Horizontal transfer of phage-defense genes can stably maintain their diversity in a microbial pan-genome despite continuous extinction and turnover of genomes

Phages and their bacterial hosts are locked in an evolutionary competition which in small and closed systems typically results in an extinction of one or the other. To resist phages bacteria have evolved numerous defense systems, which nevertheless are still susceptible to specific phage anti-defense mechanisms. These defense/anti-defense systems are a major element of microbial genetic diversity and have been demonstrated to propagate between strains by horizontal gene transfer (HGT). It has been proposed that the totality of defense systems found in microbial communities collectively form a distributed "pan-immune" system with individual elements moving between strains with via ubiquitous HGT. Here, we formulate a Lotka-Volterra type model of a host/phage system interacting via a combinatorial variety of defense/anti-defense systems and show that HGT enables stable maintenance of diverse defense/anti-defense genes in the microbial pan-genome even when individual microbial strains inevitably undergo extinction leaving only few descendants that survive thanks to immunity acquired through HGT. This mechanism of persistence for the pan-immune gene pool is fundamentally similar to the "island migration" model of ecological diversity, with genes moving between genomes instead of species migrating between islands.