Fermentation with coffee berry peels induces spatiotemporal changes in microbial communities leading to unique aroma of coffee berries

Traditionally harvested coffee berries are subjected to fermentation processes to remove the mucilage layers leaving two dried seeds. Moreover, fermentation also greatly affects coffee’s sensory quality. The present study was conducted to elucidate the spatiotemporal changes in microbial communities in Arabica coffee beans fermented with fermentation broth made by using coffee peels. The unpeeled berries were soaked for 2, 4, 6, and 8 h. Samples from each fermentation time point were collected for DNA extraction and sequencing of the 16S V4 and ITS1 regions to elucidate the structure of bacterial and fungal communities, respectively. Results revealed Firmicutes as the dominant phyla followed by Proteobacteria including Lentilactobacillus and Secundilactobacillus as the two top dominant genera followed by Acetobacter, Kosakonia, Lactipiantibacillus, and Pantoea in fermentation broth group. Ascomycota was the dominant fungal phyla, having Kazachstania as the dominant genera throughout the fermentation period. The LEfSe analysis revealed many biomarker taxa before the start of fermentation but none of the taxa decreased with fermentation time. Collectively, Acetobacter, and Secundilactobacillus from bacterial taxa and Kazachstania from fungal taxa were identified as core microbial taxa and biomarker species for both fermentation groups. The most differential metabolic pathway (N-10-formyl-tetrahydrofolate biosynthesis) was dominated by four major bacterial taxa (Secundilactobacillus, Lentilactobacillus, Pantoea, and Lactiplantibacillus) in the fermentation broth group. For fungal communities, glycolysis III was the most differential pathway which was dominated by Kazachstania fungal taxa throughout the fermentation periods in both fermentation groups. Kazachstania has been shown to produce strong flavor compounds, imparting a unique aroma to coffee beans that resulted in a red wine flavor and excellent coffee quality score (>83). The study concluded that coffee peels can be used for wet fermentation of coffee beans to improve coffee bean quality, sensory, and biological qualities for specialty coffee products while addressing environmental concerns of coffee peels as crop waste.