Fecal samples were resuspended in phosphate-buffered saline and sequentially filtered using 0.8 micron (PES) filter (Sartorius). Any remaining DNA that was not encapsidated was degraded by treating with a mixture of Benzonase Endonuclease (EMD Millipore) and Micrococcal Nuclease (New England Biolabs) followed by EDTA inactivation of DNases. The remaining supernatant was subjected to lysis and viral 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). The sterile water control contained no detectable DNA indicating no contamination of exogenous DNA during the analysis. Viral DNA from each sample was pooled into equimolar proportions and sequenced on the Illumina platform at the UCSD IGM Genomics Center.