Final published version
Research output: Contribution to Journal/Magazine › Journal article › peer-review
Research output: Contribution to Journal/Magazine › Journal article › peer-review
}
TY - JOUR
T1 - A mechanistic Individual-based Model of microbial communities
AU - Jayathilake, Pahala Gedara
AU - Gupta, Prashant
AU - Li, Bowen
AU - Madsen, Curtis
AU - Oyebamiji, Oluwole
AU - González-Cabaleiro, Rebeca
AU - Rushton, Steve
AU - Bridgens, Ben
AU - Swailes, David
AU - Allen, Ben
AU - McGough, A. Stephen
AU - Zuliani, Paolo
AU - Ofiteru, Irina Dana
AU - Wilkinson, Darren
AU - Chen, Jinju
AU - Curtis, Tom
PY - 2017/8/1
Y1 - 2017/8/1
N2 - Accurate predictive modelling of the growth of microbial communities requires the credible representation of the interactions of biological, chemical and mechanical processes. How-ever, 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 com-bine 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 emer-gent behaviour of entire microbial systems. In the model presented here, bacterial growth, division, decay, mechanical contact among bacterial cells, and adhesion between the bacte-ria and extracellular polymeric substances are incorporated. In addition, fluid-bacteria inter-action is implemented to simulate biofilm deformation and erosion. The model predicts that the surface morphology of biofilms becomes smoother with increased nutrient concentra-tion, 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.
AB - Accurate predictive modelling of the growth of microbial communities requires the credible representation of the interactions of biological, chemical and mechanical processes. How-ever, 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 com-bine 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 emer-gent behaviour of entire microbial systems. In the model presented here, bacterial growth, division, decay, mechanical contact among bacterial cells, and adhesion between the bacte-ria and extracellular polymeric substances are incorporated. In addition, fluid-bacteria inter-action is implemented to simulate biofilm deformation and erosion. The model predicts that the surface morphology of biofilms becomes smoother with increased nutrient concentra-tion, 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.
U2 - 10.1371/journal.pone.0181965
DO - 10.1371/journal.pone.0181965
M3 - Journal article
JO - PLoS ONE
JF - PLoS ONE
SN - 1932-6203
ER -