Assessment of fecal DNA extraction protocols for metagenomic study

Aiming at providing an alternative method for human fecal DNA extraction, this study compared 5 DNA extraction protocols (MagPure Stool DNA KF Kit (MP), Macherey-Nagel Nucleospin Soil kit (MN), Zymo Research Quick-DNATM Fecal/Soil Microbe kit (ZYMO), MOBIO DNeasy PowerSoil protocol (PS) and MetaHIT) with a standardized protocol Q using 1 microbial mock community (MMC) (contained 8 bacterial and 2 fungal strains) and fecal samples from 6 individuals via shotgun metagenomics sequencing. For each protocol, six technical replicates were generated on the MMC and each human fecal sample. In total, 233 qualified DNA samples (36 MMC extractions and 197 human fecal DNA extractions) were subjected to shotgun sequencing and further quantitative analyses.