A mechanistic approach to understand microbiome-viriome dynamics in nature

Facing the therapeutic impasse of antibiotics, farming systems, among which aquaculture, should consider the extraordinary resource of phages, the natural bacterial predators, for environmental friendly practices. It is, however, crucial to understand how phages can control pathogens in a sustainable and safety manner.

The goal of this project is to shed light on key ecological and evolutionary processes underlying phage-bacteria dynamics in the marine environment.

An oyster bacterial pathogen, Vibrio crassostreae and its infecting phages will be used as model system to investigate the molecular bases and evolution of phage infections in nature.

Based on a field approach, we will determine whether phages influence V. crassostreae dynamics in the wild by reducing bacterial density via predation and if co-evolution applies in this natural system.

Combining comparative and functional genomics we will identify genes involved in the phage host range, host resistance, and phage–host coevolution.

Exploring phage-vibrio interactions in culture, we will analyze whether fitness costs can constrain evolution of resistance in oyster hemolymph. We will identify vibrio virulence genes that are negatively selected by phages. In addition we will study whether phages in combination act synergistically to control V. crassostreae.

Focusing on a T4-giant phage as a model, we will assess the molecular mechanisms underpinning its broad host range and decipher its potential to spread bacterial genes by horizontal gene transfer.

We will finally revisit the phylogenomics of T4-related phages, and reconstruct the T4-giant phage ancestral genome to determine how the ability to infect multiple hosts has evolved in this group.

This project has significant potential to make truly ground breaking discoveries on phage-bacteria coevolution providing new and major knowledge for the future generation of phage therapy in aquaculture.