Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities

Abstract

Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 158 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. We find that nearly identical strains of cheese-associated bacteria contain diverse and highly variable arsenals of innate and adaptive (i.e CRISPR-Cas) immunity suggesting rapid turnover of defense mechanisms in these communities. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, suggesting that CRISPR does not provide complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. ImportanceBacteria are constantly exposed to phage predation and hence harbor highly diverse defense arsenals. According to the pan-immunity hypothesis the effective immune system of a bacterial species is not the one encoded in a single genome but in the entire community. However, few studies have investigated how defense systems are distributed within communities. Here, we carried out (meta)genomic analyses of bacterial communities used in cheesemaking. These are tractable communities of biotechnological interest which house few bacterial species and are exposed to high phage pressure. In line with the pan-immunity hypothesis, we find that nearly identical strains of cheese-associated bacteria contain highly variable arsenals of innate and adaptive immunity. We provide evidence for the functional importance of this diversity, and reveal that CRISPR alone does not provide complete immunity against all phages. Our findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry.