Human intestinal spirochetosis diagnosed with colonoscopy and analysis of partial 16S rDNA sequences of involved spirochetes

2001 ◽  
Vol 2 (1) ◽  
pp. 111-116 ◽  
Author(s):  
Wolfgang Kraatz ◽  
Ulf Thunberg ◽  
Bertil Pettersson ◽  
Claes Fellström
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rdna Sequences ◽  
Intestinal Spirochetosis ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Human Intestinal Spirochetosis ◽  
Type Strains ◽  
Rrna Sequences

AbstractDNA was extracted from colonic biopsies of 33 patients with and three without evidence of intestinal spirochetosis (IS) in the large bowel. The biopsies were subjected to PCR. A pair of primers, generating a 207 bp fragment, were designed to detect specifically the 16S rDNA gene ofBrachyspira. PCR products of the expected size were obtained from 33 samples with histologic evidence of IS. The PCR amplicons were used for sequencing. The sequences obtained were aligned to the corresponding 16S rRNA sequences of five type strains ofBrachyspira. The sequences of 23 PCR products were 99–100% identical with the correspond-ingB.aalborgitype strain sequence. Two cases showed 99–100% sequence similarity with the type strain ofB.pilosicoliP43/6/78. Six cases could not be referred to any of the known species ofBrachyspira. Two PCR products gave incomplete sequences.

scholarly journals Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea

2004 ◽  
Vol 54 (2) ◽  
pp. 487-491 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Phenotypic Properties ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Isoprenoid Quinones ◽  
Type Strains

A Gram-negative, motile, non-spore-forming, rod-shaped strain, TF-27T (=KCCM 41648T=JCM 11814T), was isolated from a tidal flat in Korea. This organism grew well at 25–35 °C, with optimum growth at 30 °C. Strain TF-27T grew optimally in the presence of 2 % NaCl; it did not grow without NaCl or in the presence of >8 % NaCl. Strain TF-27T simultaneously contained both menaquinones and ubiquinones as isoprenoid quinones. The predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acids in strain TF-27T were iso-C15 : 0 (20·6 %) and iso-C15 : 0 2-OH and/or C16 : 1 ω7c (21·1 %). The DNA G+C content of strain TF-27T was 42 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-27T falls within the radiation of the cluster that is encompassed by the genus Shewanella. Levels of 16S rDNA sequence similarity between strain TF-27T and the type strains of Shewanella species were 93·2–96·8 %. On the basis of phenotypic properties and phylogenetic data, strain TF-27T should be placed in the genus Shewanella as a novel species, for which the name Shewanella gaetbuli sp. nov. is proposed.

scholarly journals Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium

2004 ◽  
Vol 54 (3) ◽  
pp. 851-855 ◽  
Author(s):  
Wan-Taek Im ◽  
Hee-Sung Bae ◽  
Akira Yokota ◽  
Sung Taik Lee
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Rdna Sequence ◽  
The Novel ◽  
Comamonas Testosteroni ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
Degrading Bacterium ◽  
16S Rdna Sequences ◽  
Type Strains

A 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of Comamonas testosteroni, was reclassified as a member of the genus Herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16S rDNA sequences. Phylogenetic inference based on 16S rDNA sequences showed that strain CPW301T clusters in a phylogenetic branch that contains Herbaspirillum species. 16S rDNA sequence similarity of strain CPW301T to species of the genus Herbaspirillum with validly published names is in the range 98·7–98·9 %. Despite the considerably high 16S rDNA sequence similarity, strain CPW301T could be distinguished clearly from type strains of Herbaspirillum species with validly published names by DNA–DNA relatedness values, which were <15·7 %. The genomic DNA G+C content of strain CPW301T is 61·3 mol%. The predominant ubiquinone is Q-8 and the major cellular fatty acids are C16 : 0 and cyclo-C17 : 0. The strain does not fix nitrogen and is not plant-associated. It is an aerobic rod with one unipolar flagellum. On the basis of these characteristics, a novel Herbaspirillum species, Herbaspirillum chlorophenolicum sp. nov., is proposed. The type strain of the novel species is strain CPW301T (=KCTC 12096T=IAM 15024T).

Molecular bacterial diversity and distribution in waste from a steel plant

2008 ◽  
Vol 54 (12) ◽  
pp. 996-1005 ◽  
Author(s):  
Dulcecleide B. Freitas ◽  
Mariana P. Reis ◽  
Leandro M. Freitas ◽  
Paulo S. Assis ◽  
Edmar Chartone-Souza ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Sequence Similarity ◽  
Diversity Indices ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
Partial Length ◽  
16S Rdna Sequences ◽  
Novel Taxa

We characterized the bacterial diversity of newly produced steelmaking wastes (NPSW) and steelmaking wastes deposited (SWD) in a restricted land area, generated by the siderurgic industry, using the 16S rDNA clone library approach. A total of 212 partial-length sequences were analyzed, revealing 123 distinct operational taxonomic units (OTUs) determined by the DOTUR program to 97% sequence similarity. Phylogenetic analysis of bacterial 16S rDNA sequences from the NPSW and SWD libraries demonstrated that Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Planctomycetes, Firmicutes, and Bacteroidetes were represented in both libraries. Deltaproteobacteria, Acidobacteria, Chloroflexi, Deinococcus-thermus, Gemmatimonadetes, and candidate divisions OP10 and OD1 were only present in the SWD library, and Nitrospira was only present in the NPSW library. The abundance of sequences affiliated with Gammaproteobacteria was high in both libraries. Six previously unclassified OTUs may represent novel taxa. Based on diversity indices (Simpson, Shannon–Weaver, Chao1, and ACE), the SWD library had a higher diversity. LIBSHUFF comparisons of the composition of the 2 libraries showed that they were significantly different. These results indicate that the bacterial communities in steelmaking wastes present high phylogenetic diversity and complexity. A possible association between the functional diversity and the bacterial communities’ complexity requires further phenotypic investigation.

scholarly journals Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea

2004 ◽  
Vol 54 (1) ◽  
pp. 71-75 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
In-Gi Kim ◽  
Kook Hee Kang ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
Fatty Acid ◽  
16S Rdna ◽  
Type Strain ◽  
Cellular Fatty Acid ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Phenotypic Characterization ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Diamino Acid

A bacterial strain, GW-9T, which was isolated from groundwater in Korea, was subjected to a polyphasic taxonomic study using phenotypic characterization and phylogenetic and genetic methods. Phylogenetic analysis based on 16S rDNA sequences showed that strain GW-9T forms an evolutionary lineage within the radiation enclosing Nocardioides species and, in particular, a coherent cluster with Nocardioides pyridinolyticus. The cell-wall peptidoglycan type of strain GW-9T was based on ll-diaminopimelic acid as the diamino acid, indicating wall chemotype I. The predominant menaquinone was MK-8(H4). Strain GW-9T had a cellular fatty acid profile containing straight-chain, branched, unsaturated and 10-methyl fatty acids. The major fatty acid was iso-C16 : 0. The DNA G+C content of strain GW-9T was 73 mol%. The 16S rDNA of strain GW-9T was 99·2 % similar to that of the type strain of Nocardioides pyridinolyticus and 94·9–96·0 % similar to sequences of the type strains of other Nocardioides species. Differences in phenotypic characteristics and genetic distinctiveness indicate that strain GW-9T is separate from previously described Nocardioides species. Therefore, on the basis of the data presented, a novel species of the genus Nocardioides, Nocardioides aquiterrae sp. nov., is proposed. The type strain is strain GW-9T (=KCCM 41647T=JCM 11813T).

scholarly journals First Report of ‘Candidatus Phytoplasma asteris’-Related Strains Infecting Lily in Mexico

Plant Disease ◽  
2008 ◽  
Vol 92 (6) ◽  
pp. 979-979 ◽  
Author(s):  
N. E. Cortés-Martínez ◽  
E. Valadez-Moctezuma ◽  
L. X. Zelaya-Molina ◽  
N. Marbán-Mendoza
Keyword(s):  
16S Rdna ◽  
The Czech Republic ◽  
First Report ◽  
Rdna Sequences ◽  
Flower Abortion ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Total Dna ◽  
Nested Pcr Assays ◽  
Symptomatic Plant

In recent years, lily (Lilium spp.) has become an important ornamental crop in diverse regions of Mexico. Since 2005, unusual symptoms have been observed on lily plants grown from imported bulbs in both greenhouse and production plots at San Pablo Ixayo, Boyeros, and Tequexquinauac, Mexico State. Symptoms included a zigzag line pattern on leaves, dwarfism, enlargement of stems, shortened internodes, leaves without petioles growing directly from bulbs, air bulbils, death of young roots, atrophy of flower buttons, and flower abortion. Symptoms were experimentally reproduced on healthy lily plants by graft inoculation. Total DNA was extracted from 50 diseased, 10 symptomless, and 10 graft-inoculated plants by the method of Dellaporta et al. (2). DNA samples were analyzed for phytoplasma presence by two different nested PCR assays. One assay employed ribosomal RNA gene primer pair P1/P7 followed by R16F2n/R16R2 (1), whereas ribosomal protein (rp) gene primer pairs rpF1/rpR1 and rp(I)F1A/rp(I)R1A (4) were used in a second assay. A DNA fragment approximately 1.2 kb long was consistently amplified from all symptomatic plant samples only by both assays. A comparative analysis of 16S rDNA sequences (Genbank Accession Nos. EF421158–EF421160 and EU124518–EU124520) and rp gene sequences (EU277012–EU277014), derived from PCR products, revealed that phytoplasma infecting lily were most similar (99.9% to 16S rDNA and 99.7% to rp) to carrot phytoplasma sp. ca2006/5 and also were similar (99.8% to 16SrDNA and 99.2% to rp) to broccoli phytoplasma sp. br273. Both carrot and broccoli phytoplasmas were classified as members of aster yellow 16S rDNA restriction fragment length polymorphism subgroup 16SrI-B (3). Although infection of lilies by aster yellows (‘Ca. phytoplasma asteris’) subgroup 16SrI-B and 16SrI-C was reported from the Czech Republic and Poland, to our knowledge, this is the first report of ‘Ca. phytoplasma asteris’-related strains associated with lily plants in Mexico. References: (1) R. F. Davis et al. Microbiol. Res. 158:229, 2003. (2) S. L. Dellaporta et al. Plant Mol. Biol. Rep. 1:19, 1983. (3) B. Duduk et al. Bull. Insectol. 60 2:341, 2007. (4) I.-M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004.

scholarly journals TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation

2017 ◽  
Author(s):  
Ali Z Ijaz ◽  
Thomas Jeffries ◽  
Christopher Quince ◽  
Kelly Hamonts ◽  
Brajesh Singh
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Marker Gene ◽  
Evolutionary Conservation ◽  
Rrna Gene ◽  
Similarity Metric ◽  
Rdna Sequences ◽  
Fine Grain ◽  
16S Rdna Sequences ◽  
Taxonomic Annotation

Amplicon based taxonomic analysis, which determines the presence of microbial taxa in different environments on the basis of marker gene annotations, often uses percentage identity as the main metric to determine sequence similarity against databases. These data are then used to study the distribution of biodiversity as well as response of microbial communities to environmental conditions. However the 16S rRNA gene displays varying degrees of sequence conservation along its length and percentage identity does not fully utilize this information. Additionally, the prevalent usage of Operational Taxonomic Unit, or OTUs is not without its own issues and may lead to a reduction in annotation capability of the system. Hence a novel approach to taxonomic annotation is needed. Here we introduce a new taxonomic annotation pipeline, TaxaSE, which utilizes Shannon entropy to quantify evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotations. Furthermore, the system is capable of annotation of individual sequences in order to improve fine grain taxonomic annotations. We present both in-silico comparison of the new similarity metric with percentage identity, as well as comparison with the popular QIIME pipeline. The results demonstrate the new similarity metric achieves better performance especially at lower taxa levels. Furthermore, the pipeline is able to extract more fine grain taxonomic annotations compared to QIIME. These exhibit not only the effectiveness of the new pipeline but also highlight the need to shift away from both percentage identity and OTU based approaches for ecological projects.

scholarly journals Differences at Species Level and in Repertoires of Secondary Metabolite Biosynthetic Gene Clusters among Streptomyces coelicolor A3(2) and Type Strains of S. coelicolor and Its Taxonomic Neighbors

2021 ◽  
Vol 1 (3) ◽  
pp. 573-585
Author(s):  
Hisayuki Komaki ◽  
Tomohiko Tamura
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Polyketide Synthase ◽  
Streptomyces Coelicolor ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Nrps Gene ◽  
Rdna Sequences ◽  
Type Strains

Streptomyces coelicolor A3(2) is used worldwide for genetic studies, and its complete genome sequence was published in 2002. However, as the whole genome of the type strain of S. coelicolor has not been analyzed, the relationship between S. coelicolor A3(2) and the type strain is not yet well known. To clarify differences in their biosynthetic potential, as well as their taxonomic positions, we sequenced whole genomes of S. coelicolor NBRC 12854T and type strains of its closely related species—such as Streptomyces daghestanicus, Streptomyces hydrogenans, and Streptomyces violascens—via PacBio. Biosynthetic gene clusters for polyketides and non-ribosomal peptides were surveyed by antiSMASH, followed by bioinformatic analyses. Type strains of Streptomyces albidoflavus, S. coelicolor, S. daghestanicus, S. hydrogenans, and S. violascens shared the same 16S rDNA sequence, but S. coelicolor A3(2) did not. S. coelicolor A3(2) and S. coelicolor NBRC 12854T can be classified as Streptomycesanthocyanicus and S. albidoflavus, respectively. In contrast, S. daghestanicus, S. hydrogenans, and S. violascens are independent species, despite their identical 16S rDNA sequences. S. coelicolor A3(2), S. coelicolor NBRC 12854T, S. daghestanicus NBRC 12762T, S. hydrogenans NBRC 13475T, and S. violascens NBRC 12920T each harbor specific polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters in their genomes, whereas PKS and NRPS gene clusters are well conserved between S. coelicolor A3(2) and S. anthocyanicus JCM 5058T, and between S. coelicolor NBRC 12854T and S. albidoflavus DSM 40455T, belonging to the same species. These results support our hypothesis that the repertoires of PKS and NRPS gene clusters are different between different species.

scholarly journals First Report of ‘Candidatus Phytoplasma asteris’-Related Strain Associated with Peach Rosette in Canada

Plant Disease ◽  
2010 ◽  
Vol 94 (7) ◽  
pp. 916-916 ◽  
Author(s):  
S. Zunnoon-Khan ◽  
R. Michelutti ◽  
Y. Arocha-Rosete ◽  
J. Scott ◽  
W. Crosby ◽  
...  
Keyword(s):  
16S Rdna ◽  
Nested Pcr ◽  
The United States ◽  
Polymorphism Analysis ◽  
Plant Host ◽  
First Report ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Short Internodes

Prunus persica (L.) Bastch (family Rosaceae) is currently represented by 83 accessions at the Canadian Clonal Genebank. Approximately 3,200 ha are devoted to peach cultivation in Canada where Ontario Province accounts for 82% of the national production. The clonal peach accessions, also located in Ontario, are monitored routinely for symptoms of phytoplasma infection, including rosette-like symptoms (3) that are characterized by new shoots with very short internodes, loss of older shoot leaves leaving only bunches of young leaves on the tips of naked shoots, and flowers that rarely set fruit. From June to August 2009, peach accessions PRU0382 and PRU0445 showed typical peach rosette symptoms, while another 14 accessions exhibited either short internodes or no symptoms. Leaf midrib samples were collected from 16 peach accessions, including 17 symptomatic (from which 8 corresponded to accession PRU0382, 6 for PRU0445, 1 for PRU0335, 1 for PRU0179, and 1 for PRU0451) and 16 asymptomatic (from which 5 corresponded to a representative of each accession PRU0382, PRU0445, PRU0335, PRU0179, and PRU0451 and 11 to other peach accessions). Total DNA was extracted (DNeasy Plant Extraction Mini Kit, QIAGEN, Valencia, CA) from 100 mg of each sample and used as a template in a nested PCR with phytoplasma universal primers R16mF2/R1 (1) and fU5/rU3 (2). Nested PCR products of the expected size (~880 bp) were obtained from all symptomatic samples (14 of 14) of accessions PRU0382 (peach-almond cv. Kando from the Czech Republic) and PRU0445 (peach cv. HW271 from Canada) only. All other plants with or without symptoms yielded no PCR products. Amplicons were purified (Wizard PCR Clean-up, Promega, Madison, WI), cloned in pGEM-T Easy Vector (Promega), and sequenced (Robarts Institute, London, Canada). The resulting 16S rDNA sequences were identical; one of each was archived in GenBank as Accession No. GU223904. BLAST analysis determined that the P. persica phytoplasma sequence shared 99% identity with 16S rDNA sequences of ‘Candidatus Phytoplasma asteris’-related strains. This relationship was also supported by restriction fragment length polymorphism analysis (RFLP) of rDNA amplicons using AluI, RsaI, and MseI endonucleases that yielded fragment profiles indicative of phytoplasmas belonging to group 16SrI (Aster Yellows), subgroup B (16SrI-B). Among phytoplasma diseases, those attributed to group 16SrI strains are most numerous and affect the widest plant host range. They include peach rosette in the United States and Europe (3) as well as diseases of various horticultural crops in Canada, including grapevine (4). To our knowledge, this is the first report of a subgroup 16SrI-B phytoplasma affecting peach in Canada. Early detection of phytoplasmas by PCR in accessions with both European and Canadian origins underscores the importance of prompt identification of infected plants for subsequent thermotherapy treatment to maintain the health of the collection and prevent further disease spread. References: (1) D. E Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:1441, 1996. (2) K. H. Lorenz et al. Phytopathology 85:771, 1995. (3) C. Marcone et al. Acta Hortic. 386:471, 1995. (4) C. Y. Olivier et al. Plant Dis. 93:669, 2009.

scholarly journals CDC Group IV c-2: a New RalstoniaSpecies Close to Ralstonia eutropha

1999 ◽  
Vol 37 (6) ◽  
pp. 1777-1781 ◽  
Author(s):  
Didier Moissenet ◽  
Christophe P. Goujon ◽  
Antoine Garbarg-Chenon ◽  
Hoang Vu-Thien
Keyword(s):  
16S Rdna ◽  
Biochemical Characterization ◽  
Ralstonia Eutropha ◽  
Rapd Analysis ◽  
Group Iv ◽  
Clinical Isolates ◽  
Rdna Sequences ◽  
Rdna Sequencing ◽  
16S Rdna Sequences ◽  
Type Strains

CDC group IV c-2, an environmental gram-negative bacillus recently proposed for inclusion in the genus Ralstonia, has been isolated in several human infections. Biochemical characterization and 16S ribosomal DNA (rDNA) sequencing with phylogenetic analysis were used to characterize eight clinical isolates and four type strains. Other typing tools, such as pulsed-field gel electrophoresis (PFGE) and randomly amplified polymorphic DNA (RAPD) analysis, were also used. PFGE typing of clinical isolates was unsuccessful because the DNA was degraded, and RAPD analysis was poorly discriminatory. In contrast, the type strains were clearly distinguished with both PFGE and RAPD analysis. All of the 16S rDNA sequences were identical. Comparison of the 16S rDNA sequences to the GenBank sequences showed that they were consistent with CDC group IV c-2 belonging to the genusRalstonia. The closest matches were obtained withRalstonia eutropha. However, four differences in 32 biochemical tests separated R. eutropha from CDC group IV c-2, which suggests that CDC group IV c-2 is a new species of the genusRalstonia.

scholarly journals Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae

2004 ◽  
Vol 54 (3) ◽  
pp. 857-864 ◽  
Author(s):  
Wietse de Boer ◽  
Johan H. J. Leveau ◽  
George A. Kowalchuk ◽  
Paulien J. A. Klein Gunnewiek ◽  
Edwin C. A. Abeln ◽  
...  
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Biochemical Properties ◽  
Phylogenetic Position ◽  
Strictly Aerobic ◽  
Novel Genus ◽  
Physiological Characterization ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Wide Range

A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These isolates, which were found in slightly acidic dune soils in the Netherlands, were strictly aerobic, Gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili. A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. DNA G+C contents were 57–62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (>98·6 % sequence similarity) and could be assigned to the β-Proteobacteria, family ‘Oxalobacteraceae’, order ‘Burkholderiales’. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiting 95·9–96·7 % (Herbaspirillum species) and 94·3–95·6 % (Janthinobacterium species) 16S rDNA sequence similarity to the isolates. Several physiological and biochemical properties indicated that the isolates could be distinguished clearly from both of these genera. Therefore, it is proposed that the isolates described in this study are representatives of a novel genus, Collimonas gen. nov. Genomic fingerprinting (BOX-PCR), detailed analysis of 16S rDNA patterns and physiological characterization (Biolog) of the isolates revealed the existence of four subclusters. The name Collimonas fungivorans gen. nov., sp. nov. has been given to one subcluster (four isolates) that appears to be in the centre of the novel genus; isolates in the other subclusters have been tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6T (=NCCB 100033T=LMG 21973T).

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