Illumina shotgun metagenomic sequencing of S1-CAM-02_pre-enriched
Pre-enriched stool gDNA isolation from native stool was performed following the protocol for fecal samples from the Invitrogen PureLink Microbiome DNA purification kit using an 800 l aliquot of cefuroxime pre-enriched broth (i.e., bacterial/stool pellet was used after centrifugation) as starting material. Quality and quantity of pre-enriched  gDNA isolations were assessed by Nanodrop and Qubit (dsDNA High-Sensitivity kit (HS)). Libraries were prepared with the NEBNext Ultra II FS DNA Library Prep Kit and sequenced on a NovaSeq 6000 platform (2 x 150-bp paired-end) by Eurofins Genomics. Raw reads were preprocessed by removing optical duplicates with BBMap v38.18 using clumpify.sh (dedupe optical dist=12000), followed by read quality read trimming with Trimmomatic v0.36 (minimum length= 60 bp) and host decontamination (human reads) with Kneaddata v0.10.0 using both GRCh37 (hg37dec) and GRCh38 (GRCh38_noalt_decoy_as) human genome assemblies.