(Meta)genomics of bacteria and antimicrobial resistance from different food production systems (MATHER_Q22DTP2)

Applications Close: 14 February 2022

Salary: Stipend 2021/22 UKRI rate: £15,609pa

Contract Length: 4 years

During the COVID-19 pandemic, sales of organic foods had the biggest year-on-year increase in 15 years. Claims that organic or free-range food is better and healthier for people and the planet may have helped drive this trend, despite sometimes contradictory evidence. Many food production systems, such as organic and free-range, variously include practices to improve animal welfare and reduce or avoid the use of artificial fertilisers, pesticides and antibiotics but what is the underlying evidence? This studentship will further understanding of the microbial pathogens and antimicrobial resistance (AMR) burden in both conventional and non-conventional food production systems.

This multidisciplinary project will utilise comprehensive microbiological and (meta)genomic approaches to understand the microbial pathogens and antimicrobial resistance (AMR) burden, and thus the food safety, of foods produced through organic, free-range and conventional systems. This project will include both wet lab and dry lab components, including study design, culture-based microbiology and both short-read and long-read genome and metagenome sequencing. You will benefit from existing links with policymakers, including the Food Standards Agency, who will have an interest in the results of this work, and from the experience of generating and communicating data for public health action. You will develop skills in state-of-the-art bioinformatics, microbiology, molecular biology and genomic epidemiology.

You will join an interdisciplinary team that will support your training and development. Quadram Institute Bioscience provides a stimulating and supportive environment for research on bacterial genomics, microbiology, and the microbiome, and you will also work with collaborators at the Royal Veterinary College and the Wellcome Sanger Institute. You will have intellectual input into shaping the project and there will be opportunities to collaborate with partners both within and outside the institute to develop further skills and impact of the project.

This project is a Joint-Studentship with the Food Standards Agency.


Janecko, N.†, Bloomfield, S.J.†, Palau, R. and Mather, A.E. (2021) Whole genome sequencing reveals great diversity of Vibrio spp in prawns at retail. Microb. Genom. doi: 10.1099/mgen.0.000647.

†authors contributed equally

de Oliveira Martins, L., Bloomfield, S.J., Stoakes, E., Grant, A.J., Page, A.J. and Mather, A.E. (2021) Tatajuba – exploring the distribution of homopolymer tracts (preprint). https://biorxiv.org/cgi/content/short/2021.06.02.446710v1.

Mellor, K.C., Petrovska, L., Thomson, N.R., Harris, K., Reid, S.W.J. and Mather, A.E. (2019) Antimicrobial resistance diversity suggestive of distinct Salmonella Typhimurium sources or selective pressures in food-production animals. Front Microbiol. doi: 10.3389/fmicb.2019.00708.

Entry Requirements

Candidates for academic admission to a doctoral degree at UEA and for entry to the NRPDTP programme must have obtained (or be about to obtain), a First or Upper Second-class UK Honours degree, or qualifications gained outside the UK that are considered to be equivalent. Applicants with a Lower Second-class degree will be considered if they also have a Master’s degree, or have significant research or non-academic experience relevant to the proposed field of research. Studentships awarded based on predicted grades will be conditional upon final results.

English Language requirement (UEA Faculty of Science equivalent: IELTS 6.5 overall, 6 in each category).


NRPDTP studentships are funded by the UK Research and Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) and the NRPDTP Partners. Studentships are funded for 4 years.

• University of East Anglia (UEA) tuition fees paid directly to the University
• A student stipend to cover living expenses for each year of study* at the UKRI national minimum rate (2021/22 stipend is £15,609 )
• A Research Training Support Grant (£5,000 per annum)*
• PIPS or CASE placement costs

More information on eligibility and funding can be found here.

About The Norwich Research Park Biosciences Doctoral Training Partnership (NRPDTP)

The Norwich Research Park Biosciences Doctoral Training Partnership (NRPDTP) is open to UK and international candidates for entry October 2021 and offers postgraduates the opportunity to undertake a 4-year PhD research project whilst enhancing professional development and research skills through a comprehensive training programme. You will join a vibrant community of world-leading researchers. All NRPDTP students undertake a three-month professional internship placement (PIPS) during their study. The placement offers exciting and invaluable work experience designed to enhance professional development. Full support and advice will be provided by our Professional Internship team. Students with, or expecting to attain, at least an upper second class honours degree, or equivalent, are invited to apply.

Shortlisted candidates can expect to be interviewed on 15th March 2022.

Shortlisted candidates will be notified of their interview times by email by no later than 9 March 2022.

Visit our website for further information on eligibility and how to apply: https://biodtp.norwichresearchpark.ac.uk/

Our partners value diverse and inclusive work environments that are positive and supportive. Students are selected for admission without regard to gender, marital or civil partnership status, disability, race, nationality, ethnic origin, religion or belief, sexual orientation, age or social background.