Liang Kevin Y H, Orata Fabini D, Boucher Yann F, Case Rebecca J
Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
Front Microbiol. 2021 Jun 25;12:683109. doi: 10.3389/fmicb.2021.683109. eCollection 2021.
The family consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the family. Representatives of the roseobacter clade not only have different environmental adaptions from other isolates but were also found to be distinct based on genomic, phylogenetic, and -predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.
该家族由代谢、表型和生态多样的α-变形菌组成。它包括玫瑰杆菌进化枝，这是一个非正式名称，代表海洋细菌中最丰富的类群之一。在过去三十年中，新型玫瑰杆菌的发现速度很快，这意味着分类学分类的最佳实践，即利用表型、基因型和系统发育特征的多相方法，并不总是得到遵循。早期的分类工作严重依赖16S rRNA基因序列相似性，导致了许多分类学上的不一致，该家族中有几个多系和并系属。新一代测序技术使得大多数模式菌株能够获得全基因组序列，从而有可能对它们的分类学进行修订。在本研究中，我们进行了全基因组系统发育和基因型分析，并结合表型数据的荟萃分析，以审查该家族内331个模式菌株（属于119个属）的分类学分类。玫瑰杆菌进化枝的代表不仅与其他分离株有不同的环境适应性，而且根据基因组、系统发育和预测的表型数据也被发现是不同的。因此，我们建议将这组细菌归入一个新的家族，新家族。总共重新分类为327个物种和128个属，这表明在属水平上的错误鉴定比物种水平上的问题更大。通过解决该家族内模式菌株的分类学不一致问题，我们基于全基因组分析建立了一套连贯的标准，这将有助于指导未来的分类学工作并防止错误的传播。
