Pathogens past and present - reconstructing historical and ancient host jumps

病原体的过去和现在——重建历史和古代宿主跳跃

• 批准号: 2722992
• 金额: --
• 依托单位: University College London
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2022
• 资助国家: 英国
• 起止时间: 2022 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2722992
• 关键词: Pathogens; past; present; reconstructing; historical

Over the past decades, the rapid development of techniques optimised to sequencethe DNA of post-mortem, museum, and archaeological specimens, termed 'ancientDNA sequencing', has provided unprecedented opportunities to recover genomes of amultitude of species at specific points in their evolutionary history. Identification of thegenomes of microbes within ancient DNA can pinpoint when a pathogen first started tocirculate in a species, inference of past transmissions and identification of genomicdeterminants of host-adaptation and infectivity. Such observations can be combinedwith contemporary clinical and veterinary infection data in an analytical frameworkthat unveils the path to host-microbe associations today. This PhD project will harnessthe unique potential of combining ancient and modern microbial genomic data toaddress major questions including: i) How has the spread of microbes betweenhumans and other animals been maintained or changed over history? ii) What is thedirection of transmission of major microbes associated to humans and animals? iii)What genomic features are enriched in pathogens infecting specific hosts and whendid they evolve? During the PhD, the student will screen published and newlygenerated data obtained from a range of historic and archaeological material toinclude key zoonoses of humans and swine (eg. Salmonella. Erysipelothrix, Yersinia)and other relevant domesticates spanning the Neolithic through to present. Using skillsinitially learned during the rotation project, analyses will be applied includingmetagenomic classification, population genetics and phylogenetic tip-dating. Usingpan-genome reconstruction methods, proteins correlated with changing hosts will beidentified as putative adaptive mechanisms including estimation of when they evolved.Results will be contextualised via collaboration with archaeologists, epidemiologists,and microbiologists. Taken together, this PhD will take advantage of the expandingtoolkit of ancient genomics to address the contemporary challenge of zoonotic diseasefrom a novel historic perspective.

在过去的几十年中，被称为“古代DNA测序”的后验尸，博物馆和考古标本的测序DNA的快速发展，为在其进化史上在特定点上恢复了物种的娱乐基因组提供了前所未有的机会。鉴定古代DNA中微生物的基因组时，当病原体首次开始在某个物种中循环，推断过去的传播以及宿主适应性和感染性基因组确定性的鉴定时，可以确定。在分析框架中，可以将这些观察结果与当代临床和兽医感染数据相结合，这是今天揭示了宿主 - 微生物关联的途径。这个博士学位项目将利用将古代和现代微生物基因组数据结合起来的独特潜力，包括：i）在历史上，人类和其他动物之间的微生物和其他动物之间的传播是如何维持或改变的？ ii）与人类和动物相关的主要微生物的传播是什么？ iii）在感染特定宿主的病原体中，哪些基因组特征富含它们？在博士学位期间，该学生将筛选出从一系列历史和考古材料获得的新生命的数据，包括人类和猪的关键人畜共患病（例如沙门氏菌。Erysipelothrix，Yersinia，Yersinia）和其他相关的家乡，跨越了新石器时代。在旋转项目期间，将使用以技巧学习的方式进行分析，包括元素元素分类，种群遗传学和系统发育尖端约会。使用PAN基因组重建方法，将与变化的宿主相关的蛋白质将被视为推定的自适应机制，包括估算何时进化的估计。通过与考古学家，流行病学家和微生物学家的合作，将会对其进行上下文化。综上所述，该博士将利用古代基因组学的扩展台球，从一种新颖的历史观点来解决人畜共患病的当代挑战。