Table_1_Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes.XLSX

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.

尽管近年来针对归类于拟杆菌门（Bacteroidetes）的细菌的分类研究已取得长足进展，但仍需进一步厘清该门类下一个兼具多样性的类群内部的分类学关系——该类群涵盖了具有临床、水产养殖及生态学重要价值的各类生物。拟杆菌门的分类工作历来颇具难度，尤其是当分类学决策高度依赖分辨率不佳的16S rRNA基因树解读，以及有限数量的表型特征时。本研究针对超过1000株拟杆菌门及外类群模式菌株的基因组集合进行了大幅扩充，基于系统发育系统学的原理，利用全基因组规模的数据推演系统发育树。绝大多数类群被证实为单系群，但多个目、科及属——包括早年提出的拟杆菌属（Bacteroides）、噬纤维菌属（Cytophaga）与黄杆菌属（Flavobacterium）等类群，亦包括近年新增的类群，以及少数物种——均显示需要进行分类修订。据此，研究提出了新建若干目、科与属的建议，并建议将多个物种转移至其他属中。此外，本文还为多个物种提供了修订后的描述，主要补充了DNA G+C含量与（近似）基因组大小两类可作为有效分类学标记的信息。将本研究结果与现有分类体系进行比对后，我们发现了诸多不一致之处，这些不一致大概率源于分辨率不足的16S rRNA基因树或不完整的类群取样。16S rRNA基因树与全基因组树之间仅存的少量显著不一致，凸显了基于单基因序列构建系统发育树的固有缺陷，以及在系统基因组学研究中使用常规自展检验的局限性，尤其是当基因选择范围过窄时。尽管在所调研的所有表型性状中均检测到了显著的系统发育保守性，但整体拟合度差异显著——这正是过去分类学误判的潜在原因之一，恰似将祖征性状状态用作鉴别特征所带来的问题。