Bar-seq of barcoded B. theta population: in vitro expt EV, plate_well p2_B3 at passage 31
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.