Deciphering the Principles of Bacterial Biofilm Assembly through Raman Imaging: From Single Cell to Extracellular Matrix.

Bacterial biofilms are living structures formed by bacteria that attach to surfaces and become embedded in a self-secreted extracellular matrix (ECM). They have a major impact on human activities and geochemical cycles. We are currently developing a project, jointly led by LKB* and LJP*, with the aim of creating a time-resolved functional mapping of a developing biofilm by implementing a combination of conventional and compressive Raman micro-spectroscopies, assisted by the use of stable isotope probes (SIP), and complemented by multiparametric computational analysis. This hybrid strategy should enable a kinetic approach to the processes of biofilm assembly from the single-cell stage to the two- and then three-dimensional stages. An AI strategy will be implemented to decipher cell-ECM couplings up to the mature biofilm stage. We will start by imaging a simple model biofilm of Escherichia coli, followed by strains of medical and environmental interest such as Pseudomonas aeruginosa or Bacillus thuringiensis. In the longer term, the achievement of the project should allow addressing the more complex question of the functioning of multi-species communities, a key subject in modern microbiology.

The extracellular matrix:

biofilm dark matter controlling biofilm biology, function, and mechanical properties (as shown in a previous work Galy et al., 2012, Biophys. J.)

Raman Imaging and Isotopic Labeling of Escherichia coli. (A) Raman image of bacteria in micro-chamber. (B) Comparison of spectra obtained on bacteria cultured in standard medium (H₂0) and in isotopic medium (D₂O). Preliminary results

Fast compressive Raman bio-imaging will provide time- and space-resolved molecular signatures in a complex  living organization. Compressive Raman exploits new sampling paradigms based on experimental undersampling followed by computational reconstruction. Details in Soldevila, F., Dong, J., Tajahuerce, E., Gigan, S., and de Aguiar, H.B. (2019). Fast compressive Raman bio-imaging via matrix completion. Optica 6, 341-346.