StreptoBase: An oral Streptococcus mitis group genomic resource and analysis platform

Zheng, W. and Tan, T.K. and Paterson, I.C. and Mutha, N.V.R. and Siow, C.C. and Tan, S.Y. and Old, L.A. and Jakubovics, N.S. and Choo, S.W. (2016) StreptoBase: An oral Streptococcus mitis group genomic resource and analysis platform. PLoS ONE, 11 (5). e0151908. ISSN 1932-6203

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Official URL: https://doi.org/10.1371/journal.pone.0151908

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.

Item Type: Article
Uncontrolled Keywords: Genome, Bacterial; Humans; Mouth; Streptococcus mitis
Subjects: R Medicine > RK Dentistry
Divisions: Faculty of Dentistry
Depositing User: Ms. Juhaida Abd Rahim
Date Deposited: 14 May 2018 08:44
Last Modified: 14 May 2018 08:44
URI: http://eprints.um.edu.my/id/eprint/18664

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