design: Bacterial genomic DNA was extracted from fecal samples using the Qiagen PowerSoil Kit. DNA libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina) and genomic DNA was fragmented with Illumina Nextera XT fragmentation enzyme. IDT Unique Dual Indexes were added to each sample before 12 cycles of PCR amplification. AMpure magnetic Beads (Beckman Coulter) were used to purify DNA libraries which were eluted in QIAGEN EB buffer. Qubit 4 fluorometer and Qubit dsDNA HS Assay Kit were used for DNA library quantification. Libraries were then sequenced on Illumina HiSeq 4000 platform 2x150bp at a 6M read depth using by CosmosID