Modelling metabolic capability and phylogeny of host and environmental niche adaptation in E. coli (MATHER_Q21DTP)

Applications Close: 23 November 2020

Salary: stipend rate: £15,285

Contract Length: 4 years

The species Escherichia coli is a complex group of organisms which is found in a wide range of vertebrate animal hosts. The ability to colonise a given host is critical for E. coli and will require a different strategies, thus allowing for the evolution of separate lineages adapted to specific hosts. However, the high genetic diversity of E. coli means that detection of this niche adaptation is difficult. Given that there are multiple genotypic pathways to the same phenotypic endpoint, adaptation of E. coli to different host species may be more clearly observed by examination of phenotypes or metabolic pathways.

This multidisciplinary project will define the variation in E. coli from different host species through genomic and phenotypic analysis. A new understanding of bacterial niche adaptation and novel computational tools will be developed. This project will include both wet lab and dry lab components, including growth assays, phylogenetics, and construction of computational metabolic models. You will develop skills in state-of-the-art genomics, bioinformatics, microbiology, and computational biology.

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 One Health researchers at the Royal Veterinary College. 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.


de Oliveira Martins, L., et al., Taxonomic resolution of the ribosomal RNA operon in bacteria: Implications for its use with long-read sequencing. 2020. 2: p. doi: 10.1093/nargab/lqz016.

Mather, A.E., et al., New variant of multidrug-resistant Salmonella enterica serovar Typhimurium associated with invasive disease in immunocompromised patients in Vietnam. MBio, 2018. 9(5).

Seif, Y., et al., Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nat Commun, 2018. 9(1): p. 3771.

Entry Requirements:

At least UK equivalence Bachelors (Honours) 2:1 or UK equivalence Master’s degree. English Language requirement (Faculty of Science equivalent: IELTS 6.5 overall, 6 in each category).


This project is awarded with a 4-year Norwich Research Park Biosciences Doctoral Training Partnership (NRPDTP) PhD studentship. The studentship includes payment of tuition fees (directly to the University), a stipend for each year of the studentship (2020/21 stipend rate: £15,285), and a Research Training Support Grant for each year of the studentship of £5,000 p.a..

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.

This project has been shortlisted for funding by the NRPDTP programme. Shortlisted applicants will be interviewed on Thursday 7th January, Friday 8th January and Monday 11th January 2021.

Visit our website for further information on eligibility and how to apply:

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.