Phylogeny of the genus Nocardia based on reassessed 16S rRNA gene sequences reveals underspeciation and division of strains classified as Nocardia asteroides into three established species and two unnamed taxons
Phylogeny of the genus Nocardia based on reassessed 16S rRNA gene sequences reveals underspeciation and division of strains classified as Nocardia asteroides into three established species and two unnamed taxons
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DOI：
10.1128/jcm.41.2.851-856.2003
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发表时间：
2003-02-01
影响因子：
9.4
通讯作者：
Mauch, H
中科院分区：
文献类型：
--
作者：
Roth, A;Andrees, S;Mauch, H
诺卡菌在常规实验室的常规鉴定仍然存在问题，因为缺乏可靠的表型试验，而且由于被归类为小行星诺卡菌属的菌株的分类尚未解决，其中包括型菌株和具有药物模式II和VI的分离株。诺卡菌属74个代表性菌株的16S rRNA基因，包括25个已确定的物种。为准确的物种鉴定提供分子基础，并重新评估属于该物种的分类群的系统发育。该系统发育分析结果证实，亲缘关系较近的无心种的种间异质性可以相当低（N. paucivorans和N. brevicatena之间的序列差异仅为0.5%）。我们观察到序列微异质性（序列差异小于5个碱基），在11个物种中有8个物种中有一个以上的菌株被研究。发现至少有10个分类群值得作为新种描述。先前归类为N. asteroides的菌株可分为5个不同的系统发育类群：型菌株群（N. asteroides sensu strictu）、N.脓肿菌株、N. cyriacigeorgica，以及与N. carnea或N. flavorosea密切相关的两个类群。后两组中的菌株可能代表新种，有待进一步的遗传和表型评估。有限表型数据显示，N.脓肿菌、N. cyriacigeorgica和两个诺卡菌种分类群分别相当于药物模式I、VI和II。在未来，这些数据将有助于在采用更精确的命名法后，发现与N. asteroides密切相关的分离物的物种特异性标记，并解开过去从系统发育角度确定属于单独分类群的未解决菌株群的令人困惑的表型数据。
Conventional identification of Nocardia in the routine laboratory remains problematic due to a paucity of reliable phenotypic tests and due to the yet-unresolved taxonomy of strains classified as belonging to the species Nocardia asteroides, which comprises the type strain and isolates with drug pattern types II and VI. The 16S rRNA gene of 74 representative strains of the genus Nocardia, encompassing 25 established species, was sequenced in order to provide a molecular basis for accurate species identification and with the aim of reassessing the phylogeny of taxons assigned to the species N. asteroides. The result of this phylogenetic analysis confirms that the interspecies heterogeneity of closely related nocardial species can be considerably low (a sequence divergence of only 0.5% was found between N. paucivorans and N. brevicatena). We observed a sequence microheterogeneity (sequence divergence of fewer than five bases) in 8 of 11 species of which more than one strain in the species was studied. At least 10 taxons were found that merit description as new species. Strains previously classified as N. asteroides fell into five distinct phylogenetic groups: the type strain cluster (N. asteroides sensu strictu), N. abscessus, N. cyriacigeorgica, and two clusters closely related to N. carnea or N. flavorosea. The strains within the latter two groups probably represent new species, pending further genetic and phenotypic evaluation. Restricted phenotypic data revealed that N. abscessus, N. cyriacigeorgica, and the two Nocardia species taxons are equivalent to drug patterns I, VI, and II, respectively. In the future, these data will help in finding species-specific markers after adoption of a more precise nomenclature for isolates closely related to N. asteroides and unravel confusing phenotypic data obtained in the past for unresolved groups of strains that definitely belong to separate taxons from a phylogenetic point of view.