Code availability
The following programmes were used for data collection: Castor EDC (v2019.2.0-2020.2.25), EPIC (versions August 2019-November 2020), Voedingscentrum Eetmeter (v2019-2020), Freestyle Libre 1 software. The following software and codes were used for data analysis: R v4.2.1, CGDA v0.8.2, fastp v0.23.2, bbmap v38.90, metaSPAdes v3.15.5, MEGAHIT v1.2.9, virsorter v2.2.3, checkv v1.0.1, BLAST v2.12.0+, vContact2 v0.11.3, bowtie2 v2.4.2, coverm filter v0.6.1, bedtools v2.27.1, samtools v1.15.1, mOTUs v3.0.3, jgi_summarize_bam_contig_depths v2.15, metabat2 v2:2.15, checkm v1.2.1, GTDB-Tk v2.1.1, CRISPCasFinder v4.2.20, vegan R package v2.6-4, MASS R package v7.3-58.1 and ANCOM-BC v1.2.2. In the ”Methods” section any specific settings are described. Codes and scripts are publicly available online and from published literature. No custom software was developed for this project.