Coffee fermentation assisted by bacterial starter cultures enhance coffee quality in northern Peru

The Amazonas region has considerable potential for growing coffee but currently lacks established fermentation strategies. In this study, the efficacy of bacterial starter cultures (Lysinibacillus xylanilyticus, Stenotrophomonas maltophilia, and Stenotrophomonas pavanii) in directing coffee fermentation and shaping cup quality was assessed. Using a multiomic approach, it was investigated the temporal dynamics of bacterial community during fermentation. This initiated a predictable microbial succession from early enterobacterial activity to the dominance of acid-tolerant taxa. Four species (Acetobacter orientalis, Bacillus subtilis, Leuconostoc pseudomesenteroides, S. maltophilia) persisted throughout the fermentation process. Functional metagenomics revealed the upregulation of key metabolic pathways associated with carbohydrate metabolism and protein transporters, especially in inoculated fermentations. This heightened metabolic activity led to the targeted production of volatile compounds (esters and pyrazines) associated with desirable sweet-fruity-floral notes. Coffees fermented with starter cultures achieved higher sensory scores (82.9–83.9) in a shorter timeframe (36 hours) than spontaneous controls did, demonstrating that tailored starter cultures can shorten the fermentation timeline while reproducibly enhancing organoleptic quality.