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Literature DB >> 16517676

Evaluation of 23S rRNA PCR primers for use in phylogenetic studies of bacterial diversity.

Dana E Hunt¹, Vanja Klepac-Ceraj, Silvia G Acinas, Clement Gautier, Stefan Bertilsson, Martin F Polz.

Abstract

The availability of a diverse set of 23S rRNA gene sequences enabled evaluation of the specificity of 39 previously published and 4 newly designed primers specific for bacteria. An extensive clone library constructed using an optimized primer pair resulted in similar gene richness but slightly differing coverage of some phylogenetic groups, compared to a 16S rRNA gene library from the same environmental sample.

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Year: 2006 PMID： 16517676 PMCID： PMC1393206 DOI： 10.1128/AEM.72.3.2221-2225.2006

Source DB: PubMed Journal: Appl Environ Microbiol ISSN： 0099-2240 Impact factor: 4.792

22 in total

1. Amplification and direct sequence analysis of the 23S rRNA gene from thermophilic bacteria.

Authors: A Ibrahim; J Hofman-Bang; B K Ahring
Journal: Biotechniques Date: 2001-02 Impact factor: 1.993

2. Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton.

Authors: M T Suzuki; O Béjà; L T Taylor; E F Delong
Journal: Environ Microbiol Date: 2001-05 Impact factor: 5.491

3. Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability.

Authors: L Ranjard; F Poly; J C Lata; C Mougel; J Thioulouse; S Nazaret
Journal: Appl Environ Microbiol Date: 2001-10 Impact factor: 4.792

4. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array.

Authors: R M Anthony; T J Brown; G L French
Journal: J Clin Microbiol Date: 2000-02 Impact factor: 5.948

5. The European ribosomal RNA database.

Authors: Jan Wuyts; Guy Perrière; Yves Van De Peer
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

6. Fine-scale phylogenetic architecture of a complex bacterial community.

Authors: Silvia G Acinas; Vanja Klepac-Ceraj; Dana E Hunt; Chanathip Pharino; Ivica Ceraj; Daniel L Distel; Martin F Polz
Journal: Nature Date: 2004-07-29 Impact factor: 49.962

7. Microarray-based identification of bacteria in clinical samples by solid-phase PCR amplification of 23S ribosomal DNA sequences.

Authors: Georg Mitterer; Martin Huber; Ernst Leidinger; Claudia Kirisits; Werner Lubitz; Manfred W Mueller; Wolfgang M Schmidt
Journal: J Clin Microbiol Date: 2004-03 Impact factor: 5.948

8. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample.

Authors: Silvia G Acinas; Ramahi Sarma-Rupavtarm; Vanja Klepac-Ceraj; Martin F Polz
Journal: Appl Environ Microbiol Date: 2005-12 Impact factor: 4.792

9. Sequencing-independent method to generate oligonucleotide probes targeting a variable region in bacterial 16S rRNA by PCR with detachable primers.

Authors: Stefan Bertilsson; Colleen M Cavanaugh; Martin F Polz
Journal: Appl Environ Microbiol Date: 2002-12 Impact factor: 4.792

10. Environmental genome shotgun sequencing of the Sargasso Sea.

Authors: J Craig Venter; Karin Remington; John F Heidelberg; Aaron L Halpern; Doug Rusch; Jonathan A Eisen; Dongying Wu; Ian Paulsen; Karen E Nelson; William Nelson; Derrick E Fouts; Samuel Levy; Anthony H Knap; Michael W Lomas; Ken Nealson; Owen White; Jeremy Peterson; Jeff Hoffman; Rachel Parsons; Holly Baden-Tillson; Cynthia Pfannkoch; Yu-Hui Rogers; Hamilton O Smith
Journal: Science Date: 2004-03-04 Impact factor: 47.728

38 in total

1. Novel Burkholderiales 23S rRNA genes identified in ileal biopsy samples from children: preliminary evidence that a subtype is associated with perianal Crohn's disease.

Authors: W H Sim; J Wagner; D J Cameron; A G Catto-Smith; R F Bishop; C D Kirkwood
Journal: J Clin Microbiol Date: 2010-03-17 Impact factor: 5.948

2. Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes.

Authors: Jiarong Guo; James R Cole; Qingpeng Zhang; C Titus Brown; James M Tiedje
Journal: Appl Environ Microbiol Date: 2015-10-16 Impact factor: 4.792

3. Evaluation of different molecular and phenotypic methods for identification of environmental Burkholderia cepacia complex.

Authors: João Pedro Rueda Furlan; André Pitondo-Silva; Vânia Santos Braz; Inara Fernanda Lage Gallo; Eliana Guedes Stehling
Journal: World J Microbiol Biotechnol Date: 2019-02-09 Impact factor: 3.312

4. Depletion of ribosomal RNA for mosquito gut metagenomic RNA-seq.

Authors: Phanidhar Kukutla; Matthew Steritz; Jiannong Xu
Journal: J Vis Exp Date: 2013-04-07 Impact factor: 1.355

5. Differentiation of non-pylori Helicobacter species based on PCR-restriction fragment length polymorphism of the 23S rRNA gene.

Authors: Abbas Yadegar; Masoud Alebouyeh; Andy J Lawson; Tabassom Mirzaei; Ehsan Nazemalhosseini Mojarad; Mohammad Reza Zali
Journal: World J Microbiol Biotechnol Date: 2014-02-04 Impact factor: 3.312

6. Description of an unusual Neisseria meningitidis isolate containing and expressing Neisseria gonorrhoeae-Specific 16S rRNA gene sequences.

Authors: Marion Walcher; Rhonda Skvoretz; Megan Montgomery-Fullerton; Vivian Jonas; Steve Brentano
Journal: J Clin Microbiol Date: 2013-07-17 Impact factor: 5.948

10. Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion.

Authors: Pui Yi Yung; Catherine Burke; Matt Lewis; Suhelen Egan; Staffan Kjelleberg; Torsten Thomas
Journal: Nucleic Acids Res Date: 2009-11 Impact factor: 16.971