Ribosomal Database Project: data and tools for high throughput rRNA analysis

Abstract

Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines.

Quantitative analysis of ruminal bacterial populations involved in lipid metabolism in dairy cows fed different vegetable oils

“…The primers used in this study were previously validated (Tajima et al, 2001;Huws et al, 2010). Furthermore, the primers were checked using the probe match tool in the RDP (Huws et al, 2007;Cole et al, 2014). One interesting point is that the sum of the selected bacterial populations corresponded to half of the total bacterial, and this observation was independent of the diet used.…”

Emerging Infectious Disease Implications of Invasive Mammalian Species: The Greater White-Toothed Shrew (Crocidura russula) Is Associated With a Novel Serovar of Pathogenic Leptospira in Ireland

“…The 16S rRNA gene sequence identified within the newly sequenced organism described herein was used to retrieve 108 similar sequences from the Ribosomal Database Project (RDP) via the SeqMatch tool[37]. Sequences were aligned with MUSCLE[38], and divergent and ambiguously aligned alignment blocks were removed with Gblocks[39].…”

Molecular typing of bacteria for epidemiological surveillance and outbreak investigation / Molekulare Typisierung von Bakterien für die epidemiologische Überwachung und Ausbruchsabklärung

“…However, in contrast to viral diagnostics, culturebased methods are still dominating in clinical microbiology (Mancini et al, 2010). Over the past years, sequence analysis of the 16S rRNA gene has allowed identification of several new bacterial species or bacterial communities (Woo et al, 2008;Loncaric et al, 2011) and represents the "gold standard" for bacteria classification because of quality and accuracy of a sequence-based method and the availability of comprehensive databases such as the Ribosomal Database Project (RDP) (Cole et al, 2014) (Euzéby, 1997;Parte, 2014). In general, public databases such as Basic Local Alignment Search Tool (BLAST) or the RDP yield better identification results for rare or highly pathogenic bacteria than quality-controlled databases such as RIDOM or MicroSeq 500 (Ruppitsch et al, 2007b).…”