shotgun metagenomic sequences from mouse fecal pellet
Isolation of fecal DNA, sequence library preparation, and next generation sequencing was performed at CosmosID Inc. (Germantown, MD, USA). Isolation of DNA from fecal pellets was performed using QIAGEN DNeasy PowerSoil Pro Kit (Germantown, MD, USA) according to the manufacturers protocol, then quantified using Qubit 4 fluorometer and dsDNA HS Assay Kit (Thermofisher Scientific, Waltham, MA, USA). Isolated DNA was stored at -20C until library preparation. Sequence libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, USA) and Integrated DNA Technologies unique dual indexes (San Diego, CA, USA) with a total DNA input of 1ng. Genomic DNA was fragmented using a proportional amount of Illumina Nextera XT fragmentation enzyme. Unique dual indexes were added to each sample followed by 12 cycles of PCR to construct libraries. Sequence libraries were purified using AMPure magnetic beads (Beckman Coulter, Brea, CA, USA) and eluted in QIAGEN EB buffer. Sequence libraries were quantified using the Qubit 4 fluorometer and dsDNA HS Assay Kit. Libraries were then sequenced on an Illumina HiSeq X platform with 150 bp paired-end sequencing. Number of reads ranged from 1M to 5M per sample.