Supervisors: 

Main Supervisor: Dr Androniki Psifidi (apsifidi@rvc.ac.uk)

Co-Supervisor: Prof Damer Blake (dblake@rvc.ac.uk), Prof Georgios Banos (Scotland’s Rural College and University of Edinburgh) (georgios.banos@sruc.ac.uk)

Dr. Ankit Hinsu (day to day supervisor) (ahinsu@rvc.ac.uk)

Department: Clinical Science and Services

Project Details:

Campylobacter remains one of the most important foodborne pathogens worldwide, causing millions of human gastroenteritis cases each year. Chickens are the main reservoir, typically carrying the bacteria without symptoms while contributing to contamination throughout the farm‑to‑fork chain. Although management practices and environmental exposure shape colonisation levels, host biology plays a crucial role in determining whether birds become heavily colonised or naturally resistant. Genetic variation, epigenetic regulation, and transcriptional responses influence gut physiology, immune function, and host–microbe interactions, making them key components of resistance. With the growing need for sustainable, antibiotic‑free approaches to improve food safety, understanding these host factors is essential. This project leverages a unique multi‑omics dataset generated through the GCRF‑UKRI One Health Poultry Hub (https://www.onehealthpoultry.org), integrating whole‑genome sequencing, DNA methylation profiles, and RNA‑seq data from chickens with contrasting Campylobacter colonisation levels. The project aims to uncover the genetic and epigenetic determinants that underpin natural host resistance to Campylobacter by combining genomics with epigenetics and transcriptomics. Genome‑wide association studies will identify genetic variants and genomic regions linked to colonisation levels. In parallel, DNA methylation differences will be characterised using Reduced Representation Bisulfite Sequencing  (RRBS) to reveal epigenetic signatures associated with resistance or susceptibility. These datasets will then be integrated with transcriptomic data to determine whether genetic variants or methylation changes influence gene expression in pathways relevant to gut immunity and host–microbe interactions. Functional enrichment and pathway analyses will help interpret the biological significance of candidate genes and regulatory features. The strongest targets will be validated experimentally using qRT‑PCR, and genomic breeding values for resistance will be estimated to assess the potential for incorporating these findings into poultry breeding programmes. This project offers an exciting opportunity to work at the interface of animal health, genomics, and food safety. By generating a comprehensive multi‑omics view of host resistance to Campylobacter, the work has the potential to inform breeding strategies that reduce bacterial load in poultry and ultimately lower the burden of human campylobacteriosis. The student will gain experience in GWAS, epigenetic analysis, multi‑omics integration, and wet‑lab validation, developing a versatile skill set applicable across modern bioscience and quantitative genetics. The findings are expected to contribute to a peer‑reviewed publication and support future research into sustainable disease control in livestock.  

References:

1. A. Psifidi, et al. Quantitative trait loci and transcriptome signatures associated with avian heritable resistance to Campylobacter. Sci Rep. 2021; 11(1):1623. DOI:10.1038/s41598-020-79005-7

2. A. Psifidi, et al. The genomic architecture of resistance to Campylobacter jejuni intestinal colonisation in chickens. BMC Genomics. 2016; 17:293. DOI:10.1186/s12864-016-2612-7

3. G. Banos, et al. Integrating Genetic and Genomic Analyses of Combined Health Data Across Ecotypes to Improve Disease Resistance in Indigenous African Chickens. Front Genet. 2020; 11:543890. DOI:10.3389/fgene.2020.543890  

Requirements:

Essential

• Must meet our standard MRes entry requirements
• Applicants should have a genuine interest in computational and data‑driven approaches, as the project involves working with bioinformatics tools and analytical workflows. An in‑depth background in programming or advanced computation is not necessary; enthusiasm for learning and engaging with these methods is far more important.

Desirable

•  It is helpful if applicants have some prior wet lab experience and exposure to data analysis, or working in a Linux environment, although this is not essential.

This can be taken full-time project commencing in October 2026, based at RVC's Hawkshead campus.

No animal work is needed for this project.

Funding:

Partially funded: The MRes student will be expected to meet their course fees and living expenses. All other project costs will be met by the supervisors. All the datasets have already been generated as part of the One Health Poultry Hub project  

Please note that EU/EEA and Swiss national students may no longer be eligible for the “Home” rate of tuition fees, dependent on personal circumstances (including immigration status and residence history in the UK) and UK government rules which are currently being developed. For up-to-date information on fees for EU/EEA and Swiss national students following Brexit please see our fees and funding page.

How to apply

Deadline:

8th May 2026> 

For more information on the application process and English Language requirements see How to Apply.

Interviews will take place remotely (Teams, Zoom etc) within 4 weeks of the closing date.We welcome informal enquiries - these should be directed to apsifidi@rvc.ac.uk