Unveiling the role of functional strains in flavor and bioactive compound formation of Cili (Rosa roxburghii Tratt) kombucha during fermentation by microbiota and metabolome

Kombucha fermentation increases the bioactive components and reduces the sugar. • Komagataeibacter_saccharivorans and JC017_sp004296775 were identified as the key functional strains driving metabolism and flavor formation. • Kombucha fermentation promotes the production of beneficial components and reduces bitterness and volatile acids. • By integrating microbiome, metabolome and GC–MS data, the system reveals the dynamic association between microbial succession and metabolites during fermentation. Cili ( Rosa roxburghii Tratt) represents a promising novel substrate of kombucha. This study investigates the dynamic changes and interrelationships among bioactive compounds, flavor components, microbial communities, and metabolites during the fermentation of Cili kombucha. The results indicate that kombucha fermentation significantly increases the contents of organic acids, flavonoids, and polyphenols in Cili juice. An integrated multi-omics analysis identifies Komagataeibacter saccharivorans and JC017_sp004296775 as core functional strains that modulate metabolite biosynthesis and flavor regulation, which promoted the accumulation of beneficial metabolites, including D-tagatose, fumaric acid, indolelactic acid, and tryptophol. Concurrently, the fermentation process reduced the levels of raw material-derived volatile acids (acetic acid, octanoic acid, hexanoic acid, nonanoic acid) and bitter-tasting metabolites (quinic acid). This study verifies the feasibility of using Cili as a substrate for kombucha through comparative controls and provides a theoretical basis for targeted process optimization and functional product development. Download: Download high-res image (157KB) Download: Download full-size image