A mechanistic Individual-based Model of microbial communities

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.

NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities

“…These detached microbe chunks may also break-up again, re-agglomerate with other 427 clusters or re-attach to the biofilm surface (Fig 4(c)). Such deformation and detachment 428 events observed from our NUFEB simulation show qualitative agreement with both 429 experimental results [42] and other numerical simulations using different 430 methods [17,43]. The deformation reaches a pseudo-steady-state when the 431 mushroom-shaped biofilm protrusions are removed from the system.…”

“…57 Model description 58In this section, we describe and review the IbM implemented in NUFEB. We build on 59 the ideas described previously in [17] and extend them to cope with hydrodynamics and 60 chemical processes. For the sake of accuracy, in the following we use the term "microbe" 61 when describing biological and chemical processes, and use the term "particle" when 62 describing physical process.…”

“…The user can choose one of the growth models when configuring the 110 simulation to run. For exemplification, the Monod-based growth model implements the 111 work described in [17] and [18]. Three functional groups of microbes and two inert 112 states are considered.…”

“…The EPS play an important role in 144 microbial aggregation by offering a protective medium. The production process follows 145 the approach presented in [17] and [23] with the simplification that EPS are secreted by 146 heterotrophs only. Initially, EPS is accumulated as an extra shell around a HET particle 147 (note that EPS density is lower than microbe density).…”

“…Design and implementations 266 NUFEB is developed in C++ as a user package within the LAMMPS platform. A 267 prototype implementation was used in [17] to study physical behaviour of microbial 268 communities. We describe a major improvement of the tool, in which new features and 269 enhancements have been developed including coupling with fluid dynamics, chemical 270 processes, code parallelisation, and post-processing routines.…”