Summary of Study ST004075

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 PR002557. The data can be accessed directly via it's Project DOI: 10.21228/M84C32 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	ST004075
Study Title	[U-13C]Glucose Labeling in Adult Zebrafish Treated with Antimicrobials or Control
Study Summary	Glucose metabolism was traced with [U-13C]glucose in the intestine, liver, and serum of adult zebrafish with in-tact or depleted gut microbiota. We found that fish treated with antimicrobials had elevated M+6 sorbitol relative to control in these organs.
Institute	Washington University in St. Louis
Last Name	Jackstadt
First Name	Madelyn
Address	One Brookings Drive, St. Louis, Missouri, 63130, USA
Email	mjackstadt@wustl.edu
Phone	3149356405
Submit Date	2025-07-01
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-10-28
Release Version	1

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Project:

Project ID:	PR002557
Project DOI:	doi: 10.21228/M84C32
Project Title:	Intestine-derived sorbitol drives steatotic liver disease in the absence of gut bacteria
Project Summary:	The role of the gut microbiome in mediating steatotic liver disease is poorly understood. Here, we developed a model to deplete the gut microbiome in adult zebrafish and discovered that it led to steatotic liver disease in animals on standard diets. Using metabolomics and isotope tracing, we found that dietary glucose is transformed into sorbitol within the intestine. While bacteria degrade the sorbitol in control animals, sorbitol is passed to the livers of fish in which the gut microbiome has been depleted. Within the liver, sorbitol is converted into fructose 1-phosphate, which subsequently activates glucokinase. The result is increased hepatic metabolism of glucose, leading to elevated glycogen and fat content. Inhibition of sorbitol production in microbiome-depleted animals was sufficient to prevent the development of steatotic liver, and colonizing sorbitol-degrading bacteria in the intestines of microbiome-depleted fish reversed the steatotic liver phenotype. Taken together, these findings show that sorbitol-degrading bacteria in the gut protect against steatotic liver disease.
Institute:	Washington University in St. Louis
Last Name:	Jackstadt
First Name:	Madelyn
Address:	One Brookings Drive, St. Louis, Missouri, 63130, USA
Email:	mjackstadt@wustl.edu
Phone:	3149356405

Subject:

Subject ID:	SU004221
Subject Type:	Fish
Subject Species:	Danio rerio
Taxonomy ID:	7955

Factors:

Subject type: Fish; Subject species: Danio rerio (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment	Sample source
SA473348	UGlucose_Neg_Anti_31_Intestine	Antimicrobials	Intestine
SA473349	UGlucose_Neg_Anti_30_Intestine	Antimicrobials	Intestine
SA473350	UGlucose_Neg_Anti_29_Intestine	Antimicrobials	Intestine
SA473351	UGlucose_Neg_Anti_28_Intestine	Antimicrobials	Intestine
SA473352	UGlucose_Neg_Anti_27_Intestine	Antimicrobials	Intestine
SA473353	UGlucose_Neg_Anti_26_Intestine	Antimicrobials	Intestine
SA473354	UGlucose_Neg_Anti_24_Intestine	Antimicrobials	Intestine
SA473355	UGlucose_Neg_Anti_26_Liver	Antimicrobials	Liver
SA473356	UGlucose_Neg_Anti_31_Liver	Antimicrobials	Liver
SA473357	UGlucose_Neg_Anti_30_Liver	Antimicrobials	Liver
SA473358	UGlucose_Neg_Anti_29_Liver	Antimicrobials	Liver
SA473359	UGlucose_Neg_Anti_28_Liver	Antimicrobials	Liver
SA473360	UGlucose_Neg_Anti_27_Liver	Antimicrobials	Liver
SA473361	UGlucose_Neg_Anti_24_Liver	Antimicrobials	Liver
SA473362	UGlucose_Neg_Anti_31_Serum	Antimicrobials	Serum
SA473363	UGlucose_Neg_Anti_24_Serum	Antimicrobials	Serum
SA473364	UGlucose_Neg_Anti_30_Serum	Antimicrobials	Serum
SA473365	UGlucose_Neg_Anti_29_Serum	Antimicrobials	Serum
SA473366	UGlucose_Neg_Anti_28_Serum	Antimicrobials	Serum
SA473367	UGlucose_Neg_Anti_27_Serum	Antimicrobials	Serum
SA473368	UGlucose_Neg_Anti_26_Serum	Antimicrobials	Serum
SA473369	UGlucose_Neg_Ctrl_17_Intestine	Control	Intestine
SA473370	UGlucose_Neg_Ctrl_18_Intestine	Control	Intestine
SA473371	UGlucose_Neg_Ctrl_23_Intestine	Control	Intestine
SA473372	UGlucose_Neg_Ctrl_22_Intestine	Control	Intestine
SA473373	UGlucose_Neg_Ctrl_21_Intestine	Control	Intestine
SA473374	UGlucose_Neg_Ctrl_20_Intestine	Control	Intestine
SA473375	UGlucose_Neg_Ctrl_19_Intestine	Control	Intestine
SA473376	UGlucose_Neg_Ctrl_16_Intestine	Control	Intestine
SA473377	UGlucose_Neg_Ctrl_16_Liver	Control	Liver
SA473378	UGlucose_Neg_Ctrl_17_Liver	Control	Liver
SA473379	UGlucose_Neg_Ctrl_23_Liver	Control	Liver
SA473380	UGlucose_Neg_Ctrl_21_Liver	Control	Liver
SA473381	UGlucose_Neg_Ctrl_20_Liver	Control	Liver
SA473382	UGlucose_Neg_Ctrl_19_Liver	Control	Liver
SA473383	UGlucose_Neg_Ctrl_18_Liver	Control	Liver
SA473384	UGlucose_Neg_Ctrl_17_Serum	Control	Serum
SA473385	UGlucose_Neg_Ctrl_23_Serum	Control	Serum
SA473386	UGlucose_Neg_Ctrl_22_Serum	Control	Serum
SA473387	UGlucose_Neg_Ctrl_21_Serum	Control	Serum
SA473388	UGlucose_Neg_Ctrl_20_Serum	Control	Serum
SA473389	UGlucose_Neg_Ctrl_19_Serum	Control	Serum
SA473390	UGlucose_Neg_Ctrl_18_Serum	Control	Serum
SA473391	UGlucose_Neg_Ctrl_16_Serum	Control	Serum

Showing results 1 to 44 of 44

Showing results 1 to 44 of 44

Collection:

Collection ID:	CO004214
Collection Summary:	Zebrafish were anesthetized and thoroughly dried before a scalpel was used to excise the caudal fin and some attached muscle tissue. Zebrafish were then immediately placed in a spin column such that blood from the wound could flow from the fish (in a 1.5 mL microcentrifuge tube with a small hole in the bottom) to a collection tube (a 0.5 mL microcentrifuge tube) during a brief, low-speed centrifugation (40 g for 1 min at 15 C). Immediately following blood collection, whole blood was placed on ice for 10 min while organs were harvested in pre-weighed microcentrifuge tubes and snap frozen in liquid nitrogen. After clotting on ice, whole blood was centrifuged at 1600 g for 10 min at 4 C. Serum (top layer) was then pipetted into a new 0.5 mL microcentrifuge tube and snap frozen in liquid nitrogen.
Sample Type:	intestine, liver, serum

Treatment:

Treatment ID:	TR004230
Treatment Summary:	For control treatment, conditioned facility water was autoclaved prior to zebrafish exposure. For antimicrobial treatment, 2% penicillin/streptomycin, 5 ug/mL kanamycin, 100 ug/mL ampicillin, and 250 ng/mL amphotericin b were added to autoclaved facility water. Both conditions were exposed to 10 mM [U-13C]glucose.

Sample Preparation:

Sampleprep ID:	SP004227
Sampleprep Summary:	For serum extractions, samples were stored on ice until the addition of 2:2:1 methanol:acetonitrile:water (MAW) at a ratio of 1 uL serum:15 uL MAW. Samples were briefly mixed and immediately placed at -20 C for 1 h. Following incubation, samples were centrifuged at 20,000 g for 10 min at 4 C, and supernatant was transferred to LC-MS vials for analysis. For organ samples, tissues were ground in collection tubes by using a pestle while submerged in liquid nitrogen. Frozen samples in tubes were then massed, and the preweight of the tube was subtracted to yield tissue weight. 40 uL of 2:2:1 MAW were added per mg wet tissue weight, and the sample was vortexed before snap freezing in liquid nitrogen. Simultaneously, samples were extracted by thawing in room temperature water (~10 s), sonicating (5 min), vortexing (~30 s), snap freezing in liquid nitrogen (~1 min), thawing in room temperature water (~10 s), sonicating (5 min), and vortexing (~30 s) before incubating at -20 C for 1 h. Following incubation, samples were centrifuged at 20,000 g for 10 min at 4 C, and supernatant was transferred to LC-MS vials for analysis.

Sampleprep ID:

SP004227

Sampleprep Summary:

For serum extractions, samples were stored on ice until the addition of 2:2:1 methanol:acetonitrile:water (MAW) at a ratio of 1 uL serum:15 uL MAW. Samples were briefly mixed and immediately placed at -20 C for 1 h. Following incubation, samples were centrifuged at 20,000 g for 10 min at 4 C, and supernatant was transferred to LC-MS vials for analysis. For organ samples, tissues were ground in collection tubes by using a pestle while submerged in liquid nitrogen. Frozen samples in tubes were then massed, and the preweight of the tube was subtracted to yield tissue weight. 40 uL of 2:2:1 MAW were added per mg wet tissue weight, and the sample was vortexed before snap freezing in liquid nitrogen. Simultaneously, samples were extracted by thawing in room temperature water (~10 s), sonicating (5 min), vortexing (~30 s), snap freezing in liquid nitrogen (~1 min), thawing in room temperature water (~10 s), sonicating (5 min), and vortexing (~30 s) before incubating at -20 C for 1 h. Following incubation, samples were centrifuged at 20,000 g for 10 min at 4 C, and supernatant was transferred to LC-MS vials for analysis.

Chromatography:

Chromatography ID:	CH005126
Instrument Name:	Thermo Vanquish
Column Name:	HILICON iHILIC-(P) Classic (100 x 2.1mm,5um)
Column Temperature:	40
Flow Gradient:	0-0.5 min, 90% solvent B at 200 μL/min; 0.5-17.5 min, linear gradient from 90% solvent B to 45% solvent B at 200 μL/min; 17.5-19 min, from 45% solvent B to 30% solvent B at 200 μL/min; 19-19.5 min, held at 30% solvent B at 200 μL/min; 19.5-22 min, from 30% solvent B to 90% solvent B at 200 μL/min; 22-23 min, 90% solvent B at 400 μL/min; 23-31.5 min, held at 90% solvent B at 400 μL/min; 31.5-32.5 min, ramped down to 90% solvent B at 200 μL/min; 32.5-34 min, held at 90% solvent B at 200 μL/min
Flow Rate:	0-22 min, 200 μL/min; 22-31.5 min, 400 μL/min; 31.5-34 min, 200 μL/min
Solvent A:	95% water/5% acetonitrile; 20 mM ammonium acetate; 0.1% ammonium hydroxide; 5 μM medronic acid
Solvent B:	95% acetonitrile/5% water
Chromatography Type:	HILIC

Analysis:

Analysis ID:	AN006745
Analysis Type:	MS
Chromatography ID:	CH005126
Num Factors:	6
Num Metabolites:	36
Units:	Percent Labeling