Identification using partial rDNA 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.
Complete 16S rRNA gene sequence analysis including phylogenetic analysis should be part of the description of the type strain of a new species (Stackebrandt et al., 2002).

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

Dr. Cathrin Spröer

References

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
  6. 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

Identification of fungi using partial rRNA sequencing

DSMZ offers basic identification of fungal and yeast cultures using sequencing of the ribosomal ITS region which is the first common DNA-barcode for Fungi (Schoch et al. 2012). Note that a few additional DNA-markers (CAMTUBRPB1,TEF1ACT) should be applied to perform a more precise identification of some common moulds such as genera PenicilliumAspergillusCladosporiumFusarium, and Trichoderma.

Required material: A living culture (agar plate or slant) is preferred. Customers will receive identification report containing the best match among known species (or available sequences), the identification result (species name and references) and a brief comment on the species.

PD Dr. Christiane Baschien

Dr. Andrey Yurkov

References

  1. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consortium (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA. 109, 6241-6246.