Composition, diversity and response dynamics of fish skin microbiomes under environmental stress, including antibiotic exposure.

微生物组（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压力源，如抗生素暴露，反过来又会增加感染的可能性，但在这方面对鱼类几乎一无所知。用于杀死细菌的抗生素通过病人和动物的使用，通过制造工厂和/或不当处理进入英国淡水，在英国一些地表水和污水处理厂流出物/废水中的浓度可达到每升微克。人们对抗生素的关注主要集中在抗生素耐药性对人类健康的影响上，但很少关注抗生素对环境健康的影响对更广泛的环境影响。该学生将进行实地和实验室研究相结合的研究，以促进对天然水域中鱼类皮肤和鳃粘膜微生物群的了解，并评估环境中广泛存在的抗生素如何影响皮肤和鳃微生物群，以及这反过来如何影响对疾病感染的易感性。应对疾病挑战的两种病原体将是卵菌（一种在淡水生态系统中特有的真菌样病原体，与淡水物种野生种群的全球下降有关）和附着在皮肤和/或鳃上的单基因寄生蠕虫，它们在鱼类中具有广泛的适应性后果。该项目还将研究鳃和皮肤微生物组中含有的病毒与抗生素效应之间的相互作用。该项目将采用令人兴奋的尖端测序方法，包括MiSeq和MinION测序（牛津纳米孔），以分析微生物（和病毒）群落（16S和宏基因组）。鱼类研究物种是蟑螂（Rutilus Rutilus）在低地生态系统功能中的基础。学生将在专家指导和资源丰富的实验室接受广泛的技术培训，包括野外生物学、生态毒理学、疾病生物学、分子生物学、进化生态学和遗传学、微生物组学、生物信息学和大型复杂数据集分析。他们将体验不同的制度环境，包括我们的利益相关者Cefas，学生也将获得商业环境的经验

Microbiomes (the microbes associated with a host) are a fundamental component of human and animal health. Stressors that induce shifts in microbial communities, such as antibiotic exposure, in turn can increase the likelihood of infection, but almost nothing is known in this regard for fish. Antibiotics, that are designed to kill bacteria, enter UK freshwaters via patient and animal use, through manufacturing plants and/or improper disposal and can reach microgram per litre concentrations in some UK surface waters and sewerage treatment plant effluents/wastewaters. Much attention on antibiotics has been focused on their implications for human health through antimicrobial resistance (AMR) but far less attention has been focused on the wider environmental implications of antibiotic impacts to environmental health.This studentship will undertake a combination of field and laboratory based studies to advance understanding on fish skin and gill mucosal microbiomes in natural waters and assess how exposure to antibiotics that are widespread in the environment affect the skin and gill microbiomes and how, in turn, this affects susceptibility to disease infection. The two pathogens for the disease challenges will be the oomycete Saprolegnia parasitica, a fungal-like pathogen that is endemic to freshwater ecosystems and associated with global declines in wild populations of freshwater species, and monogenean parasitic worms that attach to the skins and/or gills, which have widespread fitness consequences across fishes. The project will also investigate the interactions between the viruses contained in the gill and skin microbiomes and the antibiotic effects. The studentship will employ a combination of exciitng and cutting edge sequencing methods inclduing MiSeq and also MinION sequencing (Oxford Nanopore) for profiling microbial (and viral) communities (16S and metagenomes). The fish study species is the roach (Rutilus rutilus) fundamental in lowland ecosystem function.The student will receive training in an exceptional wide range of techniques, including field biology, ecotoxicology, disease biology, molecular biology, evolutionary ecology and genetics, microbiomes, bioinformatics and the analysis of large complex datasets, under expert tuition and in labs that are very well resourced. They will experience different institutional environments including with our stakeholder Cefas, where the student will also get experience also in the business environment