Engineering microbial communities for distributed computation using bacterial micro compartments.

Chris Barnes (primary)
Cell and Developmental Biology
Stefanie Frank (secondary)
Biochemical Engineering


Building biological systems that can perform computations has long been an aim of synthetic biology. The potential utility ranges from smart diagnostics and therapeutics, sustainable bioprocessing, and bioremediation/environmental applications. Engineered bacterial communities can serve as distributed biocomputing systems capable of integrating signal information and decision making (eg logic gates, neural networks). Bacterial microcompartments (BMCs) are organelle-like structures in prokaryotes. They are important for the localisation of a myriad of metabolic processes that would normally be toxic to cells. We will expand the toolbox of biocomputing using BMCs for the control of microbial communities.


Karkaria, B.D., Fedorec, A.J.H., Barnes, C.P. (2021). Automated design of synthetic microbial communities. Nature Communications, 12 (1), doi:10.1038/s41467-020-20756-2

Fedorec, A., Karkaria, B., Sulu, M., Barnes, C. (2021). Single strain control of microbial consortia. Nature Communications, doi:10.1038/s41467-021-22240-x

Treloar, N.J., Fedorec, A.J.H., Ingalls, B., Barnes, C.P. (2020). Deep reinforcement learning for the control of microbial co-cultures in bioreactors.. PLoS Comput Biol, 16 (4), e1007783. doi:10.1371/journal.pcbi.1007783

Karkaria, B.D., Treloar, N.J., Barnes, C.P., Fedorec, A.J.H. (2020). From Microbial Communities to Distributed Computing Systems. Frontiers in Bioengineering and Biotechnology, 8 doi:10.3389/fbioe.2020.00834

Planamente, S., & Frank, S. (2019). Bio-engineering of bacterial microcompartments: a mini review. Biochem Soc Trans, 47 (3), 765-777. doi:10.1042/BST20170564

Molecules, cells and industrial biotechnology
Area of Biology
Techniques & Approaches
EngineeringImage ProcessingMathematics / StatisticsMolecular BiologySimulation / Modelling