REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
B. vulgatus cell culture	Lab stock	Bacteroides vulgatus ATCC 8482
B. subtilis cell culture	Lab stock	Bacillus subtilis str. 168 BS168
Biological samples
Human stool sample	Korpela et al., 2018	Stool sample from baby collected in Luxembourg. https://www.ebi.ac.uk/ena/browser/view/SAMEA104445596
Deposited data
Data and scripts (CheckM, Binning, Contig KEGG-KO table, Chip designs, PADS data plotting via GitHub)	This paper, deposited in the Open Science Framework	https://doi.org/10.17605/OSF.IO/6TMZK
FIJI plugin code and imaging data	This paper, deposited in Zenodo	https://doi.org/10.5281/zenodo.5748533
Genomic data	This paper, deposited in ENA	Project accession number PRJEB48713; sample 1 https://www.ebi.ac.uk/ena/browser/view/ERS8538067 and sample 2 https://www.ebi.ac.uk/ena/browser/view/ERS8538068
Oligonucleotides
Forward primer with 5’ Mod: BtnTg for Bacteroides vulgatus and dorei	Sigma-Aldrich	CAAGCTGAGAAAAGCAGCCAAA
Probe sequence with Iowa Black FQ and intermediate ZEN quencher and 5’ 6-FAM fluorophore for Bacteroides vulgatus and dorei	IDT	AGTGGCAGTAGCCGGAGGGGTA TCAGCCA
Reverse primer with 5’ Mod: BtnTg for Bacteroides vulgatus and dorei	Sigma-Aldrich	GAATGAGTTACGAAGCCCGTTG
Forward primer with 5’ Mod: BtnTg for Bacillus subtilis	Sigma-Aldrich	TCGTGCTGAGACAGTTGCTT
Probe sequence with Iowa Black FQ and intermediate ZEN quencher and 5’ 6-FAM fluorophore for Bacillus subtilis	IDT	TTGCGGGCGGCGGTATGGCAGGAGCT
Reverse primer with 5’ Mod: BtnTg for Bacillus subtilis	Sigma-Aldrich	TCTTTCCCTTCAAGGCGGAC