Understanding and predicting how bacteriophages structure the microbiome

背景：微生物组在人类健康和营养中发挥着重要作用。在更多样化的微生物组中，这些功能的表现预计会更高。因此，微生物群的生态稳定性——尤其是它们从抗生素治疗等扰动中恢复的能力——被认为是它们健康功能的重要预测指标。为了控制和改善微生物组对人类健康的益处，我们首先需要了解控制其结构和稳定性的生态和进化规则（Foster et al. 2017）。噬菌体，感染细菌的病毒，在细菌群落中是普遍存在的，驱动着它们的生态和进化（Koskella & Brockhurst 2014），但噬菌体如何影响人类微生物群的结构和稳定性目前尚不清楚。项目：本项目将探讨噬菌体如何影响人体气道微生物群落的结构和稳定性。具体来说，我们将结合生态学理论（Coyte et al. 2015）和简化的实验群落（Davies et al. 2015）来预测和测试噬菌体对微生物群落结构和稳定性的影响，无论是否有抗生素扰动。然后，我们将使用宏基因组学来跟踪人类呼吸道内噬菌体和细菌的纵向动态（Layeghifard等人，2019），在现实世界和临床相关背景下测试我们的预测。这项研究将促进对人类微生物群生态学和进化的理解。这对于改善微生物组功能（例如，通过微生物组恢复和移植）和了解抗菌治疗（例如抗生素和噬菌体治疗）对人类健康的更广泛影响至关重要。培训和监督：该项目提供广泛的跨学科培训，包括数学和计算建模，微生物学，实验进化，进化生物学，基因组学和生物信息学。管理团队提供微生物组的生态理论（Katherine Coyte, uomchesteruniversity），理解微生物生态学和进化的实验方法（Michael Brockhurst, uomchesteruniversity）以及基因组学方法和生物信息学（David Guttman, utoronto）方面的专业知识。该项目将在曼彻斯特大学进行，并在多伦多大学进行为期12个月的实习，使您能够体验不同的研究环境。你将成为充满活力的研究实验室的一员，与博士后、技术人员和学生一起研究微生物进化和生态学的相关项目，提供一个令人兴奋和支持性的培训环境。

Background: Microbiomes play important roles in human health and nutrition. The performance of these functions is expected to be higher in more diverse microbiomes. Thus, the ecological stability of microbiomes - particularly their ability to recover from perturbations like antibiotic treatment - is believed to be an important predictor of their healthy function. To control and improve the benefits of microbiomes to human health we first need to understand the ecological and evolutionary rules that govern their structure and stability (Foster et al. 2017). Bacteriophages, viruses that infect bacteria, are universal in bacterial communities, driving their ecology and evolution (Koskella & Brockhurst 2014), but how bacteriophages affect the structure and stability of human microbiomes is currently unknown. Project: In this project we will explore how bacteriophages influence the structure and stability of human airway microbiome communities. Specifically, we will use a combination of ecological theory (Coyte et al. 2015) and simplified experimental communities (Davies et al. 2015) to predict and test the impact of bacteriophages on the structure and stability of microbiome communities with or without antibiotic perturbation. Then, we will use metagenomics to track the longitudinal dynamics of bacteriophages and bacteria within human airways (Layeghifard et al. 2019), testing our predictions in a real-world and clinically-relevant context. This research will advance understanding of the ecology and evolution of the human microbiome. This is vital for improving microbiome function (e.g. though microbiome restoration and transplants) and understanding the broader impacts of antimicrobial treatments (e.g. antibiotics and phage therapy) on human health.Training and supervision: This project offers a broad interdisciplinary training, including mathematical and computational modelling, microbiology, experimental evolution, evolutionary biology, genomics and bioinformatics. The supervisory team provides expertise in ecological theory for microbiomes (Katherine Coyte, UoManchester), experimental approaches to understanding microbial ecology and evolution (Michael Brockhurst, UoManchester), and genomics methods and bioinformatics (David Guttman, UoToronto). The project will be based at UoManchester with a 12-month placement at UoToronto enabling you to experience diverse research environments. You will be part of vibrant research labs alongside postdocs, technicians and students working on related projects investigating microbial evolution and ecology, offering an exciting and supportive training environment.