Jensen Anders, Scholz Christian F P, Kilian Mogens
Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000, Denmark.
Int J Syst Evol Microbiol. 2016 Nov;66(11):4803-4820. doi: 10.1099/ijsem.0.001433. Epub 2016 Aug 17.
The Mitis group of the genus Streptococcus currently comprises 20 species with validly published names, including the pathogen S. pneumoniae. They have been the subject of much taxonomic confusion, due to phenotypic overlap and genetic heterogeneity, which has hampered a full appreciation of their clinical significance. The purpose of this study was to critically re-examine the taxonomy of the Mitis group using 195 publicly available genomes, including designated type strains for phylogenetic analyses based on core genomes, multilocus sequences and 16S rRNA gene sequences, combined with estimates of average nucleotide identity (ANI) and in silico and in vitro analyses of specific phenotypic characteristics. Our core genomic phylogenetic analyses revealed distinct clades that, to some extent, and from the clustering of type strains represent known species. However, many of the genomes have been incorrectly identified adding to the current confusion. Furthermore, our data show that 16S rRNA gene sequences and ANI are unsuitable for identifying and circumscribing new species of the Mitis group of the genus Streptococci. Based on the clustering patterns resulting from core genome phylogenetic analysis, we conclude that S. oligofermentans is a later synonym of S. cristatus. The recently described strains of the species Streptococcus dentisani includes one previously referred to as 'S. mitis biovar 2'. Together with S. oralis, S. dentisani and S. tigurinus form subclusters within a coherent phylogenetic clade. We propose that the species S. oralis consists of three subspecies: S. oralis subsp. oralis subsp. nov., S. oralis subsp. tigurinus comb. nov., and S. oralis subsp. dentisani comb. nov.
链球菌属的轻链菌群目前包含20个具有有效发表名称的物种，包括病原体肺炎链球菌。由于表型重叠和基因异质性，它们一直是许多分类学混乱的主题，这阻碍了对其临床意义的充分认识。本研究的目的是使用195个公开可用的基因组对轻链菌群的分类学进行严格的重新审视，包括用于基于核心基因组、多位点序列和16S rRNA基因序列进行系统发育分析的指定模式菌株，并结合平均核苷酸同一性（ANI）估计以及特定表型特征的计算机模拟和体外分析。我们的核心基因组系统发育分析揭示了不同的进化枝，在某种程度上，从模式菌株的聚类情况来看，这些进化枝代表了已知物种。然而，许多基因组被错误鉴定，加剧了当前的混乱。此外，我们的数据表明，16S rRNA基因序列和ANI不适用于鉴定和界定链球菌属轻链菌群的新物种。基于核心基因组系统发育分析产生的聚类模式，我们得出结论，少发酵链球菌是嵴链球菌的晚出同物异名。最近描述的龋齿链球菌菌株包括一个先前被称为“轻链链球菌生物变种2”的菌株。与口腔链球菌一起，龋齿链球菌和蒂氏链球菌在一个连贯的系统发育进化枝内形成亚聚类。我们提议将口腔链球菌物种分为三个亚种：口腔链球菌亚种oralis subsp.nov.、口腔链球菌亚种tigurinus comb.nov.和口腔链球菌亚种dentisani comb.nov.
