Skip to main content

Phage Classification and Characterization

  • Protocol
Bacteriophages

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 501))

Abstract

Prokaryote viruses include 14 officially accepted families and at least five other potential families awaiting classification. Approximately 5,500 prokaryote viruses have been examined in the electron microscope. Classification has a predictive value and is invaluable to control experimental techniques and results. In describing viruses, the choice of methods depends on structure and taxonomical position of viruses. The study of isometric, filamentous, and pleomorphic viruses requires more detailed investigations than that of tailed species.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 239.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Sneath, P.H.A. and Sokal R.R. (1973) Numerical taxonomy, The Principles and Practice of Numerical Classification. W.H. Freeman, San Francisco, pp. 23 and 110.

    Google Scholar 

  2. Sneath, P.H.A. (1989) Analysis and interpretation of sequence data for bacterial systematics: the view of a numerical taxonomist. System. Appl. Microbiol. 12, 15–31.

    Google Scholar 

  3. d’H’érelle, F., (1918) Technique de la recherche du microbe filtrant bact’ériophage (Bacteriophagum intestinale). C.R. Soc. Biol., 81, 1160–1162.

    Google Scholar 

  4. Ruska, H. (1943) Versuch zu einer Ordnung der Virusarten. Arch. Ges. Virusforsch. 2, 480–498.

    Article  Google Scholar 

  5. Holmes, F.O. (1948) Order Virales; the filterable viruses, in Bergey’s Manual of Determinative Biology, 6th ed. (Breed, R.S., Murray, E.G.D., and Hitchens, A.P., eds.), Williams & Wilkins, Baltimore, pp. 1126–1144.

    Google Scholar 

  6. Lwoff, A., Horne, R.W., and Tournier P. (1962) A system of viruses. Cold Spring Harbor Symp. Quant. Biol. 27, 51–62.

    CAS  PubMed  Google Scholar 

  7. P.C.N.V. (1965) Proposals and recommendations of the Provisional Committee on Taxonomy of Viruses (P.C.N.V.). Ann Inst Pasteur 109, 625–637.

    Google Scholar 

  8. Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball L.A., eds. (2005) Virus Taxonomy: VIIIth Report of the International Committee on Taxonomy of Viruses. Academic Press/Elsevier, London, pp. 35–116, 279–295, 443–446, 741–750.

    Google Scholar 

  9. Ackermann, H.-W. and DuBow, M.S. (1987) Viruses of Prokaryotes, Vol. 1, General Properties of Bacteriophages, CRC Press, Boca Raton, pp. 13–28 and 130–135.

    Google Scholar 

  10. Ackermann H.-W. (2005) Bacteriophage classification. In: Bacteriophages – Biology and Applications, eds. E. Kutter, A. Sulakvelidze. CRC Press, Boca Raton, FL, pp. 67–89.

    Google Scholar 

  11. Bath, C., Cukalac, T., Porter, K., Dyall-Smith, M.L. (2006) His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology. 350, 228–39.

    Article  CAS  PubMed  Google Scholar 

  12. Bradley, D.E. (1997) Ultrastructure of bacteriophages and bacteriocins. Bacteriol. Rev. 31, 230–314.

    Google Scholar 

  13. Van Regenmortel, M.H.V. (1990) Virus species, a much neglected but essential concept in virus classification. Intervirology 31:241–271.

    Google Scholar 

  14. Ackermann, H.-W. (2007) 5500 Phages examined in the electron microscope. Arch. Virol. 152:277–243.

    Article  Google Scholar 

  15. Porter, K., Kukkaro, P., Bamford, J.K.H., Bath, C., Kivelä, H.M., Dyall-Smith, M.L., and Bamford D.H. (2005) SH1: A novel, spherical halovirus isolated from an Australian hypersaline lake. Virology 335, 22–33.

    Article  CAS  PubMed  Google Scholar 

  16. Rice, G., Tang, L., Stedman, K., Roberto, F., Spuhler, J., Gillitzer, E., Johnson, J.E., Douglas, T., and Young, M. (2004) The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life. Proc. Natl. Acad. Sci. USA 101, 7716–7720.

    Article  CAS  PubMed  Google Scholar 

  17. Häring, M., Vestergaard, G., Rachel, R., Chen, L., Garrett, R.A., and Prangishvili, D. (2005) Independent virus development outside a host. Nature 436, 1101–1102.

    Article  PubMed  Google Scholar 

  18. Häring, M., Rachel, R., Peng, X., Garrett, R.A., and Prangishvili, D. (2005) Viral diversity in hot springs of Pozzuoli, Italy, and characterization of a unique bottle-shaped archaeal virus, Acidicanus bottle-shaped virus, from a new family, the Ampullaviridae. J. Virol. 79, 9904–9911.

    Article  PubMed  Google Scholar 

  19. Häring, M., Peng, X., Brügger, K., Rachel, R., Stetter, K.O., Garrett, R.A., and Prangishvili, D. (2004) Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae. Virology 323, 233–242.

    Article  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  21. Lawrence, J.G., Hatfull, G.F., and Hendrix, R.W. (2002) Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J. Bacteriol. 184, 4891–4905.

    Article  CAS  PubMed  Google Scholar 

  22. Proux, C., van Sinderen, D., Suarez, J., Garcia, P., Ladero, V., Fitzgerald, G.F., Desiere, F., and Brüssow H. (2002) The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria. J. Bacteriol. 184, 6026–6036.

    Article  CAS  PubMed  Google Scholar 

  23. Ge, F., Wang, L.-S., and Kim J. (2005) The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PloS Biol 3:e316 (8 pp.).

    Article  PubMed  Google Scholar 

  24. Rohwer, F. and Edwards, R. (2002) The Phage Proteomic Tree: a genome-based taxonomy for phage. J. Bacteriol. 184, 4529–4535.

    Article  CAS  PubMed  Google Scholar 

  25. Adams M.J. and Antoniv J.F. (2006) DPVweb: a comprehensive database of plant and fungal virus gene and genomes. Nucleic Acids Res. 34, D382–385 (Database Issue).

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Ackermann, HW. (2009). Phage Classification and Characterization. In: Clokie, M.R., Kropinski, A.M. (eds) Bacteriophages. Methods in Molecular Biology™, vol 501. Humana Press. https://doi.org/10.1007/978-1-60327-164-6_13

Download citation

  • DOI: https://doi.org/10.1007/978-1-60327-164-6_13

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-682-5

  • Online ISBN: 978-1-60327-164-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics