Characterisation of gut microbiota of farmed Chinook salmon using metabarcoding

Abstract

ABSTRACTWith the growing importance of aquaculture worldwide, characterisation of the microbial flora of high-value aquaculture species and identification of gut flora shifts induced by changes in fish physiology or nutrition is of special interest.Here we report the first metabarcoding survey of the intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and intestinal samples, and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles.Over 1,000 operational taxonomic units (OTUs) were identified within the cohort, providing a first glimpse into the gut microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae.This survey was performed amid a summer heat wave, during which the fish exhibited reduced feeding. Although the sampled fish appeared healthy, they had minimal intestinal content, and the observed intestinal flora may represent the microbiota of fasting and stressed fish. Limited comparison between Mycoplasma and Vibrio sequences from the Chinook salmon gut and published microbial sequences from the intestines of a variety of fish species (including Atlantic salmon) indicated that despite the starvation and temperature variations, the replacement of Vibrio with Mycoplasma is occurring within expected ecological parameters and does not necessarily reflect colonisation by atypical microbes.DATA SUMMARYRaw sequences from Chinook salmon intestinal microbiome 16S survey generated on the Illumina platform are publically available through NCBI Sequence Read Archive (SRA) database:Bioproject PRJNA421844SRA study SRP134829https://www.ncbi.nlm.nih.gov/bioproject/PRJNA421844IMPACT STATEMENTAlthough 16S metabarcoding surveys are becoming routine, little is still known about the microbiota of fish. This is the first survey of the intestinal microbiota of Chinook salmon, a species native to the Pacific Northwest which is farmed in New Zealand and Chile. While most intestinal microbiota studies are performed on faecal material, we directly sampled the intestine epithelium and content.During the time of sampling, the farmed fish population was experiencing stress from a summer heat wave and had little intestinal content. Over 1,000 operational taxonomic units (OTUs) were identified within the intestines of the cohort, providing a first glimpse into the gut microbiota of farmed Chinook salmon.We believe this survey will be of interest not only to those interested in fish biology and aquaculture, but also as an addition to the ongoing debate in the literature on sampling and DNA extraction methods for challenging samples.