IBD-Appendix
DNA extraction was conducted using the QIAamp Fast DNA Stool Mini Kit (QIAGEN), and the quality, size, and concentration of the extracted DNA were assessed using NanoDrop 1000 Spectrophotometers (Thermo Fisher Scientific). Whole-genome shotgun libraries were prepared after quantifying metagenomic DNA samples with the Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific) and normalizing them to a concentration of 50 ng/L. Illumina sequencing libraries were prepared from 500pg of DNA using the Shotgun Library prep protocol with the NEBNext Ultra II DNA Library Prep Kit (Illumina), following the manufacturers protocol. The pooled libraries were sequenced on NovaSeq6000 S4 PE150 platform (Illumina), generating 2x150 bp paired-end reads, with ~30M million reads per sample. The sequencing was performed at the Gnome Qubec Innovation Centre (QC, Canada).