16S of Mus musculus: adult female feces
gDNA was extracted from mouse fecal samples using the QIAamp PowerFecal Pro DNA kit. Two-stage PCR amplification of the V1-V3 variable regions of microbial 16S rRNA genes was performed using a mixture of 27F (YM, Bor, Bif, Chl, and Ato variants) and 534R primers with Fluidigm common sequence linkers CS1 and CS2. The second stage used barcoded primers from the Access Array for Illumina system with CS1 and CS2 linkers. Samples were then pooled equimolarly and sequenced using an Illumina MiSeq instrument with a V3 kit with paired-end 2 x 300 base sequencing reads.