Fig 2. B. subtilis predictions.

Correlations between measured and predicted flux of heterotrophic B. subtilis grown on 8 different carbon sources for the three FBA methods E-Flux2 (red), SPOT (gray), pFBA (blue). Double carbon sources are glutamate plus succinate (Glut + Succ) and malate plus glucose (Mal + Glcs). Horizontal dashed lines are the respectively colored mean correlations per method. The mean (μ) is the average prediction correlation per method. The standard deviation (σ) is the spread of prediction correlation above and below the mean, denoted by the error bars. (A) Respective direct carbon source (DC) supplied. pFBA was given the additional constraint of known uptake rate in the single carbon source, while E-Flux2 and SPOT were not. All methods perform consistently across the individual carbon sources, with minor drops in correlation for double carbon sources (Glut + Succ and Mal + Glcs). (B) All 8 carbon sources supplied and correlated with measured flux from single carbon growth (AC). Correlations drop in all methods, particularly for Malate. (C) All possible carbon sources in the model supplied (Full AC). All methods again lose performance, but the transcriptomic methods retain reasonable correlations. See Supplementary S1 Table for uptake rates used.