Significant Differences in Media Components and Predicted Growth Rates of 58 Escherichia coli Genome scale Models.

Citation: Tan, FL, Kuan, ZJ, Amir-Hamzah, N, Kng, X, Wee, YY, Sor, SX, Ling, MHT. 2022. Significant Differences in Media Components and Predicted Growth Rates of 58 Escherichia coli Genome-scale Models. Acta Scientific Microbiology 5(2): 56-68.

Link to [Abstract] and [PDF].

Here is the permanent [PDF], and [Data set] links to my archive.

Escherichia coli is a common host for metabolite production and genome-scale metabolic models (GSMs) is an important computational tool to aid in such experimental design. As of September 30, 2021; 58 GSMs have been registered with BiGG database. However, these GSMs had been built for different applications and no large-scale comparative study had been performed to-date. In this study, we examine the media components and predicted growth rates of these 58 GSMs using flux balance analysis across various glucose uptake rates. Only 5 out of 29 uptake rates (as proxy for media components) are common in all 58 GSMs; namely, proton, water, ammonium, oxygen, and phosphate. 74.25% (2370 of the 3192) pairwise comparisons of predicted growth rates show significant differences (p-value < 0.05) and 34 of 42 pairwise comparisons of predicted growth rates within the same strain are significantly different. Hence, our results demonstrated substantial differences in media components and significant differences in predicted growth rates between the GSMs and even within GSMs constructed for the same strain.