Snapshot of SynComSim for predicting metabolite crossfeeding strategies for a 4-strain community consisting of the gut pathogen Clostridioides difficile and three common Enterobacteriaceae species.
SynComSim was released by In Silico Fermentation in September 2024. Please continue reading this page to learn more about the application and to download this free software.
An emerging application of genome-scale metabolic reconstructions is the development of multispecies metabolic models of synthetic bacterial communities, which can be experimentally realized through in vitro cell cultures. These models can be used for a priori prediction, such as determining which strains can coexist under certain nutrient conditions, or for a posterior analyses, such as identifying putative metabolite crossfeeding strategies employed by coexisting strains. By doing so, multispecies models can guide community design and generate predictions of variables that are difficult/impossible to measure experimentally. The research literature offers an expanding suite of community modeling tools which require considerable skill with programming languages such as MATLAB. By contrast, industrial practitioners typically wish to quickly perform community simulations with minimal coding effort.
SynComSim is a MATLAB application that enables rapid development, simulation and analysis of bacterial community models. Given genome-scale metabolic reconstructions of the community strains, the GUI tool generates predictions of the community growth rate and strain abundances, nutrient uptake and product secretion rates, and metabolite crossfeeding rates. All predictions are resolved on both a community and strain-by-strain basis. The workflow allows the definition of the growth medium (compatible with MediumFBA), the crossfed metabolites, and excluded strains to mimic strain dropout experiments. Community simulations can be performed for different combinations of the user-defined model parameters and stored for visualization and comparison using the included visualization App.
The following PDF file provides an overview of how SynComSim can be used to develop and simulate a 4-strain community consisting of the gut pathogen Clostridioides difficile and three species from the family Enterobacteriaceae, which is commonly elevated in gut microbiomes of patients suffering from recurrent Clostridioides difficile infections. The four strain models were downloaded from the Virtual Metabolic Human resource.
SynComSim has the following requirements:
- Version 2021a or newer version of MATLAB.
- Installed COBRA toolbox for MATLAB.
- A linear program (LP) solver compatible with COBRA. A list of compatible LP solvers is available here.
- Genome-scale metabolic reconstructions compatible with COBRA. SynComSim has been tested with selected reconstructions from the BIGG repository and the Virtual Metabolic Human resource (i.e., AGORA1 models).
SynComSim can be freely downloaded using the link below. The software is distributed under The GNU General Public License v3.0.
The Zip file should be processed as follows:
- Download and unzip the file using Zip archive software.
- The unzipped file will contain the following files: (1) the main application, SynComSim_ver_1_0.mlappinstall; and (2) two saved App states for community models developed using metabolic reconstructions from AGORA (Clostridioides difficile/Enterobacteriaceae community) and BIGG (Bacillus subtilis/Escherichia coli/Pseudomonas putida community).
- Save the files in the desired working directory.
- To install the SynComSim application, go to the Apps tab on the main Matlab page and click “Install App”. Select the saved SynComSim_ver_1_0.mlappinstall. The SynComSim application will appear as a new icon in the Apps tab.
- Launch the application by clicking on the icon.
Please contact me by email if you have any questions or feedback about SynComSim.
