Archives of Microbiology

, Volume 195, Issue 6, pp 413–418

When should a DDH experiment be mandatory in microbial taxonomy?

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

Abstract

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.

Keywords

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

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)

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

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

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