Summary of Study ST003505
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 PR002151. The data can be accessed directly via it's Project DOI: 10.21228/M8KG00 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 | ST003505 |
| Study Title | Investigation of polyamine biosynthesis and metabolism in gut microbiome by stale isotope resolved metabolomics |
| Study Summary | Polyamines are important gut microbial metabolites known to affect host organs, yet the mechanisms behind their microbial production remain poorly understood. In this study, we used a stable isotope-resolved metabolomic (SIRM) approach to track polyamine biosynthesis in the fecal microbiome. Viable microbial cells were extracted from fresh human and mouse feces and incubated anaerobically with 13C-labeled inulin (tracer). Liquid chromatography-high resolution mass spectrometry analysis revealed distinct 13C enrichment profiles for spermidine (SPD) and putrescine (PUT), with the arginine-agmatine-SPD pathway predominating over the well acknowledged spermidine synthase pathway (PUT aminopropylation) for SPD biosynthesis. Furthermore, significant species differences were observed in the 13C enrichments of polyamines and related metabolites between the human and mouse microbiome. Further investigations using single-strain SIRM analyses (Bacteroides) identified the key microbial genes and gut microbes responsible for the polyamine biosynthesis. Taken together, this study expands our understanding of polyamine biosynthesis in the gut microbiome and will facilitate the development of precision therapies to target polyamine-associated diseases. |
| Institute | Soochow University |
| Last Name | xinwei |
| First Name | li |
| Address | School of Pharmacy, Soochow University 1113 |
| lxw9911117@163.com | |
| Phone | 19971871675 |
| Submit Date | 2024-09-23 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | API-MS |
| Release Date | 2025-02-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002151 |
| Project DOI: | doi: 10.21228/M8KG00 |
| Project Title: | Uncovering the de novo synthesis of polyamines in gut microbiome using stable isotope resolved metabolomics |
| Project Type: | metabolomics |
| Project Summary: | Using 13C-inulin as a tracer, we tracked the biosynthesis of polyamines in the human and mouse fecal microbiome. Additionally, single-strain SIRM analyses was used to explore functional gut microbes. Liquid chromatography-high resolution mass spectrometry analysis revealed distinct 13C enrichment profiles for polyamines. SIRM analyses were performed using a Q-Exactive HF mass spectrometer, equipped with an Ion Max API source and a HESI II probe, and were coupled to a Dionex UltiMate 3000 UHPLC system (Thermo Fisher Scientific). The findings revealed a novel de novo SPD biosynthesis pathway in the human gut microbiome, and Bacteroides (including B.fragilis and B.thetaiotaomicron) contributed to the biosynthesis of polyamines, underscoring the importance of polyamine bioanalysis in aligning gut microbial functions to host intestinal health. |
| Institute: | Soochow University |
| Last Name: | li |
| First Name: | xinwei |
| Address: | 199 Renai Road, Xietang Street, Suzhou, Suzhou, Jiangsu Province, 215031, China |
| Email: | lxw9911117@163.com |
| Phone: | 19971871675 |
Subject:
| Subject ID: | SU003634 |
| Subject Type: | Bacteria |
| Subject Species: | Human (Intestinal bacteria); Mouse (Intestinal bacteria); Bacteroides (B.fragilis and B.thetaiotaomicron) |
| Species Group: | Mammals |
Factors:
Subject type: Bacteria; Subject species: Human (Intestinal bacteria); Mouse (Intestinal bacteria); Bacteroides (B.fragilis and B.thetaiotaomicron) (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment Condition |
|---|---|---|---|
| SA385797 | XBPC18_13C-F3C-pos | Bacteroides fragilis cells | Fmoc-derivatization-LC-HRMS |
| SA385798 | XBPC18_13C-F2C-pos | Bacteroides fragilis cells | Fmoc-derivatization-LC-HRMS |
| SA385799 | XBPC18_13C-F1C-pos | Bacteroides fragilis cells | Fmoc-derivatization-LC-HRMS |
| SA385800 | F3P-pos | Bacteroides fragilis cells | HILIC-HRMS |
| SA385801 | F2P-pos | Bacteroides fragilis cells | HILIC-HRMS |
| SA385802 | F1P-pos | Bacteroides fragilis cells | HILIC-HRMS |
| SA385803 | XBPC18_13C-T3C-pos | Bacteroides thetaiotaomicron cells | Fmoc-derivatization-LC-HRMS |
| SA385804 | XBPC18_13C-T2C-pos | Bacteroides thetaiotaomicron cells | Fmoc-derivatization-LC-HRMS |
| SA385805 | XBPC18_13C-T1C-pos | Bacteroides thetaiotaomicron cells | Fmoc-derivatization-LC-HRMS |
| SA385806 | T2P-pos | Bacteroides thetaiotaomicron cells | HILIC-HRMS |
| SA385807 | T3P-pos | Bacteroides thetaiotaomicron cells | HILIC-HRMS |
| SA385808 | T1P-pos | Bacteroides thetaiotaomicron cells | HILIC-HRMS |
| SA385809 | Hcell3 | Human feces | Fmoc-derivatization-LC-HRMS |
| SA385810 | Hcell2 | Human feces | Fmoc-derivatization-LC-HRMS |
| SA385811 | Hcell1 | Human feces | Fmoc-derivatization-LC-HRMS |
| SA385812 | Pos_13D_2 | Human feces | HILIC-HRMS |
| SA385813 | NGE_D_13C_3 | Human feces | HILIC-HRMS |
| SA385814 | NGE_D_13C_2 | Human feces | HILIC-HRMS |
| SA385815 | NGE_D_13C_1 | Human feces | HILIC-HRMS |
| SA385816 | Pos_13D_3 | Human feces | HILIC-HRMS |
| SA385817 | Pos_13D_1 | Human feces | HILIC-HRMS |
| SA385818 | C57cell3 | mouse feces | Fmoc-derivatization-LC-HRMS |
| SA385819 | C57cell2 | mouse feces | Fmoc-derivatization-LC-HRMS |
| SA385820 | C57cell1 | mouse feces | Fmoc-derivatization-LC-HRMS |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO003627 |
| Collection Summary: | A fraction of the fecal sample was collected fresh in its native state in a sterile screw-cap container. The samples were quickly transferred to an anaerobic glove bag to ensure fecal microbiome vitality. The fresh fecal samples were dissolved in the culture media and processed with a glass rods to suspend the microorganisms and particles. Then, the suspensions were transferred to an anaerobic tube and subjected to low-speed centrifugation (600 rpm, 10 min) to remove larger particles of undigested material. The supernatants were then collected and centrifuged at 3,000 rpm for 10 min to pellet the microbes. After washing the precipitated microorganisms using culture medium, the fecal microbial cells were collected by centrifugation at 3000 rpm for 10 min. |
| Sample Type: | Feces (including human and mouse); Bacteroides (including B.fragilis and B.thetaiotaomicron) |
Treatment:
| Treatment ID: | TR003643 |
| Treatment Summary: | 13C-Inulin was added to each tube aseptically to achieve a final concentration of 2 g/L inulin. After incubating at 37ºC for 24 h, the samples were centrifuged and washed with fresh culture medium and centrifuged to collect the microbial cells for further analysis. |
Sample Preparation:
| Sampleprep ID: | SP003641 |
| Sampleprep Summary: | For the analysis of polyamines, the microbial cells were quenched immediately after collection using 200 μL of acetonitrile containing 0.2% formic acid. To each 50 μL aliquot of the sample solution, 50 μL of carbonic acid buffer (0.5 M, pH 10.2) was added, followed by 50 μL of 5 mM Fmoc-OSu solution in acetonitrile. The mixture was shaken and incubated at room temperature for 15 min. The derivatization reaction was quenched with 20 μL of formic acid, and the sample was extracted with 500 μL of ethyl acetate. After vortexing for 2 min, the sample was centrifuged and the organic phase was collected and dried under a nitrogen stream. The samples were stored at −80ºC and dissolved in acetonitrile: water (9:1, v/v) before analysis. For the untargeted metabolomic analysis (polar metabolites), the microbial cells were quenched using 450 μL cold methanol immediately after collection. 5 mL of methyl tert-butyl ether was added to each tube, and phase separation was then induced by adding 1.25 mL of deionized water. The samples were then vortexed briefly and centrifuged. Polar fractions were collected into clean tubes and lyophilized. The dried powder was stored at −80ºC and dissolved in methanol: water (8:2, v/v) before analysis. |
Chromatography:
| Chromatography ID: | CH004367 |
| Chromatography Summary: | Fmoc-derivatization-LC-HRMS |
| Instrument Name: | Thermo Q-Exactive HF |
| Column Name: | Agela Technologies Venusil XBP C18 column (50 x 2.1 mm, 5 μm) |
| Column Temperature: | 40˚C |
| Flow Gradient: | 0–10 min, linear gradient from 10% to 90% B; 10–14 min, hold at 90% B; 14–14.5 min, linear gradient to 10% B; 14.5–20 min, hold at 10% B; and stop running at 32 min. |
| Flow Rate: | 200 μL/min |
| Solvent A: | 100% Water; 0.1% Formic acid |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004368 |
| Chromatography Summary: | HILIC-HRMS |
| Instrument Name: | Thermo Q-Exactive HF |
| Column Name: | SeQuant ZIC-pHILIC column (150 x 2.1 mm, 5 μm) |
| Column Temperature: | 40˚C |
| Flow Gradient: | 0-20 min, linear gradient from 80% to 20% B;20–21 min, hold at 20% B; 21–22 min, linear gradient to 80% B; 22–28 min, hold at 80% B; and stop running at 28 min. |
| Flow Rate: | 150 μL/min |
| Solvent A: | 100% Water; 20 mM Ammonium carbonate |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN005753 |
| Analysis Type: | MS |
| Chromatography ID: | CH004367 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003505_AN005753_Results.txt |
| Units: | Peak area |
| Analysis ID: | AN005754 |
| Analysis Type: | MS |
| Chromatography ID: | CH004368 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003505_AN005754_Results.txt |
| Units: | Peak area |
| Analysis ID: | AN005755 |
| Analysis Type: | MS |
| Chromatography ID: | CH004368 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003505_AN005755_Results.txt |
| Units: | Peak area |
