Comparative metagenomic analysis of the gastrointestinal tract of the rainbow trout

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Fish, are one of the most efficient converters of feed into high quality food and increasingly recognised for nutritional and health-promoting qualities. Over the past 40 years, the aquaculture industry has developed, expanded and intensified in line with increasing global population and now produces almost 50% of the world's food fish. In order to maintain high levels of productivity, food security and allow expansion of key areas of the industry, improved fish management and effective disease control is essential. The UK aquaculture industry is diverse, with trout the second largest fish market after salmon and the cost of disease and mortalities estimated at £6 million/annum. The application of improved health management strategies is one of the contributing reasons for the success of the intensification of the UK salmon industry. If the trout industry is to continue to intensify and match this success, a greater insight into the health of the trout and subsequent response to disease is vital.In commercial rainbow trout farming, growth of female fish is preferred as they have faster growth rates and are generally less aggressive than male fish, minimising stress related complications during rearing. Triploid fish are increasingly being farmed for food as they are sterile and therefore minimise reproductive-related production loss. The host and bacterial gastrointestinal (GI) balance is known to play important role in the nutrient acquisition, immune development and tolerance and also disease resistance in fish. This balance forms an integral part of the innate immune defence system of the GI tract and allows differentiation of food particles and pathogenic bacteria from normal bacterial flora. The role that the individual microbe plays in the health and nutrition of fish is still poorly understood, making investigations of the composition of the intestinal microbiota crucial for future health management strategies for the aquaculture industry. Further to this, very little is known about the differences in immune gene expression and GI function in diploid and triploid fish and the role this has in overall fish nutrition and health.The aim of this project is to compare the expression of key immune genes related to GI health in diploid and triploid rainbow trout and to characterise the intestinal microbiota using a combination of culture based and bioinformatic assessments. This will include analysis of the expression of selected host genes and the construction of primary microbial gene catalogue, to determine if there is a difference in the gastrointestinal composition and function between the diploid and triploid species. Objective 1: To identify and characterise the microbiome of the gut in diploid and triploid rainbow trout.Bacterial cell counts and characterisation will be performed on gastrointestinal tissue and DNA isolated for genome sequencing to determine the resident bacterial population within the GI tract. These will be compared to bacteria isolated from water and food samples using typical microbiological tests including antibiotic susceptibility testing. Objective 2: To characterise and identify key immunological markers of the rainbow trout GI tract other key immune tissues.The GI tract, head kidney and spleen will be analysed to determine any differences in expression of immune gene receptors and cytokines which play a crucial role in the early innate response to infection. An understanding of differences in immune function and microbiome composition of the diploid and triploid trout will assist in the development of strategies for better health management of trout, particularly through manipulation of 'healthy' gut bacteria. This will have important implications for the overall health and welfare of farmed fish and is likely to enhance the productivity and sustainability within this industry.