Summary of Study ST001939

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 PR001227. The data can be accessed directly via it's Project DOI: 10.21228/M83Q5Z This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Study ID	ST001939
Study Title	Metabolomics characterized concentration-dependent metabolic influence of magnesium on biofilm formation in Escherichia coli (Part 2)
Study Summary	Biofilms are broadly formed by a diversity of microorganisms that enable them to adapt stressful environments. Biofilms often impose harmful influences in many niches, as they can cause food contamination, antibiotics resistance, and environmental issues. However, eradicating biofilms remains difficult since the formation mechanism of biofilms are still incompletely clarified. In this study, we aimed at exploring the regulatory role of magnesium (Mg2+) on biofilm formation in Escherichia coli (E. coli) using phenotype visualization combined with targeted metabolomics method. We found that Mg2+ could exert significant influence on biofilm formation in a concentration-dependent manner by regulating phenotypic morphology and triggering metabolic modifications of biofilm. Phenotypic imaging revealed that increasing concentration of Mg2+ gradually inhibited biofilm formation, Mg2+ was observed to restore the microstructure of E. coli strain in biofilms to that in the relevant planktonic cells. In addition, our metabolomics analysis characterized 20 differential metabolites and associated 2 metabolic pathways including nucleotide metabolism and amino acid metabolism that were notably modified during biofilm formation under the treatments of different concentrations of Mg2+. Altogether, our work provides a novel insight into the influence of Mg2+ on biofilm formation at a metabolic level, which are implicated in the novel solution to disturb biofilm formation through the regulation of Mg2+ and functional metabolite interaction, then biofilms associated harmful impacts in different niches could be well tangled accordingly.
Institute	Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University
Department	Shanghai Center for Systems Biomedicine
Laboratory	Lu Group
Last Name	Lu
First Name	Haitao
Address	800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China
Email	haitao_lu@sjtu.edu.cn
Phone	15221478139
Submit Date	2021-09-07
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2021-11-04
Release Version	1

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Project:

Project ID:	PR001227
Project DOI:	doi: 10.21228/M83Q5Z
Project Title:	Metabolomics characterized concentration-dependent metabolic influence of magnesium on biofilm formation in Escherichia coli
Project Type:	Targeted MS quantitative analysis
Project Summary:	Metabolomics characterized concentration-dependent metabolic influence of magnesium on biofilm formation in Escherichia coli
Institute:	Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University
Department:	Shanghai Center for Systems Biomedicine
Laboratory:	Lu Group
Last Name:	Lu
First Name:	Haitao
Address:	800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China
Email:	haitao_lu@sjtu.edu.cn
Phone:	15221478139

Subject:

Subject ID:	SU002017
Subject Type:	Bacteria
Subject Species:	Escherichia coli
Taxonomy ID:	562

Factors:

Subject type: Bacteria; Subject species: Escherichia coli (Factor headings shown in green)

mb_sample_id	local_sample_id	Concentration of MgSO4(w/v)
SA183157	20210227-3-C-1	0.01%
SA183158	20210227-3-C-6	0.01%
SA183159	20210227-3-C-5	0.01%
SA183160	20210227-3-C-2	0.01%
SA183161	20210227-3-C-3	0.01%
SA183162	20210227-3-C-4	0.01%
SA183163	20210227-3-30-6	0.15%
SA183164	20210227-3-30-5	0.15%
SA183165	20210227-3-30-2	0.15%
SA183166	20210227-3-30-4	0.15%
SA183167	20210227-3-30-1	0.15%
SA183168	20210227-3-30-3	0.15%
SA183169	20210227-3-50-5	0.25%
SA183170	20210227-3-50-6	0.25%
SA183171	20210227-3-50-4	0.25%
SA183172	20210227-3-50-3	0.25%
SA183173	20210227-3-50-1	0.25%
SA183174	20210227-3-50-2	0.25%
SA183175	20210227-3-80-5	0.40%
SA183176	20210227-3-80-4	0.40%
SA183177	20210227-3-80-6	0.40%
SA183178	20210227-3-80-3	0.40%
SA183179	20210227-3-80-1	0.40%
SA183180	20210227-3-80-2	0.40%
SA183181	20210227-3-100-6	0.50%
SA183182	20210227-3-100-5	0.50%
SA183183	20210227-3-100-3	0.50%
SA183184	20210227-3-100-1	0.50%
SA183185	20210227-3-100-2	0.50%
SA183186	20210227-3-100-4	0.50%

Showing results 1 to 30 of 30

Showing results 1 to 30 of 30

Collection:

Collection ID:	CO002010
Collection Summary:	After 72 hours of culture, the planktonic cells were isolated, and the biofilms were washed with PBS solvent for three times. Then, planktonic cells and biofilm solutions were centrifuged at 2000 rpm and 4°C for 15 minutes, to collect the strain pellets.
Sample Type:	Biofilm

Treatment:

Treatment ID:	TR002029
Treatment Summary:	Colony-forming antigen (CFA) medium (1% casamino acids, 0.15% yeast extract, 0.005% magnesium sulfate, and 0.0005% manganese chloride) was used to form biofilms. The E. coli strain was incubated in LB-agar plate for 12 hours, one colony was isolated to LB broth for further 4 hours incubation, then diluted the solution into CFA medium at a ratio of 1:1000 and the cultures were incubated for another 72 h at 30°C to form mature biofilms. To test the influence of MgSO4 on biofilm formation, the purified compound of MgSO4 was added to the CFA medium at different concentrations for the preparation of treated culture medium; The left cultural procedures were kept as the same as the protocol listed above.

Treatment ID:

TR002029

Treatment Summary:

Colony-forming antigen (CFA) medium (1% casamino acids, 0.15% yeast extract, 0.005% magnesium sulfate, and 0.0005% manganese chloride) was used to form biofilms. The E. coli strain was incubated in LB-agar plate for 12 hours, one colony was isolated to LB broth for further 4 hours incubation, then diluted the solution into CFA medium at a ratio of 1:1000 and the cultures were incubated for another 72 h at 30°C to form mature biofilms. To test the influence of MgSO4 on biofilm formation, the purified compound of MgSO4 was added to the CFA medium at different concentrations for the preparation of treated culture medium; The left cultural procedures were kept as the same as the protocol listed above.

Sample Preparation:

Sampleprep ID:	SP002023
Sampleprep Summary:	Each pellet sample was mixed with 2 mL of 80% ice-cold methanol, and the mixed solution was homogenized on ice for 2 minutes and repeated the same procedure for three times. Next, the collected samples were centrifuged at 12000 rpm and 4°C for 15 minutes, to collect the supernatants. The supernatants were further mixed with 800 μL of ice-cold acetonitrile for 20 minutes before further centrifuge at 12000 rpm and 4°C for 15 minutes. At last, the isolated supernatants were gone through a 0.22 μm filter membrane (nylon) before the lyophilization. The lyophilized samples were stored at -80°C for metabolomics analysis.

Sampleprep ID:

SP002023

Sampleprep Summary:

Each pellet sample was mixed with 2 mL of 80% ice-cold methanol, and the mixed solution was homogenized on ice for 2 minutes and repeated the same procedure for three times. Next, the collected samples were centrifuged at 12000 rpm and 4°C for 15 minutes, to collect the supernatants. The supernatants were further mixed with 800 μL of ice-cold acetonitrile for 20 minutes before further centrifuge at 12000 rpm and 4°C for 15 minutes. At last, the isolated supernatants were gone through a 0.22 μm filter membrane (nylon) before the lyophilization. The lyophilized samples were stored at -80°C for metabolomics analysis.

Combined analysis:

Analysis ID	AN003153	AN003154
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Agilent 1290 Infinity	Agilent 1290 Infinity
Column	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type	ESI	ESI
MS instrument type	Triple quadrupole	Triple quadrupole
MS instrument name	Agilent 6495 QQQ	Agilent 6495 QQQ
Ion Mode	NEGATIVE	POSITIVE
Units	-	-

Chromatography:

Chromatography ID:	CH002332
Chromatography Summary:	The chromatographic separation of biological samples was implemented on a Waters ACQUITY UPLC HSS T3 column (2.1×100 mm, 1.8 μm) with an optimized gradient-elution program (mobile phase A and B were 0.1% formic acid in water and acetonitrile (v/v)): 0-2 minutes, 98% A; 2-10 minutes, 98%-65% A; 10-12 minutes, 65%-20% A; 12-14 minutes, 20%-2% A; 14-30 minutes, 2% A. The column temperature was at 40°C and the flow rate was set at 0.3 mL/ minutes.
Instrument Name:	Agilent 1290 Infinity
Column Name:	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:	40
Flow Gradient:	0-2 minutes, 98% A; 2-10 minutes, 98%-65% A; 10-12 minutes, 65%-20% A; 12-14 minutes, 20%-2% A; 14-30 minutes, 2% A
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

MS:

MS ID:	MS002933
Analysis ID:	AN003153
Instrument Name:	Agilent 6495 QQQ
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Agilent MassHunter Workstation Data Acquisition Agilent MassHunter QualitativeAnalysis B.07.00 Agilent MassHunter Quantitative Analysis (for QQQ)
Ion Mode:	NEGATIVE

MS ID:	MS002934
Analysis ID:	AN003154
Instrument Name:	Agilent 6495 QQQ
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Agilent MassHunter Workstation Data Acquisition Agilent MassHunter QualitativeAnalysis B.07.00 Agilent MassHunter Quantitative Analysis (for QQQ)
Ion Mode:	POSITIVE