Abstract
The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis 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 S. mitis 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 S. mitis 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 Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis 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. Database URL: http://streptococcus.um.edu.my.
Highlights
Streptococcus is a major genus of spherical Gram-positive bacteria which belong to the phylum Firmicutes
The genomic study of diverse S. mitis group bacteria is essential in order to understand how these microorganisms transit from a commensal lifestyle in the mouth to subsequent pathogenesis
While most biological genome databases only focus on the genome content and genetic variation, we have identified a need to create functional bioinformatics tools to investigate virulence determinants within genomes through comparative pathogenomics, as well as to compare the genome content and genetic variation within the S. mitis group bacteria
Summary
Streptococcus is a major genus of spherical Gram-positive bacteria which belong to the phylum Firmicutes. Alpha-hemolysis involves the bleaching of heme iron by streptococcal hydrogen peroxide (H2O2), resulting in a greenish tinge on blood agar [1]. Alpha-hemolysis is not entirely consistent between different strains of individual Streptococcal species, and the term ‘Viridans’ is somewhat misleading and is no longer used. These organisms are more commonly known as the oral streptococci. In 2002, Facklam proposed a phenotypic identification scheme which included an additional new cluster called Sanguinis [5]. This cluster, containing S. sanguinis, S. gordonii and S. sinensis is sometimes included within the mitis group
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