Fecal DNA metagenomic shotgun sequencing
Fecal DNA was quantified using a Qubit Fluorometer (Themo Fisher Scientific, Carlsbad, United States). Sequencing libraries were prepared with Nextera XT Library kit (Illumina, San Diego, United States) following the manufacturer’s instructions. The samples were sequenced using a NovaSeq 6000 platform with paired-end reads of 151 base pairs, resulting in 45.2 million ( ± 2.8 million) paired-ends per sample. Demultiplexed reads were filtered with BBTools suite and quality filtering was performed with BBMap (version 38.36) (