Culture enrichment

Following MetaSUB protocols, swabs were directly incubated with 7 ml of Brain Heart Infusion (BHI) broth (Thermo Scientific Microbiology, CM1135B) at 37 °C until turbidity was observed (14–16 h for >95% of samples), up to a maximum of 48 h. Culture tubes were centrifuged at 3,200g for 12 min. For the first two time points, cell pellets were resuspended with 550 µl of 1× PBS, while the cell pellets for the third time point were resuspended with 1 ml of 1× PBS. Fifty microliters of resuspended cultures was then plated on each of six agar plates (without antibiotics, BHI; ampicillin: 100 µg ml^–1, AMP; streptomycin sulfate: 100 µg ml^–1, STREP; tetracycline: 10 µg ml^–1, TET; kanamycin: 50 µg ml^–1, KAN; and chloramphenicol: 35 µg ml^–1, CHLOR), and plates were incubated overnight at 37 °C. Cells were harvested by a plate sweep and were pelleted by centrifugation at 8,000g for 15 min at 4 °C for the first two time points. For the third time point, a loopful of harvested cells was streaked out on an antibiotic-free BHI plate to obtain single colonies for whole-genome sequencing. Plates were only excluded if no cells were growing on the plates or when the growth was insufficient to generate enough DNA for sequencing.