Defense systems and horizontal gene transfer in bacteria

Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defense mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defense systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defense systems across 12 bacterial species. We discovered that only six defense systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defense systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defense mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defense systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.