Dynamic interactions of fish skin microbiomes with their aquatic environments and the impacts of antibiotic exposures in aquaculture

微生物群(与宿主相关的微生物)是人类和动物健康的基本组成部分。导致微生物群落变化的应激源与人类疾病和感染的增加有关，但对鱼类来说，在这方面几乎一无所知。水产养殖提供了全球约8%的动物食品蛋白，对低收入、粮食短缺国家的粮食安全至关重要，但受到疾病的阻碍，每年损失巨大(超过60亿美元)。在水产养殖中防治这些疾病的努力包括自由使用抗生素(估计全球抗生素的水平为数十万吨)，但这些抗生素也可能导致微生物群落发生变化，这些微生物群落聚集在鱼类的外表面(和肠道)，并为疾病感染提供重要的障碍。这门课程将利用最新的DNA测序技术，并与包括环境、渔业和水产养殖科学中心在内的主要利益相关者和全球组织世界鱼类合作，努力帮助了解抗生素如何影响罗非鱼(世界第二大养殖鱼种，670万吨)的皮肤和鳃表面微生物组合，以及这些变化对抗病的影响。学生将首先通过其中一个合作伙伴(世界鱼类)牵头的重大疾病监测项目中收集的样本，表征孟加拉国养殖场的无病罗非鱼的皮肤和鳃微生物群。然后，他们将在埃克塞特、卡迪夫和塞法斯的合作实验室进行一系列实验室研究，以调查与非暴露社区相比，罗非鱼养殖中使用的抗生素暴露是如何重塑微生物群的，以及微生物群的这些变化是否改变了罗非鱼养殖中一些关键致病微生物对感染的易感性。这项工作的另一个也是重要的组成部分将研究细菌的自然病毒的存在是否可以减轻由于噬菌体和抗生素耐药性的竞争适应成本而导致的微生物群的变化。学生将获得出色的多学科培训，发展广泛的尖端分子、生态毒理学、疾病生物学、生物信息学和统计方法的技能。他们将得到经验丰富、资源充足的团队的支持，并包括主要利益相关者的参与。它们还将被整合到埃克塞特新成立的可持续水产养殖未来中心，并获得进一步的支持和网络利益。

Microbiomes (the microbes associated with a host) are a fundamental component of human and animal health. Stressors that induce shifts in microbial communities have been associated with increased disease and infection in humans, but almost nothing is known in this regard for fish. Aquaculture supplies approximately 8% of global animal food proteins and is vital for food security in Low Income, Food Deficit Countries but is hampered by disease with huge annual losses (exceeding >$6bn). Attempts to combat these diseases in aquaculture include the liberal use of antibiotics (at levels estimated in the hundreds of thousands on tonnes globally) but these antibiotics may also induce shifts in microbial communities that populate external facing (and gut) surfaces in fish and provide important barriers to disease infection. This studentship will harness the latest DNA sequencing technologies and in partnership with key stakeholders including Centre for the Environment, Fisheries, and Aquaculture Sciences, and the global organisation WorldFish, work to help understand how antibiotics affect skin and gill surface microorganism assemblages of tilapia (the second largest farmed fish species in the world; 6.7 million tonnes) and the implications of these changes for disease resistance.The student will first characterise skin and gill microbiomes in disease free tilapia from farm sites in Bangladesh through samples collected in a major disease surveillance project lead by one of the partners (WorldFish). They will then undertake a series of laboratory studies at Exeter, Cardiff and Cefas partner laboratories to investigate how exposure to antibiotics used in tilapia farming re -shapes the microbiome compared to non-exposed communities and whether these shifts in the microbiome alter susceptibility to infection to some of the key disease causing organisms in tilapia culture. An additional, and important component of this work will study whether presence of natural viruses that bacteria can mitigate antibiotic driven microbiome shifts due to competing fitness costs of phage and antibiotic resistance.The student will acquire outstanding multidisciplinary training, developing skills in a wide range of cutting edge molecular, ecotoxicology, disease biology, bioinformatics and statistical methods. They will be supported through a highly experienced and well resourced team and including major stakeholder engagement. They will also be integrated into the newly established centre for Sustainable Aquaculture Futures at Exeter with further support and network benefits.