Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J
Laboratorium voor Microbiologie, Universiteit Gent, Belgium.
Microbiol Rev. 1996 Jun;60(2):407-38. doi: 10.1128/mr.60.2.407-438.1996.
Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question.
在过去25年里，对细菌进行的分类学研究范围已大幅拓宽，逐渐取代了以往对形态学、生理学和生物化学特征的依赖。这种多相分类学考虑了所有可用的表型和基因型数据，并将它们整合到一种共识性的分类中，该分类构建在由16S rRNA序列分析得出的一般系统发育框架内。在某些情况下，这种共识性分类是一种包含最少矛盾的折衷方案。人们认为，未来可获得的参数越多，多相分类就会越稳定。在这篇综述中，我们讨论了多相分类学在四组因其相关性、复杂性或两者兼具而被挑选出来的细菌中的应用：黄单胞菌属和弯曲杆菌属、乳酸菌以及丛毛单胞菌科。我们讨论了对当前认识的评估、从中得出的结论以及多相分类学的前景，强调了物种的关键作用。分类学家未能通过使用DNA杂交百分比值来标准化物种界定。再加上缺乏物种定义的另一个“金标准”，这对细菌分类学产生了巨大影响。多相分类学面临着这个问题，它不依赖于一种理论、一个假设或一套规则，而是提出了一种达成共识性分类的务实方法，最大限度地整合所有可用数据。未来，多相分类学将不得不应对：（i）海量数据，（ii）大量菌株，以及（iii）数据融合（数据聚合），这将需要高效且集中的数据存储。未来，分类学研究将比现在更需要专业实验室的协作努力。这些未来的发展是否能保证达成更稳定的共识性分类仍是一个悬而未决的问题。
