16S rRNA gene sequence from pigs
The target V4 region was amplified using 515f/806r primers with Nextera overhangs using KAPA HiFi HotStart ReadyMix . Index primers were annealed to the amplicon product, such that each sample was given a unique combination of primer barcodes through combinatorial Nextera i5 and i7 indexing. Indexed samples were then quantified and pooled in equimolar concentrations. The pooled library was cleaned with Kapa Pure Beads before performing paired end 250bp read sequencing on a MiSeq500 at the University of California Davis DNA Technologies core.