Abstract
With the growing importance of aquaculture worldwide, characterization of the microbiota of high-value aquaculture species and identification of their shifts induced by changes in fish physiology or nutrition is of special interest. Here we report the first 16S rRNA gene metabarcoding survey of the mid-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 mid-intestinal samples and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles. Over 1000 operational taxonomic units were identified within the cohort, providing a first glimpse into the mid-intestinal 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. We anticipate that the workflow presented in this paper could be applied in other aquacultured fish species to capture variation or dysbiosis occurring as a result of changes in feed, health or environmental conditions.
Highlights
The digestive tracts of all vertebrates harbor complex assemblages of microorganisms, collectively referred to as intestinal microbiota
High throughput partial 16S rRNA gene sequencing has been increasingly employed to investigate changes in the structure of fish intestinal microbial community caused by diet, starvation, pathogens, different lifestyles and water temperature [1,4,5]
Raw sequences from Chinook salmon mid-intestinal microbiome 16S rRNA gene metabarcoding survey generated on the Illumina platform are publicly available through the NCBI Sequence Read Archive (SRA) database
Summary
The digestive tracts of all vertebrates harbor complex assemblages of microorganisms (microbial communities), collectively referred to as intestinal microbiota. The intestinal microbiota is an area of research interest universally applicable to Animalia, but the majority of studies on intestinal microbiota composition and function in vertebrates have been conducted in. The microbial community harbored in fish intestines influences host physiology and is of relevance to aquaculture. During the past few decades, substantial research has been carried out to characterize the intestinal microbiota in a wide range of fish species, focusing primarily on model organisms (i.e. zebrafish) and species relevant to aquaculture. High throughput partial 16S rRNA gene sequencing has been increasingly employed to investigate changes in the structure of fish intestinal microbial community caused by diet (including probiotics), starvation, pathogens, different lifestyles and water temperature [1,4,5]
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