Human stool samples were resuspended in phosphate-buffered saline and sequentially filtered using 0.8 micron (PES) filter. Any remaining DNA that was not encapsidated was degraded by treating with a mixture of benzonase (EMD Millipore) and micrococcal nuclease (New England Biolabs) followed by EDTA inactivation of DNases. The remaining supernatant was subjected to lysis and virome DNA and RNA were extracted using the QIAamp Viral RNA mini kit without carrier RNA (Qiagen). Amplification was performed using a modified WTA2 (Complete Transcriptome Amplification Kit) protocol from Sigma Aldrich. Library preparation was performed using an adjusted protocol for the Nextera XT DNA Library Preparation kit from Illumina. The size of amplified viral products was determined using a High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies) and concentration was measured by High Sensitivity Double Stranded DNA kit on a Qubit Fluorometer (Thermo Fisher Scientific). Viral DNA from each sample was pooled into equimolar proportions and sequenced on Illumina platforms at UCSD.