REAGENT or RESOURCE	SOURCE	IDENTIFIER
Software and algorithms
GEM mapper build 1.376	Marco-Sola et al.109	https://sourceforge.net/projects/gemlibrary/
Segata DB	Pasolli et al.44	https://github.com/SegataLab
MetaPhlAn2	Truong et al.110	https://bitbucket.org/biobakery/metaphlan2; RRID: SCR_004915
Bowtie2	Langmead et al.111	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Diamond	Buchfink et al.47	https://github.com/bbuchfink/diamond
STAR	Dobin et al.112	N/A
htseq-count	Anders et al.113	N/A
Other
Study participants data	Table S2
Untargeted mass spectrometry	Metabolon, Inc., Durham, North Carolina, USA	https://www.metabolon.com/