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

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. •Microbiome of Chinook salmon in RAS are different from fish farmed in open pens, but have similar key taxa.•The gut microbiome shares taxa with the environment (water, feed).•Alteration in lipid levels of the diet did not influence the fecal microbiome.•Host genetics might influence the fish microbiome.•Identification of core bacteria in gut microbiome