Fig. 1
Exo-metabolome profiling. a Optical densities (OD600; blue line) and instantaneous growth rate—i.e., OD600 difference between two contiguous time points divided by the time interval (red line), of an E. coli culture growing in M9 glucose minimal medium supplemented with casamino acids (CAA). Dots represent time points for withdrawal of supernatant aliquots for exo-metabolome analysis. The solid line represents the mean across four biological replicates, while the shaded region is the mean ± standard deviation. b Percentage of detected metabolites with respect to the annotated compounds in the genome-scale model of E. coli25: metabolites that can be exchanged with the external environment (white and yellow), and those that are constrained to be intracellular (red and black). c Percentage of detected metabolites exhibiting complex (yellow) or monotonic profiles, i.e., instantaneous derivative in time is always negative (green—consumed) or positive (blue—secreted). d The total incoming flux of carbon at each given time is calculated by multiplying the number of carbon atoms for each compound and the respective estimated uptake flux. The relative percentage is reported. Only those metabolites contributing for at least 2% of the total incoming carbon are listed. The remaining compounds are grouped (i.e., Various in the legend). Correspondence between metabolite IDs in the legend and metabolite names can be found in the Supplementary Data 1
