- Volume 48, Issue 2, 1998

Whole-organism protein electrophoresis was used to compare and group unidentified coryneform bacteria resembling Gardnerella vaginalis and various Actinomyces and Arcanobacterium species. The obtained clusters of strains were further characterized by whole-cell fatty acid analysis and a variety of biochemical tests. Species-specific oligonucleotide probes based on 16S rRNA gene sequences were designed. The results demonstrate that the majority of the isolates belonged to Actinomyces turicensis; the other strains belonged to Actinomyces radingae. The descriptions of both species are emended.

Two bacterial isolates, designated AMG-D1Tand AMG-D2, were recovered from 25·35-million-year-old Dominican amber. AMG-D1Tand AMG-D2 biochemically most closely resemble Staphylococcus xylosus; they differ physiologically from other staphylococci. Fatty acid analysis and comparisons with extensive databases were unable to show relatedness to any specific taxon. Moreover, AMG-D1Tand AMG-D2 contain tuberculostearic acid and meso-diaminopimelic acid, characteristic of the G+C-rich coryneform bacteria, as opposed to l-lysine characteristic of staphylococci. AMG-D1Tand AMG-D2 have a G+C ratio of 35 mol%. Phylogenetic analysis with the 16S rRNA gene indicated that AMG-D1Tand AMG-D2 were most closely related to Staphylococcus equorum, S. xylosus, Staphylococcus saprophyticus and other novobiocin-resistant staphylococci. Stringent DNA-DNA hybridization studies with AMG-D1Trevealed similarities of 38% with S. equorum, 23% with S. xylosus and 6% with S. saprophyticus. The results indicate that AMG-D1Tand AMG-D2 represent a novel species, which was named Staphylococcus succinus sp. nov. The type strain of the new species is AMG-D1 (ATCC 700337).

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.

Two groups of strains isolated from biofilters for the treatment of waste gases were assigned to the genus Paracoccus by phylogenetic and chemotaxonomic methods. All type strains of the genus Paracoccus were compared with these groups using 16S rDNA sequence analysis, fatty acid patterns and physiological reaction profiles. For both groups, the nearest related reference species was Paracoccus solventivorans based on 16S rDNA sequence similarity. However, whereas one group of isolates was identified as a member of this species by fatty acid analysis and DNA-DNA hybridization, the other group was proposed as a new species, Paracoccus alkenifer sp. nov. Fatty acid analysis showed the unusual fatty acid 20:1cis13 instead of 19:0 cyclo11–12 for P. alkenifer and P. solventivorans, and 14:1cis7 instead of 12:1cis5 for P. alkenifer and Paracoccus kocurii. By means of a GC-MS method, diaminopimelic acid was detected for P. solventivorans. Based on these results we propose an emended description for the species P. solventivorans.

Four bacterial strains were isolated from larval cultures and collectors of the scallop Pecten maximus. They showed a high level of intragroup genomic relatedness (84–95%) as determined by DNA-DNA hybridization. The cells were Gram-negative, strictly aerobic, motile, ovoid rods. They grew at temperatures from 15 to 37 °C and from pH 7·0 to 10, but did not grow in the absence of NaCl and required growth factors. They had the ability to use a wide variety of compounds as sole carbon source: d-mannose, d-galactose, d-fructose, d-glucose, d-xylose, melibiose, trehalose, maltose, cellobiose, sucrose, meso-erythritol, d-mannitol, glycerol, d-sorbitol, meso-inositol, succinate, propionate, butyrate, γ-aminobutyrate, dl-hydroxybutyrate, 2-ketoglutarate, pyruvate, fumarate, glycine, l-α-alanine, β-alanine, l-glutamate, l-arginine, l-lysine, l-ornithine and l-proline. They exhibited oxidase and catalase activities but no denitrification activity. The isolates did not contain bacteriochlorophyll a. The G+C content ranged from 57·6 to 58 mol%. Phylogenetic analyses of the 16S rRNA sequence revealed that these isolates belong to the genus Roseobacter. On the basis of quantitative hybridization data, it is proposed that these isolates should be placed in a new species, Roseobacter gallaeciensis. The type strain is Roseobacter gallaeciensis BS107T(= CIP 105210T).

Phenotypic, chemotaxonomic and 16S rDNA sequence analysis of an orange Gram-negative coccus that appeared as a contaminant on a nutrient agar plate delineated a new species of the genus Paracoccus. Phenotypic features of the strain that differ from all or most of the previously described Paracoccus species include its bright orange colour, caused by the synthesis of large amounts of carotenoids (mainly astaxanthin), and its inability to use nitrate as an electron acceptor in respiration. The name Paracoccus marcusii is proposed for this organism. The type strain is DSM 11574T.

In a survey of soil and wheat or maize rhizoplane bacteria isolated using a medium containing azelaic acid and tryptamine as sole carbon and nitrogen sources, respectively, a large proportion of Burkholderia-like bacteria were found. Among them, a homogeneous group of strains was identifiable based on phenotypic properties, fatty acid composition, DNA-DNA hybridizations and 16S rDNA sequences. According to molecular data, this group belongs to the genus Burkholderia but its weak similarity to previously described species suggests that it belongs to a novel species. Closest 16S rDNA phylogenetic neighbours of this species are Burkholderia caryophylli and two previously named Pseudomonas species which clearly appear to be part of the Burkholderia genus and were thus named Burkholderia glathei comb. nov. and Burkholderia phenazinium comb. nov. Strains of the new species are oxidase-and catalase-positive, produce indole and gelatinase, and use l-xylose, lactose, rhamnose, trehalose, d-lyxose, l-arabitol, xylitol and d-raffinose as sole carbon source. This novel taxon is named Burkholderia graminis. In the course of this study, [Pseudomonas] pyrrocinia also proved to be a member of the Burkholderia genus.

Novel Gram-negative alkaliphilic strains were isolated from soil obtained from Atsuma, Hokkaido, Japan. The isolates were strictly aerobic rods that produced subterminally located ellipsoidal spores. Chemotaxonomic characteristics of the isolates included the presence of meso-diaminopimelic acid in the cell wall and a DNA G+C content of 40·2–40·9 mol%. The major isoprenoid quinone was menaquinone-7 and the cellular fatty acid profile consisted of a significant amount of 15-C branched-chain acids, iso-C15:0 and anteiso-C15:0. The growth rate was higher at pH 8–10 than at pH 7. Comparative sequence analysis of 16S rDNA of 14 alkaliphilic Bacillus strains indicates that the isolated strain has an equidistant relationship to three already defined rRNA groups of alkaliphilic Bacillus species. Based on the morphological and physiological characteristics, as well as phylogenetic position as determined by 16S rDNA analysis and DNA-DNA relatedness data, it is concluded that these isolates should be designated as a new species, for which the name Bacillus horti is proposed. The type strain is K13T(= JCM 9943T).

Six alginolytic, facultatively anaerobic, non-motile marine bacteria were isolated from the gut of abalone Haliotis discus hannai. DNA-DNA hybridization data showed that the six strains constituted a single genospecies. Phylogenetic analyses of 16S rDNA sequences indicated that the isolates should be assigned to the genus Vibrio. The phenotypic features of the isolates were closely related to Vibrio fischeri and Vibrio pelagius biovar I, but 13 traits (motility, luminescence, alginase production, lipase production, lysine decarboxylase, indole production, growth in 1 and 6% NaCl and assimilation of five carbon compounds) distinguished these strains from V. fischeri, and 17 traits (motility, growth at 37 °C, lipase production, indole production, growth in 1 and 6% NaCl, acid from sucrose and d-sorbitol, and assimilation of nine carbon compounds) distinguished these strains from V. pelagius. The G+C content of the isolates was 41·6–43·1 mol%. According to DNA-DNA hybridization data and 16S rDNA phylogenetic analyses, it was concluded that the six isolates constitute a new species different from any other Vibrio species. The name Vibrio halioticoli sp. nov. (type strain IAM 14596T) is proposed. A set of phenotypic features which enables differentiation of the new species from other species of the Vibrionaceae family is described.

The 16S rRNA gene sequences of reference strains of Streptococcus suis serotypes 1–34 and 1/2 were determined. A comparative sequence analysis showed that the degree of sequence similarity between S. suis reference strains ranged from 93·94 to 100%. A dendrogram was constructed from the similarity matrix. Thirty-two strains representing 32 serotypes fell into a major group divided into three clusters. The other strains, S. suis serotypes 32, 33 and 34, were more distant. Biochemical characterization of the six more distant strains, including S. suis serotypes 20, 22, 26, 32, 33 and 34, revealed a profile similar to that of other S. suis serotypes. Comprison of the 16S rRNA gene sequences of S. suis reference strains with sequences of other members of the genus Streptococcus indicated that, with the exception of S. suis serotypes 32, 33 and 34, reference strains did not cluster with any other species in the genus. In conclusion, 16S rRNA gene sequence analysis defined a major group of S. suis reference strains which were very closely related and a higher divergence for S. suis serotypes 32, 33 and 34. However, to date, there is no strong evidence to reclassify strains of these serotypes in another species.

The taxonomic relationships among nine strains of Streptomyces, which have been commonly used for genetic studies, were examined by sequence analysis of their ribosomal L11(= rplK) protein genes. Phylogenetic relationships among these organisms derived from similarity sequence an lysis of the rplK genes were in good agreement with those derived from the analysis of the deduced L11 protein amino acid sequence itself, indicating complete sequence homology among Streptomyces coelicolor A3(2), ‘Streptomyces lividans 66’ and Streptomyces violaceoruber JCM 4423. S. coelicolor A3(2) related (in the order of closer relatedness) to Streptomyces antibioticus ATCC 14888, Streptomyces griseus IFO 13189, Streptomyces lavendulae MA 406 A-1 and Streptomyces virginiae MAFF 6014. Sequence analysis of the 26 N-terminal amino acid residues of ribosomal L30 proteins also resulted in similar phylogenetic relationships, except that S. griseus, S. lavendulae and S. virginiae were not differentiated from each other using this method. These findings concerning the phylogenetic relationship therefore confirm the previous conclusion that S. coelicolor A3(2), ‘S. lividans 66’ and S. violaceoruber should be recognized as a single taxon at the species level.

Phenotypic and phylogenetic studies were performed on four strains of a Gram-positive non-acid-fast coryneform-like organism isolated from the nasal cavities of common seals (Phoca vitulina). Chemotaxonomic investigations revealed the presence of corynomycolic acids in the unidentified isolates, which is consistent with corynebacteria. 16S rRNA gene sequence analysis demonstrated that the strains from seals represent a hitherto unknown subline within the genus Corynebacterium sensu stricto. Based on the results of the phylogenetic analysis and phenotypical criteria, it is proposed that the bacterium should be classified as a new species, Corynebacterium phocae. The type strain of Corynebacterium phocae is CCUG 38205T.

To establish the phylogenetic relationships between the subspecies of Salmonella enterica (official name Salmonella choleraesuis), Salmonella bongori and related members of Enterobacteriaceae, sequence comparison of rRNA was performed by maximum-likelihood analysis. The two Salmonella species were separated by 16S rRNA analysis and found to be closely related to the Escherichia coli and Shigella complex by both 16S and 23S rRNA analyses. The diphasic serotypes S. enterica subspp. I and VI were separated from the monophasic serotypes subspp. Illa and IV, including S. bongori, by 23S rRNA sequence comparison.

Some proposals are made in agreement with some Judicial Opinions placing names in the lists of conserved or rejected names.