PhD Studentship: Metagenomic Workflows for Diagnostic Applications in Gastrointestinal Infections

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.

Mode of study

Full-time

Start date

1 October 2026

Additional Funding Information

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.

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