Diversity and microbiome feature abundance quantification
All shotgun metagenomic sequencing was quality-controlled prior to analysis. We executed all quality control with a combination of bbtoolsAnnotation of microbial taxa, pathways, and gene family abundances was performed using MetaPhlAn3 and HUMAnN3 running the default settings.Shannon and Simpson diversity were computed for each phylogenetic level with the vegan package in R.