Metagenomic, metabolomic and sensorial characteristics of fermented Coffea arabica L. var. Castillo beans inoculated with microbial starter cultures

Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with "starter cultures" on the sensory and metabolic profiles, as well as in the microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, where one was inoculated with a microbial starter culture and the other, spontaneous fermentation was allowed to occur. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting a higher sweetness, reduced acidity and bitterness, and presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted coffee beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with a better sensory perception. The inoculated process featured abundant lactic acid bacteria and Kazachstania yeasts, which are linked to desirable metabolites like lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality as determined by standardized cupping and reflected by changes in the metabolic profile and microbial community structures. Future studies should focus on microbial identification and the association between species and resulting metabolic compounds, where specific bacterial and fungal groups could be isolated to be used as commercially available starter cultures for coffee fermentation. IMPORTANCEOur study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and affects the dynamics of bacterial and fungal communities during this process. We identified specific changes in microbial diversity and associated metabolite profiles resulting from inoculation. Notably, we found that inoculation influences the metabolite composition of coffee beans and identified key compounds, such as aminophenol and phenol, which are likely linked to phenolic defects. This suggests that inoculation could serve as a tool to control cup defects by modifying the fermentation microbiota. Our findings advance the understanding of coffee fermentation and open opportunities for developing techniques to produce coffee with unique and desirable qualities.