rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

By S. Stoddard, Byron J. Smith, R. Hein, Benjamin R. K. Roller, Thomas M. Schmidt. Nucleic Acids Res., 2014

1,026 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/53633edfe4e1c303c96814d6017301721c437637

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Citations in the corpus

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling (2020, methodology): “For the copy-number correction, we used the 16S copy number database rrnDB [28].”
Soil Bacterial and Fungal Response to Wildfires in the Canadian Boreal Forest Across a Burn Severity Gradient (2019, methodology): “We predicted 16S rRNA gene copy numbers using the ribosomal RNA operon database (rrnDB) (Stoddard et al., 2015).”
MiDAS: the field guide to the microbes of activated sludge (2015, background): “Such values should be considered in the interpretation of amplicon-sequencing data given that, relative to other taxa present, they influence the determined abundance (35).”
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life (2017, background): “Cyanobacteria (48) Thermotogae (11) Acetothermia (10) Dictyoglomi Coprothermo.”