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

biochemistry
food-science-and-technology
microbiology

Abstract

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. Despite its worldwide fame, civet coffee remains scarce in Vietnam, where strong consumer demand has led to widespread adulteration and the exploitation of captive civets for production. To address this context, the present study characterized the gut microbiota involved in the fermentation of ingested coffee beans and the associated secondary metabolites in Vietnamese civets, with the main aim to elucidate the underlying microbial and biochemical mechanisms.

Methods. Fecal samples were collected under two dietary conditions: one in which civets received a standardized diet of 150 g of food containing 20% protein, 6% fiber, and 0.4%–1.5% lysine, and the other one which coffee cherries were added to their diet. Then, metagenomic analysis based on 16S rRNA sequencing and untargeted metabolomic analysis were conducted.

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, Enterococcus and Escherichia/Shigella decreased, whereas Gluconobacter and Pseudomonas increased following the diet shift. Metabolomic profiling identified 46 metabolites across both ionization modes, and strong correlations were observed between microbial genera and metabolite profiles. Specifically, 6−Hydroxyangolensic acid methyl ester, 4−Aminobenzoic acid, and caffeine were more abundant in civets on a coffee-cherry diet; meanwhile, the other nine metabolites were more prevalent in the normal diet. Overall, the findings demonstrate that civet gut microbiota and metabolic output were highly responsive to dietary inputs and that coffee cherries promoted a unique fermentation environment. This represents the first integrative metagenomic and metabolomic study of civets consuming coffee in Vietnam, providing valuable insights into microbial contributions to coffee fermentation.

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