16S-seq. of sus scrofa: rectal swab
DNA extraction from swabs was performed using the MagMax Total Nucleic Acid Isolation Kit (Thermo Fischer Scientific). Samples were subjected to a PCR targeting the V4 region of the 16S rRNA gene using the Taq Platinum High Fidelity DNA Polymerase enzyme (Thermo Fischer Scientific). Sequencing libraries were prepared utilizing Illumina's protocol, with purification being made using AMPure XP beads (Agencourt), indexing using  Nextera XT index. Amplicons were sequenced on the Miseq platform, using a v3 kit with 2 x 250 bp reads.