Metagenomic and metabolomic analyses of fecal samples from civet-digested coffee in Vietnam.

Background: Civet-digested coffee originates from the feces of civets that consume coffee cherries, where microbial fermentation in the gastrointestinal tract imparts distinctive flavor attributes, thereby enhancing its global reputation and market value. Gut microbiota is considered important drivers of coffee-bean fermentation, potentially shaping the unique and region-specific flavor characteristics of civet-digested coffee. To address this context, the present study integrated metagenomic and metabolomic analyses to compare the gut microbiota and secondary metabolites involved in coffee-bean fermentation inside Vietnamese civets. Methods: Fecal samples were collected under two dietary conditions: a standardized one containing 20% protein, 6% fiber, and 0.4-1.5% lysine, and the same diet supplemented with coffee cherries. Metagenomic 16S rRNA sequencing and untargeted ultra-performance liquid chromatography quadrupole time-of-flight (UPLC-QTOF) revealed clear differences between the two groups. Results: Integrated metagenomic and metabolomic analyses revealed clear distinctions between the two groups. Civets on the coffee-cherry diet exhibited higher microbial diversity at the family and genus levels. Specifically, among 31 classified bacterial genera showing a trend toward significant differences in abundance,