REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Fecal samples	This study	N/A
Critical commercial assays
Stratec (now Invitek) Stool Collection Tubes	Stratec (now Invitek), Berlin, Germany	1038111200
Stool DNA Stabilizer PSP Spin Stool DNA	Stratec (now Invitek), Berlin, Germany	1038120200
NEBNext Ultra DNA Library Prep Kit for Illumina	New England Biolabs, Massachusetts, USA	E7645L
Deposited data
Raw sequencing data	This study	PRJNA947377
Metagenome-assembled genomes	This study	PRJNA947377
Software and algorithms
BBMap	sourceforge.net/projects/bbmap/	https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbmap-guide/
MetaPhlAn 4.0	Blanco-Miguez et al.25	https://github.com/biobakery/MetaPhlAn
GTDB-Tk v1.5.0	Chaumeil et al.61	https://github.com/ecogenomics/gtdbtk
metaWRAP v1.3.2	Uritskiy et al.64	https://github.com/bxlab/metaWRAP
VAMB v3.0.2	Nissen et al.65	https://github.com/RasmussenLab/vamb
DAS Tool v1.1.1	Sieber et al.66	https://github.com/cmks/DAS_Tool
CheckM v1.0.7	Parks et al.67	https://ecogenomics.github.io/CheckM/
Bowtie2 v2.3.5.1	Langmead and Salzberg68	https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
CMSeq v1.0.0	Pasolli et al.21	https://github.com/SegataLab/cmseq
GraPhlAn	Asnicar et al.69	https://github.com/biobakery/graphlan
PhyloPhlAn 3.0	Asnicar et al.70	https://github.com/biobakery/phylophlan
iTOL v6.0	Letunic and Bork71	https://itol.embl.de/
python package hclust2	N/A	https://github.com/SegataLab/hclust2
python package scikit-bio v0.5.7	N/A	http://scikit-bio.org/
python package scikit-learn v1.1.2	Pedregosa et al.72	https://scikit-learn.org/
python package matplotlib v3.5.0	Hunter73	https://matplotlib.org/
python package scipy v1.7.3	Virtanen et al.74	https://scipy.org/
python package seaborn v0.11.2	Waskom75	https://seaborn.pydata.org/
python package pandas v1.3.5	McKinney76	https://pandas.pydata.org/
python package statsmodels v0.12.1	Seabold and Perktold77	https://www.statsmodels.org/
python package numpy v1.21.2	Harris et al.78	https://numpy.org/
LEfSe v1.1.2	Segata et al.58	https://huttenhower.sph.harvard.edu/lefse/
R package ggplot2 v3.3.6	Wickham79	https://ggplot2.tidyverse.org/
R package ggpubr v0.4.0	N/A	https://rpkgs.datanovia.com/ggpubr
R package ComplexHeatmap v2.8.0	Gu80	https://bioconductor.org/packages/ComplexHeatmap/
R package mia v1.0.8	N/A	https://github.com/microbiome/mia
R package lfe v2.8.8	Gaure31	https://github.com/sgaure/lfe
R package vegan v2.6.2	Oksanen et al.81	https://github.com/vegandevs/vegan