Effects of feed ration and temperature on Chinook salmon (Oncorhynchus tshawytscha) microbiota in freshwater recirculating aquaculture systems

Feed ration plays a crucial role in influencing fish growth performance and maintaining optimal gut health over the seasonal temperature range. However, we have limited knowledge of how these factors affect the gut microbiota of Chinook salmon (Oncorhynchus tshawytscha) farmed in freshwater recirculating aquaculture systems (RAS). Here we examined the environmental and faecal microbiota of freshwater Chinook salmon using 16S rRNA gene V1-V3 amplicon sequencing and evaluated the relationship between faecal casts and dominant microflora. Faecal microbial communities were highly stable in terms of composition and diversity regardless of feed ration and temperature changes, whereas temperature significantly affected water microbiota. The composition of faecal microbiota significantly differed from the microbiota of water or feed. The faecal microbiota was dominated by the species Photobacterium piscicola that was more predominant in faecal samples with higher water content (high faecal scores). The relative abundance of lactic acid bacteria (LAB) in the gut was distinctly lower than that in the feed and water. Our study provides detailed information on the complex microbial communities in the freshwater RAS and farmed Chinook salmon. It increases our knowledge of potential linkages between core gut microbiota and gut health, illustrated by the relationship between faecal casts and dominant microflora, and provides useful information for sustainable land-based Chinook salmon aquaculture.