KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Enrofloxacin	Sigma-Aldrich	Prod#17849
Vancomycin	Sigma-Aldrich	Prod#V2002
Ampicillin	Sigma-Aldrich	Prod#A9393
Neomycin	Sigma-Aldrich	Prod#N6386
Metronidazole	Sigma-Aldrich	Prod#M1547
Critical commercial assays
QIAamp PowerFecal Pro DNA kit	Qiagen	Cat#51804
Quant-iT BR dsDNA kit	ThermoFisher	Cat#Q32853
Buffer EB (250 mL)	Qiagen	Cat# 19,086
HS NGS Fragment Kit (1-6000bp), 500	Agilent	Cat# DNF-474-0500
Phusion™ High-Fidelity DNA Polymerase	ThermoFisher	Cat# F350L
Qubit dsDNA HS Assay Kit	Invitrogen	Cat# Q32851
Axygen™ MAGPCRCL250	ThermoFisher	Cat# 14-223-153
MiSeq Reagent Kit v2 (500-cycles)	Illumina	Cat# MS-102-2003
Deposited data
Raw data	This paper	PRJNA689557 (cohort 1), PRJNA790931 (cohort 2)
Experimental models: Organisms/strains
Mus musculus, C57BL/6NHsd	Envigo	Order code: 044
Oligonucleotides
Primer: U515 Forward: GTGYCAGCMGCCGCGGTAA	IDT	https://doi.org/10.1128/mSystems.00009-15
Primer: 806 Reverse: GGACTACNVGGGTWTCTAAT	IDT	https://doi.org/10.1128/mSystems.00009-15
Software and algorithms
Microsoft Excel	Microsoft	https://www.microsoft.com/en-us/microsoft-365/excel
Past 3.0	National History Museum - University of Oslo	https://www.nhm.uio.no/english/research/infrastructure/past/
SigmaPlot 14	SPSS Inc.	http://www.sigmaplot.co.uk/
R version 4.0.3	The R Foundation for Statistical Computing	https://cran.r-project.org/bin/windows/base/old/4.0.3/
nlme version 3.1-152	R Core Team	https://CRAN.R-project.org/package=nlme
Psych version 2.1.9	William Revelle	https://cran.r-project.org/package=psych
dplyr version 1.0.8	Hadley Wickham	https://cran.r-project.org/package=dplyr
BiodiversityR	World Agroforestry	https://www.worldagroforestry.org/output/tree-diversity-analysis