Analysis of the molar G+C content of genomic DNA by HPLC

The mol% G+­C content of genomic DNA is required for the description of the type strain of the type species of a new genus (Stackebrandt et al., 2002).

Required material: 1-2 g wet biomass (centrifugal pellet) sent either in frozen state on dry ice or, alternatively, suspended in isopropanol/water (1:1, v/v) at ambient temperature. Lyophilized cells are suboptimal but can also be sent in the amount corresponding to 2 g wet weight. 

Dr. Peter Schumann

References

  1. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P., Kämpfer, P., Maiden, M., Nesme, X., Rossello-Mora, R., Swings, J., Trüper, 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. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159-167.
  3. Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125-128.

 

Antibiotic susceptibility testing

For the determination of antibiotic susceptibility different methods are available: Disc Diffusion Assays with a panel of 36 antibiotics are performed according to DIN 58940 on a number of Quality Control strains as a standard procedure. The results are available in BacDive. This service is offered on request for individual strains (either DSM strains or strains provided by customers) using the standard panel of antibiotic discs. In addition, specific substances provided by the customer can be applied in Disc Diffusion Assays on selected strains. Results are supplied as inhibition zones (in mm) and not interpreted by DSMZ (resistant, sensitive, intermediate).
The broth microdilution method is used to measure (semiquantitatively) the in vitro activity of an antimicrobial agent against a bacterial isolate. Determination of minimal inhibitory concentrations of specific antimicrobial substances (MIC-test) is performed in 96 well plates and can be offered for specific strains and substances.

The price for these services depends on time and effort needed for each individual strain and substance and will be provided upon request.

Required material: A living culture of the strain(s) or the substance(s) intended for testing if not available from DSMZ. 

Dr. Susanne Verbarg

 

DNA - DNA hybridization

DNA-DNA hybridization is applied in microbial species discrimination when 16S rRNA gene sequence similarities are higher than 98.5% (Stackebrandt & Ebers, 2006).

Required material: 3g of wet biomass from all strains included in the analysis suspended in isopropanol/water (1:1, v/v) (first suspend biomass in water, mix well and then mix 1:1 with isopropanol) which can be sent in tightly sealed screw cap tubes (e.g. 50 ml Falcon tubes) at ambient temperature. Alternatively centrifuged biomass on dry ice (best option). Lyophilized cells in corresponding amount can also be sent. However, the use of lyophilized cells may result in a lower DNA yield. Please specify pairings in a table:

 strain Astrain B
strain B     x     -
strain C     x     x

Dr. Cathrin Spröer

References

  1. De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133-142.
  2. Huss, V. A. R., Festl, H. & Schleifer, K. H. (1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184-192.
  3. Stackebrandt, E. & Ebers, J. (2006). Taxonomic Parameters revisited: tarnished gold standards. Microbiology Today Nov 06, 152-155.