KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
Bacteroides vulgatus ATCC 8482	ATCC	ATCC 8482
B. vulgatus Δtdk	This paper	N/A
B. vulgatus Δint	This paper	N/A
B. vulgatus ΔBV01	This paper	N/A
B. vulgatus ΔBV01 ΔtspO	This paper	N/A
B. vulgatus ΔBV01, attN::pNBU2-bla-ermGb	This paper	N/A
B. vulgatus BV01-tetQ, attN::pNBU2-bla-cfx	This paper	N/A
B. vulgatus ΔBV01, attB::BV01-tetQ, attN::pNBU2-bla-ermGb	This paper	N/A
B. vulgatus VPI-4245	Abigail Salyers	N/A
B. vulgatus VPI-2365	Abigail Salyers	N/A
B. vulgatus VPI-6186	Abigail Salyers	N/A
B. vulgatus VPI-5710	Abigail Salyers	N/A
B. vulgatus DH4096S	Abigail Salyers	N/A
B. ovatus ATCC 8483	ATCC	ATCC 8483
Chemicals, Peptides, and Recombinant Proteins
Taurocholic acid sodium salt hydrate, ≥ 95%	Sigma-Aldrich	CAS #345909–26-4
Glycocholic acid hydrate, ≥ 97%	Sigma-Aldrich	CAS #1192657–83-2
Critical Commercial Assays
Nextera XT Library Preparation Kit	Illumina	Cat. #FC-131–1096
Nextera XT Index Kit	Illumina	Cat. #FC-131–1002
NEBNext Ultra II FS Kit for Illumina	New England Biolabs	E7805L
RNeasy Kit	QIAGEN	Cat. #74104
Deposited Data
Mutant genome DNA sequencing, see Table S3	This paper	PRJNA655911
RNA sequencing, see Table S3	This paper	PRJNA622597
Wastewater virome DNA sequencing, see Table S3	This paper	PRJNA622299
Bacterial genomes, see Table S3	This paper	PRJNA622758
Phage DNA sequencing, see Table S3	This paper	PRJNA655697
Experimental Models: Organisms/Strains
Germfree C57BL/6J mice	UCR Gnotobiotic Facility	N/A
Oligonucleotides
Primers for strain construction, see Table S4	This paper	N/A
Primers for integrase activity assays, see Table S4	This paper	N/A
Primers for detection of Salyersviridae phages, see Table S4	This paper	N/A
Recombinant DNA
pKNOCK-bla-ermGb	Koropatkin et al., 2008	N/A
pExchange-tdkBV	This paper	N/A
pNBU2-bla-ermGb	Koropatkin et al., 2008	N/A
pNBU2-int	This paper	N/A
pNBU2-bla-cfx	This paper	N/A
Software and Algorithms
Breseq	Deatherage and Barrick, 2014	https://github.com/barricklab/breseq
A5ud	Riley et al., 2017	https://github.com/phdegnan/A5ud
bwa	Li and Durbin, 2009	https://github.com/lh3/bwa
Microbialomics	This paper	https://github.com/phdegnan/MICROBIALOMICS
Rockhopper	McClure et al., 2013	https://cs.wellesley.edu/~btjaden/Rockhopper/
Trimmomatic 0.38	Bolger et al., 2014	http://www.usadellab.org/cms/?page=trimmomatic
metaSPAdes v3.13.0	Nurk etal., 2017	https://github.com/ablab/spades
Other
30,000 MWCO Corning Spin-X UF 20 Concentrators	Sigma-Aldrich	Cat. #CLS431489
Vivaflow 50R 30,000 MWCO Hydrosart Filter	Sartorius	Cat. #VF05H2
Sep-Pak tC18 500 mg cartridges	Waters Corp	Cat. #WAT036790