A multiplexed amplicon library covering the 16S rDNA gene V4 region was generated from human stool sample DNA as described 58 (link). Briefly, bacterial genomic DNA was extracted using the Mo Bio Power Fecal DNA Isolation kit (Mo Bio Laboratories) according to the manufacturer's instructions. To increase the DNA yields, the following modifications were used. An additional bead beater step using the Faster Prep FP120 (Thermo) at 6 meters/second for 1 min was used instead of vortex agitation. Incubation with buffers C2 and C3 was done for 10 min at 4°C. Starting nucleic acid concentrations were determined by a Qubit Fluromoter (Life Technologies). The amplicon library was prepared using dual-index barcodes 58 (link). The aggregated library pool was size selected from 300-500 base pairs (bp) on a pippin prep 1.5% agarose cassette (Sage Sciences) according to the manufacturer's instructions. The concentration of the pool was measured by qPCR (Kapa Biosystems) and loaded onto the MiSeq Illumina instrument (300 bp kit) at 6-9pM with 40% phiX spike-in to compensate for low base diversity according to Illumina's standard loading protocol.