a, Cell diagram of bacterium–phage and phage–phage interactions that involve CRISPR targeting during superinfection. Arrows indicate CRISPR–Cas targeting of the prophage and phage genomes. Phage names indicate related groups delineated by whole-genome alignment. We only included CRISPR interactions from samples of subjects of the same human cohort. b, Maximum likelihood phylogenetic tree of Cas12 subtypes a–i. Phage-encoded Cas12i and CasΦ, the new effector, are outlined in red, with bacteria-encoded proteins in blue. Bootstrap values >90 are shown on the branches (circles). Cas14 and type V-U trees are provided separately (Supplementary Fig. 11). Scale bars indicates the number of substitutions per site. c, Top, alignment of the consensus repeats from the A9 phage array and predicted host bacterial arrays. Bottom, interaction network showing the targeting of bacteria-encoded (blue) and phage-encoded (red) CRISPR spacers. The number of edges indicate the number of spacers from the array with targets to the smaller node. Solid edges denote spacer targets with no or one mismatch, and dashed edges denote two to three mismatches (to account for degeneration in old-end phage spacers, diversity in different subjects or phage mutation to avoid targeting).