A gap-filling algorithm for prediction of metabolic interactions in microbial communities
Fig 2
Graphical representation of the toy E. coli community after the application of the community gap-filling method.
The central carbon metabolism of an E. coli core model (blue rectangular: Glycolysis, pink square: Pentose Phosphate Pathway, yellow circle: TCA cycle) was used in order to create two E. coli strains: one that consumes glucose (left) and one that consumes acetate (right), after the deletion of the reactions marked with red crosses. The best solution of the community gap-filling algorithm predicted the addition of the reactions represented by continuous blue arrows and the activation of the existing reactions represented by dashed blue arrows, in order to restore biomass production in the two models. The dashed black arrows show the exchange reactions for glucose and acetate in the community. The metabolites in bold represent biomass precursors. The numbered deleted reactions are: (1) PGM, (2) MALS, (3) SUCOAS, (4) PFL, (5) PTAr, (6) GLCpts, (7) CS. The numbered added and activated reactions are: (1) POX, (2) CS, (3) PKETF, (4) EDD and EDA, (5) PDH, (6) ACS, (7) ACKr, (8) ME1.