Snapshot of MediumFBA applied to a 4-species bacterial model system containing Clostridioides difficile.
MediumFBA was released by In Silico Fermentation in February 2024. Please continue reading this page to learn more about the application and to download this free software.
Flux balance analysis (FBA) requires a priori specification of an in silico medium containing all essential nutrients required for growth. Development of in silico growth media is highly strain dependent and becomes increasingly difficult as additional strains are incorporated. Practitioners often find the medium definition problem for novel microbes and synthetic microbial communities to be a time consuming and frustrating task.
MediumFBA is a MATLAB application that integrates the medium design and FBA problems to allow more efficient analysis of metabolic behavior. The GUI tool generates growth media that allow monoculture growth of all strains where the metabolic properties of each strain is captured with an available genome-scale reconstruction. The workflow allows the definition of nutrients to be included and excluded from the medium such that the user can guide the medium design algorithm to yield an acceptable solution. The designed medium can be modified by the user to explore the effects of nutrient uptake rates and non-essential nutrients on monoculture growth and product secretion patterns.
The following PDF file provides an overview of how MediumFBA can be used to design an in silico medium that allows monoculture growth of four species comprising a synthetic bacterial community. More specifically, this example considers the design of an anaerobic glucose minimal medium for the gut pathogen Clostridioides difficile and three strains 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.
MediumFBA 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. MediumFBA has been tested with selected reconstructions from the Virtual Metabolic Human resource (i.e., AGORA models), the BIGG repository, and the KBase platform.
MediumFBA can be freely downloaded using the link below. The software is distributed under The GNU General Public License v3.0. Based on user feedback, Version 1.1 of MediumFBA offers the following improvements over the initial release:
- Improved support for BIGG bacterial reconstructions with a periplasmic compartment.
- Fixes for coding bugs associated with building metabolic models, constructing media and saving/loading App states.
- General improvements in the App workflow.
- Example App files for co-culture models using AGORA and BIGG metabolic reconstructions.
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, MediumFBA_v1_1.mlappinstall; (2) an updated version of the COBRA function createMultipleSpeciesModel.m, which is needed to properly build medium metabolic models for BIGG reconstructions; (3) example core media containing common ions for AGORA, BIGG and KBase metabolic models; and (4) saved App states for co-culture models developed using AGORA and BIGG metabolic models.
- Save the files in the desired working directory.
- To install the MediumFBA application, go to the Apps tab on the main Matlab page and click “Install App”. Select the saved MediumFBA_v1_1.mlappinstall. The MediumFBA 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 MediumFBA.
