PhD Studentship: Detecting and Tracking Low Abundant Pathogens Using 3rd Gen Sequencing

Primary supervisor - Dr Falk Hildebrand

Microbial communities consist of thousands of species, some abundant but most actually very rare. Such rare microbes are underrepresented in metagenomic sequencing and therefore little researched. Within the Hildebrand group we love looking at these – largely ignored – microbes, because they are largely unexplored  and often play key roles in health and disease. In this 4-year PhD project, the applicant will develop novel protocols to increase our genetic resolution of three key patogenic groups: Listeria (causative of listeriosis), Enterobactericeae (including pathogens such as Klebsiella, Enterobacter, Citrobacter, Salmonella, Escherichia coli, Shigella) and Canida albicans (causing candidiasis infections). The project will rely on CRISPR-CAS9 systems and 3rd generation (Oxford Nanopore) sequencing.

During this PhD you will learn about complex molecular biology techniques, metagenomics, bioinformatics, and microbial ecology. The project is directly related to human health and wellbeing, looking not only at detecting & preventing listeriosis, but also investigating how health-promoting microbes can be inherited in families, and how they evolve and adapt during this process.

The ideal candidate will enjoy science and be very curious about biology, want to develop wetlab protocols and have an interest in strengthening their computational skills (R and Linux). We will teach different flavours of metagenomic sequencing, and how to analyse and interpret this data using bioinformatics. Visiting international conferences and training courses as well as a planned 3-month exchange with collaborators are part of student training.

The candidate will be supervised by Dr Hildebrand, Prof Nieduszynski and Dr Gilmour (Quadram and Earlham Institutes) in Norwich. Both Institutes are part of the large, multinational Norwich Research Park (NRP), that hosts a vibrant and active research community adjacent to the University of East Anglia (UEA). Norwich is a mid-sized historical, medieval city with a large student community, situated at the Norfolk coast.

For further information visit: 
https://www.falk.science
https://quadram.ac.uk/leading-canadian-microbiologist-joins-quadram-institute/
https://www.earlham.ac.uk/profile/conrad-nieduszynski

The Microbes, Microbiomes and Bioinformatics (MMB) Doctoral Training Partnership (DTP) is open to UK and International candidates with relevant undergraduate degrees for entry in October 2024 and offers the opportunity to undertake a fully-funded 4-year PhD research project supported by the UKRI Medical Research Council in microbiology and microbial bioinformatics.

Our unique and comprehensive training programme empowers students to feel comfortable running sophisticated computer analyses alongside laboratory work and emphasises problem-based learning in microbial bioinformatics, professional development and research skills. All MMB DTP students undertake a Professional Placement.

Interviews for shortlisted candidates will take place on Wednesday 15 May 2024.

The MRC DTP is committed to equality, diversity and inclusion. Students are selected without regard to age, disability, gender identity, marriage or civil partnership, pregnancy or maternity, ethnicity, religion or belief, sex or sexual orientation or social background. We value curiosity, independence of thought, plus an aptitude for research that combines laboratory work and bioinformatics.

For information on eligibility and how to apply: www.uea.ac.uk/phd/mmbdtp

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