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Background  The increase in glycerol obtained as a byproduct of biodiesel has encouraged the production of new industrial products, such as 1,3-propanediol (PDO), using biotechnological transformation via bacteria like  Clostridium butyricum . However, despite the increasing role of  Clostridium butyricum  as a bio-production platform, its metabolism remains poorly modeled.    Results  We reconstructed  i Cbu641, the first genome-scale metabolic (GSM) model of a PDO producer  Clostridium  strain, which included 641 genes, 365 enzymes, 891 reactions, and 701 metabolites. We found an enzyme expression prediction of nearly 84% after comparison of proteomic data with flux distribution estimation using flux balance analysis (FBA). The remaining 16% corresponded to enzymes directionally coupled to growth, according to flux coupling findings (FCF). The fermentation data validation also revealed different phenotype states that depended on culture media conditions; for example,  Clostridium  maximizes its biomass yield per enzyme usage under glycerol limitation. By contrast, under glycerol excess conditions,  Clostridium  grows sub-optimally, maximizing biomass yield while minimizing both enzyme usage and ATP production. We further evaluated perturbations in the GSM model through enzyme deletions and variations in biomass composition. The GSM predictions showed no significant increase in PDO production, suggesting a robustness to perturbations in the GSM model. We used the experimental results to predict that co-fermentation was a better alternative than  i Cbu641 perturbations for improving PDO yields.    Conclusions  The agreement between the predicted and experimental values allows the use of the GSM model constructed for the PDO-producing  Clostridium  strain to propose new scenarios for PDO production, such as dynamic simulations, thereby reducing the time and costs associated with experimentation.    Electronic supplementary material  The online version of this article (doi:10.1186/s12918-017-0434-0) contains supplementary material, which is available to authorized users.

Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol