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Open Access Research article

Stochastic simulations of a synthetic bacteria-yeast ecosystem

Konstantinos Biliouris1, David Babson2, Claudia Schmidt-Dannert3 and Yiannis N Kaznessis1*

Author affiliations

1 Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis, MN 55455, USA

2 University of Minnesota Biotechnology Institute, 140 Gortner Lab, 1479 Gortner Avenue, Saint Paul, MN 55108, USA

3 Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 140 Gortner Laboratory, Saint Paul, MN 55108, USA

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Citation and License

BMC Systems Biology 2012, 6:58  doi:10.1186/1752-0509-6-58

Published: 6 June 2012

Abstract

Background

The field of synthetic biology has greatly evolved and numerous functions can now be implemented by artificially engineered cells carrying the appropriate genetic information. However, in order for the cells to robustly perform complex or multiple tasks, co-operation between them may be necessary. Therefore, various synthetic biological systems whose functionality requires cell-cell communication are being designed. These systems, microbial consortia, are composed of engineered cells and exhibit a wide range of behaviors. These include yeast cells whose growth is dependent on one another, or bacteria that kill or rescue each other, synchronize, behave as predator-prey ecosystems or invade cancer cells.

Results

In this paper, we study a synthetic ecosystem comprising of bacteria and yeast that communicate with and benefit from each other using small diffusible molecules. We explore the behavior of this heterogeneous microbial consortium, composed of Saccharomyces cerevisiae and Escherichia coli cells, using stochastic modeling. The stochastic model captures the relevant intra-cellular and inter-cellular interactions taking place in and between the eukaryotic and prokaryotic cells. Integration of well-characterized molecular regulatory elements into these two microbes allows for communication through quorum sensing. A gene controlling growth in yeast is induced by bacteria via chemical signals and vice versa. Interesting dynamics that are common in natural ecosystems, such as obligatory and facultative mutualism, extinction, commensalism and predator-prey like dynamics are observed. We investigate and report on the conditions under which the two species can successfully communicate and rescue each other.

Conclusions

This study explores the various behaviors exhibited by the cohabitation of engineered yeast and bacterial cells. The way that the model is built allows for studying the dynamics of any system consisting of two species communicating with one another via chemical signals. Therefore, key information acquired by our model may potentially drive the experimental design of various synthetic heterogeneous ecosystems.

Keywords:
Stochastic modeling; Synthetic ecosystem; Cell-cell communication; Synthetic microbial consortia; Bacteria-yeast ecosystem