title: shotgun metagenomic of Equus caballus: adult female feces
design: We weighed 0.16-g portions of freshly thawed fecal samples into 2-ml bead beating tubes containing Qiagen 0.7-mm dry garnet beads. Next, we added 680 l of lysis buffer (pre-warmed to 60 C) from Qiagens QIAamp 96 PowerFecal QIAcube HT Kit to each tube, and 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 the Qiagen kit QIAcube HT recommendations (using a single-tube start protocol) for high-throughput DNA extractions. Final DNA extracts were eluted in 100 l of molecular grade water. DNA extracts were quantified using Quant-iT 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 iGenomx Riptide preparations (1:1 mixture of low GC and High GC primers), as per manufacturer specifications. We sequenced a total of 188 samples using an Illumina NovaSeq 6000 (300 cycle SP sequencing kit v1.5 2 lanes) to a target depth of 4.1M (150 bp) read pairs per sample.