A mechanistic individual-based model of microbial communities

Jayathilake, P. G. et al. (2017) A mechanistic individual-based model of microbial communities. PLoS ONE, 12(8), e0181965. (doi: 10.1371/journal.pone.0181965) (PMID:28771505) (PMCID:PMC5542553)

Abstract

Accurate predictive modelling of the growth of microbial communities requires the credible representation of the interactions of biological, chemical and mechanical processes. However, although biological and chemical processes are represented in a number of Individual-based Models (IbMs) the interaction of growth and mechanics is limited. Conversely, there are mechanically sophisticated IbMs with only elementary biology and chemistry. This study focuses on addressing these limitations by developing a flexible IbM that can robustly combine the biological, chemical and physical processes that dictate the emergent properties of a wide range of bacterial communities. This IbM is developed by creating a microbiological adaptation of the open source Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). This innovation should provide the basis for “bottom up” prediction of the emergent behaviour of entire microbial systems. In the model presented here, bacterial growth, division, decay, mechanical contact among bacterial cells, and adhesion between the bacteria and extracellular polymeric substances are incorporated. In addition, fluid-bacteria interaction is implemented to simulate biofilm deformation and erosion. The model predicts that the surface morphology of biofilms becomes smoother with increased nutrient concentration, which agrees well with previous literature. In addition, the results show that increased shear rate results in smoother and more compact biofilms. The model can also predict shear rate dependent biofilm deformation, erosion, streamer formation and breakup.

• Item Type: Articles
• Additional Information: The authors would like to thank the UK Engineering and Physical Sciences Research Council (EPSRC) for funding this work as part of the Newcastle University Frontiers in Engineering Biology (NUFEB) project (EP/K039083/1).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Gonzalez-Cabaleiro, Dr Rebeca
• Authors: Jayathilake, P. G., Gupta, P., Li, B., Madsen, C., Oyebamiji, O., González-Cabaleiro, R., Rushton, S., Bridgens, B., Swailes, D., Allen, B., McGough, A. S., Zuliani, P., Ofiteru, I. D., Wilkinson, D., Chen, J., and Curtis, T.
• College/School: College of Science and Engineering > School of Engineering > Infrastructure and Environment
• Journal Name: PLoS ONE
• Publisher: Public Library of Science
• ISSN: 1932-6203
• ISSN (Online): 1932-6203
• Copyright Holders: Copyright © 2017 Jayathilake et al.
• First Published: First published in PLoS ONE 12(8): e0181965
• Publisher Policy: Reproduced under a Creative Commons License

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