Characterising the microbial dark matter of the ovine interdigital skin microbiota through bioinformatics and culture-based approaches
Fact file
| Duration |
Three years |
|---|
| Eligibility |
Applicants should have a minimum of a 2.1 undergraduate degree or a minimum of a 2.2 degree and a Master’s degree in Agriculture, Animal Science, Veterinary Science, Nutrition or similar subjects.
This is a fully funded studentship open to UK nationals qualifying for Home fee status. This will be assessed upon application.
|
|---|
| Supervisor(s) |
Rachel Clifton, Adam Blanchard, Laura Randall, and Kate Lewis |
|---|
| Start date |
1st April 2026 or 1st July 2026 |
|---|
| Application deadline |
13th February 2026 |
|---|
About the project
Ovine footrot is the leading cause of lameness in sheep worldwide, severely affecting animal welfare and reducing flock productivity. In the UK, footrot occurs in almost all sheep flocks and costs the industry up to £80 million annually. Footrot is also a major sustainability concern: it accounts for around two thirds of all antibiotics used on UK sheep farms, contributing to antimicrobial resistance and reducing sheep longevity.
High throughput sequencing greatly improved our understanding of the bacterial communities on sheep interdigital skin. However, a major limitation remains: many bacteria detected in these communities cannot be identified using existing reference databases. This unclassified microbial “dark matter” represents a significant gap in knowledge surrounding footrot biology, disease mechanisms, and potential targets for improved control.
This multidisciplinary PhD project will use existing interdigital skin sequencing datasets to uncover previously unknown bacterial species associated with healthy and diseased feet. After identifying candidate novel species through computational analysis, the student will work to culture these bacteria from clinical samples, linking in silico discovery with wet lab validation.
Training and Skills Development
The successful applicant will gain advanced, transferable expertise in:
- Bioinformatics and microbial genomics: genome assembly and annotation from metagenome data, identification of novel species
- Statistical and computational analysis: handling large sequencing datasets, applying modern tools for microbial community profiling and statistical analysis
- Laboratory microbiology: culture based bacterial isolation, genome sequencing of novel isolates
This project suits candidates interested in microbial ecology, animal health, genomics, and computational biology, offering opportunities to contribute to both fundamental science and practical livestock health solutions.
Research Environment
Research at the School of Veterinary Medicine and Science includes established world class research groups. 85% of our research is classed as "world-leading" (4*) or "internationally excellent" (3*) and our research collaborations and networks extend nationally and internationally. Research undertaken at the School is relevant to both Veterinary Medicine and Science, One Health, and Comparative and Human Medicine.
Entry requirements
Applicants should have a minimum of a 2.1 undergraduate degree or a minimum of a 2.2 degree and a Master’s degree in Agriculture, Animal Science, Veterinary Science, Nutrition or similar subjects.
Funding notes
This is a fully funded studentship open to UK nationals qualifying for Home fee status. This will be assessed upon application.
How to apply
Informal enquiries may be addressed to the principal supervisor: rachel.clifton@nottingham.ac.uk
Candidates should and include a CV. When completing the online application form, please select the School of Veterinary Medicine and Science, then PhD Veterinary Medicine and Science (36m) and, once submitted, send your student ID number to SV-PG-VET@exmail.nottingham.ac.uk.
Any queries regarding the application process should be addressed to SV-PG-VET@exmail.nottingham.ac.uk.
Interview Date: 26th February 2026