Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities

Abstract

Fermentation of Theobroma cacao L. beans is the most critical stage in the production of cocoa products such as chocolates and its derivatives. There is a limited understanding of the complex response of microbial diversity during cocoa bean fermentation. The aim of the present study was to investigate microbial communities in the cocoa bean fermentation heap using a culture-independent approach to elucidate microbial diversity, structure, functional annotation and mapping unto metabolic pathways. Genomic DNA was extracted and purified from a sample of cocoa beans fermentation heap and was followed by library preparations. Sequence data was generated on Illumina Hiseq 2000 paired-end technology (Macrogen Inc). Taxonomic analysis based on genes predicted from the metagenome identified a high percentage of Bacteria (90.0%), Yeast (9%), and bacteriophages (1%) from the cocoa microbiome. Lactobacillus (20%), Gluconacetobacter (9%), Acetobacter (7%) and Gluconobacter (6%) dominated this study. The mean species diversity, measured by Shannon alpha-diversity index, was estimated at 142.81. Assignment of metagenomic sequences to SEED database categories at 97% sequence similarity identified a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates and aromatic amino acids. Metabolism of aromatic compounds, amino acids and their derivatives and carbohydrates occupied 0.6%, 8% and 13% respectively. Overall, these results provide insights into the cocoa microbiome, identifying fermentation processes carried out broadly by complex microbial communities and metabolic pathways encoding aromatic compounds such as phenylacetaldehyde, butanediol, acetoin, and theobromine that are required for flavour and aroma production. The results obtained will help develop targeted inoculations to produce desired chocolate flavour or targeted metabolic pathways for the selection of microbes for good aroma and flavour compounds formation.

Profile of Volatile Compounds of On-Farm Fermented and Dried Cocoa Beans Inoculated with Saccharomyces cerevisiae KY794742 and Pichia kudriavzevii KY794725

“…The metabolic method of production of phenylacetaldehyde was elucidated from the use of aromatic enzymes such as aminotransferase, which can convert amino acids (tyrosine, phenylalanine and tryptophan) in the stage of transamination of these compounds. These activities have been associated with lactic acid bacteria Lactobacillus brevis and Lactobacillus plantarum [ 37 ], the last of which is widely found in cocoa fermentations performed in the Amazonian region [ 11 ].…”

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

“…1c), in the contact of the fruit in the soil, and mainly, of the microbial groups. present in the containers that will serve for the process over the necessary time (Schwan & Wheals, 2004; Agyirifo et al ., 2019).…”

Fine Resolution Analysis of Microbial Communities Provides Insights Into the Variability of Cocoa Bean Fermentation

“…Recently, metagenomic shotgun sequencing has been used to evaluate the composition and metabolic potential of the community at one-time point of the fermentation (Blaxter et al, 2005), by extracting the microbial community DNA from different samples (Agyirifo et al, 2019), revealing a wider diversity of bacteria and yeasts, and elucidating the contributions of the distinct functional groups in the biochemical transformation of cocoa bean mass. These results suggest that culture-independent techniques are valuable tools to characterize the changes in microbiota composition and the transformation of the cocoa seeds.…”