KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
Clostridioides difficile R20291	Stabler et. al., 2009	N/A
Clostridioides difficile R20291 tcdAB::CT	This study	N/A
Chemicals, peptides, and recombinant proteins
Cefoperazone	Sigma-Aldrich	Cat#C4292
Phosphate buffered saline	Sigma-Aldrich	Cat#79383
2.6% carboxymethylcellulose	Sigma-Aldrich	Cat#419273
Dextran sulfate sodium	MP Biomedicals	Cat#02160110
9-aminoacridine	Sigma-Aldrich	Cat#A38401
Ammonium formate	Sigma-Aldrich	Cat#516961
1,5- diaminonaphthalene	Sigma-Aldrich	Cat#D21200
Hematoxylin	Sigma-Aldrich	Cat#H3136
Eosin	Sigma-Aldrich	Cat#230251
Beta-mercaptoethanol	Sigma-Aldrich	Cat#63689
Phenol:chloroform:IAA, pH 6.7	Sigma-Aldrich	Cat#P1944
Cholestyramine	Sigma-Aldrich	Cat#11041
iQ SYBR Green mix	Bio-Rad	Cat#25230
Poly-l-lysine	Sigma-Aldrich	Cat#P8920
Critical commercial assays
RNeasy Mini Kit	QIAGEN	Cat#74104
iScript cDNA synthesis kit	Bio-Rad	Cat#1708890
Wizard SV Gel and PCR clean-up system	Promega	Cat#A9281
Deposited data
Raw LC-MS/MS data	This study	Mendeley Data: https://dx.doi.org/10.17632/rhbktnpyj2.1
Experimental models: Organisms/strains
C57BL/6J mice	The Jackson Laboratory	Cat#664
Oligonucleotides
Primers for qRT-PCR: Table S1	N/A	N/A
Software and algorithms
Xcaliber Quan Browser	Thermo Fisher Scientific	Version 4.3
Prism	Graph Pad	Version 8.2
Canvas X16	Canvas	Version 16
Adobe Illustrator	Adobe	Version 16.0
SCiLS	Bruker Daltonics	Version 2020
Gen5 Data Analysis Software	BioTek	Gen5 3.0
Other
Lysing Matrix D tubes	MP Biomedicals	Cat#116913050
SecurityGuard C18 guard column (3.2 × 8 mm)	Phenomenex	Cat#AJ0-4286
Ascentis Express HPLC C18 column (25 cm × 2.1 mm, 5 um particle size)	Supelco Analytical	Cat#5811305-U
AIN-93G ± 2% cholestyramine	Dyets, Inc.	Diet#103550
Indium Tin Oxide Coated Glass Slides	Delta Technologies	Cat#NC1501896