Summary of Study ST003277

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 PR001952. The data can be accessed directly via it's Project DOI: 10.21228/M8DD95 This work is supported by NIH grant, U2C- DK119886.

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Study IDST003277
Study TitleLC-MS/MS spatial analysis of mouse GI
Study Summaryuntargeted metabolomic analysis of lumenal contents from AMX-treated and untreated mice
Institute
Brown University
Last NameBeekman
First NameChapman
AddressBMC 613, 171 Meeting Street, Providence RI 02912
EmailChapman_Beekman@brown.edu
Phone4012071832
Submit Date2024-01-17
Analysis Type DetailOther
Release Date2024-08-05
Release Version1
Chapman Beekman Chapman Beekman
https://dx.doi.org/10.21228/M8DD95
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001952
Project DOI:doi: 10.21228/M8DD95
Project Title:Spatial analysis of murine GI reveals role of small intestinal bile acid metabolism in amoxicillin-induced dysbiosis
Project Summary:Antibiotics cause collateral damage to resident microbes that is associated with various health risks. To-date, studies have largely focused on impacts of antibiotics on large intestinal and fecal microbiota. Here, we employ a GI-wide integrated multiomic approach to reveal that amoxicillin (AMX) treatment reduces overall bacterial abundance, bile salt hydrolase activity and unconjugated bile acids in the small intestine (SI). An accompanying loss of fatty acids and increase in acyl-carnitines in the large intestine corresponded with spatially-distinct expansions of proteobacteria. Parasutterella excrementihominis utilized fatty acid biosynthesis, becoming dominant in the SI while multiple Klebsiella species employed fatty acid oxidation during expansion in the large intestine. Depletion of bile acids and lipids may contribute to AMX-induced dysbiosis in the lower GI. To test this, we demonstrate that restoration of unconjugated bile acids can mitigate losses of commensals in the large intestine while also inhibiting the expansion of Proteobacteria during AMX treatment.
Institute:Brown University
Department:MMI
Laboratory:MMI, Belenky Lab
Last Name:Beekman
First Name:Chapman
Address:BMC 613, 171 Meeting Street, Providence RI 02912
Email:Chapman_Beekman@brown.edu
Phone:4012071832

Subject:

Subject ID:SU003397
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57/BL6
Animal Animal Supplier:JAX

Factors:

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

mb_sample_id local_sample_id Cage # Organ Treatment
SA354703A421 Blood Amox
SA354704A401 Blood Amox
SA354705A381 Blood Amox
SA354706A51 Cecum Amox
SA354707A111 Cecum Amox
SA354708A171 Cecum Amox
SA354709A181 Colon Amox
SA354710A61 Colon Amox
SA354711A121 Colon Amox
SA354712A101 DSI Amox
SA354713A41 DSI Amox
SA354714A161 DSI Amox
SA354715A371 Liver Amox
SA354716A411 Liver Amox
SA354717A391 Liver Amox
SA354718A91 MSI Amox
SA354719A151 MSI Amox
SA354720A31 MSI Amox
SA354721A81 PSI Amox
SA354722A21 PSI Amox
SA354723A141 PSI Amox
SA354724A11 Stomach Amox
SA354725A131 Stomach Amox
SA354726A71 Stomach Amox
SA354727A482 Blood Amox
SA354728A462 Blood Amox
SA354729A442 Blood Amox
SA354730A292 Cecum Amox
SA354731A352 Cecum Amox
SA354732A232 Cecum Amox
SA354733A242 Colon Amox
SA354734A302 Colon Amox
SA354735A362 Colon Amox
SA354736A282 DSI Amox
SA354737A342 DSI Amox
SA354738A222 DSI Amox
SA354739A472 Liver Amox
SA354740A452 Liver Amox
SA354741A432 Liver Amox
SA354742A212 MSI Amox
SA354743A332 MSI Amox
SA354744A272 MSI Amox
SA354745A322 PSI Amox
SA354746A262 PSI Amox
SA354747A202 PSI Amox
SA354748A192 Stomach Amox
SA354749A312 Stomach Amox
SA354750A252 Stomach Amox
SA354751C53 Cecum Control
SA354752C173 Cecum Control
SA354753C113 Cecum Control
SA354754C63 Colon Control
SA354755C183 Colon Control
SA354756C123 Colon Control
SA354757C43 DSI Control
SA354758C163 DSI Control
SA354759C103 DSI Control
SA354760C153 MSI Control
SA354761C93 MSI Control
SA354762C33 MSI Control
SA354763C143 PSI Control
SA354764C83 PSI Control
SA354765C23 PSI Control
SA354766C133 Stomach Control
SA354767C73 Stomach Control
SA354768C13 Stomach Control
SA354769C354 Cecum Control
SA354770C234 Cecum Control
SA354771C294 Cecum Control
SA354772C244 Colon Control
SA354773C304 Colon Control
SA354774C364 Colon Control
SA354775C284 DSI Control
SA354776C224 DSI Control
SA354777C344 DSI Control
SA354778C214 MSI Control
SA354779C274 MSI Control
SA354780C334 MSI Control
SA354781C264 PSI Control
SA354782C204 PSI Control
SA354783C324 PSI Control
SA354784C194 Stomach Control
SA354785C314 Stomach Control
SA354786C254 Stomach Control
Showing results 1 to 84 of 84

Collection:

Collection ID:CO003390
Collection Summary:Lumenal contents collected from multiple GI sites and immediately flash frozen
Sample Type:Intestine

Treatment:

Treatment ID:TR003406
Treatment Summary:Mice were treated for 24h with amoxicillin/vehicle in drinking water
Treatment Compound:Amoxicillin
Treatment Route:oral

Sample Preparation:

Sampleprep ID:SP003404
Sampleprep Summary:Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis

Combined analysis:

Analysis ID AN005365 AN005366 AN005367 AN005368
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase HILIC
Chromatography system Waters Acquity Waters Acquity Waters Acquity Waters Acquity
Column Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE NEGATIVE
Units normalized imputed data normalized imputed data normalized imputed data normalized imputed data

Chromatography:

Chromatography ID:CH004064
Chromatography Summary:Low pH polar (LC/MS Pos early)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 5% B to 80% B over 3.35 minutes
Flow Rate:0.35 mL/min
Solvent A:100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Solvent B:100% methanol; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Chromatography Type:Reversed phase
  
Chromatography ID:CH004065
Chromatography Summary:Low pH Lipophilic (LC/MS Pos late)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes.
Flow Rate:0.60 mL/min
Solvent A:100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Solvent B:50% methanol/50% acetonitrile; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Chromatography Type:Reversed phase
  
Chromatography ID:CH004066
Chromatography Summary:High pH (LC/MS Neg)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99% B in 0.5 minutes.
Flow Rate:0.35 mL/min
Solvent A:100% water; 6.5 mM ammonium bicarbonate, pH 8
Solvent B:95% methanol/5% water; 6.5 mM ammonium bicarbonate
Chromatography Type:Reversed phase
  
Chromatography ID:CH004067
Chromatography Summary:HILIC (LC/MS Polar Neg)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes.
Flow Rate:0.50 mL/min
Solvent A:15% water/5% methanol/80% acetonitrile; 10 mM ammonium formate, (effective pH 10.16 with NH4OH)
Solvent B:50% water/50% acetonitrile; 10 mM ammonium formate, (effective pH 10.60 with NH4OH)
Chromatography Type:HILIC

MS:

MS ID:MS005094
Analysis ID:AN005365
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolon (LC/MS Pos early)
Ion Mode:POSITIVE
  
MS ID:MS005095
Analysis ID:AN005366
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolon (LC/MS Pos late)
Ion Mode:POSITIVE
  
MS ID:MS005096
Analysis ID:AN005367
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolon (LC/MS Neg)
Ion Mode:NEGATIVE
  
MS ID:MS005097
Analysis ID:AN005368
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolon (LC/MS Polar)
Ion Mode:NEGATIVE
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