International journal of systematic bacteriology最新文献

Nodule isolates from 11 species of wild legumes in north-western China were characterized by numerical taxonomy, PCR-based 16S rRNA gene RFLP and sequence analyses, DNA-DNA hybridization, restriction patterns of nodDAB and nifH genes, and symbiotic properties. Based on the results of numerical taxonomy, most of the 35 new isolates were grouped into five clusters (clusters 7, 9, 12, 14 and 15). Clusters 7 and 12 were identified as Mesorhizobium amorphae and Agrobacterium tumefaciens, respectively, based on their high DNA homologies with the reference strains for these species, their 16S rRNA gene analysis and their phenotypic features. Results of 16S rDNA PCR-RFLP analysis showed that cluster 9 belonged to Rhizobium. Clusters 14 and 15 were identified as Mesorhizobium based on their moderately slow-growing, acid-producing characters and the high similarity of their 16S rDNA PCR-RFLP patterns to those of Mesorhizobium species. These two clusters were genomic species distinct from all described species based on analysis of DNA relatedness within this genus. The isolates in cluster 12 (Agrobacterium tumefaciens) failed to nodulate their original host and other selected hosts and they did not hybridize to nif or nod gene probes. The possibility of opportunistic nodulation of these isolates is discussed. Identical restriction patterns were obtained in the nif or nod gene hybridization studies from the three isolates within cluster 15, which were isolated from the same host species. The isolates from different host plants in each of clusters 9 and 14 produced different nodDAB RFLP patterns, but similar nifH RFLP patterns appeared (one band for each isolate). Different patterns were observed among different clusters from both the nod and nif gene hybridization studies. Crossnodulation was recorded among the isolates and the host plants in the same cluster and promiscuous properties were found among some of the hosts tested.

Two actinomycete strains, DF-28 and DF-32T, were isolated from soil samples collected in a deciduous dipterocarp forest in Thailand. They produced longitudinally paired spores on the tips of short sporophores alternately branched from aerial hyphae, and the chemotaxonomic properties of the isolates were the same as those of members of the family Streptosporangiaceae. These phenotypic properties, together with the results of a phylogenetic analysis based on 16S rRNA gene sequences, indicated that these isolates should be assigned to the genus Microbispora. The two isolates showed more than 93% DNA relatedness to each other, but their relatedness to any previously described species of the genus Microbispora was only 45% or less. They were distinguishable from previously described Microbispora spp. by a combination of physiological and biochemical properties. Therefore, a new species is proposed for these strains, under the name Microbispora corallina sp. nov. The type strain is strain DF-32T (= JCM 10267T).

Four strains of a previously undescribed Actinomyces-like bacterium were isolated from canine and feline clinical specimens. Phenotypic studies indicated the strains were members of the genus Actinomyces, and most closely resembled Actinomyces viscosus serotype I and Actinomyces slackii. Comparative 16S rRNA gene sequencing studies demonstrated the unknown bacterium constitutes a new subline within a group of Actinomyces species, which includes Actinomyces bovis, the type species of the genus. Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium be classified as Actinomyces bowdenii sp. nov. The type strain of Actinomyces bowdenii is CCUG 37421T.

Previous investigations demonstrated three taxonomic groups among 22 clinical isolates of Mycobacterium smegmatis. These studies were expanded to 71 clinical isolates, of which 35 (49%) (group 1) were identical to five ATCC reference strains including the type strain ATCC 19420T. Twenty-eight isolates (39%) were group 2, and eight isolates (11%) were group 3. Isolates of groups 2 and 3 were most often associated with post-traumatic or post-surgical wound infections including osteomyelitis, were susceptible to sulfamethoxazole, amikacin, imipenem and the tetracyclines, variably resistant to clarithromycin, and susceptible (group 1), intermediately resistant (group 2) or resistant (group 3) to tobramycin. The three groups were similar by routine biochemical and growth characteristics, but had different mycolic acid dimethoxy-4-coumarinylmethyl ester elution patterns by HPLC and different PCR-restriction enzyme patterns of a 439 bp fragment of the hsp-65 gene. Group 3 isolates differed from group 1 by 18 bp by 16S rRNA sequencing and exhibited < 25% homology by DNA-DNA hybridization, being most closely related to Mycobacterium mageritense. The 16S rRNA of group 1 and group 2 isolates differed by only 3 bp, but by DNA-DNA hybridization they exhibited only 40% homology. The following names are proposed: Mycobacterium goodii sp. nov. for group 2 isolates (type strain ATCC 700504T = MO69T), Mycobacterium wolinskyi sp. nov. for group 3 isolates (type strain ATCC 700010T = MO739T) and Mycobacterium smegmatis sensu stricto for group 1 isolates.

Two strains of a hitherto undescribed Gram-positive, catalase-negative, facultatively anaerobic coccus isolated from sheep were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing studies demonstrated that the unknown strains were genealogically highly related and constitute a new line close to, but distinct from, Helcococcus kunzii. The unknown bacterium was readily distinguished from H. kunzii 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 Helcococcus ovis sp. nov. The type strain of Helcococcus ovis is CCUG 37441T.

DNA sequences covering 36% of the mle gene that encodes the malolactic enzyme were determined for 13 strains of lactic acid bacteria, representing Pediococcus, Leuconostoc, Lactobacillus and Oenococcus genera. The sequences were aligned with the corresponding region of mleS in Lactococcus lactis. The phylogenetic distance matrix tree of all mle sequences was compared with the 16S rRNA phylogenetic tree. The analysis showed that the mle fragment evolved more rapidly than the 16S gene and differently. Pediococcus and Lactobacillus species were intermixed in the 16S rRNA tree whereas they were separated in the mle tree. Leuconostoc mesenteroides and Oenococcus oeni were distinct from other species in the 16S rRNA tree, whereas they were intermixed with Lactobacillus species and Lactococcus lactis in the mle tree. The amino acid sequences deduced from partial mle genes were aligned with 22 malic enzyme sequences and the corresponding phylogenetic tree was constructed. Malic and malolactic enzymes were distinct at the phylogenetic level, except for malic enzymes of yeast and Escherichia coli which were nearer the malolactic enzymes than the other malic enzymes. The analysis of conserved sites showed several interesting amino acids specific to either malic enzyme or malolactic enzyme.

Two Gram-positive coccoid, non-motile bacteria with L-ornithine as diagnostic diamino acid of the peptidoglycan and an interpeptide bridge of L-Orn<--Gly(1,2)<--D-Glu were isolated from a sample of garden soil. The major menaquinone is MK-8(H4). 13-methyl and 12-methyl tetradecanoic acids are the predominant fatty acids. The polar lipids are phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine and two unknown phospholipids. Mycolic acids are absent. The DNA base composition is 72 mol% G + C. Recent comparative 16S rDNA studies revealed that strains HKI 0125T and HKI 0131 represent a novel lineage adjacent to the family Intrasporangiaceae of the order Actinomycetales but distinct from the previously described genera of this family. On the basis of the genotypic, chemotaxonomic, morphological and physiological characteristics of these two isolates it is proposed to classify HKI 0125T and HKI 0131 in a new genus and species for which the name Ornithinicoccus hortensis gen. nov., sp. nov. is proposed. The type strain is HKI 0125T (= DSM 12335T).

A new species of the genus Gluconacetobacter, for which the name Gluconacetobacter sacchari sp. nov. is proposed, was isolated from the leaf sheath of sugar cane and from the pink sugar-cane mealy bug, Saccharicoccus sacchari, found on sugar cane growing in Queensland and northern New South Wales, Australia. The nearest phylogenetic relatives in the alpha-subclass of the Proteobacteria are Gluconacetobacter liquefaciens and Gluconacetobacter diazotrophicus, which have 98.8-99.3% and 97.9-98.5% 16S rDNA sequence similarity, respectively, to members of Gluconacetobacter sacchari. On the basis of the phylogenetic positioning of the strains, DNA reassociation studies, phenotypic tests and the presence of the Q10 ubiquinone, this new species was assigned to the genus Gluconacetobacter. No single phenotypic characteristic is unique to the species, but the species can be differentiated phenotypically from closely related members of the acetic acid bacteria by growth in the presence of 0.01% malachite green, growth on 30% glucose, an inability to fix nitrogen and an inability to grow with the L-amino acids asparagine, glycine, glutamine, threonine and tryptophan when D-mannitol was supplied as the sole carbon and energy source. The type strain of this species is strain SRI 1794T (= DSM 12717T).

By sequencing a total of 2089 bp of the 16S rRNA and phoE genes it was demonstrated that Calymmatobacterium granulomatis (the causative organism of donovanosis) shows a high level of identity with Klebsiella species pathogenic to humans (Klebsiella pneumoniae, Klebsiella rhinoscleromatis). It is proposed that C. granulomatis should be reclassified as Klebsiella granulomatis comb. nov. An emended description of the genus Klebsiella is given.

A soil isolate, which had been assigned to the genus Nocardia, was shown to have properties consistent with its classification in the genus Amycolatopsis. An almost complete nucleotide sequence of the 16S rDNA of the strain was determined following cloning and sequencing of the amplified gene. The sequence was aligned with those available for members of the family Pseudonocardiaceae and related taxa and phylogenetic trees were inferred using three tree-making algorithms. The organism consistently formed a distinct monophyletic clade with the type strain of Amycolatopsis methanolica, but DNA-DNA relatedness data showed that the two strains belonged to distinct genomic species. The organism was also distinguished from the type strains of all validly described species of Amycolatopsis using a battery of phenotypic properties. The genotypic and phenotypic data show that the strain merits recognition as a new species of the genus Amycolatopsis. The name proposed for the new species is Amycolatopsis thermoflava sp. nov. The type strain is IFO 14333T.