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Understanding and Engineering E. coli biofilm formation

Primary Supervisor: Dr Tim Overton

Secondary supervisor: Mark Simmons

PhD project title: Understanding and Engineering E. coli biofilm formation

University of Registration: University of Birmingham

Project outline:

Biofilms are communities of bacteria living together, bound by a self-produced extracellular matrix, often attached to a solid surface (Hall-Stoodley et al., 2004). Biofilms offer benefits to bacteria: protection from external stressors such as antibiotics and other chemicals; protection from host immune systems; cell to cell communication; and division of metabolic labour.

Many biofilms pose a threat to humans. Oral bacteria form a biofilm on the teeth, dental plaque, causing tooth decay if not removed. Biofilms also cause problems for industry, growing inside pipes in factories, leading to product contamination. Biofilm growth on ships leads to increased drag and thus increased fuel consumption. The economic cost of biofilms is therefore immense.

However, the very properties of biofilms that make them problematic – protection, stickiness – allow them to be used in some processes to manufacture chemicals. Biofilms can be used a biocatalysts, and have been shown to have higher yield than planktonic cells and immobilised enzymes for some reactions (Tsoligkas et al., 2011). Given that industry is interested in converting chemical processes to biologically-catalysed processes for sustainability, environmental and economic reasons, biofilms offer an exciting new prospect.

We are interested in engineering biofilm formation and development. Recent work has investigated the regulation of the adhesin curli, thought to be the initial mechanism by which E. coli cells attach to surfaces. Curli regulation is complex and influenced by multiple environmental stimuli; understanding this regulatory network could offer the ability to engineer attachment in situations where biofilms are desirable, such as in biocatalysis. 

We have also investigated pellicles, floating biofilms that form at the air-liquid interface (Kovács & Dragoš, 2019). We are interested in how pellicles form, and how regulation of adhesins and matrix components differ from surface-attached biofilms. We would also like to explore the possibility of using pellicles as a biocatalytic platform.

Finally, we are interested in the different ways in which biofilms could form. The standard model for biofilm formation (Stoodley et al., 2002) is that single cells attach to a surface via adhesins, grow into microcolonies and produce extracellular matrix, then form larger structures with a typical mushroom-shaped morphology. However, a new model is developing, whereby not only single cells can attach to solid surfaces, but also cells can form clumps in the medium, before attaching to surfaces (Kragh et al., 2016). This model could also encompass formation of clusters of cells and floating pellicles. This would allow us to investigate the use of clusters of cells as biocatalysts, which could be compatible with standard reactor systems.

This project will investigate aspects of E. coli biofilm formation and development in the context of generating useful, biocatalytic biofilms. Some of the key questions that we will aim to address are:

  • How can attachment of coli to surfaces and extracellular matrix synthesis be engineered?
  • How is curli regulation related to cell to cell communication?
  • How do pellicles differ from solid surface-attached biofilms?
  • How are curli regulated during cell cluster formation?

As the project will start in Summer 2021, the exact project objectives will be decided closer to the start, based on progress in the laboratory and other scientific literature.


  1. Hall-Stoodley et al. (2004) Nat Rev Microbiol. 2004 2(2):95-108. doi: 10.1038/nrmicro821
  2. Kovács & Dragoš A (2019) J Mol Biol. doi: 10.1016/j.jmb.2019.02.005.
  3. Kragh et al. (2016) MBio. 7(2):e00237. doi: 10.1128/mBio.00237-16
  4. Stoodley et al. (2002) Annu Rev Microbiol. 56:187-209. doi: 10.1146/annurev.micro.56.012302.160705

BBSRC Strategic Research Priority: Renewable Resources and Clean Growth: Industrial Biotechnology

Techniques that will be undertaken during the project:

Flow cytometry for physiology and gene regulation studies, molecular biology and reporter gene construction, microscopy (light/fluorescence/confocal Laser scanning), goiniometry, Mastersizer particle sizing, zeta potential determination. Other techniques as required.

Contact: Dr Tim Overton, University of Birmingham