- Volume 55, Issue 2, 2005

Strain LBB3T isolated from Bogoria soda lake in Kenya is an alkaliphilic, Gram-positive, strictly aerobic, non-motile, spore-forming bacterium. It was identified as a member of the genus Bacillus on the basis of phenotypic and phylogenetic analyses. The organism grows optimally at 37 °C and pH 10. The G+C content of the genomic DNA is 37·5 mol%. 16S rRNA gene sequence analysis showed 95 and 96 % sequence similarity with Bacillus pseudofirmus (DSM 8715T) and Bacillus alcalophilus (DSM 485T), respectively. Furthermore, DNA–DNA hybridization against these two Bacillus species showed 39·0 and 55·5 % similarity, respectively. Based on our observations, strain LBB3T is proposed to represent a novel species of the genus Bacillus, for which the name Bacillus bogoriensis sp. nov. is proposed. The type strain of B. bogoriensis is LBB3T (=ATCC BAA-922T=LMG 22234T).

A halophilic and halotolerant, facultatively alkaliphilic strain, K11T, was isolated from soil obtained from Oshyamanbe, Oshima, Hokkaido, Japan. The isolate grew at pH 7–10. It was non-motile, Gram-positive and aerobic. Cells comprised straight rods and produced ellipsoidal spores. The isolate grew in 0–20 % NaCl, with optimum growth at 7 % NaCl, and hydrolysed casein, gelatin, starch, DNA and Tweens 20, 40, 60 and 80. The major isoprenoid quinone was menaquinone-7, and the cellular fatty acid profile consisted of significant amounts of C15 branched-chain acids, iso C15 : 0 and anteiso C15 : 0. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain K11T was a member of group 6 [ Nielsen et al., FEMS Microbiol Lett 117 (1994), 61–66 ] (alkaliphiles) of the genus Bacillus. DNA–DNA hybridization revealed a low relatedness (14 %) of the isolate to its closest phylogenetic neighbour, Bacillus clausii. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic data and DNA–DNA relatedness data, it was concluded that K11T (=JCM 12663T=NCIMB 14023T) merits classification as the type strain of a novel species, for which the name Bacillus oshimensis sp. nov. is proposed.

A Gram-positive, endospore-forming, xylanase-producing bacterium isolated from a rice field was studied taxonomically. The strain grows at 10–40 °C and in the presence of lysozyme or 5 % (w/v) NaCl. Chemotaxonomic analysis revealed that MK-7 was the predominant menaquinone of the isolated strain, while the major fatty acid was anteiso-C15 : 0. Comparison of 16S rRNA gene sequences showed that strain BP-23T fell within the radiation of the cluster comprising Paenibacillus species. The highest 16S rRNA gene sequence similarities were found with Paenibacillus illinoisensis (97·4 %), Paenibacillus pabuli (97·1 %) and Paenibacillus amylolyticus (96·9 %). The DNA–DNA relatedness of strain BP-23T with respect to these three species was very low (32·7, 31·6 and 23·0 %, respectively). On the basis of phenotypic and genotypic data, strain BP-23T should be placed in the genus Paenibacillus and designated a novel species, for which the name Paenibacillus barcinonensis sp. nov. is proposed. The type strain is BP-23T (=CECT 7022T=DSM 15478T).

Comparative analysis of 16S rRNA gene sequences, DNA–DNA hybridization data and phenotypic properties revealed that ‘Sulfobacillus thermosulfidooxidans subsp. thermotolerans’ strain K1 is not a member of the genus Sulfobacillus. Phylogenetically, strain K1 is closely related to unclassified strains of the genus Alicyclobacillus: the 16S rRNA gene sequence of strain K1 is similar to that of Alicyclobacillus sp. AGC-2 (99·6 %), Alicyclobacillus sp. 5C (98·9 %) and Alicyclobacillus sp. CLG (98·6 %) and bacterium GSM (99·1 %). The 16S rRNA gene sequence similarity values for strain K1 and species of the genus Alicyclobacillus with validly published names were in the range 92·1–94·6 %, and for S. thermosulfidooxidans VKM B-1269T the value was 87·7 %. Sulfobacillus disulfidooxidans SD-11T was also phylogenetically related to strain K1 (92·6 % sequence similarity) and thus belonged to the genus Alicyclobacillus. Chemotaxonomic data, such as the major cell-membrane lipid components of strains K1 and SD-11T (ω-alicyclic fatty acids) and the major isoprenoid quinone (menaquinone MK-7) of strain K1, supported the affiliation of strains K1 and SD-11T to the genus Alicyclobacillus. Physiological and molecular biological tests allowed genotypic and phenotypic differentiation of strains K1 and SD-11T from the nine Alicyclobacillus species with validly published names. The G+C content of the DNA of strain K1 was 48·7±0·6 mol%; that of strain SD-11T was 53±1 mol%. DNA–DNA reassociation studies showed low relatedness (22 %) between strains K1 and SD-11T, and even lower relatedness (3–5 %) between these strains and Alicyclobacillus acidocaldarius subsp. acidocaldarius ATCC 27009T, DSM 446T. DNA reassociation of strains K1 and SD-11T with Alicyclobacillus cycloheptanicus DSM 4006T gave values of 15 and 21, respectively. Based on the phenotypic and phylogenetic characteristics of strains K1 and SD-11T, Alicyclobacillus tolerans sp. nov. (type strain, K1T=VKM B-2304T=DSM 16297T) and Alicyclobacillus disulfidooxidans comb. nov. (type strain, SD-11T=ATCC 51911T=DSM 12064T) are proposed.

Three Gram-positive, moderately halophilic, heterotrophic bacterial strains were isolated from a neutral saline lake in the Xin-Jiang area of China. The strains, designated 8-2T, W11-1 and 25-7T, were motile, spore-forming, aerobic rods and contained meso-diaminopimelic acid in their cell walls. Their DNA G+C contents were 37·4, 37·2 and 39·9 mol%, respectively. The main fatty acids in the cellular membranes of these novel strains were C15 and C17 methyl-branched. No species with validly published names showed 16S rRNA gene sequence similarity of more than 95 % with respect to these novel isolates; the most closely related species was a halophilic denitrifier, Bacillus halodenitrificans (94·6 %). Polyphasic taxonomic studies revealed that these strains belong to the Bacillaceae and are distantly related to other genera of the family. It is proposed that a new genus, Salinibacillus, should be created, with Salinibacillus aidingensis (type strain, 25-7T=AS 1.3565T=JCM 12389T) as the type species. Another species, Salinibacillus kushneri, is also proposed, with 8-2T (=AS 1.3566T=JCM 12390T) as the type strain.

The genetic relationship between Streptococcus agalactiae and Streptococcus difficilis was studied. S. difficilis was originally described as serologically non-typable but was later reported to be a group B, type Ib streptococcus. Upon comparative analysis of five gene sequences, it was found that S. agalactiae and S. difficilis are closely related. Sequence similarity values between these two species were 100·0 % for 16S rRNA, 99·6 % for gyrB, 98·6 % for sodA, 99·5 % for gyrA and 99·8 % for parC genes. These data strongly suggest that S. agalactiae and S. difficilis are synonyms. The biochemical characteristics of S. difficilis, which differ slightly from those of typical S. agalactiae, are similar to those of other group B, type Ib streptococci isolated from fish and frogs. Whole genome DNA–DNA hybridization values between the type strains of both species were greater than 78·6 %. On the basis of these data, it is proposed that S. difficilis is a later synonym of S. agalactiae.

Two strains (TERI-6T and TERI-7) of a novel yeast species were isolated from acidic tar sludge-contaminated soil samples collected from Digboi Refinery, Assam, India. These two yeast strains were morphologically, physiologically and phylogenetically identical to each other. No sexual reproduction was observed on corn meal, malt, Gorodkowa, YM or V8 agars. Physiologically, the novel isolates were most closely related to Candida blankii, but differed in eight physiological tests. The prominent differences were the ability of the isolates to assimilate melibiose and inulin and their inability to assimilate d-glucuronate, succinate and citrate. Phylogenetic analysis using the D1/D2 variable domain showed that the closest relative of these strains is C. blankii (2·8 % divergence). Other related species are Zygoascus hellenicus and Candida bituminiphila. The isolates differed from C. blankii by 11 base substitutions in the 18S rRNA gene sequence and by 58 base substitutions in the internal transcribed spacer sequences. The physiological, biochemical and molecular data support the contention that strains TERI-6T and TERI-7 represent a novel species, for which the name Candida digboiensis sp. nov. is proposed. The type strain is TERI-6T (=MTCC 4371T=CBS 9800T=JCM 12300T).

The new methanol-assimilating yeast species Komagataella phaffii Kurtzman sp. nov. (type strain NRRL Y-7556T=CBS 2612T) is described. Of the four known strains of this species, two were isolated from black oak trees in California, USA, one from an Emory oak in Arizona, USA, and one from an unidentified source in Mexico. The species forms hat-shaped ascospores in deliquescent asci and appears to be homothallic. Analysis of nucleotide sequences from domains D1/D2 of large-subunit (26S) rDNA separates the new species from Komagataella pastoris, the type species of the genus, and from Pichia pseudopastoris, which is here renamed Komagataella pseudopastoris (Dlauchy, Tornai-Lehoczki, Fülöp & Péter) Kurtzman comb. nov. (type strain NRRL Y-27603T=CBS 9187T=NCAIM Y 01541T). On the basis of D1/D2 26S rDNA sequence analysis, the three species now assigned to the genus Komagataella represent a clade that is phylogenetically isolated from other ascomycetous yeast genera.

The 16S–23S rRNA gene internal transcribed spacer (ITS) regions of 11 reference strains of Porphyromonas species, together with Bacteroides distasonis and Tannerella forsythensis, were analysed to examine interspecies relationships. Compared with the phylogenetic tree generated using 16S rRNA gene sequences, the resolution of the ITS sequence-based tree was higher, but species positioning and clustering were similar with both approaches. The recent separation of Porphyromonas gulae and Porphyromonas gingivalis into distinct species was confirmed by the ITS data. In addition, analysis of the ITS sequences of 24 clinical isolates of Porphyromonas asaccharolytica plus the type strain ATCC 25260T divided the sequences into two clusters, of which one was α-fucosidase-positive (like the type strain) while the other was α-fucosidase-negative. The latter resembled the previously studied unusual extra-oral isolates of ‘Porphyromonas endodontalis-like organisms' (PELOs) which could therefore be called ‘Porphyromonas asaccharolytica-like organisms' (PALOs), based on the genetic identification. Moreover, the proposal of α-fucosidase-negative P. asaccharolytica strains as a new species should also be considered.

The evolution and taxonomy of enterohepatic Helicobacter species with flexispira morphology were studied by a polyphasic approach including phenotypic characterization, analysis of 16S rRNA and ureB gene sequences and dot-blot DNA–DNA hybridization of whole genomic DNA. In addition, available phylogenetic data on the HSP60 gene were used in the analysis. The study included 14 Finnish canine and feline flexispira strains, the reference strains of Helicobacter sp. flexispira taxa 2, 3 and 8 and Helicobacter bilis ATCC 51630T. Phenotypically, all canine and feline strains were similar to H. bilis. Analysis of 16S rRNA gene sequences of these strains revealed a similarity of 97–99·5 %. Similarity of ureB nucleotide and amino acid sequences within the studied flexispira group was 97–100 % and 99–100 %, respectively, revealing close relatedness. ureB sequences of Helicobacter hepaticus had only 64–66 % similarity to the flexispira group. The similarity to Helicobacter trogontum was 81·5–82·1 %. High levels of DNA–DNA hybridization between the strains were found in dot-blot tests. Polyphasic analysis of the phenotypic and genotypic characteristics of the Finnish flexispira strains and the reference strains of taxa 2, 3 and 8 showed that they differed from other Helicobacter species and are members of the previously described species H. bilis. In addition, canine strain F56 differed in all phylogenetic analyses from the H. bilis group and probably represents a novel Helicobacter species.