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Taxonomy of Thermophilic Phages (Turkish with English Abstract)

Year 2009, Volume: 34 Issue: 4, 251 - 258, 01.08.2009

Abstract

Approximately 5100 bacteriophages have been examined to date and most of these phages belong to Siphoviridae family according to the classification of Bradley and Ackermann. Thermophilic phages, specific for S. thermophilus and L. bulgaricus strains which are used in yogurt production, are classified in B group of Bradley classification because of having icosahedral capsid and noncontractile long tail and are also classified in Siphoviridae family of Ackermann classification because of having linear double stranded DNA. Recently, phages are classified according to the polythetic species concept, developed by ICTV, which considers the properties of phages such as nucleic acid nature, particle structure, DNA hybridization, nucleotide and amino acid sequences. Besides, phages have been classified in various studies according to their restriction endonuclease and protein patterns, DNA-DNA hybridization, sequence analysis and serological properties, but, the results of these studies can be compared with each other after analyzed within the study. New classification approaches in which all kind of parameters are taken into account arouse interest as most of the methods used today do not correspond the requirements of phage taxonomy.

References

  • Ackermann H W. 2006. ClassiŞcation of Bacteriopha- ge, In The Bacteriophage, 2nd., R Calendar, pp. 8-16, Ox- ford University Press, USA.
  • Brussow H, Frémont M, Bruttin A, Sidoti J, Cons- tabla A, Fryder V. 1994a. Detection and ClassiŞcation of Streptococcus thermophilus Bacteriophages Isolated from Industrial Milk Fermentation. Appl Environ Micro- biol, 60 (12): 4537-4543.
  • Mata M, Trautwetter A, Luthaud G, Ritzenthaler P. Thirteen virulent and temperate bacteriophages of Lactobacillus bulgaricus and Lactobacillus lactis belong to a single DNA homology group. Appl Environ Micro- biol, 52 (4): 812-818. Cluzel PJ, Veaux M, Rousseau M, Accolas JP. 1987.
  • Evidence for temperate bacteriophages in two strains of Lactobacillus bulgaricus. J Dairy Res, 54: 397-405. Kivi S, Peltomäki T, Luomala K, Sarimo SS. 1987.
  • Some properties of Streptococcus thermophilus bacteri- ophages. Fotra Microbiol, 32: 101-106. Chow J, Batt CA, Sinskey AJ. 1988. Characterization of Lactobacillus bulgaricus bacteriophage ch2. Appl En- viron Microbiol, 54 (5): 1138-1142.
  • Prevots F, Relano P, Mata M, Ritzenthaler P. 1989. Clo- se relationship of virulent bacteriophages of Streptococ- cus salivarius subsp. thermophilus at both the protein and the DNA level. J Gen Microbiol, 135: 3337-3344.
  • Benbadis L, Faelen M, Slos P, Fazel A, Mercenier A. Characterization and comparison of virulent bac- teriophages of Streptococcus thermophilus isolated from yogurt. Biochimie, 72: 855-862. Lahbib-Mansais Y, Boizet B, Dupont L, Mata M, Rit- zenthaler P. 1992. Characterization of a temperate bac- teriophage of Lactobacillus delbrueckii subsp. bulgari- cus and its interactions with the host cell chromosome. J Gen Microbiol, 138: 1139-1146.
  • Fayard B, Haefliger M, Accolas JP. 1993. Interacti- on of temperate bacteriophages of Streptococcus sali- varius subsp. thermophilus with lysogenic affect phage
  • DNA restriction pattern and host ranges. J Dairy Res, 60: 399. Le Marrec C, Sinderen D, Walsh L, Stanley E, Vlegels E, Moineau S, Heinze P, Fitzgerald G, Fayard B. 1997.
  • Two groups of bacteriophages Streptococcus thermophi- lus can be distinguished on the basis of mode of packa- ging and genetic determinants for major structural pro- teins. Appl Environ Microbiol, 63 (8): 3246-3253.
  • Auad L, Raisanen L, Raya RR, Alatossava T. 1999.
  • Physical mapping and partial genetic characterizationof the Lactobacillus delbrueckii subsp. bulgaricus bacteri- ophage lb539. Arch Virol, 144: 1503-1512.
  • Quiberoni A, Auad L, Binetti AG, Suarez VB, Reinhe- imer JA, Raya RR. 2003. Comparative analysis of Strepto- coccus thermophilus bacteriophages isolated from a yog- hurt industrial plant. Food Microbiol, 20: 461-469.
  • Quiberoni A, Guglielmotti DM, Binetti A, Reinhe- imer JA. 2004. Characterization of three Lactobacillus delbrueckii subsp. bulgaricus phages and the physicoc- hemical analysis of phage adsorption. J Appl Microbiol, : 340-351.
  • Tunail N, Açık L, Acar E, Özyurt Ş, Kahraman E, Çe- lebi A. 2006. Yerel (doğal) S. thermophilus ve Lb. bulga- ricus ile özgül fajlarının edüstriyel öneme sahip özellik- ler açısından tanımlanarak alternatif starterlerin belir- lenmesi. Ankara Üniversitesi Biyoteknoloji Enstitüsü 67 nolu proje.
  • Moineau S, Levesque C. 2005. Control of Bacteriop- hages in Industrial Fermentations, In: Bacteriophages
  • Biology and Applications, E Kutter and A Sulakvelidze (eds), pp. 285- 297, CRC Press, USA. ICTV http://phene.cpmc.columbia.edu/Ictv Summers WC. 2005. Bacteriophage Research: Early
  • History, In: Bacteriophages Biology and Applications, E Kutter and A Sulakvelidze (eds), pp. 5-29, CRC Press, USA. Ackermann HW. 1987. Bacteriophage taxonomy in Microbiol Sci, 4: 214-218.
  • Ackermann HW. 1991. Phagentexonomie 1990:
  • Stand and Probleme. Bioforum, 11/91: 419-426. Ackermann HW. 2001. Frequency of morphologi- cal phage descriptions in the year 2000. Arch Virol, 146: 857.
  • Ackermann HW. 2003. Bacteriophage observations and evolution. Res Microbiol, 154: 245-251.
  • Maniloff J, Ackermann HW. 1998. Taxonomy of bac- terial viruses: establishment of tailed virus genera and the order Caudovirales. Arch Virol, 143 (10): 2051-2063.
  • Schlegel HG. 1985. Allgemeine Mikrobiologie, 6. Übe- rarbaytete Auflage. Georg Thieme Verlag, Stuttgart, pp:
  • Prescott LM, Harley JP, Klein DA. 1993. Microbio- logy, Wm. C. Brown Communication, Inc., 2nd. Edition, USA, pp. 912.
  • Hendrix RW. 2002. Bacteriophage λ and Its Relati- ves, In Modern Microbial Genetics, 2nd UN Streips and RE Yasbin (eds), A John Willey&Sons, Inc., Publication, New York.
  • Hendrix RW. 2003. Bacteriophage genomics. Cur Opin Microbiol, 6: 506-511.
  • Brussow H, Desiere F. 2006. Evolution of Tailed Pha- ges: Insights from Comparative Phage Genomics, In The Bacteriophage, 2nd., R Calendar (ed), Oxford University Press, USA, pp. 26-37.
  • Desiere F, Lucchini S, Canchaya C, Ventura M, Brus- sow H. 2002. Comparative genomics of phages and prophages in lactic acid bacteria. Antonie van Leeuwen- hoek, 82: 73-91.
  • Brussow H. 2001. Phages of dairy bacteria. Annu Rev Microbiol, 55: 283-303.
  • Brussow, H., Suarez, J. E. 2006. Lactobacillus phages,
  • In The Bacteriophage, 2nd., R Calendar (ed), Oxford Uni- versity Press, USA, pp. 653-667. Brussow H, Desiere F. 2001. Comparative phage ge- nomics and the evolution of Siphoviridae: insights from dairy phages. Mol Microbiol, 39 (2): 213-222.
  • Tremblay DM, Moineau S. 1999. Complete genomic sequence of the lytic bacteriophage DT1 of Streptococ- cus thermophilus. Virology, 255: 63-76.
  • Brussow H, Kutter E. 2005. Phage Ecology, In: Bacte- riophages Biology and Applications, E Kutter and A Su- lakvelidze (eds), CRC Press, USA, pp. 129-165.
  • Desiere F, Pridmore RD, Brussow H. 2000. Compara- tive genomics of the late gene cluster from Lactobacillus phages. Virology, 275: 294-305.
  • Accolas JP, Spillmann H. 1979. The morphology of six bacteriophage of Streptococcus thermophilus. J Appl Bacteriol, 47: 135-144.
  • Reinbold GW, Reddy MS, Hammond EG. 1982. Ult- rastructures of bacteriophages active against Streptococ- cus thermophilus, Lactobacillus bulgaricus, Lactobacil- lus lactis and Lactobacillus helveticus. J Food Prot, 45 (2): 124.
  • Krusch U, Neve H, Luschei B, Teuber M. 1987. Cha- racterization of virulent bacteriophages of Streptococ- cus salivarius subsp. thermophilus by host speciŞty and electron microscopy. Kieler Milchwirtschaftliche Fors- chungsberichte, 39 (3): 155-167.
  • Neve, H., Krusch, U., Teuber, M. 1989. ClassiŞcation of virulent bacteriophages of Streptococcus salivarius subsp. thermophilus isolated from yoghurt and Swiss- type cheese. Appl Microbiol Biotechnol, 30: 624-629.
  • Brussow H, Probst A, Fremont M, Sidoti J. 1994b.
  • Distinct Streptococcus thermophilus bacteriophages sha- re an extremely conserved DNA fragment. Virology, 200: 857. Acar E. 2002. Yoğurt starter kültür fajlarının elekt- ron mikroskobu ile morfolojik karakterizasyonu, Ankara
  • Üniversitesi Fen Bilimleri Enstitüsü Gıda Mühendisliği Anabilim Dalı Yüksek Lisans Tezi, 102 s. Ankara. Tunail N, Ayhan K, Akçelik M, Durlu Özkaya F, Do- ğan HB, Kaleli D, Tükel Ç, Acar E. 2002. Yoğurt fabrika- larında faj probleminin çözümüne yönelik araştırmalar,
  • TÜBİTAK/TARP-2106 Nolu Proje.
  • Acar Soykut E. 2007. Streptococcus thermophilus ve Lactobacillus bulgaricus virülent fajlarının replikas- yon parametreleri, kapsid protein proŞlleri ve restriksi- yon endonükleaz analizleri esas alınarak tanımlanmala- rı ve sınıflandırılmaları. Ankara Üniversitesi Fen Bilim- leri Enstitüsü Gıda Müh. Ana Bilim Dalı Doktora tezi, s, Ankara.

Termofilik Faj Taksonomisi

Year 2009, Volume: 34 Issue: 4, 251 - 258, 01.08.2009

Abstract

Bugüne kadar incelenmiş olan yaklaşık 5100 adet fajın çoğu, Bradley ve Ackermann sınıflamalarına göre Siphoviridae familyasında bulunmaktadır. Yoğurt yapımında kullanılan S. thermophilus ve L. bulgaricus suşlarına özgül termofilik fajlar da ikosahedral kapside, kontraktil olmayan uzun kuyruğa sahip olmaları nedeniyle Bradley sınıflaması B grubuna ve lineer çift sarmal DNA içermelerinden dolayı Ackermann sınıflaması Siphoviridae familyasına dahil edilmişlerdir. Günümüzde fajlar, ICTV tarafından oluşturulan ve politetik türler kavramı olarak adlandırılan, nükleik asit doğası ve partikül yapısına ek olarak DNADNA hibridizasyonu, nükleotit veya aminoasit sekansları gibi parametrelerin de dikkate alındığı taşınabilir kriterler seti ile aileye kadar sınıflandırılabilmektedir. Ayrıca fajlar, yapılan farklı araştırmalarda, konakçı özgüllükleri, restriksiyon endonükleaz kesim şablonları, DNA hibridizasyon ve sekans analizleri, yapısal protein profilleri ve serolojik test sonuçlarına göre sınıflandırılmakta ancak herbir çalışmada elde edilen sonuçlar kendi içinde değerlendirildikten sonra diğer çalışma sonuçları ile karşılaştırmaya çalışılmaktadır. Kullanılan kriterlerden çoğunun faj taksonomisine hizmet etmede yetersiz kaldığı, bununla beraber her türlü kriterin değerlendirilmeye çalışıldığı ayrıca bu konuda farklı yeni yaklaşımlar üzerinde durulduğu görülmektedir.

References

  • Ackermann H W. 2006. ClassiŞcation of Bacteriopha- ge, In The Bacteriophage, 2nd., R Calendar, pp. 8-16, Ox- ford University Press, USA.
  • Brussow H, Frémont M, Bruttin A, Sidoti J, Cons- tabla A, Fryder V. 1994a. Detection and ClassiŞcation of Streptococcus thermophilus Bacteriophages Isolated from Industrial Milk Fermentation. Appl Environ Micro- biol, 60 (12): 4537-4543.
  • Mata M, Trautwetter A, Luthaud G, Ritzenthaler P. Thirteen virulent and temperate bacteriophages of Lactobacillus bulgaricus and Lactobacillus lactis belong to a single DNA homology group. Appl Environ Micro- biol, 52 (4): 812-818. Cluzel PJ, Veaux M, Rousseau M, Accolas JP. 1987.
  • Evidence for temperate bacteriophages in two strains of Lactobacillus bulgaricus. J Dairy Res, 54: 397-405. Kivi S, Peltomäki T, Luomala K, Sarimo SS. 1987.
  • Some properties of Streptococcus thermophilus bacteri- ophages. Fotra Microbiol, 32: 101-106. Chow J, Batt CA, Sinskey AJ. 1988. Characterization of Lactobacillus bulgaricus bacteriophage ch2. Appl En- viron Microbiol, 54 (5): 1138-1142.
  • Prevots F, Relano P, Mata M, Ritzenthaler P. 1989. Clo- se relationship of virulent bacteriophages of Streptococ- cus salivarius subsp. thermophilus at both the protein and the DNA level. J Gen Microbiol, 135: 3337-3344.
  • Benbadis L, Faelen M, Slos P, Fazel A, Mercenier A. Characterization and comparison of virulent bac- teriophages of Streptococcus thermophilus isolated from yogurt. Biochimie, 72: 855-862. Lahbib-Mansais Y, Boizet B, Dupont L, Mata M, Rit- zenthaler P. 1992. Characterization of a temperate bac- teriophage of Lactobacillus delbrueckii subsp. bulgari- cus and its interactions with the host cell chromosome. J Gen Microbiol, 138: 1139-1146.
  • Fayard B, Haefliger M, Accolas JP. 1993. Interacti- on of temperate bacteriophages of Streptococcus sali- varius subsp. thermophilus with lysogenic affect phage
  • DNA restriction pattern and host ranges. J Dairy Res, 60: 399. Le Marrec C, Sinderen D, Walsh L, Stanley E, Vlegels E, Moineau S, Heinze P, Fitzgerald G, Fayard B. 1997.
  • Two groups of bacteriophages Streptococcus thermophi- lus can be distinguished on the basis of mode of packa- ging and genetic determinants for major structural pro- teins. Appl Environ Microbiol, 63 (8): 3246-3253.
  • Auad L, Raisanen L, Raya RR, Alatossava T. 1999.
  • Physical mapping and partial genetic characterizationof the Lactobacillus delbrueckii subsp. bulgaricus bacteri- ophage lb539. Arch Virol, 144: 1503-1512.
  • Quiberoni A, Auad L, Binetti AG, Suarez VB, Reinhe- imer JA, Raya RR. 2003. Comparative analysis of Strepto- coccus thermophilus bacteriophages isolated from a yog- hurt industrial plant. Food Microbiol, 20: 461-469.
  • Quiberoni A, Guglielmotti DM, Binetti A, Reinhe- imer JA. 2004. Characterization of three Lactobacillus delbrueckii subsp. bulgaricus phages and the physicoc- hemical analysis of phage adsorption. J Appl Microbiol, : 340-351.
  • Tunail N, Açık L, Acar E, Özyurt Ş, Kahraman E, Çe- lebi A. 2006. Yerel (doğal) S. thermophilus ve Lb. bulga- ricus ile özgül fajlarının edüstriyel öneme sahip özellik- ler açısından tanımlanarak alternatif starterlerin belir- lenmesi. Ankara Üniversitesi Biyoteknoloji Enstitüsü 67 nolu proje.
  • Moineau S, Levesque C. 2005. Control of Bacteriop- hages in Industrial Fermentations, In: Bacteriophages
  • Biology and Applications, E Kutter and A Sulakvelidze (eds), pp. 285- 297, CRC Press, USA. ICTV http://phene.cpmc.columbia.edu/Ictv Summers WC. 2005. Bacteriophage Research: Early
  • History, In: Bacteriophages Biology and Applications, E Kutter and A Sulakvelidze (eds), pp. 5-29, CRC Press, USA. Ackermann HW. 1987. Bacteriophage taxonomy in Microbiol Sci, 4: 214-218.
  • Ackermann HW. 1991. Phagentexonomie 1990:
  • Stand and Probleme. Bioforum, 11/91: 419-426. Ackermann HW. 2001. Frequency of morphologi- cal phage descriptions in the year 2000. Arch Virol, 146: 857.
  • Ackermann HW. 2003. Bacteriophage observations and evolution. Res Microbiol, 154: 245-251.
  • Maniloff J, Ackermann HW. 1998. Taxonomy of bac- terial viruses: establishment of tailed virus genera and the order Caudovirales. Arch Virol, 143 (10): 2051-2063.
  • Schlegel HG. 1985. Allgemeine Mikrobiologie, 6. Übe- rarbaytete Auflage. Georg Thieme Verlag, Stuttgart, pp:
  • Prescott LM, Harley JP, Klein DA. 1993. Microbio- logy, Wm. C. Brown Communication, Inc., 2nd. Edition, USA, pp. 912.
  • Hendrix RW. 2002. Bacteriophage λ and Its Relati- ves, In Modern Microbial Genetics, 2nd UN Streips and RE Yasbin (eds), A John Willey&Sons, Inc., Publication, New York.
  • Hendrix RW. 2003. Bacteriophage genomics. Cur Opin Microbiol, 6: 506-511.
  • Brussow H, Desiere F. 2006. Evolution of Tailed Pha- ges: Insights from Comparative Phage Genomics, In The Bacteriophage, 2nd., R Calendar (ed), Oxford University Press, USA, pp. 26-37.
  • Desiere F, Lucchini S, Canchaya C, Ventura M, Brus- sow H. 2002. Comparative genomics of phages and prophages in lactic acid bacteria. Antonie van Leeuwen- hoek, 82: 73-91.
  • Brussow H. 2001. Phages of dairy bacteria. Annu Rev Microbiol, 55: 283-303.
  • Brussow, H., Suarez, J. E. 2006. Lactobacillus phages,
  • In The Bacteriophage, 2nd., R Calendar (ed), Oxford Uni- versity Press, USA, pp. 653-667. Brussow H, Desiere F. 2001. Comparative phage ge- nomics and the evolution of Siphoviridae: insights from dairy phages. Mol Microbiol, 39 (2): 213-222.
  • Tremblay DM, Moineau S. 1999. Complete genomic sequence of the lytic bacteriophage DT1 of Streptococ- cus thermophilus. Virology, 255: 63-76.
  • Brussow H, Kutter E. 2005. Phage Ecology, In: Bacte- riophages Biology and Applications, E Kutter and A Su- lakvelidze (eds), CRC Press, USA, pp. 129-165.
  • Desiere F, Pridmore RD, Brussow H. 2000. Compara- tive genomics of the late gene cluster from Lactobacillus phages. Virology, 275: 294-305.
  • Accolas JP, Spillmann H. 1979. The morphology of six bacteriophage of Streptococcus thermophilus. J Appl Bacteriol, 47: 135-144.
  • Reinbold GW, Reddy MS, Hammond EG. 1982. Ult- rastructures of bacteriophages active against Streptococ- cus thermophilus, Lactobacillus bulgaricus, Lactobacil- lus lactis and Lactobacillus helveticus. J Food Prot, 45 (2): 124.
  • Krusch U, Neve H, Luschei B, Teuber M. 1987. Cha- racterization of virulent bacteriophages of Streptococ- cus salivarius subsp. thermophilus by host speciŞty and electron microscopy. Kieler Milchwirtschaftliche Fors- chungsberichte, 39 (3): 155-167.
  • Neve, H., Krusch, U., Teuber, M. 1989. ClassiŞcation of virulent bacteriophages of Streptococcus salivarius subsp. thermophilus isolated from yoghurt and Swiss- type cheese. Appl Microbiol Biotechnol, 30: 624-629.
  • Brussow H, Probst A, Fremont M, Sidoti J. 1994b.
  • Distinct Streptococcus thermophilus bacteriophages sha- re an extremely conserved DNA fragment. Virology, 200: 857. Acar E. 2002. Yoğurt starter kültür fajlarının elekt- ron mikroskobu ile morfolojik karakterizasyonu, Ankara
  • Üniversitesi Fen Bilimleri Enstitüsü Gıda Mühendisliği Anabilim Dalı Yüksek Lisans Tezi, 102 s. Ankara. Tunail N, Ayhan K, Akçelik M, Durlu Özkaya F, Do- ğan HB, Kaleli D, Tükel Ç, Acar E. 2002. Yoğurt fabrika- larında faj probleminin çözümüne yönelik araştırmalar,
  • TÜBİTAK/TARP-2106 Nolu Proje.
  • Acar Soykut E. 2007. Streptococcus thermophilus ve Lactobacillus bulgaricus virülent fajlarının replikas- yon parametreleri, kapsid protein proŞlleri ve restriksi- yon endonükleaz analizleri esas alınarak tanımlanmala- rı ve sınıflandırılmaları. Ankara Üniversitesi Fen Bilim- leri Enstitüsü Gıda Müh. Ana Bilim Dalı Doktora tezi, s, Ankara.
There are 43 citations in total.

Details

Primary Language Turkish
Journal Section Articles
Authors

Esra Acar Soykut This is me

Nezihe Tunail This is me

Publication Date August 1, 2009
Published in Issue Year 2009 Volume: 34 Issue: 4

Cite

APA Soykut, E. A. ., & Tunail, N. . (2009). Termofilik Faj Taksonomisi. Gıda, 34(4), 251-258.
AMA Soykut EA, Tunail N. Termofilik Faj Taksonomisi. The Journal of Food. August 2009;34(4):251-258.
Chicago Soykut, Esra Acar, and Nezihe Tunail. “Termofilik Faj Taksonomisi”. Gıda 34, no. 4 (August 2009): 251-58.
EndNote Soykut EA, Tunail N (August 1, 2009) Termofilik Faj Taksonomisi. Gıda 34 4 251–258.
IEEE E. A. . Soykut and N. . Tunail, “Termofilik Faj Taksonomisi”, The Journal of Food, vol. 34, no. 4, pp. 251–258, 2009.
ISNAD Soykut, Esra Acar - Tunail, Nezihe. “Termofilik Faj Taksonomisi”. Gıda 34/4 (August 2009), 251-258.
JAMA Soykut EA, Tunail N. Termofilik Faj Taksonomisi. The Journal of Food. 2009;34:251–258.
MLA Soykut, Esra Acar and Nezihe Tunail. “Termofilik Faj Taksonomisi”. Gıda, vol. 34, no. 4, 2009, pp. 251-8.
Vancouver Soykut EA, Tunail N. Termofilik Faj Taksonomisi. The Journal of Food. 2009;34(4):251-8.

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