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The interplay between viruses and bacteria in soil and human microbiome

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Closing date: Wednesday 29th May 2024, 23:59)

FUNDING: (October 2024 start - October 2028 finish): 4 year full-time PhD studentship (this covers all university tuition fees and research project costs, plus £19,237/year tax free ‘stipend’ for living expenses)
Open to: UK students only, with at least a 2:1 undergraduate degree (and/or equivalent experience) in a relevant subject area, and with widening access eligibility.
Keywords: genomics, transcriptomics, bioinformatics, microbiome, virology, microbiology, infection, bacterial immunity

We want to recruit an enthusiastic and motivated graduate into our scientific team to explore the microbial ecosystem that underpins global food security and human health. The bacterial component of both soil and human gut microbiomes has been studied extensively in the last few years. However, we would like to understand more about the viruses, known as phages, that infect these bacteria, and likely play an important role in regulating bacterial communities. We also want to look at the diverse intracellular immune mechanisms the bacteria have evolved. Thus, the student will use a range of genomic methods to understand bacterial-viral interactions and test the association of specific viral species with bacterial defence systems.

The successful student will work on collecting soil samples from ecologically different field sites to extract DNA in order to bioinformatically map microbial communities. This result will indicate, for the first time, how viruses replicate within the soil. Sean’s Research Group will provide the student with the skills and support they need to collect and analyse data on these ‘phages’. A great opportunity for anyone interested in bioinformatics, genomics, bacteria, or virology.

Your PhD community


Sean completed a degree at the University of Exeter in Biological Sciences and then a PhD on bacterial resistance. Following post-doctoral research in the US and UK, Sean was awarded a research fellowship to work in New Zealand learning the technique of metagenomics, before arriving in York to become a lecturer in 2023. The University of York is an international leader in infection, microbiology, and disease research with Sean’s group being part of over 12 teams investigating bacterial, viral, and parasitic interactions. Researchers at York work with groups from countries across the world including Brazil, Kenya, and Tanzania.

Sean (and co-supervisor James Chong) have combined expertise in microbial ecology, virology, systems biology, and metagenomics. You will work alongside both groups, including technicians and bioinformaticians who will provide support for the entire duration of your PhD studies. There is also scope to work with a wider research network to collaborate on projects involving the human gut microbiome. As a student at the University of York you will be supported with a Thesis Advisory Panel to keep you on track with data generation, research questions, and writing your thesis. You will be part of an active community of >100 PhD students in the Biology Department, plus >120 postdoctoral scientists and around 30 highly skilled technical staff.

A focus on technical skill development

The successful student will complete field work to collect soil samples, and then use bioinformatic and cell biology tools to understand viral phage activity. In addition to this we will support you to learn a number of key technical skills during your PhD. When you first begin in Sean’s team, existing lecture and workshop teaching in relevant undergraduate subject modules and training courses will be made available, alongside key primary research articles, so that you can develop a theoretical understanding. You will then also have the ability to work in our Technology Facility with experienced technical staff in order to get a practical understanding of the research skills you will need, including bioinformatics and genomic techniques. This support will create a strong mentorship network for you as you start to generate your own data. Additionally, there will be opportunities to liaise with key stakeholders in academia and travel to international conferences.