Adeolu Mobolaji, Alnajar Seema, Naushad Sohail, S Gupta Radhey
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada.
Int J Syst Evol Microbiol. 2016 Dec;66(12):5575-5599. doi: 10.1099/ijsem.0.001485. Epub 2016 Sep 11.
Understanding of the phylogeny and interrelationships of the genera within the order 'Enterobacteriales' has proven difficult using the 16S rRNA gene and other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses of the members of the order 'Enterobacteriales' which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins and four multilocus sequence analysis proteins, as well as examining the overall genome similarity amongst the members of this order. The results of these analyses all support the existence of seven distinct monophyletic groups of genera within the order 'Enterobacteriales'. In parallel, our analyses of protein sequences from the 'Enterobacteriales' genomes have identified numerous molecular characteristics in the forms of conserved signature insertions/deletions, which are specifically shared by the members of the identified clades and independently support their monophyly and distinctness. Many of these groupings, either in part or in whole, have been recognized in previous evolutionary studies, but have not been consistently resolved as monophyletic entities in 16S rRNA gene trees. The work presented here represents the first comprehensive, genome-scale taxonomic analysis of the entirety of the order 'Enterobacteriales'. On the basis of phylogenetic analyses and the numerous identified conserved molecular characteristics, which clearly distinguish members of the order 'Enterobacteriales' and the seven reported clades within this order, a proposal is made here for the order Enterobacterales ord. nov. which consists of seven families: Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov.
事实证明，使用16S rRNA基因以及其他单基因或有限的多基因方法来理解“肠杆菌目”内各属的系统发育和相互关系是困难的。在这项工作中，我们完成了对“肠杆菌目”成员的全面比较基因组分析，包括基于1548个核心蛋白、53个核糖体蛋白和4个多位点序列分析蛋白的系统发育重建，以及检查该目成员之间的整体基因组相似性。这些分析结果均支持“肠杆菌目”内存在七个不同的单系属群。同时，我们对“肠杆菌目”基因组的蛋白质序列分析确定了许多以保守特征插入/缺失形式存在的分子特征，这些特征为已鉴定分支的成员所特有，并独立支持它们的单系性和独特性。这些分类群中的许多部分或全部在先前的进化研究中已被认可，但在16S rRNA基因树中并未始终被解析为单系实体。此处展示的工作代表了对整个“肠杆菌目”的首次全面的、基因组规模的分类学分析。基于系统发育分析以及众多已鉴定的保守分子特征，这些特征清晰地区分了“肠杆菌目”的成员以及该目内报告的七个分支，在此提出肠杆菌目新目，它由七个科组成：肠杆菌科、欧文氏菌科新科、果胶杆菌科新科、耶尔森氏菌科新科、哈夫尼菌科新科、摩根氏菌科新科和布德维氏菌科新科。
