16S rRNAseq: CIA+FMC stool day 35, biol replicate 1
Total genomic DNA was extracted using the QIAamp PowerFecal DNA kit (Qiagen Inc, Carlsbad, CA).  PCR amplicons were generated using barcoded primers targeting the V3V4 variable region of the 16S rRNA gene (338F: 5ACTCCTACGGGAGGCAGCAG and 806R: 5 GGACTACHVGGGTWTCTAAT). PCR products were normalized using a SequalPrepTM kit (Invitrogen, Carlsbad, CA) and then pooled. The amplicon pool was partially lyophilized to reduce its volume, purified and concentrated using a DNA Clean and Concentrator Kit (Zymo, Irvine, CA), and then quantified using a Qubit Fluorometer 2.0 (Invitrogen, Carlsbad, CA). The pool was diluted to 4nM and denatured with 0.2 N NaOH at room temperature. The denatured DNA was diluted to 15pM and spiked with 25% of the Illumina PhiX control DNA prior to loading the sequencer. Paired-end sequencing was performed on the Illumina MiSeq platform with versions v2.4 of the MiSeq Control Software and of MiSeq Reporter, using a 600 cycle version 3 reagent kit.