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PubMed1998

Separation among species of Mycobacterium terrae complex by lipid analyses: comparison with biochemical tests and 16S rRNA sequencing.

Fatty acids, alcohols, and mycolic acid cleavage products were determined for 13 ATCC strains and 24 clinical isolates, which were initially identified by biochemical and growth characteristics as the Mycobacterium terrae complex. The clinical isolates were also analyzed by partial sequencing of the 16S rRNA gene, which divided them into five genetic entities, M. triviale (three strains), M. terrae (four strains), M. nonchromogenicum sensu stricto (seven strains), Mycobacterium sp. strain MCRO 6 (seven strains), and Mycobacterium sp. strain 31958 (one strain). After acidic methanolysis, secondary alcohols were a characteristic feature in all members of the M. terrae complex but M. triviale. In addition to the prominent secondary alcohols, 2-octadecanol and 2-eicosanol, two previously unidentified alcohols, 2-(8,15-dimethyl)docosenol and 2-(8,17-dimethyl)tetracosenol, were detected in M. nonchromogenicum, Mycobacterium sp. strain MCRO 6, and Mycobacterium sp. strain 31958. Only 2-(8,17-dimethyl)tetracosenol was detected in trace amounts in M. terrae. Genetic differences were associated with differences in phenotypic characteristics, including growth at 42 degrees C and pyrazinamidase production. Based on fatty acid and alcohol composition and biochemical and genetic characteristics, M. non-chromogenicum and Mycobacterium sp. strains MCRO 6 and 31958 were found to be a closely related group, named the M. nonchromogenicum complex. Detected genetic variations associated with phenotypic characteristics may indicate further species separation of this complex. In conclusion, the results of gas-liquid chromatography fatty acid analysis, combined with those of a Tween 80 test, enable identification of the species of the M. terrae complex and their separation from other nonpigmented slowly growing mycobacteria.

Amidohydrolases↗
PubMed2001

Re-examining the 16S rDNA sequence of Halomonas salina.

Previous reports of 16S rDNA sequencing of members of the family Halomonadaceae Franzmann et al. 1989 include two different sequences that were both attributed to the type strain of Halomonas salina (Valderrama et al. 1991) Dobson and Franzmann 1996 (basonym Deleya salina Valderrama et al. 1991). The two sequences are sufficiently different for them to belong to two different species within the genus Halomonas. In order to determine which of the two sequences corresponded to that of the type strain of Halomonas salina, the designated type strains of this species were obtained from the ATCC and the DSMZ. It was possible to show that only one of the previous sequences corresponded to the sequences obtained from DSMZ 5928T and ATCC 49509T.

DNA, Bacterial↗
PubMedDate not supplied

Nucleotide sequences of 16S rRNA from ten Serratia species.

Comparison of 16S ribosomal ribonucleic acid (rRNA) sequences has emerged as a powerful tool for bacterial phylogeny. However, earlier studies often only included one or a few species per genus, and it is not sure whether the rRNA sequences could discriminate closely related species. The genus Serratia is composed of ten species, some being up to 60% related by DNA hybridization. The reverse transcriptase/primer extension method was used to determine 1,492 to 1,509 nucleotides in each of ten Serratia 16S rRNA sequences. All rRNA sequences determined were unique. The phylogenetic tree obtained with the neighbour-joining method showed a cluster of Serratia species distinct from both Escherichia coli and Proteus vulgaris. S. fonticola--whose position in the genus Serratia is questioned--was clearly included in the Serratia branch and grouped within the psychrophilic Serratia species. Variable regions in the Serratia rRNA molecules were identified and could serve as the basis for a specific probe design.

Base Sequence↗
PubMedDate not supplied

Mitochondrial 16S rRNA sequence diversity of hominoids.

We determined nucleotide sequences of the 16S rRNA gene of mitochondrial DNA (mtDNA) (about 1.6 kb) for 35 chimpanzee, 13 bonobo, 10 gorilla, 16 orangutan, and 23 gibbon individuals. We compared those data with published sequences and estimated nucleotide diversity for each species. All the ape species showed higher diversity than human. We also constructed phylogenetic trees and networks. The two orangutan subspecies were clearly separated from each other, and Sumatran orangutans showed much higher nucleotide diversity than Bornean orangutans. Some gibbon species did not form monophyletic clusters, and variation within species was not much different from that among species in the subgenus Hylobates.

Animals↗
PubMed1997

Phylogenetic positions and assignment of swine and ovine corynebacterial isolates based on the 16S rDNA sequence.

The nucleotide sequences of the 16S ribosomal RNA gene (rDNA) of swine and ovine corynebacterial strains were determined. The sequences of the strains that identified as Corynebacterium pseudotuberculosis by their biochemical characteristics were homologous with each other. The phylogenetic position of C. pseudotuberculosis strains was closet to C. ulcerans and next closet to C. diphtheriae. The nucleotide sequence of another swine isolate, SC8, was similar to that of a recently proposed species, C. seminale, and a non-validated species, "C. glucuronolyticum," with about 0.01 to 0.02 evolutionary distances. Analysis of the predicted secondary structure of the 16S rRNA molecule agreed with the close phylogenetic relationships between C. pseudotuberculosis and C. ulcerans and between C. seminale and strain SC8.

Animals↗
PubMed1975

A possible role of the 5' terminal sequence of 16S ribosomal RNA in the recognition of initiation sequences for protein synthesis.

Extensive complementarity is found between the 5' end of 16S ribosomal RNA and protein synthesis initiation sites of bacteriophage RNA. Hybrids can be constructed from base sequences of 16S-RNA and two initiation regions on phage RNA. A model is proposed for the involvement of 16S-RNA in the unfolding of hairpin loops containing the initiation codon AUG.

Base Sequence↗
PubMed1997

Phylogeny of Photorhabdus and Xenorhabdus species and strains as determined by comparison of partial 16S rRNA gene sequences.

Partial 16S rRNA gene sequences of 16 strains of the genera Photorhabdus and Xenorhabdus were determined by direct sequencing of PCR products. Aligned sequences were subjected to phylogenetic analysis by maximum-likelihood and maximum-parsimony methods. Distance matrix and phylogenetic analysis did not separate the genera unambiguously. Taxonomic grouping of the bacteria closely paralleled taxonomic grouping of their nematode associates and their geographic origins. We found at least two well-supported taxonomic groups in Photorhabdus species, which suggests that the genus Photorhabdus is coevolving with the nematodes and may be polyspecific.

Animals↗
PubMed1995

Phylogenetic position of Rickettsia tsutsugamushi and the relationship among its antigenic variants by analyses of 16S rRNA gene sequences.

The 16S rRNA gene sequences of Rickettsia tsutsugamushi and Rickettsia sibirica were determined by PCR and DNA sequencing. Phylogenetic analysis revealed that R. sibirica is positioned in a cluster of the genus Rickettsia with a similarity value of 98.1-99.6%, whereas R. tsutsugamushi is located apart from the cluster with a similarity value of 90.2-90.6%. This evidence suggests that R. tsutsugamushi should be excluded taxonomically from the genus Rickettsia. The phylogenetic classification of six antigenic variants in R. tsutsugamushi moderately reflected their antigenic relationship known in closely and distantly related strains.

Antigens, Bacterial↗
PubMed2000

Characterization of Borrelia burgdorferi strains isolated from Korea by 16S rDNA sequence analysis and PCR-RFLP analysis of rrf (5S)-rrl (23S) intergenic spacer amplicons.

Haenam strains of Borrelia burgdorferi, which had been isolated from Ixodes granulatus and Apodemus agrarius in Haenam, Korea, were characterized by PCR-RFLP analysis of rrf (5S)-rrl (23S) intergenic spacer amplicons and by sequence analysis of the 16S rRNA gene (rDNA). The Msel and Dral restriction patterns of the 5S-23S intergenic spacer amplicons of Haenam strains differed from those of other B. burgdorferi sensu lato strains. Furthermore, in the phylogenetic tree based on the 16S rDNA sequences, Haenam strains formed a distinctive cluster, clearly separated from the other members of B. burgdorferi sensu lato. These results suggest that, apart from Borrelia garinii and Borrelia afzelii, other genotypes of B. burgdorferi sensu lato exist in Korea and the Haenam strain is a newly identified one.

Animals↗
PubMed1998

16S rRNA sequence diversity in Mycobacterium celatum strains caused by presence of two different copies of 16S rRNA gene.

Direct sequencing of the 16S rRNA gene (16S rDNA) of Mycobacterium celatum isolates showed ambiguities, suggesting heterogeneity. Cloned 16S rDNA yielded two copies of the gene, which differed by insertion of a thymine at position 214 and by additional mismatches. Restriction fragment length polymorphism analysis confirmed the presence of two copies of 16S rDNA within the bacterial chromosome.

Base Sequence↗
PubMed1999

Identification of bacteria using two degenerate 16S rDNA sequencing primers.

Two degenerate 16S rDNA primers have been designed for broad-range identification of eubacteria by PCR and automated sequencing. Using a simple method, the primers have proven useful in identification of proteobacteria (Campylobacter, Enterobacter, Escherichia, Helicobacter, Klebsiella), gram-positive bacteria (Mycobacterium, Staphylococcus, Streptococcus) and spirochetes (Borrelia) derived from clinical samples. In several cases, the samples could be identified at the species level.

Bacteria↗
PubMed2003

Sequencing of 16S rDNA of Klebsiella: taxonomic relations within the genus and to other Enterobacteriaceae.

The 16S rDNAs of 20 strains of Klebsiella were sequenced and used for construction of a phylogenetic tree together with already published Enterobacteriaceae 16S rDNA sequences. The taxonomy within the Klebsiella genus, as reflected by the 16S rDNA tree, was in agreement with existing DNA-DNA hybridisation and numerical taxonomy data, indicating that for Klebsiella, 16S rDNA sequencing is a valid method for identification and taxonomical purposes. Five closely related clusters were found in the Klebsiella genus; Cluster I, K. oxytoca; Cluster II, K. terrigena, Cluster III, K. planticola and K. ornithinolytica; Cluster IV, Enterobacter aerogenes (K. mobilis); and Cluster V, K. pneumoniae. The position of Calymmatobacterium granulomatis within the genus and closest to K. pneumoniae was confirmed. For the species K. oxytoca, data seem to indicate a subdivision into two subspecies. In addition, a biochemically aberrant Klebsiella strain (BEC441) that was included in the analysis could not be assigned to any of the known species, but was found to be closest related to K. oxytoca. Furthermore, the high sequence similarity between the two environmental species K. planticola and K. ornithinolytica does not justify a distinction of the two species. Finally, within a 165-bp stretch of the 16S rDNA sequences, species-specific nucleotides were found.

DNA, Bacterial↗
PubMed1995

16S rRNA sequence analysis of an isolate of Mycobacterium haemophilum from a heart transplant patient.

Biopsy samples from a heart transplant patient with cellulitis and bursitis yielded an isolate of Mycobacterium haemophilum. The isolate was identified on the basis of a growth requirement for haemin or ferric ammonium citrate, growth at 30 degrees C but not at 37 degrees C, negative catalase test, intracellular growth in McCoy fibroblasts and sequence identify with a portion of the 16S rRNA sequence of the type strain. In comparisons with known 16S rRNA sequences, M. haemophilum grouped with other pathogenic, slow-growing mycobacteria, showing close sequence similarity to M. marinum (98.8%) and lower similarity to M. ulcerans and M. tuberculosis complex organisms. M. haemophilum and M. marium share other features including optimal growth at 30 degrees C and the ability to cause superficial skin lesions in man.

Base Sequence↗
PubMed1998

Intervening sequences in 16S rRNA genes of Campylobacter sp.: diversity of nucleotide sequences and uniformity of location.

We found and sequenced intervening sequences (IVSs) in the PCR-amplicons of 16S rRNA genes of 3 strains of Campylobacter rectus, 2 strains of C. curvus and 2 strains of C. sputorum. The lengths of the IVSs were 140 to 233 bp. The IVSs of C. rectus were identical and had a sequence homology of 55 to 79% against those of C. curvus and C. helveticus. The IVSs of C. sputorum were 97.9-100% homologous but poorly homologous to the other IVSs. In spite of the diversities of the lengths and the nucleotide sequences, all of the IVSs were located at the same position in the 16S rRNA genes.

Base Sequence↗
PubMed1998

Identification and analysis of PCB dechlorinating anaerobic enrichments by amplification: accuracy of community structure based on restriction analysis and partial sequencing of 16S rRNA genes.

The composition of polychlorinated biphenyl (PCB) dechlorinating mixed communities was analysed by restriction fragment length polymorphism of PCR amplified rDNAs (ARDRA) and partial sequencing of 16S rRNA genes amplified from PCB degrading enrichments. Restriction analysis confirms that the 16S rRNA genes amplified from PCB dechlorinating communities vary depending on the PCB congener dechlorinated. Comparison of 16S rRNA sequences to published ribosomal databases indicates that the two most abundant Operational Taxonomic Units (OTUs) appear to be species of the genus Clostridium. The amount that the amplification procedure contributed to this result was determined by varying the amplification procedure and by creating an artificial template mixture. Varying the amount of template by sixfold in the amplification did not affect the distribution of OTUs but the number of OTUs observed decreased with decreasing template concentration. Comparison of products amplified from mixtures of 16S rDNA clones indicates that the more abundant Clostridium OTU did not amplify more efficiently than those of less abundant OTUs. Hybridization to a probe designed to detect the most abundant OTUs indicates that two other OTUs are closely related to this Clostridium species.

Bacteria, Anaerobic↗
PubMed2001

Re-evaluation of the classical Mycoplasma lipophilum cluster (Weisburg et al. 1989) and description of two new clusters in the hominis group based on 16S rDNA sequences.

The Mycoplasma lipophilum cluster (Weisburg et al. 1989) in the hominis group of the mollicutes is re-evaluated in this work to update the phylogenetic framework for classification of species within the genus Mycoplasma. Therefore, sequences of the 16S rRNA gene were determined from previously described species, and 11 were found to be closely related to the M. lipophilum cluster. A selection of members of the other hitherto defined clusters of the hominis group was included for phylogenetic analysis, revealing that the classical M. lipophilum cluster could be re-organized into two clusters, namely the M. lipophilum cluster and the Mycoplasma bovis cluster. The former was found to contain two species, while the latter contained 20 species. The two clusters were closely related, sharing an ancestral branch with the Mycoplasma synoviae cluster. Furthermore, the M. bovis cluster could be divided into subclusters. Interestingly, two species, Mycoplasma equigenitalium and Mycoplasma elephantis, formed a distinct and early branch of the M. lipophilum, M. bovis and M. synoviae clusters. This entity was termed the M. equigenitalium cluster. The clusters and subclusters could be verified by using neighbour-joining and maximum-likelihood analyses on a variety of data sets, bootstrap calculations, secondary structure analysis and signature nucleotides. Therefore, the new 16S rDNA data presented in this work were used to re-evaluate the M. lipophilum cluster, leading to the definition of two additional clusters. At present, the mollicutes belonging to the hominis group can be classified into ten evolutionary lineages.

Bacterial Typing Techniques↗
PubMed1995

Oligonucleotide probes based on 16S rRNA sequences for the identification of four Azospirillum species.

Partial sequences of the 16S rRNA molecules of nine strains belonging to four Azospirillum species were used to design species-specific oligonucleotide probes. Azospirillum strains sequences were analyzed and three homologous fragments containing 16 nucleotides were determined. These three probes were found to be characteristic of A. lipoferum (Al), A. irakense (Ai), and A. brasilense/amazonense species (Aba) and of few nontarget organisms. The specificity of these three probes was tested both against sequences in the GenBank data base and in numerous colony hybridization experiments. As a few non-target organisms hyridized with the different Azospirillum probes, the use of these probes in bulk soil hybridization is not permitted. However, their use together with specific isolation techniques is validated.

Azospirillum↗
PubMed2006

Phylogenetic and taxonomic relationships of northern Far Eastern phoxinin minnows, Phoxinus and Rhynchocypris (Pisces, Cyprinidae), as inferred from allozyme and mitochondrial 16S rRNA sequence analyses.

Analyses of allozyme (18 loci) and partial mitochondrial DNA (mtDNA) sequences (1295 bp, 16S rRNA) support the classification of phoxinin minnows from the northern Far East into 2 genera of 8 species: Phoxinus phoxinus, Rhynchocypris oxycephalus, R. perenurus, R. czekanowskii, R. kumgangensis, R. semotilus, R. lagowskii and R. sp. (bergi ?). Although R. lagowskii from Japan and the Amur basin and R. sp. from Vladivostok region to Korea have been classified into a single species by many authors as R. lagowskii, they form separate clusters in both analyses, suggesting different specific status. Some R. oxycephalus and R. perenurus had the mtDNA haplotypes of R. lagowskii and R. czekanowskii, respectively, which probably indicates that local introgression of mtDNA occurred through inter-specific hybridization. Rhynchocypris forms a monophyletic cluster with dace genera Tribolodon and Pseudaspius, not with Phoxinus. Eurasian and American Phoxinus are suggested to be paraphyletic.

Animals↗