Abstract
Viruses that infect bacteria (bacteriophages; also known as phages) were discovered 100 years ago. Since then, phage research has transformed fundamental and translational biosciences. For example, phages were crucial in establishing the central dogma of molecular biology — information is sequentially passed from DNA to RNA to proteins — and they have been shown to have major roles in ecosystems, and help drive bacterial evolution and virulence. Furthermore, phage research has provided many techniques and reagents that underpin modern biology — from sequencing and genome engineering to the recent discovery and exploitation of CRISPR–Cas phage resistance systems. In this Timeline, we discuss a century of phage research and its impact on basic and applied biology.
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References
Twort, F. W. An investigation on the nature of ultra-microscopic viruses. Bacteriophage 1, 127–129 (2011).
D'Herelle, F. On an invisible microbe antagonistic toward dysenteric bacilli: brief note by Mr. F. D'Herelle, presented by Mr. Roux. 1917. Res. Microbiol. 158, 553–554 (2007).
Summers, W. C. Bacteriophage therapy. Annu. Rev. Microbiol. 55, 437–451 (2001).
Ruska, H., von Borries, B. & Ruska, E. Die Bedeutung der Übermikroskopie für die Virusforschung. Arch. Virusforsch (Arch. Virol.) 1, 155–169 (in German) (1940).
Summers, W. C. in The Bacteriophages (ed. Calendar, R.) 3–7 (Oxford Univ. Press, 2006).
Ellis, E. L. & Delbruck, M. The growth of bacteriophage. J. Gen. Physiol. 22, 365–384 (1939).
Luria, S. E. & Delbruck, M. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28, 491–511 (1943).
Hershey, A. D. & Chase, M. Independent functions of viral protein and nucleic acid in growth of bacteriophage. J. Gen. Physiol. 36, 39–56 (1952).
Benzer, S. Fine structure of a genetic region in bacteriophage. Proc. Natl Acad. Sci. USA 41, 344–354 (1955).
Crick, F. H., Barnett, L., Brenner, S. & Watts-Tobin, R. J. General nature of the genetic code for proteins. Nature 192, 1227–1232 (1961).
Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318–356 (1961).
Bertani, G. & Weigle, J. J. Host controlled variation in bacterial viruses. J. Bacteriol. 65, 113–121 (1953).
Luria, S. E. & Human, M. L. A nonhereditary, host-induced variation of bacterial viruses. J. Bacteriol. 64, 557–569 (1952).
Pingoud, A., Wilson, G. G. & Wende, W. Type II restriction endonucleases — a historical perspective and more. Nucleic Acids Res. 42, 7489–7527 (2014).
Smith, H. O. & Wilcox, K. W. A restriction enzyme from Hemophilus influenzae: I. Purification and general properties. J. Mol. Biol. 51, 379–391 (1970).
Weiss, B. & Richardson, C. C. Enzymatic breakage and joining of deoxyribonucleic acid, I. Repair of single-strand breaks in DNA by an enzyme system from Escherichia coli infected with T4 bacteriophage. Proc. Natl Acad. Sci. USA 57, 1021–1028 (1967).
Collins, J. & Hohn, B. Cosmids: a type of plasmid gene-cloning vector that is packageable in vitro in bacteriophage λ heads. Proc. Natl Acad. Sci. USA 75, 4242–4246 (1978).
Zhu, B. Bacteriophage T7 DNA polymerase — sequenase. Front. Microbiol. 5, 181 (2014).
Kleckner, N., Roth, J. & Botstein, D. Genetic engineering in vivo using translocatable drug-resistance elements. New methods in bacterial genetics. J. Mol. Biol. 116, 125–159 (1977).
Wasylyk, B. et al. Specific in vitro transcription of conalbumin gene is drastically decreased by single-point mutation in T-A-T-A box homology sequence. Proc. Natl Acad. Sci. USA 77, 7024–7028 (1980).
Groisman, E. A. In vivo genetic engineering with bacteriophage Mu. Methods Enzymol. 204, 180–212 (1991).
Fiers, W. et al. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature 260, 500–507 (1976).
Sanger, F. et al. Nucleotide sequence of bacteriophage ΦX174 DNA. Nature 265, 687–695 (1977).
Sanger, F., Coulson, A. R., Hong, G. F., Hill, D. F. & Petersen, G. B. Nucleotide sequence of bacteriophage λ DNA. J. Mol. Biol. 162, 729–773 (1982).
Bergh, O., Borsheim, K. Y., Bratbak, G. & Heldal, M. High abundance of viruses found in aquatic environments. Nature 340, 467–468 (1989).
Bratbak, G., Heldal, M., Norland, S. & Thingstad, T. F. Viruses as partners in spring bloom microbial trophodynamics. Appl. Environ. Microbiol. 56, 1400–1405 (1990).
Proctor, L. M. & Fuhrman, J. A. Viral mortality of marine bacteria and cyanobacteria. Nature 343, 60–62 (1990).
Suttle, C., Chan, A. & Cottrell, M. Infection of phytoplankton by viruses and reduction of primary productivity. Nature 347, 467–469 (1990).
Clokie, M. R., Millard, A. D., Letarov, A. V. & Heaphy, S. Phages in nature. Bacteriophage 1, 31–45 (2011).
Breitbart, M. Marine viruses: truth or dare. Ann. Rev. Mar. Sci. 4, 425–448 (2012).
Breitbart, M. et al. Genomic analysis of uncultured marine viral communities. Proc. Natl Acad. Sci. USA 99, 14250–14255 (2002).
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).
Pope, W. H. et al. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. eLife 4, e06416 (2015).
Koskella, B. & Brockhurst, M. A. Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol. Rev. 38, 916–931 (2014).
Buckling, A., Craig Maclean, R., Brockhurst, M. A. & Colegrave, N. The Beagle in a bottle. Nature 457, 824–829 (2009).
Brussow, H., Canchaya, C. & Hardt, W. D. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68, 560–602 (2004).
Waldor, M. K. & Mekalanos, J. J. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272, 1910–1914 (1996).
Freeman, V. J. Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae. J. Bacteriol. 61, 675–688 (1951).
Neely, M. N. & Friedman, D. I. Functional and genetic analysis of regulatory regions of coliphage H-19B: location of shiga-like toxin and lysis genes suggest a role for phage functions in toxin release. Mol. Microbiol. 28, 1255–1267 (1998).
Zinder, N. D. & Lederberg, J. Genetic exchange in Salmonella. J. Bacteriol. 64, 679–699 (1952).
Modi, S. R., Lee, H. H., Spina, C. S. & Collins, J. J. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499, 219–222 (2013).
Penades, J. R., Chen, J., Quiles-Puchalt, N., Carpena, N. & Novick, R. P. Bacteriophage-mediated spread of bacterial virulence genes. Curr. Opin. Microbiol. 23, 171–178 (2015).
McDaniel, L. D. et al. High frequency of horizontal gene transfer in the oceans. Science 330, 50 (2010).
Lang, A. S., Zhaxybayeva, O. & Beatty, J. T. Gene transfer agents: phage-like elements of genetic exchange. Nat. Rev. Microbiol. 10, 472–482 (2012).
Novick, R. P., Christie, G. E. & Penades, J. R. The phage-related chromosomal islands of Gram-positive bacteria. Nat. Rev. Microbiol. 8, 541–551 (2010).
Coulthurst, S. J. The type VI secretion system — a widespread and versatile cell targeting system. Res. Microbiol. 164, 640–654 (2013).
Shikuma, N. J. et al. Marine tubeworm metamorphosis induced by arrays of bacterial phage tail-like structures. Science 343, 529–533 (2014).
Schmelcher, M. & Loessner, M. J. Application of bacteriophages for detection of foodborne pathogens. Bacteriophage 4, e28137 (2014).
Chan, B. K., Abedon, S. T. & Loc-Carrillo, C. Phage cocktails and the future of phage therapy. Future Microbiol. 8, 769–783 (2013).
Nobrega, F. L., Costa, A. R., Kluskens, L. D. & Azeredo, J. Revisiting phage therapy: new applications for old resources. Trends Microbiol. 23, 185–191 (2015).
Wright, A., Hawkins, C. H., Anggard, E. E. & Harper, D. R. A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy. Clin. Otolaryngol. 34, 349–357 (2009).
Roach, D. R. & Donovan, D. M. Antimicrobial bacteriophage-derived proteins and therapeutic applications. Bacteriophage 5, e1062590 (2015).
Schuch, R., Nelson, D. & Fischetti, V. A. A bacteriolytic agent that detects and kills Bacillus anthracis. Nature 418, 884–889 (2002).
Young, R. Phage lysis: do we have the hole story yet? Curr. Opin. Microbiol. 16, 790–797 (2013).
Briers, Y. et al. Engineered endolysin-based 'Artilysins' to combat multidrug-resistant Gram-negative pathogens. mBio 5, e01379–14 (2014).
Dubos, R. & Avery, O. T. Decomposition of the capsular polysaccharide of pneumococcus type III by a bacterial enzyme. J. Exp. Med. 54, 51–71 (1931).
Lu, T. K. & Collins, J. J. Dispersing biofilms with engineered enzymatic bacteriophage. Proc. Natl Acad. Sci. USA 104, 11197–11202 (2007).
Meyer, J. R. et al. Repeatability and contingency in the evolution of a key innovation in phage λ. Science 335, 428–432 (2012).
Liu, M. et al. Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science 295, 2091–2094 (2002).
Yacoby, I. & Benhar, I. Targeted filamentous bacteriophages as therapeutic agents. Expert Opin. Drug Deliv. 5, 321–329 (2008).
Edgar, R., Friedman, N., Molshanski-Mor, S. & Qimron, U. Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes. Appl. Environ. Microbiol. 78, 744–751 (2012).
Lu, T. K. & Collins, J. J. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc. Natl Acad. Sci. USA 106, 4629–4634 (2009).
Rakonjac, J., Bennett, N. J., Spagnuolo, J., Gagic, D. & Russel, M. Filamentous bacteriophage: biology, phage display and nanotechnology applications. Curr. Issues Mol. Biol. 13, 51–76 (2011).
Smith, G. P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228, 1315–1317 (1985).
Henry, K. A., Arbabi-Ghahroudi, M. & Scott, J. K. Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold. Front. Microbiol. 6, 755 (2015).
Fokine, A. & Rossmann, M. G. Molecular architecture of tailed double-stranded DNA phages. Bacteriophage 4, e28281 (2014).
Ackermann, H. W. Phage classification and characterization. Methods Mol. Biol. 501, 127–140 (2009).
Guo, F. et al. Visualization of uncorrelated, tandem symmetry mismatches in the internal genome packaging apparatus of bacteriophage T7. Proc. Natl Acad. Sci. USA 110, 6811–6816 (2013).
Wikoff, W. R. et al. Topologically linked protein rings in the bacteriophage HK97 capsid. Science 289, 2129–2133 (2000).
Kanamaru, S. et al. Structure of the cell-puncturing device of bacteriophage T4. Nature 415, 553–557 (2002).
Dai, W. et al. Visualizing virus assembly intermediates inside marine cyanobacteria. Nature 502, 707–710 (2013).
Dewey, J. S. et al. Micron-scale holes terminate the phage infection cycle. Proc. Natl Acad. Sci. USA 107, 2219–2223 (2010).
Hu, B., Margolin, W., Molineux, I. J. & Liu, J. The bacteriophage T7 virion undergoes extensive structural remodeling during infection. Science 339, 576–579 (2013).
Citorik, R. J., Mimee, M. & Lu, T. K. Bacteriophage-based synthetic biology for the study of infectious diseases. Curr. Opin. Microbiol. 19, 59–69 (2014).
Smith, H. O., Hutchison, C. A., Pfannkoch, C. & Venter, J. C. Generating a synthetic genome by whole genome assembly: ΦX174 bacteriophage from synthetic oligonucleotides. Proc. Natl Acad. Sci. USA 100, 15440–15445 (2003).
Fogg, P. C., Colloms, S., Rosser, S., Stark, M. & Smith, M. C. New applications for phage integrases. J. Mol. Biol. 426, 2703–2716 (2014).
Sauer, B. & Henderson, N. Site-specific DNA recombination in mammalian cells by the Cre recombinase of bacteriophage P1. Proc. Natl Acad. Sci. USA 85, 5166–5170 (1988).
Bonnet, J., Subsoontorn, P. & Endy, D. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc. Natl Acad. Sci. USA 109, 8884–8889 (2012).
Shis, D. L. & Bennett, M. R. Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants. Proc. Natl Acad. Sci. USA 110, 5028–5033 (2013).
Dy, R. L., Richter, C., Salmond, G. P. C. & Fineran, P. C. Remarkable mechanisms in microbes to resist viral infections. Annu. Rev. Virol. 1, 307–331 (2014).
Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007).
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).
Rath, D., Amlinger, L., Rath, A. & Lundgren, M. The CRISPR–Cas immune system: biology, mechanisms and applications. Biochimie (2015).
Doudna, J. A. & Charpentier, E. The new frontier of genome engineering with CRISPR–Cas9. Science 346, 1258096 (2014).
Liao, H. K. et al. Use of the CRISPR/Cas9 system as an intracellular defense against HIV-1 infection in human cells. Nat. Commun. 6, 6413 (2015).
Gantz, V. M. & Bier, E. The mutagenic chain reaction: a method for converting heterozygous to homozygous mutations. Science 348, 442–444 (2015).
Selle, K. & Barrangou, R. Harnessing CRISPR–Cas systems for bacterial genome editing. Trends Microbiol. 23, 225–232 (2015).
Martel, B. & Moineau, S. CRISPR–Cas: an efficient tool for genome engineering of virulent bacteriophages. Nucleic Acids Res. 42, 9504–9513 (2014).
Hendrix, R. W. Jumbo bacteriophages. Curr. Top. Microbiol. Immunol. 328, 229–240 (2009).
King, A. M. Q., Lefkowitz, E., Adams, M. J. & Carstens, E. B. Virus Taxonomy: Classification and Nomenclature of Viruses (Elsevier, 2011).
Lwoff, A., Horne, R. & Tournier, P. A system of viruses. Cold Spring Harb. Symp. Quant. Biol. 27, 51–55 (1962).
Westra, E. R., Buckling, A. & Fineran, P. C. CRISPR–Cas systems: beyond adaptive immunity. Nat. Rev. Microbiol. 12, 317–326 (2014).
van der Oost, J., Westra, E. R., Jackson, R. N. & Wiedenheft, B. Unravelling the structural and mechanistic basis of CRISPR–Cas systems. Nat. Rev. Microbiol. 12, 479–492 (2014).
Makarova, K. S. et al. An updated evolutionary classification of CRISPR–Cas systems. Nat. Rev. Microbiol. 13, 722–736 (2015).
Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163, 759–771 (2015).
Levy, A. et al. CRISPR adaptation biases explain preference for acquisition of foreign DNA. Nature 520, 505–510 (2015).
Goldberg, G. W., Jiang, W., Bikard, D. & Marraffini, L. A. Conditional tolerance of temperate phages via transcription-dependent CRISPR–Cas targeting. Nature 514, 633–637 (2014).
Fineran, P. C. et al. Degenerate target sites mediate rapid primed CRISPR adaptation. Proc. Natl Acad. Sci. USA 111, E1629–E1638 (2014).
Bondy-Denomy, J., Pawluk, A., Maxwell, K. L. & Davidson, A. R. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493, 429–432 (2013).
Seed, K. D., Lazinski, D. W., Calderwood, S. B. & Camilli, A. A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature 494, 489–491 (2013).
Acknowledgements
Research in the laboratory of G.P.C.S. is supported by grants from the UK Biotechnology and Biological Sciences Research Council (BBSRC) and the Cambridge Trusts, and through the financial support of the Society for General Microbiology, the Society for Applied Microbiology and the British Society for Plant Pathology. Research in the laboratory of P.C.F. is supported by the Marsden Fund, the Royal Society of New Zealand (RSNZ), a Rutherford Discovery Fellowship (RSNZ) to P.C.F., a University of Otago Research Grant, a Bequest Fund for Research in the Otago School of Medical Sciences and the Bio-Protection Centre of Research Excellence. The authors thank R. Dy for assistance with the preparation of some of the figures and R. Staals for comments on the manuscript. The authors apologize to the many phage researchers whose significant contributions could not be cited owing to space constraints.
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Salmond, G., Fineran, P. A century of the phage: past, present and future. Nat Rev Microbiol 13, 777–786 (2015). https://doi.org/10.1038/nrmicro3564
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DOI: https://doi.org/10.1038/nrmicro3564