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University of Oxford

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PhD Studentship in E. coli Genomics, Microbiome, and Infection Risk at the University of Oxford University of Oxford in United Kingdom

Degree Level

PhD

Field of study

Computer Science

Funding

Funding minimum: Home fees student. Funding maximum: International student, subject to gaining an NDM studentship.

Deadline

Dec 1, 2026

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Country

United Kingdom

University

University of Oxford

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Keywords

Computer Science
Biology
Infectious Disease
Medical Science
Salud Pública
Disease Ecology
Microbiome Research
Long-read Sequencing
Genomic
Statistics
Bioinformatic

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About this position

PhD Studentship at the University of Oxford in Oxford, England, focused on the double life of E. coli as a benign commensal and a deadly pathogen.

The project is part of the COHORT-Microbiome study, in collaboration with the Oxford Vaccine Group and the Ellison Institute of Technology. It is led within a team associated with Prof Susanna Dunachie and aims to understand how E. coli strains colonise and persist in the gut, and how this relates to future invasive infection risk.

The student will generate high-quality genomic datasets using long-read sequencing, combine these with clinical metadata from electronic health records, and apply bioinformatic methods for strain deconvolution in long-read metagenomic samples. The work will compare patients at risk of invasive disease with healthy controls and explore the ecology of E. coli within the wider microbiome.

There may also be opportunities for in vitro laboratory studies to test hypotheses about strain colonisation dynamics, microbiome background, and antibiotic exposure, plus collaborative analysis of microbiome and immunological datasets.

This studentship is suitable for an ambitious candidate who wants to build skills across both wet lab and dry lab research in an interdisciplinary clinical microbiology setting. Funding is stated for Home fees students, with international students possible subject to gaining an NDM studentship.

Deadline: 1 December 2026.

Funding details

Funding minimum: Home fees student. Funding maximum: International student, subject to gaining an NDM studentship.

What's required

Applicants should be ambitious and keen to develop skills across wet-lab and dry-lab work in an interdisciplinary team. The project suits a student interested in genomic datasets, long-read sequencing, bioinformatics, longitudinal microbiome analysis, and in vitro laboratory studies. Funding is listed for Home fees students, with international students possible subject to gaining an NDM studentship.

How to apply

Apply via the jobs.ac.uk listing linked in the post. Review the project details and submit an application through the application portal on that page before the deadline.

More information can be found here

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