7188–7196 Nucleic Acids Research, 2007, Vol. 35, No. 21 doi:10.1093/nar/gkm864 Published online 18 October 2007 SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Elmar Pruesse1,2, Christian Quast1,3, Katrin Knittel4, Bernhard M. Fuchs4, Wolfgang Ludwig5, Jo¨ rg Peplies6 and Frank Oliver Glo¨ ckner1,3,* 1Microbial Genomics Group, Max Planck Institute for Marine Microbiology, 2University Bremen, Center for Computing Technologies, D-28359, 3Jacobs University Bremen gGmbH, D-28759, 4Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, D-28359 Bremen, 5Department for Microbiology, Technical University Munich, D-85354 Freising and 6Ribocon GmbH, D-28359 Bremen Received May 26, 2007; Revised August 18, 2007; Accepted September 14, 2007 ABSTRACT Sequencing ribosomal RNA (rRNA) genes is cur- rently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB soft- ware 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 phyloge- netic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleo- tides 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. INTRODUCTION Initiated by the pioneering studies of Fox and Woese (1) 30 years ago and later on pursued by Pace, Olsen, Giovannoni, and Ward (2–5), the ribosomal RNA (rRNA) molecule has been established as the ‘gold- standard’ for the investigation of the phylogeny and ecology of microorganisms (6,7). Today the more than 500 000 publicly available small and large subunit (SSU and LSU) rRNA sequences ask for specialized quality controlled databases and appropriate software tools. In anticipation of this impending deluge of rRNA data, the development of the ARB software suite and the curation of its associated databases began more than 12 years ago (8). The software suite oﬀers a graphical user interface and a wide variety of interacting software tools built around a common database. Furthermore, the ARB project provides structured, integrative knowledge data- bases for small and large subunit rRNAs. Based on regularly oﬀered international workshops and the ARB mailing list it is currently estimated that the ARB software suite and its databases are employed worldwide by several thousand users from academia and industry. In addition to the ARB approach, there are currently three projects oﬀering access to a set of curated ribosomal RNA sequence and alignment databases: the European rRNA databank at the University of Gent (http://www.psb. ugent.be/rRNA/) (9), the Ribosomal Database Project II (http://rdp.cme.msu.edu/) at Michigan State University in East Lansing, MI (10,11), and the greengenes project (http://greengenes.lbl.gov/) maintained by the Lawrence Berkeley National Laboratory in Berkeley, CA (12). All four projects oﬀer at least one 16S rRNA dataset, but vary in the amount of sequences, quality checks, alignments, and update procedures. However, the ARB project is the *To whom correspondence should be addressed. Tel: +49 421 2028970; Fax: +49 421 2028580; Email: fog@mpi-bremen.de The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors. 2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.