title: Whole metagenome sequencing (host-depleted) of stool DNA
design: DNA extractions from 0.2 grams of stool were carried out using the vacuum protocol of PowerSoil DNA Isolation Kit (MoBio Laboratories, Inc., Carlsbad, CA, USA) according to the manufacturer's standard protocol. The extracted DNA was stored at -80 C. DNA samples were quantified by Quant-iT PicoGreen dsDNA Assay (Life Technologies) and normalized to a concentration of 50 pg mL Illumina sequencing libraries were prepared from 100-250 pg DNA using the Nextera XT DNA Library Preparation kit (Illumina) according to the manufacturers recommended protocol, with reaction volumes scaled accordingly. Metagenomic libraries were sequenced on the Illumina HiSeq 2500 platform, targeting 2.5 Gb of sequence per sample with 101 bp paired end reads.