The defensome of Acinetobacter baumannii reveals two genome groups according to their innate defense systems and phage profile

Phages are guilty of killing daily almost half of bacterial cells, while bacteria have developed defense mechanisms that number in the dozens. Individual defense systems are gained and lost by genomes of the same species, depending on their fitness advantage. Thus, some genomes have a certain combination of defense systems, while other genomes act as a reservoir for the rest of the systems, thus constituting the so-called pan-immune system of the species. The study of this system, also called defensome, requires a good representation of genomes of the same species. Here we have analyzed thousands of genomes of the bacterium Acinetobacter baumannii , an opportunistic pathogen of humans of great clinical concern. We have found 81 different defense systems, heterogeneously distributed. By analyzing how these systems combine, we have found that restriction-modification (R-M) systems can act synergistically with CRISPR-Cas systems, in addition to other combinations not described so far. Notably, more than half of the genomes lack the universal DNA-methylating R-M systems and have the alternative innate SspBCDE system that made a DNA phosphorothioate modification. The presence of one or the other could modulate the evolution of the genomes of this species, causing them to present a different profile of phages integrated or prophages. Finally, we found that the presence of many defense systems is associated with the presence of a greater number of prophages, which may be due to the fact that the prophage carries the system, as in the case of PD-T4 systems, or that the bacterium would not need these systems in environments where the phage is absent.