KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Antibodies used for flow cytometry or cell sorting are listed in Supp. Table S2.	N/A	N/A
Bacterial and virus strains
Citrobacter rodentium (bioluminescent)	Gad Frankel	Wiles, S., Pickard, K.M., Peng, K., MacDonald, T.T., and Frankel, G. (2006). In vivo bioluminescence imaging of the murine pathogen Citrobacter rodentium. Infect Immun 74, 5391–5396. 10.1128/IAI.00848-06.
Critical commercial assays
Ovation RNA-seq System V2	Tecan, Mannëdorf, Switzerland	N/A
RNAeasy Micro Kit	Qiagen	N/A
Deposited data
Bulk RNA-seq colonic Treg cells	This paper	GEO: GSE208621
16S sequencing data	This paper	SRA: PRJNA860604
Single-cell RNA-seq ileal Crohn’s Disease from Martin et al.	Martin et al.51	Martin, J.C., Chang, C., Boschetti, G., Ungaro, R., Giri, M., Grout, J.A., Gettler, K., Chuang, L. shiang, Nayar, S., Greenstein, A.J., et al. (2019). Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy. Cell 178, 1493–1508.e20. 10.1016/j.cell.2019.08.008.
Experimental models: Organisms/strains
RorctdTomato mouse	This paper	N/A
Il23rflox/flox mouse	Philip Rosenstiel	Aden, K., Rehman, A., Falk-Paulsen, M., Secher, T., Kuiper, J., Tran, F., Pfeuffer, S., Sheibani-Tezerji, R., Breuer, A., Luzius, A., et al. (2016). Epithelial IL-23R Signaling Licenses Protective IL-22 Responses in Intestinal Inflammation. Cell Rep 16, 2208–2218. 10.1016/j.celrep.2016.07.054.
RT-qPCR primers are in Table S1	N/A	N/A
Software and algorithms
Prism 9	Graphpad	RRID:SCR_002798
FACSDiva	BD	RRID:SCR_001456
FlowJo	FlowJo	RRID:SCR_008520
Illustrator	Adobe	RRID:SCR_010279
R	r-project.org	RRID SCR_001905
Other
Code for reanalysis of single-cell RNA-seq ileal Crohn’s Disease	This paper	https://github.com/Ken-Lau-Lab/IL23Ranalysis
Code for analysis of bulk RNA-seq data and 16S	This paper	Data S1