International journal of systematic bacteriology最新文献

'Gastrospirillum suis' is an uncultured, tightly spiral micro-organism that has been associated with ulcer disease in the stomachs of pigs. It was the purpose of this study to determine the phylogenetic position of 'G. suis'. Stomachs of five slaughterhouse pigs, originating from different Belgian and Dutch farms, were selected on the basis of the presence of 'G. suis'-like bacteria, as demonstrated by biochemical, immunohistochemical and electron microscopical data. Bacterial 16S rDNA was amplified by PCR using broad-range primers and five helicobacter-like sequences were determined either by direct or indirect sequence analysis. An inter-sequence homology of 99.7% was observed, suggesting that the sequences originated from strains belonging to a single species. Phylogenetic analysis of the consensus sequence placed the organism within the genus Helicobacter, where it formed a distinct sub-group together with other gastrospirillum-like bacteria (Helicobacter felis, Helicobacter bizzozeronii, Helicobacter salomonis and 'Helicobacter heilmannii' types 1 and 2). Diagnostic PCR primers and a probe were developed that differentiated the porcine sequences from all known helicobacters. These results indicate that the porcine sequences represent a single taxon within the genus Helicobacter. The low similarity level towards H. salomonis (96.6%), its closest validly named neighbour, strongly suggests that this taxon is a novel Helicobacter species. In situ hybridization experiments linked the reference sequence to the 'G. suis'-like bacteria. On the basis of these results, we propose the name 'Candidatus Helicobacter suis' for this gastric helicobacter from pigs.

The taxonomic position of the genus Planopolyspora comprising a single species, Planopolyspora crispa, was reviewed. This genus was originally characterized by formation of long, curly and sometimes branching sporangia containing numerous zoospores arranged in a single row and by the presence of meso-diaminopimelic acid and madurose (3-O-methyl-D-galactose) in whole-cell hydrolysates. However, our chemotaxonomic analyses of the type strain of P. crispa did not agree with the original description. The peptidoglycan contained L-lysine but not meso-diaminopimelic acid, and the whole-cell hydrolysate contained xylose as the characteristic sugar but not madurose. These characteristics and other chemotaxonomic profiles (e.g. menaquinone, phospholipid and cellular fatty acid compositions) of the genus Planopolyspora coincided with those of the genus Catenuloplanes. These two genera also had very similar morphological characteristics, but in the original description of the genus Catenuloplanes the presence of sporangia was not referred to. This difference is considered to originate from a divergence of views owing to the ambiguity of the definition of the term 'sporangium' in actinomycete morphology. Phylogenetic analysis based on 16S rDNA sequences also supported the proposal that the genera Planopolyspora and Catenuloplanes should be combined into one genus. Levels of DNA relatedness among the type strains of P. crispa and six Catenuloplanes species and their cultural, physiological and biochemical characteristics indicated that P. crispa should be classified as an independent species of the genus Catenuloplanes, which has priority over the genus Planopolyspora. Therefore, it is proposed that Planopolyspora crispa be transferred to the genus Catenuloplanes as Catenuloplanes crispus comb. nov.

In this study, the phylogenetic relationships between the two biovars and 14 serovars of Ureaplasma urealyticum were studied using the sequences of four different genes or genetic regions, namely: 16S rRNA genes; 16S-23S rRNA gene spacer regions; urease gene subunits ureA, ureB, partial ureC and adjoining regions upstream of ureA, ureA-ureB spacer and ureB-ureC spacer; the 5'-ends of the multiple-banded antigen (MBA) genes. U. urealyticum genotypes, based on all four genomic sequences, could be clearly separated into two clusters corresponding with currently recognized biovars 1 and 2. Sequences were generally conserved within each biovar. However, there was heterogeneity within the 5'-end regions of the MBA genes of the four serovars of biovar 1; the sequence of serovar 3 was identical with the previously published sequence and differed by only three bases from that of serovar 14; but there were significant differences between the sequences of serovars 3 and 14 and those of serovars 1 and 6. Based on the phylogenetic analysis, support is given to previous recommendations that the two biovars of U. urealyticum be classified as distinct species, namely U. parvum and U. urealyticum for biovars 1 and 2, respectively. In the future, the relationship between the new species and clinical manifestations of ureaplasma infections should be studied.

The 16S rRNA sequences of the Korean Borrelia strains 5MT and 9MT, isolated from Ixodes nipponensis, showed identities of 99.0-99.1% to that of B. afzelii. The strains were tentatively classified as belonging to the B. afzelii-related group. In this study, Korean isolates, including these strains, were characterized further and compared with recently described new species. These strains generated a RFLP pattern that has not been found previously in RFLP analysis of the 5S-23S rRNA intergenic spacer and the flagellin gene. When phylogenetic trees were constructed, based on the 5S-23S rRNA intergenic spacer, flagellin gene and 16S rRNA sequences, these Korean isolates formed a cluster with the Borrelia strain Am501 isolated from Ixodes columnae in Japan and Borrelia valaisiana strains VS116T and UK isolated from Ixodes ricinus in Europe and were distinguishable from the other species. However, these three groups of strains were divergent from each other in the molecular masses of the putative outer surface protein A (OspA) and in the sequences of the ospA gene. These findings suggest that these Korean isolates and one Japanese isolate are members of B. valaisiana and that OspA of this species is divergent, as is that of Borrelia garinii. This led to the speculation that B. valaisiana strains are adapted to the vector ticks found in each locality.

beta-Haemolytic, Lancefield group C streptococci within the anginosus-species group were shown by genetic and phenotypic criteria to be heterogeneous and to constitute two distinct taxa related at subspecies level to Streptococcus constellatus and Streptococcus anginosus, respectively. The first group, referred to here as DNA group 1, comprised six strains with 86-100% intragroup overall genomic DNA relatedness; five of the strains were originally isolated from the human throat and one was from an abdominal mass. They shared 61-77% DNA relatedness (delta Tm values = 1.2-1.5 degrees C) with reference strains of S. constellatus and were clearly differentiated from S. constellatus (now named Streptococcus constellatus subsp. constellatus) by the ability to produce beta-N-acetylgalactosaminidase, beta-N-acetylglucosaminidase, beta-D-fucosidase, beta-D-galactosidase and beta-D-glucosidase. The name S. constellatus subsp. pharyngis is proposed for these strains on the grounds that they are genetically and phenotypically distinct and exhibit a predeliction for the human throat, being isolated also from cases of pharyngitis. The DNA G + C content is 35-37 mol%. The type strain is MM9889aT (= NCTC 13122T). The second group (DNA group 2) was formed by five beta-haemolytic, Lancefield group C strains originally isolated from various human infections. DNA group 2 strains (81-100% intragroup DNA relatedness) shared 60-72% DNA relatedness (delta Tm values = 2.1-4.1 degrees C) with S. anginosus strains NCTC 10713T and MAS 283 but were not clearly differentiated phenotypically from S. anginosus, showed no clear pattern of clinical association, and therefore are not formally proposed as a new subspecies here.

Two aerobic, Gram-positive bacteria, strains HKI 0122T and HKI 0132, were isolated from a cave. Cells are not acid-fast, non-motile, non-spore-forming and exhibit a rod-coccus growth cycle. The cell wall peptidoglycan contains lysine in position 3 of the peptide subunit and an interpeptide bridge of L-Lys<--L-Glu. The major menaquinone is MK-8(H4), 13-methyl and 12-methyl tetradecanoic acids are the predominating fatty acids. The polar lipids consist of phosphatidylinositol, diphosphatidylglycerol and three unknown phospholipids. Mycolic acids are absent. The DNA base composition is 71 mol% G + C. Phylogenetic analysis revealed that strain HKI 0122T forms a novel taxon among the families and unassigned genera of the suborder Micrococcineae, within the order Actinomycetales. On the basis of the genotypic, chemotaxonomic, morphological and physiological characteristics of these two isolates it is proposed to assign strains HKI 0122T and HKI 0132 to a new genus and species for which the name Beutenbergia cavernae gen. nov., sp. nov. is proposed. The type strain is HKI 0122T (= DSM 12333T).

Seven strains of three new yeast species were isolated from soil, flowers and leaves in the Nansei Islands, Japan. These isolates most closely resembled Kluyveromyces phaffii in physiological characteristics and nuclear DNA base composition (30-32 mol% G + C), but on the basis of DNA-DNA hybridization and electrophoretic karyotyping they were categorized into three new species different from K. phaffii. Phylogenetic analysis using 18S rRNA gene sequences showed that the three new species and K. phaffii were highly related to one another and phylogenetically separate from the members of other species. On the basis of phylogeny and physiological characters, it is proposed that the three new species represent novel taxa and should be designated Tetrapisispora iriomotensis gen. nov., sp. nov. (type strain IFO 10929T), Tetrapisispora nanseiensis gen. nov., sp. nov. (type strain IFO 10899T) and Tetrapisispora arboricola gen. nov., sp. nov. (type strain IFO 10925T), while Kluyveromyces phaffii becomes Tetrapisispora phaffii comb. nov.

Five psychrophilic, Gram-negative, sulfate-reducing bacteria were isolated from marine sediments off the coast of Svalbard. All isolates grew at the in situ temperature of -1.7 degrees C. In batch cultures, strain PSv29T had the highest growth rate at 7 degrees C, strains ASv26T and LSv54T had the highest growth rate at 10 degrees C, and strains LSv21T and LSv514T had the highest growth rate at 18 degrees C. The new isolates used the most common fermentation products in marine sediments, such as acetate, propionate, butyrate, lactate and hydrogen, but only strain ASv26T was able to oxidize fatty acids completely to CO2. The new strains had growth optima at neutral pH and marine salt concentration, except for LSv54T which grew fastest with 1% NaCl. Sulfite and thiosulfate were used as electron acceptors by strains ASv26T, PSv29T and LSv54T, and all strains except PSv29T grew with Fe3+ (ferric citrate) as electron acceptor. Chemotaxonomy based on cellular fatty acid patterns and menaquinones showed good agreement with the phylogeny based on 16S rRNA sequences. All strains belonged to the delta subclass of Proteobacteria but had at least 9% evolutionary distance from known sulfate reducers. Due to the phylogenetic and phenotypic differences between the new isolates and their closest relatives, establishment of the new genera Desulfotalea gen. nov., Desulfofaba gen. nov. and Desulfofrigus gen. nov. is proposed, with strain ASv26T as the type strain of the type species Desulfofrigus oceanense sp. nov., LSv21T as the type strain of Desulfofrigus fragile sp. nov., PSv29T as the type strain of the type species Desulfofaba gelida sp. nov., LSv54T as the type strain of the type species Desulfotalea psychrophila sp. nov. and LSv514T as the type strain of Desulfotalea arctica sp. nov.

The taxonomic position of Photorhabdus strains was examined through the results of DNA relatedness (S1 nuclease method) studies associated with the determination of delta Tm, 16S rRNA phylogenetic inferences and phenotypic characterization, including morphological, auxanographic, biochemical and physiological properties. Three genomic species were delineated on a consensus assessment. One of these species corresponded to Photorhabdus luminescens, since strains were at least 50% related to the type strain of this species with delta Tm less than 7 degrees C. The two other species were novel genomic species II and III, which were less than 40% related to each other with delta Tm higher than 9 degrees C. A comparison of the complete 16S rDNA sequences of several representatives of genomic species II and genomic species III revealed that each of them formed a stable lineage independent of the cluster generated by P. luminescens strains. The genomic species differed in their maximum temperatures for growth. A correlation with the ecological origin of the bacterial samples was noticed. The heat-tolerant group I (maximum growth temperature 35-39 degrees C) corresponded to the symbionts of Heterorhabditis bacteriophora groups Brecon and HP88 and Heterorhabditis indica, nematodes living in warm and tropical countries, respectively. Group II (maximum growth temperature 33-35 degrees C) encompassed symbionts from Heterorhabditis megidis, Heterorhabditis zealandica and group NC1 of H. bacteriophora, nematodes isolated in temperate climates. Group III were bacteria isolated from human specimens. Two new species, Photorhabdus temperata sp. nov. (type strain CIP 105563T) and Photorhabdus asymbiotica sp. nov. (type strain ATCC 43950T), are proposed for genomic species II and III, respectively. Species I and II can be separated into sub-groups on the basis of high DNA-DNA relatedness (more than 80% DNA binding with delta Tm < 1.5 degrees C), 16S rDNA branching and phenotypic characters. Therefore, we propose that the two species P. luminescens and P. temperata should be subdivided into subspecies as follows: P. luminescens subsp. luminescens subsp. nov. (type strain ATCC 29999T), P. luminescens subsp. akhurstii subsp. nov. (type strain CIP 105564T), P. luminescens subsp. laumondii subsp. nov. (type strain CIP 105565T) and P. temperata subsp. temperata subsp. nov.

Phenotypic and phylogenetic studies were performed on a hitherto undescribed micro-organism isolated from the human vagina. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strain constituted a new subline within the genus Atopobium. The unknown bacterium was readily distinguished from other Atopobium species by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Atopobium vaginae sp. nov. The type strain of Atopobium vaginae is CCUG 38953T.