shotgun metagenomic of Equus caballus: adult female feces
We weighed 0.2-g portions of 16 freshly thawed fecal samples into 2-ml bead beating tubes containing Qiagen 0.7-mm garnet beads, added 750 l of PowerBead Solution and 60 l of C1 buffer from Qiagens QIAamp PowerFecal DNA Kits to each tube, vortexed each tube for 2 seconds, and incubated tubes for 10 min at 60C. After incubation, we bead beat samples for 10 min on a Vortex-Genie 2 fitted with Qiagens Vortex Adapter (cat. No 13000-V1-24). All other extraction steps were completed as per Qiagen kit recommendations (single-tube extraction protocol). Final DNA extracts were eluted in 100 l of molecular grade water.  DNA extracts were quantified using Qubit dsDNA Broad Range Assays. Extracts were sent to the University of Calgary Centre for Health Genomics and Informatics, where shotgun metagenomic libraries were created using v1 Illumina Nextera XT Index Kit preparations, as per manufacturer specifications. Normalized libraries were sequenced on an Illumina NextSeq 500 High Output Flow Cell to a target depth of 30M (150 bp) read pairs per sample.