BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies

Abstract

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.Database URL: www.biosurfdb.org

Potential Biotechnological Strategies for the Cleanup of Heavy Metals and Metalloids

“…The rapidly accumulated knowledge on biosurfactants derived by computational biologists and bioinformaticians allowed the development of computational methods that are especially tailored for biosurfactant discovery as well as online resources to collect the accumulated data/knowledge in centralized resources. For instance, the BioSurf database provides curated information about biosurfactants and their organisms, proteins, metabolic pathways as well as associated algorithms and bioinformatics tools used for biosurfactant discovery ( Oliveira et al, 2015 ). Biosurfactants and their applications have been reviewed in detail in several recent reports ( Müller et al, 2012 ; Kiran et al, 2015 ; Mnif and Ghribi, 2015 ).…”

Genome sequence of Pseudomonas aeruginosa PA1-Petro—A role model of environmental adaptation and a potential biotechnological tool

“…To identify proteins and metabolic pathways related to hydrocarbon degradation and biosurfactant production, the three genomes were aligned against the BioSurfDB ( Oliveira et al., 2015 ), which comprises domain-specific databases, including nucleotide and protein sequences, available at www.biosurfdb.org . We chose the BLASTx alignment tool, which uses a protein database to align with nucleotide sequences, with an E-value of 1e−3.…”

Microbial Culture in Minimal Medium With Oil Favors Enrichment of Biosurfactant Producing Genes

“…Taxonomic analyses were performed using MG-RAST, with the default parameters, against the SILVA Databases (Quast et al, 2013). The biodegradation functional analyses of hydrocarbons and biosurfactant production were performed using the BLAST program (Gish et al, 1990) against the protein database of the Biosurfactant and Biodegradation Database (BioSurfDB) (Oliveira et al, 2015). For this analysis, Trimmomatic (Bolger et al, 2014) was used to remove quality index bases < 20, as well as fragments of sizes less than 30 bp.…”