Specific enrichment of DNA fragments (GeneBeads)

Metagenomics is a promising approach for the study of microbial communities, opening the opportunity to study microbial genomes directly from environmental sources. However classic metagenomic studies require a considerable effort, as libraries consisting of up to hundreds of thousands of large construct clones have to be screened (and / or sequenced), specifically if the microbial diversity in the studied system is large. For many research questions it would be more appropriate to specifically target only a subgroup of the entire diversity that is of interest instead of cloning the entire metagenome. Several approaches are possible, ranging from classical enrichment to size selection to cell sorting with a flow cytometer. In the GeneBeads project we are testing a magnetic beads based capture method to specifically enrich genome fragments. The goal is to evaluate the suitability of this approach as a universal approach for performing targeted metagenomics. For this end we are evaluating, among other parameters, the enrichment efficiency, specificity, the size of retrieved fragments, and suitability of the enrichments for downstream applications.

Funding

Eawag Seed Project 2008