16S rRNA-Seq of mus musculus: stool
V3/V4 region of the 16S rRNA gene was amplified and double indexed using barcoding primers modeled after Kozich et al. PCR fragments were indexed with Nextera XT DNA Library Preparation Kit (Ilumina, USA) and afterwards purified using magnetic AMPure XP beads (Beckman Coulter, USA) according to manufacturers instructions. Finally, a 4pM indexed library was spiked with PhiX control (Ilumina) at 20% and sequenced on Illumina MiSeq with Reagent Kit v3 (Ilumina) for 600 cycles of paired-end reads.