Key resources table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Bacterial and virus strains
Biological samples
Stool and blood samples from the Arivale Cohort	This paper
Chemicals, peptides, and recombinant proteins
Critical commercial assays
Deposited data
Stool 16S rRNA sequencing data	This paper	Sequence Read Archive (SRA) Accession numbers: PRJNA826530 PRJNA826648
Demographics, clinical, and metabolomics data	This paper	Data S3
Experimental models: Cell lines
Experimental models: Organisms/strains
Oligonucleotides
Recombinant DNA
Software and algorithms
DADA2 (version 1.20.0)	Callahan et al. 2016	https://benjjneb.github.io/dada2/
DECIPHER (version 2.20.0)	Wright 2015	http://www2.decipher.codes/AlignSequences.html
mbtools (version 0.38.0)	This paper	https://github.com/Gibbons-Lab/mbtools
FastTree (version 2.1.11)	Price et al. 2010	http://www.microbesonlineorg/fasttree/
Phyloseq (version 1.30.0)	McMurdie & Holmes 2013	https://joey711.github.io/phyloseq/
DirichletMultinomial (version 1.28.0)	Holmes et al. 2012	https://microbiome.github.io/tutorials/DMM.html
vegan (version 2.5–7)	Oksanen et al. 2020	https://cran.r-project.org/web/packages/vegan/index.html
RDP	Wang et al. 2007	http://rdp.cme.msu.edu/classifier/classifier.jsp
Statsmodels (version 0.10.2)	Skipper & Perktold 2010	https://www.statsmodels.org/stable/index.html#
Other
SILVA Database (version 132)	Quast et al. 2013	https://www.arb-silva.de/
Metacardis Cohort dataset	Fromentin et al. 2022	https://www.nature.com/articles/s41591–022-01688–4#data-availability