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At least 595 records · Page 33Linked to original sources
PubMed2006

Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences.

Phylogenetic relationships within the halophilic archaea were inferred from comparisons of the 16S rRNA gene sequences from 61 strains, representing 18 genera with validly published names within the order Halobacteriales. Trees produced using distance-matrix (least-squares and neighbour-joining) methods affirm with strong bootstrap support that the members of the order Halobacteriales are a monophyletic group. Ten genera were supported as monophyletic groups [Haloarcula, Halobiforma, Halococcus, Haloferax, Halorubrum, Halosimplex (multiple sequences from a single strain), Natrialba, Natrinema, Natronococcus and Natronorubrum] and eight genera were represented by a single strain (Halobacterium, Halobaculum, Halogeometricum, Halomicrobium, Halorhabdus, Halosimplex, Natronobacterium and Natronomonas). The genus Haloterrigena was always paraphyletic, and the phylogenetic placement of and sister groups to Halobacterium and Natronomonas could not be resolved. Both treeing methods failed to resolve the deep branching patterns within the order Halobacteriales and the relationships between the major clades. Additional representation from the currently monospecific genera and/or the use of other macromolecules may be required to resolve the relationships within the order Halobacteriales.

Base Sequence↗
PubMed1999

Phylogenetic relationships of three amino-acid-utilizing anaerobes, Selenomonas acidaminovorans, 'Selenomonas acidaminophila' and Eubacterium acidaminophilum, as inferred from partial 16S rDNA nucleotide sequences and proposal of Thermanaerovibrio acidaminovorans gen. nov., comb. nov. and Anaeromusa acidaminophila gen. nov., comb. nov.

16S rRNA gene sequences of three previously described amino-acid-fermenting anaerobes, Selenomonas acidaminovorans, 'Selenomonas acidaminophila' and Eubacterium acidaminophilum, were determined. All three were found to cluster within the Clostridium and related genera of the subphylum of the Gram-positive bacteria. The thermophile, S. acidaminovorans, formed an individual line of descent and was equidistantly placed between Dethiosulfovibrio peptidovorans and Anaerobaculum thermoterrenum (similarity of 85%), both of which also form single lines of descent. 'S. acidaminophila' was related to Clostridium quercicolum, a member of cluster IX, with a similarity of 90%, whereas E. acidaminophilum was closely related to Clostridium litorale (similarity of 96%) as a member of cluster XI. Based on the phylogenetic data presented in this report and the phenotypic descriptions of these bacteria published previously, it is recommended that S. acidaminovorans be transferred to a new genus, Thermanaerovibrio gen. nov., as Thermanaerovibrio acidaminovorans comb. nov. and 'Selenomonas acidaminophila' be transferred to a new genus, Anaeromusa gen. nov., as Anaeromusa acidaminophila comb. nov. Though the transfer of E. acidaminophilum to a new taxon is justified, this is not recommended until the taxonomic status of all the members of cluster XI has been reviewed.

Amino Acids↗
PubMed1998

Recombination between rRNA operons created most of the ribotype variation observed in the seventh pandemic clone of Vibrio cholerae.

Individual rrn operons and their flanking regions have been analysed in a study of the molecular basis of ribotype variation in the seventh pandemic clone of Vibrio cholerae. The genome of an early isolate of the seventh pandemic clone had nine rrn operons of which two were in tandem with other rrn operons. The site for BglI, the most discriminatory enzyme used for ribotyping, was found to be present in the 16S sequence of three of the operons of the earliest isolate. This site was observed to be gained or lost in specific operons in many later isolates, presumably by recombination, and this gave most of the ribotype variation. Additional rrn recombination events were uncovered by analysis of the 16S-23S intergenic spacers associated with each operon. Spacers of 431, 509, 607 and 711 bp were found. A total of at least eight rrn recombination events were detected. Three rrn loci were primarily involved in this recombination, with four new forms generated from that in the early strains for operon B and two new forms each for operons C and G. In addition there was variation due to deletion of tandem operons. The frequency of recombination between rrn operons was very high as there were nine new ribotypes found among 47 isolates sampled over the 33 year period of study. This means that any variation could undergo precise reversion by the same recombination event within the time frame covered by the study. Recombination between rrn operons may be a factor in ribotype variation in all systems. The recombination observed is thought to be that which results in concerted evolution and the data give an indication of the rate involved.

Bacterial Typing Techniques↗
PubMed1996

Bacillus piliformis infection (Tyzzer's disease) in a patient infected with HIV-1: confirmation with 16S ribosomal RNA sequence analysis.

Bacillus piliformis is a long, rod-shaped bacterium that has never been grown in cell-free medium and whose taxonomic classification is uncertain. B. piliformis is the causative agent of Tyzzer's disease, which is frequently reported in laboratory, wild, and domesticated animals. The spectrum and severity of this disease is wide in animals. Although many infections are rapidly fatal, subclinical infections are also common. To date, there have been no reports of B. piliformis infection in human beings, although elevated antibody levels have been reported in pregnant women. We describe the first case of human B. piliformis infection, in a man with HIV-1 infection and chronic, localized, crusted verrucous lesions. The diagnosis was confirmed by ribosomal RNA sequencing. The spectrum of organisms leading to infection and the spectrum of diseases caused by these organisms continue to expand, as new infections are identified and as patients with HIV-1 live longer with more severe immune suppression. The extreme difficulty in culturing B. piliformis and the lack of clinical and histopathologic experience with this organism in human beings mean that B. piliformis is potentially another infectious agent to be considered in human beings. Also, when an infectious organism is a strong clinical consideration, silver stains may be of use when results of routine bacterial staining are negative.

AIDS-Related Opportunistic Infections↗
PubMed2003

A description of the second species of the family Dipteromimidae (Insecta, Ephemeroptera), and genetic relationship of two dipteromimid mayflies inferred from mitochondrial 16S rRNA gene sequences.

A new mayfly species, Dipteromimus flavipterus sp. nov., of the family Dipteromimidae is described on the basis of specimens of males, females and mature nymphs collected from Ofunato, Iwate Prefecture, Japan. This new Dipteromimus species is characterized by a large body size, a yellowish body color (especially the frontal border of the forewings), short penis lobes, a slight elongation backwards of the female 7th abdominal sternum, and a rounded backward projection of the female 9th abdominal sternum, etc., in comparison with another known dipteromimid mayfly Dipteromimus tipuliformis McLachlan, 1875. Full descriptions of males, females, mature nymphs and eggs of this new species have been provided. We also examined and discussed the genetic relationship of two dipteromimid mayflies to settle the taxonomic status, inferred from the partially sequenced large mitochondrial ribosomal subunit (16S rRNA) genes. Consequently, phenetic and molecular phylogenetic analyses agreed in terms of clustering.

Animal Structures↗
PubMed1996

Phylogeny of Prosthecobacter, the fusiform caulobacters: members of a recently discovered division of the bacteria.

Prosthecobacter fusiformis is morphologically similar to caulobacters; however, it lacks a dimorphic life cycle. To determine the relatedness of the genus Prosthecobacter to dimorphic caulobacters and other prosthecate members of the alpha subgroup of the Proteobacteria (alpha-Proteobacteria), we isolated and sequenced 16S rRNA genes from four Prosthecobacter strains. Surprisingly, the results of phylogenetic analyses placed the fusiform caulobacters in a deeply rooted division of the Bacteria that was most closely affiliated with the Planctomyces-Chlamydia group and only distantly related to the alpha-Proteobacteria. The genus Prosthecobacter shares a common lineage in this division with Verrucomicrobium spinosum, a polyprosthecate, heterotrophic bacterium. Consistent with this phylogenetic placement, menaquinones were isolated from Prosthecobacter strains and menaquinones have been isolated from Verrucomicrobium strains and planctomycetes but not from members of the alpha-Proteobacteria. Thus, the genus Prosthecobacter is a second genus in the recently described order Verrucomicrobiales. Members of the genus Prosthecobacter are susceptible to beta-lactam antibiotics and contain mesodiaminopimelic acid, indicating that they, unlike members of the Planctomycetales or Chlamydiales, have peptidoglycan cell walls. This major phenotypic difference, together with the phylogenetic independence of the verrucomicrobia, indicates that these bacteria and the sources of related 16S ribosomal DNAs obtained from soils, freshwater, and the marine pelagic environment represent an unrecognized division of the Bacteria.

Base Sequence↗
PubMed1999

Complete DNA sequence analysis for 16S ribosomal RNA gene of the leproma-derived, cultivable and nerve-invading mycobacterium HI-75.

The complete 1493 nucleotide sequence of the 16SrRNA gene of the leproma-derived and cultivable mycobacterium HI-75 strain was analyzed to elucidate the taxonomic characteristics by direct sequencing of the polymerase chain reaction (PCR) products. The results revealed that the sequence of mycobacterium HI-75 was mostly similar to that of Mycobacterium scrofulaceum with 5 bases differences in the sequenced 1493 bases (0.35%) of the 16SrRNA gene. M. leprae differed from the strain with 47 bases (3.3%). Sasaki and Hamit reported the nerve-invasive activity of the inoculated mycobacterium HI-75 in nude mice or the 131I-treated immunocompromised Swiss mice. The results indicate that mycobacterium HI-75 could be a mutant of M. scrofulaceum possessing the ability to invade the peripheral nerve in addition to developing leproma-like lesions.

Base Sequence↗
PubMed1998

Genetic analyses of the genus Nocardioides and related taxa based on 16S-23S rDNA internally transcribed spacer sequences.

The 16S-23S internally transcribed spacer (ITS) sequences were analysed to clarify inter- and intraspecific relationships among strains of the genus Nocardioides and the relationship between two Aeromicrobium species. The 16S-23S ITS regions from 33 Nocardioides strains, two Aeromicrobium species and Terrabacter tumescens were sequenced directly after polymerase chain reaction (PCR0 amplification and gamma exonuclease treatment. The genomes of some Nocardioides strains included two types of 16S-23S ITS sequences. The sizes of the 16S-23S ITS sequences of Nocardioides strains ranged from 328 to 539 bp. The 16S-23S ITS sequences of Aeromicrobium erythreum NSP37T, Aeromicrobium fastidiosum NSP38T and T. tumescens NSP39T were 349, 355 and 386 bp long, respectively. Nucleotide similarity among 16S-23S ITS sequences of Nocardioides albus strains and of Nocardioides simplex strains was 84.1-100% and 97.7-100%, respectively. The 16S-23S ITS sequence of Nocardioides luteus was identical to that of 'Nocardioides fulvus' NSP32T and was only 1 bp different from that of 'Nocardioides flavus' strains. However, the 16S-23S ITS sequences of 'N. fulvus' NSP33 showed only a low degree of similarity to 'N. fulvus' NSP32T (54.8%). The degree of 16S-23S ITS similarity between N. luteus NSP20T and N. ablus strains ranged from 85 to 93%. The mean nucleotide similarity values between the type strains of validly described Nocardioides species were highly divergent at 68:1 +/- 16.8%. The two Aeromicrobium species showed a level of 16S-23S ITS similarity of 71.2%. In this study, 16S-23S ITS sequences of the members of the genera Nocardioides and Aeromicrobium were useful for inferring the relationships between closely related strains and species. However, they were not found to be appropriate for elucidating the phylogenetic relationships between distantly related organisms at the genus level.

Actinomycetales↗
PubMed2001

Routine molecular identification of enterococci by gene-specific PCR and 16S ribosomal DNA sequencing.

For 279 clinically isolated specimens identified by commercial kits as enterococci, genotypic identification was performed by two multiplex PCRs, one with ddl(E. faecalis) and ddl(E. faecium) primers and another with vanC-1 and vanC-2/3 primers, and by 16S ribosomal DNA (rDNA) sequencing. For 253 strains, phenotypic and genotypic results were the same. Multiplex PCR allowed for the identification of 13 discordant results. Six strains were not enterococci and were identified by 16S rDNA sequencing. For 5 discordant and 10 concordant enterococcal strains, 16S rDNA sequencing was needed. Because many supplementary tests are frequently necessary for phenotypic identification, the molecular approach is a good alternative.

DNA Primers↗
PubMed2006

Phylogenetic analysis of gamma-proteobacteria inferred from nucleotide sequence comparisons of the house-keeping genes adk, aroE and gdh: comparisons with phylogeny inferred from 16S rRNA gene sequences.

Nucleotide sequence comparisons of three house-keeping genes, adenylate kinase (adk), shikimate dehydrogenase (aroE), and glucose-6-phosphate dehydrogenase (gdh), were used to infer the phylogeny of 33 gamma-proteobacteria. Phylogenetic trees inferred from each gene, and from the concatenated sequences of all three genes, are, in general, similar to a 16S rRNA gene-inferred tree. Similar grouping of bacteria are revealed at the family, genus, species and strain levels in all five trees. The house-keeping genes, however, show a higher rate of nucleotide sequence substitutions. Consequently, they can possibly probe deeper branches of a phylogenetic tree than the 16S rRNA gene. However, because their nucleotide sequences are not as highly conserved among gamma-proteobacteria, family- or genus-specific primers would need to be designed for the amplification of any of these three house-keeping genes. Since these genes are used in multilocus sequence typing, it is expected that the number of sequences publicly available for many taxa will increase over time proving them very useful either at complementing 16S rRNA-inferred phylogenies or for specific, targeted, phylogenetic analysis.

Adenylate Kinase↗
PubMed2002

16S ribosomal DNA sequencing confirms the synonymy of Vibrio harveyi and V. carchariae.

Seventeen bacterial strains previously identified as Vibrio harveyi (Baumann et al. 1981) or V. carchariae (Grimes et al. 1984) and the type strains of V. harveyi, V. carchariae and V. campbellii were analyzed by 16S ribosomal DNA (rDNA) sequencing. Four clusters were identified in a phylogenetic analysis performed by comparing a 746 base pair fragment of the 16S rDNA and previously published sequences of other closely related Vibrio species. The type strains of V. harveyi and V. carchariae and about half of the strains identified as V. harveyi or V. carchariae formed a single, well-supported cluster designed as 'bona fide' V. harveyi/carchariae. A second more heterogeneous cluster included most other strains and the V. campbellii type strain. Two remaining strains are shown to be more closely related to V. rumoiensis and V. mediterranei. 16S rDNA sequencing has confirmed the homogeneity and synonymy of V. harveyi and V. carchariae. Analysis of API20E biochemical profiles revealed that they are insufficient by themselves to differentiate V. harveyi and V. campbellii strains. 16S rDNA sequencing, however, can be used in conjunction with biochemical techniques to provide a reliable method of distinguishing V. harveyi from other closely related species.

Animals↗
PubMed2002

Sequence analysis of 16S rRNA gene of cyanobacteria associated with the marine sponge Mycale (Carmia) hentscheli.

Marine sponges frequently contain a complex mixture of bacteria, fungi, unicellular algae and cyanobacteria. Epifluorescent microscopy showed that Mycale (Carmia) hentscheli contained coccoid cyanobacteria. The 16S rRNA gene was amplified, fragments cloned and analysed using amplified rRNA gene restriction analysis. The nearly complete 16S rRNA gene of distinct clones was sequenced and aligned using ARB. The phylogenetic analysis indicated the presence of four closely related clones which have a high (8%) sequence divergence from known cyanobacteria, Cyanobacterium stanieri being the closest, followed by Prochloron sp. and Synechocystis sp. All belong to the order Chroococcales. The lack of non-molecular evidence prevents us from proposing a new genus.

Animals↗
PubMed2004

PCR detection and 16S rRNA sequence-based phylogeny of a novel Propionibacterium acidipropionici applicable for enhanced fermentation of high moisture corn.

AIMS: The aims of this study were to develop a sensitive and more rapid detection of Propionibacterium acidipropionici DH42 in silage and rumen fluid samples, and to explore its 16S rRNA sequence-based phylogeny. METHODS AND RESULTS: Nested polymerase chain reaction (PCR) was used with DH42-specific primers dhb1 and dhb2 for the secondary amplification of a 1267-bp fragment of 16S rRNA encoding gene. Using the established protocols for PCR amplification, as low as 10(2) and 10(3) CFU ml(-1) of strain DH42 in silage extracts and rumen fluid, respectively, were detected. To determine phylogenetic relationships between DH42 and other representatives of Propionibacterineae, a 1529-bp fragment of its 16S rRNA was amplified by PCR and sequenced. The propionibacterium DH42 formed a cluster with Eubacterium combesii, P. acidipropionici and P. microaerophilus. CONCLUSIONS: 16S rRNA-based PCR detection technique was developed for DH42 in silage and rumen fluid samples. The 16S rRNA sequence confirmed the earlier identification of strain DH42 as P. acidipropionici. However, variable nucleotide positions were revealed. SIGNIFICANCE AND IMPACT OF THE STUDY: Variability of 16S rRNA sequence within the species P. acidipropionici, determined in this study, poses the need of re-sequencing for some species of the suborder Propionibacterineae for a more reliable classification.

Animals↗
PubMed2005

Novel major bacterial candidate division within a municipal anaerobic sludge digester.

In a previous study, we analyzed the molecular diversity of Planctomycetales by PCR amplification and sequencing of 16S rRNA clone libraries generated from a municipal wastewater plant, using planctomycete-specific and universal primer sets (R. Chouari, D. Le Paslier, P. Daegelen, P. Ginestet, J. Weissenbach, and A. Sghir, Appl. Environ. Microbiol. 69:7354-7363, 2003). Only a small fraction (4%) of the 16S rRNA gene sequences of the digester clone library corresponded to the Planctomycetales division. Importantly, 85.9% of the digester clone sequences are grouped into two different clusters named WWE1 (81.4% of the sequences) and WWE2 (4.5%) and are distantly affiliated with unidentified bacterial sequences retrieved from a methanogenic reactor community and from a termite gut, respectively. In phylogenetic analysis using 16S rRNA gene sequence representatives of the main phylogenetic bacterial divisions, the two clusters are monophyletic, branch apart from each other, and are distantly related to Planctomycetales and other bacterial divisions. A novel candidate division is proposed for WWE1, while the WWE2 cluster strongly affiliates with the recently proposed Lentisphearae phylum. We designed and validated a 16S rRNA probe targeting WWE1 16S rRNA sequences by both fluorescent in situ hybridization (FISH) and dot blot hybridization (DBH). Results of FISH analysis show that WWE1 representative microorganisms are rods or filamentous shaped, while DBH shows that WWE1 accounts for 12% of the total bacterial rRNA within the anaerobic digester. The remaining 16S rRNA gene sequences are affiliated with Verrucomicrobia or recently described candidate divisions with no known pure culture representatives, such as OD1, BRC1, or NBL-UPA2, making up less than 3.5% of the clone library, respectively. This inventory expands the known diversity of the latter bacterial division-level lineages.

Bacteria, Anaerobic↗
PubMed1999

Novel 16S rRNA gene sequences retrieved from highly saline brine sediments of kebrit deep, red Sea

In this study, we report on first 16S rRNA gene sequences from highly saline brine sediments taken at a depth of 1,515 m in the Kebrit Deep, northern Red Sea. Microbial DNA extracted directly from the sediments was subjected to PCR amplification with primers specific for bacterial and archaeal 16S rRNA gene sequences. The PCR products were cloned, and a total of 11 (6 bacterial and 5 archaeal) clone types were determined by restriction endonuclease digestion. Phylogenetic analysis revealed that most of the cloned sequences were unique, showing no close association with sequences of cultivated organisms or sequences derived from environmental samples. The bacterial clone sequences form a novel phylogenetic lineage (KB1 group) that branches between the Aquificales and the Thermotogales. The archaeal clone sequences group within the Euryarchaeota. Some of the sequences cluster with the group II and group III uncultivated archaea sequence clones, while two clone groups form separate branches. Our results suggest that hitherto unknown archaea and bacteria may thrive in highly saline brines of the Red Sea under extreme environmental conditions.

Journal Article↗
PubMed1995

Staphylococcus pulvereri sp. nov., isolated from human and animal specimens.

A new coagulase-negative species of the genus Staphylococcus, Staphylococcus pulvereri, was isolated from human and animal specimens. The complete 16S rRNA sequence of the type strain of S. pulvereri, NT215, was determined and compared with the sequences of 16S rRNAs from the other staphylococci. Strains of S. pulvereri were differentiated from other novobiocin-resistant Staphylococcus species by their biochemical activities, cell wall composition, and levels of genetic relatedness. The type strain of this species is NT215 (= PCM 2443T).

Animals↗
PubMed1992

Uncultivated cyanobacteria, Chloroflexus-like inhabitants, and spirochete-like inhabitants of a hot spring microbial mat.

Analysis of 16S rRNA sequences retrieved as cDNA (16S rcDNA) from the Octopus Spring cyanobacterial mat has permitted phylogenetic characterization of some uncultivated community members, expanding our knowledge or diversity within this microbial community. Two new cyanobacterial 16S rRNA sequences were discovered, raising to four the number of cyanobacterial sequence types known to occur in the mat. None of the sequences found is that of the cultivated thermophilic cyanobacterium Synechococcus lividus. A new 16S rRNA sequence characteristic of green nonsulfur bacteria and their relatives was discovered, raising to two the number of such sequences known to exist in the mat. Both are unique among the 16S rRNA sequences of cultivated members of this group, including an Octopus Spring isolate of Chloroflexus aurantiacus and Heliothrix oregonensis, whose sequences we report herein. Two spirochete-like 16S rRNA sequences were discovered. One can be placed in the leptospira subdivision of the spirochete group, but the other has such a loose affiliation with the spirochete group that it might actually belong to an as yet unrecognized subdivision or even to a new eubacterial line of descent.

Bacteria↗