WGA of Sus scrofa gut metagenome: Pen Wall and Floor of Treated pigs 0 days post weaning of farm 6
The DNA was extracted using the QIAamp PowerFecal Pro DNA Kit (Qiagen, Crawley, West Sussex, UK) following the manufacturers instructions, using 200  50 mg of faecal content from samples. Environmental samples were previously thawed on ice, centrifuged at 15.000 rpm for 1 min at 4 C, the supernatant was discarded and pellet was used for DNA extraction. A Qubit fluorometer (Qubit 3, BioSciences, Dublin, Ireland) was used to determine the total DNA concentration. Paired-end sequencing libraries were prepared from the extracted DNA using the Illumina Nextera XT Library Preparation Kit (Illumina Inc., San Diego, CA) followed by sequencing on the Illumina NextSeq 500 platform using high-output chemistry (2  150 bp) according to the manufacturers instructions. Libraries size from each sample was assessed on an Agilent Technology 21000 Bioanalyzer using a High Sensitivity DNA chip.