Prokaryotic taxonomy in the sequencing era – the polyphasic approach revisited

Summary The ultimate goal of taxonomy is to establish a system that mirrors the ‘order in nature’. In prokaryote microbiology, almost all taxonomic concepts try to mirror the whole evolutionary order back to the origin of life with the cell as basic unit. The introduction of the 16S rRNA gene as molecular marker allowed for the first time the creation of a hierarchical taxonomic system based on one practical molecular marker. With the development of new and rapid sequencing technologies a wealth of new data can and will be used for critical evaluation of the taxonomic system. Comprehensive analyses of other molecular markers as well as total or partial genome comparisons confirmed the 16S rRNA based hierarchical system as ‘backbone of prokaryote taxonomy’ at least at the genus level and above. A tendency is visible to classify novel taxa more and more based on the genotype, i.e. comparative analyses of 16S rRNA and/or other gene sequence data (in multilocus sequence analysis, MLSA) at the genus and the species level, sometimes contrary to the indications of other (often phenotypic) data. The understanding of all the information behind these data is lagging far beh