KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
Escherichia coli strain MG1655	Huang lab strain collection	N/A
Evolved S1-36	This paper	N/A
lacI* mut	This paper	N/A
[flhE-flhD] mutant	This paper	N/A
gyrBD87G mutant	This paper	N/A
gyrAE466D mutant	This paper	N/A
Critical commercial assays
Biolog PM1 and PM2A microplates	Biolog Inc.	Cat. #12111,12112
PicoGreen dsDNA quantification kit	Thermo Fisher	Cat. #P7589
MiniPrep kit	Macherey-Nagel	Cat. #740588.50
Oligonucleotides
lacI mutant oligo	C*C*A* T*TA AGT TCT GTC TCG GCG CGT CTG CGT CTG GCT GGC TGG CTG GCA TAA ATA TCT CAC TCG CAA TCA AAT TCA GCC GAT AGC GGA ACG, (where * indicates a phosphorothioated base)	N/A
lacI Sanger sequencing forward primer	Fwd: 5’-TGGCTGGCTGGCTGGCATAAAT	N/A
lacI Sanger sequencing reverse primer	Rev: 5’-CGCAGCCCGGACTCGGTAAT	N/A
Barcode sequencing forward primer #1	Fwd: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNTCGCTAAGGATGATTTCTGGA NNN = unique molecular identifier	N/A
Barcode sequencing reverse primer #1	Rev: 5’-GACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNNNNNNNNNTCGCTTGGACTCCTGTTGAT NNN = unique molecular identifier	N/A
Barcode sequencing forward primer #2	Fwd: 5’-AATGATACGGCGACCACCGAGATCTACACnnnnnnAAACACTCTTTCCCTACACGACGCTCTTCCGATCT nnnnnn = multiplexing indices	N/A
Barcode sequencing reverse primer #2	Rev: 5’-CAAGCAGAAGACGGCATACGAGATAAnnnnnnGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT nnnnnn = multiplexing indices	N/A
Experimental models: Organisms/strains
Swiss Webster Mice – Germ Free	Taconic	SW GF
Recombinant DNA
DNA barcode plasmids	(Cira et al., 2018)	N/A
Gentamicin cassette containing plasmid (pUC18-mini-Tn7T-Gm-lux)	(Choi et al., 2005)	Addgene Ref. 64963
Software and algorithms
MATLAB	Mathworks	v. 2017a
SeqPrep	https://github.com/jstjohn/SeqPrep	v. 1.2
Tableau Desktop	Tableau	v. 2018.3
Breseq	https://github.com/barricklab/breseq	v. 0.33.1
PTR	https://github.com/christophertbrown/iRep	v. 1.10
Transmission model code	https://bitbucket.org/kchuanglab/bacterial_transmission_model/src/master/	N/A
Growth rate and lag time analysis code	https://github.com/sv1714/Plate_reader_analysis	N/A
Other
PowerSoil-htp kit	Qiagen	Ref. 12955-4
Platinum Pfx DNA polymerase	Thermo Fisher	Ref. 11708-021
Ampure XP Beads	Beckman Coulter	Ref. A63881
MiSeq	Illumina	N/A
NovaSeq S4	Illumina	N/A