A comprehensive DNA-DNA hybridization study was performed by using 183 strains of the genus Xanthomonus. This genus was shown to comprise 20 DNA homology groups which are considered genomic species. Four groups corresponded to the previously described species Xanthomonas albilineans, Xanthomonas fiagariae, Xanthomonas oryzae, and Xanthomonas populi. The previously described species Xanthomonas campestris was heterogeneous and was divided into 16 DNA homology groups. One of these groups exhibited a high level of DNA homology with Xanthomonas axonopodis. The 62 pathovars represented in this study were. allocated to appropriate species. Our results, together with previous taxonomic data, supported a comprehensive revision of the classification of the genus Xanthomonas. The species X. albilineans, X. jiagarke, X. oryme, and X. populi are not affected. The type species of the genus,X. campestris (Pammell895) Dowson 1939, is emended to include only the pathovars obtained from crucifers (i.e., X. campestris pv. aberrans, X. campestris pv. armoraciae, X. campestris pv. barbareae, X. campestris pv. campestris, X. campestris pv. incanae, and X. campestris pv. raphani). vesicatoria. Differentiating characteristics were determined for the new species on the basis of metabolic activity on a range of carbon substrates by using the Biolog GN microplate system. X. axonopodisIn the past, the taxonomy of bacteria has been dominated by a phenetic approach, and many classification systems have been and still are based on what were thought to be important phenotypic properties. The taxonomy of the genus Xanthomonas has followed this tendency in that a single phenotypic feature, host specificity, has determined the classification of the genus. Since the first report of a xanthomonad (55) until 1974, it was common practice to define a plant-pathogenic xanthomonad isolated from a new host plant as a new Xanthomonas species. The unreasonable number of nomenspecies resulting from this practice was drastically reduced by Dye and Lelliott (19), who justified their reclassification by referring to the impossibility of differentiating nomenspecies by any feature other than host specificity (10,17). Later, names of former nomenspecies were preserved in a special-purpose classification (18) as Xanthomonas campestris pathovar names.The original classification of the genus Xanthomonas, in which all of the phytopathological variants of X campestris were recognized as separate species, was not sound taxonomically. With the exception of the ambiguous feature of host specificity, few biochemical and phenotypic characteristics were used to differentiate the species. In the last few years, * Corresponding author. Mailing address: Laboratorium voor Microbiologie, Universiteit Gent, Ledeganckstraat 35, B-9000 Ghent, Belgium.workers have provided evidence that the current classification, in whichX. campestris contains more than 140 pathovars, is not a reflection of genomic relationships. The first DNA hybridization experiments performed with Xanthomonas...

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.

No abstract

The genus Xanthomonas contains a large number of strains, which have been characterized by a variety of phenotypic and genotypic classification methods. The Xanthomonas collection constitutes one of the largest groups of bacteria that have been characterized phylogenetically by DNA-DNA homology studies and genomic fingerprinting. Presently, a total genomic DNA-DNA homology value of 70 % represents an internationally accepted criterion to define bacterial species levels. However, the complexity of DNA-DNA reassociation kinetics methods precludes the rapid analysis of large numbers of bacterial isolates, which is imperative for molecular microbial diversity studies. Therefore, the aim of this study was to compare more facile PCR-based genomic fingerprinting techniques, such as repetitive-sequence-based (rep)-PCR and AFLP genomic fingerprinting, to DNA-DNA hybridization studies. Using three different primer sets, rep-PCR genomic fingerprint patterns were generated for 178 Xanthomonas strains, belonging to all 20 previously defined DNA-DNA homology groups, and one Stenotrophomonas maltophilia strain. In addition, AFLP genomic fingerprints were produced for a subset of 80 Xanthomonas strains belonging to the 20 DNA-DNA homology groups and for the S. maltophilia strain. Similarity values derived from rep-PCR-and AFLPgenerated fingerprinting analyses were calculated and used to determine the correlation between rep-PCR-or AFLP-derived relationships and DNA-DNA homology values. A high correlation was observed, suggesting that genomic fingerprinting techniques truly reveal genotypic and phylogenetic relationships of organisms. On the basis of these studies, we propose that genomic fingerprinting techniques such as rep-PCR and AFLP can be used as rapid, highly discriminatory screening techniques to determine the taxonomic diversity and phylogenetic structure of bacterial populations.

The phylogenetic relationships of all validly described species of the genus Xanthomonas and the type strain of Stenotrophomonas maltophilia were analyzed by sequencing and comparing 16s ribosomal DNAs (rDNAs). The two genera exhibited a mean sequence similarity value of 96.6%, corresponding to differences at 50 nucleotide positions on average. The species of the genus Xanthomonas exhibited relatively high levels of overall sequence similarity; the mean similarity value was 98.2%, which corresponds to an average of 14 mutual nucleotide differences. Within the genus Xanthomonas, a group containing Xanthomonas albilineans, Xanthomonas hyacinthi, Xanthornonas theicoh, and Xanthomonas translucens clustered apart from the main Xanthomonas core, whereas Xanthomonas sacchari formed a third phylogenetic lineage. Due to the very restricted variability in 16s rDNA sequences within the genusxanthomonas, rDNA signatures that have possible diagnostic value for differentiating the Xanthomonas species could not be determined with certainty. When sequence similarities were compared with DNA-DNA pairing data determined previously, there was only a limited correlation. This illustrates the different resolving powers of the techniques for determining phylogenetic hierarchies and for species delineation.The phytopathogenic specialization and the broad host range of members of the genus Xanthomonas (30) have made these microorganisms the subject of numerous taxonomic studies (for a review, see reference 59). Traditional methods used for the detection and identification of xanthomonads, such as biochemical (55), serological, and pathogenicity tests (3, 4, 5, 31, 45, 48), have been extended by molecular methods based on protein profiling (57, 60) and fatty acid analysis (7, 63).Currently, molecular approaches are being used increasingly in studies of the taxonomy and epidemiology of Xanthomonas species (15, 19). This has led to the development of different probes for detection and identification by hybridization or by PCR amplification (17, 18, 20, 21, 24, 25, 27, 32,40) and to analyses of the genetic structures of field populations (1,4,26, 28, 29).A polyphasic approach, such as the approach described by Vandamme et al. (54), could utilize all of these methods to contribute to the classification of the genus Xanthomonas. In practice, however, DNA reassociation, which provides a measure of the overall similarity of chromosomal genomes, is generally used for species delineation. This strategy has been used by Vauterin et al. (58), who recently reclassified the genus Xanthomonas and recognized and described 20 genomic species.Ideally, a comparison of the complete nucleotide sequences of genomes would probably be the most informative technique and thus the best method for determining the overall taxonomic relatedness of bacterial taxa. As sequencing entire genomes on a routine basis for taxonomy purposes is still impractical, techniques such as the sequencing of "molecular chronometers" like rRNA genes have been developed during the las...