title: rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development.
abstract: Microbiologists utilize ribosomal RNA genes as molecular markers of taxonomy in surveys of microbial communities. rRNA genes are often co-located as part of an rrn operon, and multiple copies of this operon are present in genomes across the microbial tree of life. rrn copy number variability provides valuable insight into microbial life history, but introduces systematic bias when measuring community composition in molecular surveys. Here we present an update to the ribosomal RNA operon copy number database (rrnDB), a publicly available, curated resource for copy number information for bacteria and archaea. The redesigned rrnDB (http://rrndb.umms.med.umich.edu/) brings a substantial increase in the number of genomes described, improved curation, mapping of genomes to both NCBI and RDP taxonomies, and refined tools for querying and analyzing these data. With these changes, the rrnDB is better positioned to remain a comprehensive resource under the torrent of microbial genome sequencing. The enhanced rrnDB will contribute to the analysis of molecular surveys and to research linking genomic characteristics to life history.
authors.affiliation: Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Steven F
authors.initials: SF
authors.lastname: Stoddard
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Byron J
authors.identifier: http://orcid.org/0000-0002-0182-404X
authors.initials: BJ
authors.lastname: Smith
authors.affiliation: Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Hein
authors.affiliation: Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
authors.forename: Benjamin R K
authors.identifier: http://orcid.org/0000-0003-4458-8267
authors.initials: BR
authors.lastname: Roller
authors.affiliation: Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA schmidti@umich.edu.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Schmidt
mesh_terms: D001105:Archaea / Q000145:classification; D001419:Bacteria / Q000145:classification; D030561:Databases, Nucleic Acid; D018628:Gene Dosage; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D020459:Genes, rRNA; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D020407:Internet; D009876:Operon; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S