2025
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 Master2 internship fits into this overall program by focusing on the SIP strategy. The objective is to determine the set of isotopic markers (e.g., D₂O, C13-glucose, N15-Nitrogen, ...) providing the most effective hyperspectral data set (Raman images) for establishing the functional mapping of the biofilm. This involves optimal spatiotemporal and spectral resolutions as well as distinguishable cellular and matrix signatures. Preliminary experiments conducted in deuterated water (D₂O) have already demonstrated the feasibility of these approaches (see figure).
Raman Imaging and Isotopic Labeling of Escherichia coli. (A) Raman image of bacteria in a micro-chamber. (B) Comparison of spectra obtained on bacteria grown in standard medium (H₂O) and isotopic medium (D₂O).
This work will involve microbiology experiments for the culture of bacteria and biofilm, experimental devices microfabrication, Raman images acquisition as well as algorithmic processing and modeling approaches for large data sets. To accomplish this project, the intern will benefit from the dual scientific environment of LJP and LKB and the dual supervision of Nelly Henry and Hilton De Aguiar.
This biophysics project is ideally aimed at a Master2 candidate at the interface of physics or physico-chemistry and biology. However, strong motivation for interdisciplinarity will also be favorably considered for a candidate without dual training.
The internship is expected to continue into a PhD.
Contact: nelly.henry@sorbonne-universite.fr and h.aguiar@phys.ens.fr
*Laboratoire Jean Perrin (LJP)
Campus Pierre et Marie Curie
4, Place Jussieu, Paris 5e
*Laboratoire Kastler Brossel (LKB)
Campus ENS Ulm
24 rue Lhomond, Paris 5e
References:
1. P. Thomen, J. D. P. Valentin, A. F. Bitbol, N. Henry, Spatiotemporal pattern formation in E.coli biofilms explained by a simple physical energy balance. Soft Matter 16, 494-504 (2020)
2. Monmeyran et al., The inducible chemical-genetic fluorescent marker FAST outperforms classical fluorescent proteins in the quantitative reporting of bacterial biofilm dynamics. Sci Rep 8, 10336 (2018)
3. P. Thomen et al., Bacterial biofilm under flow: First a physical struggle to stay, then a matter of breathing. PLoS ONE 12, e0175197 (2017)
4. O. Galy et al., Mapping of bacterial biofilm local mechanics by magnetic microparticle actuation. Biophysical journal 5, 1400-1408 (2012).
5. S. H. Donaldson Jr., H. B. de Aguiar. Molecular Imaging of Cholesterol and Lipid Distributions in Model Membranes. J. Phys. Chem. Lett. 9 1528 (2018)
6. B. Sturm, F. Soldevila, E. Tajahuerce, S. Gigan, H. Rigneault, H. B. de Aguiar. High-sensitivity high-speed compressive spectrometer for Raman imaging. ACS Photonics 6, 1409–1415 (2019)
7. F. Soldevila, J. Dong, E. Tajahuerce, S. Gigan, H. B. de Aguiar. Fast compressive Raman bio-imaging via matrix completion. Optica 6, 341–346 (2019)