Summary of Study ST001651

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 PR001057. The data can be accessed directly via it's Project DOI: 10.21228/M82Q48 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.

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Study ID	ST001651
Study Title	Analysis of metabolites in gut microbioal culture media and microbial cells
Study Summary	We developed an untargeted stable isotope-resolved metabolomics (SIRM) approach for the holistic study of gut microbial metabolites
Institute	University of Kentucky
Last Name	Deng
First Name	Pan
Address	789 South Limestone
Email	pde233@uky.edu
Phone	8595623039
Submit Date	2020-12-11
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2021-03-01
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001057
Project DOI:	doi: 10.21228/M82Q48
Project Title:	Untargeted stable-isotope probing of the gut microbiota metabolome using 13C-labeled dietary fibers
Project Summary:	The gut microbiome generates numerous metabolites that exert local effects and enter the circulation to affect the functions of many organs. Despite extensive sequencing-based characterization of the gut microbiome, there remains a lack of understanding of microbial metabolism. Here, we developed an untargeted stable isotope-resolved metabolomics (SIRM) approach for the holistic study of gut microbial metabolites.
Institute:	University of Kentucky
Last Name:	Deng
First Name:	Pan
Address:	789 South Limestone
Email:	pde233@uky.edu
Phone:	8595623039

Subject:

Subject ID:	SU001728
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Gender:	Female

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA151719	Cellulose_Cell_2	13C-Cellulose
SA151720	Cellulose_Cell_3	13C-Cellulose
SA151721	Cellulose_Media_1	13C-Cellulose
SA151722	Cellulose_Cell_1	13C-Cellulose
SA151723	Cellulose_Media_2	13C-Cellulose
SA151724	Cellulose_Media_3	13C-Cellulose
SA151725	Inulin_Cell_3	13C-Inulin
SA151726	Inulin_Media_2	13C-Inulin
SA151727	Inulin_Cell_2	13C-Inulin
SA151728	Inulin_Cell_1	13C-Inulin
SA151729	Inulin_Media_3	13C-Inulin
SA151730	Inulin_Media_1	13C-Inulin

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO001721
Collection Summary:	Fresh fecal pellets were collected from each mouse (23 weeks old) and immediately placed in a sterile microcentrifuge tube. Samples were quickly transferred to an anaerobic chamber for immediate experimental setup to ensure microbial viability.
Sample Type:	Feces
Storage Conditions:	Described in summary

Treatment:

Treatment ID:	TR001741
Treatment Summary:	Fresh fecal samples (ca. 110 mg) from each mouse were weighed and dispensed in 3 mL of prepared medium separately in an anaerobic chamber. The samples were pestled to suspend the microorganisms and particles. The suspensions were subjected to low-speed centrifugation and the supernatants were then collected and centrifuged to pellet microbes. The microbial cells were then suspended in 4 mL of culture medium, and divided equally into two Hungate tubes. To each paired tube was amended with either 13C-Inulin or 13C-cellulose aseptically to achieve a final concentration of 4 g/L fibers. The sealed Hungate tubes were incubated in a water bath (37°C) for 24 h. After incubation, the samples were centrifuged (3,000 g, 5 min) to collect supernatant (culture medium). Each pellet was washed with 1 mL of fresh culture medium and centrifuged to collect the microbial cells. All procedures were performed under anaerobic conditions.

Treatment ID:

TR001741

Treatment Summary:

Fresh fecal samples (ca. 110 mg) from each mouse were weighed and dispensed in 3 mL of prepared medium separately in an anaerobic chamber. The samples were pestled to suspend the microorganisms and particles. The suspensions were subjected to low-speed centrifugation and the supernatants were then collected and centrifuged to pellet microbes. The microbial cells were then suspended in 4 mL of culture medium, and divided equally into two Hungate tubes. To each paired tube was amended with either 13C-Inulin or 13C-cellulose aseptically to achieve a final concentration of 4 g/L fibers. The sealed Hungate tubes were incubated in a water bath (37°C) for 24 h. After incubation, the samples were centrifuged (3,000 g, 5 min) to collect supernatant (culture medium). Each pellet was washed with 1 mL of fresh culture medium and centrifuged to collect the microbial cells. All procedures were performed under anaerobic conditions.

Sample Preparation:

Sampleprep ID:	SP001734
Sampleprep Summary:	The collected medium was weighed, and equal amounts of medium (50% of total medium weight) were accurately aliquoted from each sample and lyophilized. The microbial cells were quenched using 450 μL cold methanol right after collection. After brief agitation by vortex, the samples were transferred into glass tubes. Then 5 mL of methyl tert-butyl ether was added to each tube and the samples were mixed on a multi-tube vortexer (600 rpm, 30 min). Phase separation was then induced by adding 1.25 mL of Millipore deionized water. Samples were then vortexed again for 1 min, incubated at 4 °C for 10 min to allow phase separation and centrifuged (3,000 g, 10 min, 4 °C). Polar fractions were collected into clean tubes and lyophilized.

Sampleprep ID:

SP001734

Sampleprep Summary:

The collected medium was weighed, and equal amounts of medium (50% of total medium weight) were accurately aliquoted from each sample and lyophilized. The microbial cells were quenched using 450 μL cold methanol right after collection. After brief agitation by vortex, the samples were transferred into glass tubes. Then 5 mL of methyl tert-butyl ether was added to each tube and the samples were mixed on a multi-tube vortexer (600 rpm, 30 min). Phase separation was then induced by adding 1.25 mL of Millipore deionized water. Samples were then vortexed again for 1 min, incubated at 4 °C for 10 min to allow phase separation and centrifuged (3,000 g, 10 min, 4 °C). Polar fractions were collected into clean tubes and lyophilized.

Combined analysis:

Analysis ID	AN002697	AN002698
Analysis type	MS	MS
Chromatography type	HILIC	HILIC
Chromatography system	Thermo Dionex Ultimate 3000	Thermo Dionex Ultimate 3000
Column	SeQuant ZIC-HILIC (150 x 2.1mm,5um)	SeQuant ZIC-HILIC (150 x 2.1mm,5um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	peak area	peak area

Chromatography:

Chromatography ID:	CH001990
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	SeQuant ZIC-HILIC (150 x 2.1mm,5um)
Column Temperature:	40
Flow Gradient:	0–20 min, linear gradient from 80% to 20% B; 20–21 min, hold at 20% B min; 21-22 min, linear gradient to 80% B; 22-28 min, re-equilibrate at 80% B
Flow Rate:	0.150 ml/min
Solvent A:	100% water; 20 mM ammonium carbonate; 0.1% ammonium hydroxide
Solvent B:	100% acetonitrile
Chromatography Type:	HILIC

MS:

MS ID:	MS002495
Analysis ID:	AN002697
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The mass spectrometer was operated in positive and negative ionization modes. Initial metabolite identification was performed using Compound Discoverer 3.1 (Thermo Fisher Scientific).Metabolites were further confirmed by comparison of the ion features in the samples with an in-house reference library of authentic chemical standards. Peak areas of metabolites and isotopologues were integrated and exported to Excel via the TraceFinder 5.0 software package (Thermo Fisher Scientific).
Ion Mode:	POSITIVE

MS ID:	MS002496
Analysis ID:	AN002698
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The mass spectrometer was operated in positive and negative ionization modes. Initial metabolite identification was performed using Compound Discoverer 3.1 (Thermo Fisher Scientific).Metabolites were further confirmed by comparison of the ion features in the samples with an in-house reference library of authentic chemical standards. Peak areas of metabolites and isotopologues were integrated and exported to Excel via the TraceFinder 5.0 software package (Thermo Fisher Scientific).
Ion Mode:	NEGATIVE