ArticleScientific reports2020
ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial Communities.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment.PLoS computational biology · 2024Article
- Discretised Flux Balance Analysis for Reaction-Diffusion Simulation of Single-Cell Metabolism.Bulletin of mathematical biology · 2024Article
- Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0.PLoS computational biology · 2024Article
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations.Briefings in bioinformatics · 2023Review
- Multiscale models driving hypothesis and theory-based research in microbial ecology.Interface focus · 2023Review
- A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia.PLoS computational biology · 2023Article
- From Spatial-Temporal Multiscale Modeling to Application: Bridging the Valley of Death in Industrial Biotechnology.Bioengineering (Basel, Switzerland) · 2023Review
- Developing a metabolic model-based fed-batch feeding strategy for Pichia pastoris fermentation through fine-tuning of the methanol utilization pathway.Microbial biotechnology · 2023Article
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- A Systematic Strategy to Find Potential Therapeutic Targets forFrontiers in molecular biosciences · 2021Article
- Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools.Computational and structural biotechnology journal · 2020Review
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2 authors.
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Abstract
The development of new methods capable of more realistic modeling of microbial communities necessitates that their results be quantitatively comparable with experimental findings. In this research, a new integrated agent and constraint based modeling framework abbreviated ACBM has been proposed that integrates agent-based and constraint-based modeling approaches. ACBM models the cell population in three-dimensional space to predict spatial and temporal dynamics and metabolic interactions. When used to simulate the batch growth of C. beijerinckii and two-species communities of F. prausnitzii and B. adolescent., ACBM improved on predictions made by two previous models. Furthermore, when transcriptomic data were integrated with a metabolic model of E. coli to consider intracellular constraints in the metabolism, ACBM accurately predicted growth rate, half-rate constant, and concentration of biomass, glucose, and acidic products over time. The results also show that the framework was able to predict the metabolism changes in the early stationary compared to the log phase. Finally, ACBM was implemented to estimate starved cells under heterogeneous feeding and it was concluded that a percentage of cells are always subject to starvation in a bioreactor with high volume.
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