The antiviral defence arsenal of the Bacillus cereus group

The pressure of phage infection on bacteria has resulted in the evolution of multiple defence mechanisms that are known as the prokaryotic immune system. As antiphage defence genes tend to cluster in prokaryotic genomes within defence islands, new systems have been uncovered located in proximity of these islands. However, few studies have set out to capture the diversity of such antiviral arsenal outside of a limited number of model organisms. Considering the broad potential of phages as an antibacterial alternative against members of the Bacillus cereus group, it is of prime interest to evaluate the prevalence of antiviral defence systems within this group, along with their potential to be transferred by the abundant MGEs present in these species. Therefore, in this work, we used DefenseFinder1 and PADLOC2 bioinformatics tools to systematically identify in silico the defence arsenal encoded in more than 6300 B. cereus sensu lato genomes. Our results highlight that almost all studied B. cereus assemblies possess at least one defence system. Out of the ninety thousand systems identified across the group, restriction-modification (RM) and abortive infection (Abi) are the main strategies detected, which are indeed common defences in prokaryotes. Most detected systems are small (one or two proteins) and thus easily mobilizable. No significant difference in the type or abundance of systems was identified between species. The analysis of the detected systems that matched between DefenseFinder and PADLOC indicated that they can be encoded on either the chromosome or plasmids, though some systems tend to occupy specific genetic elements. For instance, RM systems are often found on the chromosome while Nhi, PD-T7-3, and AbiO are plasmid encoded. Overall, these analyses improve our understanding of the multi-layered defensome in the B. cereus group and pave the way for studying co-existing strategies displayed by this bacterial group to subvert phages-attacks. 1 Tesson F., et al., 2022. Nature Communications 13(1) 2 Payne L.J., et al., 2021. Nucleic Acids Research 49(19), 10868–10878