Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species
Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species
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DOI：
10.1099/ijsem.0.004475
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发表时间：
2020-01-01
影响因子：
2.8
通讯作者：
Chen, Shu
中科院分区：
文献类型：
--
作者：
Gupta, Radhey S.;Patel, Sudip;Chen, Shu
为了阐明芽孢杆菌属物种的进化关系和分类，对超过300个芽孢杆菌/芽孢杆菌科基因组进行了全面的基因组学和比较分析。多个基因组规模的系统发育树初步重建，以确定不同的单系分支的芽孢杆菌物种。平行地，对基因组的蛋白质序列进行详细分析以鉴定对每个鉴定的进化枝特异的保守标签插入缺失（CSI）。我们发现，在不同的重建树，大多数的芽孢杆菌属物种，除了Subarcus和Cereus分支，始终形成17个新的不同的分支。此外，一些芽孢杆菌属物种可靠地归为嗜碱菌属、嗜热碱芽孢杆菌属、嗜热芽孢杆菌属、Salibacterium属和Salisediminibacterium属。已鉴定的芽孢杆菌物种进化枝的独特性得到了128个已鉴定的CS I的独立有力支持，这些CS I是这些进化枝的独特特征，为它们的划分提供了可靠的手段。基于强有力的系统发育和分子证据，我们建议这17个芽孢杆菌属分支应被视为新属，命名为Alteribacter gen. nov.，Eccinogen. nov.，Evansella gen. nov.，Ferdinandcohnia gen. nov.，Gottfriedia gen. nov.，Heyndrickxia gen. nov.，Lederbergia gen. nov.，Litchfieldia gen. nov.，Margalitia gen. nov.，Niallia gen. nov.，Priestia gen. nov.，Robertmurraya gen. nov.，Rossellomorea gen. nov.，Schinkia gen. nov.，Siminovitchia gen. nov.，我们还建议将“京畿芽孢杆菌”转移到京畿罗伯拉菌新种（模式菌株：NB 22 =JCM 17569 T =DSM 26768）。此外，我们报告了31个CSIs，这些CSIs是亚种分支（包含模式种B）成员的独特特征。subtilis）或Cereus进化枝（含有B.炭疽菌和B. B. cereus）。由于大多数芽孢杆菌属的物种，这不是这两个分支的一部分，现在可以分配到其他属，我们提出了一个修订的描述属芽孢杆菌，以限制它只有Subarcus和Cereus分支的成员。
To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic- scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.