Genome-Scale Metabolic Reconstruction of 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation.

386B is a candidate functional starter culture for the cocoa bean fermentation process. To allow simulations of its related metabolism in response to different environmental conditions, a genome-scale metabolic model for 386B was reconstructed. This is the first genome-scale metabolic model reconstruction for a member of the genus . The metabolic network reconstruction process was based on extensive genome re-annotation and comparative genomics analyses. The information content related to the functional annotation of metabolic enzymes and transporters was placed in a metabolic context by exploring and curating a Pathway/Genome Database of 386B using the Pathway Tools software. Metabolic reactions and curated gene-protein-reaction associations were bundled into a genome-scale metabolic model of 386B, named iAp386B454, containing 454 genes, 322 reactions, and 296 metabolites embedded in two cellular compartments. The reconstructed model was validated by performing growth experiments in a defined medium, which revealed that lactic acid as the sole carbon source could sustain growth of this strain. Further, the reconstruction of the 386B genome-scale metabolic model revealed knowledge gaps concerning the metabolism of this strain, especially related to the biosynthesis of its cell envelope and the presence or absence of metabolite transporters.