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NAR Molecular Biology Database Collection entry number 43
Schmidt, Thomas; Stoddard, Steven; Smith, Byron; Hein, Robert; Roller, Benjamin
1 Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA 2 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA 3 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA 4 Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA

Database Description

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database, hosted by the Center for Microbial Ecology at Michigan State University, which contains annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon on prokaryotic genomes, yet the rRNA genes can vary from 1 to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes on a genome is not readily accessible. In an attempt to understand the evolutionary and ecological implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed, and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using rRNA gene sequences.

Recent Developments

Major improvements to the website and database include: expanded organism taxonomies to include both the National Center for Biotechnology Information (NCBI) and the Ribosomal Database Project (RDP) systems, new statistical summaries for 16S copy number in search results, downloadable copy number data optimized for use in copy number corrections in 16S molecular surveys, a new download area for sharing database contents, improved searching of records enabled by the availability of additional metadata, on-line 16S rRNA gene sequence classification based on the "RDP Classifier" tool (6) with copy number adjustment based on rrnDB data, and additional links to related external resources. Major changes in the data sources underlying the rrnDB records, as well as new data curation protocols, have been implemented to keep rrnDB concurrent with new bacterial and archaeal genomes as they become available. The new version of rrnDB serves the needs of a broader community than previous versions, and is better positioned for integration of gene-function data with the 16S copy number information as an anticipated future development.


The authors thank Jim Cole, Qiang Wang and Benli Chen of the Ribosomal Database Project for helpful discussions and for incorporating rrnDB 16S copy number data into RDP Classifier. Funding: National Institutes of Health [M0099549 to T.M.S.]; National Science Foundation’s Long-Term Ecological Research Program [DEB 1027253 to T.M.S]; Department of Energy Office of Science Graduate Fellowship Program [DOE SCGF to B.R.K.R., in part] by the American Recovery and Reinvestment Act of 2009, administered by ORISE-ORAU [DE-AC05–06OR23100].


1. Klappenbach,J.A., Saxman,P.R., Cole,J.R. and Schmidt,T.M. (2001) rrndb: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res., 29, 181–184.
2. Klappenbach,J.A., Dunbar,J.M. and Schmidt,T.M. (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol., 66, 1328–1333.
3. Dethlefsen,L. and Schmidt,T.M. (2007) Performance of the translational apparatus varies with the ecological strategies of bacteria. J. Bacteriol., 189, 3237–3245.
4. Eichorst,S.A., Breznak,J.A. and Schmidt,T.M. (2007) Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Appl. Environ. Microbiol., 73, 2708–2717.
5. Cavicchioli,R., Ostrowski,M., Fegatella,F., Goodchild,A. and Guixa-Boixereu,N. (2003) Life under nutrient limitation in oligotrophic marine environments: an eco/physiological perspective of Sphingopyxis alaskensis (formerly Sphingomonas alaskensis). Microb. Ecol., 45, 203–217.
6. Cole,J.R., Wang,Q., Fish,J.A., Chai,B., McGarrell,D.M., Sun,Y., Brown,C.T., Porras-Alfaro,A., Kuske,C.R. and Tiedje,J.M. (2014) Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res., 42, D633–D642.

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