Bacterial communities shaping the sensory quality of Veracruz coffee: Impact of planting altitude, processing method, and fermentation times

The microbial composition of coffee fruits plays an important role in the sensory quality of coffee beverages; therefore, understanding its dynamics is essential for optimizing production processes. This study evaluated the effects of planting altitude, post-harvest processing (dry and wet), and fermentation duration on bacterial diversity associated with coffee fruits and fermentation must during coffee processing in Veracruz, Mexico. We also investigated whether variations in bacterial diversity were associated with the sensory quality of the resulting coffee beverage. Coffee fruit and must samples were collected during fermentation, from which bacterial DNA was extracted and sequenced, focusing on the V3–V4 region of the 16S rRNA gene. A total of 6,527,736 high-quality reads were obtained. Principal Coordinate Analysis (PCoA) revealed distinctive beta diversity patterns, showing clear separation among treatments according to altitude and processing method. Alpha diversity analysis revealed differences in richness, evenness, and overall bacterial diversity before and during fermentation. The dominant bacterial phyla were Proteobacteria , Bacteroidota , and Firmicutes . The interaction among planting altitude, processing method, and fermentation time significantly influenced the sensory characteristics of the coffee beverage. Wet-processed coffees from higher altitudes exhibited superior sensory scores, while naturally (dry) fermented coffees performed better at lower altitudes. These findings suggest that the development of bacterial consortia adapted to different agroecological contexts can optimize fermentation and contribute to improving coffee quality, sustainability, and competitiveness.