title: Metagenome shotgun sequencing of Mus musculus: cecum sham
design: All laboratory procedures were conducted under a hood with laminar flow (LabGarda ES Energy Sever Classe II Laminar Flow, NuAire Inc., Plymouth, Minnesota) to limit environmental contamination. Total DNA was extracted from 20-50 mg aliquots from the previously frozen stool and caecum content using the ZymoBIOMICS DNA Miniprep Kit (ZYMO Research Europe GmbH, Freiburg, Germany) with slight modifications for better mechanical disruption (for more information see Supplementary Methods). Isolated DNA concentration was measured by Qubit (Thermo Fisher Scientific, Waltham, WA), DNA integrity and purity were assayed using a 5400 Fragment Analyzer (Agilent, Santa Clara, CA, United States). All isolated DNA passed the quality control measures. Metagenomics library preparation and sequencing (Illumina NovaSeq 6000 PE150, at minimum of 6G raw data per sample) was performed by Novogene (Novogene (UK) Company Limited).