The metataxonomic diversity and microbial composition of microorganisms during the coffee fermentation process as well as their relationship with coffee quality were determined across 20 farms in the department of Cesar, Colombia, by sampling coffee fruits from Coffea arabica; Var. Castillo General^®, Var. Colombia, and Var. Cenicafé 1. In each farm, the fruits were processed and the fermentation process took place between 10 and 42 h following this. Three samples of mucilage and washed coffee seeds were collected per farm during the fermentation process. The microorganisms present in the mucilage were identified using metataxonomic methods by amplifying the 16S rRNA gene for bacteria and ITS for fungi. The microorganisms’ morphotypes were isolated and identified. The analysis of bacteria allowed for the identification of the following genera: Gluconobacter, Leuconostoc, Acetobacter, Frateuria, Pantoea, Pseudomonas, Tatumella, and Weisella, as well as unclassified enterobacteria; the Lactobacillacea and Secundilactobacillus families were only identified in the Var. Cenicafé 1. For fungi, the top 11 genera and families found included Hanseniaspora, Candida, Meyerozyma, Wickerhamomyces, Pichia, f-Saccharomycodaceae, f-Nectriciae, unclassified fungi, and Saccharomycetaceae, which were only found in Cenicafé 1. A total of 92% of the coffee samples obtained scored between 80.1 and 84.9, indicating “Very Good” coffee (Specialty Coffee Association (SCA) scale). Farms with the longest fermentation times showed better coffee attributes related to acidity, fragrance, and aroma. During coffee fermentation, there is a central microbiome. The differences between the microorganisms’ genera could be influenced by the coffee variety, while the specific conditions of each farm (i.e., altitude and temperature) and its fermentation processes could determine the proportions of and interactions between the microbial groups that favor the sensory characteristics responsible for coffee cup quality.

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.