I am now making a central carbon metabolic (CCM) model for a bacterium, but I don't know how to formulate the biomass equation. I have a genome-scale metabolic model (GEM) for the bacterium but its biomass equation is beyond the scope of the CCM model. Some of the metabolites in the GEM biomass equation are not involved in the CCM model. Could you please tell me how to simplify the GEM biomass equation?
I do not have a solution to this issue but there is a suggestion. I would prefer convert the equation from GEM from the aspect of element balances.
The complicity of the final equation depends on the scale of your CCM model and the elements it involves. There will be definitely some compromises on the accuracy of the final equation in the end. You can list available intracellular compounds (in pool), such as amino acids, phosphate sugars, polysaccharides, fatty acid (if any) etc, and calculate the stoichiometry of equation from these pools based on element balances and redox balance. Simplification could be done furhter if you are only interested in C H O N (P) but not other trace elements.
Here I attached an old publication from Walter van Gulik who established a metabolic pathway model of Penicillium chrysogenum previously, which is much simpler to a current GEM model. Hope it can help you to work out your CCM model.
Best,
Wenjun
Article Application of metabolic flux analysis for the identificatio...
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