2.5. DNA Extraction

DNA was extracted from intestinal samples using an E.Z.N.A.^® Stool DNA Kit (Omega Bio-tek, Inc.; Norcross, GA, USA) according to the manufacturer’s instructions, applying the following modifications: 700 µL of lysis buffer SL2 provided in the kit was added to 250 mg of intestinal digesta. Samples were disrupted in a FastPrep-24TM benchtop homogenizer using metal beads instead of Glass Beads X, to enhance obtained DNA concentration. DNA was eluted in a final volume of 50 µL of elution buffer, DNA purity (OD260/OD280 ratio of ~1.8) was evaluated with the Nanodrop ND1000 (Thermo Scientific, Waltham, MA, USA), and quantified fluorometrically with Qubit 3.0 HS dsDNA assay (Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA ). DNA concentrations were adjusted to 5 ng/μL using DNase I, RNase-free water (Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA ), instead of the elution buffer, as the elution buffer had an inhibitory effect on the PCR.