Bacterial Taxonomy and Methods in Identifying New Species

Abstract

 The system which separates the microorganisms into the different groups by considering the similar and different characteristics of the microorganisms is named taxonomy. Molecular diagnostic methods as alternatives to conventional methods used for classification and naming of bacteria have been developed, including the 16S rRNA sequence analysis and DNA: DNA hybridization methods have been put forward as the most current techniques. Strains showing 70% or more DNA: DNA hybridization and 97% or more 16S rRNA sequence homology is considered to be the same species. As a result of these rates, strains which have been identified as different bacterial species can be published in various scientific journals and by entering the national culture collection thought monitoring official protocols. In this paper, requisite methods to identify new bacterial species are summarized briefly explaining the conditions to enter into the national culture collections.

Keywords

• Bacteria,hybridization,taxonomy,16S rRNA

Bakteriyel Taksonomi ve Yeni Türlerin Belirlenmesinde Kullanılan Yöntemler

Abstract

Mikroorganizmaların farklı ve benzer özelliklerini dikkate alarak gruplara ayırma ve belirleme işlemlerinin oluşturduğu sisteme taksonomi denir. Bakterilerin sınıflandırması ve adlandırması için kullanılan konvansiyonel yöntemlere alternatif olarak moleküler tanı yöntemleri geliştirilmiş, bunlar arasında da 16S rRNA dizi analizi ve DNA:DNA hibridizasyon yöntemleri en geçerli teknikler olarak ortaya konulmuştur. Sınıflandırmada %70 veya daha fazla DNA:DNA hibridizasyonu gösteren ve 16S rRNA sekanslamasında %97 veya daha fazla benzerlik gösteren suşlar aynı tür olarak dikkate alınır. İdentifiye edilen türler belirlenen kurallara göre çeşitli bilimsel dergilerde yayımlanır ve resmi protokoller izlenerek ulusal kültür koleksiyonlarında yer alırlar. Bu derlemede, yeni bakteri türlerini tanımlayabilmek için gerekli olan metotlar kısaca anlatılarak bu türlerin sınıflandırılması ve ulusal kültür koleksiyonlarına girebilmesi için gerekli koşullar özetlenmiştir.

Keywords

• Bakteri,hibridizasyon,taksonomi,16S rRNA

References

1. 1. Achtman M, Wain J, Weill FX, Nair S, Zhou Z, Sangal V, Krauland MG, Hale JL, Harbottle H, Uesbeck A,Dougan G, Harrison LH, Brisse S, the S. enterica MLST study group. Multilocus sequence typing as a replacement for serotyping in Salmonella enterica. PLoS Pathogens. 2012; 8(6):e1002776.
2. 2. Arda M. Temel Mikrobiyoloji. Dördüncü baskı. Ankara: Medisan, 2000; p.1-13
3. 3. Chairman JFI. International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of phototrophic bacteria. Minutes of the closed on-line meeting, June 10–30, 2014; Tubingen-Germany.
4. 4. Chakravorty S, Helb D, Burday M, Connell N, Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Meth. 2007; 69(2):330-9.
5. 5. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol. 2014;64(Pt 2):316-24.
6. 6. Erişim adresi: http://141.150.157.117.8080/prokPUB/index.htm. Erişim tarihi: 02.10.14.
7. 7. Erişim adresi: http://mlst.warwick.ac.uk/mlst/dbs/Senterica. Erişim tarihi: 10.11.14.
8. 8. Erişim adresi: http://www.bacterio.net/-news.html. Erişim tarihi: 16.11.14.

9. 9. Erişim adresi: http://www.dsmz.de/bactnom/bactname.htm. Erişim tarihi: 16.11.14.
10. 10. Erişim adresi: http://www.ncbi.nlm.nih.gov/BLAST. Erişim tarihi: 01.11.14.
11. 11. Erişim adresi: http://rdp.cme.msu.edu/html. Erişim tarihi:14.09.14.
12. 12. Erişim adresi: http://www.bergeys.org/pubinfo.html. Erişim tarihi:21.11.14.
13. 13. Erişimadresi:www.uab.cat/servlet/Satellite?cid=1096481466574&pagename=UABDivulga%2Fage%2FTemplatePageDetallArticleInvestigar¶m1=1096483529658.Erişim tarihi:19.11.14.
14. 14. Freeman S, Herron JC. Evolutionary Analysis. Fourth edition. Pearson Education. 2009.
15. 15. Kaya İB, Karacan N, Özdal M, Mete Ş, Diker KS. Veteriner Klinik Örneklerde Direkt 16S rRNA Dizi Analizi İle Bakteriyel Tanı. 8. Ulusal Moleküler ve Tanısal Mikrobiyoloji Kongresi. 4-7 Haziran 2014/ANKARA. 2014.
16. 16. Klein G, Pack A, Bonaparte C, Reuter G. Taxonomy and physiology of probiotic lactic acid bacteria. Int J Food Microbiol. 1998;41(2):103-25.
17. 17. Klijn N, Weerkamp AH, de Vos WM. Identification of mesophilic lactic acid bacteria by using polymerase chain reaction-amplified variable regions of 16S rRNA and specific DNA probes. Appl Environ Microbiol. 1991; 57(11):3390-3.
18. 18. Michael TM, John MM. Brock Biology of Microorganisms, 13th Edition. Pearson Education, Inc. Publishing as Prentice Hall. O-13-144329-1. 2012.
19. 19. Nogales B, Moore ER, Llobet-Brossa E, Rossello-Mora R, Amann R, Timmis K.N. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol. 2001;67(4):1874-84.
20. 20. Palmer KL, Kos VN, Gilmore MS. Horizontal gene transfer and the genomics of enterococcal antibiotic resistance. Curr Opin Microbiol. 2010;13(5):632-9.
21. Piccirillo A, Giacomelli M, Salata C, Bettanello S, De Canale E, Palù G. Multilocus sequence typing of Campylobacter jejuni and Campylobacter coli from humans and chickens in North-Eastern Italy. New Microbiol. 2014; 37(4):557-62.
22. 22. Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M, Sentausa E, Raoult D, Fournier PE. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol. 2014; 64(Pt 2):384-91.
23. 23. Rudi K, Skulberg OM, Larsen F, Jakobsen KS. Strain characterization and classification of oxyphotobacteria in clone cultures on the basis of 16S rRNA sequences from the variable regions V6, V7, and V8. Appl Environ Microbiol. 1997; 63(7):2593-9.
24. 24. Stackebrandt E, Teuber M. Molecular taxonomy and phylogenetic position of lactic acid bacteria. Biochimie. 1988; 70(3):317-24.
25. 25. Stackebrant E, Goebel BM. Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology Int J Syst Bacteriol October 1994 44:846.849
26. 26. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL. Microbial genomic taxonomy. BMC Genomics. 2013; 14: 913.
27. 27. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev. 1996; 60(2):407-38.
28. 28. Willems A, Collins MD. Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences. Int J Syst Bacteriol. 1993; 43(2):305-13
29. 29. Wuyts J, Van de Peer Y, Winkelmans T, De Wachter R. The European database on small subunit ribosomal RNA. Nucleic Acids Res. 2002; 30(1):183-5.
30. 30. Xu XB, Yuan ZA, Jin HM, Xiao WJ, Gu BK, Chen M, Ran L, Diao BW, Cui ZG, Hu QH, Kan B. Study on the epidemiological characteristics and molecular typing of Salmonella enterica subsp. enterica serovar Senftenberg in Shanghai. Zhonghua Liu Xing Bing Xue Za Zhi. 2009;30(9):933-7.