Shotgun metagenomic sequencing
Library preparation was then carried out using the standard input workflow on 200 ng DNA per sample using the Illumina DNA PCR-Free Prep, Tagmentation Kit and IDT for Illumina DNA/RNA UD Indexes (Sets A-D) as described in the Illumina reference guide. Dual-indexed paired-end single-stranded DNA Libraries (450 bp average library size) were then quantified using the CollibriTM Library Quantification kit (ThermoFisher Scientific) on a LightCycler 96 Instrument (Roche Diagnostics Ltd.), adjusted to 2.0 nM and pooled. The pooled library was further checked by sequencing on a MiSeq 300 cycle cartridge (Illumina MiSeq System) and adjusted to 1.5 nM based on sequence reads before deep sequencing on an Illumina NovaSeq 6000 Sequencing System (paired-end 2  150 bp flow cell) with NovaSeq S4 cartridge v1.5 (300 cycles) and 1 % PhiX control