Gut metagenome from participant 11340at visit 0
Swab samples were extracted using bead-beating with Lysing Matrix E beads (MP Biomedicals, Burlingame, CA) in RLT-Plus lysis buffer from the AllPrep DNA/RNA isolation kit (Qiagen). DNA extraction was completed using the AllPrep DNA/RNA isolation kit per manufacturers protocol. Sponge samples were first eluted as previously described25, then extraction was performed as described above for swabs. Barcoded libraries were prepared using the Qiagen FX DNA Library Kit following manufacturers protocols and sequenced using Illumina NextSeq500 2x150bp v2 chemistry to a target depth of 10 million read pairs per sample.