title: Whole metagenome sequencing (host-depleted) of stool DNA
design: Total DNA was extracted from 200 mg of fecal material using the QIAamp DNA Stool minikit (Qiagen) according to the manufacturers instructions, with an additional series of mechanical disruption steps (4 x 60 s). This was followed by bead-based purification. Metagenomic sequencing libraries were prepared for 1,377 stool samples using 2 ng of input DNA with the Nextera XT DNA Library Preparation kit (Illumina) according to the manufacturers recommended protocol. Prior to sequencing, libraries were pooled by collecting equal volumes of each library. Insert sizes and concentrations for each pooled library were determined using an Agilent Bioanalyzer DNA 1000 kit (Agilent Technologies) prior to sequencing on an Illumina NovaSeq 6000 with 151 bp paired-end reads.