Phage co-infection: a missing link in deciphering phage co-evolutionary dynamics

Introduction

Phage genomes represent an impressive mosaicism with different genomic regions having distinct evolutionary histories resulting from horizontal gene transfer. By initiating an estimated 10^25 bacterial infections globally every second, phages encounter and recombine with DNA of the host or of prophage origin, further adding to their genome mosaicism.

Co-infection and Genome Evolution

Accumulating evidence, including from my work, suggests that the simultaneous infection of a bacterial host by multiple phages (co-infection) could also be an important driver of phage genome evolution. However, methodological limitations have so far prevented rigorous testing of this hypothesis due to the failure of studying phage co-infection in natural settings.

Objectives of MULTIPHAGE

MULTIPHAGE will overcome these limitations by developing a novel approach for precisely deciphering how phage co-infection governs the co-evolutionary dynamics of phage genomes by pursuing three objectives:

1. Quantifying Prevalence: My team will quantify the prevalence of phage co-infection by constructing phage-host infection networks.
2. Deciphering Co-evolutionary Relations: We will decipher the co-evolutionary relations of phage genes with no detectable sequence homology, using the novel concept of clusters of orthologous structures (COSs) and reconstructing structural phylogeny.
3. Unearthing Interaction Strategies: Finally, we will unearth phage-phage interaction and co-infection strategies in high resolution by taking advantage of cultured model systems containing multiple phages co-infecting a single bacterial host population.

Methodology

To achieve these objectives, we will combine integrated omics methods (metaHiC proximity ligation, long-read metagenomic sequencing, and single-cell amplified genomics), COSs and structural phylogeny with high-resolution experimental confirmation of co-infection strategies.

Impact of MULTIPHAGE

With its ground-breaking approach, MULTIPHAGE will transform our view of phage-host co-evolution by uncovering how phage co-infection and broad host range modulate the complexity of the infection network, clarifying its enigmatic co-evolutionary dynamics.