Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov.
Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov.
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DOI：
10.1099/ijs.0.048371-0
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发表时间：
2013-09-01
影响因子：
2.8
通讯作者：
Chai, Yujuan
中科院分区：
文献类型：
--
作者：
Gupta, Radhey S.;Chen, Wan Jun;Chai, Yujuan
目前，芽孢杆菌与其他细菌的区别主要是基于它们在16S rRNA基因树上的分枝。目前还没有可靠的分子标记能将这类细菌与其他生物区分开来。在这里，我们报告了详细的系统发育和比较分析的结果，从22个测序的基因组从科里细菌纲成员。这里报道的对这些基因组的蛋白质序列的详细比较分析已经在广泛分布的蛋白质中发现了66个保守的特征插入或缺失(即indels)(CSIS)，这些蛋白质在多个系统发育水平上是Coribacteriia纲的一些不同分支所特有的，这也得到了系统发育分析的支持。一组在不同蛋白质中的24个CSI是针对所有被测序的芽孢杆菌类成员所特有的，为区分和界定这一类提供了新的分子标记。另外一个CSI是唯一存在于柯里杆菌纲和放线菌门的所有成员中的，支持他们在这个细菌门中的位置。发散蛋白中的一组16个CSI是在所有物种的基因组中唯一发现的，这些物种的序列来自发酵葡萄糖的柯里杆菌属、Collinsella属、Atopobium属和Olsenella属，但它们不存在于任何其他细菌中。根据连接的蛋白质序列和16S rRNA，这些属的物种还在系统发育树中形成了一个强有力的支系(支系I)。另外10个不同蛋白质中的CSIS专门存在于已有序列数据的阿糖分解属Eggerthella、隐杆菌、Slackia和Gordonibacter的所有成员中。由这些属组成的一个分支(分支II)也得到了我们的系统发育分析的支持。在第一支系中，两个较小的支系，一个由柯氏杆菌属和Collinsella属组成，另一个由Atopobium属和Olsenella属组成，分别由多个CSIS(分别为8个和7个)和我们的系统发育分析支持。根据系统发育研究的结果和已鉴定的分子标记，在不同的系统发育深度上明确地区分和划分了上述所示的科里细菌分类支系，我们建议将科里细菌划分为两个目(即。铜绿假单胞菌和球藻亚目。11月)和三个家庭(即芽孢杆菌科、隐杆菌科。11月和鹅膏科(Eggerthellaceae Fam.)11月)。此外，还对柯氏杆菌纲、柯氏杆菌目和柯氏藻科的描述进行了校订。
The species of the class Coriobacteriia are currently distinguished from other bacteria primarily on the basis of their branching in the 16S rRNA gene trees. No reliable molecular marker is known that distinguishes the bacteria of this class from other organisms. We report here the results of detailed phylogenetic and comparative analyses on 22 sequenced genomes from members of the class Coriobacteriia. Detailed comparative analyses on protein sequences from these genomes, reported here, have identified 66 conserved signature inserts or deletions (i.e. indels) (CSIs) in widely distributed proteins that are specific for a number of different clades of the class Coriobacteriia at multiple phylogenetic levels, which are also supported by phylogenetic analyses. A set of 24 CSIs in different proteins are specific for all sequenced members of the class Coriobacteriia, providing novel molecular markers distinguishing and delimiting this class. One additional CSI is uniquely present in all members of the class Coriobacteriia and the phylum Actinobacteria supporting their placement within this bacterial phylum. A set of 16 CSIs in divergent proteins are uniquely found in the genomes of all species for which sequences are available from the glucose-fermenting genera Coriobacterium, Collinsella, Atopobium and Olsenella, but they are not present in any other bacteria. The species from these genera also form a strongly supported clade (Clade I) in the phylogenetic trees based upon concatenated protein sequences and the 16S rRNA. An additional 10 CSIs in different proteins are specifically present in all members of the asaccharolytic genera Eggerthella, Cryptobacterium, Slackia and Gordonibacter for which sequence data is available. A clade consisting of these genera (Clade II) is also supported by our phylogenetic analyses. Within Clade I, two smaller clades, one consisting of the genera Coriobacterium and Collinsella and the other containing the genera Atopobium and Olsenella, are independently supported by multiple CSIs (eight and seven respectively) and our phylogenetic analyses. Based upon the results of phylogenetic studies and the identified molecular markers, which clearly distinguish and demarcate the above indicated clades of the class Coriobacteriia at different phylogenetic depths, we propose division of the class Coriobacteriia into two orders (viz. Coriobacteriales and Eggerthellales ord. nov.) and three families (viz. Coriobacteriaceae, Atopobiaceae fam. nov. and Eggerthellaceae fam. nov.). Additionally, descriptions of the class Coriobacteriia, the order Coriobacteriales and the family Coriobacteriaceea are also emended.