16S rDNA metabarcoding analyses from the goat digestive tract
Genomic DNA was extracted using MoBio DNeasy Powerlyzer DNA isolation Kit (Qiagen, The Netherlands), following the manufacturers instructions. DNA concentration and quality were determined using Nanodrop (Thermo Scientific) and by a 1% agarose gel electrophoresis, respectively. Genomic DNA was stored at -20C, until further analysis. Ten genomic DNA samples were sequenced at the Genoinseq Laboratory(Cantanhede, Portugal, https://www.cnc.uc.pt/en/services) in an Illumina Miseq V2 platform.The bacterial and archaeal structural diversity was determined by metabarcoding sequencing thehypervariable regions V3-V4 and V4-V5, respectively, of the metagenomic 16S rRNA gene with theset of primers 357wF 5 CCTACGGGNGGCWGCAG -3 and 926wR 5CCGTCAATTYMTTTRAGTTT -3 for domain Bacteria (Cilieborg, Boye, Thymann, Jensen, &amp;Sangild, 2011; Herlemann et al., 2011) and 517F 5 GCYTAAAGSRNCCGTAGC -3 and 909R 5TTTCAGYCTTGCGRCCGTAC -3 for domain Archaea (Baker, Smith, &amp; Cowan, 2003; Burggraf,Huber, &amp; Stetter, 1997).