Evaluation of 23S rRNA PCR Primers for Use in Phylogenetic Studies of Bacterial Diversity

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.

[1]  Guy Perrière,et al.  The European ribosomal RNA database , 2004, Nucleic Acids Res..

[2]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[3]  W. Ludwig,et al.  Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny. , 2000, International journal of systematic and evolutionary microbiology.

[4]  J. Heesemann,et al.  Development of rRNA-Targeted PCR and In Situ Hybridization with Fluorescently Labelled Oligonucleotides for Detection of Yersinia Species , 1998, Journal of Clinical Microbiology.

[5]  S. Acinas,et al.  Fine-scale phylogenetic architecture of a complex bacterial community , 2004, Nature.

[6]  Oded Béjà,et al.  Different SAR86 subgroups harbour divergent proteorhodopsins. , 2004, Environmental microbiology.

[7]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[8]  E. Delong,et al.  Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. , 2001, Environmental microbiology.

[9]  Stefan Bertilsson,et al.  Sequencing-Independent Method To Generate Oligonucleotide Probes Targeting a Variable Region in Bacterial 16S rRNA by PCR with Detachable Primers , 2002, Applied and Environmental Microbiology.

[10]  D. Lane.  16S/23S rRNA sequencing , 1991 .

[11]  V. Stanisich,et al.  New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. , 1996, Microbiology.

[12]  M. Weizenegger,et al.  Complete 23S Ribosomal RNA Sequences of Gram-positive Bacteria with a Low DNA G+C Content , 1992 .

[13]  B. K. Ahring,et al.  Amplification and direct sequence analysis of the 23S rRNA gene from thermophilic bacteria. , 2001, BioTechniques.

[14]  D. Karl,et al.  A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature , 1996, Applied and environmental microbiology.

[15]  Rupert De Wachter,et al.  Amplification and sequencing of variable regions in bacterial 23S ribosomal RNA genes with conserved primer sequences , 1993, Current Microbiology.

[16]  Vanja Klepac-Ceraj,et al.  PCR-Induced Sequence Artifacts and Bias: Insights from Comparison of Two 16S rRNA Clone Libraries Constructed from the Same Sample , 2005, Applied and Environmental Microbiology.

[17]  G. L. French,et al.  Rapid Diagnosis of Bacteremia by Universal Amplification of 23S Ribosomal DNA Followed by Hybridization to an Oligonucleotide Array , 2000, Journal of Clinical Microbiology.

[18]  C. Sorlini,et al.  Comparison of Different Primer Sets for Use in Automated Ribosomal Intergenic Spacer Analysis of Complex Bacterial Communities , 2004, Applied and Environmental Microbiology.

[19]  Nina Springer,et al.  Comparative Sequence Analysis of 23S rRNA from Proteobacteria , 1995 .

[20]  K. Schleifer,et al.  Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. , 1994, FEMS microbiology reviews.

[21]  E. Stackebrandt,et al.  Nucleic acid techniques in bacterial systematics , 1991 .

[22]  E. Triplett,et al.  Automated Approach for Ribosomal Intergenic Spacer Analysis of Microbial Diversity and Its Application to Freshwater Bacterial Communities , 1999, Applied and Environmental Microbiology.

[23]  F. Rodríguez-Valera,et al.  Intraspecific Diversity of the 23S rRNA Gene and the Spacer Region Downstream in Escherichia coli , 1999, Journal of bacteriology.

[24]  E. Delong,et al.  Phylogenetic Screening of Ribosomal RNA Gene-Containing Clones in Bacterial Artificial Chromosome (BAC) Libraries from Different Depths in Monterey Bay , 2004, Microbial Ecology.

[25]  M. W. Mueller,et al.  Microarray-Based Identification of Bacteria in Clinical Samples by Solid-Phase PCR Amplification of 23S Ribosomal DNA Sequences , 2004, Journal of Clinical Microbiology.

[26]  J. Thioulouse,et al.  Characterization of Bacterial and Fungal Soil Communities by Automated Ribosomal Intergenic Spacer Analysis Fingerprints: Biological and Methodological Variability , 2001, Applied and Environmental Microbiology.

[27]  H. Noller,et al.  Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. , 1981, Journal of molecular biology.