Mushegian, A. R. Are there 1031 virus particles on earth, or more, or fewer? J. Bacteriol. 202, e00052–20 (2020).

Article  PubMed  Google Scholar 

Hendrix, R. W., Smith, M. C., Burns, R. N., Ford, M. E. & Hatfull, G. F. Evolutionary relationships among diverse bacteriophages and prophages: all the world’s a phage. Proc. Natl Acad. Sci. USA 96, 2192–2197 (1999).

Article  CAS  PubMed  Google Scholar 

Luria, S. E. & Delbrück, M. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28, 491–511 (1943).

Article  CAS  PubMed  Google Scholar 

Hershey, A. D. & Chase, M. Independent functions of viral protein and nucleic acid in growth of bacteriophage. J. Gen. Physiol. 36, 39–56 (1952).

Article  CAS  PubMed  Google Scholar 

van der Oost, J. & Patinios, C. The genome editing revolution. Trends Biotechnol. 41, 396–409 (2023).

Article  PubMed  Google Scholar 

Doudna, J. A. & Charpentier, E. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).

Article  PubMed  Google Scholar 

Nair, A. & Kis, Z. Bacteriophage RNA polymerases: catalysts for mRNA vaccines and therapeutics. Front. Mol. Biosci. 11, 1504876 (2024).

Article  CAS  PubMed  Google Scholar 

Dion, M. B., Oechslin, F. & Moineau, S. Phage diversity, genomics and phylogeny. Nat. Rev. Microbiol. 18, 125–138 (2020).

Article  CAS  PubMed  Google Scholar 

Lederberg, E. M. & Lederberg, J. Genetic studies of lysogenicity in Escherichia coli. Genetics 38, 51–64 (1953).

Article  CAS  PubMed  Google Scholar 

Lederberg, E. M. Lysogenicity in Escherichia coli strain K-12. Microb. Genet. Bull. 1, 5–8 (1950).

Google Scholar 

Lwoff, A. Lysogeny. Bacteriol. Rev. 17, 269–337 (1953).

Article  CAS  PubMed  Google Scholar 

Ptashne, Mark. A Genetic Switch: Phage Lambda Revisited (Cold Spring Harbor Laboratory Press, 2004).

Correa, A. M. S. et al. Revisiting the rules of life for viruses of microorganisms. Nat. Rev. Microbiol. 19, 501–513 (2021).

Article  CAS  PubMed  Google Scholar 

Howard-Varona, C., Hargreaves, K. R., Abedon, S. T. & Sullivan, M. B. Lysogeny in nature: mechanisms, impact and ecology of temperate phages. ISME J. 11, 1511–1520 (2017).

Article  PubMed  Google Scholar 

Herskowitz, I. & Hagen, D. The lysis-lysogeny decision of phage lambda: explicit programming and responsiveness. Annu. Rev. Genet. 14, 399–445 (1980).

Article  CAS  PubMed  Google Scholar 

Gandon, S. Why be temperate: lessons from bacteriophage λ. Trends Microbiol. 24, 356–365 (2016).

Article  CAS  PubMed  Google Scholar 

Brady, A. et al. Molecular basis of lysis–lysogeny decisions in gram-positive phages. Annu. Rev. Microbiol. 75, 563–581 (2021).

Article  CAS  PubMed  Google Scholar 

Feiner, R. et al. A new perspective on lysogeny: prophages as active regulatory switches of bacteria. Nat. Rev. Microbiol. 13, 641–650 (2015).

Article  CAS  PubMed  Google Scholar 

Hobbs, Z. & Abedon, S. T. Diversity of phage infection types and associated terminology: the problem with ‘lytic or lysogenic’. FEMS Microbiol. Lett. 363, fnw047 (2016).

Article  PubMed  Google Scholar 

Mäntynen, S., Laanto, E., Oksanen, H. M., Poranen, M. M. & Díaz-Muñoz, S. L. Black box of phage–bacterium interactions: exploring alternative phage infection strategies. Open Biol. 11, 210188 (2021).

Article  PubMed  Google Scholar 

Taylor, V. L., Fitzpatrick, A. D., Islam, Z. & Maxwell, K. L. The diverse impacts of phage morons on bacterial fitness and virulence. Adv. Virus Res. 103, 1–31 (2019).

Article  CAS  PubMed  Google Scholar 

Touchon, M., Bernheim, A. & Rocha, E. P. Genetic and life-history traits associated with the distribution of prophages in bacteria. ISME J. 10, 2744–2754 (2016).

Article  CAS  PubMed  Google Scholar 

López-Leal, G. et al. Mining of thousands of prokaryotic genomes reveals high abundance of prophages with a strictly narrow host range. mSystems 7, e0032622 (2022).

Article  PubMed  Google Scholar 

Kim, M.-S. & Bae, J.-W. Lysogeny is prevalent and widely distributed in the murine gut microbiota. ISME J. 12, 1127–1141 (2018).

Article  CAS  PubMed  Google Scholar 

Ohnishi, M., Kurokawa, K. & Hayashi, T. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol. 9, 481–485 (2001).

Article  CAS  PubMed  Google Scholar 

Winstanley, C. et al. Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Res. 19, 12–23 (2009).

Article  CAS  PubMed  Google Scholar 

Juhala, R. J. et al. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J. Mol. Biol. 299, 27–51 (2000).

Article  CAS  PubMed  Google Scholar 

Argov, T. et al. Temperate bacteriophages as regulators of host behavior. Curr. Opin. Microbiol. 38, 81–87 (2017).

Article  CAS  PubMed  Google Scholar 

Gummalla, V. S., Zhang, Y., Liao, Y.-T. & Wu, V. C. H. The role of temperate phages in bacterial pathogenicity. Microorganisms 11, 541 (2023).

Article  CAS  PubMed  Google Scholar 

Fortier, L.-C. & Sekulovic, O. Importance of prophages to evolution and virulence of bacterial pathogens. Virulence 4, 354–365 (2013).

Article  PubMed  Google Scholar 

Tsao, Y.-F. et al. Phage morons play an important role in Pseudomonas aeruginosa phenotypes. J. Bacteriol. 200, e00189–18 (2018).

Article  CAS  PubMed  Google Scholar 

Freeman, V. J. Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae. J. Bacteriol. 61, 675–688 (1951).

Article  CAS  PubMed  Google Scholar 

Wirtz, C., Witte, W., Wolz, C. & Goerke, C. Transcription of the phage-encoded Panton–Valentine leukocidin of Staphylococcus aureus is dependent on the phage life-cycle and on the host background. Microbiology 155, 3491–3499 (2009).

Article  CAS  PubMed  Google Scholar 

Gerlach, D. et al. Methicillin-resistant Staphylococcus aureus alters cell wall glycosylation to evade immunity. Nature 563, 705–709 (2018).

Article  CAS  PubMed  Google Scholar 

Figueroa-Bossi, N. & Bossi, L. Inducible prophages contribute to Salmonella virulence in mice. Mol. Microbiol. 33, 167–176 (1999).

Article  CAS  PubMed