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Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

Cited 2789 time in Web of Science Cited 2675 time in Scopus
Authors
Yoon, Seok-Hwan; Ha, Sung-Min; Kwon, Soonjae; Lim, Jeongmin; Kim, Yeseul; Seo, Hyungseok; Chun, Jongsik
Issue Date
2017-05
Citation
International Journal of Systematic and Evolutionary Microbiology, Vol.67 No.5, pp.1613-1617
Keywords
16S rRNA genegenomeaverage nucleotide identityidentificationdatabase
Abstract
The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by qualitycontrolled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.
ISSN
1466-5026
URI
https://hdl.handle.net/10371/165734
DOI
https://doi.org/10.1099/ijsem.0.001755
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College of Natural Sciences (자연과학대학)Dept. of Biological Sciences (생명과학부)Journal Papers (저널논문_생명과학부)
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