Bacterial DNA Extraction from Stool Samples

Genomic DNA was extracted from bacterial suspensions obtained from stool samples, as previously described (Molino et al., 2021 (link)). Both the MagNA Pure LC JE379 platform (Roche), with DNA Isolation Kit III (Bacteria, Fungi) (REF 03264785001), and the eMAG Magnetic Extraction System (Biomerieux) (REF 418591) were used for DNA extraction, following the manufacturer’s instructions, with a previous lysis with lysozyme at a final concentration of 0.1 mg/ml. These two DNA extraction methods were previously proven to produce reliable and comparable results in our laboratory. DNA integrity was determined by agarose gel electrophoresis (0.8% w/v agarose in Tris-acetate-EDTA buffer) and DNA samples were quantified using a Qubit 3⋅0 Fluorometer (Invitrogen). All DNA samples were stored at −20°C until further processing.