REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Brain tissue	This study	N/A
Fecal samples	This study	N/A
Chemicals, peptides, and recombinant proteins
Penicillin G	Sigma, St. Louis MO	P3032
Critical commercial assays
PowerSoil-htp 96-Well DNA Isolation Kit	MoBio, Carlsbad CA	Cat # 12855-50
Quant-iT PicoGreen dsDNA assay kit	Life Technologies, Eugene OR	Cat # P11496
Qiaquick PCR purification kit	Qiagen, Valencia CA	Cat # 28104
high-sensitivity dsDNA assay kit	Life Technologies, Eugene OR	Cat # Q33120
mRNAeasy Micro Kit	Qiagen, Valencia CA	Cat # 74004
TruSeq RNA Sample Preparation Kit v2	Illumina, San Diego CA	Cat # RS-122-2001
Deposited data
Raw 16S rRNA and RNA-Seq data	This paper	SRA Accession #’s PRJNA731131(16S); PRJNA730313 (RNA -Seq)
Mouse genome	https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/	GRCm38 (mm10)
Silva 138	[Pruesse et al., 2007 #15858]	Release of December 2019
Experimental models: Organisms
Mice	Jackson Laboratories, Bar Harbor ME	C57BL/6 mice
Oligonucleotides
Primers 515F/806R	Walters et al. (2015)	IDT
Software and algorithms
TrimGalore	bioinformatics.babraham.ac.uk	v. 0.5.0
Bbmap	jgi.doe.gov/data-and-tools/bbtools/bb-tools-user- guide/bbmap-guide/	v. 38.25
Samtools	http://www.htslib.org/doc/	v. 1.9
featureCounts	[Liao et al., 2014 #15514]	Subread package v.1.6.3
DESeq2 package	https://bioconductor.org/packages/release/bioc/html/DESeq2.html	v 1.22.2
QIIME2	https://qiime2.org/	v. 2020.8
DADA2	[Callahan et al., 2016 #15857]	v. 1.16
MaAsLin2	https://huttenhower.sph.harvard.edu/maaslin/	R package version 1.4.0
GraphPadPrism® software	Graph Pad Software, San Diego CA	v. 6