REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-GADD153/CHOP	SCBT	sc-166682
Anti-Tubulin	Abcam	ab176560
Anti-EPCAM	BD Biosciences	563214
Anti-4 Hydroxynonenal	Abcam	ab48506
Bacterial and virus strains
Adherent-invasive E. Coli pathotype (AIEC), NRG857c strain (O83:H1)	Small et al.24	N/A
Chemicals, peptides, and recombinant proteins
tauroursodeoxycholic acid (TUDCA)	Sigma-Aldrich	T0266
Ulex Europaeus Agglutinin I (UEA I), DyLight™ 649	Vector Laboratories	DL-1068-1
Fixable Viability Stain 510	BD Biosciences	564406
Salubrinal	Enzo	ALX-270-428
Thapsigargin	Sigma-Aldrich	T9033
Dextran sulfate sodium colitis grade, 36,000 - 50,000 Da	MP Biomedicals	SKU: 02160110-CF
Compound 147 (AA147)	Abbexa	abx283245
IL-22-Fc	Genentech	PRO312045
Critical commercial assays
TLR4 HEK-Blue™ reporter cells	Invivogen	hkb-mtlr4
TLR5 HEK-Blue™ reporter cells	Invivogen	hkb-mtlr5
RNeasy Universal kit	Qiagen	73404
Purelink™ Microbiome DNA Purification Kit	Invitrogen	A29790
AMPure magnetic beads	Beckman Coulter	A63880
Lcn-2 ELISA kit	R&D systems	DY1857-05
NOD1 HEK-Blue™ reporter cells	Invivogen	hkb-mnod1
NOD2 HEK-Blue™ reporter cells	Invivogen	hkb-mnod2
TLR9 HEK-Blue™ reporter cells	Invivogen	hkb-mtlr9
Deposited data
RNA sequencing	This paper	GSE220457
16S rRNA gene sequencing	This paper	GSE220883
Experimental models: Organisms/strains
Mouse: C57BL/6JOlaHsd	Envigo Israel	2BL
Mouse: Becn1F121A (C57BL/6)	Fernández et al.5	N/A
Mouse: Nod2flox/flox (C57BL/6)	Kim et al.35	N/A
Mouse: B6.129X1(Cg)-Bcl2tm1.1Sjk/J	The Jackson Laboratory	#018430
Mouse: Germ-free Mice/Swiss Webster	Taconic Biosciences	SW-F/SW-M
Mouse: B6.129S7-Rag1tm1Mom/J	The Jackson Laboratory	# 002216
Mouse: B6.129P2(SJL)-Myd88tm1Defr/J	The Jackson Laboratory	# 008888
Mouse: B6.C-Tg(CMV-cre)1Cgn/J	The Jackson Laboratory	# 006054
Mouse: B6.Cg-Tg(Vil1-cre)997Gum/J	The Jackson Laboratory	# 004586
Oligonucleotides
515F - (barcode) 5′-AATGATACGGCGACCACCGAG ATCTACACGCTAGCCTTCGTCGCTATGGTAATTGT G TGYCAGCMGCCGCGGTAA-3′	DeSantis et al.36	N/A
806 R 5′- CAAGCAGAAGACGGCATACGAGATAG TCAGTCAGCCGGACTACHVGGGTWTCTAAT -3′	DeSantis et al.36	N/A
Software and algorithms
Quantitative Insights into Microbial Ecology 2 (QIIME2)	Bolyen et al.37	N/A
PRISM	Graphpad	N/A
FIJI	Schindelin et al.38	N/A
Divisive Amplicon Denoising Algorithm (DADA2)	DeSantis et al.36	N/A