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

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 investig...

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Autores principales: Agyirifo, Daniel S., Wamalwa, Mark, Otwe, Emmanuel Plas, Galyuon, Isaac, Runo, Steven, Takrama, Jemmy, Ngeranwa, Joseph
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667825/
https://www.ncbi.nlm.nih.gov/pubmed/31388591
http://dx.doi.org/10.1016/j.heliyon.2019.e02170
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author Agyirifo, Daniel S.
Wamalwa, Mark
Otwe, Emmanuel Plas
Galyuon, Isaac
Runo, Steven
Takrama, Jemmy
Ngeranwa, Joseph
author_facet Agyirifo, Daniel S.
Wamalwa, Mark
Otwe, Emmanuel Plas
Galyuon, Isaac
Runo, Steven
Takrama, Jemmy
Ngeranwa, Joseph
author_sort Agyirifo, Daniel S.
collection PubMed
description 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.
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spelling pubmed-66678252019-08-06 Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities Agyirifo, Daniel S. Wamalwa, Mark Otwe, Emmanuel Plas Galyuon, Isaac Runo, Steven Takrama, Jemmy Ngeranwa, Joseph Heliyon Article 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. Elsevier 2019-07-30 /pmc/articles/PMC6667825/ /pubmed/31388591 http://dx.doi.org/10.1016/j.heliyon.2019.e02170 Text en © 2019 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
Agyirifo, Daniel S.
Wamalwa, Mark
Otwe, Emmanuel Plas
Galyuon, Isaac
Runo, Steven
Takrama, Jemmy
Ngeranwa, Joseph
Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities
title Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities
title_full Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities
title_fullStr Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities
title_full_unstemmed Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities
title_short Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities
title_sort metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667825/
https://www.ncbi.nlm.nih.gov/pubmed/31388591
http://dx.doi.org/10.1016/j.heliyon.2019.e02170
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