Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers. INTRODUCTIONThe characterization of a strain is a key element in prokaryote systematics. Although various new methodologies have been developed over the past 100 years, both the newer methodologies and those considered to be 'traditional' remain key elements in determining whether a strain belongs to a known taxon or constitutes a novel one. In the case of a known taxon, a selected set of tests may be used to determine whether a strain has been identified as a member of an existing taxon. However, in the case of a strain or set of strains shown to be novel taxa, they should be characterized as comprehensively as possible. The goal of this characterization is to place them within the hierarchical framework laid down by the Bacteriological Code (1990 revision) (Lapage et al., 1992), as well as to provide a description of the taxa. Strains should be allocated to species (and/or subspecies), but the nature of the 'species name' (a binomial or combination) dictates that it must also be assigned to a genus. The genus may be either an existing or a novel genus. The Bacteriological Code also recommends that the placement of a genus in a family should be mentioned, and this can be extended to the other hierarchical levels as these become defined. Although this approach may appear novel, with much emphasis currently being placed on the species, the advent of 16S rRNA gene sequencing forces us to choose between primers that are specific for members of the Archaea or for members of the Bacteria, so the first step in that direction is already routine in many laboratories. However, such a classification system is only possible if strains are comprehensively and properly characterized. A further key element is the way in which datasets are compared and it is here too that some degree of guidance and a discussion of the potential problems needs to be provided. In the case of species, various recommendations have been made with respect to the ways in which species may be delineated and it is important to consider these aspects when considering how new strains are to be placed in novel species. However, far too little attention has been paid to the way in which taxa above the rank of species should be characterized a...

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.

A numerical study of the fatty acid patterns of 263 reference strains belonging to the genera Arthrobacter, Aureobacterium, Brevibacterium, Cellulomonas, Clavibacter, Corynebacterium, Curtobacterium, Erysipelothrix, Microbacterium, and Rhodococcus was undertaken based on cultural and chemical standardized techniques. Clustering was by the unweighted pair group method using the correlation coefficient. Two cluster groups could be defined at the 62% level, one containing strains characterized by saturated and monounsaturated fatty acids and the second group characterized by iso- and anteiso-branched fatty acids. Within the first cluster group, a clear separation of strains assigned to the genera Rhodococcus, Erysipelothrix, and Corynebacterium could be achieved. Furthermore, strains of the species Corynebacterium glutamicum, Corynebacterium ammoniagenes, Corynebacterium diphtheriae, 'Corynebacterium ulcerans,' and Erysipelothrix rhusiopathiae could be found in distinct clusters, based on quantitative differences in fatty acid patterns. Within the second cluster group, a high degree of similarity between the genera Aureobacterium, Cellulomonas, Clavibacter, Curtobacterium, and Microbacterium found in phylogenetically based studies could be shown also by fatty acid patterns. Several strains of the plant pathogenic coryneform bacteria assigned to the genus Clavibacter and Curtobacterium flaccumfaciens were found within one cluster, indicating a high similarity between these genera. Strains of the genus Arthrobacter were grouped into three adjacent clusters and could not be differentiated by fatty acid patterns. The results of the study are essentially in line with a previously published numerical survey and with other chemotaxonomic and genetic data. Thus, quantitative fatty acid patterns are recommended for identification of several coryneform bacterial genera. In some cases an identification at the species level is possible.Key words: fatty acid analysis, coryneform bacteria, differentiation, numerical analysis.

Minimal standards for describing new taxa within the aerobic endospore-forming bacteria are proposed, following Recommendation 30b of the Bacteriological Code (1990 Revision). These minimal standards are recommended as guidelines to assist authors in the preparation of descriptions for novel taxa. They encourage broad polyphasic characterization and the construction of descriptions that are practically useful in routine diagnostic laboratories. The proposals have been endorsed by the Subcommittee on the Taxonomy of the Genus Bacillus and Related Organisms of the International Committee on Systematics of Prokaryotes

Two Gram-negative, non-motile, non-spore-forming, coccoid bacteria (strains CCM 4915 T and CCM 4916), isolated from clinical specimens of the common vole Microtus arvalis during an epizootic in the Czech Republic in 2001, were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA (rrs) and recA gene sequence similarities, both isolates were allocated to the genus Brucella. Affiliation to Brucella was confirmed by DNA-DNA hybridization studies. Both strains reacted equally with Brucella M-monospecific antiserum and were lysed by the bacteriophages Tb, Wb, F1 and F25. Biochemical profiling revealed a high degree of enzyme activity and metabolic capabilities not observed in other Brucella species. The omp2a and omp2b genes of isolates CCM 4915 T and CCM 4916 were indistinguishable. Whereas omp2a was identical to omp2a of brucellae from certain pinniped marine mammals, omp2b clustered with omp2b of terrestrial brucellae. Analysis of the bp26 gene downstream region identified strains CCM 4915 T and CCM 4916 as Brucella of terrestrial origin. Both strains harboured five to six copies of the insertion element IS711, displaying a unique banding pattern as determined by Southern blotting. In comparative multilocus VNTR (variable-number tandem-repeat) analysis (MLVA) with 296 different genotypes, the two isolates grouped together, but formed a separate Abbreviations: MLST, multilocus sequence typing; MLVA, multilocus VNTR (variable-number tandem-repeat) analysis; RTD, routine test dilution.The GenBank/EMBL/DDBJ accession numbers for the gene sequences omp22, omp25, omp25b, omp31 and omp31b of strain CCM 4915

The taxonomic position of Pseudomonas sp. B13 T , isolated as a 3-chlorobenzoate-degrading organism and used for several groundbreaking studies on the enzymology and genetics of the degradative pathway for haloaromatic compounds, was studied in detail. The previously performed physiological studies, the detection of ubiquinone Q-9, the polyamine pattern with putrescine and spermidine as major polyamines, a fatty acid profile with C 18 : 1 v7c, summed feature 3 and C 16 : 0 as quantitatively the most important constituents and the 16S rRNA gene sequence demonstrated that Pseudomonas sp. B13 T indeed belongs to the genus Pseudomonas. The sequence of the Pseudomonas sp. B13 T 16S rRNA gene demonstrated a high degree of similarity with that of Pseudomonas citronellolis DSM 50332 T (98.9 %), Pseudomonas nitroreducens DSM 14399 T (98.7 %), Pseudomonas jinjuensis DSM 16612 T (98.1 %) and Pseudomonas multiresinivorans DSM 17553 T (98.7 %). Thus it was shown that strain Pseudomonas sp. B13 T can be distinguished from related species by the ability/inability to assimilate N-acetylgalactosamine, D-galactose, putrescine, trans-aconitate and mesaconate and some differences in the fatty acid profile. The positioning of Pseudomonas sp. B13 T as a separate taxon was finally verified by DNA hybridization, which demonstrated less than 45 % DNA-DNA similarity between strain Pseudomonas sp. B13 T and the reference strains. On the basis of these results, Pseudomonas sp. B13 T represents a novel species for which the name Pseudomonas knackmussii sp. nov. is proposed. The type strain is B13 T (=DSM 6978 T =LMG 23759 T ).Pseudomonas sp. B13 T was one of the first micro-organisms described that utilizes halogenated aromatic compounds as sole source of carbon and energy. The strain was isolated from a continuous enrichment in a chemostat with 3-chlorobenzoate. The original inoculum of the chemostat was obtained from a sewage treatment plant in Göttingen, Germany (Dorn et al., 1974). The isolate was subsequently used to elaborate the degradative pathway of 3-chlorobenzoate and other halogenated aromatic compounds (e.g. Dorn & Knackmuss, 1978a, b; Reineke & Knackmuss, 1978a, b; Schmidt & Knackmuss, 1980a, b;Kaschabek & Reineke, 1992). Furthermore, Pseudomonas sp. B13 T was used for the first experiments that demonstrated the feasibility of in vivo and in vitro approaches for the construction of organisms with new metabolic capabilities (Reineke & Knackmuss, 1979, 1980Rubio et al., 1986;Ramos et al., 1986;Rojo et al., 1987). Very recently it was demonstrated that the ability to degrade 3-and 4-chlorocatechol is encoded on a selftransferable DNA element in Pseudomonas sp. B13 T (Gaillard et al., 2006). Affilation of Pseudomonas sp. B13 T to the genus Pseudomonas sensu stricto has already been demonstrated by Busse et al. (1989) based on analysis of the quinone system and polyamine pattern.Cells of Pseudomonas sp. B13 T are Gram-negative, polarly flagellated, motile short rods. The oxidase and catalase reactions were positive. Based on these...

No abstract

A Gram-negative, non-motile, non-spore-forming coccoid bacterium (strain BO1 T ) was isolated recently from a breast implant infection of a 71-year-old female patient with clinical signs of brucellosis. Affiliation of strain BO1T to the genus Brucella was confirmed by means of polyamine pattern, polar lipid profile, fatty acid profile, quinone system, DNA-DNA hybridization studies and by insertion sequence 711 (IS711)-specific PCR. Strain BO1 T harboured four to five copies of the Brucella-specific insertion element IS711, displaying a unique banding pattern, and exhibited a unique 16S rRNA gene sequence and also grouped separately in multilocus sequence typing analysis. Strain BO1 T reacted with Brucella M-monospecific antiserum. Incomplete lysis was detected with bacteriophages Tb (Tbilisi), F1 and F25. Biochemical profiling revealed a high degree of enzymic activity and metabolic capabilities. In multilocus VNTR (variable-number tandem-repeat) analysis, strain BO1 T showed a very distinctive profile and clustered with the other 'exotic' Brucella strains, including strains isolated from marine mammals, and Brucella microti, Brucella suis biovar 5 and Brucella neotomae. Comparative omp2a and omp2b gene sequence analysis revealed the most divergent omp2 sequences identified to date for a Brucella strain. The recA gene sequence of strain BO1 T differed in seven nucleotides from the Brucella recA consensus sequence. Using the Brucella species-specific multiplex PCR assay, strain BO1T displayed a unique banding pattern not observed in other Brucella species. From the phenotypic and molecular analysis it became evident that strain BO1 T was clearly different from all other Brucella species, and therefore represents a novel species within the genus Brucella. Because of its unexpected isolation, the name Brucella inopinata with the type strain BO1 T (5BCCN