Shotgun metagenomic sequencing of human stool sample
Genomic DNA was extracted from fecal specimens using a Maxwell RSC instrument (Promega Corporation, Madison, WI, United States) for automated nucleic acid recovery. Libraries were prepared using a Nextera library preparation kit (Illumina, San Diego, CA, United States) according to manufacturer instructions. Five control specimens were used. Libraries were pooled and sequenced on an Illumina MiniSeq sequencer; based on the relative abundance of reads generated, specimens were repooled and sequenced on a 300-cycle kit implemented on an Illumina NovaSeq 6000 sequencer.