WGS of mus musculus fecal sample
Individual libraries constructed from each sample were loaded onto the HiSeq platform (Illumina) and sequenced using the 2 x 100 base pair (bp) pair-end read protocol. Illumina paired-end libraries were constructed from total genomic DNA isolated from each sample. The DNA was sheared into approximately 400600 bp fragments followed by ligation of Illumina adaptors containing molecular barcodes for downstream de-multiplexing. These products were then amplified through ligation-mediated PCR (LM-PCR) using KAPA HiFi DNA Polymerase (Kapa Biosystems, Wilmington, MA, USA). Following bead purification with Agencourt AMPure XP (Beckman Coulter, Brea, CA, USA), quantification and size distribution of the LM-PCR product was determined using the LabChip GX electrophoresis system (PerkinElmer, Akron, OH, USA). Libraries were pooled in equimolar amounts at six samples per pool and prepared for sequencing with TruSeq PE Cluster Generation Kit (Illumina). Each library pool was loaded onto one lane of a HiSeq 2000 flow cell spiked with 1% PhiX control library.