Microbial community dynamics during Coffea arabica cv. Arara fermentation and their relationship with specialty coffee quality.

Fermentation stands out as a promising strategy for the valorization of specialty coffees, directly impacting the sensory profile of the beverage. This study investigated the microbial dynamics during the self-induced anaerobic fermentation (SIAF) of Coffea arabica L. cv. Arara cherries, under different conditions of time (0, 24, 48, and 72 h), temperature (ambient and 27 °C), processing type (solid-state or submerged), and the presence or absence of a starter culture. Metataxonomic analyses (16 S rRNA and ITS1) were performed, revealing significant shifts in the diversity and structure of bacterial and fungal communities throughout the process. A predominance of the genera Lactobacillus and Kazachstania was observed, with fungal diversity being strongly affected, showing a marked reduction within the first 24 h. Decision tree-based predictive models revealed correlations between specific microorganisms and sensory attributes of the beverage, highlighting Leuconostoc, Lactobacillus, and Pichia as potential positive markers. These findings indicate that controlling fermentation conditions enables modulation of the microbiome, promoting desirable sensory profiles and contributing to the development of targeted starter cultures and the standardization of high-quality coffees.