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

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Study IDST004051
Study TitleSynergistic action of specialized metabolites from divergent biosynthesis in human oral microbiome
Study SummaryIn 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 NameYao
First NameMcKenna
AddressStanley Hall University Dr
Emailmckenna_yao@berkeley.edu
Phone4803266096
Submit Date2024-11-08
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-08-11
Release Version1
McKenna Yao McKenna Yao
https://dx.doi.org/10.21228/M86828
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA46774213411341-knockout bacteria
SA46774313461346-knockout bacteria
SA46774413511351-knockout bacteria
SA46774513561356-knockout bacteria
SA467746ffsffs-knockout bacteria
SA467748mcgbmcgb-knockout bacteria
SA467749mcgdmcgd-knockout bacteria
SA467750mcgmmcgm-knockout bacteria
SA467751mcgnmcgn-knockout bacteria
SA467747mcgomcgO-knockout bacteria
SA467752Smu102 wtwt 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).

Combined analysis:

Analysis ID AN006697
Chromatography ID CH005088
MS ID MS006396
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent Technologies 6545 Accurate-Mass QTOF LC-MS
Column ZORBAX RR Eclipse Plus C18 (100 mm x 4.6 mm, 3.5 µm)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6445 Q-TOF
Ion Mode POSITIVE
Units Peak height

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

MS:

MS ID:MS006396
Analysis ID:AN006697
Instrument Name:Agilent 6445 Q-TOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS data were collected at a fragmentation voltage of 110 V. MS/MS data were collected throughout the run method using three fragmentation voltages (10, 30, and 50 V). Data analysis was performed using MassHunter software and comparative metabolomics with MS-DIAL69. No feature assignment was performed.
Ion Mode:POSITIVE
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