Title: MicroBQs: a centralized database for use in studying bacterial biofilms and quorum sensing Authors
Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: May 1, 2009
Publication Date: June 1, 2009
Citation: Yan, X., Gui, J., Fratamico, P.M. 2009. MicroBQs: a centralized database for use in studying bacterial biofilms and quorum sensing. Book Chapter. Oxford, UK: Woodhead Publishing Ltd. p. 152-166. Biofilms in the Food and Beverage Industries, P.M. Fratamico, B.A. Annous, and N.W. Gunther (Ed.) Technical Abstract: Biofilm formation in many bacterial species may be negatively or positively regulated by cell-to-cell signaling systems referred to as quorum sensing (QS). To assist in understanding research related to biofilms, QS, and the role of QS in biofilm formation, a comprehensive, centralized database, known as MicroBQs was generated. The database consists of the following: (1) relevant references in the literature; (2) genomic and proteomic information, including genes involved in QS and biofilm formation, DNA and protein sequences, and publicly available microarray data; (3) research tools, including bioinformatics tools, reporter strains, plasmids, PCR primers, and signaling molecules and other compounds needed to conduct research on biofilm formation and QS; (4) methods used to study biofilms and QS; and (5) embedded tools for functional predictions and pathway re-engineering. This database includes a collection of bacterial genomes, genes, proteins, and signaling molecules, and information on domains, pathways, mechanisms, and various types of mutants, which are all relevant to biofilm formation and QS. Some of candidate genes involved in biofilm formation and QS have been identified by genome-comparisons. The database also includes information on computer modeling of biofilm formation and QS based on literature mining and also on quorum quenching/inhibition methods that can potentially be used to prevent QS and biofilm formation. In our next release the text-mining and data-mining software will be embedded in the database, and scripts are being generated to mine the information by linking to the public databases, including but not limited to the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and PubMed and GenBank at NCBI. Information in the database will be updated regularly through the use of these scripts. The MicroBQs database can be accessed at http://microbqs.arserrc.gov.