Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France.
Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):384-391. doi: 10.1099/ijs.0.057091-0.
Currently, bacterial taxonomy relies on a polyphasic approach based on the combination of phenotypic and genotypic characteristics. However, the current situation is paradoxical in that the genetic criteria that are used, including DNA-DNA hybridization, 16S rRNA gene sequence nucleotide similarity and phylogeny, and DNA G+C content, have significant limitations, but genome sequences that contain the whole genetic information of bacterial strains are not used for taxonomic purposes, despite the decreasing costs of sequencing and the increasing number of available genomes. Recently, we diversified bacterial culture conditions with the aim of isolating uncultivated bacteria. To classify the putative novel species that we cultivated, we used a polyphasic strategy that included phenotypic as well as genomic criteria (genome characteristics as well as genomic sequence similarity). Herein, we review the pros and cons of genome sequencing for taxonomy and propose that the incorporation of genome sequences in taxonomic studies has the advantage of using reliable and reproducible data. This strategy, which we name taxono-genomics, may contribute to the taxonomic classification of bacteria.
目前，细菌分类学依赖于一种基于表型和基因型特征相结合的多相方法。然而，目前的情况是矛盾的，因为所使用的遗传标准，包括 DNA-DNA 杂交、16S rRNA 基因序列核苷酸相似性和系统发育以及 DNA G+C 含量，都有很大的局限性，但包含细菌菌株全部遗传信息的基因组序列并没有被用于分类目的，尽管测序成本不断降低，可用基因组数量不断增加。最近，我们多样化了细菌培养条件，旨在分离未培养的细菌。为了对我们培养的假定新物种进行分类，我们采用了一种多相策略，包括表型和基因组标准（基因组特征以及基因组序列相似性）。在此，我们综述了基因组测序在分类学中的优缺点，并提出将基因组序列纳入分类学研究具有利用可靠和可重复数据的优势。我们将这种策略命名为分类基因组学，它可能有助于细菌的分类学分类。
