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Facility‐specific ‘house’ microbiome ensures the maintenance of functional microbial communities into coffee beans fermentation: implications for source tracking
Author(s) -
Silva Vale Alexander,
Melo Pereira Gilberto Vinícius,
Carvalho Neto Dão Pedro,
Sorto Ruben Dario,
GoésNeto Aristóteles,
Kato Rodrigo,
Soccol Carlos Ricardo
Publication year - 2021
Publication title -
environmental microbiology reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.229
H-Index - 69
ISSN - 1758-2229
DOI - 10.1111/1758-2229.12921
Subject(s) - biology , fermentation , microbiome , phyllosphere , microorganism , leuconostoc , food science , microbial population biology , food spoilage , microbial ecology , horticulture , botany , agronomy , microbiology and biotechnology , bacteria , lactobacillus , bioinformatics , genetics
This work aimed at studying the unconfirmed hypothesis predicting the existence of a connection between coffee farm microbiome and the resulting spontaneous fermentation process. Using Illumina‐based amplicon sequencing, 360 prokaryotes and 397 eukaryotes were identified from coffee fruits and leaves, over‐ripe fruits, water used for coffee de‐pulping, depulped coffee beans, soil, and temporal fermentation samples at an experimental farm in Honduras. Coffee fruits and leaves were mainly associated with high incidence of Enterobacteriaceae, Pseudomonas , Colletotrichum , and Cladosporium . The proportion of Enterobacteriaceae was increased when leaves and fruits were collected on the ground compared to those from the coffee tree. Coffee farm soil showed the richest microbial diversity with marked presence of Bacillus . Following the fermentation process, microorganisms present in depulped coffee beans ( Leuconostoc , Gluconobater , Pichia , Hanseniaspora , and Candida ) represented more than 90% of the total microbial community, which produced lactic acid, ethanol, and several volatile compounds. The community ecology connections described in this study showed that coffee fruit provides beneficial microorganisms for the fermentation process. Enterobacteria, Colletotrichum , and other microbial groups present in leaves, fruit surface, over‐ripe fruits, and soil may transfer unwanted aromas to coffee beans, so they should be avoided from having access to the fermentation tank.