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The microbiome of Chinook salmon (Oncorhynchus tshawytscha) in a recirculation aquaculture system


Steiner, K and Heasman, K and Laroche, O and Pochon, X and Preece, M and Bowman, JP and Walker, SP and Symonds, JE, The microbiome of Chinook salmon (Oncorhynchus tshawytscha) in a recirculation aquaculture system, Aquaculture, 534 Article 736227. ISSN 0044-8486 (2021) [Refereed Article]

Copyright Statement

2020 Elsevier B.V. All rights reserved.

DOI: doi:10.1016/j.aquaculture.2020.736227


The intestinal microbiome has recently been described for a variety of fish species and has been shown to influence host biology, including physiology, health and behavior. Knowledge of the intestinal microbiome of a species and how it can favorably be modulated to enhance production in different rearing systems is therefore of benefit for farmed fish. Here we describe the microbiome of the digesta (feces) of Chinook salmon (Oncorhynchus tshawytscha) reared in a seawater recirculation aquaculture system (RAS) and compare it to the microbiome found in the surrounding water and feed. The effects of varying lipid levels in three different diets were also investigated. We used high-throughput sequencing of the V3/V4 region of the 16S rRNA gene to determine the microbial community in the different samples. The dominant phyla in Chinook salmon feces were Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria. Most of the taxa dominating feces samples were also present in the surrounding water or feed, suggesting that the microbiome is partially shared with the ambient environment. About 40% of all taxa were only present in feces, indicating that these bacterial taxa were either acquired previously and could belong to the attached, rather than transient, microbiome or were at levels below detection in the surrounding environment but grew well in the gut. Differences among individuals were detected and could suggest host-specific variability, which requires further investigation. Variation in dietary lipid levels did not alter the microbiome among cohorts. Identifying the key bacterial communities in the Chinook salmon gut microbiome will help establish strategies to reliably attain and maintain a healthy gut microbiome in fish reared in RAS systems.

Item Details

Item Type:Refereed Article
Keywords:digesta microbiome, Chinook salmon, RAS, diet, next generation sequencing, 16S rRNA gene, King salmon Oncorhynchus tshawytscha, hatchery, bacteria, feed aquaculture
Research Division:Agricultural, Veterinary and Food Sciences
Research Group:Fisheries sciences
Research Field:Aquaculture
Objective Division:Animal Production and Animal Primary Products
Objective Group:Fisheries - aquaculture
Objective Field:Aquaculture fin fish (excl. tuna)
UTAS Author:Bowman, JP (Associate Professor John Bowman)
ID Code:142666
Year Published:2021
Web of Science® Times Cited:12
Deposited By:TIA - Research Institute
Deposited On:2021-02-04
Last Modified:2021-09-28

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