The catabolism of 3-ketolactose in Agrobacterium

The existence of a novel enzyme, catalyzing the hydrolysis of 3-ketolactose, is described in the different genetic groups of the genus Agrobacterium. The enzyme differs from the other glycosidases formed by Agrobacterium during growth on lactose. The inducibility of the enzyme could be demonstrated in a strain from biotype 1, but not in a strain from biotype 2. The specific activity of the 3-ketolactose hydrolase is higher in extracts of strains belonging to biotype 2 than to biotype 1. The optimum pH of the enzyme in Tris-HCl buffer is 8.4-8.5. The K(m) value for 3-ketolactose is 2.2 × 10(-2) M. The 3-ketolactose hydrolase is stimulated by Mg(2+) and Mn(2+), and inhibited by Zn(2+). Mercaptoethanol promotes the reaction rate in extracts of strains of biotype 1 but not in extracts of strains of bio-type 2.

Differentiation of Lactobacillus plantarum, L. pentosus and L. paraplantarum species by RAPD-PCR and AFLP

Two high-resolution genotypic techniques (RAPD-PCR and AFLP) were evaluated for their possibility to discriminate the species Lactobacillus plantarum, Lactobacillus pentosus and Lactobacillus paraplantarum and to type these taxa at the infra-species level. In total 23 strains of L. plantarum, three strains of L. pentosus, two strains of L. paraplantarum and two related strains for which the species assignment was not clear, were studied. For RAPD-PCR, suitable oligonucleotides and amplification conditions were selected and tested. For AFLP, a double digest of total genomic DNA was used and a subset of restriction fragments was selectively amplified and visualised using different primer combinations. Both methodologies generated, species-specific electrophoretic profiles. Moreover, the presence of distinct subgroups was revealed within the species L. plantarum.

Classification of metal-resistant bacteria from industrial biotopes as Ralstonia campinensis sp. nov., Ralstonia metallidurans sp. nov. and Ralstonia basilensis Steinle et al. 1998 emend

Thirty-one heavy-metal-resistant bacteria isolated from industrial biotopes were subjected to polyphasic characterization, including 16S rDNA sequence analysis, DNA-DNA hybridizations, biochemical tests, whole-cell protein and fatty-acid analyses. All strains were shown to belong to the Ralstonia branch of the beta-Proteobacteria. Whole-cell protein profiles and DNA-DNA hybridizations revealed two clearly distinct groups, showing low similarity to known Ralstonia species. These two groups, of 8 and 17 isolates, were assigned to two new species, for which the names Ralstonia campinensis sp. nov. and Ralstonia metallidurans sp. nov. are proposed. The type strains are WS2T (= LMG 19282T = CCUG 44526T) and CH34T (= LMG 1195T = DSM 2839T), respectively. Six isolates were allocated to Ralstonia basilensis, which presently contains only the type strain; an emendation of the latter species description is therefore proposed.

Phenotypic and genetic diversity of enterococci isolated from Italian cheeses

In the present study, 124 enterococcal strains, isolated from traditional Italian cow, goat and buffalo cheeses, were characterized using phenotypic features and randomly amplified polymorphic DNA polymerase chain reaction (RAPD-PCR). The RAPD-PCR profiles obtained with four primers and five different amplification conditions were compared by numerical analysis and allowed an inter- and intraspecific differentiation of the isolates. Whole cell protein analysis by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was used as a reference method for species identification. The strains were identified as Enterococcus faecalis (82 strains), E. faecium (27 strains), E. durans (nine strains), E. gallinarum (four strains) and E. hirae (two strains). Species recognition by means of RAPD-PCR was in agreement with the SDS-PAGE results except for eight strains of E. faecium that clustered in separated groups. On the other hand, phenotypic identification based on carbohydrate fermentation profiles, using the rapid ID 32 STREP galleries, gave different results from SDS-PAGE in 12.1% of the cases. The majority of the strains had weak acidifying and proteolytic activities in milk. One E. faecium strain showed vanA (vancomycin resistance) genotype while four strains showed a beta-haemolytic reaction on human blood. Several strains showed antagonistic activity towards indicator strains of Listeria innocua, Clostridium tyrobutyricam and Propionibacterium freudenreichii subsp. shermanii.

Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system

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 AFLP-generated 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.

Modification of the aggregation behaviour of the environmental Ralstonia eutropha-like strain AE815 is reflected by both surface hydrophobicity and amplified fragment length polymorphism (AFLP) patterns

After inoculation of the plasmid-free non-aggregative Ralstonia eutropha-like strain AE815 in activated sludge, followed by reisolation on a selective medium, a mutant strain A3 was obtained, which was characterized by an autoaggregative behaviour. Strain A3 had also acquired an IncP1 plasmid, pLME1, co-aggregated with yeast cells when co-cultured, and stained better with Congo red than did the AE815 strain. Contact angle measurements showed that the mutant strain was considerably more hydrophobic than the parent strain AE815, and scanning electron microscopy (SEM) revealed the production of an extracellular substance. A similar hydrophobic mutant (AE176R) could be isolated from the AE815-isogenic R. eutropha-like strain AE176. With the DNA fingerprinting technique repetitive extragenic palindromic-polymerase chain reaction (REP-PCR), no differences between these four strains, AE815, A3, AE176 and AE176R, could be revealed. However, using the amplified fragment length polymorphism (AFLP) DNA fingerprinting technique with three different primer combinations, small but clear reproducible differences between the banding patterns of the autoaggregative mutants and their non-autoaggregative parent strains were observed for each primer set. These studies demonstrate that, upon introduction of a strain in an activated sludge microbial community, minor genetic changes readily occur, which can nevertheless have major consequences for the phenotype of the strain and its aggregation behaviour.

Polyphasic characterization of rhizobia that nodulate Phaseolus vulgaris in West Africa (Senegal and Gambia)

Fifty-eight new isolates were obtained from root nodules of common bean (Phaseolus vulgaris) cultivated in soils originating from different agroecological areas in Senegal and Gambia (West Africa). A polyphasic approach including both phenotypic and genotypic techniques was used to study the diversity of the 58 Rhizobium isolates and to determine their taxonomic relationships with reference strains. All the techniques performed, analysis of multilocus enzyme electrophoretic patterns, SDS-PAGE profiles of total cell proteins, PCR-RFLP analysis of the genes encoding 16S rRNA and of the 16S-23S RNA intergenic spacer region (ITS-PCR-RFLP), auxanographic tests using API galleries and nodulation tests lead to the consensus conclusion that the new rhizobial isolates formed two main distinct groups, I and II, belonging to Rhizobium tropici type B and Rhizobium etli, respectively. By MLEE R. etli and group II strains showed several related electrophoretic types, evidencing some extent of internal heterogeneity among them. This heterogeneity was confirmed by other techniques (ITS-PCR-RFLP, SDS-PAGE and host-plant-specificity) with the same nine distinct strains of group II showing some differences from the core of group II (54 strains).

A polyphasic taxonomic study of Chryseobacterium strains isolated from dairy sources

A polyphasic taxonomic study, employing protein electrophoresis (SDS-PAGE), gas chromatographic analysis of cellular fatty acids (FAME), mol% G+C determination and DNA-DNA hybridizations, was undertaken on 103 dairy isolates shown to belong to Chryseobacterium. Reference strains of the Chryseobacterium species, CDC group IIb and Embedobacter brevis were included. SDS-PAGE analysis yielded good differentiation between the investigated species. About half of the strains could be clustered into nine major groups while the other half occupied a separate position. With FAME analysis no clear differentiation of the Chryseobacterium species (except C. meningosepticum) and SDS-PAGE groups could be achieved. FAME analysis, however, gave good differentiation between the Chryseobacterium and Empedobacter strains. The mol% G+C of the isolates tested, ranged between 36.4 and 39.0. The combination of SDS-PAGE and DNA-DNA hybridization identified a large group of dairy isolates as C. indologenes, one isolate as C. gleum and two new genotypic groups, comprising five and 15 dairy isolates respectively, emerged from the polyphasic study. Another large part of strains have a separate or uncertain position in Chryseobacterium and remained classified as Chryseobacterium species CDC group IIb.

A polyphasic approach towards the identification of strains belonging to Lactobacillus acidophilus and related species

A set of 98 strains belonging to nine species of the Lactobacillus acidophilus rRNA-group have been analysed by SDS-PAGE of cellular proteins, RAPD-PCR and AFLP with fluorescently labeled primers in order to find improved methods for their identification. Strains of the following phenotypically highly similar species were examined: L. acidophilus, L. amylovorus, L. crispatus, L. johnsonii, L. gasseri, L. gallinarum, L. helveticus, L. iners and L. amylolyticus. Although the majority of the species can be differentiated by SDS-PAGE of whole-cell proteins, the latter technique showed poor discrimination between L. gasseri and L. johnsonii strains and between some strains of L. amylovorus and L. gallinarum. However, this study shows that the RAPD-PCR (using at least 3 different primers followed by numerical analysis of the combined patterns) and AFLP are most suitable genomic fingerprinting techniques for the differentiation of all the species listed above, and that databases for identification can be constructed, particularly when commercially available molecular tool-kits are used. The separate species status of the recently described L. amylolyticus and L. iners was fully confirmed.

Identification of Burkholderia species and genomovars from cystic fibrosis patients by AFLP fingerprinting

AFLP is a genomic fingerprinting technique based on the selective amplification of restriction fragments from a total double-digest of genomic DNA. The applicability of this method to differentiate between species and genomovars of the genus Burkholderia was tested, with particular emphasis on taxa occurring in cystic fibrosis patients. In this study, 78 well-characterized strains and field isolates were investigated by two methods of AFLP fingerprinting. In the manual procedure, a radioactively labelled primer was used, amplified fragments were separated by conventional PAGE and the patterns were revealed by autoradiography. In the automated procedure, a fluorescently labelled primer was used in combination with electrophoresis and on-line data collection by means of an automated DNA sequencer. Overall, there was good agreement between the two AFLP procedures and the data were mostly consistent with results obtained from SDS-PAGE of whole-cell proteins and DNA-DNA hybridization experiments. The automated AFLP procedure has considerable technical advantages compared with the manual AFLP procedure, but a thorough visual analysis of the DNA profiles was required to avoid misidentification of some Burkholderia cepacia genomovar III strains.

Lactobacillus perolens sp. nov., a soft drink spoilage bacterium

Lactic acid bacteria that are able to spoil soft drinks with low pH comprise a limited number of acidotolerant or acidophilic species of the genera Lactobacillus, Leuconostoc and Weissella. Various Gram-positive rods causing turbidity and off-flavour were isolated from orange lemonades. Physiological and biochemical studies including SDS-PAGE whole-cell protein analysis showed a homogeneous group of organisms. The 16S rRNA gene sequence analysis of two representatives revealed that they formed a phylogenetically distinct line within the genus Lactobacillus. All strains were facultatively heterofermentative, producing L-lactic acid. Based on the data presented a new species L. perolens is proposed. The name refers to the off-flavour caused by high amounts of diacetyl. The type strain of L. perolens is DSM 12744 (LMG 18936). A rRNA targeted oligonucleotide probe was designed that allows a fast and reliable identification of L. perolens.

Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998

A polyphasic study of strains originally received as Bacillus (now Virgibacillus) pantothenticus, along with strains representing species belonging to Bacillus, Halobacillus and Paenibacillus, was undertaken using amplified rDNA restriction analysis (ARDRA), fatty acid methyl ester (FAME) analysis, SDS-PAGE of whole-cell proteins and routine diagnostic characters comprising 61 biochemical tests in the API system and 15 observations of vegetative cell and sporangial morphology. It revealed the presence within Virgibacillus of an as yet undescribed new species, for which the name Virgibacillus proomii is proposed; V. proomii can be distinguished from V. pantothenticus and members of Bacillus sensu stricto, and from members of Paenibacillus and other aerobic endospore-forming bacteria, by routine phenotypic tests. The type strain of Virgibacillus proomii is LMG 12370T.

Streptococcus intestinalis Robinson et al. 1988 and Streptococcus alactolyticus Farrow et al. 1984 are phenotypically indistinguishable

The one-dimensional whole-cell protein patterns and a variety of biochemical characteristics of the type and reference strains of Streptococcus intestinalis and Streptococcus alactolyticus were studied. All the data revealed that strains of both species were indistinguishable. Reported differences in haemolytic activity and presence of Lancefield antigens were not reproduced. All strains were alpha-haemolytic. The S. intestinalis type strain possessed the group G antigen, but a second S. intestinalis reference strain and all of the S. alactolyticus strains possessed the group D antigen. All strains produced urease activity (albeit some after prolonged incubation), a characteristic considered important for S. intestinalis. Given the congruence between whole-cell protein electrophoresis and percentage of DNA-DNA hybridization, these data suggest that Streptococcus intestinalis Robinson et al. 1988 is a junior synonym of Streptococcus alactolyticus Farrow et al. 1984.

Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov

A polyphasic taxonomic study that included DNA-DNA hybridizations, DNA base ratio determinations, 16S rDNA sequence analysis, whole-cell protein and fatty acid analyses, AFLP (amplified fragment length polymorphism) fingerprinting and an extensive biochemical characterization was performed on 10 strains provisionally identified as Alcaligenes faecalis-like bacteria. The six environmental and four human isolates belonged to the genus Ralstonia and were assigned to a new species for which the name Ralstonia gilardii sp. nov. is proposed. The type strain is LMG 5886T.

Assignment of Centers for Disease Control group IVc-2 to the genus Ralstonia as Ralstonia paucula sp. nov

An integrated genotypic and phenotypic analysis of 12 Centers for Disease Control (CDC) group IVc-2 strains revealed that this taxon represents a novel species belonging to the genus Ralstonia. Comparative 16S rDNA sequence analysis allocated a representative CDC group IVc-2 strain to the Ralstonia branch of the beta subclass of the Proteobacteria. DNA-DNA hybridizations did not detect significant binding levels towards any presently known Ralstonia species, including Ralstonia pickettii. Its DNA base ratio is between 65 and 67 mol%. The name Ralstonia paucula sp. nov. is proposed, with strain LMG 3244 (= CDC E6793), isolated from a human respiratory tract, as the type strain. R. paucula can be differentiated from other Ralstonia species by whole-cell protein analysis, amplified rDNA restriction analysis and a variety of classical biochemical tests. Strains have been isolated from various human clinical and environmental sources.

Burkholderia cocovenenans (van Damme et al. 1960) Gillis et al. 1995 and Burkholderia vandii Urakami et al. 1994 are junior synonyms of Burkholderia gladioli (Severini 1913) Yabuuchi et al. 1993 and Burkholderia plantarii (Azegami et al. 1987) Urakami et al. 1994, respectively

Reference strains of Burkholderia cocovenenans and Burkholderia vandii were compared with strains of other Burkholderia species using SDS-PAGE of whole-cell proteins, DNA-DNA hybridization and extensive biochemical characterization. Burkholderia gladioli and B. cocovenenans were indistinguishable in the chemotaxonomic and biochemical analyses. Burkholderia plantarii and B. vandii had indistinguishable whole-cell protein patterns but the B. vandii type strain differed from B. plantarii strains in several biochemical tests. The DNA-DNA binding levels (higher than 70%) indicated that (i) B. gladioli and B. cocovenenans, and (ii) B. plantarii and B. vandii each represent a single species. It is concluded that B. cocovenenans and B. vandii are junior synonyms of B. gladioli and B. plantarii, respectively.

Application of temperature-gradient gel electrophoresis in taxonomy of coryneform bacteria

Strains belonging to the Gram-positive coryneform soil bacteria were screened genotypically by temperature-gradient gel electrophoresis (TGGE). This method allows the sequence-specific separation of amplified fragments of 16S rRNA genes. A total of 115 reference strains representing the majority of the species of the genera Aeromicrobium, Agromyces, Arthrobacter, Aureobacterium, Cellulomonas, Curtobacterium, Nocardioides and Terrabacter were characterized. Depending on the genus investigated, the resolution limit of the technique appeared to be at the species or genus level or intermediate between the two. Aberrant TGGE profiles of strains within particular taxa revealed genomic heterogeneity and generic misclassification of nine strains studied. Beyond that, indications of 16S rRNA gene heterogeneity were found within the genomes of three Curtobacterium strains. The misclassifications revealed by TGGE were confirmed using whole-cell fatty acid methyl ester analysis and subsequent comparison with a database. TGGE has been demonstrated to be a useful tool in bacterial taxonomy.

Differentiation between Streptococcus gallolyticus strains of human clinical and veterinary origins and Streptococcus bovis strains from the intestinal tracts of ruminants

Strains formerly identified as Streptococcus bovis were allotted to two groups by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of whole-cell proteins. Strains from humans with infections, mostly patients with endocarditis, and strains from pigeons with septicemia clustered with the recently described species Streptococcus gallolyticus. The original S. bovis type strain and strains exclusively from ruminants formed the second cluster. The findings indicate that S. gallolyticus is more likely to be involved in human and animal infections than S. bovis. Growth characteristics and several biochemical reactions were found to be useful in the differentiation of S. gallolyticus from S. bovis.

Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal

A group of nodule isolates from Neptunia natans, an indigenous stemnodulated tropical legume found in waterlogged areas of Senegal, was studied. Polyphasic taxonomy was performed, including SDS-PAGE of total proteins, auxanography using API galleries, host-plant specificity, PCR-RFLP of the internal transcribed spacer region between the 16S and the 23S rRNA coding genes, 16S rRNA gene sequencing and DNA-DNA hybridization. It was demonstrated that this group is phenotypically and phylogenetically separate from the known species of Rhizobium, Sinorhizobium, Mesorhizobium, Agrobacterium, Bradyrhizobium and Azorhizobium. Its closest phylogenetic neighbour, as deduced by 16S rRNA gene sequencing, is Agrobacterium vitis (96.2% sequence homology). The name Allorhizobium undicola gen. nov., sp. nov., is proposed for this group of bacteria, which are capable of efficient nitrogen-fixing symbiosis with Neptunia natans, and the type strain is ORS 992T (= LMG 11875T).

Identification of streptococci from Greek Kasseri cheese and description of Streptococcus macedonicus sp. nov

Taxonomic studies were performed on some Streptococcus-like organisms isolated from naturally fermented Greek Kasseri cheese. By SDS-PAGE analysis of whole-cell proteins the group was found to be quite different from Streptococcus thermophilus. Comparative 16S and 23S rRNA sequence analyses showed that the isolates represent a new species within the genus Streptococcus, where they are most closely related to the Streptococcus bovis cluster. On the basis of these phylogenetic results and some phenotypic differences, a new species, Streptococcus macedonicus, is proposed. The type strain is ACA-DC 206.

Pelistega europaea gen. nov., sp. nov., a bacterium associated with respiratory disease in pigeons: taxonomic structure and phylogenetic allocation

Twenty-four strains isolated mainly from infected respiratory tracts of pigeons were characterized by an integrated genotypic and phenotypic approach. An extensive biochemical examination using conventional tests and several API microtest systems indicated that all isolates formed a phenotypically homogeneous taxon with a DNA G + C content between 42 and 43 mol%. Whole-cell protein and fatty acid analysis revealed an unexpected heterogeneity which was confirmed by DNA-DNA hybridizations. Four main genotypic sub-groups (genomovars) were delineated. 16S rDNA sequence analysis of a representative strain indicated that this taxon belongs to the beta-subclass of the Proteobacteria with Taylorella equigenitalis as its closest neighbour (about 94.8% similarity). A comparison of phenotypic and genotypic characteristics of both taxa suggested that the pigeon isolates represented a novel genus for which the name Pelistega is proposed. In the absence of differential phenotypic characteristics between the genomovars, it was preferred to include all of the isolates into a single species, Pelistega europaea, and strain LMG 10982 was selected as the type strain. The latter strain belongs to fatty acid cluster I and protein electrophoretic sub-group 1, which comprise 13 and 5 isolates, respectively. It is not unlikely that the name P. europaea will be restricted in the future to organisms belonging to fatty acid cluster I, or even to protein electrophoretic sub-group 1, upon discovery of differential diagnostic features.

Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov

Sixteen heparinase-producing isolates, related to Sphingobacterium heparinum, were grouped into three major clusters by SDS-PAGE and DNA-rRNA hybridizations. Based on a polyphasic approach, it was shown that isolates of two of these clusters and S. heparinum species belong to a new genus for which the name Pedobacter is proposed. The genus consists of Pedobacter heparinus comb. nov. (formerly Sphingobacterium heparinum), which is the type species, Pedobacter piscium comb. nov. (formerly Sphingobacterium piscium), Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. and four as-yet-unnamed DNA hybridization groups. All the previously named taxa can be discriminated by phenotypic features, but have strong overall similarities with representatives of the genus Sphingobacterium and the misclassified species [Flexibacter] canadensis. All these organisms constitute a separate rRNA branch in rRNA superfamily V for which the family Sphingobacteriaceae fam. nov. is proposed.

Whole-cell protein electrophoretic analysis of viridans streptococci: evidence for heterogeneity among Streptococcus mitis biovars

One hundred reference strains representing all species belonging to the different phylogenetic lineages of the viridans streptococci were examined by means of one-dimensional whole-organism protein electrophoresis. For most of the species examined, multiple strains characterized by DNA-DNA hybridization were included and, wherever described, representatives of different biochemical variants were analysed. Most species were clearly differentiated. The data support the viewpoint that members of the Streptococcus anginosus group constitute a single species and indicate that Streptococcus mitis biovar 2 is a heterogeneous taxon comprising strains from several streptococcal species.

Occurrence of multiple genomovars of Burkholderia cepacia in cystic fibrosis patients and proposal of Burkholderia multivorans sp. nov

We performed an integrated genotypic and phenotypic analysis of 128 strains of the genera Burkholderia, Ralstonia, and Pseudomonas in order to study the taxonomic structure of Burkholderia cepacia and its relationships with other Burkholderia species. Our data show that presumed B. cepacia strains isolated from cystic fibrosis patients belong to at least five distinct genomic species, one of which was identified as Burkholderia vietnamiensis. This group of five phenotypically similar species is referred to as the B. cepacia complex. The name Burkholderia multivorans is proposed for one of these genomic species, which was formerly referred to as B. cepacia genomovar II; the remaining B. cepacia groups are referred to as genomovars I, III, and IV, pending additional differential phenotypic tests. The role and pathogenic potential of each of these taxa, particularly in view of the potentially fatal infections in cystic fibrosis patients, need further evaluation. The data presented also demonstrate that Pseudomonas glathei and Pseudomonas pyrrocinia should be reclassified as Burkholderia species.

Inclusion of Aeromonas DNA hybridization group 11 in Aeromonas encheleia and extended descriptions of the species Aeromonas eucrenophila and A. encheleia

The recently reported chemotaxonomic and genotypic description of two well-separated subgroups (I and II) in Aeromonas eucrenophila and their affiliation to Aeromonas encheleia and the unnamed Aeromonas DNA hybridization group (HG) 11 (G. Huys, M. Altwegg, M.-L. Hänninen, M. Vancanneyt, L. Vauterin, R. Coopman, U. Torck, J. Lüthy-Hottenstein, P. Janssen, and K. Kersters, Syst. Appl. Microbiol. 19:616-623, 1996) has questioned the original species descriptions of A. eucrenophila and A. encheleia. In order to elucidate the unclear taxonomic status of these taxa in the genus Aeromonas, we have further investigated a collection of 14 reference strains and 14 related isolates encompassing the taxa A. eucrenophila subgroups I and II, A. encheleia, and HG11 by DNA-DNA hybridization (on 17 of the 28 strains) and phenotypic characterization (on all 28 strains). Genotypically, the investigated strains could be grouped into two DNA hybridization groups that exhibited between-group homologies ranging from 42 to 52%. The members of DNA homology group I (DNA binding, 76 to 100%) were strains of A. eucrenophila subgroup I, including the type strain LMG 3774, and two A. eucrenophila-like isolates, leading to the conclusion that these strains should be considered true representatives of the species A. eucrenophila. The strains of A. eucrenophila subgroup II, HG11, and A. encheleia, on the other hand, were closely joined in DNA homology group II (DNA binding, 74 to 105%) together with two presumptive A. encheleia isolates. The fact that strain LMG 16330T of A. encheleia was the only type strain residing in DNA homology group II implies that HG11 and A. eucrenophila subgroup II should be classified in the species A. encheleia. Except for the somewhat aberrant phenotypic positions of HG11 strains LMG 13075 and LMG 13076, the establishment of DNA homology groups I and II was supported by the delineation of phena 1 and 2 (level of correlation, 90%), respectively, as revealed by numerical analysis of 136 phenotypic test results. These data indicate that A. eucrenophila and A. encheleia are phenotypically highly related but can be easily separated by testing the production of acid from D-cellobiose and lactose and the assimilation of D-cellobiose. Extended descriptions of both species are given.

Aeromonas popoffii sp. nov., a mesophilic bacterium isolated from drinking water production plants and reservoirs

We examined the taxonomic position of seven Aeromonas isolates, recovered from Flemish and Scottish drinking water production plants and reservoirs, which were previously recognized by numerical analysis of genomic AFLP fingerprints as members of an unknown Aeromonas taxon that most closely resembled the species Aeromonas bestiarum (DNA hybridization group [HG] 2). The new phenotypic and DNA-DNA hybridization data obtained in this study show that the A. bestiarum-like strains constitute a separate Aeromonas species, for which the name Aeromonas popoffii sp. nov. is being proposed. The new species exhibited an internal DNA relatedness ranging from 79 to 100% and was 22 to 63% related to the type or reference strains of other Aeromonas spp. The highest DNA binding values were determined with A. bestiarum (51 to 63%), followed by Aeromonas hydrophila sensu stricto (HG1; 50 to 60%) and Aeromonas salmonicida (HG3; 39 to 55%). Although fingerprints generated by ribotyping and cellular fatty acid analysis often were highly similar, minor differences between the respective fingerprints were of significance for the differentiation of A. popoffii from its closest taxonomic neighbors, HG1, HG2, and HG3. Phenotypically, all seven strains of A. popoffii were positive for acid and gas production from D-glucose and glycerol, growth in KCN broth, arginine dihydrolase, DNase, Voges-Proskauer reaction, and resistance to vibriostatic agent O/129 and ampicillin but displayed negative reactions for production of urease, tryptophan deaminase, ornithine decarboxylase, and lysine decarboxylase (LDC). None of the strains displayed strong hemolytic activity. The lack of D-sucrose fermentation and LDC production and the ability to utilize DL-lactate as the sole energy and carbon source were useful characteristics for the biochemical separation of A. popoffii from A. bestiarum. Other Aeromonas spp. could be differentiated phenotypically from the new species by at least two features. The chromosomal G+C content of A. popoffii ranges from 57.7 to 59.6 mol%. Strain LMG 17541 is proposed as the type strain.

Discrimination of Acinetobacter genomic species by AFLP fingerprinting

AFLP is a novel genomic fingerprinting method based on the selective PCR amplification of restriction fragments. The usability of this method for the differentiation of genomic species in the genus Acinetobacter was investigated. A total of 151 classified strains (representing 18 genomic species, including type, reference, and field strains) and 8 unclassified strains were analyzed. By using a single set of restriction enzymes (HindIII and TaqI) and one particular set of selective PCR primers, all strains could be allocated to the correct genomic species and all groups were properly separated, with minimal intraspecific similarity levels ranging from 29 to 74%. Strains belonging to genomic species 8 (Acinetobacter lwoffii sensu stricto) and 9 grouped together in one cluster. The closely related DNA groups 1 (Acinetobacter calcoaceticus), 2 (Acinetobacter baumannii), 3 and 13TU (sensu Tjernberg & Ursing 1989) were clearly distinguishable, with intraspecific linkage levels above 50%. Strains of the independently described genomic species 13BJ (sensu Bouvet & Jeanjean 1989) and 14TU linked together at a relatively low level (33%). Although a previous DNA-DNA hybridization study seemed to justify the unification of these genomic species, AFLP analysis actually divides the 13BJ-14TU group into three well-separated subgroups. Finally, four unclassified strains obtained from diverse sources and origins grouped convincingly together, with a similarity linkage level of approximately 50%. These strains showed no similarities in their AFLP patterns with any of the other 155 strains studied and may represent a thus-far-undescribed Acinetobacter species. Based on these results, AFLP should be regarded as an important auxiliary method for the delineation of genomic species. Furthermore, because AFLP provides a detailed insight into the infraspecific structure of Acinetobacter taxa, the method also represents a highly effective means for the confirmation of strain identity in the epidemiology of acinetobacters.

Streptococcus hyovaginalis sp. nov. and Streptococcus thoraltensis sp. nov., from the genital tract of sows

Two groups of strains isolated from sows were shown to belong to new sublines in the genus Streptococcus. Based on phenotypic and phylogenetic analyses, we propose that these bacteria should be classified as two new species, Streptococcus hyovaginalis sp. nov. and Streptococcus thoraltensis sp. nov. These two species are found in the genital tract, but the capnophilic species S. thoraltensis may also occur in the intestinal tract of pigs. The type strain of S. hyovaginalis is SHV515 (= LMG 14710), and S69 (= LMG 13593) is the type strain of S. thoraltensis.

Diversity, persistence, and virulence of Aeromonas strains isolated from drinking water distribution systems in Sweden

The Aeromonas populations in 13 Swedish drinking water distribution systems, representing different treatments, were investigated. From each system, water samples were collected four times during the period from May to September 1994 from raw water and water after treatment and at two to five sites within the distribution system. In total, 220 water samples were collected. From samples containing presumptive Aeromonas, up to 32 colonies were analyzed by the PhenePlate Aeromonas (PhP-AE) system, which is a highly discriminating biochemical fingerprinting method. Selected isolates from different phenotypes (PhP types) were further identified by the API 20 NE system and by gas-liquid chromatography analysis of fatty acid methyl esters (FAMEs). Selected isolates were also assayed for their potential to produce hemolysin and cytotoxin and for their ability to adhere to human intestinal cells. In total, 117 water samples (53%) contained presumptive Aeromonas which numbered up to 10(6) CFU/100 ml in raw water and up to 750 CFU/100 ml in tap water. Among the 2,117 isolates that were subjected to typing by the PhP-AE system, more than 300 distinct PhP types were found, of which the majority occurred only sporadically. Raw (surface) water samples usually contained many different PhP types, showing high diversity indices (Di) (median Di = 0.95). The Aeromonas populations in samples collected from within the distribution systems were less diverse (median Di = 0.58) and were often dominated by one major PhP type that was found on several sampling occasions. Seventeen such major PhP types could be found and were represented in 1,037 isolates (49%). Identification by API 20 NE and FAME analysis revealed that most of the major PhP types were Aeromonas hydrophila or belonged to unidentified Aeromonas species. Hemolysin and cytotoxin production was observed in most major PhP types (representing 87 and 54% of the assayed isolates, respectively), and adherence was found in 89% of the isolates that produced cytotoxin. Thus, the data presented here show that although raw water may contain very diverse Aeromonas populations, the populations seemed to be remarkably stable within the studied water distribution systems, and that some potentially pathogenic Aeromonas strains could persist for several months in drinking water.

Characterization of Aeromonas spp. isolated from humans with diarrhea, from healthy controls, and from surface water in Bangladesh

Aeromonas isolates from patients with diarrhea in Bangladesh (n = 69), from healthy controls (n = 11), and from surface water (n = 40) were analyzed with respect to their hybridization groups (HGs) by the aid of fatty acid methyl ester (FAME) characterization and DNA fingerprinting by AFLP, biochemical phenotypes (Phe-nePlate [PhP] types), and the production of hemolysin and cytotoxin. The aim of the investigation was to find out whether certain strains carrying virulence factors predominated among patient isolates. According to FAME and/or AFLP analysis, most human isolates were allocated to DNA HGs 4 (Aeromonas caviae) and 1 (A. hydrophila). Most environmental strains were allocated to HG8 (A. veronii biogroup sobria) and HG4 (A. caviae), and only one was of HG1. According to PhP typing, the diversity among patient isolates was lower than that among other strains, and two dominating PhP types (types BD-1 and BD-2) were identified in 29 and 30% of the patient isolates, respectively. PhP type BD-1 was also common among the environmental isolates, whereas PhP type BD-2 was only identified in two of the other isolates. Twenty-five of 26 isolates belonging to HG1 were of the same PhP type (BD-2), whereas isolates of other common HGs were more diverse according to their PhP types. Hemolytic and cytotoxin-producing strains occurred more frequently among the environmental isolates than among patient isolates. However, the hemolytic and cytotoxic activities among human isolates was strongly correlated to the HG1/BD-2 type, which, in addition, showed high cytotoxin titers (median values, 1/512 compared to 1/128 for cytotoxin-positive isolates belonging to other types). Thus, the HG1/BD-2 type may represent a pathogenic A. hydrophila type that is able to produce diarrhea in humans.

A 4-year study of the diversity and persistence of coliforms and Aeromonas in the water of a Swedish drinking water well

Coliforms and Aeromonas, isolated over a sampling period of 4 years from a Swedish drinking water well, were analysed for their phenotypical diversity and for their ability to persist in the well water. From each of the 40 water samples collected from the well, 32 bacterial isolates were subjected to typing by the PhenePlate (PhP) biochemical fingerprinting system. Strains able to persist in the well water were further characterized using the API 20E system, gas-liquid chromatographic cellular fatty acid analysis, and the DNA fingerprinting technique AFLP. Using the PhP system, a total of 170 different phenotypes were identified among 1143 studied isolates. Most phenotypes were only represented by a few isolates and (or) were restricted to one or two sampling occasions. However, one particular phenotype (RV-C01), identified as Aeromonas hydrophila using the API 20E system and fatty acid analysis, reoccurred in 28 samples distributed over the whole study period and often dominated the bacterial population in the well water. AFLP analysis revealed that the RV-C01 isolates displayed basically identical fingerprints. Our results thus suggest that a genetically stable Aeromonas clone resided in the well water over the whole 4-year study, whereas other bacterial strains studied were only transient inhabitants of the well.

Streptococcus difficile is a nonhemolytic group B, type Ib Streptococcus

Whole-cell protein electrophoretic analysis of the type strain of Streptococcus difficile (LMG 15799) revealed that this organism was indistinguishable from Streptococcus agalactiae strains. Although LMG 15799T (T = type strain) was originally described as serologically untypeable, we found that this strain was a group B streptococcus belonging to the capsular polysaccharide antigen type Ib group. The biochemical reactivity of S. difficile, which differed from the biochemical reactivity of typical S. agalactiae strains mainly by being less versatile, is similar to the biochemical reactivity of other group B, type Ib streptococci isolated from poikilothermic animals, such as fish and frogs.

A polyphasic reassessment of the genus Paenibacillus, reclassification of Bacillus lautus (Nakamura 1984) as Paenibacillus lautus comb. nov. and of Bacillus peoriae (Montefusco et al. 1993) as Paenibacillus peoriae comb. nov., and emended descriptions of P. lautus and of P. peoriae

Seventy-seven strains representing 10 species in the Paenibacillus polymyxa 16S rRNA group and 3 other species that exhibit phenetic relatedness to members of this group, Bacillus lautus, "Bacillus longisporus," and Bacillus peoriae, were characterized genotypically and phenotypically by performing an amplified ribosomal DNA restriction analysis, a randomly amplified polymorphic DNA analysis, a fatty acid methyl ester analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins, pyrolysis mass spectrometry, and API and other routine phenotypic tests. These analyses revealed distinct clusters representing Paenibacillus alvei, Paenibacillus amylolyticus, Paenibacillus azotofixans, Paenibacillus durum, Paenibacillus larvae subsp. larvae, Paenibacillus larvae subsp. pulvifaciens, B. lautus, Paenibacillus macerans, Paenibacillus macquariensis, B. peoriae, P. polymyxa, and Paenibacillus validus, which confirmed the distinctness of these species, but appreciable within-species heterogeneity was observed in P. alvei, B. lautus, P. macerans, P. polymyxa, and P. validus. The type strain of Paenibacillus pabuli did not cluster with other strains of this species, and in several analyses a relationship between strains of P. pabuli and "B. longisporus" was observed. As the analyses showed that B. lautus and B. peoriae are closely related to the genus Paenibacillus, these species are reclassified as members of this genus.

Bordetella trematum sp. nov., isolated from wounds and ear infections in humans, and reassessment of Alcaligenes denitrificans Rüger and Tan 1983

Ten strains recognized on the basis of a computer-assisted numerical comparison of whole-cell protein patterns as members of a novel species belonging to the family Alcaligenaceae were examined by using an integrated phenotypic and genotypic approach. This species, for which we propose the name Bordetella trematum sp. nov., was more closely related to the type species of the genus Bordetella (Bordetella pertussis) than to the type species of the genus Alcaligenes (Alcaligenes faecalis) and had the general characteristics of members of this family (i.e., a DNA base ratio in the range from 57 to 70 mol%, a fatty acid profile characterized by high percentages of 16:0, 17:0 cyclo, and 14:0 3OH, nonsaccharolytic metabolism, and several classical biochemical characteristics, including aerobic and microaerobic growth, catalase activity, assimilation of citrate, an absence of anaerobic growth, and an absence of acetylmethylcarbinol and indole production, gelatin liquefaction, and esculin hydrolysis). A reevaluation of the criteria used to classify Alcaligenes denitrificans Rüger and Tan 1983 and Achromobacter xylosoxidans Yabuuchi and Ohyama 1971 as subspecies of Alcaligenes xylosoxidans and additional evidence provided in recent studies revealed that, consistent with present standards, it is appropriate to consider these two taxa distinct species of the genus Alcaligenes.

Acidification of methyl-alpha-D-glucopyranoside: a useful test to differentiate Enterococcus casseliflavus and Enterococcus gallinarum from Enterococcus faecium species group and from Enterococcus faecalis

Enterococcus gallinarum and E. casseliflavus are difficult to differentiate from other enterococci, particularly E.faecium. The former two species were found to produce acid from methyl-alpha-D-glucopyranoside in phenol red broth, while E.faecalis strains and strains of the E.faecium species group, including E.faecium, E.durans, E. hirae, and E.mundtii, failed to produce acid from this substrate.

The presence of two S-layer-protein-encoding genes is conserved among species related to Lactobacillus acidophilus

Previously we have shown that the type strain of Lactobacillus acidophilus possesses two S-protein-encoding genes, one of which is silent, on a chromosomal segment of 6 kb. The S-protein-encoding gene in the expression site can be exchanged for the silent S-protein-encoding gene by inversion of this slp segment. In this study the presence of S-protein and corresponding S-protein-encoding genes of strains belonging to species that are closely related to L. acidophilus was determined. All strains investigated were identified by numerical comparison of highly standardized one-dimensional SDS-PAGE whole-cellular-protein patterns. Western blot and Southern blot methods were used to identify the presence of, and homology between, S-proteins and S-protein-encoding genes. From these analyses we conclude that strains of L. acidophilus, L. crispatus, L. amylovorus and L. gallinarum possess an S-layer and contain two slp genes. Strains of L. helveticus possess an S-layer but have only one intact slp gene. Strains of L. gasseri, L. johnsonii and L. delbrueckii subsp. bulgaricus have neither an S-layer nor S-protein-encoding genes hybridizing with probes derived from the L. acidophilus slpA or slpB region. The presence of a highly conserved 5' region in the slp genes of strains of L. acidophilus, L. crispatus, L. amylovorus and L. gallinarum suggests that S-layer variation is a common feature for strains of these species.

Evaluation of the DNA fingerprinting method AFLP as an new tool in bacterial taxonomy

We investigated the usefulness of a novel DNA fingerprinting technique, AFLP, which is based on the selective amplification of genomic restriction fragments by PCR, to differentiate bacterial strains at the subgeneric level. In totals, 147 bacterial strains were subjected to AFLP fingerprinting: 36 Xanthomonas strains, including 23 pathovars of Xanthomonas axonopodis and six pathovars of Xanthomonas vasicola, one strain of Stenotrophomonas, 90 genotypically characterized strains comprising all 14 hybridization groups currently described in the genus Aeromonas, and four strains of each of the genera Clostridium, Bacillus, Acinetobacter, Pseudomonas and Vibrio. Depending on the genus, total genomic DNA of each bacterium was digested with a particular combination of two restriction endonucleases and the resulting fragments were ligated to restriction halfsite-specific adaptors. These adaptors served as primer-binding sites allowing the fragments to be amplified by selective PCR primers that extend beyond the adaptor and restriction site sequences. Following electrophoretic separation on 5% (w/v) polyacrylamide/8.3 M urea, amplified products could be visualized by autoradiography because one of the selective primers was radioactively labelled. The resulting banding patterns, containing approximately 30-50 visualized PCR products in the size range 80-550 bp, were captured by a high-resolution densitoscanner and further processed for computer-assisted analysis to determine band-based similarity coefficients. This study reveals extensive evidence for the applicability of AFLP in bacterial taxonomy through comparison of the newly obtained data with results previously obtained by well-established genotypic and chemotaxonomic methods such as DNA-DNA hybridization and cellular fatty acid analysis. In addition, this study clearly demonstrates the superior discriminative power of AFLP towards the differentiation of highly related bacterial strains that belong to the same species or even biovar (i.e. to characterize strains at the infrasubspecific level), highlighting the potential of this novel fingerprinting method in epidemiological and evolutionary studies.

Isolation and identification of poly(3-hydroxyvalerate)-degrading strains of Pseudomonas lemoignei

By using selective enrichment of polyhydroxyalkanoate-degrading bacteria and poly(3-hydroxyvalerate)-containing granules from Chromobacterium violaceum as the carbon source, 10 new Pseudomonas lemoignei strains were isolated; these strains were able to degrade poly(3-hydroxyvalerate), as well as poly(3-hydroxybutyrate), in vitro. The new isolates were characterized and identified by comparing them with P. lemoignei LMG 2207(T) (T = type strain). Like P. lemoignei LMG 2207(T) cells, the cells of the 10 new isolates contained mainly hexadecenoic, hexadecanoic, octadecenoic, and dodecanoic acids, as well as hydroxylated fatty acids, and exhibited respiration in the presence of methylpyruvate, 3-hydroxybutyrate, and 4-hydroxybutyrate, but not in the presence of the 92 other carbon sources included in Biolog GN microplates. The protein patterns of the new isolates were almost identical to each other and very similar to the protein pattern of P. lemoignei LMG 2207(T). Some of the new isolates, but not P. lemoignei LMG 2207(T), contained megaplasmids that were about 200 kbp long. The 16S ribosomal DNA genes of strain A62, a representative of the 10 new isolates, and of P. lemoignei LMG 2207(T) exhibited more than 0.99 sequence similarity. The DNA-DNA reassociation value for two representative strains was 100%, and the levels of DNA-DNA reassociation between these strains and the type strain were 60 and 61%. The taxonomy of P. lemoignei is briefly discussed.

Taxonomic study of lancefield streptococcal groups C, G, and L (Streptococcus dysgalactiae) and proposal of S. dysgalactiae subsp. equisimilis subsp. nov

Streptococcus dysgalactiae consists of at least five distinct subgroups on the basis of serogroups, biotypes, and hosts. A chemotaxonomic and phenotypic examination of 80 S. dysgalactiae strains representing the known diversity within this species and 49 reference strains representing all members of the streptococcal pyogenic species group revealed two subpopulations of strains within S. dysgalactiae. The name S. dysgalactiae subsp. dysgalactiae is proposed for strains of animal origin. These strains belong to Lancefield serogroups C and L, are alpha-, beta-, or nonhemolytic, and do not exhibit streptokinase activity on human plasminogen or proteolytic activity on human fibrin. The name S. dysgalactiae subsp. equisimilis is proposed for human isolates. These strains belong to Lancefield serogroups C and G, are beta-hemolytic, and exhibit streptokinase activity on human plasminogen and proteolytic activity on human fibrin.

Emended description of Herbaspirillum; inclusion of [Pseudomonas] rubrisubalbicans, a milk plant pathogen, as Herbaspirillum rubrisubalbicans comb. nov.; and classification of a group of clinical isolates (EF group 1) as Herbaspirillum species 3

[Pseudomonas] rubrisubalbicans, a mild plant pathogen. Herbaspirillum seropedicae, and EF group 1 strains (clustered by an immunological method) were investigated by a polyphasic approach with DNA-rRNA and DNA-DNA hybridizations and auxanography on 147 substrates. Our results show that they all belong to the genus Herbaspirillum. In addition to H. seropedicae, two other species are described: Herbaspirillum rubrisubalbicans and a new unnamed species, Herbaspirillum species 3, containing mainly strains of clinical origin. The three species can be differentiated on the basis of their auxanographic features and DNA-DNA similarities. The type strain of H. rubrisubalbicans is NCPPB 1027 (=LMG 2286); representative strains of the third Herbaspirillum species are strains CCUG 189 (=LMG 5523), CCUG 10263 (=LMG 5934), and CCUG 11060 (=LMG 5321). It has been confirmed that H. rubrisubalbicans is an endophytic diazotroph. It colonizes the roots, the stems, and predominantly the leaves of sugarcane (Saccharum spp.), while Herbaspirillum seropedicae colonizes in large numbers many different species of the Gramineae. Both diazotrophic Herbaspirillum species could be differentiated with meso-erythritol and N-acetylglucosamine. Oligonucleotide probes based on partial sequences of the 23S rRNA of H. seropedicae and H. rubrisubalbicans (HS and HR probes, respectively), were constructed and used as diagnostic probes.

Polyphasic approach to the classification and identification of Gardnerella vaginalis and unidentified Gardnerella vaginalis-like coryneforms present in bacterial vaginosis

A taxonomic study of Gardnerella vaginalis and G. vaginalis-like coryneforms was performed in order to clarify the phylogenetic affiliation of these organisms and to improve future identification. We examined 50 strains by performing whole-cell protein and fatty acid analyses, a 16S rRNA sequence analysis, and an extensive phenotypic characterization analysis. The results of both chemotaxonomic techniques which we used divided the organisms into two main clusters, and the 16S rRNA sequence analysis revealed that the clusters represent different genera, which were easily distinguished by the results of classical phenotypic tests. The cluster I strains were identified as G. vaginalis, which was shown to be a close relative of the genus Bifidobacterium. An improved description of G. vaginalis is presented. The cluster II strains belong to or are closely related to Actinomyces turicensis.

Polyphasic analysis of strains of the genus Capnocytophaga and Centers for Disease Control group DF-3

A polyphasic approach was used to determine the relationships between well-characterized reference strains representing all seven Capnocytophaga species. One Centers for Disease Control (CDC) group DF-3 strain, a presumed relative of the genus Capnocytophaga, and 15 field isolates were included as well. Fourteen isolates were assigned to named Capnocytophaga species, all of which could be differentiated by means of whole-organism protein electrophoresis. A separate position was occupied by the CDC group DF-3 strain and by one field isolate representing a novel Capnocytophaga species. The phylogenetic position of each taxon was determined by means of 16S rRNA sequence analysis. A considerable genotypic heterogeneity within the genus Capnocytophaga was detected in spite of the minimal phenotypic differences. Comparative 16S rRNA sequence analysis revealed that CDC group DF-3 is not a close relative of the capnocytophagas but constitutes a separate genus that clusters together with Bacteroides forsythus and Bacteroides distasonis, two generically misclassified Bacteroides species. The degree of protein similarity correlated with our and published DNA-DNA binding values. Percentage 16S rRNA similarity values of greater than 97% did not guarantee conspecificity. All Capnocytophaga strains had very similar fatty acid contents characterized by significant amounts of 14:0, 15:0 iso (greater than 55%), 16:0, 16:0 3OH, and 17:0 iso 3OH. PCR-mediated DNA fingerprinting allowed discrimination of most species, although some strains could not be classified efficiently because of DNA polymorphisms.

Polyphasic taxonomy, a consensus approach to bacterial systematics

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.

High-resolution genotypic analysis of the genus Aeromonas by AFLP fingerprinting

We investigated the ability of a recently developed genomic fingerprinting technique, named AFLP, to differentiate the 14 currently defined DNA hybridization groups (HGs) in the genus Aeromonas. We also determined the taxonomic positions of the phenospecies Aeromonas allosaccharophila, Aeromonas encheleia, Aeromonas enteropelogenes, and Aeromonas ichthiosmia, which have not been assigned to HGs yet. A total of 98 Aeromonas type and reference strains were included in this study. For the AFLP analysis, the total genomic DNA of each strain was digested with restriction endonucleases ApaI and TaqI. Subsequently, restriction fragments were selectively amplified under high-stringency PCR conditions. The amplification products were electrophoretically separated on a polyacrylamide gel and visualized by autoradiography. Following high-resolution densitometric scanning of the resulting band patterns, AFLP data were further processed for a computer-assisted comparison. A numerical analysis of the digitized fingerprints revealed 13 AFLP clusters which, in general, clearly supported the current Aeromonas taxonomy derived from DNA homology data. In addition, our results indicated that there is significant genotypic heterogeneity in Aeromonas eucrenophila (HG6), which may lead to a further subdivision of this species. A. allosaccharophila and A. encheleia did not represent a separate AFLP cluster but were found to be genotypically related to HG8/10 and HG6, respectively. In addition, the results of the AFLP analysis also confirmed the phylogenetic findings that A. enteropelogenes and A. ichthiosmia are in fact identical to Aeromonas trota (HG13) and Aeromonas veronii (HG8/10), respectively. The results of this study clearly show that the AFLP technique is a valuable new high-resolution genotypic tool for classification of Aeromonas species and also emphasize that this powerful DNA fingerprinting method is important for bacterial taxonomy in general.

Survival potential of Aeromonas hydrophila in freshwaters and nutrient-poor waters in comparison with other bacteria

The survival of a genetically-marked Aeromonas hydrophila strain was studied in water microcosms using viable counts. Aeromonas hydrophila AWWX1 was shown to survive without decline in viable counts for at least 10 d in three of four filtered-autoclaved freshwaters (surface water and groundwater) and in all examined filtered-autoclaved nutrient-poor waters (bottled spring water, Milli-Q and tap water). However, in the unfiltered waters, a rapid decrease in viable counts of Aer. hydrophila AWWX1 was observed after 1-5 d. The survival of Aer. hydrophila AWWX1 in nutrient-poor waters was compared with that of Pseudomonas fluorescens P17 and Spirillum strain NOX. Survival characteristics were organism- and water-dependent. In the filtered-autoclaved waters, viable counts of Spirillum strain NOX were ca 1 log-unit higher than for Aer. hydrophila AWWX1 and Ps. fluorescens P17. The tested strains Aer. hydrophila AWWX1 and Ps. fluorescens P17 survived 3 to 20, respectively 2 to 4 times better in the filtered-autoclaved waters compared to the unfiltered waters. Apparently, any inherent capability of these micro-organisms to adapt to low-nutrient environments was undone by the presence of the autochthonous microbiota. The present findings that Aer. hydrophila survives very poorly in several drinking waters is of utmost importance towards public health and arises questions about the mechanisms involved.