Facility-specific 'house' microbiome ensures the maintenance of functional microbial communities into coffee beans...

Area of Science:

• Microbiology
• Food Science
• Agricultural Science

Background:

• The spontaneous fermentation of coffee is crucial for flavor development but poorly understood.
• The role of the coffee farm's microbial community in this process remains largely uncharacterized.

Purpose of the Study:

• To investigate the connection between the coffee farm's microbiome and the spontaneous coffee fermentation process.
• To identify key microbial players and their origins throughout coffee processing.

Main Methods:

• Illumina-based amplicon sequencing was employed to analyze microbial communities.
• Samples were collected from various sources including coffee fruits, leaves, soil, water, and fermentation stages at an experimental farm in Honduras.

Main Results:

• A diverse range of prokaryotes and eukaryotes were identified across different sample types.
• Coffee fruits and leaves harbored Enterobacteriaceae, Pseudomonas, Colletotrichum, and Cladosporium, with higher Enterobacteriaceae on fallen fruits.
• Coffee farm soil exhibited rich microbial diversity, notably Bacillus species.
• During fermentation, Leuconostoc, Gluconobater, Pichia, Hanseniaspora, and Candida dominated depulped coffee beans (>90%), producing key fermentation compounds.
• The coffee fruit itself was found to be a significant source of beneficial microbes for fermentation.

Conclusions:

• The coffee fruit microbiome plays a vital role in providing beneficial microorganisms for spontaneous fermentation.
• Microbial groups from soil, leaves, and over-ripe fruits (e.g., Enterobacteria, Colletotrichum) can negatively impact coffee flavor and should be prevented from entering fermentation tanks.