Temporal shotgun metagenomic dissection of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria

Vasileios Pothakos; Luc De Vuyst; Jiyuan Sophia Zhang; Florac De Bruyn; Marko Verce; Julio Torres; Michael Callanan; Cyril Moccand; Stefan Weckx

doi:10.1016/j.crbiot.2020.02.001

Temporal shotgun metagenomic dissection of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria

Vasileios Pothakos, Luc De Vuyst, Jiyuan Sophia Zhang, Florac De Bruyn, Marko Verce, Julio Torres, Michael Callanan, Cyril Moccand, Stefan Weckx

Research output: Contribution to journal › Article › peer-review

72 Citations (Scopus)

422 Downloads (Pure)

Abstract

Temporal shotgun metagenomics of multiple samples of an Arabica wet coffee fermentation process, which was exam-ined microbiologically and metabolomically before, was performed to complement these microbiological and bio-chemical data with an in-depthin silicoanalysis of the structure and functions of the coffee microbiome. Thetaxonomic analysis of a massive sequence dataset ofca.16 Gbp identified>150 microbial species and distinguishedthree 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 onca.138,000 coding sequences, facilitated the gene repertoireoverview of this ecosystem, showcasing differences in each fermentation stage. Initial prototrophic characters, plantcell wall-degrading activities, and pectinolytic activitieswerefollowed by a moreauxotrophic and saccharolytic micro-bial profile, due to an increasing relative abundance of LAB. The almost full genome of 22 bacterial species was recon-structed and additional coffee-specific features were identified. This temporal metagenomic analysis of a case ofreproducible wet coffee fermentation processes carried out in a coffee plantation near Nanegal, Ecuador, constitutesa breakthrough for the study of wet coffee processing and the contribution of the growth and activities of different mi-croorganisms, in particular LAB, to this process

Original language	English
Pages (from-to)	1-15
Number of pages	15
Journal	Current Research in Biotechnology
Volume	2
DOIs	https://doi.org/10.1016/j.crbiot.2020.02.001
Publication status	Published - Nov 2020

Bibliographical note

Funding Information:
The authors would like to acknowledge their financial support from the Research Council of the Vrije Universiteit Brussel ( SRP7 and IOF342 projects), the Hercules Foundation (grants UABR09004 and UAB13002 ), and Nestec S.A. , a subsidiary of Nestlé S.A. Part of the computational resources and services were provided by the Shared ICT Services Centre funded by the Vrije Universiteit Brussel, the Flemish Supercomputer Center (VSC), and the Research Foundation – Flanders ( FWO-Vlaanderen ).

Funding Information:
The authors would like to acknowledge their financial support from the Research Council of the Vrije Universiteit Brussel (SRP7 and IOF342 projects), the Hercules Foundation (grants UABR09004 and UAB13002), and Nestec S.A., a subsidiary of Nestlé S.A. Part of the computational resources and services were provided by the Shared ICT Services Centre funded by the Vrije Universiteit Brussel, the Flemish Supercomputer Center (VSC), and the Research Foundation – Flanders (FWO-Vlaanderen). Experiments on the coffee plantation: FDB, VP, JT, and MC. Conceptualization, methodology, and organization of sequencing: SW; investigation, bioinformatics analysis, and writing original draft: VP; contribution to interpretation and discussion of the scientific findings: VP, SJZ, FDB, MV, MC, CM, SW, and LDV; review and editing, funding acquisition, resources, project management, and supervision: LDV. All six metagenomic datasets were submitted to the European Nucleotide Archive of the European Bioinformatics Institute (ENA/EBI) and are accessible under the study accession number PRJEB24129.

Publisher Copyright:
© 2020 The Authors

Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.

Keywords

Coffee bean fermentation
Wet processing
shotgun metagenomics
Taxonomic analysis
functional analysis
Leuconostoc pseudomesenteroides
Lactobacillus

Access to Document

10.1016/j.crbiot.2020.02.001Licence: CC BY-NC-ND

1-s2.0-S2590262820300034-mainFinal published version, 4.65 MBLicence: CC BY-NC-ND

Handle.net

Persistent link

Cite this

@article{6dff4966b9d24f048e260ee986b52703,

title = "Temporal shotgun metagenomic dissection of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria",

abstract = "Temporal shotgun metagenomics of multiple samples of an Arabica wet coffee fermentation process, which was exam-ined microbiologically and metabolomically before, was performed to complement these microbiological and bio-chemical data with an in-depthin silicoanalysis of the structure and functions of the coffee microbiome. Thetaxonomic analysis of a massive sequence dataset ofca.16 Gbp identified>150 microbial species and distinguishedthree 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 onca.138,000 coding sequences, facilitated the gene repertoireoverview of this ecosystem, showcasing differences in each fermentation stage. Initial prototrophic characters, plantcell wall-degrading activities, and pectinolytic activitieswerefollowed by a moreauxotrophic and saccharolytic micro-bial profile, due to an increasing relative abundance of LAB. The almost full genome of 22 bacterial species was recon-structed and additional coffee-specific features were identified. This temporal metagenomic analysis of a case ofreproducible wet coffee fermentation processes carried out in a coffee plantation near Nanegal, Ecuador, constitutesa breakthrough for the study of wet coffee processing and the contribution of the growth and activities of different mi-croorganisms, in particular LAB, to this process",

keywords = "Coffee bean fermentation, Wet processing, shotgun metagenomics, Taxonomic analysis, functional analysis, Leuconostoc pseudomesenteroides, Lactobacillus",

author = "Vasileios Pothakos and {De Vuyst}, Luc and Zhang, {Jiyuan Sophia} and {De Bruyn}, Florac and Marko Verce and Julio Torres and Michael Callanan and Cyril Moccand and Stefan Weckx",

note = "Funding Information: The authors would like to acknowledge their financial support from the Research Council of the Vrije Universiteit Brussel ( SRP7 and IOF342 projects), the Hercules Foundation (grants UABR09004 and UAB13002 ), and Nestec S.A. , a subsidiary of Nestl{\'e} S.A. Part of the computational resources and services were provided by the Shared ICT Services Centre funded by the Vrije Universiteit Brussel, the Flemish Supercomputer Center (VSC), and the Research Foundation – Flanders ( FWO-Vlaanderen ). Funding Information: The authors would like to acknowledge their financial support from the Research Council of the Vrije Universiteit Brussel (SRP7 and IOF342 projects), the Hercules Foundation (grants UABR09004 and UAB13002), and Nestec S.A., a subsidiary of Nestl{\'e} S.A. Part of the computational resources and services were provided by the Shared ICT Services Centre funded by the Vrije Universiteit Brussel, the Flemish Supercomputer Center (VSC), and the Research Foundation – Flanders (FWO-Vlaanderen). Experiments on the coffee plantation: FDB, VP, JT, and MC. Conceptualization, methodology, and organization of sequencing: SW; investigation, bioinformatics analysis, and writing original draft: VP; contribution to interpretation and discussion of the scientific findings: VP, SJZ, FDB, MV, MC, CM, SW, and LDV; review and editing, funding acquisition, resources, project management, and supervision: LDV. All six metagenomic datasets were submitted to the European Nucleotide Archive of the European Bioinformatics Institute (ENA/EBI) and are accessible under the study accession number PRJEB24129. Publisher Copyright: {\textcopyright} 2020 The Authors Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

year = "2020",

month = nov,

doi = "10.1016/j.crbiot.2020.02.001",

language = "English",

volume = "2",

pages = "1--15",

journal = "Current Research in Biotechnology",

issn = "2590-2628",

publisher = "Elsevier",

}

TY - JOUR

T1 - Temporal shotgun metagenomic dissection of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria

AU - Pothakos, Vasileios

AU - De Vuyst, Luc

AU - Zhang, Jiyuan Sophia

AU - De Bruyn, Florac

AU - Verce, Marko

AU - Torres, Julio

AU - Callanan, Michael

AU - Moccand, Cyril

AU - Weckx, Stefan

N1 - Funding Information: The authors would like to acknowledge their financial support from the Research Council of the Vrije Universiteit Brussel ( SRP7 and IOF342 projects), the Hercules Foundation (grants UABR09004 and UAB13002 ), and Nestec S.A. , a subsidiary of Nestlé S.A. Part of the computational resources and services were provided by the Shared ICT Services Centre funded by the Vrije Universiteit Brussel, the Flemish Supercomputer Center (VSC), and the Research Foundation – Flanders ( FWO-Vlaanderen ). Funding Information: The authors would like to acknowledge their financial support from the Research Council of the Vrije Universiteit Brussel (SRP7 and IOF342 projects), the Hercules Foundation (grants UABR09004 and UAB13002), and Nestec S.A., a subsidiary of Nestlé S.A. Part of the computational resources and services were provided by the Shared ICT Services Centre funded by the Vrije Universiteit Brussel, the Flemish Supercomputer Center (VSC), and the Research Foundation – Flanders (FWO-Vlaanderen). Experiments on the coffee plantation: FDB, VP, JT, and MC. Conceptualization, methodology, and organization of sequencing: SW; investigation, bioinformatics analysis, and writing original draft: VP; contribution to interpretation and discussion of the scientific findings: VP, SJZ, FDB, MV, MC, CM, SW, and LDV; review and editing, funding acquisition, resources, project management, and supervision: LDV. All six metagenomic datasets were submitted to the European Nucleotide Archive of the European Bioinformatics Institute (ENA/EBI) and are accessible under the study accession number PRJEB24129. Publisher Copyright: © 2020 The Authors Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2020/11

Y1 - 2020/11

N2 - Temporal shotgun metagenomics of multiple samples of an Arabica wet coffee fermentation process, which was exam-ined microbiologically and metabolomically before, was performed to complement these microbiological and bio-chemical data with an in-depthin silicoanalysis of the structure and functions of the coffee microbiome. Thetaxonomic analysis of a massive sequence dataset ofca.16 Gbp identified>150 microbial species and distinguishedthree 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 onca.138,000 coding sequences, facilitated the gene repertoireoverview of this ecosystem, showcasing differences in each fermentation stage. Initial prototrophic characters, plantcell wall-degrading activities, and pectinolytic activitieswerefollowed by a moreauxotrophic and saccharolytic micro-bial profile, due to an increasing relative abundance of LAB. The almost full genome of 22 bacterial species was recon-structed and additional coffee-specific features were identified. This temporal metagenomic analysis of a case ofreproducible wet coffee fermentation processes carried out in a coffee plantation near Nanegal, Ecuador, constitutesa breakthrough for the study of wet coffee processing and the contribution of the growth and activities of different mi-croorganisms, in particular LAB, to this process

AB - Temporal shotgun metagenomics of multiple samples of an Arabica wet coffee fermentation process, which was exam-ined microbiologically and metabolomically before, was performed to complement these microbiological and bio-chemical data with an in-depthin silicoanalysis of the structure and functions of the coffee microbiome. Thetaxonomic analysis of a massive sequence dataset ofca.16 Gbp identified>150 microbial species and distinguishedthree 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 onca.138,000 coding sequences, facilitated the gene repertoireoverview of this ecosystem, showcasing differences in each fermentation stage. Initial prototrophic characters, plantcell wall-degrading activities, and pectinolytic activitieswerefollowed by a moreauxotrophic and saccharolytic micro-bial profile, due to an increasing relative abundance of LAB. The almost full genome of 22 bacterial species was recon-structed and additional coffee-specific features were identified. This temporal metagenomic analysis of a case ofreproducible wet coffee fermentation processes carried out in a coffee plantation near Nanegal, Ecuador, constitutesa breakthrough for the study of wet coffee processing and the contribution of the growth and activities of different mi-croorganisms, in particular LAB, to this process

KW - Coffee bean fermentation

KW - Wet processing

KW - shotgun metagenomics

KW - Taxonomic analysis

KW - functional analysis

KW - Leuconostoc pseudomesenteroides

KW - Lactobacillus

UR - http://www.scopus.com/inward/record.url?scp=85088989981&partnerID=8YFLogxK

U2 - 10.1016/j.crbiot.2020.02.001

DO - 10.1016/j.crbiot.2020.02.001

M3 - Article

SN - 2590-2628

VL - 2

SP - 1

EP - 15

JO - Current Research in Biotechnology

JF - Current Research in Biotechnology

ER -

Temporal shotgun metagenomic dissection of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria

Abstract

Bibliographical note

Keywords

Access to Document

Handle.net

Other files and links

Fingerprint

SRP7: Strategic Research Programme: Understanding the competitiveness and functional role of microorganisms in fermented food ecosystems

Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem

Cite this

Temporal shotgun metagenomic dissection of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria

Abstract

Bibliographical note

Keywords

Access to Document

Handle.net

Other files and links

Fingerprint

Projects

SRP7: Strategic Research Programme: Understanding the competitiveness and functional role of microorganisms in fermented food ecosystems

Datasets

Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem

Cite this