Total DNA was isolated from 0.2 g of faeces using the QIAamp DNA Mini Kit (QIAGEN, GmbH, Hilden, Germany), according to the manufacturer’s protocol, but with a modification for lysis of bacterial cells. Instead of enzymatic lysis of bacterial cell walls, we used bead beating with 0.1 mm zirconium/silica beads (Biospec Products INC, Bartlesville, OK, USA) for 2 × 45 s at setting 5.0 in a FastPrep®-24 benchtop homogeniser (MP Biomedicals, Solon, OH, USA) as bead beating improves the lysis of bacterial cell walls [31 (link)]. The isolated DNA was stored at -20 °C until further analysis.
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