Harnessing the immune system of S. thermophilus to counter bacteriophages in the dairy industry by Audrey Leprince (Université Laval, Canada)

Bacteriophages (phages) are currently experiencing a renewed interest as antimicrobials, but in the dairy industry they represent a major threat due to their ability to infect and kill lactic acid bacteria (LAB), resulting in poor-quality products. In this context, it is essential to understand the strategies evolved by bacteria to counteract phage infection to carefully select or construct phage-resistant industrial strains. Among LAB, Streptococcus thermophilus is commonly used in the manufacture of certain types of cheese (mozzarella, Swiss, etc.) and yoghurt. In this LAB, CRISPR-Cas systems are widespread and have been deeply investigated due to their ability to provide robust phage resistance. However, some phages infecting S. thermophilus encode anti-CRISPR (ACR) proteins that neutralize the Cas9 nuclease, enabling them to bypass this line of defense. This compels us to investigate alternative defense mechanisms to further improve industrial strains. In this work, we are exploring the diversity of anti-phage mechanisms in S. thermophilus to identify defense systems to which ACR-producing phages are susceptible. An in-silico analysis was first performed to predict putative defense systems using a dataset of 263 genomes of S. thermophilus. So far, 28 groups of anti-phage systems were retrieved with, as expected, CRISPR-Cas and restriction modification systems being the most abundant. In addition, other defense systems which have been recently identified in other bacteria, were also highlighted in our analysis. Several systems are currently experimentally tested to establish their efficiency against S. thermophilus phages, particularly those coding for ACR proteins. The bioinformatic analysis also led to the discovery of 26 genomic islands enriched in phage defense systems in S. thermophilus. These genomic islands are often associated with mobile genetic elements such as Integrative and conjugative elements (ICE) and transposons and constitute a reservoir of genes involved in anti-phage mechanisms, as well as genes of unknown function potentially involved in new, uncharacterized defense systems.