State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.
Int J Syst Evol Microbiol. 2010 Mar;60(Pt 3):696-703. doi: 10.1099/ijs.0.012419-0. Epub 2009 Aug 5.
Streptomyces griseus and related species form the biggest but least well-defined clade in the whole Streptomyces 16S rRNA gene tree. Multilocus sequence analysis (MLSA) has shown promising potential for refining Streptomyces systematics. In this investigation, strains of 18 additional S. griseus clade species were analysed and data from a previous pilot study were integrated in a larger MLSA phylogeny. The results demonstrated that MLSA of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is better than the previous six-gene scheme, as it provides equally good resolution and stability and is more cost-effective; MLSA using three or four of the genes also shows good resolution and robustness for differentiating most of the strains and is therefore of value for everyday use. MLSA is more suitable for discriminating strains that show >99 % 16S rRNA gene sequence similarity. DNA-DNA hybridization (DDH) between strains with representative MLSA distances revealed a strong correlation between the data of MLSA and DDH. The 70 % DDH value for current species definition corresponds to a five-gene MLSA distance of 0.007, which could be considered as the species cut-off for the S. griseus clade. It is concluded that the MLSA procedure can be a practical, reliable and robust alternative to DDH for the identification and classification of streptomycetes at the species and intraspecies levels. Based on the data from MLSA and DDH, as well as cultural and morphological characteristics, 18 species and three subspecies of the S. griseus clade are considered to be later heterotypic synonyms of 11 genomic species: Streptomyces griseinus and Streptomyces mediolani as synonyms of Streptomyces albovinaceus; Streptomyces praecox as a synonym of Streptomyces anulatus; Streptomyces olivoviridis as a synonym of Streptomyces atroolivaceus; Streptomyces griseobrunneus as a synonym of Streptomyces bacillaris; Streptomyces cavourensis subsp. washingtonensis as a synonym of Streptomyces cyaneofuscatus; Streptomyces acrimycini, Streptomyces baarnensis, Streptomyces caviscabies and Streptomyces flavofuscus as synonyms of Streptomyces fimicarius; Streptomyces flavogriseus as a synonym of Streptomyces flavovirens; Streptomyces erumpens, 'Streptomyces ornatus' and Streptomyces setonii as synonyms of Streptomyces griseus; Streptomyces graminofaciens as a synonym of Streptomyces halstedii; Streptomyces alboviridis, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces luridiscabiei as synonyms of Streptomyces microflavus; and Streptomyces californicus and Streptomyces floridae as synonyms of Streptomyces puniceus.
灰色链霉菌和相关种形成了整个灰色链霉菌 16S rRNA 基因树中最大但定义最不明确的分支。多位点序列分析（MLSA）已显示出在细化链霉菌系统发育方面有很大的潜力。在这项研究中，分析了 18 种额外的灰色链霉菌群种，并且将之前的一项初步研究的数据整合到更大的 MLSA 系统发育中。结果表明，五个看家基因（atpD、gyrB、recA、rpoB 和 trpB）的 MLSA 优于之前的六基因方案，因为它提供了同样好的分辨率和稳定性，并且更具成本效益；使用三个或四个基因的 MLSA 也可以很好地区分大多数菌株，因此对于日常使用具有价值。MLSA 更适合于区分具有 >99% 16S rRNA 基因序列相似性的菌株。具有代表性 MLSA 距离的菌株之间的 DNA-DNA 杂交（DDH）表明 MLSA 和 DDH 数据之间存在很强的相关性。目前物种定义的 70% DDH 值对应于 0.007 的五基因 MLSA 距离，这可以被认为是灰色链霉菌群的种间切割值。结论是，MLSA 程序可以作为一种实用、可靠和稳健的替代方法，用于在种内和种间水平上鉴定和分类链霉菌。基于 MLSA 和 DDH 以及培养和形态特征的数据，灰色链霉菌群的 18 个种和 3 个亚种被认为是 11 个基因组种的异质同形同义词：灰色链霉菌和中介链霉菌是白色链霉菌的同义词；变铅青链霉菌是轮环链霉菌的同义词；橄榄绿链霉菌是暗橄榄色链霉菌的同义词；灰色短杆菌是枯草芽孢杆菌的同义词；华盛顿沙福克链霉菌亚种是蓝灰链霉菌的同义词；棘孢小单孢菌、巴恩斯链霉菌、滑液链霉菌和黄褐链霉菌是纤细链霉菌的同义词；灰色链霉菌是黄色链霉菌的同义词；棘孢链霉菌、华丽链霉菌和塞托尼链霉菌是灰色链霉菌的同义词；链霉菌产黄菌素是黄色链霉菌的同义词；链霉菌灰色变种、灰色链霉菌 alpha 亚种、灰色链霉菌 cretosus 亚种和链霉菌卢里迪斯卡比是微黄色链霉菌的同义词；加利福尼亚链霉菌和佛罗里达链霉菌是紫色链霉菌的同义词。
