In a new work just published in Current Research in Biotechnology, the author team applies temporal shotgun metagenomics of an Ecuadorian coffee fermentation process, which yielded the reconstruction of full genomes of 22 microbial species and 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 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.
Read full text: 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, Volume 2, 2020, Pages 1-15, https://doi.org/10.1016/j.crbiot.2020.02.001.
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