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

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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 languageEnglish
Pages (from-to)1-15
Number of pages15
JournalCurrent Research in Biotechnology
Publication statusPublished - Nov 2020


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


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