The oesophageal microbiome in health and disease (PALLEN_Q24MMB)

Primary supervisor – Prof Mark Pallen

Secondary supervisor – Prof Mark Webber

The human oesophagus is home to a complex but poorly understood resident microbial community, the oesophageal microbiome. By analogy with other sites in the gut, this community is predicted to play key roles in health and disease, including influencing progression to oesophageal cancer. However, despite decades of work, microbiologists have only a poor, low-resolution view of this microbial community, making it impossible to assess its role in the maintenance of health across the human lifespan. 

This PhD project will deliver an exciting multidisciplinary exploration of the oesophageal microbiome, bridging the gap between basic science and translational medicine and between laboratory research and advanced computational analyses. 

The student will conduct a pioneering genome-resolved census of the oesophageal microbiome in health and disease, leveraging cutting-edge culturomics, genome sequencing and metagenomics to revolutionize our understanding of this neglected microbial community. 

The student will work in a supportive multi-disciplinary research and clinical environment with—housed under one roof—a strategically funded research institute, with world-leading laboratory, sequencing and bioinformatics facilities and a state-of-the-art Endoscopy Unit, one of the largest in Europe, performing at least 40,000 endoscopic procedures a year. The PhD candidate will work wtihin a multidisciplinary team that includes a clinician, experts in microbial genomics and metagenomics and a core bioinformatician.

The student will gain hands-on experience in collecting and analyzing oesophageal samples, optimising culture of microbes, genome and metagenome sequencing and state of the art bioinformatics analyses to achieve an integrated view of the oesophageal microbiome. Anticipated outcomes include a microbial gene and genome catalogue, the discovery of new microbial species and fresh insights into the microbial biodiversity and ecology associated with disease progression in the oesophagus.

The Microbes, Microbiomes and Bioinformatics (MMB) Doctoral Training Partnership (DTP) is open to UK and International candidates with relevant undergraduate degrees for entry in October 2024 and offers the opportunity to undertake a fully-funded 4-year PhD research project supported by the UKRI Medical Research Council in microbiology and microbial bioinformatics.

Our unique and comprehensive training programme empowers students to feel comfortable running sophisticated computer analyses alongside laboratory work and emphasises problem-based learning in microbial bioinformatics, professional development and research skills. All MMB DTP students undertake a Professional Placement. 

Interviews for shortlisted candidates will take place on Wednesday 15 May 2024.

The MRC DTP is committed to equality, diversity and inclusion. Students are selected without regard to age, disability, gender identity, marriage or civil partnership, pregnancy or maternity, ethnicity, religion or belief, sex or sexual orientation or social background. We value curiosity, independence of thought, plus an aptitude for research that combines laboratory work and bioinformatics.

For information on eligibility and how to apply: www.uea.ac.uk/phd/mmbdtp

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).

Start date

October 2024

Mode of study

Full-time