Summary of Study ST004051
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 PR002541. The data can be accessed directly via it's Project DOI: 10.21228/M86828 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 | ST004051 |
| Study Title | Synergistic action of specialized metabolites from divergent biosynthesis in human oral microbiome |
| Study Summary | In this project, we report the discovery of three specialized metabolites, MC-584, MC-586, and MC-602 from the mutanoclumpin NRPS/PKS gene cluster from Streptococcus mutans, which MC-584 and MC-586 (major metabolites) are both required for robust biofilm formation in Streptococcus mutans. Submitted are the raw metabolomics data of wildtype Streptococcus mutans Smu102 (that has the three metabolites) and its gene knockouts. |
| Institute | University of California, Berkeley |
| Last Name | Yao |
| First Name | McKenna |
| Address | Stanley Hall University Dr |
| mckenna_yao@berkeley.edu | |
| Phone | 4803266096 |
| Submit Date | 2024-11-08 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-08-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002541 |
| Project DOI: | doi: 10.21228/M86828 |
| Project Title: | Synergistic action of specialized metabolites from divergent biosynthesis in human oral microbiome |
| Project Summary: | In this project, we report the discovery of two specialized metabolites from one NRPS/PKS gene cluster which are both required for robust biofilm formation in Streptococcus mutans. Submitted are the raw metabolomics data of wildtype Streptococcus mutans Smu102 and its knockouts. |
| Institute: | University of California, Berkeley |
| Last Name: | Yao |
| First Name: | McKenna |
| Address: | Stanley Hall University Dr Berkeley, CA 94720 |
| Email: | mckenna_yao@berkeley.edu |
| Phone: | 4803266096 |
| Funding Source: | National Institute of Dental & Craniofacial Research of the National Institutes of Health under Award Number R01DE032732 |
| Publications: | Synergistic action of specialized metabolites from divergent biosynthesis in human oral microbiome |
Subject:
| Subject ID: | SU004197 |
| Subject Type: | Bacteria |
| Subject Species: | Streptococcus mutans |
| Taxonomy ID: | 1309 |
| Genotype Strain: | Smu102 |
Factors:
Subject type: Bacteria; Subject species: Streptococcus mutans (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor | Sample source |
|---|---|---|---|
| SA467742 | 1341 | 1341-knockout | bacteria |
| SA467743 | 1346 | 1346-knockout | bacteria |
| SA467744 | 1351 | 1351-knockout | bacteria |
| SA467745 | 1356 | 1356-knockout | bacteria |
| SA467746 | ffs | ffs-knockout | bacteria |
| SA467748 | mcgb | mcgb-knockout | bacteria |
| SA467749 | mcgd | mcgd-knockout | bacteria |
| SA467750 | mcgm | mcgm-knockout | bacteria |
| SA467751 | mcgn | mcgn-knockout | bacteria |
| SA467747 | mcgo | mcgO-knockout | bacteria |
| SA467752 | Smu102 wt | wt | bacteria |
| Showing results 1 to 11 of 11 |
Collection:
| Collection ID: | CO004190 |
| Collection Summary: | To carry out comparative metabolomic analysis, strains were grown in 5 mL CDM for 16 hours. Cultures were extracted with 1 volume of 95:5 ethyl acetate:methanol. Mixtures were vortexed and centrifuged (16,000×g, 5 min). The organic layer was pipetted into a new tube and dried under N2, then resuspended in methanol. |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR004206 |
| Treatment Summary: | No treatment was performed. Only bacterial growth and extraction for comparative metabolomics. |
Sample Preparation:
| Sampleprep ID: | SP004203 |
| Sampleprep Summary: | For each experiment, strains were first streaked out on Todd Hewitt Broth (THB) agar plates and grown for two days at 37°C. For S. mutans, single colonies were then inoculated into Chemically Defined Medium (CDMB) with 4% (v/v) BD™ Difco™ Brain Heart Infusion at 37°C in a standing incubator (CDMB). Growth of S. mutans in liquid was carried out at 37°C without shaking for 16hours. Unless specified, cultures were grown with 1M Dextrose (D-glucose). |
Chromatography:
| Chromatography ID: | CH005088 |
| Chromatography Summary: | 100 μL cell culture equivalent was analyzed on an Agilent Technologies 6545 Accurate-Mass QTOF LC-MS instrument after separation on an Agilent Eclipse Plus C18 column (4.6×100 mm) 3.5um pour size. Samples were separated using a linear gradient of 2-98% acetonitrile (v/v) over 30 minutes in H2O with 0.1% formic acid (v/v) at a flow rate of 0.5 mL/min. |
| Instrument Name: | Agilent Technologies 6545 Accurate-Mass QTOF LC-MS |
| Column Name: | ZORBAX RR Eclipse Plus C18 (100 mm x 4.6 mm, 3.5 µm) |
| Column Temperature: | 28°C |
| Flow Gradient: | 0-2 min: 2% B; 2-32 min: 2% B - 98% B; 32-37 min: 98% B; 37-37.1 min: 98% B - 2% B; 37-41 min: 2% B |
| Flow Rate: | 0.5 mL/min |
| Solvent A: | 100% Water |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN006697 |
| Analysis Type: | MS |
| Chromatography ID: | CH005088 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST004051_AN006697_Results.txt |
| Units: | Peak height |
