The NEBNext® Microbiome DNA enrichment kit can separate microbial DNA from host DNA. The kit utilizes the MBD2-Fc protein, which can bind to CpG-methylated DNA (including human genomic DNA) with high specificity. The MDB2-Fc protein is attached to Protein A-coated magnetic beads, allowing for the 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.