PhD Studentship: The Dual Role of *E. coli* in Human Health and Disease
Explore the molecular ecology of *E. coli* to understand its transition from gut commensal to deadly pathogen.
Best for:Best for ambitious PhD students with a background in microbiology, genomics, or bioinformatics, eager to bridge computational and experimental research in infectious disease.
Overview
This PhD project investigates the dual role of *Escherichia coli* as a harmless gut microbe and a leading cause of severe infections. Based at the University of Oxford’s Nuffield Department of Medicine, the student will generate high-quality genomic datasets using long-read sequencing to study *E. coli* strain dynamics in patients across a health-to-disease spectrum. By integrating microbiome data with clinical metadata, the project aims to uncover how *E. coli* colonisation patterns influence infection risk. The work spans both computational and wet-lab approaches, offering interdisciplinary training in genomics, bioinformatics, and microbiology. Suitable candidates will thrive in a collaborative environment addressing critical clinical challenges.
What you'll do
- Generate high-quality genomic datasets using long-read sequencing technologies to profile *E. coli* strains in patient samples.
- Develop and apply bioinformatic pipelines for strain deconvolution in metagenomic data to study colonisation dynamics.
- Integrate genomic data with clinical metadata from electronic health records to correlate microbiome profiles with infection risk.
- Conduct *in vitro* experiments to investigate strain-specific colonisation patterns, microbiome interactions, and antibiotic resistance.
- Collaborate with interdisciplinary teams to explore combined microbiome and immunological datasets for translational insights.
- Present findings at national/international conferences and publish results in peer-reviewed journals.
- Contribute to the broader COHORT study’s objectives, including longitudinal faecal sampling and immunological profiling.
Requirements
Degree required: A Master’s degree (or equivalent) in Microbiology, Genetics, Bioinformatics, Computational Biology, or a related discipline.
Degree offered: PhD
Language: English; proficiency suitable for academic research (no formal test score specified).
Instruction: English
- Proven experience in molecular biology techniques (e.g., PCR, DNA sequencing).
- Familiarity with bioinformatics tools for genomic data analysis (e.g., long-read sequencing pipelines).
- Strong computational skills (e.g., programming in Python/R, experience with Linux/Unix systems).
- Ability to work with clinical datasets and electronic health records.
- Experience with *in vitro* experimental techniques (e.g., bacterial culture, antibiotic susceptibility testing).
- Open to UK/EU/International applicants (funding available for Home and International students, subject to securing an NDM studentship).
- No age restrictions, but typical PhD entry requirements apply (e.g., prior academic excellence).
Funding & terms
How to apply
Deadline: 2026-12-01
Applicants must apply directly through the University of Oxford’s DPhil (PhD) application portal for the Nuffield Department of Medicine. Include a CV, academic transcripts, a research proposal (if required), and two references. Shortlisted candidates will be interviewed. For project-specific details, visit the NDM DPhil projects page.
- Curriculum Vitae (CV)
- Academic transcripts (BSc and MSc)
- Two reference letters
- Research proposal (if requested)
- Proof of English proficiency (if applicable)
Contact
Susanna Dunachie· Principal Investigator
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