The NEBNext® Microbiome DNA Enrichment Kit uses a novel method to separate microbial DNA from host DNA, thereby reducing the high cost of sequencing microbiome DNA to a more practical level.

Microbiome samples are commonly dominated by host DNA (up to 99%). This complicates the genetic analyses of these samples, particularly total microbiome DNA sequencing studies. Since only a small percentage of sequencing reads pertain to the microbes of interest, obtaining sufficient sequence coverage of the microbiome DNA can become cost-prohibitive or even technically infeasible.

The NEBNext Microbiome DNA Enrichment Kit utilizes the MBD2-Fc protein, which binds to CpG-methylated DNA (including human genomic DNA) with very high specificity. The MDB2-Fc protein is attached to Protein A-coated magnetic beads, enabling quick and easy removal of the contaminating host DNA in about 30 minutes. The microbial DNA-enriched sample is then ready to be processed for multiple downstream applications, including next generation sequencing, qPCR and endpoint PCR.

"Although microbiome whole genome sequencing provides more information than other methods, such as 16S analysis, this method has proven difficult for many samples, due to the presence of contaminating host genomic DNA," says Fiona Stewart, Product Marketing Manager, Next Generation Sequencing at NEB. "The NEBNext Microbiome DNA Enrichment Kit makes it possible to substantially enrich samples for non-host, microbial DNA, while retaining microbial diversity, thereby improving the quality and cost-effectiveness of downstream analyses."