Summary of Study ST004251
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002680. The data can be accessed directly via it's Project DOI: 10.21228/M87G0W This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST004251 |
| Study Title | Metagenomic and metabolomic analyses of fecal samples from civet-digested coffee in Vietnam |
| Study Summary | 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. 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 where coffee cherries were added to their diet. A clear differentiation was displayed between the metabolomic profiles associated with the coffee-cherry and normal diets. 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 specific fecal metabolites were closely associated with diet-driven variations in the civet gut microbiota. |
| Institute | University of Science and Technology of Hanoi |
| Department | Life Sciences |
| Laboratory | BEAM |
| Last Name | Nguyen |
| First Name | Nhung Phuong |
| Address | 18 Hoang Quoc Viet |
| nguyen-phuong.nhung@usth.edu.vn | |
| Phone | +84-0865309954 |
| Submit Date | 2025-09-08 |
| Num Groups | 2 |
| Total Subjects | 18 |
| Num Females | 18 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | abf |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-10-28 |
| Release Version | 1 |
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Project:
| Project ID: | PR002680 |
| Project DOI: | doi: 10.21228/M87G0W |
| Project Title: | Metagenomic and metabolomic analyses of fecal samples from civet-digested coffee in Vietnam |
| Project Summary: | 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. 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 where coffee cherries were added to their diet. Integrated metagenomic and metabolomic analyses revealed clear distinctions between the two groups. |
| Institute: | University of Science and Technology of Hanoi |
| Department: | Life Sciences |
| Laboratory: | BEAM |
| Last Name: | Nguyen |
| First Name: | Nhung Phuong |
| Address: | 18 Hoang Quoc Viet, Hanoi, Hanoi, 11355, Vietnam |
| Email: | nguyen-phuong.nhung@usth.edu.vn |
| Phone: | +84-0865309954 |
| Funding Source: | University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, project number USTH.GED.01/24-25 |
| Contributors: | Tam Thi Thanh Tran , Oanh Thi Kieu Nguyen, Phuong Hanh Hoang, Nhung Phuong Nguyen, Huong Thi Mai To, Hoa Quynh Nguyen |
Subject:
| Subject ID: | SU004403 |
| Subject Type: | Mammal |
| Subject Species: | Paradoxurus hermaphroditus |
| Taxonomy ID: | 71117 |
| Gender: | Female |
Factors:
Subject type: Mammal; Subject species: Paradoxurus hermaphroditus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Diet | Sample source |
|---|---|---|---|
| SA496488 | B14.T1 | Coffee-cherry diet | Civet feces |
| SA496489 | B18.T1 | Coffee-cherry diet | Civet feces |
| SA496490 | B17.T1 | Coffee-cherry diet | Civet feces |
| SA496491 | B16.T1 | Coffee-cherry diet | Civet feces |
| SA496492 | B15.T1 | Coffee-cherry diet | Civet feces |
| SA496493 | A18.T1 | Coffee-cherry diet | Civet feces |
| SA496494 | B13.T1 | Coffee-cherry diet | Civet feces |
| SA496495 | B12.T1 | Coffee-cherry diet | Civet feces |
| SA496496 | A19.T1 | Coffee-cherry diet | Civet feces |
| SA496497 | B13.T2 | Normal diet | Civet feces |
| SA496498 | A18.T2 | Normal diet | Civet feces |
| SA496499 | B12.T2 | Normal diet | Civet feces |
| SA496500 | B15.T2 | Normal diet | Civet feces |
| SA496501 | B16.T2 | Normal diet | Civet feces |
| SA496502 | A19.T2 | Normal diet | Civet feces |
| SA496503 | B17.T2 | Normal diet | Civet feces |
| SA496504 | B18.T2 | Normal diet | Civet feces |
| SA496505 | B14.T2 | Normal diet | Civet feces |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO004396 |
| Collection Summary: | Civet fecal samples used in this study were sourced from Kien Cuong Civet Coffee Company in Buon Ma Thuot City, Dak Lak Province, Vietnam. Samples were collected twice in April 2024 from nine female Asian palm civets (Paradoxurus hermaphroditus) of Vietnam origin. The first collection occurred when the civets were fed exclusively with coffee cherries, meanwhile the second collection followed a normal diet consisting of 150 g of food containing 20% protein, 6% fibre, and 0.4%-1.5% lysine. Feces were recuperated the following morning, placed in separate plastic bags, and transported by air to the University of Science and Technology of Hanoi on the same day. All samples were stored at -80 ºC until DNA extraction. |
| Sample Type: | Feces |
| Collection Location: | Buon Ma Thuot City, Dak Lak Province, Vietnam |
| Collection Duration: | 1 month |
| Storage Conditions: | -80℃ |
| Additives: | None |
Treatment:
| Treatment ID: | TR004412 |
| Treatment Summary: | 18 fecal samples were divided into 2 groups (n=9): eating coffee cherries and a normal diet consisting of 150 g of food containing 20% protein, 6% fibre, and 0.4%-1.5% lysine. Fecal samples were analyzed by untargeted lipidomics. The lipidomic profile of two groups were compared to examine the effects of coffee eating on the metabolism of the civets and elucidate the correlation between gut microbiome and metabolome of the civets. |
Sample Preparation:
| Sampleprep ID: | SP004409 |
| Sampleprep Summary: | Fifty milligrams of each fecal sample were dissolved in 1 mL of 80% methanol containing 3.25 ppm of 10-camphorsulfonic acid, followed by ultrasonic sonication for 15 min. Samples were then incubated at 65 °C for 45 min and centrifuged at 14000 × g for 10 min. The resulting supernatants were filtered through 0.22-µm nylon syringe filters prior to analysis by a UPLC-QToF system. |
| Processing Storage Conditions: | On ice |
| Extract Storage: | -80℃ |
Chromatography:
| Chromatography ID: | CH005371 |
| Chromatography Summary: | Metabolite analysis was performed using an ACQUITY UPLC I-Class Plus system coupled to a Xevo G3 ESI/QTOF high-resolution mass spectrometer (Waters Corporation, Massachusetts, USA). Chromatographic separation was conducted on an ACQUITY UPLC BEH C18 (1.7 µm, 2.1 x 50 mm, 130 Å) using a composition of solvent A (H 2 O with 0.1% FA) and solvent B (acetonitrile with 0.1% FA) as the mobile phase. The gradient program was as follows: 20% B for 2 min, ramped to 95% B over 10 min, held at 95% B for 5 min, decreased to 20% B over 3 min, and re-equilibrated for 2 min. The flow rate was set at 0.3 mL/min, with an injection volume of 5 µL. |
| Instrument Name: | Waters Acquity I-Class |
| Column Name: | Waters ACQUITY UPLC BEH C18 (50 x 2.1mm, 1.7um, 130 Å) |
| Column Temperature: | 60 |
| Flow Gradient: | 20% B for 2 min, ramped to 95% B over 10 min, held at 95% B for 5 min, decreased to 20% B over 3 min, and re-equilibrated for 2 min. |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% Water; 0.1% formic acid |
| Solvent B: | 100% Acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN007074 |
| Laboratory Name: | BEAM |
| Analysis Type: | MS |
| Chromatography ID: | CH005371 |
| Num Factors: | 2 |
| Num Metabolites: | 46 |
| Units: | Normalized total ion count |
