The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
Open accessAbstract
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.
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Quantitative microbiome profiling links gut community variation to microbial load
Vandeputte, D., Kathagen, G., D’hoe, K., Vieira-Silva, S., Valles-Colomer, M., Sabino, J., Wang, J., Tito, R. Y., De Commer, L., Darzi, Y., et al. (2017) · Nature · doi:10.1038/nature24460 · Cited by 1,218
The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies
Pollock, J., Glendinning, L., Wisedchanwet, T., & Watson, M. (2018) · Applied and Environmental Microbiology · doi:10.1128/aem.02627-17 · Cited by 575
Dynamic modulation of the gut microbiota and metabolome by bacteriophages in a mouse model
Hsu, B. B., Gibson, T. E., Yeliseyev, V., Liu, Q., Lyon, L., Bry, L., Silver, P. A., & Gerber, G. K. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.05.001 · Cited by 573
Dai, T., Wen, D., Bates, C. T., Wu, L., Guo, X., Liu, S., Su, Y., Lei, J., Zhou, J., & Yang, Y. (2022) · Nature Communications · doi:10.1038/s41467-021-27857-6 · Cited by 470
Metadata
- Authors
- Stoddard, S. F., Smith, B. J., Hein, R., Roller, B. R. K., & Schmidt, T. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-11-20
- Volume
- 43
- Issue
- D1
- Pages
- D593-D598
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2135293770
- Cited by
- 1,112
- References
- 23
- FWCI
- 18.25
- Type
- journal article
- Language
- en
- Open access
- gold
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- Stoddard, S. F., Smith, B. J., Hein, R., Roller, B. R. K., & Schmidt, T. M. (2015). rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Research. https://doi.org/10.1093/nar/gku1201
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