REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-MUC2	Santa Cruz Biotechnology	Cat#sc-15334; AB_2146667
anti-ZO-1	Invitrogen	Cat # 61–7300; RRID:AB_2533938
XCR1-BV421 (clone ZET)	Biolegend	Cat #148216; RRID:AB_2565230
CD172α-FITC (clone P84)	BD Biosciences	Cat #560316; RRID:AB_1645240
CD4-PeCy5.5 (clone RM4-5)	eBioscience	Cat #35-0042-82; RRID:AB_11218300
CD11c-PeCy7 (clone N418)	Biolegend	Cat #117318; RRID:AB_493568
BST2-APC (clone 927)	Biolegend	Cat #127016; RRID:AB_1967127
CMHII-A700 (clone M5/114.15.2)	eBioscience	Cat #56-5321-82; RRID:AB_494009
CD11b-APC/Cy7 (clone M1/70)	Biolegend	Cat #101226; RRID:AB_830642
CD45-BUV395 (clone 30-F11)	BD Biosciences	Cat #564279; RRID:AB_2651134
PD-1-BV605 (clone J43)	BD Biosciences	Cat #563059; RRID:AB_2737980
CD62L-BV786 (clone MEL-14)	BD Biosciences	Cat #564109; RRID:AB_2738598
CD8α-AF488 (clone 53-6.7)	Biolegend	Cat #100723; RRID:AB_389304
CXCR5-PE (clone 2G8)	BD Biosciences	Cat #551959; RRID:AB_394300
RORγt-Pe-eFluor610 (clone B2D)	eBioscience	Cat #61-6981-80; RRID:AB_2574649
Foxp3-APC (clone FJK-16S)	eBioscience	Cat #17-5773-82; RRID:AB_469457
CD44-A700 (clone IM7)	eBioscience	Cat #56-0441-82; RRID:AB_494011
CD43-BUV737 (clone S7)	BD Biosciences	Cat #564398; RRID:AB_2738790
CD3-eFluor450 (clone 17A2)	eBioscience	Cat #48-0032-80; RRID:AB_1272229
Siglec-F-BV421 (clone E50-2440)	BD Biosciences	Cat #565934; RRID:AB_2739398
CD19-BV605 (clone 6D5)	Biolegend	Cat #115539; RRID:AB_11203538
B220-BV786 (clone RA3-6B2)	BD Biosciences	Cat #563894; RRID:AB_2738472
IgM-biotin (clone II/41)	eBioscience	Cat #13-5790-82; RRID:AB_466675
IgA-PE (clone mA-6E1)	eBioscience	Cat #12-4204-81; RRID:AB_465916
IgD-Pe/Cy7 (clone 11-26c.2a)	Biolegend	Cat #405719; RRID:AB_2561875
GL-7-eF660 (GL-7)	eBioscience	Cat #50-5902-82; RRID:AB_2574252
Streptavidin PE-CF594	BD Biosciences	Cat #562284; RRID:AB_11154598
Rat anti-MerTK (clone DS5MMER)	eBioscience	Cat #14-5751-82; RRID:AB_2688282
armenian hamster anti-CD11c (clone N418)	Biolegend	Cat #117301; RRID:AB_313771
rabbit anti-lysozyme (polyclonal)	Abcam	Cat# ab2408; RRID:AB_303050
SIPR-α-AF594 (clone P84)	Biolegend	Cat #144020; RRID:AB_2629588
CD4-eFluor450 (clone RM4-5)	eBioscience	Cat #48-0042-82; RRID:AB_1272194
CD4-eF570 (clone RM4-5)	Invitrogen	Cat #41-0042-82; RRID:AB_2573595
EpCAM-eF450 (clone G8.8)	eBioscience	Cat #48-5791-82; RRID:AB_10717090
Donkey anti-rat IgG Cy3	Jackson Immuno-research	Cat #712-165-153; RRID:AB_2340667
Donkey anti-rat IgG AF488	Invitrogen	Cat #A21208; RRID:AB_2535794
Goat anti-Armenian hamster IgG AF594	Jackson Immuno-research	Cat #127-585-160; RRID:AB_2338999
Goat anti-Armenian hamster IgG Cy3	Jackson Immuno-research	Cat #127-165-160; RRID:AB_2338989
Goat anti-rabbit IgG AF514	Invitrogen	Cat #A-31558; RRID:AB_2536173
CD11c microbeads	Miltenyi Biotec	Cat #130-125-835
Chemicals, peptides, and recombinant proteins
4-kDA Fluorescein isothiocyanate–dextran	Sigma-Aldrich	Cat #60842-46-8
Critical commercial assays
IgA mouse uncoated ELISA kit	Invitrogen	Cat #88-50450-88
Mouse NGAL ELISA kit, ELISAGenie	Ozyme	Cat #MOFI00997
E.Z.N.A Tissue DNA Kit	Omega bio-tek	Cat #D3396-00S
Deposited data
Row fastq files 16s rRNA sequencing	This study	Zenodo https://doi.org/10.5281/zenodo.7107337
Workflow microbiome profiling of the terminal ileum and caecal contents	This study	Zenodo https://doi.org/10.5281/zenodo.7079338
Experimental models: Organisms/strains
C57BL6/J mouse 21 days old	This study	Parents from Janvier
Oligonucleotides
pan-bacteria probe Eub338-Alexa 555 5-GCTGCCTCCCGTAGGAGT-3′	Invitrogen	https://doi.org/10.1128/aem.56.6.1919-1925.1990
Segmented Filamentous Bacteria (SFB) 1008-AF594 probe 5-GCGAGCTTCCCTCATTACAAGG-3′	Invitrogen	https://doi.org/10.1099/00207713-45-4-780
Software and algorithms
PRISM 9	GraphPad	N/A
Photoshop CC 2019	Adobe	N/A
MetaboAnalyst 5.0	https://doi.org/10.1093/nar/gkq329	https://www.metaboanalyst.ca/home.xhtml
QIIME 2	https://doi.org/10.1038/s41587-019-0209-9	https://qiime2.org/
ZEN Lite 2.3 SP1	Carl Zeiss Microscopy	https://www.zeiss.com/microscopy/us/RRID:SCR_013672
Other
Safe® A03, regular diet	SAFE	Cat #U8200G10R
MAIS +1800 mg/kg Sodium, SAFE R8960A01R 00128, SAM diet	SAFE	This study