Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria
Temporal shotgun metagenomics of multiple samples of an Arabica wet coffee fermentation process, which was examined microbiologically and metabolomically before, was performed to complement these microbiological and biochemical data with an in-depth in silico analysis of the structure and functions...
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| Format: | Article |
| Language: | English |
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Elsevier
2020-11-01
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| Series: | Current Research in Biotechnology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2590262820300034 |
| _version_ | 1818663323610120192 |
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| author | Vasileios Pothakos Luc De Vuyst Sophia Jiyuan Zhang Florac De Bruyn Marko Verce Julio Torres Michael Callanan Cyril Moccand Stefan Weckx |
| author_facet | Vasileios Pothakos Luc De Vuyst Sophia Jiyuan Zhang Florac De Bruyn Marko Verce Julio Torres Michael Callanan Cyril Moccand Stefan Weckx |
| author_sort | Vasileios Pothakos |
| collection | DOAJ |
| description | Temporal shotgun metagenomics of multiple samples of an Arabica wet coffee fermentation process, which was examined microbiologically and metabolomically before, was performed to complement these microbiological and biochemical data with an in-depth in silico analysis of the structure and functions of the coffee microbiome. The taxonomic analysis of a massive sequence dataset of ca. 16 Gbp identified >150 microbial species and distinguished three successive, microbial phases: (i) enterobacteria, acetic acid bacteria, and some yeasts prevailing at the start; (ii) lactic acid bacteria (LAB) in the second phase; and (iii) acid-tolerant LAB at the end of the fermentation process. The functional analysis of prokaryotic genes, based on ca. 138,000 coding sequences, facilitated the gene repertoire overview of this ecosystem, showcasing differences in each fermentation stage. Initial prototrophic characters, plant cell wall-degrading activities, and pectinolytic activities were followed by a more auxotrophic and saccharolytic microbial profile, due to an increasing relative abundance of LAB. The almost full genome of 22 bacterial species was reconstructed and additional coffee-specific features were identified. This temporal metagenomic analysis of a case of reproducible wet coffee fermentation processes carried out in a coffee plantation near Nanegal, Ecuador, constitutes a breakthrough for the study of wet coffee processing and the contribution of the growth and activities of different microorganisms, in particular LAB, to this process. |
| first_indexed | 2024-12-17T05:15:01Z |
| format | Article |
| id | doaj.art-f74ae4ed736b492c9b96fe6ae7395f3d |
| institution | Directory Open Access Journal |
| issn | 2590-2628 |
| language | English |
| last_indexed | 2024-12-17T05:15:01Z |
| publishDate | 2020-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Current Research in Biotechnology |
| spelling | doaj.art-f74ae4ed736b492c9b96fe6ae7395f3d2022-12-21T22:02:09ZengElsevierCurrent Research in Biotechnology2590-26282020-11-012115Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteriaVasileios Pothakos0Luc De Vuyst1Sophia Jiyuan Zhang2Florac De Bruyn3Marko Verce4Julio Torres5Michael Callanan6Cyril Moccand7Stefan Weckx8Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, BelgiumResearch Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium; Corresponding author.Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, BelgiumResearch Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, BelgiumResearch Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, BelgiumNestlé R&D Centre Tours, 101 Avenue Gustave Eiffel, B.P. 49716, 37097 Tours Cedex 2, France; Nestlé Ecuador, El Inca, EC 170124, Quito, EcuadorNestlé Research, Route du Jorat 57, Vers-chez-les-Blancs, CH-1000 Lausanne 26, SwitzerlandNestlé Research, Route du Jorat 57, Vers-chez-les-Blancs, CH-1000 Lausanne 26, SwitzerlandResearch Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, BelgiumTemporal shotgun metagenomics of multiple samples of an Arabica wet coffee fermentation process, which was examined microbiologically and metabolomically before, was performed to complement these microbiological and biochemical data with an in-depth in silico analysis of the structure and functions of the coffee microbiome. The taxonomic analysis of a massive sequence dataset of ca. 16 Gbp identified >150 microbial species and distinguished three successive, microbial phases: (i) enterobacteria, acetic acid bacteria, and some yeasts prevailing at the start; (ii) lactic acid bacteria (LAB) in the second phase; and (iii) acid-tolerant LAB at the end of the fermentation process. The functional analysis of prokaryotic genes, based on ca. 138,000 coding sequences, facilitated the gene repertoire overview of this ecosystem, showcasing differences in each fermentation stage. Initial prototrophic characters, plant cell wall-degrading activities, and pectinolytic activities were followed by a more auxotrophic and saccharolytic microbial profile, due to an increasing relative abundance of LAB. The almost full genome of 22 bacterial species was reconstructed and additional coffee-specific features were identified. This temporal metagenomic analysis of a case of reproducible wet coffee fermentation processes carried out in a coffee plantation near Nanegal, Ecuador, constitutes a breakthrough for the study of wet coffee processing and the contribution of the growth and activities of different microorganisms, in particular LAB, to this process.http://www.sciencedirect.com/science/article/pii/S2590262820300034Coffee bean fermentationWet processingShotgun metagenomicsTaxonomic analysisFunctional analysisLeuconostoc pseudomesenteroides |
| spellingShingle | Vasileios Pothakos Luc De Vuyst Sophia Jiyuan Zhang Florac De Bruyn Marko Verce Julio Torres Michael Callanan Cyril Moccand Stefan Weckx Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria Current Research in Biotechnology Coffee bean fermentation Wet processing Shotgun metagenomics Taxonomic analysis Functional analysis Leuconostoc pseudomesenteroides |
| title | Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria |
| title_full | Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria |
| title_fullStr | Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria |
| title_full_unstemmed | Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria |
| title_short | Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria |
| title_sort | temporal shotgun metagenomics of an ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria |
| topic | Coffee bean fermentation Wet processing Shotgun metagenomics Taxonomic analysis Functional analysis Leuconostoc pseudomesenteroides |
| url | http://www.sciencedirect.com/science/article/pii/S2590262820300034 |
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