Summary of Study ST004181

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 PR002637. The data can be accessed directly via it's Project DOI: 10.21228/M8SK0W 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 IDST004181
Study TitleThe Ability of Dietary Polyunsaturated Fatty Acids to Protect Against Liver Inflammation and Non-Alcoholic Steatohepatitis (NASH) is Dependent on Gut Microbes
Study SummaryTo test the hypothesis that the ability of dietary PUFAs to suppress NASH and cardiometabolic diseases is dependent on microbe-host co-metabolism of lipids, we fed either conventionally raised or germ-free C57BL6/N mice six sterile diets with well-defined levels of either saturated monounsaturated, ω6 PUFAs, or ω3 PUFAs and comprehensively examined the diet-microbe-host interactions as they relate to NAFLD progression. Compared to a SFA control diet (palm oil with lard), which effectively promoted obesity and NASH, both ω6 (borage oil) and ω3 PUFAs (fish oil) reduced body weight and liver weight in conventional, but not germ-free mice. Furthermore, the ability of dietary SFA, MUFA, and PUFAs to uniquely alter the hepatic lipidome was clearly altered in germ-free versus conventional mice. Of particular interest, the ability of dietary ω3 PUFAs to increase certain species of pro-resolving lipid mediators in the liver was prevented in germ-free mice. Collectively, this study provides a comprehensive lipidomic analysis defining unique dietary fatty acid-microbe-host interactions and have uncovered new insights into how meta-organismal metabolism impacts liver diseases and metabolic disorders.
Institute
Cleveland Clinic
DepartmentCardiovascular and Metabolic Sciences
LaboratoryBrown Lab
Last NameBrown
First NameJ. Mark
Address9500 Euclid Avenue, Cleveland, Ohio, 44196, USA
Emailbrownm5@ccf.org
Phone+1 216 444 8340
Submit Date2025-08-25
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-09-28
Release Version1
J. Mark Brown J. Mark Brown
https://dx.doi.org/10.21228/M8SK0W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002637
Project DOI:doi: 10.21228/M8SK0W
Project Title:The Ability of Dietary Polyunsaturated Fatty Acids to Protect Against Liver Inflammation and Non-Alcoholic Steatohepatitis (NASH) is Dependent on Gut Microbes
Project Summary:Non-alcoholic steatohepatitis (NASH) is a rapidly expanding form of liver disease associated with increased risk of cardiometabolic pathologies. Several clinical trials have shown that dietary ω3 polyunsaturated fatty acid (PUFA) supplementation, in particular eicosapentaenoic acid (EPA, 20:5,ω3) and docosahexaenoic acid (DHA, 22:6,ω3), improves health outcomes in NASH patients and lowers cardiovascular diseases. It is shown that ω3 PUFAs can suppress hepatic lipogenesis, resolve hepatic inflammation, and lower plasma triglycerides by reducing the production of hepatic very low-density lipoprotein. In parallel, there is emerging evidence that the gut microbiome can powerfully impact NASH via similar mechanisms. Although dietary PUFA supplementation can strongly impact host lipid metabolic pathways in the liver, it is often overlooked that gut microbiota can also synthesize and degrade diverse lipids. Here, we hypothesized that the ability of dietary PUFAs to suppress NASH and cardiometabolic diseases is dependent on microbe-host co-metabolism of lipids. This study provides a comprehensive lipidomic analysis defining unique dietary fatty acid-microbe-host interactions and have uncovered new insights into how meta-organismal metabolism impacts liver diseases and metabolic disorders.
Institute:Cleveland Clinic
Department:Cardiovascular and Metabolic Sciences
Laboratory:Brown Lab
Last Name:Brown
First Name:J. Mark
Address:9500 Euclid Avenue, Cleveland, Ohio, 44196, USA
Email:brownm5@ccf.org
Phone:216 444 8340

Subject:

Subject ID:SU004332
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 Genotype Treatment
SA4825406502C48LIVER GF BORAGE
SA4825416497C47LIVER GF BORAGE
SA4825426502HIL48LIVER GF BORAGE
SA4825436497HIL47LIVER GF BORAGE
SA4825446496HIL46LIVER GF BORAGE
SA4825456503HIL45LIVER GF BORAGE
SA4825466495HIL44LIVER GF BORAGE
SA4825476495C44LIVER GF BORAGE
SA4825486503C45LIVER GF BORAGE
SA4825496496C46LIVER GF BORAGE
SA4825506517HIL39LIVER GF ECHIUM
SA4825516507C40LIVER GF ECHIUM
SA4825526517C39LIVER GF ECHIUM
SA4825536514C43LIVER GF ECHIUM
SA4825546514HIL43LIVER GF ECHIUM
SA4825556507HIL40LIVER GF ECHIUM
SA4825566516HIL41LIVER GF ECHIUM
SA4825576515HIL42LIVER GF ECHIUM
SA4825586515C42LIVER GF ECHIUM
SA4825596516C41LIVER GF ECHIUM
SA4825606525C54LIVER GF FISH
SA4825616519C55LIVER GF FISH
SA4825626521C56LIVER GF FISH
SA4825636526C57LIVER GF FISH
SA4825646528C58LIVER GF FISH
SA4825656525HIL54LIVER GF FISH
SA4825666519HIL55LIVER GF FISH
SA4825676521HIL56LIVER GF FISH
SA4825686526HIL57LIVER GF FISH
SA4825696528HIL58LIVER GF FISH
SA4825706534HIL63LIVER GF HLS
SA4825716532HIL62LIVER GF HLS
SA4825726533HIL61LIVER GF HLS
SA4825736534C63LIVER GF HLS
SA4825746532C62LIVER GF HLS
SA4825756533C61LIVER GF HLS
SA4825766539C60LIVER GF HLS
SA4825776530C59LIVER GF HLS
SA4825786539HIL60LIVER GF HLS
SA4825796530HIL59LIVER GF HLS
SA4825806544C53LIVER GF HOS
SA4825816549HIL50LIVER GF HOS
SA4825826542C51LIVER GF HOS
SA4825836549C50LIVER GF HOS
SA4825846551C49LIVER GF HOS
SA4825856553C52LIVER GF HOS
SA4825866551HIL49LIVER GF HOS
SA4825876544HIL53LIVER GF HOS
SA4825886553HIL52LIVER GF HOS
SA4825896542HIL51LIVER GF HOS
SA4825906488HIL64LIVER GF PALM
SA4825916482HIL65LIVER GF PALM
SA4825926487HIL66LIVER GF PALM
SA4825936483HIL67LIVER GF PALM
SA4825946492HIL68LIVER GF PALM
SA4825956492C68LIVER GF PALM
SA4825966483C67LIVER GF PALM
SA4825976487C66LIVER GF PALM
SA4825986482C65LIVER GF PALM
SA4825996488C64LIVER GF PALM
SA4826006425C38LIVER MPF BORAGE
SA4826016424C34LIVER MPF BORAGE
SA4826026431HIL36LIVER MPF BORAGE
SA4826036427HIL37LIVER MPF BORAGE
SA4826046425HIL38LIVER MPF BORAGE
SA4826056429HIL35LIVER MPF BORAGE
SA4826066429C35LIVER MPF BORAGE
SA4826076431C36LIVER MPF BORAGE
SA4826086427C37LIVER MPF BORAGE
SA4826096424HIL34LIVER MPF BORAGE
SA4826106438C31LIVER MPF ECHIUM
SA4826116435C32LIVER MPF ECHIUM
SA4826126442C33LIVER MPF ECHIUM
SA4826136437C29LIVER MPF ECHIUM
SA4826146441C30LIVER MPF ECHIUM
SA4826156437HIL29LIVER MPF ECHIUM
SA4826166442HIL33LIVER MPF ECHIUM
SA4826176438HIL31LIVER MPF ECHIUM
SA4826186441HIL30LIVER MPF ECHIUM
SA4826196435HIL32LIVER MPF ECHIUM
SA4826206453C28LIVER MPF FISH
SA4826216451C23LIVER MPF FISH
SA4826226454C24LIVER MPF FISH
SA4826236450C25LIVER MPF FISH
SA4826246449C27LIVER MPF FISH
SA4826256455C26LIVER MPF FISH
SA4826266451HIL23LIVER MPF FISH
SA4826276454HIL24LIVER MPF FISH
SA4826286450HIL25LIVER MPF FISH
SA4826296455HIL26LIVER MPF FISH
SA4826306449HIL27LIVER MPF FISH
SA4826316453HIL28LIVER MPF FISH
SA4826326458HIL69LIVER MPF HLS
SA4826336464HIL70LIVER MPF HLS
SA4826346469C73LIVER MPF HLS
SA4826356459C72LIVER MPF HLS
SA4826366466C71LIVER MPF HLS
SA4826376464C70LIVER MPF HLS
SA4826386466HIL71LIVER MPF HLS
SA4826396459HIL72LIVER MPF HLS
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Collection:

Collection ID:CO004325
Collection Summary:We fed age-matched male C57BL6/N mice either without (germ-free) or with gut microbes (specific-pathogen-free, SPF), 6 diets with varying saturated versus monounsaturated versus polyunsaturated diets for a period of 18 weeks. Following experimental feeding, liver samples were collected to examine the ability of gut microbes to influence the effects of dietary fatty acids on obesity-related metabolic disturbance.
Sample Type:Liver

Treatment:

Treatment ID:TR004341
Treatment Summary:Conventionally raised or germ-free C57BL6/N mice were fed with six sterile diets (palm, borage, fish, echium, high linoleic safflower, high oleic safflower) with well-defined levels of either saturated monounsaturated, ω6 PUFAs, or ω3 PUFAs and these were used to comprehensively examined diet-microbe-host interactions as they relate to NAFLD progression.

Sample Preparation:

Sampleprep ID:SP004338
Sampleprep Summary:Sixty one liver samples were prepared for untargeted metabolomics. . In brief, tissues were initially thawed on ice. About 50mg were cut and placed into 1.5mL MPbio lysing matrix D tubes. 600 µL of chilled 70% methanol/20%water/10% chloroform containing 50 µM heavy-labeled internal standards (Table 1) were pipetted into each tube and homogenized using 6x3mm Zirconium beads 3x at high speed (4000 rpm) in 30 second intervals with rest on ice. Bead containing blank tubes with no tissue were also set up as quality check and treated similarly as samples. Both blank and tissue tubes were homogenized. Homogenates were then vortexed for 10 seconds and kept on ice for 5 minutes (x2) followed by centrifugation at 10,000xg for 15 min at 4°C. The supernatants were dried overnight in a speed vacuum and dried extracts were re-suspended in 95:5 water/acetonitrile (%v/v) and normalized based on dilution to control for different tissue weights. Each sample was then randomized and subjected to LC-MS analysis. 2 µL from each sample was taken and pooled and this pooled QC sample was analyzed every 5th injection.
Processing Storage Conditions:On ice
Extract Storage:-80℃
Sample Resuspension:95:5 water/acetonitrile (%v/v)

Chromatography:

Chromatography ID:CH005269
Instrument Name:Thermo Vanquish
Column Name:Thermo Accucore C18 (100 x 2.1 mm, 2.6 µm)
Column Temperature:60℃
Flow Gradient:0.2-1 min:5%B; 1-8 min :15%B; 8-10 min:95%B; 10-12 min:95%B; 12-15 min:5%B
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
  
Chromatography ID:CH005270
Instrument Name:Thermo Vanquish
Column Name:Waters XBridge BEH Amide Column (150 x 2.1 mm, 2.5 µm
Column Temperature:60℃
Flow Gradient:0-2 min:70%B; 2-4 min :60%B; 4-5.5 min:60%B; 5.5-10.5 min:50%B; 10.5-11.5 min:50%B;11.5-12 min:100%B; 12-16 min:100%B
Flow Rate:0.2 mL/min
Solvent A:100% Water; 10 mM ammonium acetate; 0.125% acetic acid
Solvent B:95% acetonitrile/5% Water; 10 mM ammonium acetate; 0.125% acetic acid
Chromatography Type:HILIC

Analysis:

Analysis ID:AN006940
Laboratory Name:Cleveland Clinic LRI Metabolomics Core
Analysis Type:MS
Chromatography ID:CH005269
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST004181_AN006940_Results.txt
Units:Peak abundance
  
Analysis ID:AN006941
Laboratory Name:Cleveland Clinic LRI Metabolomics Core
Analysis Type:MS
Chromatography ID:CH005269
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST004181_AN006941_Results.txt
Units:Peak abundance
  
Analysis ID:AN006942
Laboratory Name:Cleveland Clinic LRI Metabolomics Core
Analysis Type:MS
Chromatography ID:CH005270
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST004181_AN006942_Results.txt
Units:Peak abundance
  
Analysis ID:AN006943
Laboratory Name:Cleveland Clinic LRI Metabolomics Core
Analysis Type:MS
Chromatography ID:CH005270
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST004181_AN006943_Results.txt
Units:Peak abundance
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