Gut health and immune function: the emerging role of gut microbiota in sustainable aquaculture

全球鲑鱼产量约为150万吨，其中英国目前约为17万吨，每年对英国经济的价值约为10亿GB。英国大部分三文鱼水产养殖业位于苏格兰，占苏格兰全部食品出口的40%以上。三文鱼养殖业是一个不断增长的食品工业部门，苏格兰的雄心是到2020年将其产量提高50%。这一增长的一个主要瓶颈是提供不会对鲑鱼健康造成不利影响的高质量饲料。三文鱼是食鱼性的，传统的三文鱼饲料依赖野生来源的鱼蛋白和鱼油，已不能满足全球水产养殖业的需求。为了克服这一不足，在水产养殖饲料中使用植物蛋白和植物油来取代野生来源的鱼。这种替代存在许多主要问题和限制，包括营养物质消化率降低、肠道炎症、肠道微生物失衡和对病原体的抵抗力减弱。在这个项目中，我们将对大西洋鲑鱼和用鱼粉和植物性饲料喂养的斑马鱼模型进行一系列实验，以了解这些不同的饲料如何影响肠道早期发育、免疫功能和肠道微生物区系之间的关系。斑马鱼提供了一个独特的模型来研究这种复杂的关系，因为它们是半透明的，并建立了许多先进的实验技术，包括生成无菌幼虫，用荧光标记的细菌对幼虫进行活体成像，以及用荧光蛋白标记的炎性细胞生成鱼类。这些技术目前都不适用于鲑鱼或其他养殖鱼。通过进行鲑鱼饲养试验，我们将确定植物性饮食如何影响肠道健康(肠道形态和基因表达谱的变化)，以及它们如何改变肠道微生物区系的丰度和多样性。肠道微生物区系的多样性将由最先进的下一代16S rRNA测序决定。肠道健康的关键是建立一个平衡的肠道微生物群落，这经常发生在第一次喂养时。在这个阶段，肠道免疫系统还不成熟，可以由共生细菌物种在肠道上定居。我们将使用斑马鱼来研究这些早期生命事件，关键目标是测试肠道微生物区系的操纵是否提高了对高植物蛋白和植物油含量的可持续水产养殖饲料的口服耐受性。因此，以鱼或植物为基础的饲料喂养的斑马鱼幼体之间的微生物群交换可能为研究改善养殖鱼类的健康和免疫功能的途径开辟新的途径。最后，不同饮食模式的三文鱼(以及肠道微生物区系的相关变化)和肠道微生物区系受到操纵的斑马鱼都将暴露在细菌病原体中，以确定鱼类抵抗感染的能力是否取决于先前的肠道状况和微生物群落。该项目的重要部分将是开发鱼肠道微生物区系的分子诊断工具，使快速筛选鱼肠道中有益和有害的细菌组成为可能。该项目的主要成果包括：1)确定与养殖鱼类(鲑鱼)和模式物种(斑马鱼)的肠道健康和肠道功能障碍有关的关键微生物区系物种。2)评估肠道微生物区系改变肠道功能的能力和肠道微生物区系转移的适用性，以提高养殖鱼类对植物性饲料的口服耐受性。

Global salmon production is ~1.5 million tonnes, with the UK currently at ~170,000 tonnes, which is worth approximately £1 billion to the UK economy annually. The majority of UK salmon aquaculture is located in Scotland and it represents over 40% of all Scottish food exports. Salmon farming is a growing food industry sector and Scotland has an ambition to increase its production by 50% by 2020. A major bottleneck of this growth is the provision of high quality feed that does not adversely impact salmon health. Salmon are piscivorous and traditional salmon feeds rely on wild sources of fish protein and fish oil that can no longer meet the demand from the global aquaculture industry. To overcome this shortfall, plant proteins and vegetable oils are being used to replace the wild sourced fish in aquaculture feeds. There are a number of major problems and constraints associated with this replacement, including reduced nutrient digestibility, gut inflammation, gut microbial imbalance and impaired resistance to pathogens. In this project, we will perform a series of experiments on Atlantic salmon and a zebrafish model fed with fish meal and plant-based diets to understand how these different diets shape the relationship between early intestinal development, immune function and gut microbiota. Zebrafish provide a unique model to study such a complex relationship because they are translucent and have established many advanced experimental techniques, including generation of germ-free larvae, live imaging of larvae colonised with fluorescent-tagged bacteria and generation of fish with fluorescent protein labelled inflammatory cells. None of these techniques are currently available for salmon or other farmed fish. By performing salmon feeding trial, we will establish how plant-based diets affect gut health (changes in gut morphology and gene expression profile) and how they change the abundance and diversity of gut microbiota. The diversity of gut microbiota will be determined by the state-of-the-art next-generation sequencing of 16S rRNA. Crucial to intestinal health is the establishment of a well-balanced gut microbiota community, which frequently happens at the time of first feeding. At this stage, the intestinal immune system is not mature and allows colonisation of the gut by symbiotic bacterial species. We will use zebrafish to study these early life events, with the key goal to test whether manipulation of gut microbiota improves the oral tolerance to sustainable aquaculture diets with high inclusion of plant proteins and vegetable oils. Thus, the microbiota swap between zebrafish larvae fed with fish- or plant-based diets may open up new avenues for investigating pathways to improved health and immune function in farmed fish. Finally, both salmon on different dietary regimes (and associated changes in gut microbiota) and zebrafish with manipulated gut microbiota will be exposed to a bacterial pathogen to determine whether the capacity of the fish to fight the infection depends on prior intestinal condition and microbiota community. The important part of the project will be development of molecular diagnostic tools for fish gut microbiota, enabling rapid screening for beneficial and detrimental sets of bacteria in fish guts. The main outputs of the project include:1) Identification of key microbiota species associated with gut health and intestinal dysfunction in farmed fish (salmon) and a model species (zebrafish).2) Evaluation of the capacity of gut microbiota to modify gut function and applicability of gut microbiota transfer to improve oral tolerance of farmed fish to plant-based diets.3) Development of assays for detection of microbiota species, which can be used to create diagnostic tests for gut health.