Summary of Study ST004074

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.

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Study IDST004074
Study TitleMetabolite Pools in Adult Zebrafish Treated with Antimicrobials or Control
Study SummaryTo examine alterations to metabolism as a result of gut microbiota depletion, we exposed adult zebrafish to treatment with antimicrobials or untreated control and analyzed systemic metabolite pools. We identified various changes in tissues across the fish, including in the brain, eye, fin, heart, intestine, liver, muscle, and serum.
Institute
Washington University in St. Louis
Last NameJackstadt
First NameMadelyn
AddressOne Brookings Drive, St. Louis, Missouri, 63130, USA
Emailmjackstadt@wustl.edu
Phone3149356405
Submit Date2025-07-01
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-10-28
Release Version1
Madelyn Jackstadt Madelyn Jackstadt
https://dx.doi.org/10.21228/M84C32
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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:SU004220
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
SA473060Neg_Anti_2_BrainAntimicrobials Brain
SA473061Pos_Anti_10_BrainAntimicrobials Brain
SA473062Pos_Anti_9_BrainAntimicrobials Brain
SA473063Pos_Anti_8_BrainAntimicrobials Brain
SA473064Pos_Anti_7_BrainAntimicrobials Brain
SA473065Pos_Anti_6_BrainAntimicrobials Brain
SA473066Pos_Anti_5_BrainAntimicrobials Brain
SA473067Pos_Anti_4_BrainAntimicrobials Brain
SA473068Pos_Anti_3_BrainAntimicrobials Brain
SA473069Pos_Anti_2_BrainAntimicrobials Brain
SA473070Pos_Anti_1_BrainAntimicrobials Brain
SA473071Neg_Anti_1_BrainAntimicrobials Brain
SA473072Neg_Anti_6_BrainAntimicrobials Brain
SA473073Neg_Anti_5_BrainAntimicrobials Brain
SA473074Neg_Anti_10_BrainAntimicrobials Brain
SA473075Neg_Anti_9_BrainAntimicrobials Brain
SA473076Neg_Anti_8_BrainAntimicrobials Brain
SA473077Neg_Anti_7_BrainAntimicrobials Brain
SA473078Neg_Anti_4_BrainAntimicrobials Brain
SA473079Neg_Anti_3_BrainAntimicrobials Brain
SA473080Pos_Anti_10_EyeAntimicrobials Eye
SA473081Pos_Anti_6_EyeAntimicrobials Eye
SA473082Pos_Anti_7_EyeAntimicrobials Eye
SA473083Pos_Anti_5_EyeAntimicrobials Eye
SA473084Pos_Anti_4_EyeAntimicrobials Eye
SA473085Pos_Anti_3_EyeAntimicrobials Eye
SA473086Pos_Anti_2_EyeAntimicrobials Eye
SA473087Pos_Anti_8_EyeAntimicrobials Eye
SA473088Pos_Anti_9_EyeAntimicrobials Eye
SA473089Pos_Anti_1_EyeAntimicrobials Eye
SA473090Neg_Anti_8_EyeAntimicrobials Eye
SA473091Neg_Anti_7_EyeAntimicrobials Eye
SA473092Neg_Anti_5_EyeAntimicrobials Eye
SA473093Neg_Anti_4_EyeAntimicrobials Eye
SA473094Neg_Anti_9_EyeAntimicrobials Eye
SA473095Neg_Anti_10_EyeAntimicrobials Eye
SA473096Neg_Anti_6_EyeAntimicrobials Eye
SA473097Neg_Anti_2_EyeAntimicrobials Eye
SA473098Neg_Anti_3_EyeAntimicrobials Eye
SA473099Neg_Anti_1_EyeAntimicrobials Eye
SA473100Pos_Anti_9_FinAntimicrobials Fin
SA473101Pos_Anti_3_FinAntimicrobials Fin
SA473102Pos_Anti_5_FinAntimicrobials Fin
SA473103Pos_Anti_2_FinAntimicrobials Fin
SA473104Pos_Anti_1_FinAntimicrobials Fin
SA473105Pos_Anti_6_FinAntimicrobials Fin
SA473106Pos_Anti_8_FinAntimicrobials Fin
SA473107Pos_Anti_10_FinAntimicrobials Fin
SA473108Pos_Anti_4_FinAntimicrobials Fin
SA473109Neg_Anti_10_FinAntimicrobials Fin
SA473110Neg_Anti_9_FinAntimicrobials Fin
SA473111Neg_Anti_1_FinAntimicrobials Fin
SA473112Neg_Anti_2_FinAntimicrobials Fin
SA473113Neg_Anti_3_FinAntimicrobials Fin
SA473114Neg_Anti_4_FinAntimicrobials Fin
SA473115Pos_Anti_7_FinAntimicrobials Fin
SA473116Neg_Anti_5_FinAntimicrobials Fin
SA473117Neg_Anti_6_FinAntimicrobials Fin
SA473118Neg_Anti_7_FinAntimicrobials Fin
SA473119Neg_Anti_8_FinAntimicrobials Fin
SA473120Pos_Anti_3_HeartAntimicrobials Heart
SA473121Pos_Anti_4_HeartAntimicrobials Heart
SA473122Pos_Anti_5_HeartAntimicrobials Heart
SA473123Pos_Anti_7_HeartAntimicrobials Heart
SA473124Pos_Anti_8_HeartAntimicrobials Heart
SA473125Pos_Anti_9_HeartAntimicrobials Heart
SA473126Pos_Anti_10_HeartAntimicrobials Heart
SA473127Pos_Anti_1_HeartAntimicrobials Heart
SA473128Pos_Anti_6_HeartAntimicrobials Heart
SA473129Neg_Anti_4_HeartAntimicrobials Heart
SA473130Neg_Anti_10_HeartAntimicrobials Heart
SA473131Neg_Anti_9_HeartAntimicrobials Heart
SA473132Neg_Anti_8_HeartAntimicrobials Heart
SA473133Neg_Anti_7_HeartAntimicrobials Heart
SA473134Neg_Anti_6_HeartAntimicrobials Heart
SA473135Neg_Anti_5_HeartAntimicrobials Heart
SA473136Pos_Anti_2_HeartAntimicrobials Heart
SA473137Neg_Anti_3_HeartAntimicrobials Heart
SA473138Neg_Anti_2_HeartAntimicrobials Heart
SA473139Neg_Anti_1_HeartAntimicrobials Heart
SA473140Pos_Anti_2_IntestineAntimicrobials Intestine
SA473141Pos_Anti_1_IntestineAntimicrobials Intestine
SA473142Pos_Anti_5_IntestineAntimicrobials Intestine
SA473143Pos_Anti_6_IntestineAntimicrobials Intestine
SA473144Pos_Anti_7_IntestineAntimicrobials Intestine
SA473145Pos_Anti_8_IntestineAntimicrobials Intestine
SA473146Pos_Anti_9_IntestineAntimicrobials Intestine
SA473147Pos_Anti_10_IntestineAntimicrobials Intestine
SA473148Neg_Anti_10_IntestineAntimicrobials Intestine
SA473149Neg_Anti_9_IntestineAntimicrobials Intestine
SA473150Neg_Anti_8_IntestineAntimicrobials Intestine
SA473151Neg_Anti_7_IntestineAntimicrobials Intestine
SA473152Neg_Anti_6_IntestineAntimicrobials Intestine
SA473153Neg_Anti_5_IntestineAntimicrobials Intestine
SA473154Neg_Anti_4_IntestineAntimicrobials Intestine
SA473155Neg_Anti_3_IntestineAntimicrobials Intestine
SA473156Neg_Anti_2_IntestineAntimicrobials Intestine
SA473157Neg_Anti_1_IntestineAntimicrobials Intestine
SA473158Pos_Anti_3_IntestineAntimicrobials Intestine
SA473159Pos_Anti_4_IntestineAntimicrobials Intestine
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 288

Collection:

Collection ID:CO004213
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:brain, eye, fin, heart, intestine, liver, muscle, serum

Treatment:

Treatment ID:TR004229
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.

Sample Preparation:

Sampleprep ID:SP004226
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:CH005125
Instrument Name:Thermo Dionex
Column Name:HILICON iHILIC-(P) Classic (100 x 2.1mm,5um)
Column Temperature:40
Flow Gradient:0-1 min, 90% solvent B at 250 μL/min; 1-13 min, linear gradient from 90% solvent B to 30% solvent B at 250 μL/min; 13-14 min, held at 30% solvent B at 250 μL/min; 14-14.5 min, 30% solvent B at 150 μL/min; 14.5-15 min, 10% solvent B at 150 μL/min; 15-17 min, held at 10% solvent B at 150 μL/min; 17-17.5 min, 90% solvent B at 150 μL/min; 17.5-18 min, 90% solvent B at 150 μL/min; 18- 18.5 min, ramped to 90% solvent B at 250 μL/min; 18.5-19 min, held at 90% solvent B at 250 μL/min; 19-19.5 min, 90% solvent B at 400 μL/min; 19.5-23.5 min, held at 90% solvent B at 400 μL/min; 23.5-24 min, 90% solvent B at 250 μL/min; 24-25 min, held at 90% solvent B at 250 μL/min.
Flow Rate:0-14 min, 250 μL/min; 14-18 min, 150 μL/min; 18-19 min, 250 μL/min; 19-23.5 min, 400 μL/min; 23.5-25 min, 250 μL/min.
Solvent A:95% water/5% acetonitrile; 20 mM ammonium bicarbonate; 0.1% ammonium hydroxide; 2.5 μM medronic acid
Solvent B:95% acetonitrile/5% water; 2.5 μM medronic acid
Chromatography Type:HILIC

Analysis:

Analysis ID:AN006743
Analysis Type:MS
Chromatography ID:CH005125
Num Factors:16
Num Metabolites:172
Units:Peak Areas
  
Analysis ID:AN006744
Analysis Type:MS
Chromatography ID:CH005125
Num Factors:16
Num Metabolites:42
Units:Peak Areas
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