Fig. 1

Formulation and solution of the multispecies biofilm metabolic model. a Schematic representation of the chronic wound biofilm model of constant thickness W with glucose provided at the tissue-biofilm interface (z = 0), oxygen supplied at the biofilm-air interface (z = W) and the metabolic byproducts acetate, succinate and lactate removed at the tissue-biofilm interface. b Schematic representation of the biofilm metabolic model solution procedure. The multispecies biofilm with temporal and spatial variations is described by a spatiotemporal model that accounts for the diffusion of nutrients and byproducts. PDEs are written with respect to the bacterial species concentration (X _i) and the metabolite concentrations (M _j) assuming that spatial variations are limited to a single direction z. Lexicographic linear program solution of the genome-scale reconstruction of each species is performed to predict the growth rate, nutrient uptake rates and byproduct secretion rates. The PDEs are spatially discretized to yield a large-set of ODEs with embedded LPs that are integrated with the MATLAB code DFBAlab [78] to generate time and spatially resolved predictions