A mechanistic Individual-based Model of microbial communities

Area of Science:

• Microbial Ecology
• Computational Biology
• Biophysics

Background:

• Accurate microbial community growth prediction necessitates integrating biological, chemical, and mechanical processes.
• Existing Individual-based Models (IbMs) often lack comprehensive integration of these factors, with limitations in representing mechanical interactions or detailed biological/chemical processes.
• A gap exists in flexible models capable of robustly combining diverse processes for predicting bacterial community emergent properties.

Purpose of the Study:

• To develop a flexible Individual-based Model (IbM) that integrates biological, chemical, and physical processes for predicting bacterial community behavior.
• To address limitations in current models by incorporating mechanical interactions alongside detailed biological and chemical processes.
• To provide a "bottom-up" predictive framework for the emergent behavior of diverse bacterial communities.

Main Methods:

• Development of a microbiological adaptation of the open-source Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS).
• Incorporation of bacterial growth, division, decay, cell-cell mechanical contact, and adhesion to extracellular polymeric substances.
• Implementation of fluid-bacteria interaction to simulate biofilm deformation and erosion.

Main Results:

• The model predicts smoother biofilm morphology with increased nutrient concentration, consistent with existing literature.
• Increased shear rate leads to smoother and more compact biofilms.
• The model successfully predicts shear rate-dependent biofilm deformation, erosion, streamer formation, and breakup.

Conclusions:

• The developed Individual-based Model (IbM) offers a robust framework for integrating diverse processes in bacterial communities.
• This approach enables "bottom-up" prediction of emergent behaviors in microbial systems.
• The model's predictions align with experimental observations, validating its utility in microbial ecology and biophysics.