- Volume 50, Issue 1, 2000

Bacteria isolates phenotypically related to Pseudomonas corrugata have frequently been isolated from the rhizosphere of Arabidopsis thaliana and Brassica napus grown on different soils. 16S rDNA (rrs) gene sequencing, DNA-DNA hybridization, biochemical characterization and siderophore typing showed that these isolates belong to two different species that are distinct from other species of the genus Pseudomonas, including P. corrugata. A description of properties of these two new species is given based on the study of 16 isolates. Proposed names are Pseudomonas brassicacearum (10 strains studied) and Pseudomonas thivervalensis (6 strains studied). The type strain of Pseudomonas brassicacearum is CFBP 11706T and that of Pseudomonas thivervalensis is CFBP 11261T.

Paralactobacillus selangorensis gen. nov., sp. nov. is described. This organism, isolated from a Malaysian food ingredient called chili bo, is an obligatory homofermentative, rod-shaped lactic acid bacterium. The G+C content is 46.1-46.2+/-0.3 mol%. Earlier 16S rRNA studies showed that this organism constitutes a new taxon distantly related to the Lactobacillus casei-Pediococcus group. A phenotypic description that distinguishes Paralactobacillus selangorensis from other genera of lactic acid bacteria is presented. The type strain of Paralactobacillus selangorensis is LMG 17710T.

A new moderately thermophilic, alkaliphilic, sulfate-reducing, chemolithoheterotrophic bacterium, strain S1T, was isolated from a mixed cow/pig manure with neutral pH. The bacterium is an obligately anaerobic, non-motile, Gram-positive, spore-forming curved rod growing within a pH range of 8.0-9.15 (optimal growth at pH 8.6-8.7) and temperature range of 30-58 degrees C (optimal growth at 50-55 degrees C). The optimum NaCl concentration for growth is 0.1%. Strain S1T is an obligately carbonate-dependent alkaliphile. The G+C content of the DNA is 40.9 mol%. A limited number of compounds are utilized as electron donors, including H2+acetate, formate, ethanol, lactate and pyruvate. Sulfate, sulfite and thiosulfate, but not sulfur or nitrate, can be used as electron acceptors. Strain S1T is able to utilize acetate or yeast extract as sources of carbon. Analysis of the 16S rDNA sequence allowed strain S1T (= DSM 12257T) to be classified as a representative of a new species of the genus Desulfotomaculum, Desulfotomaculum alkaliphilum sp. nov.

The taxonomic position of two bacterial strains, BN6T and N,N, with the ability to degrade xenobiotic aromatic compounds (naphthalenesulfonates or N,N-dimethylaniline) was investigated. The 165 rRNA gene sequence, the G+C content of the DNA (62-63 mol%) and the detection of ubiquinone Q-10, 2-hydroxymyristic acid and the sphingoglycolipid present clearly placed the two strains into the genus Sphingomonas. Both strains are representatives of one species according to the level of DNA relatedness (70.7%). The strains could be separated from all validly described taxa of the genus Sphingomonas, according to the 16S rRNA gene sequence (the highest sequence similarity observed was 96 % to Sphingomonas yanoikuyae), the pattern of the polar lipids and physiological characteristics. Therefore, the new species Sphingomonas xenophaga is proposed to accommodate strains BN6T (= DSM 6383T) and N,N (= DSM 8566).

Using a combination of 16S rRNA analysis and antigenic fingerprinting consisting of new and published data, the phylogenetic position of 18 thermophilic isolates currently classified as Methanobacterium species was reinvestigated. The results were verified by independent methods, including, where applicable, plasmid and phage typing. Comparative analysis of 16S rRNA data for 30 strains belonging to the order Methanobacteriales strongly suggested that mesophilic and thermophilic Methanobacterium isolates are distantly related and should be assigned to separate genera. For the thermophilic strains the genus Methanothermobacter was initially proposed by Boone, Whitman and Rouvière. Furthermore, the results support a reclassification of 15 isolates in three species within the proposed genus: (i) Methanothermobacter thermautotrophicus comb. nov., containing eight isolates, six of which are able to utilize formate (type strain deltaHT); (ii) Methanothermobacter wolfeii comb. nov., containing four formate-utilizing isolates (type strain DSM 2970T); (iii) Methanothermobacter marburgensis sp. nov., containing three obligately autotrophic isolates (type strain MarburgT). Of the nine isolates formerly referred to as Methanobacterium thermoformicicum, six were reclassified as Methanothermobacter thermautotrophicus and three as Methanothermobacter wolfeii.

Taxonomic studies were performed on an unusual oral Streptococcus strain isolated from Sprague-Dawley rats. The isolates were alpha-haemolytic, bile-tolerant, aesculin-hydrolytic and unable to grow in 6.5% NaCl. They fermented lactose, sucrose and trehalose. They were distinguished from other recognized species of oral and viridans streptococci by several biochemical characteristics and by Lancefield's group antigen, as well as by unique DNA-DNA hybridization characteristics. 16S rDNA sequence studies confirmed the genealogical distinctiveness of the species. The results of the study demonstrated that the isolates represented a new species of the oral and viridans streptococci. The name Streptococcus orisratti sp. nov. is proposed for the new species. The type strain is A63T (= ATCC 700640T).

An intracellular bacterium, strain L13, was observed infecting an environmental isolate of an Acanthamoeba species. The bacterium could not be recovered on axenic medium but was recovered and cultivated in vitro using cultures of Acanthamoeba polyphaga. The 16S rRNA gene sequence of L13 was found to be new, sharing less than 84% similarity with other sequences in the GenBank/EMBL database. L13 was found to be a member of the alpha-Proteobacteria, sharing an evolutionary line of descent with a group of uniquely obligate intracellular organisms comprised of Caedibacter and Holospora species and the NHP bacterium. Viable bacteria appeared to be highly motile within amoebae. Ultrastructural analysis of the bacterium demonstrated that it is rod-shaped and possesses a typical Gram-negative cell wall, but has no other outstanding features except small vesicle-like structures often associated with the outer surface of each bacterium. The host range of L13 was found to be limited to the genus Acanthamoeba. In A. polyphaga, L13 infection was slow to manifest when cultures were incubated below 30 degrees C, but at higher temperatures bacteria multiplied prolifically and induced host cell lysis. The protein profile of the bacterium purified from the amoebae was assessed by SDS-PAGE and its G+C content was estimated to be 41 mol%. Although these results support the proposal of L13 as a new species, its obligate intracellular nature prevented isolation of a definitive type strain. L13 is therefore proposed as 'Candidatus Odyssella thessalonicensis' gen. nov., sp. nov.

Sixteen strains isolated from different soils and marine sediments and 'Nocardiopsis trehalosi' VKM Ac-942T were subjected to taxonomic analyses. The morphological and chemotaxonomic characteristics of the strains matched those described for members of the Nocardiopsis. Based on 16S rDNA sequence analysis, DNA-DNA hybridization values and phenotypic characteristics, including the composition of menaquinones and cell wall teichoic acids, two new species are proposed, Nocardiopsis tropica sp. nov. (type strain VKM Ac-1457T) and Nocardiopsis trehalosi sp. nov., nom. rev. (type strain VKM Ac-942T = JCM 3357T = NRRL 12026T). Nocardiopsis dassonvillei VKM Ac-1882T (formerly Nocardiopsis albirubida) differs from other strains of this species by the presence of MK-10 as the major menaquinone, cell wall teichoic acid structure, and numerical analysis based on 115 growth and physiological characteristics. The strain is reclassified as the subspecies Nocardiopsis dassonvillei subsp. albirubida, with VKM Ac-1882T (= DSM 43465T = ATCC 23612T = ISP 5465T) designated the type.

A new Pseudomonas species, for which the name Pseudomonas plecoglossicida is proposed, was isolated from cultured ayu (Plecoglossus altivelis) with bacterial haemorrhagic ascites. The causative agent was similar to Pseudomonas putida biovar A in its phenotypic characteristics and on the basis of 16S rRNA gene sequence analysis, but it reduced nitrate to nitrite. Furthermore, it was distinguished phenotypically from Pseudomonas putida biovar A by utilization of D-malate, L-(+)-tartrate, m-tartrate and nicotinate. The levels of DNA-DNA hybridization between the isolate strain FPC 951T and other reference strains of Pseudomonas species, including Pseudomonas putida, were less than 50%. The G+C content of the DNA of FPC 951T was 62.8 mol%. Strain FPC 951T (= ATCC 700383T) is designated the type strain of the new species.

The genomic relatedness was evaluated by DNA-DNA hybridization for 23 strains (21 were pathogenic and two were saprophytic strains) isolated from lesions of common and netted scab in France and 19 strains from other countries, including type strains of Streptomyces species. Three genomospecies were defined within the conventional species of Streptomyces scabies, and these genomospecies were different from other pathogenic described species (Streptomyces acidiscabies, Streptomyces caviscabies) based on previously published phenotypic data. Two of these genomospecies (1 and 3) correspond to new species, for which the names Streptomyces europaeiscabiei sp. nov. (with type strain CFBP 4497T) and Streptomyces stelliscabiei sp. nov. (with type strain CFBP 4521T) are proposed. Genomospecies 2 corresponds to S. scabies (with type strain CFBP 4517T = ATCC 49173T), and includes only one French strain. The pathogenic strains associated with netted scab lesions constituted a new species that was named Streptomyces reticuliscabiei sp. nov. (with type strain CFBP 4531T). The G+C content of DNA from the three strains CFBP 4497T (S. europaeiscabiei), CFBP 4521T (S. stelliscabiei), CFBP 4531T (S. reticuliscabiei) was 71.3, 71.0 and 69.8 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the type strain CFBP 4497T was very similar to the type strain of S. scabies, whereas, the type strain of S. stelliscabiei, CFBP 4521T, was very similar to the type strain of Streptomyces bottropensis. On the basis of 16S rRNA gene sequences, the type strain of S. reticuliscabiei, CFBP 4531T, differed extensively from the other strains of Streptomyces tested.

Morphological features, genomic DNA base composition and 16S rDNA sequence similarities, as well as a distinct phospholipid pattern, whole-cell fatty acid distribution and the occurrence of the lipoquinone 'lipid F', indicate that Clostridium quercicolum belongs to the Sporomusa-Pectinatus-Selenomonas phyletic group and possesses only a remote relationship to members of the genus Clostridium sensu stricto. On the basis of these results, the new genus and combination Dendrosporobacter quercicolus gen. nov., comb. nov. are proposed.

Two psychrophilic Clostridium strains, DB1AT and R26, were isolated from incidences of 'blown-pack' spoilage of vacuum-packed chilled lamb. Vacuum packs of meat inoculated with these strains developed gas bubbles and pack distension within 14 d storage at 2 degrees C. The two main gases responsible for pack distension were carbon dioxide and hydrogen. 1-Butanol, butyric and acetic acid and butyl esters were the major volatile compounds produced by the strains in the artificially inoculated packs. The unknown strains were Gram-positive motile rods producing elliptical subterminal spores during the late-stationary growth phase. At pH 7.0, they grew from -1.5 to 26 degrees C, and their optimum growth temperature was 20-22 degrees C. At 20 degrees C, the pH range for growth was 5.4-8.9 and the optimum pH for growth was 6.2-8.6. In peptone/yeast extract broth, the organisms grew little or not at all in the absence of fermentable carbohydrates. Both strains hydrolysed gelatin, aesculin and starch. The fermentation products formed in peptone yeast extract glucose starch broth were ethanol, acetate, butyrate, lactate, butanol, carbon dioxide and hydrogen. The G+C contents of the DNA of strains DB1AT and R26 were 29.4 and 28.3 mol%, respectively. Phylogenetic analyses indicated that the strains belong to cluster I of the genus Clostridium (sensu Collins et al. 1994). The new strains differed from the phylogenetically related clostridia in cellular fatty acid composition, soluble protein profiles and phenotypic properties. On the basis of rDNA analysis and phenotypic and phylogenetic characterization, the strains were assigned to a new species for which the name Clostridium gasigenes is proposed. Strain DB1AT (= DSM 12272T) is designated as the type strain.

A new phenotypic group of Bifidobacterium strains, isolated from an anaerobic digester for the treatment of waste water from a bean-curd farm, was described previously. In this study, the DNA-DNA relatedness between strain 36 (type strain, AS 1.2282T) of this new group and the type strains of other described Bifidobacterium species was analysed. The low level of DNA homology (0-58.9%) as well as comparison of the 16S rDNA sequences confirmed the distinct phylogenetic position of strain 36. In addition, the new species differed from other Bifidobacterium species in its phenotypic characteristics, such as its growth at moderately thermophilic conditions (49.5 degrees C) and at relatively low pH (4.0), as well as its sugar-fermentation pattern. On the basis of phenotypic, genetic and phylogenetic studies, a new Bifidobacterium species, Bifidobacterium thermacidophilum sp. nov., was designated.

The phylogenetic structure of genus Micromonospora within actinomycetes was examined by analysing the gyrB sequences of 15 validly described species and four subspecies. All but one of the Micromonospora strains formed a tight cluster, as had previously been demonstrated by a 16S rDNA-based phylogenetic analysis. However, the intrageneric relationships deduced from the gyrB-based phylogeny were different from those based on their 16S rDNA sequences. To examine which phylogeny would be more relevant for classifying genus Micromonospora, DNA-DNA hybridization experiments were performed. The gyrB-based classification agrees with the results of the DNA-DNA hybridization studies, indicating that this classification method is useful for analysing the phylogenetic relationships of high G+C Gram-positive bacteria at the level of the genomic species. Genus Micromonospora was reclassified into the following 14 species: Micromonospora echinospora, Micromonospora pallida, Micromonospora nigra, Micromonospora purpureochromogenes, Micromonospora aurantiaca, Micromonospora carbonacea, Micromonospora chalcea, Micromonospora chersina, Micromonospora coerulea, Micromonospora gallica, Micromonospora halophytica, Micromonospora inositola, Micromonospora olivasterospora and Micromonospora rosaria.

Phenotypic and phylogenetic studies were performed on a Gram-negative, rod-shaped bacterium isolated from the uterus of a porpoise. Biochemical and physiological studies indicated that the bacterium was related to the family Pasteurellaceae. Comparative 16S rRNA gene sequencing studies confirmed these findings and demonstrated that the bacterium represents a hitherto unknown subline within this family of organisms. Based on the results of the phylogenetic analysis and phenotypic criteria, it is proposed that the bacterium be assigned to a new genus, Phocoenobacter uteri gen. nov., sp. nov. The type strain of Phocoenobacter uteri sp. nov. is NCTC 12872T.

The 16S rRNA gene of Alteromonas distincta KMM 638T was amplified, cloned and sequenced. The nucleotide sequence was aligned with sequences of representative strains of Alteromonas, Moritella, Pseudoalteromonas and Shewanella. Results of phylogenetic analysis, using neighbour-joining and Fitch-Margoliash methods, clearly indicated that this species should be assigned to the genus Pseudoalteromonas. On the basis of polyphasic data obtained from previous work and this study, it is proposed that the species Alteromonas distincta be reclassified as Pseudoalteromonas distincta comb. nov. with type strain KMM 638T (= ATCC 700518T).

During studies of the bacterial flora in the intestines of mice, we isolated characteristic strains which lowered the pH of peptone-yeast broth containing Fildes' digest. Based on 16S rRNA sequence comparison, these isolates were considered to belong to the Bacteroides cluster in the bacteroides subgroup of the Cytophaga-Flavobacterium-Bacteroides phylum, and were divided into two groups. Their phenotypic characteristics, i.e. growth in 20% bile, aesculin hydrolysis, and glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6PGDH) activity, were the same as those of the 'Bacteroides fragilis group'. The low level of DNA-DNA hybridization with type strains in the Bacteroides cluster confirmed the novel species status of these isolates. It is proposed that these isolates be named Bacteroides acidifaciens, the type strain of which is A40T (= JCM 10556T).

The sequence of the RNase P RNA gene (rnpB) was determined for 60 strains representing all nine species in the family Chlamydiaceae and for the related Chlamydiales species, Parachlamydia acanthamoebae and Simkania negevensis. These sequences were used to infer evolutionary relationships among the Chlamydiaceae. The analysis separated Chlamydophila and Chlamydia into two lineages, with Chlamydophila forming three distinct clusters: the Chlamydophila pneumoniae strains; the Chlamydophila pecorum strains; and a third cluster comprising the species Chlamydophila psittaci, Chlamydophila abortus, Chlamydophila caviae and Chlamydophila felis. The Chlamydia line of descent contained two clusters, with the Chlamydia suis strains distinctly separated from strains of Chlamydia trachomatis and Chlamydia muridarum. This analysis indicated that the rnpB sequence and structure are distinctive markers for species in the Chlamydiaceae. It was also demonstrated that the RNase P RNA derived from Chlamydia trachomatis is able to cleave a tRNA precursor in the absence of protein. These findings are discussed in relation to the structure of Chlamydia RNase P RNA.