Gut microbiota of farmed Chinook salmon (Oncorhynchus tshawytscha)

The fish gut microbiota plays vital roles in digestion, growth, immunity and resistance against invasive pathogens. In the past decades, high throughput next-generation sequencing has increased our understanding of the diversity and complexity of finfish gut microbial communities and their relationship with health and disease. However, our knowledge of Chinook salmon gut microbiota is limited. Here the multiple effects of biotic and abiotic factors on the gut microbiota of Chinook salmon farmed in New Zealand were evaluated by analysing the 16S rRNA gene V1-V3 region. Furthermore, the relationship between the gut microbiota and fish health and growth performance was determined. In chapter 2, investigations were conducted on the effects of salinity, temperature, farming location and fish age on the gut microbiota of Chinook salmon sourced from five commercial farms. Significant differences in gut microbial diversity and composition were observed between freshwater and saltwater farmed Chinook salmon. Fish age was more influential than the water temperature and farming location on gut microbial diversity within each ecosystem (freshwater and marine) of farmed Chinook salmon. In chapter 3, the effects of feed ration and temperature on Chinook salmon gut microbiota together with the feed and water microbiota in freshwater recirculating aquaculture systems (RAS) were evaluated. Microbial communities in the gut significantly differed from those in water and feed, especially with a high relative abundance of Photobacterium. Gut microbial composition and diversity were not affected by either feed ration or temperature changes, whereas temperature significantly affected the water microbiota. In chapter 4, a continuing investigation of the gut microbiota of Chinook salmon farmed in freshwater RAS was conducted and further determination of the relationship between the gut microbiota and fish health and growth was performed. The dominant gut microbiota shifted from Firmicutes to Proteobacteria. A potential microbial dysbiosis was detected in the gut of freshwater Chinook salmon with fluid in their swim bladders. In chapter 5, research moved to investigate the gut microbiota of Chinook salmon in saltwater RAS and evaluate the fish family genetic effects on the gut microbial diversity and composition and its association with fish growth, feed intake and feed conversion efficiency. In contrast to Chinook salmon raised in freshwater RAS, Firmicutes was the most abundant phylum in salmon in saltwater RAS. Significant variations in terms of gut microbial diversity and composition were found in salmon with different genetic backgrounds, while the effect of host family divergence on gut microbial diversity attenuated at the later stage of the experiment when the growth and feed consumption of the fish varied. Overall, results from this thesis provide fundamental knowledge of the gut microbiota of farmed Chinook salmon in New Zealand and its association with fish health. It has implications for developing strategies to improve Chinook salmon growth performance and productivity by using beneficial strains, as well as gaining a deeper understanding of gut microbial characteristics in teleost fish.