. Author manuscript; available in PMC: 2025 Feb 14.

Published in final edited form as: Cell Host Microbe. 2024 Jan 11;32(2):209–226.e7. doi: 10.1016/j.chom.2023.12.013

KEY RESOURCES TABLE.

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
Veillonella parvula SKV38	Shared by Prof. Justin Merritt from Oregon Health and Science University, USA	N/A
Veillonella parvula SKV38 xdh::cat* [DR214]	This study	N/A
Veillonella parvula SKV38 pucD::cat* [DR213]	This study	N/A
Biological Samples
Stool samples	PROTECT study
Plasma samples	PROTECT study
Chemicals, Peptides, and Recombinant Proteins
6-mercaptopurine	Sigma	852678
Azathioprine	Sigma	A4638
Hypoxanthine	Fluka	H9377
Xanthine	Fluka	X0626
Adenine	Fluka	1830
Guanine	Fluka	G11950
Urate	Fluka	U2625
L-Tryptophan	Sigma	93659–10G
Indolelactic acid	Sigma	I5508–250MG-A
Indoleacetic acid	Sigma	I5508–250MG-A
Indole-3-propionic acid	Sigma	57400–5G-F
Deposited Data
Stool metagenomic sequencing	Sequence Read Archive	PRJNA436359
Stool and plasma metabolomics	National Metabolomics Data Repository	Project DOI: PR001596
Oligonucleotides
P4675’-atcgggtctcaggaggaaggcgtagatgaagttctacg-3’	This paper	N/A
P4685’-atcaggtctctgagtagctcgcaagaaatcaattaaacg-3’	This paper	N/A
P4695’-atcaggtctctgccgccaaaaaatcacgttgcctatgg-3’	This paper	N/A
P4705’-atcgggtctcaatggaattggcaaatgcatagcttgtg-3’	This paper	N/A
P4715’-atcgggtctcaggagtgatgagatgttgctagatacattgc-3’	This paper	N/A
P4725’-atcaggtctctgagtgaactacagggtccaaaataagcg-3’	This paper	N/A
P4735’-atcaggtctctgccggatatcgtaccattcgatccagg-3’	This paper	N/A
P4745’-atcgggtctcaatgggctgaatcaatcgattccaatagg-3’	This paper	N/A
P965’-atcaggtctcgactcagtaaaatgcaggcgagtgaag-3’	This paper	N/A
P3825’-atcaggtctcgcggccattaactatttatcaattcctgcaattcg-3’	This paper	N/A
Recombinant DNA
pDRT004	Rojas-Tapias et al., 2022	N/A
pDRT004 + pucD(cat*)	This paper	N/A
pDRT004 + xdh(cat*)	This paper	N/A
Software and Algorithms
KneadData v0.7.2	http://huttenhower.sph.harvard.edu/kneaddata
MetaPhlAn2	Segata et al., 2012⁹⁸	https://huttenhower.sph.harvard.edu/metaphlan/
MEGAHIT	Li et al., 2015⁹⁹	https://github.com/voutcn/megahit
MegaBLAST	Morgulis et al., 2008¹⁰³	https://blast.ncbi.nlm.nih.gov/Blast.cgi??DATABASE=nr&PAGE=MegaBlast&FILTER=L&QUERY=AL954329
MSPminer	Plaza Oñate et al., 2019¹⁰⁴
MaAsLin2	Mallick et al., 2021¹⁰⁵	https://huttenhower.sph.harvard.edu/maaslin/
PanPhlAn	Scholz et al., 2016¹⁰⁶	http://segatalab.cibio.unitn.it/tools/panphlan/
gutSMASH	Pascal Andreu et al., 2023²⁹	https://gutsmash.bioinformatics.nl/
GapSeq v1.2	Zimmermann et al., 2021⁹⁷	https://github.com/jotech/gapseq
SIRIUS v5.6.3	Dührkop et al., 2019⁹³	https://bio.informatik.uni-jena.de/software/sirius/
Prodigal	Hyatt et al., 2010¹⁰¹	https://github.com/hyattpd/Prodigal