Physical–Chemical and Metataxonomic Characterization of the Microbial Communities Present during the Fermentation of Three Varieties of Coffee from Colombia and Their Sensory Qualities

The microbial composition and physical-chemical characteristics were studied during the coffee fermentation of three Coffea arabica L. varieties, Var. Tabi, Var. Castillo General ® and Var. Colombia. Mucilage and washed coffee seeds samples were collected at different stages of fermentation. Mucilage microbiology characterization and metataxonomic analysis were performed using 16S rDNA sequencing to determine bacterial diversity and ITS sequencing for fungal diversity. Additionally, the microorganisms were isolated into pure cultures. The molecular diversity analyses showed similarities in microorganisms present during the fermentation of Var. Castillo General and Var. Colombia, which are genetically closely related; mixed-acid bacteria (Enterobacteriaceae, Tatumella sp.) and lactic acid bacteria ( Leuconostoc sp., Weissella sp. and Lactobacillaceae ) were common and predominant, while in Var. Tabi, acetic acid bacteria ( Gluconobacter sp. and Acetobacter sp.) and Leuconostoc sp. were predominant. At the end of the fermentation period, the fungi Saccharomycodaceae , Pichia and Wickerhamomyces were found in Var. Castillo General and Var. Colombia, while in Var. Tabi, Saccharomycodaceae , Pichia and Candida were recorded. Sensory analyses of the coffee beverages were carried out (SCA methodology) for all samples. Var. Tabi had the highest SCA score, between 82.7 and 83.2, while for Var. Colombia, the score ranged between 82.1 and 82.5. These three coffee varieties showed potential for the production of specialty coffees influenced by spontaneous fermentation processes that depend on microbial consortia rather than a single microorganism.