Fecal sample collection, DNA isolation, and 16S rRNA gene sequencing

Fecal samples were collected from 8 mice per group (32 mice total) before treatment and once per week for 5 weeks. Fecal samples were frozen immediately after collection and stored at −80°C. Bacterial DNA was extracted from the samples with the DNeasy PowerSoil Kit (Qiagen) and stored at −80°C. The V4 hypervariable region of the 16S rRNA gene was PCR amplified with primers 515F and 806R (39). The reverse primers contained unique 12-bp Golay barcodes that were incorporated into the PCR amplicons (39). Amplicon sequence libraries were prepared at the Scripps Research Institute Next Generation Sequencing Core Facility, where the libraries were sequenced on an Illumina MiSeq as previously described (27).