title: 16S rRNA gene amplicon sequencing of sow cervical, vaginal and fecal microbial communities
design: genomic DNA from each sample was amplified using Platinum Taq DNA Polymerase (Thermo Fisher Scientific, Waltham, MA) with one replicate per sample using universal 16S rRNA gene bacterial primers  [515F (5-GTGYCAGCMGCCGCGGTAA-3; Parada et al., 2016 ), and 806R (5-GGACTACNVGGGTWTCTAAT-3; Apprill et al., 2015 )] for the variable region V4, as previously described (Kozich et al., 2013). All samples underwent PCR with an initial denaturation step at 94C for 3 min, followed by 45 s of denaturing at 94C, 20 s of annealing at 50C, and 90 s of extension at 72C. This was repeated for 35 total PCR cycles and finished with a 10 min extension at 72C. All the PCR products were then purified with the QIAquick 96 PCR Purification Kit (Qiagen Sciences Inc, Germantown, MD) according to the manufacturers recommendations. PCR bar-coded amplicons were mixed at equal molar ratios and used for Illumina MiSeq paired-end sequencing with 150 bp read length and cluster generation with 10% PhiX control DNA on an Illumina MiSeq platform (Illumina Inc., San Diego, CA).