Fig. 7. Cryptic-coinfection models reconcile sparse killing overlap with prevalent recombination in phages.

We propose that two classes of cryptic (as in rarely observed in the laboratory) co-infections are key in unifying two at first contradictory observations - that in natural microbial communities overlap in killing is rare among tailed phages, yet recombinant phage genomes are common. First a, co-infections in rarely observed broadly sensitive hosts killed by multiple phage types (indicated by filled in squares in the figure) may be an important source of phage recombinants in local microbial communities. Where there is an inverse relationship between phage sensitivity and relative abundance and growth rate, broadly sensitive host strains may be ecologically important but systematically underrepresented in isolation studies. Second b, co-infections in commonly observed defended hosts that are only killed by a few phage types (indicated by both filled in and empty squares) may also be an important source of recombinant phage progeny, particularly where phage encoded recombinases are expressed in the presence of phage genome fragments generated by host anti-phage defense systems. In both scenarios, where phages are associated with hosts through states of lysogeny or pseudolysogeny, the probability of co-infections, and thus potential for generation of recombinants, will be even greater. Figure created with BioRender.com.