title: StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform.
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.
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Wenning
authors.initials: W
authors.lastname: Zheng
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Tze King
authors.identifier: 0000-0003-1623-615X
authors.initials: TK
authors.lastname: Tan
authors.affiliation: Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.|Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Ian C
authors.initials: IC
authors.lastname: Paterson
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Naresh V R
authors.initials: NV
authors.lastname: Mutha
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Cheuk Chuen
authors.initials: CC
authors.lastname: Siow
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Shi Yang
authors.initials: SY
authors.lastname: Tan
authors.affiliation: Center for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom.
authors.forename: Lesley A
authors.initials: LA
authors.lastname: Old
authors.affiliation: Center for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom.|Genome Solutions Sdn Bhd, Suite 8, Innovation Incubator UM, Level 5, Research Management & Innovation Complex, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Nicholas S
authors.initials: NS
authors.lastname: Jakubovics
authors.affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.|Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.
authors.forename: Siew Woh
authors.initials: SW
authors.lastname: Choo
mesh_terms: D016680:Genome, Bacterial; D006801:Humans; D009055:Mouth / Q000382:microbiology*; D034361:Streptococcus mitis / Q000235:genetics*