rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

Abstract

A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1–15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.

Bacterial Communities in Different Sections of a Municipal Wastewater Treatment Plant Revealed by 16S rDNA 454 Pyrosequencing

“…To our best knowledge, this is the first study introducing a method to differentiate the "gene percentage" and "cell percentage" by refereeing to the rrnDB (Lee et al 2009). This approach successfully demonstrated the underestimation or overestimation of some bacterial populations using 16S rRNA gene percentage only.…”

“…So, the cell percentages may disagree with the 16S rRNA gene percentages. In this study, we converted the 16S rRNA gene numbers into cell number at the genus level referring to the rrnDB and linked the two percentages commonly used in environmental microbiology (Lee et al 2009). Figure 5 shows the comparison of the percentage of 16S rRNA gene and cells of the four samples, i.e., activated sludge, digestion sludge, influent, and effluent.…”

The Skin Microbiome of <i>Gambusia affinis</i> Is Defined and Selective

“…Since the organisms in the skin microbiome can only be identified to the genus level, the exact number of 16S copies in the bacteria cannot be known for certain. Using the Ribosomal RNA Database [17], the number can be estimated. The database contains 11 species of Acinetobacter, which contain four to seven 16S gene copies, with an average of six.…”

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

“…The abundance of detectable dsrB genes in biofilm samples allowed the conclusion that these signatures were derived from bacteria and not from the dominant SM1 Euryarchaeon (three-log difference in archaeal 16S rRNA and dsrB gene abundance). Moreover, the one-log difference of bacterial 16S rRNA and dsrB genes can be attributed to the fact that ribosomal genes can have up to 15 copies per genome (Klappenbach et al, 2001;Lee et al, 2009), whereas dsrB genes generally appear once (Heidelberg et al, 2004).…”