Metabolic modeling for probiotic and prebiotic production to treat inflammatory disorders

Conceptual scheme of the strategy to integrate Genome–Scale Metabolic Models and Flux Balance Analysis for studying, designing, and testing novel probiotics. • Metabolic diversity of microbial communities allows for widespread applications. • Genome–Scale Metabolic Models are useful tools for studying microbial communities. • Flux Balance Analysis arises as a promising tool for probiotics design and testing. • Metabolic modeling is used for testing probiotics in inflammatory disorders. • Probiotics can complement treatments to increase effectiveness and life quality. The importance of bacterial communities has been acknowledged over the past decades. Their applications span from the study of their role in ecosystems, the use of biofilms in nature and industry, the use of bacterial cultures for biotechnological purposes (such as the production of compounds and photovoltaic energy, and bioremediation), to their investigation in human health, particularly the gut microbiome, for the modulation of the metabolism and the immune system. Here we propose a perspective highlighting the importance of engineering microbial communities to leverage Genome-Scale Metabolic Models (GSMMs) for testing probiotics with therapeutic potential. Specifically, we envision that multispecies genome-scale community metabolic models can be employed to decipher metabolic routes for probiotic and prebiotic production to treat inflammatory diseases.