PhD Studentship: Mapping Phage Diversity through Population-Scale Metagenomics in the Hunt for Novel Antimicrobials

Supervisors:

Dr Lucy van Dorp

Prof Joanne Santini

Abstract

Phages - viruses that infect bacteria - are rich sources of molecular diversity with potential applications in antimicrobial discovery. This project will use large-scale metagenomic mining to uncover novel phage-host associations and identify phage-encoded enzymes, such as endolysins, with antibacterial activity. By integrating evolutionary genomics, microbial ecology, and bioinformatics, the project will generate a curated catalogue of phages host relationships, and enzymes for future experimental validation.

Approach and Methods

• Metagenomic mining and assembly to recover host-phage associations.
• Phylogenetic analysis of recovered co-evolutionary relationships.
• Gene annotation and comparative genomics to identify candidate antimicrobial enzymes.
• Mapping bacterial defence systems to infer predictive features of co-evolutionary dynamics.

Impact and Outlook

This project will:
• Advance understanding of microbial co-evolution.
• Deliver a curated resource of phage-host-enzyme associations.
• Identify promising candidates for phage-derived antimicrobials.

Training and Student Development

The successful applicant will gain expertise in:

• Large-scale metagenomic assembly and genome recovery
  • Comparative genomics and molecular evolution
  • Machine-learning-based protein prediction
  • Data integration, bioinformatics and phylogenetics
  • Scientific reasoning and interdisciplinary communication

Research Environment

The project will be hosted in two collaborative, interdisciplinary labs with expertise in:

• Evolutionary microbial genomics and phylogenetics/population genetics (van Dorp Lab)
  • Environmental microbiology, phage biology and metagenomics (Santini Lab)
  
  Both labs promote open research culture and have a strong track record of PhD supervision.

Desirable Prior Experience

Previous experience working in the field of microbial genomics, bioinformatics or computational biology would be desirable

How to apply

This project is offered as part of the Centre for Doctoral Training in Engineering Solutions for Antimicrobial Resistance. Further details about the CDT and programme can be found at AMR CDT webiste.

Applications should be submitted by 12^th January 2026.

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