Archives of Microbiology

, Volume 195, Issue 6, pp 413–418 | Cite as

When should a DDH experiment be mandatory in microbial taxonomy?

  • Jan P. Meier-Kolthoff
  • Markus GökerEmail author
  • Cathrin Spröer
  • Hans-Peter Klenk
Original Paper


DNA–DNA hybridizations (DDH) play a key role in microbial species discrimination in cases when 16S rRNA gene sequence similarities are 97 % or higher. Using real-world 16S rRNA gene sequences and DDH data, we here re-investigate whether or not, and in which situations, this threshold value might be too conservative. Statistical estimates of these thresholds are calculated in general as well as more specifically for a number of phyla that are frequently subjected to DDH. Among several methods to infer 16S gene sequence similarities investigated, most of those routinely applied by taxonomists appear well suited for the task. The effects of using distinct DDH methods also seem to be insignificant. Depending on the investigated taxonomic group, a threshold between 98.2 and 99.0 % appears reasonable. In that way, up to half of the currently conducted DDH experiments could safely be omitted without a significant risk for wrongly differentiated species.


DNA–DNA hybridization Species concept 16S rRNA gene Generalized linear model BLAST Smith–Waterman Substitution model Microbial taxonomy 



We are grateful to Prof. Erko Stackebrandt for providing data and for helpful comments.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

203_2013_888_MOESM1_ESM.xls (374 kb)
Supplementary material 1 (XLS 373 kb)
203_2013_888_MOESM2_ESM.pdf (1.2 mb)
Supplementary material 2 (PDF 1262 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Jan P. Meier-Kolthoff
    • 1
  • Markus Göker
    • 1
    Email author
  • Cathrin Spröer
    • 1
  • Hans-Peter Klenk
    • 1
  1. 1.Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweigGermany

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