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

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。引起微生物群落变化的压力因素，如抗生素暴露，反过来会增加感染的可能性，但对鱼类来说，在这方面几乎一无所知。抗生素，旨在杀死细菌，通过病人和动物使用，通过制造工厂和/或不当处置进入英国淡水，在英国一些地表水和污水处理厂废水/废水中可达到每升微克浓度。抗生素通过抗菌素耐药性(AMR)对人类健康的影响一直是人们关注的焦点，但对抗生素对环境健康的更广泛的环境影响的关注要少得多。这个学生将进行现场和实验室相结合的研究，以促进对自然水域中鱼皮肤和鳃粘膜微生物群的了解，并评估暴露于环境中广泛存在的抗生素如何影响皮肤和鳃微生物群，以及如何影响疾病感染的易感性。挑战这种疾病的两种病原体将是卵菌属寄生腐霉，这是一种淡水生态系统特有的类似真菌的病原体，与全球淡水物种野生种群的减少有关，以及附着在皮肤和/或鳃上的单殖寄生蠕虫，这种寄生虫在鱼类中会产生广泛的适应后果。该项目还将研究鳃和皮肤微生物群中包含的病毒之间的相互作用和抗生素效应。学生将使用现有和尖端测序方法的组合，包括MiSeq和Minion测序(牛津纳米孔)，以描绘微生物(和病毒)群落(16S和元基因组)。鱼类研究物种是低地生态系统功能的基础蟑螂(Rutilus Rutilus)。学生将在专家的指导下和资源丰富的实验室接受非常广泛的技术培训，包括田间生物学、生态毒理学、疾病生物学、分子生物学、进化生态学和遗传学、微生物群、生物信息学和大型复杂数据集的分析。他们将体验不同的机构环境，包括与我们的利益相关者Cefas，在那里，学生还将获得商业环境方面的经验

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