Equation-Based Integration of Flux Balance Analysis with Diffusion for Spatio-Temporal Simulation of Microbial Communities
Senya, Frederick
Senya, Frederick
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Abstract
Spatio-temporal interactions shape microbial community dynamics. Metabolism, through competition and cross-feeding, is a foundational mechanism of these interactions. Flux balance analysis enables efficient simulation of steady-state metabolism. Integrating these simulations through time, using dynamic flux balance analysis, provides temporal predictions of growth and metabolism. Incorporating spatial context, through partial differential equations, enables spatio-temporal simulation of microbial communities. In this work, we step through this sequential process, moving from steady-state, to temporal, to spatio-temporal simulation of microbial community metabolism. As an illustrative example, we used the modeling software COMETS (Computation of Microbial Ecosystems in Time and Space) to simulate the metabolism of interacting bacterial colonies of Bifidobacterium longum subsp. infantis and Anaerobutyricum hallii. Within this simulation, both competition and cross-feeding influenced the production of butyrate, leading to a non-trivial impact of spatial structure on metabolite production. We outline each step and provide annotated open-source code such that this simulation can serve as a template for future spatio-temporal simulations of microbial community metabolism.
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Date
1/1/2026
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Graduate Student
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Poster
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Mathematics
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College of Engineering and Mathematical Sciences
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Mathematical Science