Comparative metagenomic analysis of the gastrointestinal tract of the rainbow trout

虹鳟鱼胃肠道的比较宏基因组分析

• 批准号: 1644442
• 金额: --
• 依托单位: University of Nottingham
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-1644442
• 关键词: Comparative; metagenomic; analysis; gastrointestinal; tract

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.

鱼类是将饲料转化为高质量食物的最有效的转化器之一，并且越来越多地被认为具有营养和促进健康的品质。在过去的40年里，水产养殖业随着全球人口的增长而发展、扩大和加强，现在生产了世界上近50%的食用鱼。为了保持高水平的生产力、粮食安全和扩大渔业的关键领域，必须改善鱼类管理和有效控制疾病。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，疾病和死亡的成本估计为每年600万英镑。改进健康管理策略的应用是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发展并取得同样的成功，那么更深入地了解鳟鱼的健康状况以及随后对疾病的反应至关重要。在商业虹鳟鱼养殖中，雌性鱼的生长是首选，因为它们的生长速度更快，而且通常比雄性鱼攻击性更低，从而最大限度地减少饲养过程中与压力相关的并发症。三倍体鱼越来越多地被养殖作为食物，因为它们是不育的，因此最大限度地减少了与繁殖相关的生产损失。宿主和细菌胃肠道（GI）的平衡在鱼类的营养获取、免疫发育和耐受性以及抗病性中起着重要作用。这种平衡形成了胃肠道先天免疫防御系统的组成部分，并允许将食物颗粒和致病菌与正常细菌植物群区分开来。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，关于二倍体和三倍体虹鳟鱼的免疫基因表达和GI功能的差异以及这在整体鱼类营养和健康中的作用知之甚少。本项目的目的是比较二倍体和三倍体虹鳟鱼中与GI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监测肠道微生物群。这将包括分析所选宿主基因的表达和构建主要微生物基因目录，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。目标一：为了识别和鉴定二倍体和三倍体虹鳟鱼肠道的微生物组，将对胃肠道组织和分离用于基因组测序的DNA进行细菌细胞计数和表征，以确定胃肠道内的常驻细菌种群。这些细菌将与使用典型微生物测试（包括抗生素敏感性测试）从水和食物样本中分离的细菌进行比较。目标二：为了鉴定虹鳟鱼胃肠道其他关键免疫组织的关键免疫学标志物，将分析胃肠道、头肾和脾脏，以确定免疫基因受体和细胞因子表达的任何差异，这些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的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策略，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。