Whole metagenome sequencing of human oral, vaginal, and rectal microbiome samples

The purpose of this study was to evaluate if systematic differences occur when different commercially available DNA extraction kits are used for whole metagenomic sequencing (WMS) analysis of the human microbiome. Oral, vaginal, and rectal swabs were collected in replicates of four by a healthcare provider from five participants and randomized to one of four DNA extraction kits. Two extraction blanks and three replicate mock community samples were also extracted using each extraction kit. WMS was completed with NovaSeq 6000 for all samples.