Lysing matrix e kit

All chemicals, solvents, and reagents were purchased from Sigma-Aldrich unless otherwise noted. Half of the collected swab samples, one of the two swab samples collected each collection day, were processed for DNA sequencing, and the other half remained at −80°C and were used as backup in case of contamination during the sample preparation process. Swab samples were thawed to room temperature during a 10-min centrifugation at 6,000 × g and then transferred to bead tubes from the MP Biomedicals (Irvine, CA) lysing matrix E kit. Extraction was then performed with the DNA/RNA 96 kit (Qiagen AllPrep; Germantown, MD) following the manufacturer’s protocol after homogenization for 1 min at speed 6.5 using MP Biomedicals FastPrep-24 5G Instrument followed by incubation for 5 min at 4°C and 10 min of centrifugation at 15,000 rpm. Five extraction control blanks were included per extraction plate.

After the mechanical lysing of bacteria using the Lysing Matrix E kit (MP Biomedical), from 150 mg of faeces, DNA extraction was performed using the Stool Mini Kit (Qiagen). The yield and purity of DNA extracts were quantified using a Nanodrop 2000 (Thermo Fisher Scientific) and DNA quality was tested on 1.5% agarose gel electrophoresis.