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

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 quality-controlled 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/.

Genome Sequence of Lysinibacillus sphaericus, a Lignin-Degrading Bacterium Isolated from Municipal Solid Waste Soil

“…fusiformis NBRC 15717 T , and 99.60% with L. mangiferihumi M-GX18 T , as analyzed using the EzBioCloud Web server identity tool (9). …”

Draft Genome Sequence of Bacillus sp. Strain YSP-3, a Halophilic, Alkaliphilic Bacterium Isolated from a Salt Lake

“…In sodium bicarbonate-buffered medium (1), growth occurred at 1% to 13% (wt/vol) NaCl (optimum, 8% NaCl), pH 8.0 to 10.5 (optimum, 9.0), and 15°C to 45°C (optimum, 35°C). Pairwise sequence similarities of 16S rRNA genes were calculated using a global alignment algorithm implemented by applying the EzBioCloud server (2). The result revealed that YSP-3 had the highest 16S rRNA gene sequence similarities with Bacillus aurantiacus K1-5 T (97.9  %) and Bacillus populi FJAT-45347 T (97.01%).…”

Draft Genome Sequences of Alloscardovia macacae UMA81211 and UMA81212, Isolated from the Feces of a Rhesus Macaque (Macaca mulatta)

“…The sequences of the 16S rRNA marker genes were obtained from the RAST annotations of UMA81211 and UMA81212 and showed 98.67% and 98.27% similarity to Alloscardovia macacae M8, respectively (3, 4). The next highest similarity scores were for Alloscardovia criceti DSM17774 (UMA81211, 96.54%; UMA81212, 96.31%) and Alloscardovia omnicolens DSM21503 (UMA81211, 96.54%; UMA81212, 95.93%) (3, 5).…”