Comparative metagenomic analysis of the gastrointestinal tract of the rainbow trout

鱼类是将饲料转化为高质量食品的最有效途径之一，其营养和促进健康的品质日益得到认可。在过去40年里，随着全球人口的增长，水产养殖业得到了发展、扩大和强化，目前生产了世界上近50%的食用鱼。为了保持高水平的生产力、粮食安全并扩大该行业的关键领域，改进鱼类管理和有效控制疾病至关重要。英国水产养殖业是多样化的，鳟鱼是仅次于鲑鱼的第二大鱼类市场，每年的疾病和死亡成本估计为600万英镑。改进的健康管理战略的应用是促成英国鲑鱼产业集约化成功的原因之一。如果鳟鱼产业要继续加强和匹配这一成功，更深入地了解鳟鱼的健康状况和随后对疾病的反应是至关重要的。在商业虹鳟鱼养殖中，雌性鱼的生长速度更快，通常比雄性鱼更不具攻击性，最大限度地减少了饲养过程中与压力相关的并发症。三倍体鱼越来越多地被用于食用，因为它们是不育的，因此可以最大限度地减少与生殖有关的生产损失。宿主和细菌胃肠道（GI）平衡在鱼类的营养获取、免疫发育和耐受性以及疾病抵抗中起着重要作用。这种平衡形成了胃肠道先天免疫防御系统的一个组成部分，并允许食物颗粒和致病菌与正常菌群的分化。单个微生物在鱼类健康和营养中的作用仍然知之甚少，因此调查肠道微生物群的组成对于水产养殖业未来的健康管理策略至关重要。此外，人们对二倍体和三倍体鱼类免疫基因表达和GI功能的差异及其在鱼类整体营养和健康中的作用知之甚少。该项目的目的是比较二倍体和三倍体虹鳟鱼中与胃肠道健康相关的关键免疫基因的表达，并使用基于培养和生物信息学评估的组合来表征肠道微生物群。这将包括分析选定宿主基因的表达和构建初级微生物基因目录，以确定二倍体和三倍体物种之间的胃肠道组成和功能是否存在差异。目的1：鉴定和表征二倍体和三倍体虹鳟鱼肠道微生物群。将对胃肠道组织和分离的DNA进行细菌细胞计数和表征，以进行基因组测序，以确定胃肠道内的常驻细菌种群。这些将与从水和食品样品中分离的细菌进行比较，使用典型的微生物试验，包括抗生素敏感性试验。目的2：表征和鉴定虹鳟鱼胃肠道及其他关键免疫组织的关键免疫标志物。将对胃肠道、头部肾脏和脾脏进行分析，以确定免疫基因受体和细胞因子表达的差异，这些基因受体和细胞因子在感染的早期先天反应中起着至关重要的作用。了解二倍体和三倍体鳟鱼免疫功能和微生物组组成的差异，将有助于制定更好地管理鳟鱼健康的战略，特别是通过操纵“健康”的肠道细菌。这将对养殖鱼类的整体健康和福利产生重要影响，并可能提高该行业的生产力和可持续性。

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.