BioSurfDB

BioSurfDB provides a curated relational database integrating organismal, gene, protein, metabolic pathway, metagenomic and experimental data related to biosurfactant production and pollutant biodegradation to support bioremediation research.

Key Features:

• Metagenomic Data Integration: Includes metagenomes from uncultured microorganisms to capture surfactant-producing and/or oil-degrading bacteria in environmental samples.
• Organismal Information: Contains detailed records of organisms involved in bioremediation processes.
• Genes and Proteins: Catalogs genes relevant to biodegradation, associated proteins, and metabolic pathways underpinning biosurfactant production and pollutant degradation.
• Experimental Results: Stores results from bioremediation experiments, including treatment efficiencies for specific pollutants such as crude oil using surfactant-producing organisms.
• Biosurfactant Curated List: Provides a curated list of biosurfactants organized by producing organism, surfactant name, class, and reference.
• Computational Tools: Offers computational tools for analyzing genomic and metagenomic data.

Scientific Applications:

• Microbial community characterization: Identification of surfactant-producing and oil-degrading bacteria from metagenomes in contaminated environments.
• Gene and pathway discovery: Exploration of genes, proteins, and metabolic pathways involved in biosurfactant production and pollutant biodegradation.
• Bioremediation strategy assessment: Comparison and evaluation of treatment efficiencies for pollutants, including crude oil, using experimental data.
• Biosurfactant candidate selection: Selection of potential biosurfactants by organism, name, class, and literature reference for application in bioremediation.

Methodology:

Curation and integration of metagenomic, organismal, gene/protein, metabolic pathway, and experimental data into a relational database and provision of computational tools for genomic and metagenomic analysis.