Planetary-scale metagenomic analysis reveals CRISPR targeting dynamics across ecosystems

Interactions between microorganisms and their mobile genetic elements (MGEs), including viruses and plasmids, impact microbiome dynamics. CRISPR–Cas systems are important regulators of these host–MGE interactions, but a global understanding of the diversity, activity and roles of CRISPR spacers across Earth’s biomes is still lacking. Here we develop a computational approach to search short-read data and collect 794 million CRISPR spacers across 367,609 public metagenomes, from which we identified 1.18 billion hits between 41 million spacers and 2.5 million viruses and plasmids. While spacers were highly variable across samples, those matching known viruses were more prevalent and conserved, consistent with a positive selection pressure associated with phage targeting. Among these, however, we find evidence suggestive of recurrent entry of phage genomes into non-host microbial cells, further blurring the line between CRISPR targeting and virus–host interactions. These results highlight key drivers of CRISPR targeting patterns likely to influence strain-level diversification and selection processes in microbiomes. Screening millions of CRISPR spacers across globally distributed metagenomes reveals unexpected dynamics of phage–host interactions, including many cases where phage genomes seem to repeatedly enter non-host cells.