Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26, Giessen,
Antonie Van Leeuwenhoek. 2012 Jan;101(1):3-11. doi: 10.1007/s10482-011-9660-4. Epub 2011 Nov 1.
The term taxonomy is often used synonymously with systematics but it should be regarded more as a specific part of the latter and comprises the orderly arrangements of (defined) units in addition to the nomenclature, i.e. labelling of these units defined by classification, and also identification of these units defined by classification and labeled by nomenclature. Similar to all biological disciplines, taxonomic approaches in microbiology aim at the establishment of a system that mirrors the "order in nature" as closely as possible with the ultimate goal to describe the whole evolutionary order back to the origin of life. With the recognition of molecular markers present in all organisms (here in particular the small subunit rRNAs, ssRNSs), the achievement of this goal has become more and more feasible and the generation of gene and increasing numbers of genome sequences allow nowadays the generation of large amounts of data and often a very detailed insight into the genetic potential of prokaryotes. The possibility to generate whole genome sequences in a very short period of time leads to a strong tendency to base the taxonomic system more and more on sequence data. However, a comprehensive understanding of all the information behind sequence data is lagging far behind their accumulation. Genes and genomes may (or may not) function only in a given "environment", with the cell as basic entity for the display of this potential. Prokaryotic taxonomy still has its focus on the whole organism. In this context, natural selection drives evolution selecting the existing phenotypes and it is the phenotype that "exhibits" this process both in a given cellular and also environmental context. The term polyphasic taxonomy, which was coined almost 40 years ago and aimed at the integration of many levels of information (from molecular to ecological data) thereby allowing a more holistic view, should be revisited in the light of the enormous potential of the novel information associated with large data sets.
分类学一词常与系统学同义，但它更应被视为后者的一个特定部分，除了命名法（即通过分类定义的单位的标签）外，还包括（定义的）单位的有序排列，即对通过分类定义并通过命名法标记的这些单位进行识别。与所有生物学学科一样，微生物分类学方法旨在建立一个尽可能反映“自然界秩序”的系统，最终目标是回溯生命起源描述整个进化秩序。随着对所有生物存在的分子标记（特别是小亚基 rRNAs，ssRNSs）的认识，这一目标变得越来越可行，基因和越来越多的基因组序列的产生使得现在能够生成大量数据，并且通常能够非常详细地了解原核生物的遗传潜力。在很短的时间内生成整个基因组序列的可能性导致越来越倾向于更多地基于序列数据构建分类系统。然而，对序列数据背后所有信息的全面理解远远落后于其积累。基因和基因组可能（也可能不）仅在给定的“环境”中发挥作用，细胞是展示这种潜力的基本实体。原核分类学仍然关注整个生物体。在这种情况下，自然选择推动进化，选择现有的表型，正是表型在给定的细胞和环境背景下“表现”出这一过程。多相分类学一词是在近 40 年前创造的，旨在整合多个层次的信息（从分子到生态数据），从而可以更全面地观察，应该根据与大型数据集相关的巨大潜力重新审视这一术语。
