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

Abstract

Acetobacter pasteurianus 386B is a candidate functional starter culture for the cocoa bean fermentation process. To allow in silico simulations of its related metabolism in response to different environmental conditions, a genome-scale metabolic model for A. pasteurianus 386B was reconstructed. This is the first genome-scale metabolic model reconstruction for a member of the genus Acetobacter. 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 A. pasteurianus 386B using the Pathway Tools software. Metabolic reactions and curated gene-protein-reaction associations were bundled into a genome-scale metabolic model of A. pasteurianus 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 A. pasteurianus 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.

The microbiota diversity identified during the cocoa fermentation and the benefits of the starter cultures use: an overview

“…Thanks to the acetic acid produced from the oxidation of ethanol (produced by yeasts) and the consequent increase in the mass temperature, the cocoa seed loses its germinative power due to the death of the embryo, which initiates several structural and chemical reactions inside (Soumahoro et al ., 2020). The oxidation reactions of lactic acid to acetoin occur via the α‐acetolactate pathway and in a low proportion in acetic acid, since bacteria of the genus Acetobacter have low production and activity of the enzyme decarboxylase pyruvate (Pelicaen et al ., 2019; De Vuyst & Leroy, 2020).…”

Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media

“…We approached the study through metabolic modeling, a method widely used for genome-scale biochemical networks analysis 19 – 26 . We previously described the development of a genome-scale, constraint-based model (GEM) of M. pneumoniae metabolism, iJW145 11 , and its use to carry out predictions related to growth rate and medium design, relying upon a biomass composition that had been formulated from literature 3 , sequencing, proteomics and mass spectrometry data.…”

Potential of Bacteria from Alternative Fermented Foods as Starter Cultures for the Production of Wheat Sourdoughs

“…The substrate consumption and metabolite production kinetics during those fermentations correlated with their carbohydrate consumption patterns, whereby fructose was not consumed. Instead, the concentrations of fructose increased, likely due to its continuous release from sucrose through invertase activity or by oxidation of mannitol by a polyol oxidoreductase [ 37 , 41 ]. Furthermore, the high concentrations of acetic acid and gluconic acid showed the oxidation of ethanol and glucose, respectively [ 37 , 55 ].…”

“…Moreover, food-grade microorganisms originating from food matrices other than sourdoughs and/or different from LAB could provide interesting metabolic properties to sourdoughs and hence change the organoleptic properties of the concomitant breads. Therefore, microorganisms originating from other fermented food matrices, such as fermenting cocoa pulp-bean mass, fermented sausage, and water kefir, whether or not belonging to species or genera frequently isolated from sourdoughs, are worth investigating regarding their use as candidate starter cultures, as strains of many of these species have been studied thoroughly [ 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 ]. Specialized metabolic traits needed for their prevalence in these non-sourdough matrices could confer additional metabolic flexibilities to these strains in the sourdough ecosystem, provided they can grow and be metabolically active in the latter, and hence further contribute to the final quality of the sourdoughs and breads produced therefrom.…”