Figure 3. Nutrients uptaken and that stimulate growth in the presence of minimal media for the organisms in the training set.

A, E. coli and B. subtilis have the largest number of uptaken nutrients whereas M. barkeri has the fewest. This reflects the current understanding of M. barkeri as a specialized methanogen [68]. B, E. coli and B. subtilis are able to catabolize half of the nutrients they uptake whereas M. barkeri can catabolize less than 10% of the nutrients it uptakes. C, Number of uptaken nutrients by nutrient class. Within each class, the four organisms uptake approximately the same number of nutrients. Exceptions are M. barkeri—which does not uptake neither Fatty acids nor Sugars, and only one Sugar derivative—and B. subtilis—which is not assumed to uptake Fatty acids in the in silico reconstruction. D, Fraction of uptaken nutrients that stimulate growth by nutrient class. There is a consistent pattern of growth stimulation across all four species for six nutrient classes: Sugars, Sugar derivatives, and Purines are catabolized whilst Inorganic compounds, Pyrimidines, Cofactors, and compounds involved in the formation of the cell membrane or cell wall (Cell boundary class) are not catabolized.