BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies

• Published in: Database : the journal of biological databases and curation Vol. 2015
• Main Authors: Oliveira, Jorge S., Araújo, Wydemberg, Lopes Sales, Ana Isabela, Brito Guerra, Alaine de, Silva Araújo, Sinara Carla da, de Vasconcelos, Ana Tereza Ribeiro, Agnez-Lima, Lucymara F., Freitas, Ana Teresa
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 2015
• Subjects: Biodegradation; Biodegradation, Environmental; Bioremediation; Databases, Genetic; Metagenome; Metagenomics; Organisms; Original; Petroleum - metabolism; Petroleum Pollution; Soil Microbiology; Surface-Active Agents; Surfactants
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/bav033

Crude oil extraction, transportation and use provoke the contamination of countless ecosystems. Therefore, bioremediation through surfactants mobilization or biodegradation is an important subject, both economically and environmentally. Bioremediation research had a great boost with the recent advances in Metagenomics, as it enabled the sequencing of uncultured microorganisms providing new insights on surfactant-producing and/or oil-degrading bacteria. Many research studies are making available genomic data from unknown organisms obtained from metagenomics analysis of oil-contaminated environmental samples. These new datasets are presently demanding the development of new tools and data repositories tailored for the biological analysis in a context of bioremediation data analysis. This work presents BioSurfDB, www.biosurfdb.org, a curated relational information system integrating data from: (i) metagenomes; (ii) organisms; (iii) biodegradation relevant genes; proteins and their metabolic pathways; (iv) bioremediation experiments results, with specific pollutants treatment efficiencies by surfactant producing organisms; and (v) a biosurfactant-curated list, grouped by producing organism, surfactant name, class and reference. The main goal of this repository is to gather information on the characterization of biological compounds and mechanisms involved in biosurfactant production and/or biodegradation and make it available in a curated way and associated with a number of computational tools to support studies of genomic and metagenomic data.