Shotgun sequencing of feces from Mus Musculus
Mouse fecal samples were placed in individual tubes containing DNA stabilization buffer and shipped for DNA extraction, library preparation, and sequencing by Transnetyx (Cordova, TN USA). DNA extraction is performed using the Qiagen DNeasy 96 PowerSoil Pro QIAcube HT extraction kit and protocol. After DNA extraction and quality control (QC), genomic DNA was converted into sequencing libraries using a method optimized for minimal bias. Unique dual indexed (UDI) adapters were used to ensure that reads and/or organisms are not misassigned. Library preparation is performed using the KAPA HyperPlus library preparation protocol. After QC, the libraries were sequenced using the Illumina NovaSeq instrument and the shotgun sequencing method (a depth of 2 million 2x150 bp read pairs).