StreptoBase: An Oral <i>Streptococcus mitis</i> Group Genomic Resource and Analysis Platform

<div><p>The oral streptococci are spherical Gram-positive bacteria categorized under the phylum <i>Firmicutes</i> which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The <i>Streptococcus mitis</i> group is comprised of 13 species including some of the most common human oral colonizers such as <i>S</i>. <i>mitis</i>, <i>S</i>. <i>oralis</i>, <i>S</i>. <i>sanguinis</i> and <i>S</i>. <i>gordonii</i> as well as species such as <i>S</i>. <i>tigurinus</i>, <i>S</i>. <i>oligofermentans</i> and <i>S</i>. <i>australis</i> that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 <i>S</i>. <i>mitis</i> group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of <i>S</i>. <i>mitis</i> group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of <i>Streptococcus</i> strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different <i>S</i>. <i>mitis</i> group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. <b>Database URL</b>: <a href="http://streptococcus.um.edu.my" target="_blank">http://streptococcus.um.edu.my</a>.</p>