Summary of Study ST003683

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 PR002283. The data can be accessed directly via it's Project DOI: 10.21228/M8HZ6G 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	ST003683
Study Title	Ketogenic diet suppresses colorectal cancer through the gut microbiome long chain fatty acid stearate - untargeted LCMS data from mouse plasma samples
Study Summary	Mouse plasma samples from the SD/KD-fed SPF mice were analyzed by a LC-MS. Metabolites were extracted from human plasma samples as described in the method file. Resulting samples were used for LC-MS untargeted metabolomics screen using a Vanquish UHPLC (ThermoFisher Scientific), coupled to a Q Exactive HF mass spectrometer (ThermoFisher Scientific).
Institute	University of Luxembourg
Last Name	Letellier
First Name	Elisabeth
Address	6, avenue du Swing, Belval, Esch, 4367, Luxembourg
Email	madita.brauer@uni.lu
Phone	(+352) 46 66 44 6954
Submit Date	2025-01-20
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-01-27
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002283
Project DOI:	doi: 10.21228/M8HZ6G
Project Title:	Ketogenic diet suppresses colorectal cancer through the gut microbiome long chain fatty acid stearate
Project Summary:	Our manuscript entitled “Ketogenic diet suppresses colorectal cancer through the gut microbiome long chain fatty acid stearate” describes a reduced colonic tumor burden upon ketogenic diet (KD) consumption in a CRC mouse model with a humanized microbiome. Importantly, we demonstrate a causal relationship through microbiome transplantation into germ-free mice, whereby alterations in the gut microbiota were maintained in the absence of continued selective pressure from the KD. Specifically, we identify a shift toward bacterial species that produce stearic acid in ketogenic conditions, whereas consumers were depleted, resulting in elevated levels of free stearate in the gut lumen. This microbial product demonstrates tumor-suppressing properties by inducing apoptosis in cancer cells and decreasing colonic Th17 immune cell populations. As part of this study, we used different metabolomics workflows to study metabolites in mouse fecal and plasma samples as well as the used rodent diet.
Institute:	University of Luxembourg
Last Name:	Letellier
First Name:	Elisabeth
Address:	6, avenue du Swing, Belval, Esch, 4367, Luxembourg
Email:	madita.brauer@uni.lu
Phone:	(+352) 46 66 44 6954

Subject:

Subject ID:	SU003815
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

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

mb_sample_id	local_sample_id	Sample source	Condition
SA402318	KD_12	Blood plasma	KD
SA402319	KD_24	Blood plasma	KD
SA402320	KD_23	Blood plasma	KD
SA402321	KD_22	Blood plasma	KD
SA402322	KD_11	Blood plasma	KD
SA402323	KD_21	Blood plasma	KD
SA402324	KD_13	Blood plasma	KD
SA402325	SD_19	Blood plasma	SD
SA402326	SD_20	Blood plasma	SD
SA402327	SD_18	Blood plasma	SD
SA402328	SD_17	Blood plasma	SD
SA402329	SD_16	Blood plasma	SD
SA402330	SD_1	Blood plasma	SD
SA402331	SD_2	Blood plasma	SD
SA402332	SD_3	Blood plasma	SD
SA402333	SD_4	Blood plasma	SD

Showing results 1 to 16 of 16

Showing results 1 to 16 of 16

Collection:

Collection ID:	CO003808
Collection Summary:	Plasma samples from SPF mice fed a ketogenic or standard diet were taken and stored in plasma collection tube at -80℃ until use for metabolite extraction.
Sample Type:	Blood (plasma)
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR003824
Treatment Summary:	Mice were subjected to AOM/DSS treatment and received either a ketogenic diet (KD) or a standard diet (SD) as described in Tsenkova et al. (2025). Briefly, mice were administered a single intraperitoneal injection of sterile-filtered AOM (10 mg/kg mouse body weight). SPF mice were administered a sterile-filtered antibiotic mix (vancomycin hydrochloride (Sigma-Aldrich, 500 mg/L), ampicillin (Sigma-Aldrich, 1 g/L), neomycin (Sigma-Aldrich, 1 g/L) and metronidazole (Sigma-Aldrich, 1 g/L)) via their drinking water for one week prior to AOM injection. Microbiomes were replaced with donor microbiomes via oral gavage. Mice were administered a total of three cycles of DSS, with a two-week-long recovery period between each cycle. DSS was refreshed mid-cycle. Half of the mice were randomly allocated to each dietary condition at the end of the last cycle of DSS.

Treatment ID:

TR003824

Treatment Summary:

Mice were subjected to AOM/DSS treatment and received either a ketogenic diet (KD) or a standard diet (SD) as described in Tsenkova et al. (2025). Briefly, mice were administered a single intraperitoneal injection of sterile-filtered AOM (10 mg/kg mouse body weight). SPF mice were administered a sterile-filtered antibiotic mix (vancomycin hydrochloride (Sigma-Aldrich, 500 mg/L), ampicillin (Sigma-Aldrich, 1 g/L), neomycin (Sigma-Aldrich, 1 g/L) and metronidazole (Sigma-Aldrich, 1 g/L)) via their drinking water for one week prior to AOM injection. Microbiomes were replaced with donor microbiomes via oral gavage. Mice were administered a total of three cycles of DSS, with a two-week-long recovery period between each cycle. DSS was refreshed mid-cycle. Half of the mice were randomly allocated to each dietary condition at the end of the last cycle of DSS.

Sample Preparation:

Sampleprep ID:	SP003822
Sampleprep Summary:	Plasma samples were thawed on ice and centrifuged at 15000g for three minutes at 4°C. An ISM was prepared (1 mg/mL of 6-chloropurine riboside, 2-chloroquinoline-3-carboxylic acid, 4-chloro-DL-phenylalanine, Nε-trifluoroacetyl-L-lysine, sucralose, caffeine-trimethyl in MilliQ® water). 20 μL of the ISM was added to 20 μL of plasma at 4°C and the samples were vortexed thoroughly. Proteins were precipitated by the addition of 151 μL of methanol to 38 μL of sample at 4°C and vortexed thoroughly. Samples were incubated for 15 minutes at -20°C, then centrifuged for five minutes at 4°C in a ThermoMixer. Phospholipids were removed by diluting samples in 300μL of methanol, then transferring them to a Phree phospholipid removal plate and vacuum for 2-7 inches Hg was applied until the filtrate collected in the deep well plate. 350 μL were transferred into 1.5mL Eppendorf tubes and the solvents were evaporated in a SpeedVac® at 4°C overnight. Then, the temperature of the SpeedVac® was increased to room temperature for 25 minutes to avoid water condensation on the surface of the tube. Samples were stored at -80°C until LC-MS analysis was performed.

Sampleprep ID:

SP003822

Sampleprep Summary:

Plasma samples were thawed on ice and centrifuged at 15000g for three minutes at 4°C. An ISM was prepared (1 mg/mL of 6-chloropurine riboside, 2-chloroquinoline-3-carboxylic acid, 4-chloro-DL-phenylalanine, Nε-trifluoroacetyl-L-lysine, sucralose, caffeine-trimethyl in MilliQ® water). 20 μL of the ISM was added to 20 μL of plasma at 4°C and the samples were vortexed thoroughly. Proteins were precipitated by the addition of 151 μL of methanol to 38 μL of sample at 4°C and vortexed thoroughly. Samples were incubated for 15 minutes at -20°C, then centrifuged for five minutes at 4°C in a ThermoMixer. Phospholipids were removed by diluting samples in 300μL of methanol, then transferring them to a Phree phospholipid removal plate and vacuum for 2-7 inches Hg was applied until the filtrate collected in the deep well plate. 350 μL were transferred into 1.5mL Eppendorf tubes and the solvents were evaporated in a SpeedVac® at 4°C overnight. Then, the temperature of the SpeedVac® was increased to room temperature for 25 minutes to avoid water condensation on the surface of the tube. Samples were stored at -80°C until LC-MS analysis was performed.

Combined analysis:

Analysis ID	AN006045
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Thermo Vanquish
Column	SeQuant ZIC- pHILIC (150 x 2.1 mm, 5 μm)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive HF-X Orbitrap
Ion Mode	UNSPECIFIED
Units	area

Chromatography:

Chromatography ID:	CH004594
Instrument Name:	Thermo Vanquish
Column Name:	SeQuant ZIC- pHILIC (150 x 2.1 mm, 5 μm)
Column Temperature:	50°C
Flow Gradient:	90 % B for 1.5 min, followed by a decrease to 20% B within 15 min, then 20% B for 2 min, increase to 90% B within 2 min, then 90% B for 13 min
Flow Rate:	200 µL/mL
Solvent A:	100% Water; 0.01% formic acid
Solvent B:	90% Acetonitrile/10% Water; 0.1% formic acid; 20 mM ammonium acetate
Chromatography Type:	HILIC

MS:

MS ID:	MS005754
Analysis ID:	AN006045
Instrument Name:	Thermo Q Exactive HF-X Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Resolution - 120,000, m/z range - 60-900, AGC target - 1e6, maximum injection time – 70 ms. ddMS2 was applied using the following settings: Resolution - 30,000, AGC target - 5e5, maximum injection time – 70, topN - 5, Normalized collision energy – 20. Samples were acquired in positive and negative ionization mode simultaneously (polarity switching).
Ion Mode:	UNSPECIFIED