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

TLDR

Microbiologists use rRNA genes as taxonomic markers, but their variable copy numbers across genomes bias community composition measurements while also revealing life‑history traits. The study updates rrnDB, a publicly available, curated database of rRNA operon copy numbers for bacteria and archaea. The updated rrnDB expands genome coverage, enhances curation, links genomes to NCBI and RDP taxonomies, and offers refined query and analysis tools. The updated rrnDB improves comprehensiveness amid rapid genome sequencing and supports analysis of molecular surveys and studies linking genomic traits to life history.

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.