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