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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2019
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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. |
format | Online Article Text |
id | pubmed-6667825 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
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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