Publication Details

Category Text Publication
Reference Category Journals
DOI 10.3389/fbioe.2020.00574
Licence creative commons licence
Title (Primary) μBialSim: Constraint-based dynamic simulation of complex microbiomes
Author Popp, D.; Centler, F.
Source Titel Frontiers in Bioengineering and Biotechnology
Year 2020
Department UMB
Volume 8
Page From art. 574
Language englisch
Keywords microbial communities, metabolic modeling, constraint-based modeling, cross-feeding, microbiome dynamics
Abstract Microbial communities are pervasive in the natural environment, associated with many hosts, and of increasing importance in biotechnological applications. The complexity of these microbial systems makes the underlying mechanisms driving their dynamics difficult to identify. While experimental meta-OMICS techniques are routinely applied to record the inventory and activity of microbiomes over time, it remains difficult to obtain quantitative predictions based on such data. Mechanistic, quantitative mathematical modeling approaches hold the promise to both provide predictive power and shed light on cause-effect relationships driving these dynamic systems. We introduce μbialSim (pronounced “microbial sim”), a dynamic Flux-Balance-Analysis-based (dFBA) numerical simulator which is able to predict the time course in terms of composition and activity of microbiomes containing 100s of species in batch or chemostat mode. Activity of individual species is simulated by using separate FBA models which have access to a common pool of compounds, allowing for metabolite exchange. A novel augmented forward Euler method ensures numerical accuracy by temporarily reducing the time step size when compound concentrations decrease rapidly due to high compound affinities and/or the presence of many consuming species. We present three exemplary applications of μbialSim: a batch culture of a hydrogenotrophic archaeon, a syntrophic methanogenic biculture, and a 773-species human gut microbiome which exhibits a complex and dynamic pattern of metabolite exchange. Focusing on metabolite exchange as the main interaction type, μbialSim allows for the mechanistic simulation of microbiomes at their natural complexity. Simulated trajectories can be used to contextualize experimental meta-OMICS data and to derive hypotheses on cause-effect relationships driving community dynamics based on scenario simulations. μbialSim is implemented in Matlab and relies on the COBRA Toolbox or CellNetAnalyzer for FBA calculations. The source code is available under the GNU General Public License v3.0 at
Persistent UFZ Identifier
Popp, D., Centler, F. (2020):
μBialSim: Constraint-based dynamic simulation of complex microbiomes
Front. Bioeng. Biotechnol. 8 , art. 574 10.3389/fbioe.2020.00574