Bacteriophages were labelled as described previously37 (link). Briefly, 100 μL of purified vibriophages with a concentration of 1012 plaque forming units (PFU) per mL were mixed with sodium carbonate (0.1 M final) and then incubated with 0.1 mg Alexa Fluor 488 5-TFP (A30005, Thermo Fisher Scientific) for 1 h at room temperature under continuous shaking. The reaction mixture was first dialyzed at 4 °C against 500 mL of phosphate-buffered saline (PBS) for 3 hours and then dialyzed overnight at 4 °C against 2 L of PBS. This was done to separate phages from unbound dye. This stock of fluorescently labelled phages was stored at 4 °C.
Biofilms of the mRuby3-expressing V. cholerae WT strain (KDV657) were grown for 24 h, before the inflowing M9 medium was exchanged to contain tetracycline for 6 h and fluorescently labelled phages (a 1:100 dilution of the fluorescently labelled phage stock). As a control treatment, M9 medium without tetracycline, but containing the same concentration of vibriophages was added for 6 h. Biofilms were imaged for the 6 h of phage exposure with a time resolution of 2 h (Extended Data Fig. 9c ).
Biofilms of the mRuby3-expressing V. cholerae WT strain (KDV657) were grown for 24 h, before the inflowing M9 medium was exchanged to contain tetracycline for 6 h and fluorescently labelled phages (a 1:100 dilution of the fluorescently labelled phage stock). As a control treatment, M9 medium without tetracycline, but containing the same concentration of vibriophages was added for 6 h. Biofilms were imaged for the 6 h of phage exposure with a time resolution of 2 h (
