Summary of Study ST004156
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 PR002618. The data can be accessed directly via it's Project DOI: 10.21228/M87R8P 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 | ST004156 |
| Study Title | Valerate maintains ammonia homeostasis through modulating microbial amino acid metabolism |
| Study Summary | By using an in vitro simulated intestinal fermentation system, the influence of valeric acid on the metabolites of the microbial community was investigated. There are four groups measured in this study: (1)Control; (2) PS (polystyrene, 0.1 mg/mL); (3) PLV (PS+0.01 mg/mL valeric acid); (4) PMV(PS+0.1 mg/mL valeric acid). We conducted a comprehensive analysis of metabolic alterations in the fermentation broth. Partial Least Squares Discriminant Analysis (PLS-DA) revealed significant metabolic variations across the four experimental groups. Volcano plot and Venn diagram analyses identified 102 differentially expressed metabolites between the PS and control groups, comprising 65 upregulated and 37 downregulated species. Notable differential metabolites included Isotocin, Isoleucyl-Lysine, and D-glutamine. Sankey diagram analysis further demonstrated the involvement of Deoxyadenosine, Xanthine, and Adenine in enriched pathways such as ABC transporters, purine metabolism, and nucleotide metabolism. Comparative analysis between the PMV and PS groups revealed 177 upregulated and 157 downregulated metabolites. Agmatine and specific amino acids emerged as common differential metabolites in both PS-vs-Control and PMV-vs-PS comparisons. Notably, ammonia levels exhibited strong associations with amino acid metabolism, with amino acid-related metabolites constituting 34.23% of all differential metabolites. These included pathways such as arginine biosynthesis, arginine-proline metabolism, and D-amino acid synthesis. Arginine participates in the urea cycle to promote urea formation, which is subsequently hydrolyzed into ammonia via urease activity. Intriguingly, the valerate-treated group exhibited downregulated enzymatic activity compared to the PS group, accompanied by reduced levels of key metabolites including Agmatine, L-glutamic acid, L-ornithine, and L-aspartic acid. Collectively, these findings indicate that arginine metabolism serves as a critical regulatory target of valeric acid. By modulating gut microbiota composition, valeric acid suppresses enzymatic activity involved in arginine synthesis and degradation cycles, thereby attenuating overall pathway flux and ultimately reducing microbial ammonia production. |
| Institute | Zhejiang University |
| Department | Food Science and Nutrition |
| Laboratory | Key Laboratory for Exploration and High-Value Utilization of Agricultural Products |
| Last Name | Yan |
| First Name | Fujie |
| Address | Yuhangtang Road, Hangzhou, Zhejiang, 310058, China |
| fjyan@zju.edu.cn | |
| Phone | +86 15068185696 |
| Submit Date | 2025-08-20 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-09-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002618 |
| Project DOI: | doi: 10.21228/M87R8P |
| Project Title: | Influence of valeric acid fermentation on metabolites of human fecal microbial community |
| Project Summary: | By using an in vitro simulated intestinal fermentation system, the influence of valeric acid on the metabolites of the microbial community was investigated. Results: Notable differential metabolites included Isotocin, Isoleucyl-Lysine, and D-glutamine. Sankey diagram analysis further demonstrated the involvement of Deoxyadenosine, Xanthine, and Adenine in enriched pathways such as ABC transporters, purine metabolism, and nucleotide metabolism. Comparative analysis between the PMV and PS groups revealed 177 upregulated and 157 downregulated metabolites. Agmatine and specific amino acids emerged as common differential metabolites in both PS-vs-Control and PMV-vs-PS comparisons. The findings indicate that arginine metabolism serves as a critical regulatory target of valeric acid. |
| Institute: | Zhejiang University |
| Last Name: | Yan |
| First Name: | Fujie |
| Address: | Yuhangtang Road, Hangzhou, Zhejiang, 310058, China |
| Email: | fjyan@zju.edu.cn |
| Phone: | +86 15068185696 |
Subject:
| Subject ID: | SU004307 |
| Subject Type: | Bacteria |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Bacteria; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Sample source |
|---|---|---|---|
| SA480735 | C-6 | Control | Supernatant of fecal fermentation broth |
| SA480736 | C-2 | Control | Supernatant of fecal fermentation broth |
| SA480737 | C-1 | Control | Supernatant of fecal fermentation broth |
| SA480738 | C-5 | Control | Supernatant of fecal fermentation broth |
| SA480739 | C-3 | Control | Supernatant of fecal fermentation broth |
| SA480740 | C-4 | Control | Supernatant of fecal fermentation broth |
| SA480741 | LV-6 | Intervention-1 | Supernatant of fecal fermentation broth |
| SA480742 | LV-5 | Intervention-1 | Supernatant of fecal fermentation broth |
| SA480743 | LV-4 | Intervention-1 | Supernatant of fecal fermentation broth |
| SA480744 | LV-2 | Intervention-1 | Supernatant of fecal fermentation broth |
| SA480745 | LV-3 | Intervention-1 | Supernatant of fecal fermentation broth |
| SA480746 | LV-1 | Intervention-1 | Supernatant of fecal fermentation broth |
| SA480747 | MV-1 | Intervention-2 | Supernatant of fecal fermentation broth |
| SA480748 | MV-2 | Intervention-2 | Supernatant of fecal fermentation broth |
| SA480749 | MV-3 | Intervention-2 | Supernatant of fecal fermentation broth |
| SA480750 | MV-4 | Intervention-2 | Supernatant of fecal fermentation broth |
| SA480751 | MV-5 | Intervention-2 | Supernatant of fecal fermentation broth |
| SA480752 | MV-6 | Intervention-2 | Supernatant of fecal fermentation broth |
| SA480753 | PS-6 | Model | Supernatant of fecal fermentation broth |
| SA480754 | PS-5 | Model | Supernatant of fecal fermentation broth |
| SA480755 | PS-4 | Model | Supernatant of fecal fermentation broth |
| SA480756 | PS-3 | Model | Supernatant of fecal fermentation broth |
| SA480757 | PS-2 | Model | Supernatant of fecal fermentation broth |
| SA480758 | PS-1 | Model | Supernatant of fecal fermentation broth |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO004300 |
| Collection Summary: | Fresh fecal samples were collected from three healthy volunteers and immediately transferred to a sterile laminar flow hood. A 10 g aliquot of feces was homogenized in 80 mL of sterile phosphate-buffered saline (PBS) using a sterile glass rod, followed by filtration through triple-layered sterile gauze. Side-arm test tubes were sealed at the lower port, and 27 mL of sterilized intestinal fermentation medium and 3 mL of fecal filtrate were aseptically introduced into each tube. The mixture was thoroughly vortexed, and anaerobic conditions were established by purging the headspace with nitrogen gas for 5 min. Tubes were incubated at 37 ℃ in a shaking incubator (180 rpm) for 24 h to stabilize the microbial community. Following stabilization, indicated concentrations of PS/valeric acid were introduced into the fermentation broth. The anaerobic environment was re-established by nitrogen gas purging (5 min), and tubes were returned to the 37 ℃ shaking incubator for continued fermentation. Fermentation broth samples (3 mL) were collected at 24-hour intervals over a 72-hour period. The supernatant obtained after centrifugation of the fermentation broth was used for metabolomics determination. |
| Sample Type: | Fecal fermentation broth |
Treatment:
| Treatment ID: | TR004316 |
| Treatment Summary: | Healthy individuals' feces were selected for in vitro fermentation. One day later, polystyrene microplastics (PS, 0.1 mg/mL)and different concentrations of valeric acid (PLV, 0.01 mg/mL; PMV, 0.1 mg/mL) were added to the fermentation liquid. Three days later, the fermentation supernatant was collected for metabolomics analysis. There are four groups: Control, PS, PLV, PMV. |
Sample Preparation:
| Sampleprep ID: | SP004313 |
| Sampleprep Summary: | 100 μL liquid sample was added to a 1.5 mL centrifuge tube with 800 μL solution (acetonitrile: methanol = 1:1(v:v)) containing four internal standards (0.02 mg/mL L-2-chlorophenylalanine, etc.) to extract metabolites. The samples were mixed by vortex for 30 s and low-temperature sonicated for 30 min (5°C, 40 KHz)。The samples were placed at -20°C for 30 min to precipitate the proteins. Then the samples were centrifuged for 15 min (4°C, 13000 g). The supernatant was removed and blown dry under nitrogen. The sample was then re-solubilized with 100 µL solution (acetonitrile: water = 1:1) and extracted by low-temperature ultrasonication for 5 min (5°C, 40 KHz), followed by centrifugation at 13000 g and 4°C for 10 min.The supernatant was transferred to sample vials for LC-MS/MS analysis. |
Chromatography:
| Chromatography ID: | CH005239 |
| Chromatography Summary: | Solvent A: 0.1% formic acid in water:acetonitrile (2:98, v/v); Solvent B: 0.1% formic acid in acetonitrile |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0min, 100% A; 3min, 80% A; 4.5min, 65% A; 15.5min, 15% A; 16min, 3% A; 18min, 3% A; 18.1min, 100% A; 21min, 100% A |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 2% water/98% acetonitrile; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006899 |
| Analysis Type: | MS |
| Chromatography ID: | CH005239 |
| Has Mz: | 1 |
| Rt Units: | No RT data |
| Results File: | ST004156_AN006899_Results.txt |
| Units: | peak intensity |
| Analysis ID: | AN006900 |
| Analysis Type: | MS |
| Chromatography ID: | CH005239 |
| Has Mz: | 1 |
| Rt Units: | No RT data |
| Results File: | ST004156_AN006900_Results.txt |
| Units: | peak intensity |
