KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological Samples
Human fecal and plasma samples	This study	N/A
Critical Commercial Assays
DNeasy PowerSoil Kit	QIAGEN	12888-100
Nextera XT DNA Library Preparation Kit	Illumina	FC-131-1096
Nextera XT Index Kit v2, Set A/B/C/D	Illumina	FC-131-2001/2/3/4
Quant-iT™ PicoGreen™ dsDNA Assay Kit	ThermoFisher Scientific	P7589
High Sensitivity NGS Fragment Analysis Kit (1-6000 bp), 500 Samples	Agilent Technologies, Inc.	DNF-474-0500
HiSeq PE Cluster Kit v4 cBot	Illumina	PE-401-4001
HiSeq SBS Kit V4 250 Cycle Kit	Illumina	FC-401-4003
TaqMan™ Fast Universal PCR Master Mix (2X), no AmpErase™ UNG	ThermoFisher Scientific	CAT# 4352042
Deposited Data
Metagenomics sequencing	This paper	SUB7782171
Human genome	NCBI	GRCh38.p4
Metabolomics data	This paper	http://dx.doi.org/10.17632/ykb5wh3gn3.1
Stool metabolomics data: identified metabolites from HILIC-pos, C8-pos, HILIC-neg, and C18-neg methods	National Metabolomics Data Repository (www.metabolomicsworkbench.org)	Accession number: PR001024
Stool metabolomics data: unknown peak data from HILIC-pos, C8-pos, HILIC-neg, and C18-neg methods	National Metabolomics Data Repository (www.metabolomicsworkbench.org)	Accession number: PR001024
Plasma metabolomics data: identified metabolites from HILIC-pos, C8-pos, HILIC-neg, and C18-neg methods	National Metabolomics Data Repository (www.metabolomicsworkbench.org)	Accession number: PR001024
Plasma metabolomics data: unknown peak data from HILIC-pos, C8-pos, HILIC-neg, and C18-neg methods	National Metabolomics Data Repository (www.metabolomicsworkbench.org)	Accession number: PR001024
Oligonucleotides
BSF8, 16S qPCR forward primer: AGAGTTTGATCCTGGCTCAG	Hill et al, 2010	N/A
BSR357, 16S qPCR reverse primer: CTGCTGCCTYCCGTA	Hill et al., 2010	N/A
16S qPCR probe (+ indicates locked nucleic acid base): /56-FAM/TAA +CA+C ATG +CA+A GT+C GA/3BHQ_1/	Hill et al., 2010	N/A
Software and Algorithms
Demultiplexing software	This paper	https://github.com/PennChopMicrobiomeProgram/dnabc
Trimmomatic	Bolger et al., 2014	https://github.com/PennChopMicrobiomeProgram/illqc, http://www.usadellab.org/cms/index.php?page=trimmomatic
Bwa2	Li et al., 2009	https://github.com/PennChopMicrobiomeProgram/decontam
MetaPhlAn2	Truong et al., 2015	https://huttenhower.sph.harvard.edu/metaphlan
Gene assignments	This paper	https://github.com/PennChopMicrobiomeProgram/PathwayAbundanceFinder
RAPSearch2 and DIAMOND search	Zhao et al., 2012 Buchfink et al., 2015	https://omics.informatics.indiana.edu/mg/RAPSearch2/ http://www.diamondsearch.org/index.php
The Human Metabolome Database	Wishart et al., 2018	www.hmdb.ca/