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Journal articles on the topic '16S rDNA sequencing of E'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Roshni, V. "Bacterial Diversity in Fluoride - Contaminated Soils Using 16S rDNA Sequencing." International Journal of Science and Research (IJSR) 12, no. 11 (2023): 337–40. http://dx.doi.org/10.21275/sr231031141716.

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2

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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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

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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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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Liao, Feng, Yilan Xia, Wenpeng Gu, Xiaoqing Fu, and Bing Yuan. "Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls." PeerJ 11 (November 3, 2023): e16394. http://dx.doi.org/10.7717/peerj.16394.

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Background Shotgun metagenomic and 16S rDNA sequencing are commonly used methods to identify the taxonomic composition of microbial communities. Previously, we analysed the gut microbiota and intestinal pathogenic bacteria configuration of migratory seagulls by using 16S rDNA sequencing and culture methods. Methods To continue in-depth research on the gut microbiome and reveal the applicability of the two methods, we compared the metagenome and 16S rDNA amplicon results to further demonstrate the features of this animal. Results The number of bacterial species detected by metagenomics graduall

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7

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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Alsanie, Walaa, Ebaa Felemban, Mona Farid, Mohamed Hassan, Ayman Sabry, and Ahmed Gaber. "Molecular Identification and Phylogenetic Analysis of Multidrug-resistant Bacteria using 16S rDNA Sequencing." Journal of Pure and Applied Microbiology 12, no. 2 (2018): 489–96. http://dx.doi.org/10.22207/jpam.12.2.07.

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9

Kim, Daeyoo, Gil Young Park, Dong Yeon Lee, Dong-Oh Lee, and Youngsik Yoon. "Nanopore 16S Amplicon Sequencing Enhances the Understanding of Pathogens in Medically Intractable Diabetic Foot Infections." Foot & Ankle Orthopaedics 7, no. 4 (2022): 2473011421S0072. http://dx.doi.org/10.1177/2473011421s00723.

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Category: Diabetes Introduction/Purpose: Diabetic foot infections (DFIs) cause substantial morbidity and mortality. The mainstay of the treatment is empiric antibiotics and surgical debridement in severe cases. Methods: In this study, we performed nanopore 16S rDNA sequencing from the debridement specimens of DFIs. Fifty-four surgical debridement specimens obtained from 45 patients with medically intractable DFI were included. The 16S rDNA PCR was performed on each specimen, and Nanopore sequencing was performed for up to 3 h. The reads were aligned to the BLAST database, and the results were

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10

Lawton, Samantha J., Allison M. Weis, Barbara A. Byrne, et al. "Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing." Journal of Veterinary Diagnostic Investigation 30, no. 3 (2018): 354–61. http://dx.doi.org/10.1177/1040638718762562.

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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared to conventional biochemical testing methods and nucleic acid analyses (16S rDNA sequencing, hippurate hydrolysis gene testing, whole genome sequencing [WGS]) for species identification of Campylobacter isolates obtained from chickens ( Gallus gallus domesticus, n = 8), American crows ( Corvus brachyrhynchos, n = 17), a mallard duck ( Anas platyrhynchos, n = 1), and a western scrub-jay ( Aphelocoma californica, n = 1). The test results for all 27 isolates were in 100% agreement between MALDI

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11

Agudelo-Pérez, Sergio, A. Melissa Moreno, Juliana Martínez-Garro, et al. "16S rDNA Sequencing for Bacterial Identification in Preterm Infants with Suspected Early-Onset Neonatal Sepsis." Tropical Medicine and Infectious Disease 9, no. 7 (2024): 152. http://dx.doi.org/10.3390/tropicalmed9070152.

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Background: The high prevalence of suspected early-onset neonatal sepsis among preterm infants leads to immediate antibiotic administration upon admission. Notably, most blood cultures for suspected early-onset neonatal sepsis do not yield a causative pathogen. This study aimed to assess polymerase chain reaction (PCR) targeting the variable region V4 of the 16S ribosomal gene (16S rDNA) and Sanger sequencing for bacterial identification in preterm infants with suspected early-onset neonatal sepsis. Methods: Therefore, this prospective study was conducted. Preterm infants with suspected early-

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12

Korczak, Bożena, Henrik Christensen, Stefan Emler, Joachim Frey, and Peter Kuhnert. "Phylogeny of the family Pasteurellaceae based on rpoB sequences." International Journal of Systematic and Evolutionary Microbiology 54, no. 4 (2004): 1393–99. http://dx.doi.org/10.1099/ijs.0.03043-0.

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Sequences of the gene encoding the β-subunit of the RNA polymerase (rpoB) were used to delineate the phylogeny of the family Pasteurellaceae. A total of 72 strains, including the type strains of the major described species as well as selected field isolates, were included in the study. Selection of universal rpoB-derived primers for the family allowed straightforward amplification and sequencing of a 560 bp fragment of the rpoB gene. In parallel, 16S rDNA was sequenced from all strains. The phylogenetic tree obtained with the rpoB sequences reflected the major branches of the tree obtained wit

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13

Hoogenkamp, Michel A., Bernd W. Brandt, Alexa M. G. A. Laheij, Johannes J. de Soet, and Wim Crielaard. "16S rDNA sequencing and metadata of Dutch dental unit water." Data in Brief 37 (August 2021): 107221. http://dx.doi.org/10.1016/j.dib.2021.107221.

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14

Hiraishi, Akira, Yong Kook Shin, Yoko Ueda, and Junta Sugiyama. "Automated sequencing of PCR-amplified 16S rDNA on ‘Hydrolink’ gels." Journal of Microbiological Methods 19, no. 2 (1994): 145–54. http://dx.doi.org/10.1016/0167-7012(94)90046-9.

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15

Boye, Kit, Estrid Høgdall, and Martin Borre. "Identification of bacteria using two degenerate 16S rDNA sequencing primers." Microbiological Research 154, no. 1 (1999): 23–26. http://dx.doi.org/10.1016/s0944-5013(99)80030-5.

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16

Roux, V., and D. Raoult. "Phylogenetic analysis of the genus Rickettsia by 16S rDNA sequencing." Research in Microbiology 146, no. 5 (1995): 385–96. http://dx.doi.org/10.1016/0923-2508(96)80284-1.

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17

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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18

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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19

Hinrikson, Hans Peter, Fabrizio Dutly, and Martin Altwegg. "Evaluation of a Specific Nested PCR Targeting Domain III of the 23S rRNA Gene of “Tropheryma whippelii” and Proposal of a Classification System for Its Molecular Variants." Journal of Clinical Microbiology 38, no. 2 (2000): 595–99. http://dx.doi.org/10.1128/jcm.38.2.595-599.2000.

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“Tropheryma whippelii”-associated infections are usually confirmed histopathologically by using light microscopy. PCR assays targeting the 16S rRNA gene (16S rDNA) of “T. whippelii” are increasingly being applied for this purpose. Compared to microscopic analysis, PCR seems to be more sensitive, as indicated by the fact that several cases of Whipple's disease with negative histopathological findings but positive PCR results have been reported. Considering the lack of pathognomonic clinical features for this disease and the fact that “T. whippelii” DNA has repeatedly been found in patients with

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20

Miyajima, M., M. Matsuda, S. Haga, S. Kagawa, B. C. Millar, and J. E. Moore. "Cloning and sequencing of 16S rDNA and 16S-23S rDNA internal spacer region (ISR) from urease-positive thermophilic Campylobacter (UPTC)." Letters in Applied Microbiology 34, no. 4 (2002): 287–89. http://dx.doi.org/10.1046/j.1472-765x.2002.01082.x.

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21

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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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

Storey, James R., Linda A. Doros-Richert, Cindy Gingrich-Baker, et al. "Molecular Cloning and Sequencing of Three Granulocytic Ehrlichia Genes Encoding High-Molecular-Weight Immunoreactive Proteins." Infection and Immunity 66, no. 4 (1998): 1356–63. http://dx.doi.org/10.1128/iai.66.4.1356-1363.1998.

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ABSTRACT Granulocytic Ehrlichia was isolated from canine blood obtained from animals challenged with field-collected Ixodes scapularis and propagated in HL60 cells. PCR primers specific for the 16S ribosomal DNA (rDNA) of the Ehrlichia genogroup comprising E. equi, E. phagocytophila, and the agent of human granulocytic ehrlichiosis (HGE) amplified DNA from extracts of these cells. Sequence analysis of this amplified DNA revealed that it is identical to the 16S rDNA sequence of the HGE agent. A genomic library was constructed with DNA from granulocyticEhrlichia and screened with pooled sera fro

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Singh, Ruby, O. Colin Stine, David L. Smith, John K. Spitznagel, Mohamed E. Labib, and Henry N. Williams. "Microbial Diversity of Biofilms in Dental Unit Water Systems." Applied and Environmental Microbiology 69, no. 6 (2003): 3412–20. http://dx.doi.org/10.1128/aem.69.6.3412-3420.2003.

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ABSTRACT We investigated the microbial diversity of biofilms found in dental unit water systems (DUWS) by three methods. The first was microscopic examination by scanning electron microscopy (SEM), acridine orange staining, and fluorescent in situ hybridization (FISH). Most bacteria present in the biofilm were viable. FISH detected the β and γ, but not the α, subclasses of Proteobacteria. In the second method, 55 cultivated biofilm isolates were identified with the Biolog system, fatty acid analysis, and 16S ribosomal DNA (rDNA) sequencing. Only 16S identified all 55 isolates, which represente

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Tian, Yang, and Yan Hong Li. "Comparative analysis of bacteria associated with different mosses by 16S rRNA and 16S rDNA sequencing." Journal of Basic Microbiology 57, no. 1 (2016): 57–67. http://dx.doi.org/10.1002/jobm.201600358.

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26

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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27

Pallavi, P., P. Bhavani, J. Komali, and T. Manjusha. "Molecular Identification of Lipase Producing Bacteria based on 16S rDNA Sequencing." International Journal of Current Microbiology and Applied Sciences 6, no. 5 (2017): 2067–71. http://dx.doi.org/10.20546/ijcmas.2017.605.230.

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28

Burton, Aaron S., Sarah E. Stahl, Kristen K. John, et al. "Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing." Genes 11, no. 1 (2020): 76. http://dx.doi.org/10.3390/genes11010076.

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The MinION sequencer has made in situ sequencing feasible in remote locations. Following our initial demonstration of its high performance off planet with Earth-prepared samples, we developed and tested an end-to-end, sample-to-sequencer process that could be conducted entirely aboard the International Space Station (ISS). Initial experiments demonstrated the process with a microbial mock community standard. The DNA was successfully amplified, primers were degraded, and libraries prepared and sequenced. The median percent identities for both datasets were 84%, as assessed from alignment of the

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Petrini, Björn. "16S rDNA Sequencing in the Species Identification of Non-tuberculous Mycobacteria." Scandinavian Journal of Infectious Diseases 35, no. 8 (2003): 519–20. http://dx.doi.org/10.1080/00365540310012370.

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30

Mosher, Jennifer J., Brett Bowman, Erin L. Bernberg, et al. "Improved performance of the PacBio SMRT technology for 16S rDNA sequencing." Journal of Microbiological Methods 104 (September 2014): 59–60. http://dx.doi.org/10.1016/j.mimet.2014.06.012.

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31

Shi, T., R. H. Reeves, D. A. Gilichinsky, and E. I. Friedmann. "Characterization of Viable Bacteria from Siberian Permafrost by 16S rDNA Sequencing." Microbial Ecology 33, no. 3 (1997): 169–79. http://dx.doi.org/10.1007/s002489900019.

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32

Keller, Alexander, Hannes Horn, Frank Förster, and Jörg Schultz. "Computational integration of genomic traits into 16S rDNA microbiota sequencing studies." Gene 549, no. 1 (2014): 186–91. http://dx.doi.org/10.1016/j.gene.2014.07.066.

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33

Both, Beatrix, Guido Krupp, and Erko Stackebrandt. "Direct sequencing of double-stranded polymerase chain reaction-amplified 16S rDNA." Analytical Biochemistry 199, no. 2 (1991): 216–18. http://dx.doi.org/10.1016/0003-2697(91)90092-8.

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34

Loong, Shih Keng, Chee Sieng Khor, Faizatul Lela Jafar, and Sazaly AbuBakar. "Utility of 16S rDNA Sequencing for Identification of Rare Pathogenic Bacteria." Journal of Clinical Laboratory Analysis 30, no. 6 (2016): 1056–60. http://dx.doi.org/10.1002/jcla.21980.

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35

Zhu, H., W. Y. Zhou, M. Xu, Y. L. Shen, and D. Z. Wei. "Molecular characterization of Serratia marcescens strains by RFLP and sequencing of PCR-amplified 16S rDNA and 16S?23S rDNA intergenic spacer." Letters in Applied Microbiology 45, no. 2 (2007): 174–78. http://dx.doi.org/10.1111/j.1472-765x.2007.02166.x.

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Payne, Michael, Robert Azana, and Linda M. N. Hoang. "Review of 16S and ITS Direct Sequencing Results for Clinical Specimens Submitted to a Reference Laboratory." Canadian Journal of Infectious Diseases and Medical Microbiology 2016 (2016): 1–6. http://dx.doi.org/10.1155/2016/4210129.

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We evaluated the performance of 16S and internal transcribed spacer (ITS) region amplification and sequencing of rDNA from clinical specimens, for the respective detection and identification of bacterial and fungal pathogens. Direct rDNA amplification of 16S and ITS targets from clinical samples was performed over a 4-year period and reviewed. All specimens were from sterile sites and submitted to a reference laboratory for evaluation. Results of 16S and ITS were compared to histopathology, Gram and/or calcofluor stain microscopy results. A total of 277 16S tests were performed, with 64 (23%)

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Tan, Zhi Lei, Yu Qiao Wei, Shuang Liang, Ran Zhang, Miao Liu, and Shi Ru Jia. "Rapid Identification of Microorganisms Isolated from Pickled Vegetables by MALDI-TOF Mass Spectrometry." Advanced Materials Research 712-715 (June 2013): 494–97. http://dx.doi.org/10.4028/www.scientific.net/amr.712-715.494.

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Matrix-assisted laser desorption/ionization time-off light mass spectrometry (MALDI-TOF MS) is increasingly used as a microbial diagnostic method for species identification of pathogens. However, MALDI-TOF MS identification of food bacteria was seldom reported. Ten strains isolated from different pickled vegetables were rapid identified by MALDI-TOF MS. The results of MALDI-TOF MS were confirmed by 16S rDNA sequencing method. Different score values in MALDI-TOF MS revealed nineLeuconostoc mesenteroides and oneStaphylococcus.Identification success at the species and genus levels was 90% (9/10)

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Song, Wen Feng, De Sheng Ma, You Yi Zhu, Xiao Fang Wei, and Jie Wu. "Diversity and Distribution of Sulfate-Reducing Bacteria in Jilin Oilfield." Advanced Materials Research 937 (May 2014): 297–302. http://dx.doi.org/10.4028/www.scientific.net/amr.937.297.

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To better understand the roles of microorganisms in oil production, diversity and distribution of microbes in Jilin oilfield was studied. Firstly, chromosomal DNA wassuccessfully extracted directly from crude oil samples. Diversity and distribution of microbes was then analyzed based on 16S rDNA libraries. There were totally 21 OTUs were obtained through 16S rDNA sequencing. Of those OTUs, 13 are bacteria in whichProteobacteriais the major family, while 8 are archaea in whichMethanomicrobiais the dominant. Finally, SRB was found in all samples by amplifying theapsAgene using PCR. SRB found in

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Rangel-Castro, J. Ignacio, Jolanta J. Levenfors, and Eric Danell. "Physiological and genetic characterization of fluorescentPseudomonasassociated withCantharellus cibarius." Canadian Journal of Microbiology 48, no. 8 (2002): 739–48. http://dx.doi.org/10.1139/w02-062.

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Fluorescent Pseudomonas spp. isolated from fruiting bodies (FB) of Cantharellus cibarius were characterized physiologically and genetically and were compared with fluorescent Pseudomonas from forest soil and with sequences from the GenBank database. Pseudomonas spp. from FB differed physiologically from isolates from soil lacking FB and had some similarities with the strains obtained from soil underneath the FB. Analyses of the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) patterns and partial sequencing analysis of the 16S-rDNA region indicated that the b

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40

LI, Xin, Xiao-fei ZHU, Cheng-fei ZHANG, Peter Cathro, Seneviratne CJ, and Song SHEN. "Endodontic bacteria from primary and persistent endodontic lesions in Chinese patients as identified by cloning and 16S ribosomal DNA gene sequencing." Chinese Medical Journal 126, no. 4 (2013): 634–39. http://dx.doi.org/10.3760/cma.j.issn.0366-6999.20122285.

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Background Few literatures pertain to the 16S ribosomal DNA (16S rDNA) analysis of bacteria contributing to primary and persistent endodontic lesions, with no information available for the Chinese population. As such, we investigated endodontic bacteria associated with primary and persistent endodontic lesions in adult Chinese patients living in Beijing, China using 16S rDNA gene sequencing techniques. Methods Endodontic microbial samples were obtained from fourteen adult Chinese patients and subjected to DNA extraction. Pllymerase chain reaction (PCR) products were cloned and 100 clones from

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Schlunck, Günther, Philip Maier, Barbara Maier, et al. "Next-Generation Sequencing of the Human Aqueous Humour Microbiome." International Journal of Molecular Sciences 25, no. 11 (2024): 6128. http://dx.doi.org/10.3390/ijms25116128.

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The microbiome of the ocular surface has been characterised, but only limited information is available on a possible silent intraocular microbial colonisation in normal eyes. Therefore, we performed next-generation sequencing (NGS) of 16S rDNA genes in the aqueous humour. The aqueous humour was sampled from three patients during cataract surgery. Air swabs, conjunctival swabs from patients as well as from healthy donors served as controls. Following DNA extraction, the V3 and V4 hypervariable regions of the 16S rDNA gene were amplified and sequenced followed by denoising. The resulting Amplico

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da Silva, Cleiziane Bispo, Hellen Ribeiro Martins dos Santos, Phellippe Arthur Santos Marbach, et al. "First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds." PeerJ 7 (November 20, 2019): e7452. http://dx.doi.org/10.7717/peerj.7452.

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Background Intragenomic variability in 16S rDNA is a limiting factor for taxonomic and diversity characterization of Bacteria, and studies on its occurrence in natural/environmental populations are scarce. In this work, direct DNA amplicon sequencing coupled with frequent-cutter restriction analysis allowed detection of intragenomic 16S rDNA variation in culturable endophytic bacteria from cacao seeds in a fast and attractive manner. Methods Total genomic DNA from 65 bacterial strains was extracted and the 16S rDNA hyper variable V5–V9 regions were amplified for enzyme digestion and direct San

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Knox, C. Michele, Vickey Cevellos, and Deborah Dean. "16S Ribosomal DNA Typing for Identification of Pathogens in Patients with Bacterial Keratitis." Journal of Clinical Microbiology 36, no. 12 (1998): 3492–96. http://dx.doi.org/10.1128/jcm.36.12.3492-3496.1998.

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The identification of pathogens in patients with bacterial keratitis remains problematic because standard diagnostic tests are negative for 40 to 60% of patients. A cross-sectional study was undertaken to determine if PCR and sequence analysis of 16S ribosomal DNA (rDNA) could be used to detect bacterial pathogens in patients with keratitis. Corneal specimens were collected for culture and rDNA typing. Variable segments of each rDNA specimen were amplified by PCR, sequenced, and aligned with the sequences in GenBank. Eleven patients had microbiologically documented bacterial keratitis, while 1

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Gu, F., Y. Li, C. Zhou, et al. "Bacterial 16S rRNA/rDNA Profiling in the Liquid Phase of Human Saliva." Open Dentistry Journal 3, no. 1 (2009): 80–84. http://dx.doi.org/10.2174/1874210600903010080.

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Human saliva can be separated by centrifugation into cell pellet and cell-free supernatant, which are called cellular phase and liquid phase in this study. While it is well documented that the cellular phase of saliva contains hundreds of oral bacteria species, little is known whether the liquid phase of saliva contains any information related to oral microbiota. In this study, we analyzed the bacterial nucleic acid contents of the liquid phase of saliva. Using primers universal to most eubacterial 16S rDNA, we detected large amounts of bacterial 16S rRNA and rDNA in the cell-free phase of sal

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Silveira, Érico Leandro da, Rodrigo Matheus Pereira, Denilson César Scaquitto, et al. "Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis." Pesquisa Agropecuária Brasileira 41, no. 10 (2006): 1507–16. http://dx.doi.org/10.1590/s0100-204x2006001000008.

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Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversity of sympatric communities within soils from two areas, a native forest (NFA) and an eucalyptus arbore

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Siddiqui, Huma, Karin Lagesen, Alexander J. Nederbragt, Lars M. Eri, Stig L. Jeansson, and Kjetill S. Jakobsen. "Pathogens in Urine from a Female Patient with Overactive Bladder Syndrome Detected by Culture-independent High Throughput Sequencing: A Case Report." Open Microbiology Journal 8, no. 1 (2014): 148–53. http://dx.doi.org/10.2174/1874285801408010148.

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Introduction:Overactive bladder syndrome (OAB) is described as urgency, with or without urgency incontinence. A range of medical conditions shares the symptoms of OAB, however the diagnosis is contingent on the exclusion of urinary tract infection (UTI). Knowing that urine dipstick and routine culture of bacteria can miss UTI diagnosis caused by low-count bacteriuria or “difficult-to-culture” pathogens, we examined a case of OAB with a culture-independent approach.Case presentation:A 61-year-old Norwegian female with a long history of urinary symptoms and a diagnosis of OAB was selected as a s

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Carvalho-Netto, Osmar Vaz de, Daniel Dias Rosa, and Luis Eduardo Aranha Camargo. "Identificarion of contaminant bacteria in cachaça yeast by 16s rDNA gene sequencing." Scientia Agricola 65, no. 5 (2008): 508–15. http://dx.doi.org/10.1590/s0103-90162008000500010.

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Cachaça is a typical Brazilian liquor produced from the distillation of fermented sugarcane juice mainly by Saccharomyces cerevisiae. Most of the domestic production is artisanal, and producers usually are not concerned regarding microbiological control of the fermentation. This study aimed to characterize the contaminant bacterial community of the yeast used in the production of cachaça in an artisanal still. Four samples were collected, of which one (NA) was used for comparison purposes and was collected one year earlier. The remaining samples were collected at three different periods: at th

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Sun, Mengyue, Yuanyuan Liu, Shan Tang, Yiming Li, Ridong Zhang, and Li Mao. "Characterization of Intestinal Flora in Osteoporosis Patients Based on 16S rDNA Sequencing." International Journal of General Medicine Volume 17 (September 2024): 4311–24. http://dx.doi.org/10.2147/ijgm.s468654.

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de Melo, Fabiana, Cássio do Nascimento, Diogo Onofre Souza, and Rubens F. de Albuquerque. "Identification of oral bacteria on titanium implant surfaces by 16S rDNA sequencing." Clinical Oral Implants Research 28, no. 6 (2016): 697–703. http://dx.doi.org/10.1111/clr.12865.

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Xia, Y., T. M. Embley, and A. G. O'Donnell. "Phylogenetic Analysis of Azospirillum by Direct Sequencing of PCR Amplified 16S rDNA." Systematic and Applied Microbiology 17, no. 2 (1994): 197–201. http://dx.doi.org/10.1016/s0723-2020(11)80007-x.

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