ArticlePloS one2017
A mechanistic Individual-based Model of microbial communities.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Agent-based modeling of erosion and sloughing during growth of Pseudomonas aeruginosa biofilms.NPJ biofilms and microbiomes · 2026Article
- Wrinkle-like structures emerge from matrix complementarity and mechanical discontinuity in heterogenous biofilms.NPJ biofilms and microbiomes · 2026Article
- Dissecting the physics of bacterial biofilms with agent-based simulations.Current opinion in solid state & materials science · 2025Article
- Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities.NPJ biofilms and microbiomes · 2024Article
- Computer simulation study of nutrient-driven bacterial biofilm stratification.Journal of the Royal Society, Interface · 2024Article
- Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions.Microbial ecology · 2024Review
- From microbiome composition to functional engineering, one step at a time.Microbiology and molecular biology reviews : MMBR · 2023Review
- Bayesian estimation ofBiofilm · 2023Article
- Climate change impacts on plant pathogens, food security and paths forward.Nature reviews. Microbiology · 2023Review
- Quantifying drift-selection balance using an agent-based biofilm model of identical heterotrophs under low-nutrient conditions.Interface focus · 2023Article
- A subcellular biochemical model for T6SS dynamics reveals winning competitive strategies.PNAS nexus · 2023Article
- Active layer dynamics drives a transition to biofilm fingering.NPJ biofilms and microbiomes · 2023Article
- BCM3D 2.0: accurate segmentation of single bacterial cells in dense biofilms using computationally generated intermediate image representations.NPJ biofilms and microbiomes · 2022Article
- Agent-Based Modeling of Microbial Communities.ACS synthetic biology · 2022Review
- Calibrating spatiotemporal models of microbial communities to microscopy data: A review.PLoS computational biology · 2022Review
- Coupled CFD-DEM modeling to predict how EPS affects bacterial biofilm deformation, recovery and detachment under flow conditions.Biotechnology and bioengineering · 2022Article
- Translational challenges and opportunities in biofilm science: a BRIEF for the future.NPJ biofilms and microbiomes · 2022Review
- Ecological modelling approaches for predicting emergent properties in microbial communities.Nature ecology & evolution · 2022Review
- Understanding photosynthetic biofilm productivity and structure through 2D simulation.PLoS computational biology · 2022Article
- Interacting Bioenergetic and Stoichiometric Controls on Microbial Growth.Frontiers in microbiology · 2022Article
Corrections and comments
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.