Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia).
Two Gram-positive, aerobic spherical actinobacteria were isolated from the rhizoplane of narrow-leaved cattail (Typha angustifolia) collected from a floating mat in the Soroksar tributary of the Danube river, Hungary. Sequence comparisons of the 16S rDNA indicated these isolates to be phylogenetic neighbours of members of the genus Kocuria, family Micrococcaceae, in which they represent two novel lineages. The phylogenetic distinctness of the two organisms TA68T and TAGA27T was supported by DNA-DNA similarity values of less than 55% between each other and with the type strains of Kocuria rosea, Kocuria kristinae and Kocuria varians. Chemotaxonomic properties supported the placement of the two isolates in the genus Kocuria. The diagnostic diamino acid of the cell-wall peptidoglycan is lysine, the interpeptide bridge is composed of three alanine residues. Predominant menaquinone was MK-7(H2). The fatty acid pattern represents the straight-chain saturated iso-anteiso type. Main fatty acid was anteiso-C15:0. The phospholipids are diphosphatidylglycerol, phosphatidylglycerol and an unknown component. The DNA base composition of strains TA68T and TAGA27T is 69.4 and 69.6 mol% G+C, respectively. Genotypic, morphological and physiological characteristics are used to describe two new species of Kocuria, for which we propose the names Kocuria palustris, type strain DSM 11925T and Kocuria rhizophila, type strain DSM 11926T. (+info)
Polyamine profiles within genera of the class Actinobacteria with LL-diaminopimelic acid in the peptidoglycan.
Polyamine patterns of coryne- and nocardioform representatives of the class Actinobacteria with LL-diaminopimelic acid in the peptidoglycan, comprising strains of the genera Aeromicrobium, Nocardioides, Intrasporangium, Terrabacter, Terracoccus, Propioniferax, Friedmanniella, Microlunatus, Luteococcus and Sporichthya, were analysed. The different polyamine patterns were in good agreement with the phylogenetic heterogeneity within this group of actinomycetes. Strains of the closely related genera Nocardioides and Aeromicrobium were characterized by the presence of cadaverine. The second cluster, consisting of the type strains of the species Friedmanniella antarctica, Propioniferax innocua, Microlunatus phosphovorus and Luteococcus japonicus, displayed as a common feature the presence of the two predominant compounds spermidine and spermine. The presence of putrescine was common to the type strains of the species Intrasporangium calvum, Terrabacter tumescens and Terracoccus luteus. Sporichthya polymorpha, which is a representative of a separate line of descent, displayed spermidine as the predominant polyamine. These data indicate that polyamine patterns are suitable for the classification of actinomycetes with LL-diaminopimelic acid in the peptidoglycan. (+info)
Whipple's arthritis: direct detection of Tropheryma whippelii in synovial fluid and tissue.
We describe 2 patients presenting with polyarthritis in whom the synovial fluid (1 patient) or synovial tissue (1 patient) was positive for Tropheryma whippelii, the Whipple's disease-associated bacillus, when examined by polymerase chain reaction (PCR) and DNA sequencing. Histopathologic findings were consistent with articular Whipple's disease in the synovial fluid of 1 patient and the synovial tissue of the other. In both patients, bowel mucosal specimens were negative for Whipple's disease features by histologic and PCR methods. One patient was positive for T whippelii in the peripheral blood. Control synovial fluid specimens from 40 patients with other arthritides, including Lyme arthritis, were negative. Sequencing of a 284-basepair region of the 16S ribosomal RNA gene confirmed that the sequence is closely related to the known T whippelii sequence. Both patients responded to treatment with antibiotics. (+info)
Characterization of a novel Atopobium isolate from the human vagina: description of Atopobium vaginae sp. 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. (+info)
Detection of three different types of 'Tropheryma whippelii' directly from clinical specimens by sequencing, single-strand conformation polymorphism (SSCP) analysis and type-specific PCR of their 16S-23S ribosomal intergenic spacer region.
The 16S-23S rDNA intergenic spacer region of organisms identical with or closely related to 'Tropheryma whippelii', the uncultivated causative agent of Whipple's disease, was analysed directly from 38 clinical specimens of 28 patients using a specific nested PCR followed by direct sequencing. As compared to the reference sequence in public databases, two novel 'T. whippelii' spacer types were recognized. In the absence of DNA-DNA hybridization data it is uncertain whether the three types found represent subtypes of a single species or three different but closely related species. Methods were developed to detect all three variants by single-strand conformation polymorphism analysis and by type-specific PCR assays, thus allowing the screening of large numbers of specimens. Further studies may provide a clue to the possible associations between the type of infecting strain and the various clinical presentations of Whipple's disease. (+info)
Evaluation of a specific nested PCR targeting domain III of the 23S rRNA gene of "Tropheryma whippelii" and proposal of a classification system for its molecular variants.
"Tropheryma whippelii"-associated infections are usually confirmed histopathologically by using light microscopy. PCR assays targeting the 16S rRNA gene (16S rDNA) of "T. whippelii" are increasingly being applied for this purpose. Compared to microscopic analysis, PCR seems to be more sensitive, as indicated by the fact that several cases of Whipple's disease with negative histopathological findings but positive PCR results have been reported. Considering the lack of pathognomonic clinical features for this disease and the fact that "T. whippelii" DNA has repeatedly been found in patients without clinical Whipple's disease, such PCR results should be confirmed by additional tests. We have, therefore, evaluated a "T. whippelii"-specific nested PCR targeting domain III of the 23S rDNA with 41 clinical specimens known to contain "T. whippelii" 16S rDNA. All of these specimens were also positive for "T. whippelii" 23S rDNA. The specificity of the test was shown by sequencing of the amplicons and by the absence of amplicons in 38 negative controls. We consider this PCR test to be a suitable tool for confirming the presence of "T. whippelii" DNA in specimens with inconclusive histopathological findings. The information derived from sequencing of the partial "T. whippelii" 23S rDNA was then combined with our recent data of the 16S-23S rDNA spacer region of this organism. Overall, four different rDNA types are recognized in our proposed classification system for molecular variants of "T. whippelii." This preliminary scheme may provide a basis for further epidemiological and clinical studies with "T. whippelii" and associated diseases. (+info)
Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed probes for their detection and quantitation.
Laboratory-scale sequencing batch reactors (SBRs) as models for activated sludge processes were used to study enhanced biological phosphorus removal (EBPR) from wastewater. Enrichment for polyphosphate-accumulating organisms (PAOs) was achieved essentially by increasing the phosphorus concentration in the influent to the SBRs. Fluorescence in situ hybridization (FISH) using domain-, division-, and subdivision-level probes was used to assess the proportions of microorganisms in the sludges. The A sludge, a high-performance P-removing sludge containing 15.1% P in the biomass, was comprised of large clusters of polyphosphate-containing coccobacilli. By FISH, >80% of the A sludge bacteria were beta-2 Proteobacteria arranged in clusters of coccobacilli, strongly suggesting that this group contains a PAO responsible for EBPR. The second dominant group in the A sludge was the Actinobacteria. Clone libraries of PCR-amplified bacterial 16S rRNA genes from three high-performance P-removing sludges were prepared, and clones belonging to the beta-2 Proteobacteria were fully sequenced. A distinctive group of clones (sharing >/=98% sequence identity) related to Rhodocyclus spp. (94 to 97% identity) and Propionibacter pelophilus (95 to 96% identity) was identified as the most likely candidate PAOs. Three probes specific for the highly related candidate PAO group were designed from the sequence data. All three probes specifically bound to the morphologically distinctive clusters of PAOs in the A sludge, exactly coinciding with the beta-2 Proteobacteria probe. Sequential FISH and polyphosphate staining of EBPR sludges clearly demonstrated that PAO probe-binding cells contained polyphosphate. Subsequent PAO probe analyses of a number of sludges with various P removal capacities indicated a strong positive correlation between P removal from the wastewater as determined by sludge P content and number of PAO probe-binding cells. We conclude therefore that an important group of PAOs in EBPR sludges are bacteria closely related to Rhodocyclus and Propionibacter. (+info)
Cultivation of the bacillus of Whipple's disease.
BACKGROUND: Whipple's disease is a systemic bacterial infection, but to date no isolate of the bacterium has been established in subculture, and no strain of this bacterium has been available for study. METHODS: Using specimens from the aortic [corrected] valve of a patient with endocarditis due to Whipple's disease, we isolated and propagated a bacterium by inoculation in a human fibroblast cell line (HEL) with the use of a shell-vial assay. We tested serum samples from our patient, other patients with Whipple's disease, and control subjects for the presence of antibodies to this bacterium. RESULTS: The bacterium of Whipple's disease was grown successfully in HEL cells, and we established subcultures of the isolate. Indirect immunofluorescence assays showed that the patient's serum reacted specifically against the bacterium. Seven of 9 serum samples from patients with Whipple's disease had IgM antibody titers of 1:50 or more, as compared with 3 of 40 samples from the control subjects (P<0.001). Polyclonal antibodies against the bacterium were generated by inoculation of the microorganism into mice and were used to detect bacteria in the excised cardiac tissue from our patient on immunohistochemical analysis. The 16S ribosomal RNA gene of the cultured bacterium was identical to the sequence for Tropheryma whippelii identified previously in tissue samples from patients with Whipple's disease. The strain we have grown is available in the French National Collection. CONCLUSIONS: We cultivated the bacterium of Whipple's disease, detected specific antibodies in tissue from the source patient, and generated specific antibodies in mice to be used in the immunodetection of the microorganism in tissues. The development of a serologic test for Whipple's disease may now be possible. (+info)