The Ribosomal Database Project: Sequences and Software for High‐Throughput rRNA Analysis

Cole, James R.; Wang, Qiong; Chai, Benli; Tiedje, James M.

doi:10.1002/9781118010518.ch36

Cited by 26 publications

(26 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The RDPipeline is a new tool suite designed to replace our previous Pyrosequencing Pipeline (30), offering extended processing and analysis tools reflecting recent shifts in amplicon sequencing technologies and techniques. Researchers can utilize the tools in the RDPipeline tool suite in one of two ways.…”

Section: Tool Descriptionsmentioning

confidence: 99%

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

et al. 2013

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Tool Descriptionsmentioning

confidence: 99%

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

et al. 2013

Self Cite

View full text Add to dashboard Cite

show abstract

“…Chimeric sequences were detected with UCHIME (Edgar et al, 2011) and subsequently removed from the dataset. Taxonomic affiliation of 16S rRNA genes was performed with a Bayesian classifier (Wang et al, 2007) (80% bootstrap confidence score) against the 16S rRNA gene training set (v9) of the Ribosomal Database Project (Cole et al, 2011). Unclassified sequences or sequences belonging to Eukaryota, Archaea, chloroplasts or mitochondria were discarded.…”

Section: Sequence Analysesmentioning

confidence: 99%

“…Only abundant OTUs representing at least 0.1% of the library size were conserved for microbial community analyses (Barret et al, 2015). Taxonomic affiliation of these OTUs was done using BLAST+ and RDP against the different databases: NCBI, BIBI and RDP (Cole et al, 2011;Devulder et al, 2003;The NCBI Handbook, 2013).…”

Section: Sequence Analysesmentioning

confidence: 99%

Characterization of relative abundance of lactic acid bacteria species in French organic sourdough by cultural, qPCR and MiSeq high-throughput sequencing methods

Michel

Monfort

Deffrasnes

et al. 2016

International Journal of Food Microbiology

View full text Add to dashboard Cite

In order to contribute to the description of sourdough LAB composition, MiSeq sequencing and qPCR methods were performed in association with cultural methods. A panel of 16 French organic bakers and farmer-bakers were selected for this work. The lactic acid bacteria (LAB) diversity of their organic sourdoughs was investigated quantitatively and qualitatively combining (i) Lactobacillus sanfranciscensis-specific qPCR, (ii) global sequencing with MiSeq Illumina technology and (iii) molecular isolates identification. In addition, LAB and yeast enumeration, pH, Total Titratable Acidity, organic acids and bread specific volume were analyzed. Microbial and physico-chemical data were statistically treated by Principal Component Analysis (PCA) and Hierarchical Ascendant Classification (HAC). Total yeast counts were 6 log to 7.6 logCFU/g while LAB counts varied from 7.2 log to 9.6 logCFU/g. Values obtained by L. sanfranciscensis-specific qPCR were estimated between 7.2 and 10.3 logCFU/g, except for one sample at 4.4 logCFU/g. HAC and PCA clustered the sixteen sourdoughs into three classes described by their variables but without links to bakers' practices. L. sanfranciscensis was the dominant species in 13 of the 16 sourdoughs analyzed by Next Generation Sequencing (NGS), by the culture dependent method this species was dominant only in only 10 samples. Based on isolates identification, LAB diversity was higher for 7 sourdoughs with the recovery of L. curvatus, L. brevis, L. heilongjiangensis, L. xiangfangensis, L. koreensis, L. pontis, Weissella sp. and Pediococcus pentosaceus, as the most representative species. L. koreensis, L. heilongjiangensis and L. xiangfangensis were identified in traditional Asian food and here for the first time as dominant in organic sourdough. This study highlighted that L. sanfranciscensis was not the major species in 6/16 sourdough samples and that a relatively high LAB diversity can be observed in French organic sourdough.

show abstract

“…The taxonomic assignment of these OTUs was matched to results in the Ribosomal Database Project. 40 Alpha and Beta diversities were determined using QIIME. 41 Beta-dispersion was quantified with betadisper (vegan::betadisper) and additional analyses were performed with the R package phylosEquation.…”

Section: Faecal Sample Preparation and 16s Rrna Gene Sequence Analysismentioning

confidence: 99%

Outbreak of acute larval cyathostominosis – A “perfect storm” of inflammation and dysbiosis

Walshe

Mulcahy

Crispie

et al. 2020

Equine Veterinary Journal

View full text Add to dashboard Cite

show abstract

The Ribosomal Database Project: Sequences and Software for High‐Throughput rRNA Analysis

Cited by 26 publications

References 36 publications

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

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

Characterization of relative abundance of lactic acid bacteria species in French organic sourdough by cultural, qPCR and MiSeq high-throughput sequencing methods

Outbreak of acute larval cyathostominosis – A “perfect storm” of inflammation and dysbiosis

Contact Info

Product

Resources

About