Metagenomic Workflows for Diagnostic Applications in Gastrointestinal Infections (MATHERA_Q26NIHR)
Key Details
- Application Deadline
- 26 March 2026 (midnight UK time)
- Location
- UEA
- Funding type
- Externally funded project (Home applicants only)
- Start date
- 1 October 2026
- Mode of study
- Full-time
- Programme type
- PhD
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Project description
Primary supervisor - Prof Alison Mather
The UKHSA genomic strategy prioritizes "democratization" of sequencing—moving diagnostics closer to the point-of-care. Metagenomics offers a "catch-all" tool to identify pathogens and antimicrobial resistance (AMR) without slow bacterial culture. This PhD aims to bridge the gap between research-grade metagenomics and surveillance utility for gastrointestinal (GI) infections.
Current PCR methods are limited by detecting only pre-specified targets. Leveraging shotgun metagenomics and advanced bioinformatics, this project will establish the evidence base for: direct-from-sample diagnostics by -
1) Benchmarking Pathogen Detection: Investigate analytical sensitivity and "diagnostic cut-offs" to distinguish active infection from healthy asymptomatic carriage.
2) AMR Profiling: Map the baseline carriage of resistance genes in healthy vs. diseased populations, using metagenome-assembled genomes to link AMR determinants to specific microbes.
3) Workflow Optimization: Develop laboratory and analytical protocols to maximize microbial DNA yield and improve detection of low abundant pathogens in food.
4) Advanced Innovation: Applying skills to specialized areas like functional metagenomics to investigate pathogen virulence and plasmid-chromosome associations.
You will gain a unique interdisciplinary skillset:
Molecular Biology: DNA extraction, host depletion, and metagenome sequencing.
Bioinformatics: Pathogen detection pipelines and metagenomic assembly.
Based at Quadram Institute Bioscience, with opportunities at the UKHSA Gastrointestinal Bacteria Reference Unit, you will be prepared for a career at the intersection of public health and genomic research.
UK candidates require a microbiology or molecular biology background. Genomics/Bioinformatics is desirable.
Entry requirements
At least UK equivalence Bachelors (Honours) 2:1 or UK equivalence Masters degree.
Funding
This project is awarded with a 4-year fully funded NIHR PhD studentship which covers Home tuition fees, an annual tax-free maintenance stipend set at the UKRI rate (£20,780 for 2025/6), and research training support funding.
References
Besser, J. M., Carleton, H. A., Gerner-Smidt, P., Lindsey, R. L., & Trees, E. (2018). Next-generation sequencing technologies and their application to the study and control of bacterial infections. Clinical Microbiology and Infection, 24(4), 335–341.
Bloomfield, S.J., Hildebrand, F., Zomer, A.L., Palau, R., & Mather, A.E. (2025). Ecological insights into the microbiology of food using genomics and its potential surveillance applications. Microbial Genomics, 11, 001337.
Chiu, C. Y., & Miller, S. A. (2019). Clinical metagenomics. Nature Reviews Genetics, 20(6), 341–355.
Cunningham-Oakes, E., Perez-Sepulveda, B. M., Li, Y., Hinton, J. C. D., Darby, A. C., et al. (2025). Enhancing infectious intestinal disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples. Genome Medicine, 17(1), 55.
Dziegiel, A.H., Duong, V.T., Bloomfield, S.J., Thomson, N.R., Maskell, D.J., Wain, J., Janecko, N., Baker, S., & Mather, A.E. (2025). Metagenomic identification of disease-causing Salmonella enterica serovars and antimicrobial resistance genes from paediatric faecal samples. Microbial Genomics, 11, 001547.
Forbes, J. D., Knox, N. C., Ronholm, J., Pagotto, F., & Reimer, A. (2017). Metagenomics: The Next Culture-Independent Game Changer. Frontiers in Microbiology, 8, 1069.