The bacterial species definition in the genomic era
The bacterial species definition in the genomic era
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DOI：
10.1098/rstb.2006.1920
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发表时间：
2006-11-29
影响因子：
6.3
通讯作者：
Tiedje, James M.
中科院分区：
文献类型：
--
作者：
Konstantinidis, Konstantinos T.;Ramette, Alban;Tiedje, James M.
细菌种类的定义，尽管在鉴定、诊断、检疫和多样性调查方面具有显著的实际意义，但仍然是一个很难推进的问题。基因组学现在为物种内多样性提供了新的见解，并有可能出现一个更健全的基础系统。虽然我们也很兴奋，但我们认为，现在对这个定义进行普遍的改变还为时过早，因为目前的知识是基于太少的系统发育群和太少的自然种群样本。然而，我们对五种重要细菌群的分析表明，当对基因含量和生态独特性有了深入的了解时，更严格的物种标准可能是合理的。我们的分析还揭示了根据目前的标准，在全基因组序列和基因含量多样性方面，一个物种实际上包含了什么，并表明这与所检查的环境伯克霍尔德氏菌和希瓦氏菌属的连贯集群不一致。相比之下，具有非常有限的生态位的强制性病原体确实表现出集群。因此，适用于大多数真核生物的具有生物学意义的多样性集群的想法可能并不普遍适用于微生物世界，或者如果存在这样的集群，它们可能在不同的区分水平上被发现。
The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction.