REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, Peptides, and Recombinant Proteins
BamHI-HF	NEB	R3136S
HindIII-HF	NEB	R3104S
NotI-HF	NEB	R3189S
BglII	NEB	R0144S
NheI	NEB	R0131S
XhoI	NEB	R0146S
4-Nitroquinoline N-oxide	Sigma	N8141
Gibson Assembly Master Mix	NEB	E2611S
Phusion High-Fidelity PCR Master Mix	Thermo	F531S
Nano-Glo Luciferase Assay System	Promega	N1130
Critical Commercial Assays
Nextera XT DNA Library Preparation Kit	Illumina	(FC-131-1024)
GeneJET PCR Purification Kit	Thermo	K0701
GeneJET Genomic DNA purification Kit	Thermo	K0722
MasterPure complete DNA and RNA Purification Kit	Epicenter	MC85200
QIAquick PCR Purification Kit	QIAGEN	28106
Deposited Data
All fastq files and descriptions uploaded to Sequence Read Archive	NCBI SRA SUB4542953	Bioproject: PRJNA492467
Experimental Models: Cell Lines
Human: Caco-2 epithelial cell line	ATCC	HTB-37; RRID:CVCL_0025
Harvested Bone Marrow Macrophages from BALB/c mice	N/A	Miller Lab
Experimental Models: Organisms/Strains
B. subtilis trpC2 pheA1	Brehm et al., 1973	HM1
B. subtilis trpC2 uvrA::mls	Bacillus stock center	HM713
B. subtilis trpC2 mfd::mls	Bacillus stock center	HM1720
S. typhimurium ST19	Hayden et al., 2016	HM1996
P. aeruginosa CF127	Wolfgang et al., 2003	HM2212
P. aeruginosa CF127 Δmfd	This study	HM2260
E. coli F’(kan) placOL2-62-lacZ	Dove et al., 1997	HM2295
B. subtilis mfd::mls, trpC2 pheA1	Million-Weaver et al., 2015	HM2521
E. coli F’(kan) placOL2-62, pSIM27(tet)	This study	HM2602
B. subtilis uvrA::mls, trpC2 pheA1	Million-Weaver et al., 2015	HM2633
E. coli FW102 OL2-62-Nanoluc(hyg), pSIM27	This study	HM2747
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI, pBRα Plac-a-ST19rpoB(19-142)	This study	HM2838
E. coli FW102 OL2-62-Nanoluc(hyg), pBRα, pACλCI Plac-CI-ST19mfd(1-450)	This study	HM2875
S. typhimurium ST19, pUC19	This study	HM2880
S. typhimurium ST19 mfd::cat, pUC19	This study	HM2881
S. typhimurium ST19 mfd::cat, pUC19-ST19mfd	This study	HM2882
S. typhimurium ST19 mfd::cat, pUC19-ST19mfdL499R	This study	HM2886
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-ST19mfd(1-450), pBRα Plac-a-ST19UvrA(88-505)	This study	HM2913
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-ST19rpoB(19-142), pBRα Plac-a-ST19mfd (RID)	This study	HM2920
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-ST19rpoB(19-142), pBRα Plac-a-ST19mfd (RID) L499R	This study	HM2921
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-ST19rpoB(19-142), pBRα	This study	HM2925
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI, pBRα Plac-a-ST19mfd (RID)	This study	HM2926
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI, pBRα Plac-a-ST19UvrA(88-505)	This study	HM2949
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-ST19mfdR165A, pBRα Plac-a-ST19UvrA(88-505)	This study	HM2962
S. typhimurium ST19 mfd::cat, pUC19-Mtbmfd	This study	HM3134
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-Mtbmfd(334-651), pBRα	This study	HM3193
E. coli FW102 OL2-62-Nanoluc(hyg), pACλCI Plac-CI-Mtbmfd(334-651), pBRα Plac-a-ST19rpoB(19-142)	This study	HM3225
S. typhimurium ST19 uvrA::kan	This study	HM3245
S. typhimurium ST19 ST19mfd::Mtbmfd-kan	This study	HM3406
S. typhimurium ST19 mfd::cat	This study	HM3429
S. typhimurium ST19, pMMB67EH	This study	HM3585
S. typhimurium ST19 mfd::cat, pMMB67EH	This study	HM3586
S. typhimurium ST19 mfd::cat, pMMB67EH-ST19mfd	This study	HM3590
S. typhimurium ST19 mfd::cat, pMMB67EH-ST19mfdR165A	This study	HM3666
S. typhimurium ST19 mfd::cat, pMMB67EH-ST19mfdL499R	This study	HM3667
M. tuberculosis H37Rv	ATCC	ATCC 27294
M. tuberculosis H37Rv mfd::hyg	This study	MR02
Oligonucleotides
Primer sequences provided in Table S3	N/A	N/A
Recombinant DNA
pHM443	This study	pHM443
pHM453	This study	pHM453
pHM457	This study	pHM457
pHM458	This study	pHM458
pHM474	This study	pHM474
pHM480	This study	pHM480
pHM481	This study	pHM481
pHM484	This study	pHM484
pHM494	This study	pHM494
pHM499	This study	pHM499
pHM550	This study	pHM550
pHM566	This study	pHM566
pHM629	This study	pHM629
pHM649	This study	pHM649
pHM650	This study	pHM650
pHM651	This study	pHM651
pHM661	This study	pHM661
pHM662	This study	pHM662
pBRα	Addgene	Addgene 53731
pBRα-β-flap	Addgene	Addgene 53734
pACλCI	Addgene	Addgene 53730
pACλCI-β-flap	Addgene	Addgene 53733
pEX18	Gift from Dr. Matthew Parsek	pEX18
pKD3	Addgene	Addgene 45604
pKD13	Miller Lab Stock	pKD13
pKD46	Miller Lab Stock	pKD46
pMMBEH67	Miller Lab Stock	pMMBEH67
pNIT	Sherman Lab Stock	pNIT
pNL1.1	Promega	Promega N1441
pSIM27	Gift from Dr. Don Court	pSIM27
pUC19	Addgene	Addgene 50005
Software and Algorithms
SAMtools	Li et al., 2009	N/A
Bowtie 2	Langmead and Salzberg, 2012	N/A
breseq	Deatherage and Barrick, 2014	N/A
Prism 7 Graphpad	N/A	N/A