Susanna Dunachie

[Funding minimum: Home fees student. Funding maximum: International student subject to gaining an NDM studentship.] PhD Studentship at the University of Oxford focused on understanding the double life of Escherichia coli as both a benign gut commensal and a deadly pathogen. This project, based at the John Radcliffe Hospital , forms part of the wider COHORT study led by Professor Susanna Dunachie in collaboration with the Oxford Vaccine Group and the Ellison Institute of Technology . The COHORT study investigates immune responses to E. coli across a spectrum from health to disease, while COHORT-Microbiome adds longitudinal faecal sampling to examine how microbiome profiles change over time in the same participants. The successful student will generate high-quality genomic datasets using long-read sequencing facilities, link them to rich clinical metadata from electronic healthcare records, and apply bioinformatic methods for strain deconvolution in long-read metagenomic samples. The aim is to identify how E. coli colonises and persists in the gut, how this relates to infection risk, and whether particular strains are more likely to cause invasive disease. The project combines wet-lab and dry-lab research. In addition to computational analysis, there may be opportunities for in vitro experiments to explore interactions between colonisation dynamics, microbiome background, and antibiotic exposure . There may also be collaborative analyses integrating microbiome and immunological datasets. This is a strong fit for an ambitious doctoral student interested in microbiology, microbial genomics, microbiome science, and infectious disease , especially someone who wants to work in an interdisciplinary setting with both experimental and computational components. Funding : the advert states funding minimum for a Home fees student and funding maximum for an International student , subject to gaining an NDM studentship . Deadline : 1 December 2026. Apply via the project page and follow the Oxford application process for the DPhil project.