Investigating how E. coli exploits bacterial competition in the microbiome

About the Project

Project Overview:

E. coli is one of the most significant causes of disease in the world, responsible for >950,000 deaths per year. It can cause outbreaks of severe gastric disease or it can reside harmlessly in the gut before seeding life-threatening infections in other body sites, such as the urinary tract, lungs and bloodstream. To survive in the gut, E. coli has to compete with a dense community of commensal bacteria known as the human gut microbiome. In response to this fierce competition, bacteria have evolved a wide variety of mechanisms to steal nutrients from competitors or inhibit them using toxic proteins. In this project, you will investigate how different competition mechanisms work together on a single plasmid to increase the ability of pathogenic E. coli strains to thrive within the human gut microbiome and cause disease. The finding revealed by this proposed research could suggest novel intervention strategies that prevent serious infections.

In this project you will receive training in experimental microbiology and bioinformatics experimental microbiology and bioinformatics, with receive specific training in:

• Metagenomic analysis
• In vitro gut modelling
• Genetic engineering
• Protein purification
• Statistics and bioinformatics

This PhD project will provide the applicant with training in bioinformatics, genomics, molecular microbiology, protein engineering and experimental evolution. In addition, the project offers an opportunity to research the globally significant problem of antimicrobial resistance.

The Sharp Microbial Ecology Group:

The Sharp group uses a combination of bioinformatics, biochemistry and ecology to understand how bacterial interactions impact pathogen invasion of the gut microbiome and drive disease. The group focusses on the protein weaponry that bacteria can use to compete with each other, uncovering the molecular strategies that determine competitive success and exploiting protein bacteriocins as a platform for developing next‑generation antimicrobials.

School of Biological Sciences, University of Reading:

The University of Reading, located west of London, England, provides world-class research education programs. The University’s main Whiteknights Campus is set in 120 hectares of beautiful parkland, a 30-minute train ride to central London and 40 minutes from London Heathrow airport.

Our School of Biological Sciences conducts high-impact research, tackling current global challenges faced by society and the planet. Our research ranges from understanding and improving human health and combating disease, through to understanding evolutionary processes and uncovering new ways to protect the natural world. In 2020, we moved into a stunning new ~£60 million Health and Life Sciences Building. This state-of-the-art facility is purpose-built for science research and teaching. It houses the Cole Museum of Zoology, a café and social spaces.

In the School of Biological Sciences, you will be joining a vibrant community of ~180 PhD students representing ~40 nationalities. Our students publish in high-impact journals, present at international conferences, and organise a range of exciting outreach and public engagement activities.

During your PhD at the University of Reading, you will expand your research knowledge and skills, receiving supervision in one-to-one and small group sessions. You will have access to cutting-edge technology and learn the latest research techniques. We also provide dedicated training in important transferable skills that will support your career aspirations. If English is not your first language, the University's excellent International Study and Language Institute will help you develop your academic English skills.

The University of Reading is a welcoming community for people of all faiths and cultures. We are committed to a healthy work-life balance and will work to ensure that you are supported personally and academically.

Eligibility:

Applicants should have a good degree (minimum of a UK Upper Second (2:1) undergraduate degree or equivalent) in biology or a strongly-related discipline.

Due to the nature of the funding, this studentship is only open to candidates who are eligible for UK/Republic of Ireland fees. With a commitment to improving diversity in science and engineering, we encourage applications from underrepresented groups.

How to apply:

Submit an application for a PhD in Biomedical Sciences via our online application system.

Please upload a CV and cover letter with your application. If the application system prompts you to submit a research proposal, paste in the project title and move on to the next step.

Please quote studentship reference number DRC26-030 on your application.

Informal enquiries: Dr Connor Sharp: c.sharp@reading.ac.uk

Further information:

https://www.reading.ac.uk/biological-sciences/research

Funding Notes

• Maintenance allowance of £21,805 per year
• UK tuition fees covered
• 3 year studentship
• Starts October 2026

References

Sharp, C., Foster, K.R. Bacterial warfare is associated with virulence and antimicrobial resistance. Nat Commun 16, 9329 (2025). doi: 10.1038/s41467-025-64363-5

Sharp C, Bray J, Housden NG, Maiden MCJ, Kleanthous C. Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models. PLoS Comput Biol. 2017 Jul 17;13(7):e1005652. doi: 10.1371/journal.pcbi.1005652.

Atanaskovic I, Sharp C, Press C, Kaminska R, Kleanthous C. Bacterial Competition Systems Share a Domain Required for Inner Membrane Transport of the Bacteriocin Pyocin G from Pseudomonas aeruginosa. mBio. 2022 Apr 26;13(2):e0339621. doi: 10.1128/mbio.03396-21