REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-mouse CD16/CD32 purified	eBioscience	cat#16-0161-86; RRID: AB_468900
APC anti-mouse/human CD11b, clone M1/70	Biolegend	cat#101212; RRID: AB_312795
APC anti-mouse CD3ε, clone 145-2C11	Biolegend	cat#100312; RRID: AB_312677
APC anti-mouse Ly-6G/Ly-6C (Gr-1), clone RB6-8C5	Biolegend	cat#108412; RRID: AB_313377
APC anti-mouse CD19, clone 6D5	Biolegend	cat#115512; RRID: AB_313647
APC anti-mouse TCR-β chain, clone H57-597	Biolegend	cat#109212; RRID: AB_313435
APC anti-mouse TCRγδ, clone eBioGL3	eBioscience	cat#17-5711-82; RRID: AB_842757
PE-Cy7 anti-mouse CD90.2 (Thy1), clone 53-2.1	BD Bioscience	cat#561642; RRID: AB_10895975
Alexa Fluor 700 anti-Mouse CD45, clone 30-F11	BD Bioscience	cat#560510; RRID: AB_1645208
BV650 anti-mouse RORγt, clone Q31-378	BD Bioscience	cat#564722; RRID: AB_2738915
PE anti-mouse CD4, clone RMA-5	Biolegend	cat#100512; RRID: AB_312715
PercPcy5.5 anti-mouse TCR-β, clone H57-597	Biolegend	cat#109228; RRID: AB_1575173
APC anti-mouse IL-22, clone IL22JOP	eBioscience	cat#17-7222-82; RRID: AB_10597583
Pacific Blue anti-mouse IL-17A, clone TC11-18H10.1	Biolegend	cat#506918; RRID: AB_893544
PE-Cy7 anti-mouse IFN-γ, clone XMG1.2	Biolegend	cat#505826; RRID: AB_2295770
PE anti-mouse CD11c, clone N418	Biolegend	cat#117308; RRID: AB_313777
APC anti-mouse I-A/I-E (MHC class II), clone M5/114.15.2	Biolegend	cat#107614; RRID: AB_313329
Pacific blue anti-mouse CD45, clone 30-F11	Biolegend	cat#103126; RRID: AB_493535
Bacterial and Virus Strains
C. rodentium infection strain ICC169	Dr.Gad Frankel, Imperial College London	N/A
His-EspA-expressing E. coli	Dougan Gordon, Sanger Institute	NA
Chemicals, Peptides, and Recombinant Proteins
DPBS, no calcium, no magnesium	ThermoFisher	cat#14190250
Iscove’s Modified Dulbecco’s Medium	Sigma-Aldrich	cat#I3390
Fetal Bovine Serum	Sigma-Aldrich	cat#F7524
UltraPure 0.5M EDTA	ThermoFisher	cat#15575020
HEPES solution	Sigma-Aldrich	cat#H0887
penicillin/streptomycin	Sigma-Aldrich	cat#P7539
L-Glutamine (200 mM)	ThermoFisher	cat#25030149
Dithiothreitol (DTT)	ThermoFisher	cat#R0862
DNase I	Roche	cat#11284932001
Liberase TL	Sigma-Aldrich	cat#5401020001
Collagenase VIII	Sigma-Aldrich	cat#C2139
Collagenase D	Roche	cat#11088882001
Percoll	GE healthcare	cat#17-0891-01
phorbol-12-myristate-13 acetate (PMA)	Sigma-Aldrich	cat#P8139
ionomycin	Sigma-Aldrich	cat#I0634
Brefeldin A	Sigma-Aldrich	cat#B7651
Formaldehyde solution	Sigma-Aldrich	cat#F8775
1M Tris pH 8.0	Ambion	cat#AM9856
5M NaCl	Ambion	cat#AM9760G
20% Sodium dodecyl sulfate (SDS)	Ambion	cat#AM9820
phenol:chloroform:isoamyl alcohol (25:24:1)	Ambion	cat#AM9730
3M Sodium acetate pH 5.5	ThermoFisher	cat#AM9740
Bovine serum albumin (BSA)	New England BioLabs	cat#B90005
FTY720	Cayman Chemical	cat#10006292
Dimethyl sulfoxide (DMSO)	Sigma-Aldrich	cat#D2650
Emulsion containing MOG35–55 and killed Mycobacterium tuberculosis	Hooke Laboratories	cat#EK-0111
Pertussis toxin, Bordetella pertussis	Calbiochem	cat#516560
Propidium iodide	Sigma-Aldrich	cat#P4170
SFB peptide (NYU_003340) LVFDVQFSGAVPNKT	Crick Peptide Chemistry	N/A
Poly-D-Lysine	Sigma-Aldrich	cat#A-003-E
MitoTracker Red CMXRos	Thermofisher	cat#M7512
4’,6-diamidino-2-phenylindole (DAPI)	Sigma-Aldrich	cat#D9542
Alexa Fluor 488 Phalloidin	Thermofisher	cat#A12379
Critical Commercial Assays
MILLIPLEX MAP mouse Th17 Magnetic Bead Panel kit	Merck	cat#MTH17-MAG-47K
LIVE/DEAD Fixable Near-IR Dead Cell	Thermofisher	cat#L10119
Fix/Perm buffer	eBioscience	cat#00-5523-00
SMART-Seq V4 ultra low input RNA kit	Takara	cat#634890
miRNeasy Micro kit	Qiagen	cat#217084
RiboPure RNA purification kit	Thermofisher	cat#AM1924
QIAquick PCR Purification kit	Qiagen	cat#28106
QuantiFAST SYBR Green	Qiagen	cat#204056
ThermoScript RT-PCR System kit	Thermofisher	cat#11146024
PCR Master Mix	Thermofisher	cat#4318157
EasySep Mouse CD4+ T Cell Isolation kit	Stemcell technologies	cat#19752
Ni-NTA Spin kit	Qiagen	cat#31314
Seahorse XFp Cell Mito Stress Test kit	Agilent	cat#103010-100
Deposited Data
RNA-seq data	This paper	GEO: GSE130302
Experimental Models: Organisms/Strains
Il17aCreR26ReYFPmice	Jackson Laboratory	Stock No. 016879
Oligonucleotides
B2m (Mm00437762_m1)	Applied Biosystem	cat#4331182
Saa1 (Mm00656927_g1)	Applied Biosystem	cat#4331182
Fut2 (Mm00440152_s1)	Applied Biosystem	cat#4331182
Duoxa2 (Mm00470560_m1)	Applied Biosystem	cat#4331182
Il23a (Mm00518984_m1)	Applied Biosystem	cat#4331182
Cxcl1 (Mm00433859_m1)	Applied Biosystem	cat#4331182
Cxcl2 (Mm00436450_m1)	Applied Biosystem	cat#4331182
Il1b (Mm01336189_m1)	Applied Biosystem	cat#4331182
UniF340 (5′-ACTCCTACGGGAGGCAGCAGT-3′)	Thermofisher	N/A
UniR514 (5′-ATTACCGCGGCTGCTGGC-3′)	Thermofisher	N/A
SFB736F (5′-GACGCTGAGGCATGAGAGCAT-3′)	Thermofisher	N/A
SFB844R (5′-GACGGCACGGATTGTTATTCA-3′)	Thermofisher	N/A
Software and Algorithms
GraphPad Prism 7.0c	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
FlowJo LLC version 10.4.2	Becton Dickinson	https://www.flowjo.com/solutions/flowjo/downloads
Ingenuity Pathway Analysis (IPA)	QIAGEN	www.qiagen.com/ingenuity
Bowtie2	Langmead and Salzberg, 2012	N/A
RSEM	Li and Dewey, 2011	N/A
DESeq2 (version 1.16.1)	Love et al., 2014	N/A
R (version 3.4.1)	R Development Core Team, 2015	N/A
Limma package	Ritchie et al., 2015	N/A
DAVID analysis	Huang da et al., 2009	N/A
PIANO R package	Väremo et al., 2013	N/A
Mouse genome-scale metabolic model	Mardinoglu et al., 2015	N/A
WAVE (version 2.6)	Agilent	https://www.agilent.com/en/products/cell-analysis/cell-analysis-software/data-analysis/wave-desktop-2-6
ImageJ/Fiji	Schindelin et al., 2012	https://fiji.sc/#download
SVI Huygens	Scientific Volume Imaging (SVI)	https://svi.nl/Huygens-Essential
Mitochondrial Network Analysis (MiNA) macro for ImageJ/Fiji	Schindelin et al., 2012, Valente et al., 2017	N/A