REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-mouse CD45 BV650 (30-F11)	Biolegend	103151
anti-mouse CD45 PerCPCy5.5 (30-F11)	BD	550994
anti-mouse/human CD45R/B220 PerCPCy5.5 (RA3-6B2)	Biolegend	103234
anti-mouse CD45R/B220 APC (RA3-6B2)	eBioscience	Cat # 17-0452-81
anti-mouse CD45R/B220 PE-Cy7 (RA3-6B2)	eBioscience	25-0452-82
anti-mouse IgG1 APC (A85-1)	BD	560089
anti-mouse IgA PE (mA-6E1)	eBioscience	12-4204-82
Fab Anti-Mouse IgM FITC	Jackson Immuno Research Labs	115-097-020
anti-mouse CD95 (FAS) FITC (SA367H8)	Biolegend	152606
anti-mouse CD38 PE (90)	Biolegend	102707
anti-mouse CD3 BV785 (17A2)	Biolegend	100232
anti-mouse CD3 BV510 (145-2C11)	BD	563024
anti-mouse CD19 BV510 (6D5)	Biolegend	115546
anti-mouse CD19 e450 (1D3)	eBioscience	48-0193-80
anti-mouse CD2⅓5 APC/Cy7 (7E9)	Biolegend	123417
anti-mouse CD23 PE/Cy7 (B3B4)	eBioscience	25–0232082
Zombie UV Fixable Viability Dye	Biolegend	423108
Bacterial Strains
Bifidobacterium longum	Blaser Lab; Bokulich et al. (2016)4	HMXZ001
Escherichia coli	Dr. Giulio Quarta	MG1655
Biological Samples
Mouse fecal pellets	This study
Mouse ileal samples	This study
Mouse cecal samples	This study
Mouse colonic samples	This study
Mouse serum samples	This study
Human fecal samples	Blaser Lab
Chemicals, Peptides, and Recombinant Proteins
Amoxicillin	Sigma Aldrich	A8523
Azithromycin Oral Suspension	Teva	00093-2026-23
Anerobic transport medium	Anaerobic Systems	AS-911
Bifidobacterium selective agar	Anaerobic Systems	AS-6423
Bifidus Selective Medium	Sigma Aldrich	Cat # 90273
Critical Commercial Assays
DNeasy PowerSoil-HTP 96 Well Soil DNA Isolation Kit	Qiagen	Cat # 12955-4
DNeasy PowerLyzer Powersoil kit	Qiagen	Cat # 12855-100
Quant-iT PicoGreen dsDNA assay kit	Life Technologies	Cat #P11496
Qiaquick PCR purification kit	Qiagen	Cat # 28104
IgA Mouse Uncoated ELISA Kit	Invitrogen	Cat # 88-50450-77
IgG (Total) Mouse Uncoated ELISA Kit with Plates	Invitrogen	Cat # 88-50400-22
BCA Assay	Pierce	Cat # 23225
Deposited Data
16S rRNA data	This study	Early-life microbiome composition and GALT immune development - ID 14759
Experimental Models: Organisms/Strains
C57BL/6J Mice	The Jackson Laboratory	Strain #:000664, RRID:IMSR_JAX:000664
C57BL/6JRj Mice	Javier
C57BL/6NTac	Taconic Bioscience	C57BL/6NTac Germ Free
Oligonucleotides
V4 16S rRNA Universal Primers	Walters et al. (2016)65	F515/R806
Software and Algorithms
DESeq2 package	Love et al., (2014)66	version 1.30.1
QIIME2	Bolyen et al., (2019)67	QIIME2-2022.2.1
Prism 9 for macOS	GraphPad Software	Version 9.5.1
qiime2R	Bisanz et al., (2018)68	version 0.99.6
vegan	Oksanen et al., (2022)69	Version 2.5–7
ComplexHeatmap	Gu et al., (2016)70	Version 2.6.2
MAAFT	Katoh et al., (2013)71	Version 7
DADA2	Callahan et al., (2016)72	version 0.99.8
FlowJo	BD	Version 10.8.1