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

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 comprise...

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Main Authors: Zheng, W., Tan, T.K., Paterson, I.C., Mutha, N.V.R., Siow, C.C., Tan, S.Y., Old, L.A., Jakubovics, N.S., Choo, S.W.
Format: Article
Published: Public Library of Science 2016
Subjects:
RK Dentistry
Online Access:http://eprints.um.edu.my/18664/
https://doi.org/10.1371/journal.pone.0151908
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spelling my.um.eprints.186642018-05-14T08:44:03Z http://eprints.um.edu.my/18664/ StreptoBase: An oral Streptococcus mitis group genomic resource and analysis platform Zheng, W. Tan, T.K. Paterson, I.C. Mutha, N.V.R. Siow, C.C. Tan, S.Y. Old, L.A. Jakubovics, N.S. Choo, S.W. RK Dentistry 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. Public Library of Science 2016 Article PeerReviewed 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 https://doi.org/10.1371/journal.pone.0151908 doi:10.1371/journal.pone.0151908
institution Universiti Malaya
building UM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaya
content_source UM Research Repository
url_provider http://eprints.um.edu.my/
topic RK Dentistry
spellingShingle RK Dentistry
Zheng, W.
Tan, T.K.
Paterson, I.C.
Mutha, N.V.R.
Siow, C.C.
Tan, S.Y.
Old, L.A.
Jakubovics, N.S.
Choo, S.W.
StreptoBase: An oral Streptococcus mitis group genomic resource and analysis platform
description 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.
format Article
author Zheng, W.
Tan, T.K.
Paterson, I.C.
Mutha, N.V.R.
Siow, C.C.
Tan, S.Y.
Old, L.A.
Jakubovics, N.S.
Choo, S.W.
author_facet Zheng, W.
Tan, T.K.
Paterson, I.C.
Mutha, N.V.R.
Siow, C.C.
Tan, S.Y.
Old, L.A.
Jakubovics, N.S.
Choo, S.W.
author_sort Zheng, W.
title StreptoBase: An oral Streptococcus mitis group genomic resource and analysis platform
title_short StreptoBase: An oral Streptococcus mitis group genomic resource and analysis platform
title_full StreptoBase: An oral Streptococcus mitis group genomic resource and analysis platform
title_fullStr StreptoBase: An oral Streptococcus mitis group genomic resource and analysis platform
title_full_unstemmed StreptoBase: An oral Streptococcus mitis group genomic resource and analysis platform
title_sort streptobase: an oral streptococcus mitis group genomic resource and analysis platform
publisher Public Library of Science
publishDate 2016
url http://eprints.um.edu.my/18664/
https://doi.org/10.1371/journal.pone.0151908
_version_ 1643690759040270336
score 13.211869

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