Colony Size Characterization and Quantification
Keio wild-type and ΔybeX strains were grown overnight in LB or defined MOPS minimal medium (Neidhardt et al. , 1974). Well-grown bacterial cell cultures were serially diluted and plated on LB agar plates using glass beads (Hecht Assistent, #41401004). We aimed to have approximately 100-125 colonies per plate. The plates were incubated overnight at 37°C or 42°C and scanned using EPSON Expression 1680pro scanner. The images were subjected to AutoCellSeg software (Khanet al. , 2018). The colonies were first picked automatically using program default settings, and then, as a second step, manual picking was applied (picking small colonies, deselecting adherent colonies, etc.). The data were analyzed in the R packages tidyverse and visualized with ggplot2 (Wickham et al. , 2019; R Core Team, 2022).