title: Shotgun sequencing of mouse fecal microbiome: fed with HMOs
design: DNA was extracted from fecal samples using NucleoSpin 96 Soil (Macherey-Nagel). Bead beating was done on a Vortex-Genie 2 horizontally for 5 min. The quality of the DNA samples was evaluated using agarose gel electrophoresis, NanoDrop 2000 spectrophotometry and Qubit 2.0 fluorometer quantitation. The genomic DNA was randomly sheared into fragments of around 350 bp. The fragmented DNA was used for library construction using NEBNext Ultra Library Prep Kit for Illumina (New England Biolabs). The prepared DNA libraries were evaluated using Qubit 2.0 fluorometer quantitation and Agilent 2100 Bioanalyzer for the fragment size distribution. Quantitative real-time PCR (qPCR) was used to determine the concentration of the final library before sequencing. The library was sequenced using 2 x 150 bp paired-end sequencing on an Illumina platform.