SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs.

[1]  James R. Cole,et al.  The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data , 2006, Nucleic Acids Res..

[2]  Dawn Field,et al.  Meeting report: eGenomics: Cataloguing our Complete Genome Collection II. , 2006, Omics : a journal of integrative biology.

[3]  Susan M. Huse,et al.  Microbial diversity in the deep sea and the underexplored “rare biosphere” , 2006, Proceedings of the National Academy of Sciences.

[4]  C. Pedrós-Alió,et al.  Marine microbial diversity: can it be determined? , 2006, Trends in microbiology.

[5]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[6]  John Bunge,et al.  Predicting microbial species richness. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Renzo Kottmann,et al.  Megx.net—database resources for marine ecological genomics , 2005, Nucleic Acids Res..

[8]  A. J. Jones,et al.  At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies , 2005, Applied and Environmental Microbiology.

[9]  Olivier Poch,et al.  BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark , 2005, Proteins.

[10]  George Garrity,et al.  eGenomics: Cataloguing our Complete Genome Collection , 2005, Comparative and functional genomics.

[11]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[12]  James R. Cole,et al.  The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis , 2004, Nucleic Acids Res..

[13]  Jörg Peplies,et al.  Comparative sequence analysis and oligonucleotide probe design based on 23S rRNA genes of Alphaproteobacteria from North Sea bacterioplankton. , 2004, Systematic and applied microbiology.

[14]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[15]  Jan Sapp,et al.  Microbial Phylogeny and Evolution: concepts and controversies. , 2004 .

[16]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

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

[18]  T. Z. DeSantis,et al.  Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA , 2003, Bioinform..

[19]  Alessandro Minelli,et al.  DNA points the way ahead in taxonomy , 2002, Nature.

[20]  Christopher J. Lee,et al.  Multiple sequence alignment using partial order graphs , 2002, Bioinform..

[21]  Yves Van de Peer,et al.  The European Large Subunit Ribosomal RNA database , 2000, Nucleic Acids Res..

[22]  W. Wade,et al.  Design and Evaluation of Useful Bacterium-Specific PCR Primers That Amplify Genes Coding for Bacterial 16S rRNA , 1998, Applied and Environmental Microbiology.

[23]  N. Pace.  A molecular view of microbial diversity and the biosphere. , 1997, Science.

[24]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[25]  R. Gutell,et al.  Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. , 1994, Microbiological reviews.

[26]  A. Uitterlinden,et al.  Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA , 1993, Applied and environmental microbiology.

[27]  E. Delong.  Archaea in coastal marine environments. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[28]  D. M. Ward,et al.  16S rRNA sequences reveal numerous uncultured microorganisms in a natural community , 1990, Nature.

[29]  Phylogenetic Group-Specific Oligodeoxynucleotide Probes for Identification of Single Microbial Cells , 1988 .

[30]  G J Olsen,et al.  Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells , 1988, Journal of bacteriology.

[31]  N. Pace,et al.  Microbial ecology and evolution: a ribosomal RNA approach. , 1986, Annual review of microbiology.

[32]  George E. Fox,et al.  Comparative Cataloging of 16S Ribosomal Ribonucleic Acid: Molecular Approach to Procaryotic Systematics , 1977 .

[33]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.