A mechanistic Individual-based Model of microbial communities

Authored by Steve Rushton, David Swailes, Ben Bridgens, Tom Curtis, Jinju Chen, Rebeca Gonzalez-Cabaleiro, Pahala Gedara Jayathilake, Prashant Gupta, Bowen Li, Curtis Madsen, Oluwole Oyebamiji, Ben Allen, A Stephen McGough, Paolo Zuliani, Irina Dana Ofiteru, Darren Wilkinson

Date Published: 2017

DOI: 10.1371/journal.pone.0181965

Sponsors: United Kingdom Engineering and Physical Sciences Research Council (EPSRC)

Platforms: C++ LAMMPS

Model Documentation: ODD Mathematical description

Model Code URLs: https://github.com/nufeb/NUFEB

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.

Tags

Dynamics Simulations growth Protocol Transport Cellular-automaton approach Surfaces Detachment mechanisms Multispecies biofilms Nanoindentation