Bar-seq of barcoded B. theta population: experiment E2 mouse 12 at day 55 from feces
DNA was extracted using PowerSoil HTP 96 kits (for homogenized fecal pellets, ceca, and small intestines) and UltraClean 96 microbial kits (for in vitro cultures) [Qiagen]. The barcode locus was amplified using custom primers and a two-stage Phusion High-fidelity DNA polymerase PCR [NEB]. In a three-cycle PCR, adapter regions and unique molecular identifier (UMI) barcodes were added to each template. Primers were removed using Ampure XP Beads [Beckman Coulter]. Labeled templates were then amplified over thirty cycles of a second PCR with TruSeq unique dual indices [Illumina] attached to permit pooled sequencing and demultiplexing.  Clean up on pooled libraries was performed with Ampure XP Beads [Beckman Coulter] prior to sequencing.