REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CD16/CD32 Monoclonal Antibody	eBioscience	Cat# 14-0161-86; RRID: AB_467135
CD45 Monoclonal Antibody, APC-Cyanine7	eBioscience	Cat# A15395; RRID: AB_2534409
Mouse Hematopoietic Lineage Antibody Cocktail, eFluor 450	eBioscience	Cat# 88-7772-72; RRID: AB_10426799
CD335 (NKp46) Monoclonal Antibody, Super Bright 645	eBioscience	Cat# 64-3351-82; RRID: AB_2688145
CD127 Monoclonal Antibody, FITC	eBioscience	Cat# 11-1271-82; RRID: AB_465195
CD117 (c-Kit) Monoclonal Antibody, PE-Cyanine7	eBioscience	Cat# 25-1172-82; RRID: AB_469646
ROR gamma (t) Monoclonal Antibody, PE	eBioscience	Cat# 12-6988-82; RRID: AB_1834470
IL-22 Monoclonal Antibody, APC	eBioscience	Cat# 17-7222-82; RRID: AB_10597583
Rabbit polyclonal to ZO1 tight junction protein	Abcam	Cat# ab216880; RRID: AB_2909434
Rabbit monoclonal to Occludin	Abcam	Cat# ab216327; RRID: AB_ 2,737,295
IL-22 Monoclonal Antibody	eBioscience	Cat# 16-7222-85; RRID: AB_2016574
MUC2 Polyclonal antibody	PeproTech	Cat# 27675-1-AP; RRID: AB_ M94132
Rabbit monoclonal to Cyp1a1	Abcam	Cat# ab79819; RRID: AB_1603487
Rabbit monoclonal [SP6] to Ki67	Abcam	Cat# ab16667; RRID: AB_302459
Rabbit monoclonal [E247] to beta Catenin	Abcam	Cat# ab32572; RRID: AB_725966
Rabbit monoclonal [EP1238Y] to Notch1	Abcam	Cat# ab52627; RRID: AB_881725
Biological samples
Human fecal samples	Southern Hospital of Southern Medical University	N/A
Human blood samples	Southern Hospital of Southern Medical University	N/A
Chemicals, peptides, and recombinant proteins
Fixable Viability Dye, eFluor 780	eBioscience	Cat# 65-0865-14;
Vancomycin	Macklin	Cat# 1404-93-9;
Neomycin sulfate	Macklin	Cat# 1405-10-3;
Metronidazole	Macklin	Cat# 443-48-1;
Ampicillin	Macklin	Cat# 69-53-4;
Milnacipran	MedChemExpress	Cat# HY-B0168;
Ficz	MedChemExpress	Cat# HY-12451;
Fluorescein isothiocyanate-dextran (FITC)-dextran	Sigma–Aldrich	Cat# 46944;
Recombinant Murine IL-23	R&D Systems	1887-ML-010
Recombinant Murine IL-15	PeproTech	210–15
Recombinant Murine IL-2	PeproTech	210–12
Recombinant Murine IL-7	PeproTech	210–17
Recombinant Murine IL-22	PeproTech	210–22
Critical commercial assays
Cell Counting Kit-8 (CCK-8)	Dojindo	CK04
lactate dehydrogenase (LDH) assays	Nanjing Jiancheng	A020
human IFABP ELISA Kit	Bio-Swamp	HM10888
human citrulline ELISA Kit	USCN	CEA505Ge
human diamine oxidase ELISA Kit	Cusabio	CSB-E10137h
alanine aminotransferase (ALT) assay kit	Nanjing Jiancheng	C009-2-1
aspartate aminotransferase (AST) assay kit	Nanjing Jiancheng	C010-2-1
blood urea nitrogen (BUN) assay kit	Nanjing Jiancheng	C013-2-1
Deposited data
Raw sequencing data	http://www.ncbi.nim.nih.gov/sra	PRJNA824296 PRJNA823886.
Experimental models: Cell lines
Intestinal organoids	This paper	N/A
Mouse small intestine LP single cells	This paper	N/A
Experimental models: Organisms/strains
Intestinal epithelial-specific AHR knockout mice	Cyagen Biosciences Inc	N/A
IL-22-deficient mice	Cyagen Biosciences Inc	N/A
Oligonucleotides
Primers for RT–PCR, see Table S2	This paper	N/A
Software and algorithms
FlowJo, v10.6.2	BD Biosciences	https://www.flowjo.com/
ImageJ	National Institutes of Health	https://imagej.nih.gov/ij/index.html
QIIME2	QIIME2 Software	https://qiime2.org/
Picrust2	Picrust2 Software	https://picrust.github.io/picrust/
TraceFinderTM	Thermo Fisher Scientific Corp	https://www.thermofisher.cn/order/catalog/product/OPTON-31001
GraphPad Prism v7	GraphPad	https://www.graphpad.com/