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

Abstract

Coffee is one of the most important, and most widely consumed drinks around the world. Fermentation is a key step in determining the quality of the final cup of coffee. Although this process was initially done to simply remove the mucilage from the coffee beans, coffee producers have begun to use microbial starter cultures to improve cup sensory profiles. In the present case study, freshly harvested Arabica coffee beans were processed through two different wet fermentation methods, in which one was inoculated with starter cultures, to determine the microbial communities involved in the fermentation process and the metabolomic and sensorial profiles of the resulting green and roasted coffee beans. The bacterial and fungal composition were followed throughout the wet processing of the beans implementing metagenomic DNA extraction and high-throughput sequencing. Moreover, the metabolomic profiles of the resulting green and roasted coffee beans were studied with non-targeted metabolite profiling analysis. A quantitative descriptive analysis was applied to measure certain sensory attributes, including odor, flavor, and texture, to describe the sensorial profiles of the roasted and brewed coffee beans. The results indicated that Leuconostoc was the most common bacterial genus overall, and that lactic acid bacteria were more abundant during the inoculated fermentation, including genera such as Weissella and Fructobacillus. Acetic acid bacteria belonging to the genus Acetobacter were more prevalent in the standard processing method. The most abundant fungal groups were Kazachstania humilis, Torulaspora delbrueckii, and Wickerhamomyces anomalus. K. humilis was more abundant in the inoculated fermentation when compared to the standard processing. Over 400 unique molecular masses were identified for the green and roasted coffee beans with a non-targeted metabolomics approach. After manual annotation, we identified 32 and 24 metabolic compounds that differed significantly between fermentation methods for the green and roasted coffee beans, respectively. The inoculated coffee had a higher cupping score overall, meaning the beverage had more notes that are preferred by consumers in contrast to the coffee processed with a standard wet fermentation method. Consequently, coffee producers should be aware of the potential and safety of utilizing starter cultures to improve the final quality of the brewed and consumed coffee. Future studies should focus on microbial identification at a deeper level and the correlation between certain species and their resulting metabolic compounds, where specific bacterial and fungal groups could be isolated and grown to be used as commercially available starter cultures for wet processed coffee fermentation.