Application of comparative genomics of Acetobacter species facilitates genome-scale metabolic reconstruction of the Acetobacter ghanensis LMG 23848T and Acetobacter senegalensis 108B cocoa strains

Rudy Pelicaen; Stefan Weckx; Didier Gonze; Luc De Vuyst

doi:10.3389/fmicb.2022.1060160

Application of comparative genomics of Acetobacter species facilitates genome-scale metabolic reconstruction of the Acetobacter ghanensis LMG 23848^T and Acetobacter senegalensis 108B cocoa strains

Front Microbiol. 2022 Nov 24:13:1060160. doi: 10.3389/fmicb.2022.1060160. eCollection 2022.

Authors

Rudy Pelicaen^{1

2}, Stefan Weckx^{1

2}, Didier Gonze^{2

3}, Luc De Vuyst¹

Affiliations

¹ Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
² ULB-VUB Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium.
³ Unité de Chronobiologie Théorique, Service de Chimie Physique, Faculté des Sciences, Université libre de Bruxelles, Brussels, Belgium.

Abstract

Acetobacter species play an import role during cocoa fermentation. However, Acetobacter ghanensis and Acetobacter senegalensis are outcompeted during fermentation of the cocoa pulp-bean mass, whereas Acetobacter pasteurianus prevails. In this paper, an in silico approach aimed at delivering some insights into the possible metabolic adaptations of A. ghanensis LMG 23848^T and A. senegalensis 108B, two candidate starter culture strains for cocoa fermentation processes, by reconstructing genome-scale metabolic models (GEMs). Therefore, genome sequence data of a selection of strains of Acetobacter species were used to perform a comparative genomic analysis. Combining the predicted orthologous groups of protein-encoding genes from the Acetobacter genomes with gene-reaction rules of GEMs from two reference bacteria, namely a previously manually curated model of A. pasteurianus 386B (iAp386B454) and two manually curated models of Escherichia coli (EcoCyc and iJO1366), allowed to predict the set of reactions present in A. ghanensis LMG 23848^T and A. senegalensis 108B. The predicted metabolic network was manually curated using genome re-annotation data, followed by the reconstruction of species-specific GEMs. This approach additionally revealed possible differences concerning the carbon core metabolism and redox metabolism among Acetobacter species, pointing to a hitherto unexplored metabolic diversity. More specifically, the presence or absence of reactions related to citrate catabolism and the glyoxylate cycle for assimilation of C2 compounds provided not only new insights into cocoa fermentation but also interesting guidelines for future research. In general, the A. ghanensis LMG 23848^T and A. senegalensis 108B GEMs, reconstructed in a semi-automated way, provided a proof-of-concept toward accelerated formation of GEMs of candidate functional starter cultures for food fermentation processes.

Keywords: Acetobacter metabolism; cocoa fermentation; comparative genomics; flux balance analysis; genome-scale metabolic modelling.