When should a DDH experiment be mandatory in microbial taxonomy?
When should a DDH experiment be mandatory in microbial taxonomy?
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DOI：
10.1007/s00203-013-0888-4
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发表时间：
2013-06-01
影响因子：
2.8
通讯作者：
Klenk, Hans-Peter
中科院分区：
文献类型：
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作者：
Meier-Kolthoff, Jan P.;Goeker, Markus;Klenk, Hans-Peter
当16 S rRNA基因序列相似性达到97%或更高时，DNA-DNA杂交（DDH）在微生物物种区分中起关键作用。使用真实世界的16 S rRNA基因序列和DDH数据，我们在这里重新调查是否，以及在哪些情况下，这个阈值可能过于保守。这些阈值的统计估计计算一般以及更具体地为一些门，经常受到DDH。在几种推断16 S基因序列相似性的方法中，分类学家常用的大多数方法似乎非常适合这项任务。使用不同的DDH方法的效果似乎也是微不足道的。根据所调查的分类组，98.2%和99.0%之间的阈值似乎是合理的。通过这种方式，目前进行的DDH实验中多达一半可以安全地省略，而不会出现错误区分物种的重大风险。
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.