Comparison of DNA extraction protocols from stool samples

The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to select a unique and best performing DNA extraction protocol for both metagenomic sequencing methods. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Stand-alone versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMerieux) in order to facilitate DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium Difficile infection were extracted with all protocols and sequenced with both metagenomic methods. Protocols were ranked using wet- and dry-lab criteria, including quality control of extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates.