Kombucha inoculated fermentation reshapes microbial ecology and flavour metabolism in Yunnan Arabica coffee

This study evaluates the flavor-enhancing effects of kombucha-inoculated fermentation on Coffea arabica L. and uncovers regulatory mechanisms across microbial succession, physicochemical shifts, amino acid remodeling, and volatile formation. Controlled fermentations using kombucha symbiotic consortium for 144 h was comparedwith spontaneous fermentation. At endpoint, bacterial richness in the KT group was 34% higher compared to the CK group. The KT group exhibited a significantly lower pH (4.21) than the CK group (4.95). Komagataeibacter and Zygosaccharomyces were enriched 2-6 fold, while Enterobacter and Aspergillus were suppressed. Kombucha coffee showed lower pH, titratable acidity increased by 64%, and reducing sugars decreased by 43%. Sweet-taste FAAs increased and bitter FAAs decreased, correlating with floral-fruity esters (r ≥ 0.74). Volatiles such as phenylethyl alcohol (42%), phenethyl acetate (200%), and ethyl isovalerate (89%), while off-flavor acids and smoky phenols decreased. Sensory scores improved in floral, fruity, and sweet attributes. Multi-omics linked dominant taxa to upregulated pathways (ester biosynthesis, aromatic amino acid degradation, Maillard products) and key functional genes. These results establish kombucha Inoculated Fermentation as a reproducible, mechanism-based strategy for targeted flavor optimization in speciality coffee and other high-value agricultural products.