Because a natural entity "species" cannot be recognized as a group of strains that is genetically well separated from its phylogenetic neighbors, a pragmatic approach was taken to define a species by a polyphasic approach ( Since today the primary structure of 16s rRNA is easier to determine than hybridization between DNA strands, the strength of the sequence analysis is to recognize the level at which DNA pairing studies need to be performed, which certainly applies to similarities of 97% and higher.

Bacterial taxonomy, which began as a largely intuitive process, has become increasingly objective with the advent of numerical taxonomy and techniques for the measurement of evolutionary divergence in the structure of semantides, i.e., large, information-bearing molecules such as nucleic acids and proteins. These developments have forced the

A new hierarchic classification structure for the taxa between the taxonomic levels of genus and class is proposed for the actinomycete line of descent as defined by analysis of small subunit (16s) rRNA and genes coding for this molecule (rDNA). While the traditional circumscription of a genus of the actinomycete subphylum is by and large in accord with the 16s rRNA/rDNA-based phylogenetic clustering of these organisms, most of the higher taxa proposed in the past do not take into account the phylogenetic clustering of genera. The rich chemical, morphological and physiological diversity of phylogenetically closely related genera makes the description of families and higher taxa so broad that they become meaningless for the description of the enclosed taxa. Here we present a classification system in which phylogenetically neighboring taxa at the genus level are clustered into families, suborders, orders, subclasses, and a class irrespective of those phenotypic characteristics on which the delineation of taxa has been based in the past. Rather than being based on a listing of a wide array of chemotaxonomic, morphological, and physiological properties, the delineation is based solely on 16s rDNA/rRNA sequence-based phylogenetic clustering and the presence of taxon-specific 16s rDNA/RNA signature nucleotides.In their publication "On the nature of global classification," Wheelis et al. (177) based the definition of higher taxa on the molecular level of universally homologous functions. This statement is derived from the high correlation of genealogical trees inferred from several such molecules, e.g., genes coding for 16s rRNA (16s rDNA) (179), 23s rDNA (96), elongation factors involved in the translation process, and the P-subunit of ATPase (97). The authors (177) stress that a basic requirement of a global classification is uniformity in methods and characteristics used in defining and ranking taxa. Nonhomologous characteristics, on the other hand, may be useful in confirming the molecular groupings. Application of this classification strategy led to the description of domains for the three highest taxa recognized today, the Archaea, Bacteria, and Eucarya Within the domain Bacteria, more than 15 lineages, which in phylogenetic uniqueness and ancestry are comparable to the archaeal kingdoms, have been identified. The taxonomic rank of kingdom has not yet been proposed for any of these lineages. The taxon class Proteobacteria has been proposed for a phylogenetically broad cluster of gram-negative genera, and several orders have been described for some of the phylogenetic lineages that emerged from the comparison of evolutionarily conserved macromolecules, e.g., Aquificales (19, Thermotogales (67), Verrucomicrobiales (173), and Planctomycetales (138). These phylogenetically coherent taxa are now used side by side with higher taxa that were described at the beginning of the pre-molecular era, i.e., before or around 1984. While the phylogenetic coherence of the division Firmacutes (53), the class Mollicutes, and the ord...

There is no widely accepted concept of species for prokaryotes, and assignment of isolates to species is based on measures of phenotypic or genome similarity. The current methods for defining prokaryotic species are inadequate and incapable of keeping pace with the levels of diversity that are being uncovered in nature. Prokaryotic taxonomy is being influenced by advances in microbial population genetics, ecology and genomics, and by the ease with which sequence data can be obtained. Here, we review the classical approaches to prokaryotic species definition and discuss the current and future impact of multilocus nucleotide-sequence-based approaches to prokaryotic systematics. We also consider the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters.

An ad hoc committee for the re-evaluation of the species definition in bacteriology met in Gent, Belgium, in February 2002. The committee made various recommendations regarding the species definition in the light of developments in methodologies available to systematists.