REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
C. difficile strain 630
C. difficile strain BAA-1805	ATCC	ATCC BAA-1805
C. difficile strain VA20	VA Medical Center, University of North Texas Health Science Center	VA20
Biological Samples
N/A	N/A	N/A
Chemicals, Peptides, and Recombinant Proteins
C. difficle agar base	Oxoid	OXCM0601
Defibrinated horse blood	Lampire Biological Laboratories	50-414-517
moxalactam	Santa Cruz Biotechnology	sc-250419
norfloxacin	Sigma-Aldrich	N9890-1G
L-cysteine hydrochloride	Fisher	50-668-778
Reinforced Clostridial medium	Oxoid	CM0149
Ebselen	Bogyo Lab	N/A
Vancomycin	Sigma-Aldrich	V1130
Dimethyl Sulfoxide	Santa Cruz Biotechnology	sc-358801
Tween-80	Sigma-Aldrich	P4780
Kanamycin sulfate	Genlantis	M150010
Gentamycin sulfate	Sigma-Aldrich	G3632
Colistin	Sigma-Aldrich	C4461
Metronidazole	Fluka	M3761-5G
Clindamycin	Cayman	15006
Critical Commercial Assays
PowerSoil-htp 96 well DNA isolation Kit	MoBio	12955-12
DNeasy PowerSoil HTP 96 Kit	QIAGEN	12955-4
Platinum Hot Start PCR Master Mix	ThermoFisher	13000013
UltraClean PCR Clean-Up Kit	MoBio	12596
UltraClean 96 PCR Cleanup Kit	QIAGEN	12596-4
Quant-iT dsDNA Assay Kit, high sensitivity	Invitrogen	Q33120
Lipocalin-2/NGAL DuoSet ELISA kit	R&D Biosystems	DY1857-05
Deposited Data
dada2 DSVs, .biom table, and mapping files	This study	https://purl.stanford.edu/nv308sc8099
Experimental Models: Cell Lines
C. difficile strain 630	ATCC	BAA-1382
C. difficile strain BAA-1805	ATCC	ATCC BAA-1805
C. difficile strain VA20	VA Medical Center, University of North Texas Health Science Center	VA20
Experimental Models: Organisms/Strains
Swiss-Webster mice	Taconic	SWEF
Golden Syrian hamsters	Envigo (Harlan) laboratories	089
Oligonucleotides
515fB	Earth Microbiome Project	http://www.earthmicrobiome.org/protocols-and-standards/16s/
806rB	Earth Microbiome Project	http://www.earthmicrobiome.org/protocols-and-standards/16s/
Software and Algorithms
QIIME 1.9.1	Quantitative Insights Into Microbial Ecology	http://qiime.org/install/install.html
GraphPad Prism 7 and 8	GraphPad	https://www.graphpad.com
EMPeror	Vázquez-Baeza et al.43	https://biocore.github.io/emperor/