Perfilyev, A.; Shen, A.; Hooton, S.; Zahran, S. A.; Winther-Have, C. S.; Kalatzis, P.; Wilkinson, R. C.; Thanki, A. M.; Petersen, B.; Liu, Z.; Zhang, Q.; Liu, Y.; Ibarra-Chavez, R.; Gigante, A.; Lv, Q.; Atterbury, R.; Millard, A. D.; Clokie, M. R. J.; Sicheritz-Ponten, T.

Phages are typically classified as temperate, integrating into host genomes, or lytic, replicating and killing bacteria. Lytic phages are not expected in bacterial genome sequences, yet our analysis of 3.6 million bacterial assemblies from 1,226 species revealed >100,000 complete lytic phage genomes, which we term Bacterial Assembly-associated Phage Sequences (BAPS). This represents a ~five-fold increase in the number of phages with known hosts and fundamentally reshapes our understanding of phage biology. Identifying BAPS has enabled the discovery of entirely novel phage clusters, including clusters distantly related to Salmonella Goslarviruses in E. coli, and Shigella, while significantly expanding known genera such as Seoulvirus (from 16 to >300 members). Notably, close relatives of therapeutic lytic phages were also detected, suggesting clinical isolate sequencing unknowingly archives viable phage candidates. The discovery of complete, lytic phage genomes within bacterial assemblies challenges long-standing assumptions and reveals a vast, untapped reservoir of phages.