Optimized DNA isolation from human stool samples for microbiome analysis

Fast and reproducible DNA isolation methods are needed to handle large sample collections in expanding microbiome studies. We used Chemagic 360 chemistry and MSM1 instrument to compare two sample preservatives and four different pre-treatment protocols to find an optimal high-throughput method for DNA isolation on fecal samples. The pre-treatments included bead-beating, sample handling in tube and plate format and proteinase K incubation. Three human fecal samples (adult, senior and infant) with technical replicates were extracted. The extraction included negative controls (OMNIgeneGUT, DNA/RNA shield fluid and Chemagic Lysis Buffer 1) and Zymobiomics Gut Microbiome Standard as a positive control. DNA quantity was measured using Qubit-fluorometer, DNA purity and quality using gel electrophoresis, and taxonomic signatures with 16S rRNA gene-based sequencing with V3V4 and V4 regions.