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Journal articles on the topic '16S rDNA'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Fessehaie, A., S. H. De Boer, and C. A. Lévesque. "Molecular characterization of DNA encoding 16S23S rRNA intergenic spacer regions and 16S rRNA of pectolyticErwiniaspecies." Canadian Journal of Microbiology 48, no. 5 (2002): 387–98. http://dx.doi.org/10.1139/w02-026.

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Sequences of 16S rDNAs and the intergenic spacer (IGS) regions between the 16S and 23S rDNA of bacterial strains from genus Erwinia were determined. Comparison of 16S rDNA sequences from different species and subspecies clearly revealed intraspeciessubspecies homology and interspecies heterogeneity. Phylogenetic analyses of 16S rDNA sequence data revealed that Erwinia spp. formed a discrete monophyletic clade with moderate to high bootstrap values. PCR amplification of the 16S23S rDNA regions using primers complementary to the 3' end of 16S and 5' end of 23S rRNA genes generated two DNA frag

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2

Fukatsu, Takema, and Naruo Nikoh. "Two Intracellular Symbiotic Bacteria from the Mulberry Psyllid Anomoneura mori (Insecta, Homoptera)." Applied and Environmental Microbiology 64, no. 10 (1998): 3599–606. http://dx.doi.org/10.1128/aem.64.10.3599-3606.1998.

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ABSTRACT We characterized the intracellular symbiotic bacteria of the mulberry psyllid Anomoneura mori by performing a molecular phylogenetic analysis combined with in situ hybridization. In its abdomen, the psyllid has a large, yellow, bilobed mycetome (or bacteriome) which consists of many round uninucleated mycetocytes (or bacteriocytes) enclosing syncytial tissue. The mycetocytes and syncytium harbor specific intracellular bacteria, the X-symbionts and Y-symbionts, respectively. Almost the entire length of the bacterial 16S ribosomal DNA (rDNA) was amplified and cloned from the whole DNA o

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3

Wang, Haiyin, Pengcheng Du, Juan Li, et al. "Comparative analysis of microbiome between accurately identified 16S rDNA and quantified bacteria in simulated samples." Journal of Medical Microbiology 63, no. 3 (2014): 433–40. http://dx.doi.org/10.1099/jmm.0.060616-0.

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Although 16S rRNA gene (rDNA) sequencing is the gold standard for categorizing bacteria or characterizing microbial communities its clinical utility is limited by bias in metagenomic studies, in either the experiments or the data analyses. To evaluate the efficiency of current metagenomic methods, we sequenced seven simulated samples of ten bacterial species mixed at different concentrations. The V3 region of 16S rDNA was targeted and used to determine the distribution of bacterial species. The number of target sequences in individual simulated samples was in the range 1–1000 to provide a bett

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4

Riley, Donald E., Richard E. Berger, David C. Miner, and John N. Krieger. "Diverse and Related 16S rRNA-Encoding DNA Sequences in Prostate Tissues of Men with Chronic Prostatitis." Journal of Clinical Microbiology 36, no. 6 (1998): 1646–52. http://dx.doi.org/10.1128/jcm.36.6.1646-1652.1998.

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Treatment of chronic prostatitis/chronic pelvic pain syndrome is often empirical because clinical culture methods fail to detect prostate-associated pathogens in >90% of patients. Previously, we tested a variety of specific-microorganism PCRs and began a DNA sequence study after we found that 77% of prostatitis patients were PCR positive for prokaryotic rRNA-encoding DNA sequences (rDNAs) despite negative cultures using optimal techniques. In the present study, 36 rDNA clones from 23 rDNA-positive patients were sequenced. This study represents more than twice the total rDNA sequence and mor

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5

Dahllöf, Ingela, Harriet Baillie, and Staffan Kjelleberg. "rpoB-Based Microbial Community Analysis Avoids Limitations Inherent in 16S rRNA Gene Intraspecies Heterogeneity." Applied and Environmental Microbiology 66, no. 8 (2000): 3376–80. http://dx.doi.org/10.1128/aem.66.8.3376-3380.2000.

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ABSTRACT Contemporary microbial community analysis frequently involves PCR-amplified sequences of the 16S rRNA gene (rDNA). However, this technology carries the inherent problem of heterogeneity between copies of the 16S rDNA in many species. As an alternative to 16S rDNA sequences in community analysis, we employed the gene for the RNA polymerase beta subunit (rpoB), which appears to exist in one copy only in bacteria. In the present study, the frequency of 16S rDNA heterogeneity in bacteria isolated from the marine environment was assessed using bacterial isolates from the red alga Delisea p

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6

Reischl, U., K. Feldmann, L. Naumann, et al. "16S rRNA Sequence Diversity in Mycobacterium celatum Strains Caused by Presence of Two Different Copies of 16S rRNA Gene." Journal of Clinical Microbiology 36, no. 6 (1998): 1761–64. http://dx.doi.org/10.1128/jcm.36.6.1761-1764.1998.

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Direct sequencing of the 16S rRNA gene (16S rDNA) ofMycobacterium 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.

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BAO, Qiongli, Long-Jun DING, Yizong HUANG, and Keqing XIAO. "Effect of rice straw and/or nitrogen fertiliser inputs on methanogenic archaeal and denitrifying communities in a typical rice paddy soil." Earth and Environmental Science Transactions of the Royal Society of Edinburgh 109, no. 3-4 (2018): 375–86. http://dx.doi.org/10.1017/s1755691018000580.

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ABSTRACTTo understand better the microbial functional populations which are involved in methanogenesis and denitrification in paddy soils with rice straw (RS) and/or nitrogen fertiliser (potassium nitrate, N) application, the dynamics of methanogens and the denitrifying community were monitored simultaneously during the incubation period. The results show that the community structure of methanogens remained relatively stable among treatments based on 16S rDNA analysis, but fluctuated based on 16S rRNA. The Methanocellaceae and Methanosarcinaceae dominated all treatments at 16S rDNA and 16S rRN

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8

Lamy, Brigitte, Fréderic Laurent, and Angeli Kodjo. "Validation of a partialrpoBgene sequence as a tool for phylogenetic identification of aeromonads isolated from environmental sources." Canadian Journal of Microbiology 56, no. 3 (2010): 217–28. http://dx.doi.org/10.1139/w10-006.

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A collection of 50 aeromonads isolated from environmental sources were studied, together with all known Aeromonas nomenspecies, by phenotypic, amplified 16S rDNA restriction analysis (16S rDNA RFLP) and by partial sequence alignment of both 16S rDNA and rpoB genes. Although most of the type strain showed a unique phenotypic pattern, a database constructed on type strain phenotype allowed the identification of only 24% of the isolates. Analysis of 16S rDNA RFLP and the rpoB sequence were almost concordant in identifying environmental isolates at the species level, except for strains belonging t

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9

Hashavya, S., I. Gross, A. Michael-Gayego, N. Simanovsky, and R. Lamdan. "The efficacy of 16S ribosomal DNA sequencing in the diagnosis of bacteria from blood, bone and synovial fluid samples of children with musculoskeletal infections." Journal of Children's Orthopaedics 12, no. 2 (2018): 204–8. http://dx.doi.org/10.1302/1863-2548.12.170049.

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Background Musculoskeletal infections are among the most common bacterial infections in children leading to hospitalization, invasive procedures and prolonged antibiotic administration. Blood, synovial and sometimes tissue cultures are essential for the diagnosis and treatment of musculoskeletal infections; 16S ribosomal DNA (rDNA) sequencing is a novel diagnostic tool for the detection of bacteria. While the yield of 16S rDNA sequencing in synovial fluid was previously assessed, data regarding the efficacy of this method from blood samples or partially treated children with suspected musculos

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10

Bauernfeind, Adolf, Ines Schneider, Renate Jungwirth, and Carsten Roller. "Discrimination of Burkholderia multivorans and Burkholderia vietnamiensis fromBurkholderia cepacia Genomovars I, III, and IV by PCR." Journal of Clinical Microbiology 37, no. 5 (1999): 1335–39. http://dx.doi.org/10.1128/jcm.37.5.1335-1339.1999.

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We present a PCR procedure for identification of Burkholderia cepacia, Burkholderia multivorans, andBurkholderia vietnamiensis. 16S and 23S ribosomal DNAs (rDNAs) of B. multivorans and B. vietnamiensiswere sequenced and aligned with published sequences for definition of species-specific 18-mer oligonucleotide primers. Specific antisense 16S rDNA primers (for B. cepacia, 5′-AGC ACT CCC RCC TCT CAG-3′; for B. multivorans, 5′-AGC ACT CCC GAA TCT CTT-3′) and 23S rDNA primers (for B. vietnamiensis, 5′-TCC TAC CAT GCG TGC AA-3′) were paired with a general sense primer of 16S rDNAs (5′-AGR GTT YGA TY

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11

O'Donnell, Anthony G., and Heike E. Görres. "16S rDNA methods in soil microbiology." Current Opinion in Biotechnology 10, no. 3 (1999): 225–29. http://dx.doi.org/10.1016/s0958-1669(99)80039-1.

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12

Asil, A., No author No author, S. Sanousi, et al. "Molecular identification of nontuberculous mycobacteria isolated from pyogenic bovine tissues in South Darfur State and Alsabalouga slaughterhouse at Omdurman area, Sudan." Open Veterinary Journal 5, no. 2 (2014): 16. http://dx.doi.org/10.5455/ovj.2014.v4.i1.p16.

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This study identified nontuberculous mycobacteria (NTM) recovered from bovine pyogenic affections obtained at necropsy using the molecular target 16S-23S rDNA internal transcribed spacer region. Postmortem inspection of cattle was conducted at South Darfur State abattoirs and Alsabalouga Slaughterhouse at Omdurman area during 2007-2009. Specimens were examined for the presence of acid fast bacteria (AFB) using microscopic and standard culturing techniques. AFB were identified phenotypically and confirmed by 16S-23S rDNA ITS. Fifty nine NTM were recovered and confirmed as acid fast filaments ou

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13

Rodríguez-García, Raquel, María Ángeles Rodríguez-Esteban, Jonathan Fernández-Suárez, et al. "Evaluation of 16S rDNA Heart Tissue PCR as a Complement to Blood Cultures for the Routine Etiological Diagnosis of Infective Endocarditis." Diagnostics 11, no. 8 (2021): 1372. http://dx.doi.org/10.3390/diagnostics11081372.

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Identification of the causative pathogen is required to optimize the effective therapy in infective endocarditis (IE). The aim of this study was to assess a 16S rDNA PCR to identify bacteria from heart valve tissues and to evaluate its usefulness as a complement to blood and removed valves cultures. A total of 266 patients diagnosed with IE from January 2015 to December 2019 were evaluated. Results between 16S rDNA PCR from heart valve tissues were compared with microbiological cultures. Blood cultures were positive in 83.5% of patients diagnosed with IE, while 39.6% and 71.8% of the evaluated

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14

Drancourt, Michel, Claude Bollet, Antoine Carlioz, Rolland Martelin, Jean-Pierre Gayral, and Didier Raoult. "16S Ribosomal DNA Sequence Analysis of a Large Collection of Environmental and Clinical Unidentifiable Bacterial Isolates." Journal of Clinical Microbiology 38, no. 10 (2000): 3623–30. http://dx.doi.org/10.1128/jcm.38.10.3623-3630.2000.

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Some bacteria are difficult to identify with phenotypic identification schemes commonly used outside reference laboratories. 16S ribosomal DNA (rDNA)-based identification of bacteria potentially offers a useful alternative when phenotypic characterization methods fail. However, as yet, the usefulness of 16S rDNA sequence analysis in the identification of conventionally unidentifiable isolates has not been evaluated with a large collection of isolates. In this study, we evaluated the utility of 16S rDNA sequencing as a means to identify a collection of 177 such isolates obtained from environmen

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15

Reinoso, Elina, Silvana Dieser, Luis Calvinho, Cristina Bogni, and Liliana Odierno. "Phenotyping and genotyping of streptococci in bovine milk in Argentinean dairy herds." Acta Veterinaria Hungarica 58, no. 3 (2010): 287–95. http://dx.doi.org/10.1556/avet.58.2010.3.2.

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Most veterinary and milk hygiene laboratories identify streptococci and enterococci based on serological and biochemical tests. The analysis of 16S rDNA was suggested to be used for more exact identification; however, its use has not been considered so far in monitoring studies. The objective of the present study was to compare a conventional phenotypic method with restriction fragment length polymorphism analysis of 16S rDNA (16S rDNA RFLP) for identification of streptococci isolated from composite milk samples collected in connection with intramammary infection (IMI) in six Argentinean dairy

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16

Hinrikson, Hans Peter, Fabrizio Dutly, and Martin Altwegg. "Homogeneity of 16S-23S Ribosomal Intergenic Spacer Regions of Tropheryma whippelii in Swiss Patients with Whipple’s Disease." Journal of Clinical Microbiology 37, no. 1 (1999): 152–56. http://dx.doi.org/10.1128/jcm.37.1.152-156.1999.

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The current genetic strategies used to identify Tropheryma whippelii, the putative agent of Whipple’s disease, are based on PCR-mediated amplification of a part of its 16S rRNA gene (16S rDNA). Because there is very little intraspecies variation in these molecules, they are not suitable as targets for epidemiologic investigations. However, the intergenic spacer region between the 16S and 23S rDNAs is usually much more variable and has repeatedly been used for epidemiologic purposes. We have therefore amplified the spacer region of T. whippelii directly from clinical specimens from nine indepen

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17

Prüß, Birgit M., Kevin P. Francis, Felix von Stetten, and Siegfried Scherer. "Correlation of 16S Ribosomal DNA Signature Sequences with Temperature-Dependent Growth Rates of Mesophilic and Psychrotolerant Strains of the Bacillus cereusGroup." Journal of Bacteriology 181, no. 8 (1999): 2624–30. http://dx.doi.org/10.1128/jb.181.8.2624-2630.1999.

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ABSTRACT Sequences of the 16S ribosomal DNA (rDNA) from psychrotolerant and mesophilic strains of the Bacillus cereus group revealed signatures which were specific for these two thermal groups of bacteria. Further analysis of the genomic DNA from a wide range of food and soil isolates showed that B. cereus group strains have between 6 and 10 copies of 16S rDNA. Moreover, a number of these environmental strains have both rDNA operons with psychrotolerant signatures and rDNA operons with mesophilic signatures. The ability of these isolates to grow at low temperatures correlates with the prevalen

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18

Delbès, C., M. Leclerc, E. Zumstein, J. J. Godon, and R. Moletta. "A molecular method to study population and activity dynamics in anaerobic digestors." Water Science and Technology 43, no. 1 (2001): 51–57. http://dx.doi.org/10.2166/wst.2001.0013.

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The applicability of a new molecular fingerprinting method (Single Strand Conformation Polymorphism) to study the microbial populations of anaerobic digestors was investigated. After extraction of total nucleic acids, the 16S rDNA and 16S rRNA molecules were amplified and the amplicons were separated by SSCP electrophoresis. Characteristic and complex peak patterns were obtained, where each peak could be correlated with the 16S rDNA sequence of one micro-organism. The rDNA peak patterns should consist of the most abundant sequences and thus would reflect the diversity of prominent species of d

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19

Grahn, Niclas, Mounira Hmani-Aifa, Karin Fransén, Peter Söderkvist, and Hans-Jürg Monstein. "Molecular identification of Helicobacter DNA present in human colorectal adenocarcinomas by 16S rDNA PCR amplification and pyrosequencing analysis." Journal of Medical Microbiology 54, no. 11 (2005): 1031–35. http://dx.doi.org/10.1099/jmm.0.46122-0.

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Seroepidemiological studies have indicated that Helicobacter pylori infection might be a possible risk factor for colorectal adenocarcinoma (CRC) development. However, limited information is available as to whether or not Helicobacter species are present in CRC tissues. In this study the presence of Helicobacter DNA in 77 CRC biopsies was investigated by means of a Helicobacter species-specific 16S rDNA PCR assay and real-time DNA pyrosequencing of the 16S rDNA variable V3 region. Pyrosequencing revealed the presence of Helicobacter DNA sequences in 21 of 77 biopsy specimens (27 %). 16S rDNA s

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20

Lange, Carla C., Maria A. V. P. Brito, José R. F. Brito, et al. "Uso de PCR e sequenciamento do rDNA 16S para identificação de bactérias do gênero Staphylococcus isoladas de mastite bovina." Pesquisa Veterinária Brasileira 31, no. 1 (2011): 36–40. http://dx.doi.org/10.1590/s0100-736x2011000100006.

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O objetivo deste trabalho foi identificar espécies de Staphylococcus (n=100) isoladas de mastite em rebanhos bovinos do Estado de Minas Gerais. Para esta finalidade foram utilizadas reações de PCR empregando oligonucleotídeos iniciadores descritos anteriormente para amplificar genes específicos de S. aureus (femA), S. intermedius (rDNA 16S) e S. hyicus (rDNA 16S-23S) e o sequenciamento do rDNA 16S. De acordo com as reações de PCR, 83 isolados foram identificados como S. aureus, 13 isolados como S. intermedius, dois como S. hyicus e dois isolados não foram identificados. Foram submetidos ao seq

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Björnsson, Lovisa, Philip Hugenholtz, Gene W. Tyson, and Linda L. Blackall. "Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal c cThe EMBL accession numbers for the sequences reported in this paper are X84472 (strain SBR1029 16S rDNA), X84474 (strain SBR1031 16S rDNA), X84498 (strain SBR1064 16S rDNA), X84565 (strain SBR2022 16S rDNA), X84576 (strain SBR2037 16S rDNA) and X84607 (strain SBR2076 16S rDNA)." Microbiology 148, no. 8 (2002): 2309–18. http://dx.doi.org/10.1099/00221287-148-8-2309.

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22

Devloo-Delva, Floriaan, Roger Huerlimann, Gladys Chua, et al. "How does marker choice affect your diet analysis: comparing genetic markers and digestion levels for diet metabarcoding of tropical-reef piscivores." Marine and Freshwater Research 70, no. 1 (2019): 8. http://dx.doi.org/10.1071/mf17209.

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Tropical reefs are highly diverse ecosystems, and reliable biomonitoring, through diet metabarcoding, is needed to understand present and future trophic relationships in this changing habitat. Several studies have assessed the reliability and effectiveness of single molecular markers; however, a cross-marker validation has rarely been performed. This study identified crucial properties for 12S rDNA, 16S rDNA and COI metabarcoding in tropical-reef piscivores (Plectropomus spp.). In addition, three new versatile primer sets for 16S were designed in silico for metabarcoding of reef fish. Results

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23

Heuer, Holger, Kathrin Hartung, Gabriele Wieland, Ina Kramer, and Kornelia Smalla. "Polynucleotide Probes That Target a Hypervariable Region of 16S rRNA Genes To Identify Bacterial Isolates Corresponding to Bands of Community Fingerprints." Applied and Environmental Microbiology 65, no. 3 (1999): 1045–49. http://dx.doi.org/10.1128/aem.65.3.1045-1049.1999.

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ABSTRACT Temperature gradient gel electrophoresis (TGGE) is well suited for fingerprinting bacterial communities by separating PCR-amplified fragments of 16S rRNA genes (16S ribosomal DNA [rDNA]). A strategy was developed and was generally applicable for linking 16S rDNA from community fingerprints to pure culture isolates from the same habitat. For this, digoxigenin-labeled polynucleotide probes were generated by PCR, using bands excised from TGGE community fingerprints as a template, and applied in hybridizations with dot blotted 16S rDNA amplified from bacterial isolates. Within 16S rDNA, t

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Chatellier, Sonia, Nathalie Mugnier, Françoise Allard, et al. "Comparison of two approaches for the classification of 16S rRNA gene sequences." Journal of Medical Microbiology 63, no. 10 (2014): 1311–15. http://dx.doi.org/10.1099/jmm.0.074377-0.

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The use of 16S rRNA gene sequences for microbial identification in clinical microbiology is accepted widely, and requires databases and algorithms. We compared a new research database containing curated 16S rRNA gene sequences in combination with the lca (lowest common ancestor) algorithm (RDB-LCA) to a commercially available 16S rDNA Centroid approach. We used 1025 bacterial isolates characterized by biochemistry, matrix-assisted laser desorption/ionization time-of-flight MS and 16S rDNA sequencing. Nearly 80 % of isolates were identified unambiguously at the species level by both classificat

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MOHAMMED-GEBA, KHALED, EMAN M. ABBAS, HAMDY O. AHMED, et al. "Comparing genetic markers’ efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori." Zootaxa 5092, no. 5 (2022): 559–75. http://dx.doi.org/10.11646/zootaxa.5092.5.4.

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Sea cucumber (bêche-de-mer, Echinodermata: Holothuroidea) is one of the top internationally traded seafood varieties. Besides its direct nutritional benefits, it is continuously used in the traditional medicine in different areas and cultures in the world. This world-wide interest triggered various issues related to stocks´ declining and risks of species extinction. For these reasons, the current study was designed to provide molecular tools for accurate discrimination between two sea cucumber species that prevail the Mediterranean of these echinoderms in Egypt, that are Holothuria polii and H

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Marcone, Carmine, Bernd Schneider, and Erich Seemüller. "‘Candidatus Phytoplasma cynodontis’, the phytoplasma associated with Bermuda grass white leaf disease." International Journal of Systematic and Evolutionary Microbiology 54, no. 4 (2004): 1077–82. http://dx.doi.org/10.1099/ijs.0.02837-0.

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Bermuda grass white leaf (BGWL) is a destructive, phytoplasmal disease of Bermuda grass (Cynodon dactylon). The causal pathogen, the BGWL agent, differs from other phytoplasmas that cluster in the same major branch of the phytoplasma phylogenetic clade in <2·5 % of 16S rDNA nucleotide positions, the threshold for assigning species rank to phytoplasmas under the provisional status ‘Candidatus’. Thus, the objective of this work was to examine homogeneity of BGWL isolates and to determine whether there are, in addition to 16S rDNA, other markers that support delineation of the BGWL agent at th

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Allen, Julie M., J. Gordon Burleigh, Jessica E. Light, and David L. Reed. "Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice." PeerJ 4 (July 19, 2016): e2187. http://dx.doi.org/10.7717/peerj.2187.

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Phylogenetic trees can reveal the origins of endosymbiotic lineages of bacteria and detect patterns of co-evolution with their hosts. Although taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships are based on few available bacterial sequences. Here we examined how different sampling strategies ofGammaproteobacteriasequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and

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Satokari, Reetta M., Elaine E. Vaughan, Antoon D. L. Akkermans, Maria Saarela, and Willem M. de Vos. "Bifidobacterial Diversity in Human Feces Detected by Genus-Specific PCR and Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 67, no. 2 (2001): 504–13. http://dx.doi.org/10.1128/aem.67.2.504-513.2001.

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ABSTRACT We describe the development and validation of a method for the qualitative analysis of complex bifidobacterial communities based on PCR and denaturing gradient gel electrophoresis (DGGE).Bifidobacterium genus-specific primers were used to amplify an approximately 520-bp fragment from the 16S ribosomal DNA (rDNA), and the fragments were separated in a sequence-specific manner in DGGE. PCR products of the same length from different bifidobacterial species showed good separation upon DGGE. DGGE of fecal 16S rDNA amplicons from five adult individuals showed host-specific populations of bi

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Patel, Amani, Kathryn A. Harris, and Felicity Fitzgerald. "What is broad-range 16S rDNA PCR?" Archives of disease in childhood - Education & practice edition 102, no. 5 (2017): 261–64. http://dx.doi.org/10.1136/archdischild-2016-312049.

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Gosalbes, M. J., J. J. Abellan, A. Durban, A. E. Perez-Cobas, A. Latorre, and A. Moya. "Metagenomics of human microbiome: beyond 16s rDNA." Clinical Microbiology and Infection 18 (July 2012): 47–49. http://dx.doi.org/10.1111/j.1469-0691.2012.03865.x.

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Grady, Ruth, Michael Anderson, David Drucker, and David Denning. "Partial 16S rDNA analysis of oral Treponema." Reviews in Medical Microbiology 8 (1997): S25. http://dx.doi.org/10.1097/00013542-199712001-00012.

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Ruiz, A., M. Poblet, A. Mas, and J. M. Guillamón. "Identification of acetic acid bacteria by RFLP of PCR-amplified 16S rDNA and 16S-23S rDNA intergenic spacer." International Journal of Systematic and Evolutionary Microbiology 50, no. 6 (2000): 1981–87. http://dx.doi.org/10.1099/00207713-50-6-1981.

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Subandiyah, Siti, Toru Iwanami, Shinji Tsuyumu, and Hiroyuki Ieki. "Comparison of 16S rDNA and 16S/23S Intergenic Region Sequences Among Citrus Greening Organisms in Asia." Plant Disease 84, no. 1 (2000): 15–18. http://dx.doi.org/10.1094/pdis.2000.84.1.15.

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Polymerase chain reaction was used to amplify and sequence the 16S ribosomal RNA gene (rDNA) and 16S/23S intergenic region of several isolates of citrus greening organism (GO) from Japan, the Philippines, Indonesia, and Thailand. The sequences of 16S rDNA were identical among all the isolates studied, very similar to the published sequences of Thai (99.4 to 100% identity), Nepalese (100% identity), and Indian (98.8% identity) strains, and less similar to an African strain (97.5% identity). The sequences of the intergenic region between 16S and 23S rDNA were also identical among the isolates ex

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Wood, Jacqueline, Karen P. Scott, Gorazd Avguštin, C. James Newbold, and Harry J. Flint. "Estimation of the Relative Abundance of DifferentBacteroides and Prevotella Ribotypes in Gut Samples by Restriction Enzyme Profiling of PCR-Amplified 16S rRNA Gene Sequences." Applied and Environmental Microbiology 64, no. 10 (1998): 3683–89. http://dx.doi.org/10.1128/aem.64.10.3683-3689.1998.

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ABSTRACT We describe an approach for determining the genetic composition ofBacteroides and Prevotellapopulations in gut contents based on selective amplification of 16S rRNA gene sequences (rDNA) followed by cleavage of the amplified material with restriction enzymes. The relative contributions of different ribotypes to total Bacteroides andPrevotella 16S rDNA are estimated after end labelling of one of the PCR primers, and the contribution ofBacteroides and Prevotellasequences to total eubacterial 16S rDNA is estimated by measuring the binding of oligonucleotide probes to amplified DNA.Bacter

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Ritchie, Nancy J., and David D. Myrold. "Phylogenetic placement of unculturedCeanothusmicrosymbionts using 16S rRNA gene sequences." Canadian Journal of Botany 77, no. 9 (1999): 1208–13. http://dx.doi.org/10.1139/b99-080.

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Full-length 16S rDNA sequences were amplified directly from the nodules of Ceanothus americanus L. and Ceanothus thyrsiflorus Eschsch. using the polymerase chain reaction. Sequences were determined using an automated sequencer, compared against those in GenBank, and assembled into consensus sequences. The sequences were aligned with other full-length Frankia 16S rDNA sequences available from the data base. Phylogenetic trees were obtained using three different algorithms: neighbor joining, parsimony, and the maximum-likelihood method. All three methods showed that these Ceanothus L. microsymbi

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Zoetendal, Erwin G., Antoon D. L. Akkermans, and Willem M. De Vos. "Temperature Gradient Gel Electrophoresis Analysis of 16S rRNA from Human Fecal Samples Reveals Stable and Host-Specific Communities of Active Bacteria." Applied and Environmental Microbiology 64, no. 10 (1998): 3854–59. http://dx.doi.org/10.1128/aem.64.10.3854-3859.1998.

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ABSTRACT The diversity of the predominant bacteria in the human gastrointestinal tract was studied by using 16S rRNA-based approaches. PCR amplicons of the V6 to V8 regions of fecal 16S rRNA and ribosomal DNA (rDNA) were analyzed by temperature gradient gel electrophoresis (TGGE). TGGE of fecal 16S rDNA amplicons from 16 individuals showed different profiles, with some bands in common. Fecal samples from two individuals were monitored over time and showed remarkably stable profiles over a period of at least 6 months. TGGE profiles derived from 16S rRNA and rDNA amplicons showed similar banding

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Li, Yong Feng, Yi Xuan Wang, Lu Wang, and Zhan Qing Wang. "Sequence Length Variation of Internal Genic Space of 16S rDNA-23S rDNA in Bacterium with High Yield of Hydrogen Production." Advanced Materials Research 183-185 (January 2011): 1413–16. http://dx.doi.org/10.4028/www.scientific.net/amr.183-185.1413.

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To develop the identification of species for fermentative biohydrogen-producing bacterium, scholars have found a method which is based on PCR amplification of the 16S rRNA gene (rDNA)-23S rDNA intergenic regions. In the study, a large fragment of the rDNA operon, including the 16S rDNA, the intergenic spacer region (ISR) and approximately 2000 bases of the 23S rDNA, were polymerasechain reaction (PCR) amplified. The PCR amplification of the genomic DNA of Leptonema ilk strain 3055 using primers directed against conserved regions of the rRNA operon provided evidence that the 16S and 23S rRNA ge

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Robinson, K. G., H. M. Dionisi, G. Harms, A. C. Layton, I. R. Gregory, and G. S. Sayler. "Molecular assessment of ammonia- and nitrite-oxidizing bacteria in full-scale activated sludge wastewater treatment plants." Water Science and Technology 48, no. 8 (2003): 119–26. http://dx.doi.org/10.2166/wst.2003.0460.

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Nitrification was assessed in two full-scale wastewater treatment plants (WWTPs) over time using molecular methods. Both WWTPs employed a complete-mix suspended growth, aerobic activated sludge process (with biomass recycle) for combined carbon and nitrogen treatment. However, one facility treated primarily municipal wastewater while the other only industrial wastewater. Real time PCR assays were developed to determine copy numbers for total 16S rDNA (a measure of biomass content), the amoA gene (a measure of ammonia-oxidizers), and the Nitrospira 16S rDNA gene (a measure of nitrite-oxidizers)

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Tanner, Michael A., Brett M. Goebel, Michael A. Dojka, and Norman R. Pace. "Specific Ribosomal DNA Sequences from Diverse Environmental Settings Correlate with Experimental Contaminants." Applied and Environmental Microbiology 64, no. 8 (1998): 3110–13. http://dx.doi.org/10.1128/aem.64.8.3110-3113.1998.

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ABSTRACT Phylogenetic analysis of 16S ribosomal DNA (rDNA) clones obtained by PCR from uncultured bacteria inhabiting a wide range of environments has increased our knowledge of bacterial diversity. One possible problem in the assessment of bacterial diversity based on sequence information is that PCR is exquisitely sensitive to contaminating 16S rDNA. This raises the possibility that some putative environmental rRNA sequences in fact correspond to contaminant sequences. To document potential contaminants, we cloned and sequenced PCR-amplified 16S rDNA fragments obtained at low levels in the a

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Texeira, D. C., J. Ayres, E. W. Kitajima, et al. "First Report of a Huanglongbing-Like Disease of Citrus in Sao Paulo State, Brazil and Association of a New Liberibacter Species, “Candidatus Liberibacter americanus”, with the Disease." Plant Disease 89, no. 1 (2005): 107. http://dx.doi.org/10.1094/pd-89-0107a.

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Huanglongbing (HLB) (ex-greening) is one of the most serious diseases of citrus. The causal agent is a noncultured, sieve tube-restricted α-proteobacterium, “Candidatus Liberibacter africanus” in Africa and “Candidatus Liberibacter asiaticus” in Asia (2). The disease has never been reported from the American continent. However, Diaphorina citri, the Asian psyllid vector of HLB, is found in South, Central, and North America (Florida and Texas). Early in 2004, leaf and fruit symptoms resembling those of HLB were observed in several sweet orange orchards near the city of Araraquara, Sao Paulo Sta

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Ramírez-Saad, Hugo, Jaap D. Janse, and Antoon DL Akkermans. "Root nodules ofCeanothus caeruleuscontain both the N2-fixingFrankiaendophyte and a phylogetically related Nod-/Fix-actinomycete." Canadian Journal of Microbiology 44, no. 2 (1998): 140–48. http://dx.doi.org/10.1139/w97-138.

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Attempts to isolate the N2-fixing endophyte of Ceanothus caeruleus (Rhamnaceae) root nodules, led to the isolation of nine actinomycetous strains. Owing to their inability to fix nitrogen (Fix-) and nodulate (Nod-), they could not be regarded as the effective endophyte. Characterization was done based on morphological and physiological features and 16S rDNA sequence analysis. The effective Frankia endophyte was characterized without cultivation by amplification, cloning, and sequencing of nearly full length 16S rDNA and partial nifH genes. Phylogenetic analysis based on 16S rDNA revealed that

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BjÃ¯Â¿Â½rkroth, K. Johanna, Rolf Geisen, Ulrich Schillinger, et al. "Characterization of Leuconostoc gasicomitatum sp. nov., Associated with Spoiled Raw Tomato-Marinated Broiler Meat Strips Packaged under Modified-Atmosphere Conditions." Applied and Environmental Microbiology 66, no. 9 (2000): 3764–72. http://dx.doi.org/10.1128/aem.66.9.3764-3772.2000.

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ABSTRACT Lactic acid bacteria (LAB) associated with gaseous spoilage of modified-atmosphere-packaged, raw, tomato-marinated broiler meat strips were identified on the basis of a restriction fragment length polymorphism (RFLP) (ribotyping) database containing DNAs coding for 16S and 23S rRNAs (rDNAs). A mixed LAB population dominated by aLeuconostoc species resembling Leuconostoc gelidum caused the spoilage of the product. Lactobacillus sakei, Lactobacillus curvatus, and a gram-positive rod phenotypically similar to heterofermentativeLactobacillus species were the other main organisms detected.

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Jomantiene, R. R., J. L. Maas, F. Takeda, and R. E. Davis. "Molecular Identification and Classification of Strawberry Phylloid Fruit Phytoplasma in Group 16SrI, New Subgroup." Plant Disease 86, no. 8 (2002): 920. http://dx.doi.org/10.1094/pdis.2002.86.8.920c.

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Plants of commercial strawberry (Fragaria × ananassa Duch., cv. Camarosa) exhibiting extensive fruit phyllody (development of leafy structures from achenes) were observed in a winter greenhouse production facility in West Virginia. In July 2001, 95 dormant, cold-stored plants were purchased from a California strawberry nursery, potted and grown in this West Virginia facility. Five of the plants developed fruits with phylloid growths. These fruits were assessed for phytoplasma infection using nested polymerase chain reactions (PCRs) in which initial ribosomal (r) DNA amplification was primed by

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Fu, Yue, Xiang-Liang Fang, Xin-Hua Wang, Mi Shen, and Yun-Li Xiao. "Corynoneura Winnertz species from Hunan Province, Oriental China, delineated with morphological and 16S rDNA data (Diptera, Chironomidae)." ZooKeys 1082 (January 19, 2022): 87–102. http://dx.doi.org/10.3897/zookeys.1082.73019.

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The genus Corynoneura Winnertz, 1846 from Hunan Province in Oriental China is reviewed. Four new species, C. enormis Fu sp. nov., C. gibbera Fu sp. nov., C. incuria Fu sp. nov., and C. longshanensis Fu sp. nov. are described and illustrated based on adult males. Sequence data from the 16S rDNA gene were used to infer relationships between these species and complement morphological delineation. Sequences from the mitochondrial large ribosomal subunit (16S rDNA) from these species are uploaded to the National Center for Biotechnology Information (NCBI). Relationships were inferred using the Neig

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Fu, Yue, Xiang-Liang Fang, Xin-Hua Wang, Mi Shen, and Yun-Li Xiao. "Corynoneura Winnertz species from Hunan Province, Oriental China, delineated with morphological and 16S rDNA data (Diptera, Chironomidae)." ZooKeys 1082 (January 19, 2022): 87–102. https://doi.org/10.3897/zookeys.1082.73019.

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The genus Corynoneura Winnertz, 1846 from Hunan Province in Oriental China is reviewed. Four new species, C. enormis Fu sp. nov., C. gibbera Fu sp. nov., C. incuria Fu sp. nov., and C. longshanensis Fu sp. nov. are described and illustrated based on adult males. Sequence data from the 16S rDNA gene were used to infer relationships between these species and complement morphological delineation. Sequences from the mitochondrial large ribosomal subunit (16S rDNA) from these species are uploaded to the National Center for Biotechnology Information (NCBI). Relationships were inferred using the Neig

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Janz, V., J. Schoon, C. Morgenstern, et al. "Rapid detection of periprosthetic joint infection using a combination of 16s rDNA polymerase chain reaction and lateral flow immunoassay." Bone & Joint Research 7, no. 1 (2018): 12–19. http://dx.doi.org/10.1302/2046-3758.71.bjr-2017-0103.r2.

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Objectives The objective of this study was to develop a test for the rapid (within 25 minutes) intraoperative detection of bacteria from synovial fluid to diagnose periprosthetic joint infection (PJI). Methods The 16s rDNA test combines a polymerase chain reaction (PCR) for amplification of 16s rDNA with a lateral flow immunoassay in one fully automated system. The synovial fluid of 77 patients undergoing joint aspiration or primary or revision total hip or knee surgery was prospectively collected. The cohort was divided into a proof-of-principle cohort (n = 17) and a validation cohort (n = 60

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Ruta, Christine, Arne Nygren, Vincent Rousset, et al. "Phylogeny of Hesionidae (Aciculata, Polychaeta), assessed from morphology, 18S rDNA, 28S rDNA, 16S rDNA and COI." Zoologica Scripta 36, no. 1 (2007): 99–107. http://dx.doi.org/10.1111/j.1463-6409.2006.00255.x.

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Vinuesa, Pablo, Jan L. W. Rademaker, Frans J. de Bruijn, and Dietrich Werner. "Genotypic Characterization ofBradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing." Applied and Environmental Microbiology 64, no. 6 (1998): 2096–104. http://dx.doi.org/10.1128/aem.64.6.2096-2104.1998.

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ABSTRACT We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers

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Arif, I. A., and H. A. Khan. "Molecular markers for biodiversity analysis of wildlife animals: a brief review." Animal Biodiversity and Conservation 32, no. 1 (2009): 9–17. http://dx.doi.org/10.32800/abc.2009.32.0009.

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Molecular markers are indispensable tools for determining the genetic variation and biodiversity with high levels of accuracy and reproducibility. These markers are mainly classified into two types; mitochondrial and nuclear markers. The widely used mitochondrial DNA markers with decreasing order of conserved sequences are 12S rDNA > 16S rDNA > cytochrome b > control region (CR); thus the 12S rDNA is highly conserved and the CR is highly variable. The most commonly used nuclear markers for DNA fingerprinting include random amplified polymorphic DNA (RAPD), amplified fragment length

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Clawson, Michael L., Jeffrey Gawronski, and David R. Benson. "Dominance ofFrankiastrains in stands ofAlnus incanasubsp.rugosaandMyrica pensylvanica." Canadian Journal of Botany 77, no. 9 (1999): 1203–7. http://dx.doi.org/10.1139/b99-070.

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To address issues of dominance and diversity of Frankia spp. strains, we sequenced 16S rRNA genes from root nodules and strains collected from Alnus incana subsp. rugosa (Du Roi) R.T. Clausen and Myrica pensylvanica Loisel. stands. Of 22 strains isolated previously from A. incana, 16 had the same partial rDNA sequence; the remaining 6 strains composed five additional groups. The groups identified by 16S rDNA analysis corresponded to phenotypic groups established previously by one- and two-dimensional polyacrylamide gel analysis, colony and hyphal morphology, and carbon source utilization patte

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