StaphyloBase: a specialized genomic resource for the staphylococcal research community

A H Yazdi,G J Wong,S W Choo,H Heydari,N V R Mutha,M I Mahmud,W Y Wee,C C Siow,M Y Ang

doi:10.1093/database/bau010

Abstract

With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations. We anticipate this resource platform will facilitate the analysis of staphylococcal genomic data, particularly in comparative analyses. StaphyloBase currently has a collection of 754 032 protein-coding sequences (CDSs), 19 258 rRNAs and 15 965 tRNAs from 292 genomes of different staphylococcal species. Information about these features is also included, such as putative functions, subcellular localizations and gene/protein sequences. Our web implementation supports diverse query types and the exploration of CDS- and RNA-type information in detail using an AJAX-based real-time search system. JBrowse has also been incorporated to allow rapid and seamless browsing of staphylococcal genomes. The Pairwise Genome Comparison tool is designed for comparative genomic analysis, for example, to reveal the relationships between two user-defined staphylococcal genomes. A newly designed Pathogenomics Profiling Tool (PathoProT) is also included in this platform to facilitate comparative pathogenomics analysis of staphylococcal strains. In conclusion, StaphyloBase offers access to a range of staphylococcal genomic resources as well as analysis tools for comparative analyses. Database URL: http://staphylococcus.um.edu.my/

Highlights

The genus Staphylococcus in the bacterial family Staphylococcaceae is a common bacterial genus that is widely distributed throughout the world
We present StaphyloBase, a staphylococcal genomic resource platform powered by advanced web technologies and in-house developed analysis tools for the staphylococcal research community
With StaphyloBase, we aim to provide a one-stop resource platform that will make it easy to access and analyse whole-genome genomic data and information for staphylococcal bacteria through an organized and user-friendly interface

Summary

Introduction

The genus Staphylococcus in the bacterial family Staphylococcaceae is a common bacterial genus that is widely distributed throughout the world. Some known Staphylococcus species are part of the natural fauna present on the body and can be found on mucus membranes and skin. Staphylococci are facultative anaerobic gram-positive spherical bacteria that occur in microscopic clusters resembling grapes. Staphylococcal pathogens are resistant to many antibiotics, forcing researchers to find better ways of fighting these pathogens. Staphylococcus aureus and Staphylococcus epidermidis are the two most characterized and studied staphylococcal bacteria, and S. aureus is a significant human pathogen worldwide.

Objectives

Conclusion