Abstract
The analysis of DNA or RNA molecules has been used in a large number of studies on bacterial taxonomy and typing and for diversity studies. Undoubtedly, these methods presently dominate modern taxonomic studies as a consequence of technological progress, but primarily because the present view on classification is that it should reflect the natural relationships as encoded in the DNA. Some of these methods are not fully sequence-based, although in a number of cases they have provided considerably more information than traditional phenotypic methods (1).
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References
Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. and Swings, J. (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60, 407–438.
Gürtler, V. and Mayall, C. (2001) Genomic approaches to typing, taxonomy and evolution of bacterial isolates. Int. J. Syst. Evol. Microbiol. 51, 3–16.
Garcia-Martinez, J., Acinas, S. G., Anton, A. I., and Rodriguez-Valera, F. (1999) Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J. Microbiol. Methods 36, 55–64.
Rosselló-Mora, R. and Amann, R. (2001) The species concept for prokaryotes. FEMS Microbiol. Rev. 25, 39–67.
Yoon, J.-H., Lee, S. T., Kim, S.-B., Goodfellow, M., and Park, Y.-H. (1997) Inter and intraspecific genetic analysis of the genus Saccharomonospora with 16S to 23S ribosomal DNA (rDNA) and 23S to 5S rDNA internally transcribed spacer sequences. Int. J. Syst. Bacteriol. 47, 661–669.
Zhang, Z., Kudo, T., Nakajima, Y., and Wang, Y. (2001) Clarification of the relationship between the members of the family Thermomonosporaceae on the basis of 16S rDNA, 16S-23S rRNA internal transcribed spacer and 23S rDNA sequences and chemotaxonomic analyses. Int. J. Syst. Evol. Microbiol. 51, 373–383.
Aakra, A., Utaker, J. B., and Nes, I. F. (1999) RFLP of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidizing bacteria: a phylogenetic approach. Int. J. Syst. Bacteriol. 49, 123–130.
Gürtler, V., Rao, Y., Pearson, S. R., Bates, S. M., and Mayall, B. C. (1999) DNA sequence heterogeneity in the three copies of the long 16S-23S rDNA spacer of Enterococcus faecalis isolates. Microbiology 145, 1785–1796.
Gürtler, V. and Stanisich, V.A. (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3–16.
Mendoza, M., Meugnier, H., Bes, M., Etienne, J., and Freney, J. (1998) Identification of Staphylococcus species by 16S-23S rDNA intergenic spacer PCR analysis. Int. J. Syst. Bacteriol. 48, 1049–1055.
Daffonchio, D., Borin, S., Frova, G., Manachini, P., and Sorlini, C. (1998) PCR fingerprinting of whole genomes: the spacers between the 16S and 23S rRNA genes and of intergenic tRNA gene regions reveal a different intraspecific genomic variability of Bacillus cereus and Bacillus licheniformis. Int. J. Syst. Bacteriol. 48, 107–116.
Senesi, S., Celandroni, F., Tavanti, A., and Ghelardi, E. (2001) Molecular characterization and identification of Bacillus clausii strains marketed for use in bacteriotherapy. Appl. Environ. Microbiol. 67, 834–839.
Nakasone, K., Masui, N., Takaki, Y., Sasaki, R., Maeno, G., Sakiyama, Y., et al. (2000) Characterization and comparative study of the rrn operons of alkaliphilic Bacillus halodurans C-125. Extremophiles 4, 209–214.
Mehta, A. and Rosato, Y. B. (2001) Phylogenetic relationships of Xylella fastidiosa strains from different hosts, based on 16S rDNA and 16S-23S intergenic spacer sequences. Int. J. Syst. Evol. Microbiol. 51, 311–318.
Martínez, M. A., Delgado, O. D., Breccia, J., Baigor, M. D., and Siñeriz, F. (2002) Revision on taxonomic position of the xylanolytic Bacillus sp. MIR32 strain reidentified as Bacillus halodurans and plasmid-mediated transformation of B. halodurans species. Extremophiles, in press.
Hain, T., Ward-Rainey, N., Kroppenstedt, R. M., Stackebrandt, E., and Rainey, F. A. (1997) Discrimination of Streptomyces albidoflavus strains based on the size and number of 16S-23S ribosomal DNA intergenic spacers. Int. J. Syst. Bacteriol. 47, 202–206.
Gürtler, V. (1999) The role of recombination and mutation in 16S-23S rDNA spacer rearrangements. Gene 238, 241–252.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
Jensen, M. A., Webster, J. A., and Straus, N. (1993) Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA polymorphism. Appl. Environ. Microbiol. 59, 945–952.
Nour, M. (1998) 16S-23S and 23S-5S intergenic spacer regions of lactobacilli: nucleotide sequence, secondary structure and comparative analysis. Res. Microbiol. 149, 433–448.
Christensen, H., Jorgensen, K., and Olsen, J. E. (1999) Differentiation of Campylobacter coli and C. jejuni by length and DNA sequence of the 16S-23S rRNA internal spacer region. Microbiology 145, 99–105.
Salazar, O., Morón, R., and Genilloud, O. (2000) New genus-specific primers for the PCR identification of members of the genus Saccharomonospora and evaluation of the microbial diversity of wild-type isolates of Saccharomonospora detected from soil DNAs. Intl J. Syst. Evol. Microbiol. 50, 2043–2055.
Wunschel, D., Fox, K. F., Black, G. E., and Fox, A. (1994) Discrimination among B. cereus group, in comparison to B. subtilis, by structural carbohydrate profiles and ribosomal RNA spacer region PCR. Syst. Appl. Microbiol. 17, 625–635.
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Martínez, M.A., Siñeriz, F. (2004). PCR Fingerprinting of rRNA Intergenic Spacer Regions for Molecular Characterization of Environmental Bacteria Isolates. In: Walker, J.M., Spencer, J.F.T., Ragout de Spencer, A.L. (eds) Environmental Microbiology. Methods in Biotechnology, vol 16. Humana Press. https://doi.org/10.1385/1-59259-765-3:159
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DOI: https://doi.org/10.1385/1-59259-765-3:159
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