FAQ: If my sample DNA is particularly degraded, as is the case with fecal microbiome samples, are there any protocol modifications that will enhance the performance of the NEBNext Microbiome DNA Enrichment Kit with these samples?

While the NEBNext Microbiome DNA Enrichment Kit was designed for high-quality, intact DNA, users report successfully modifying the protocol to better repair low-quality DNA samples. Recommendations for how to adjust the protocol can be found in Chiou and Bergey 2018, Scientific Reports (2018) 8:1975 DOI:10.1038/s41598-018-20427-9; they include:

  • Extra washes.
  • Adjusting the ratio of beads/ host DNA based on qPCR results.
  • 2 rounds of enrichment separated by an NaCl elution

Please also see a protocol here: