Computational protocol: Halogenated indoles eradicate bacterial persister cells and biofilms

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Protocol publication

[…] Escherichia coli BW25113 and S. aureus cells were cultured in 96-well polystyrene plates (SPL Life Sciences, Korea) without shaking with or without 5-iodoindole. Biofilms were stained with carboxyfluorescein diacetate succinimidyl ester (Invitrogen, Molecular Probes, Inc., Eugene, OR, USA) (Weston and Parish ). Planktonic cells were removed by washing with PBS three times, and static biofilms were visualized by excitation using an Ar laser 488 nm (emission wavelengths 500–550 nm) under a confocal laser microscope (Nikon Eclipse Ti, Tokyo) using a 20× objective (Kim et al. ). Color confocal images were constructed using NIS-Elements C version 3.2 (Nikon eclipse). For each experiment, at least 10 random positions in two independent cultures were chosen for microscopic analysis.To quantify biofilm formation, color confocal images (20 image stacks) were converted to gray scale using ImageJ. COMSTAT biofilm software (Heydorn et al. ) was used to determine biomasses (μm3 μm−2), mean thicknesses (μm), and substratum coverages (%). Thresholding value was fixed for all image stacks, and at least 4 positions and 20 planar images per position were analyzed. […]

Pipeline specifications

Software tools ImageJ, Comstat
Applications Laser scanning microscopy, Microscopic phenotype analysis
Organisms Escherichia coli, Staphylococcus aureus, Epipremnum aureum
Diseases Bacterial Infections