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 Evolution

Accumulating evidence, including from my work, suggests that the simultaneous infection of bacterial hosts 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 Co-infection 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. Uncovering 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.