Small Viruses, Big Battles: Experimental exploration of phage diversity and anti-phage defence mechanisms

Bacteriophages exert strong selective pressure on bacterial populations and play a central role in shaping microbial evolution. In response to phage predation, bacteria have evolved diverse antiphage defence mechanisms that interfere with viral replication through a wide range of molecular strategies. Recent genomic studies have revealed a rapidly expanding repertoire of candidate defence systems, many of which remain experimentally uncharacterised and are frequently associated with mobile genetic elements such as plasmids, prophages, and phage-plasmids. At the same time, bacteriophages themselves exhibit enormous genetic and ecological diversity, providing a rich experimental landscape for investigating phage-host interactions and bacterial defence strategies.
Despite the growing catalogue of predicted defence systems, experimental understanding of how these systems function during phage infection remains limited. Many defences are identified through genomic organisation or sequence similarity, while their phenotypic effects, molecular requirements, and physiological consequences during infection remain poorly understood. Experimental approaches that integrate systematic phage biology with functional analysis of defence systems are therefore essential for understanding how bacteria restrict phage replication and how these interactions shape microbial evolution.
The work presented in this thesis addresses this gap through experimental exploration of bacteriophage diversity and antiphage defence mechanisms. Environmental E. coli-infecting bacteriophages were isolated and characterised to expand the experimental landscape for phage-host studies. Defence systems encoded within the variable mat-lxc locus of P1-like phage-plasmids were experimentally validated and functionally analysed, revealing several enzymatic defence modules with distinct activities. In addition, metabolic labelling revealed that activation of the PARIS defence system rapidly inhibits protein synthesis. Together, these findings provide experimental insight into the diversity and functional behaviour of bacterial antiphage defence systems.