-L (p<0.05) based on alpha diversity. Meanwhile, beta diversity indicated significant differences in microbial assemblages between the ARS-FY-H and ARS-FY-L (F1,36= 4.7, p<0.05, R2=11.9%). Tax4Fun analyses predicted characteristic functional capabilities of microbial communities in the ARS-FY-H and ARS-FY-L genetic line samples. In another study, RNA-seq of the fish pathogenic bacterium, Flavobacterium psychrophilum (Fp), and its outer membrane vesicles (OMVs) identified sRNAs that potentially target immune genes in the rainbow trout host. qPCR results revealed characteristic reciprocal expression of the sRNAs and their targets in whole-body lysates of rainbow trout resistant (ARS-Fp-R) and susceptible (ARS-Fp-S) genetic lines. Whole transcriptome analyses identified transcripts associated with pathogenesis, including cell lysis, virulence factors, quorum sensing, and biofilm formation. The present studies explore the potential contributions of microbial assemblages to phenotypic variation in important fish traits, muscle accretion, and growth rate. These studies also highlight bacterial small RNA (sRNA) involvement in suppressing host immunity during host-pathogen interaction between Fp and rainbow trout. Identification of genes associated with virulence and cell lysis in Fp might further understanding of the mechanism of pathogenesis during the host-pathogen interaction.