Illumina MiSeq paired end sequencing
Random shotgun seq
Total metagenomic DNA was extracted using the NorDiag Arrow Stool DNA Extraction kit (NorDiag, Oslo, Norway). An extra beadbeating step was added to facilitate cell lysis as studies have shown that this can increase extraction of DNA from Gram-positive bacteria. DNA was quantified using the Nanodrop 1000 and Qubit. The indexed paired-end libraries were prepared for whole genome sequencing using the Nextera XT Kit (Illumina, San Diego, CA, USA), according to the manufacturer's instructions