title: Shotgun metagenome prairie vole stool microbiome, Sample_31_female_voleS16_post_live_treated
design: DNA was prepared from -80oC-frozen stool samples using the MoBio/QiaAmp PowerFecal DNA kit, according to manufacturers instructions (Qiagen-USA, Germantown, MD). Isolated DNA was quantified by absorbance at 260 nm on a Nanodrop spectrophotometer and by fluorescence using the dsDNA HS DNA Assay on a Qubit fluorometer (both instruments by ThermoFisher, Waltham, MA, USA). Genomic DNA was sheared using a Covaris E220 focused-ultrasonicator. Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA), following the manufacturer's protocol.  500 ng total DNA was found to be sufficient for high-yield libraries. For the 32 samples from the 16 L. reuteri-treated females, the average library fragment size was 885 bp. Sequencing library and library pool quantifications were performed with the KAPA Library Quantification Kit for Illumina platforms (Roche, Basel, Switzerland). Whole-genome shotgun sequencing of libraries was performed on an Illumina HiSeq 2500 sequencer in the Florida State College of Medicine Translational Science Laboratory. Paired-end 250-base sequence reads were generated in the cBOT Rapid Run protocol. The shotgun metagenome sequencing of 32 samples from the 16 L. reuteri-treated females was performed on the HiSeq, with paired-end 250-base sequence reads generated in the cBOT Rapid Run protocol.