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，英国目前约为17万吨，每年为英国经济带来约10亿英镑的价值。英国大部分鲑鱼养殖业位于苏格兰，占苏格兰食品出口的40%以上。三文鱼养殖是一个不断增长的食品工业部门，苏格兰有雄心到2020年将其产量增加50%。这种增长的一个主要瓶颈是提供不会对鲑鱼健康产生不利影响的高质量饲料。鲑鱼是食鱼的，传统的鲑鱼饲料依赖于野生来源的鱼蛋白和鱼油，不再能满足全球水产养殖业的需求。为了克服这一不足，植物蛋白和植物油被用来取代水产养殖饲料中的野生鱼类。这种替代存在许多主要问题和限制，包括营养消化率降低、肠道炎症、肠道微生物失衡和对病原体的抵抗力受损。在这个项目中，我们将对大西洋鲑鱼和用鱼粉和植物性饮食喂养的斑马鱼模型进行一系列实验，以了解这些不同的饮食如何塑造早期肠道发育，免疫功能和肠道微生物群之间的关系。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，并且已经建立了许多先进的实验技术，包括无菌幼虫的产生，荧光标记细菌定殖的幼虫的实时成像以及荧光蛋白标记炎症细胞的鱼的产生。目前这些技术都不适用于鲑鱼或其他养殖鱼类。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群的丰度和多样性。肠道微生物群的多样性将由最先进的下一代16S rRNA测序确定。对肠道健康至关重要的是建立一个平衡的肠道微生物群，这通常发生在第一次进食时。在这个阶段，肠道免疫系统还不成熟，允许共生细菌在肠道中定植。我们将使用斑马鱼来研究这些早期生命事件，主要目标是测试肠道微生物群的操纵是否可以提高对可持续水产养殖饮食的口服耐受性，这些饮食含有高含量的植物蛋白和植物油。因此，用鱼类或植物性饮食喂养的斑马鱼幼虫之间的微生物群交换可能为研究改善养殖鱼类健康和免疫功能的途径开辟新的途径。最后，不同饮食方案的鲑鱼（以及肠道微生物群的相关变化）和具有操纵的肠道微生物群的斑马鱼将暴露于细菌病原体，以确定鱼抵抗感染的能力是否取决于先前的肠道状况和微生物群群落。该项目的重要组成部分将是开发鱼肠道微生物群的分子诊断工具，从而能够快速筛选鱼肠道中的有益和有害细菌。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相关的关键微生物群物种。2）评估肠道微生物群改变肠道功能的能力和肠道微生物群转移的适用性，以提高养殖鱼类对植物性饮食的口服耐受性。3）开发检测微生物群物种的测定方法，可用于创建肠道健康的诊断测试。

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.