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Identification using RNA sequencing

Partial 16S rRNA gene sequence analysis is a useful tool for preliminary identification of a strain. 
Complete 16S rRNA gene sequencing is used for a more detailed discrimination of isolates against validly described type strains.

Required material: A living culture (agar plate or slant) is preferred. Lyophilized material might as well be sent.

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Dr. Cathrin Spröer

Senior scientist

References

  1. Kumar, S., Stecher, G. & Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution (accepted)
  2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215:403-410
  3. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P., Kampfer, P., Maiden, M., Nesme, X., Rossello-Mora, R., Swings, J., Truper, H. G., Vauterin, L., Ward, A. C. & Whitman, W. B. (2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043-1047.
  4. Rainey, F. A., Ward-Rainey, N., Kroppenstedt, R. M. & Stackebrandt, E. (1996). The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage; proposal of Nocardiopsaceae fam. nov. Int. J. Sys. Bacteriol. 46, 1088-1092.
  5. Maidak, B. L., Cole, J.R., Parker, C.T.Jr., Garrity, G.M., Larsen, N., Li, B., Lilburn, T.G., McCaughey, M.J., Olsen, G.J., Overbeek, R., Pramanik, S., Schmidt, T.M., Tiedje, J.M. & Woese, C.R. (1999). A new version of the RDP (Ribosomal Database Project). Nucl. Acids Res. 27, 171-173.
  6. Pruesse, E., Quast, C., Knittel, K., Fuchs, B., Ludwig, W., Peplies, J. & Glöckner, F.O. (2007). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl. Acids Res. 35, 7188-7196.
  7. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
  8. Jukes, T. H. & Cantor C. R. (1969). Evolution of protein molecules. In Mammalian protein metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic press