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

• Published in: Current research in biotechnology Vol. 2; pp. 1 - 15
• Main Authors: Pothakos, Vasileios, De Vuyst, Luc, Zhang, Sophia Jiyuan, De Bruyn, Florac, Verce, Marko, Torres, Julio, Callanan, Michael, Moccand, Cyril, Weckx, Stefan
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.11.2020; Elsevier
• Subjects: Coffee bean fermentation; Functional analysis; Lactobacillus; Leuconostoc pseudomesenteroides; Shotgun metagenomics; Taxonomic analysis; Wet processing; Leuconostoc pseudomesenteroides; Coffee bean fermentation; Taxonomic analysis; Functional analysis; Wet processing; Shotgun metagenomics; Lactobacillus
• ISSN: 2590-2628; 2590-2628
• DOI: 10.1016/j.crbiot.2020.02.001

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. [Display omitted] •Wet coffee fermentation consists of three consecutive microbial phases.•The three fermentation stages are characterised by a different gene repertoire.•Leuconostoc pseudomesenteroides is present throughout the fermentation process.•Coffee-specific features could be identified.•Full genomes of 22 microbial species could be reconstructed.