16S of gut microbiome of Sus scrofa domesticus
DNA extraction was performed using the MagMAXTM Pathogen RNA/DNA kit (Thermo Fisher Scientific, Waltham, MA, USA) and a Kingfisher Flex instrument (Thermo Fisher Scientific) following the instructions of the manufacturer. Samples were then submitted to the Iowa State University DNA Facility for library preparation and 16S metagenomics sequencing. Extracted total DNA was amplified using primers (515F and 806R) specific to the V4 regions of the bacterial 16S rRNA gene and library preparation was performed as previously described (3841).  Following library preparation samples were run on 150 paired-end cycles on an Illumina MiSeq instrument. A total of 721 samples were submitted and sequenced on three lanes with a maximum number of samples per lane of 240.  Negative controls consisting of sterile swabs in DPBS as well as a negative extraction control were included; positive controls consisting of Zymobiomics Microbial Community standards (catalog #D6305 and D6300; Zymo Research Corporation, Irvine, CA) were also included on all plates to ensure consistency across plates in sequencing.