Structure and Physiology of Microbial Biofilms Lab


Our work addresses a topic of relevance for Public Health, particularly with regard to infectious diseases, as it is the formation of biofilms by pathogenic bacteria. Biofilms are multicellular communities that bacteria form over surfaces by producing an extracellular matrix (ECM) that protects and holds the cells together. Within biofilms, certain bacterial subpopulations recurrently tolerate and survive antibiotic treatments, which ultimately allow the resurgence of biofilm community. As a consequence, biofilm formation allows many bacterial infections to persist, compromising the chance of cure.

Using the Gram-negative bacterium Escherichia coli as model organism, we are interested in understanding how cell subpopulations physiologically differentiate inside complex structures of biofilms and how this physiological heterogeneity shapes patterns of differential antibiotic tolerance. Understanding these aspects is crucial to design more effective therapeutic strategies, able to kill all cell subpopulations within the biofilms. In line with this, we are also interested in discovering compounds that inhibit biofilm formation by E. coli strains, including diverse pathogenic variants, and in characterizing their molecular mechanisms of action.

Our studies involve the application of approaches that combine microbiology, molecular biology and microscopy techniques. Specially, we seek to take advantage of our recent advances in the use of cryosectioning along with high-resolution fluorescence and electron microscopy as imaging tools to examine the biofilm communities in great detail.

Research Lines

Microbial biofilms typically adopt very complex architectures, whose formation essentially depends on the production by bacteria of an extracellular matrix (ECM) that promotes cohesion among cells and mechanical stability to the overall biofilm structure. In biofilms of E. coli, our model organism, this architectural role is largely fulfilled by two major ECM components: amyloid curli and the exopolysaccharide phosphoethanolamine(pEtN)-cellulose; both occurring in the form of fibers with different, but complementary, structural and mechanical properties.


An intrinsic consequence of the structural complexity of biofilms is the generation of highly heterogeneous internal environments shaped by gradients of nutrients, metabolic products and signaling compounds. Here, bacterial cells essentially adjust their physiology according to the local conditions, which ultimately causes the stratification of the biofilms into physiologically distinct regions. Our work suggests that this physiological stratification not only represents a “division of labor”, where cell subpopulations locally specialize in fulfilling specific tasks, such as for example the production of ECM, but it also endows cell subpopulations with different capacities to cope with stresses as it is the case of antibiotic treatments. Our group is interested in characterizing this physiological stratification in biofilms of commensal and pathogenic E. coli strains and in understanding how this physiological heterogeneity influences the chances of cells to survive antibiotic treatments depending on their location within the biofilm. In particular, we seek to clarify how heterogeneity in the production of ECM components (amyloid curli and pEtN-cellulose), in stress responses, and in metabolism/growth among cell subpopulations influence antibiotic tolerance in E. coli biofilms. Knowledge of these aspects is crucial to design therapies that can target all cell subpopulations that coexist within these communities, irrespective of their physiological state and spatial location.


Recognizing the need for solutions to combat biofilm-based infections, we are also interested in discovering anti-biofilm compounds and characterizing their molecular mechanisms of action. In particular, we search for compounds that can interfere with the production of amyloid curli and pEtN-cellulose, the major architectural elements of E. coli biofilms. As platform for the search of inhibitors we are exploring microbial interactions in biofilms. While antagonistic interactions among microorganisms have been intensely exploited in the search for antibiotics, i.e., compounds that directly kill or inhibit bacterial growth, these interactions have been overlooked regarding their potential as sources for compounds that, rather than killing the bacteria, modulate or interfere with other bacterial behaviors such as the formation of biofilms. The use of anti-biofilm compounds is crucial in the fight to eradicate biofilm-based infections as they can considerably increase the effectiveness of antibiotics in combined therapies or enhance the efficacy of clearance by the host immune system.

Selected Publications

- Serra D.O. and Hengge R. (2019) A c-di-GMP-based switch controls local heterogeneity of extracellular matrix synthesis which is crucial for integrity and morphogenesis of Escherichia coli macrocolony biofilms. J Mol Biol. 431(23):4775-4793. doi: 10.1016/j.jmb.2019.04.001

- Klauck G., Serra D.O., Possling A. and Hengge R. (2018) Spatial organisation of different sigma factor activities and c-di-GMP signalling within the 3D landscape of a bacterial biofilm. Open Biology. 8: 180066.

- Thongsomboon W., Serra D.O., Possling A., Hadjineophytou C., Hengge R. and Cegelski L. (2018) Phosphoethanolamine cellulose: a naturally produced chemically modified cellulose. Science. 359, 334-338. doi: 10.1126/science.aao4096

This article was highlighted in:

1) Science|Perspectives Vol. 359, Issue 6373, pp. 276-277 doi: 10.1126/science.aar5253


2) Nature |Research highlights (

3) Nat Rev Microbiol. 2018;16(3):123. doi: 10.1038/nrmicro.2018.22.


- Serra D.O., Mika F., Richter A. and Hengge R. (2016) The green tea polyphenol EGCG inhibits Escherichia coli biofilm formation by impairing amyloid curli fibre assembly and down-regulating the biofilm regulator CsgD via the σE-dependent sRNA RybB. Mol Microbiol. 101(1):136–151. doi: 10.1111/mmi.13379

Article selected for the cover of issue I (Vol 101, Number 1, Jul 2016) of Mol Microbiol.

- Serra D.O.*, Klauck G.* and Hengge R. (2015) Vertical stratification of matrix production is essential for physical integrity and architecture of macrocolony biofilms of Escherichia coli. Environ Microbiol. 17(12):5073-88. doi: 10.1111/1462-2920.12991

* both authors contributed equally to this work

- Serra D.O. and Hengge R. (2014) Stress responses go 3D – the spatial order of physiological differentiation in bacterial macrocolony biofilms. Environ. Microbiol. 16(6):1455-71. Review.

Article selected for the cover of issue 6 (Vol16) of Environ. Microbiol.

- Serra D.O.*, Richter A.M.* and Hengge R. (2013) Cellulose as an architectural element in spatially structured Escherichia coli biofilms. J. Bacteriol. 195(24):5540-54. doi: 10.1128/JB.00946-13

* both authors contributed equally to this work

Article selected for the cover of issue 24 (Vol 195) of J. Bacteriol.

- Serra D.O., Richter A.M., Klauck G., Mika F. and Hengge R. (2013) Microanatomy at cellular resolution and spatial order of physiological differentiation in a bacterial biofilm. mBio 4(2):e00103-13. doi:10.1128/mBio.00103-13. doi:10.1128/mBio.00103-13

Article highlighted in Nature Reviews Microbiology (2013) 11, 300–301


Fernando Soncini (IBR-CONICET, Rosario, ARG)

Natalia Gottig (IBR-CONICET, Rosario, ARG)

Regine Hengge (Humboldt University, Berlin, GER)

Cécile Bidan (Max Planck Institute of Colloids and Interfaces, Golm, GER)

Natalia Tschowri (Humboldt University, Berlin, GER)

Lars Dietrich (Columbia University, New York, US)


Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT)

Alexander von Humboldt Foundation (AvH, GER)

Director de Grupo

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Serra, Diego
Core CCT
Phone: +54-341-4237070 int 658
Laboratory Extension: 6