Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes
Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes
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DOI：
10.3389/fmicb.2019.02083
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发表时间：
2019-09-23
影响因子：
5.2
通讯作者：
Goeker, Markus
中科院分区：
文献类型：
--
作者：
Garcia-Lopez, Marina;Meier-Kolthoff, Jan P.;Goeker, Markus
尽管近年来在拟杆菌门细菌分类方面取得了相当大的进展，但仍然需要进一步澄清包括具有临床、鱼类养殖和生态重要性的生物体在内的不同组合内的分类学关系。拟杆菌门分类已被证明是困难的，尤其是当分类学决策很大程度上依赖于解析不佳的 16S rRNA 基因树和有限数量的表型特征的解释时。在这里，使用了 1000 多种拟杆菌和外群类型菌株的基因组序列草图，利用系统发育系统学的原理，从基因组规模的数据推断系统发育树。大多数类群被发现是单系的，但有几个目、科和属，包括很久以前提出的类群，如拟杆菌属、噬细胞菌属和黄杆菌属，还有最近出现的类群，以及一些物种被证明需要修订。据此提出了承认新目、科和属以及将多种物种转移到其他属的建议。此外，对许多物种进行了修订描述，主要涉及 DNA G+C 含量和（大约）基因组大小的信息，这两者都可以被认为是有价值的分类标记。在将本研究的结果与现有分类进行比较时，我们发现了许多不一致之处，这似乎是由于 16S rRNA 基因树解析不充分或分类单元采样不完整造成的。 16S rRNA 基因和全基因组树之间发现的少数显着不一致性强调了基于单基因序列的系统发育固有的陷阱以及在系统发育组研究中使用普通自举法的障碍，特别是当与太窄的基因选择相结合时。虽然在所有研究的表型性状中都检测到了显着程度的系统发育保守性，但与树的整体拟合差异很大，这是过去错误分类的可能原因之一，就像使用拟形性状状态作为诊断特征一样。
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.