Comparative genome analysis of the candidate functional starter culture strains Lactobacillus fermentum 222 and Lactobacillus plantarum 80 for controlled cocoa bean fermentation processes

Abstract

BackgroundLactobacillus fermentum 222 and Lactobacillus plantarum 80, isolates from a spontaneous Ghanaian cocoa bean fermentation process, proved to be interesting functional starter culture strains for cocoa bean fermentations. Lactobacillus fermentum 222 is a thermotolerant strain, able to dominate the fermentation process, thereby converting citrate and producing mannitol. Lactobacillus plantarum 80 is an acid-tolerant and facultative heterofermentative strain that is competitive during cocoa bean fermentation processes. In this study, whole-genome sequencing and comparative genome analysis was used to investigate the mechanisms of these strains to dominate the cocoa bean fermentation process.ResultsThrough functional annotation and analysis of the high-coverage contigs obtained through 454 pyrosequencing, plantaricin production was predicted for L. plantarum 80. For L. fermentum 222, genes encoding a complete arginine deiminase pathway were attributed. Further, in-depth functional analysis revealed the capacities of these strains associated with carbohydrate and amino acid metabolism, such as the ability to use alternative external electron acceptors, the presence of an extended pyruvate metabolism, and the occurrence of several amino acid conversion pathways. A comparative genome sequence analysis using publicly available genome sequences of strains of the species L. plantarum and L. fermentum revealed unique features of both strains studied. Indeed, L. fermentum 222 possessed genes encoding additional citrate transporters and enzymes involved in amino acid conversions, whereas L. plantarum 80 is the only member of this species that harboured a gene cluster involved in uptake and consumption of fructose and/or sorbose.ConclusionsIn-depth genome sequence analysis of the candidate functional starter culture strains L. fermentum 222 and L. plantarum 80 revealed their metabolic capacities, niche adaptations and functionalities that enable them to dominate the cocoa bean fermentation process. Further, these results offered insights into the cocoa bean fermentation ecosystem as a whole and will facilitate the selection of appropriate starter culture strains for controlled cocoa bean fermentation processes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1927-0) contains supplementary material, which is available to authorized users.

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

“…Limosilactobacillus fermentum IMDO 222, previously isolated from a fermenting cocoa pulp-bean mass, was able to prevail during cocoa fermentation processes when applied as a starter culture [ 70 ]. Similarly, as shown in the present study, this strain prevailed during Type II/2 sourdough productions, which might be related to its enhanced competitiveness when growing on maltose (thanks to the presence of a maltose phosphorylase) as an energy source and using fructose as an alternative external electron acceptor [ 71 ]. Furthermore, it produces buttery flavored compounds, in accordance with its genetic potential [ 69 , 71 ].…”

Genetic and Biochemical Characterization of an Exopolysaccharide With in vitro Antitumoral Activity Produced by Lactobacillus fermentum YL-11

“…However, it is necessary to investigate the mechanism of EPS biosynthesis by combining the genomic data. Although the genomic information related to EPS biosynthesis has been found in a few strains, including L. fermentum F-6 (Sun et al, 2015), L. fermentum 222 (Illeghems et al, 2015), L. fermentum 3872 (Lehri et al, 2017), and L. fermentum MTCC 25067 (Formerly TDS030603) (Aryantini et al, 2017), the mechanism of EPS biosynthesis requires detailed study. In the present study, the gene features and mechanism of EPS biosynthesis in the novel strain L. fermentum YL-11 were determined, which might provide the basis for further metabolic engineering and applications of EPS.…”

Pan-genomic and transcriptomic analyses of Leuconostoc mesenteroides provide insights into its genomic and metabolic features and roles in kimchi fermentation

“…With the development of high-throughput and low-cost sequencing technologies, genomic information-based approaches have been extensively considered for the comprehensive understanding of metabolic properties and lifestyle traits of a microorganism. In particular, with the recent explosive increase of genome sequencing data, the concept of pan-genome has been introduced to explore the genomic and metabolic diversity of a given phylogenetic clade 20 – 23 . Because a pan-genome describes the entire genomic repertoire, representing all possible metabolic and physiological properties of a given phylogenetic clade and encodes for all possible lifestyles of a bacterial species, a pan-genome analysis provides insights into the genomic and metabolic features as well as a comprehensive understanding of the genome diversities and lifestyle traits of a bacterial species 24 – 29 .…”