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Radial topographies of biofilm colonies


Bravo, Pablo et al. (2023), Radial topographies of biofilm colonies, Dryad, Dataset,


During the biofilm life cycle, bacteria attach to a surface and then reproduce, forming crowded, growing communities. Difficulties in accurately measuring biofilm height across relevant time and length scales have prevented testing diverse biophysical models empirically. Using white light interferometry, we measure the heights of microbial colonies with nanometer precision from inoculation to their final equilibrium height, producing a novel and detailed empirical characterization of vertical growth dynamics. This dataset corresponds to the profiles of developing biofilms, measured through white-light interferometry. This dataset represents novel high-resolution characterizations of developing biofilms in the vertical direction, empirical measurements that can be utilized to test models for biofilm development, ranging from bulk-dynamics to surface fluctuations. 


Measurements represent novel topographic measurements with 1 nanometer resolution in the z axis, and 0.2 micrometers in plane of developing biofilms. Time between measurements allows the study of short and long time scales (10 minutes to 14 days) of a diverse cohort of  microorganisms (Aeromonas veronii, Escherichia coli, Saccharomyces cerevisiae, Vibrio cholerae, Klebsiella pneumoniae, Bacillus cereus, Staphylococcus aureus).

Data was obtained using a Zygo ZeGage Pro Optical Profilometer, using the 1000x200@800Hz measuring mode, across the width of the colony. Images were then averaged over the 200 pixels in the y-direction (~32μm), and background from the growing substrate was removed.

 We also provide scripts for fitting and evaluating vertical growth dynamics using diverse biophysical models. 

Usage notes

All interferometric measurements are provided in csv format. For a detailed description of the files refer to the document and the accompanying article. 

For analysis and topography analysis scripts:

- Python for cleaning script, and loading sample .datx data.

- Julia for differential equation modeling, and parameter optimization.


National Institute of General Medical Sciences, Award: 1R35GM138354-01

National Science Foundation, Award: BMAT2003721