Megasphaera MJR8396C - MSc Thesis
This GitHub repository contains the code and data generated as part of the MSc thesis conducted by Joy van Geerestein.
Initial Validation: The tool memote was used to test the viability of the provided genome-scale metabolic model (GEM) for Megasphaera MJR8396C, which yielded a satisfactory memote test score.
Metabolic Flux Analysis: General metabolic fluxes in a gut-like medium were tested using pFBA (code: generalpfba). The effects of varying amino acids and carbohydrates on the growth of Megasphaera MJR8396C were assessed (code: AAvscarbohydrates). Attempts to add pectin to the GEM to test growth on this substrate were made, but did not yield feasible results (code: add_pectin_to_model).
Stickland Metabolism Analysis: Stickland metabolism pairs were simulated by pairing two amino acids and conducting pFBA (code: SticklandpairspFBA). Heatmaps were created using pandas and seaborn in Python to visualize interaction effects (code: interactioneffectheatmap). Stickland reactions were searched for in all reactions in the GEM (code: reactionstoexcel) Specific Stickland metabolites without exchange reactions were added to the model, but this also did not yield feasible results (code: add_stickland_metabolites).
Butyrate Production Analysis: Butyrate production was assessed using production envelope and double robustness analysis (code: productionenvelope and doublerobustnessanalysis). Optimization algorithms were then employed (code: Optforcebutyrate and OptKnockbutyrate).
Community Simulations: A multi-species model was created for community simulations with Bifidobacterium adolescentis (code: multiplespeciesmodel), resulting in the community model pairedModel_Bifidobacterium_adolescentis_BM.xml_Megasphaera_sp_MJR8396C.xml.mat. FBA simulations on the community model were performed with initial minimal medium for each microbe (code: minimalmedium). Pairwise interactions were analyzed (code: pairwiseinteraction), resulting in interactions pairwise.mat. BacArena was used for community growth simulations over time (BacArenacode).
Data Availability: All generated data from the above simulations can be found in the file "JVG MSc thesis data file"