Summary of Study ST001756

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 PR001126. The data can be accessed directly via it's Project DOI: 10.21228/M8569X 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 IDST001756
Study TitleMetabolomics of mouse feces comparing GF and CONV-R mice
Study Typeuntargeted metabolomics
Study SummaryUsing high coverage metabolomics, we profiled feces, blood sera and cerebral cortical brain tissues of germ-free C57BL/6 mice and their age-matched conventionally raised counterparts. Results revealed for all three sample matrices metabolomic signatures owing to microbiota, yielding hundreds of identified metabolites including 533 altered for feces, 231 for sera and 58 for brain tissues with numerous significantly enriched pathways involving aromatic amino acids and neurotransmitters.
Institute
University of North Carolina at Chapel Hill
DepartmentDepartment of Environmental Sciences and Engineering
Last NameLai
First NameYunjia
Address1104 MHRC, 135 Dauer Dr., Chapel Hill, NC 27599
Emailyunjia.lai@outlook.com
Phone9194805489
Submit Date2021-04-26
Num Groups2
Total Subjects24
Num Males12
Num Females12
PublicationsNature Communications
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2021-07-26
Release Version1
Yunjia Lai Yunjia Lai
https://dx.doi.org/10.21228/M8569X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001126
Project DOI:doi: 10.21228/M8569X
Project Title:High-coverage metabolomics annotation uncovers microbiota-driven biochemical landscape of interorgan transport and gut-brain communication
Project Type:untargeted metabolomics
Project Summary:The mammalian gut harbors a complex and dynamic microbial ecosystem: the microbiota. While emerging studies support that microbiota regulates brain function with a few molecular cues suggested, the overall biochemical landscape of the “microbiota-gut-brain axis” remains largely unclear. Using high coverage metabolomics, we profiled feces, blood sera and cerebral cortical brain tissues of germ-free C57BL/6 mice and their age-matched conventionally raised counterparts. Results revealed for all three sample matrices metabolomic signatures owing to microbiota, yielding hundreds of identified metabolites including 533 altered for feces, 231 for sera and 58 for brain tissues with numerous significantly enriched pathways involving aromatic amino acids and neurotransmitters. Multicompartmental comparative analyses singled out microbiota-derived metabolites potentially implicated in interorgan transport and the gut-brain axis, exemplified by indoxyl sulfate and trimethylamine-N-oxide. Gender-specific characteristics of these landscapes were discussed. Our findings may be valuable for future research probing microbial influences on host metabolism and gut-brain communication.
Institute:University of North Carolina at Chapel Hill
Department:Department of Environmental Sciences and Engineering
Last Name:Lai
First Name:Yunjia
Address:1104 MHRC, 135 Dauer Dr., Chapel Hill, NC, 27599, USA
Email:yunjia.lai@outlook.com
Phone:9194805489
Funding Source:NIEHS

Subject:

Subject ID:SU001833
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6
Age Or Age Range:7-8 week old
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id Experimental factor
SA164002feces_Neg_CN_30A2B_MConventionally-raised (CONV-R)
SA164003feces_Neg_CN_30A2C_MConventionally-raised (CONV-R)
SA164004feces_Neg_CN_30A2A_MConventionally-raised (CONV-R)
SA164005feces_Neg_CN_30A1C_MConventionally-raised (CONV-R)
SA164006feces_Neg_CN_30A1B_MConventionally-raised (CONV-R)
SA164007feces_Neg_CN_9A1C_FConventionally-raised (CONV-R)
SA164008feces_Neg_CN_9A2A_FConventionally-raised (CONV-R)
SA164009feces_Neg_CN_9A2E_FConventionally-raised (CONV-R)
SA164010feces_Neg_CN_9A2D_FConventionally-raised (CONV-R)
SA164011feces_Neg_CN_9A2C_FConventionally-raised (CONV-R)
SA164012feces_Neg_CN_9A2B_FConventionally-raised (CONV-R)
SA164013feces_Pos_CN_30A1A_MConventionally-raised (CONV-R)
SA164014feces_Neg_CN_30A1A_MConventionally-raised (CONV-R)
SA164015feces_Pos_CN_9A2A_FConventionally-raised (CONV-R)
SA164016feces_Pos_CN_9A2B_FConventionally-raised (CONV-R)
SA164017feces_Pos_CN_9A2C_FConventionally-raised (CONV-R)
SA164018feces_Pos_CN_9A2D_FConventionally-raised (CONV-R)
SA164019feces_Pos_CN_30A2C_MConventionally-raised (CONV-R)
SA164020feces_Pos_CN_30A2B_MConventionally-raised (CONV-R)
SA164021feces_Pos_CN_30A1B_MConventionally-raised (CONV-R)
SA164022feces_Pos_CN_30A1C_MConventionally-raised (CONV-R)
SA164023feces_Pos_CN_30A2A_MConventionally-raised (CONV-R)
SA164024feces_Pos_CN_9A2E_FConventionally-raised (CONV-R)
SA164025feces_Pos_CN_9A1C_FConventionally-raised (CONV-R)
SA164026feces_Neg_GF_27F7Germ-free (GF)
SA164027feces_Neg_GF_27M1Germ-free (GF)
SA164028feces_Neg_GF_27F6Germ-free (GF)
SA164029feces_Neg_GF_27F5Germ-free (GF)
SA164030feces_Neg_GF_27F4Germ-free (GF)
SA164031feces_Neg_GF_27M2Germ-free (GF)
SA164032feces_Neg_GF_27M5Germ-free (GF)
SA164033feces_Pos_GF_27F5Germ-free (GF)
SA164034feces_Neg_GF_27M9Germ-free (GF)
SA164035feces_Neg_GF_27M8Germ-free (GF)
SA164036feces_Neg_GF_27M7Germ-free (GF)
SA164037feces_Neg_GF_27F3Germ-free (GF)
SA164038feces_Neg_GF_27F2Germ-free (GF)
SA164039feces_Pos_GF_27M7Germ-free (GF)
SA164040feces_Pos_GF_27M8Germ-free (GF)
SA164041feces_Pos_GF_27M9Germ-free (GF)
SA164042feces_Pos_GF_27F3Germ-free (GF)
SA164043feces_Pos_GF_27M5Germ-free (GF)
SA164044feces_Pos_GF_27F4Germ-free (GF)
SA164045feces_Pos_GF_27F6Germ-free (GF)
SA164046feces_Pos_GF_27F7Germ-free (GF)
SA164047feces_Pos_GF_27M1Germ-free (GF)
SA164048feces_Pos_GF_27M2Germ-free (GF)
SA164049feces_Pos_GF_27F2Germ-free (GF)
Showing results 1 to 48 of 48

Collection:

Collection ID:CO001826
Collection Summary:Prior to sacrifice and sample harvest, all mice were observed under their original housing conditions for one week; animals were not considered if they exhibited significant signs of serious injury or morbidity (e.g. malocclusion or fight wounds). Upon euthanization in CO2 chambers, feces, bulk brain, and heart blood sera were harvested, snap-frozen, and stored in -80 ºC freezer before analysis.
Sample Type:Feces
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001846
Treatment Summary:Steady states only: C57BL/6 mouse littermates of ~7 weeks old raised under GF and conventional conditions were age-matched upon selection for sacrifice and analyses, resulting in a final total of 24 mice, including 12 GF mice and 12 SPF CONV-R mice with 6 males and 6 females included in each. The animals were raised under the following conditions: 22ºC, 40-70% humidity, and a daily 12:12 hour light-dark cycle. For dietary administration, we consistently fed all mice the same purified (and sterile) standard rodent diets and provided tap water ad libitum.

Sample Preparation:

Sampleprep ID:SP001839
Sampleprep Summary:Fecal matter, blood sera, and brain tissues (of the cerebral cortical region) were aliquoted and extracted for metabolome analyses. To maximize coverage and throughput, extraction procedures were kept as simple and non-selective as can be.
Sampleprep Protocol Filename:Protocol_sample_extraction.docx

Combined analysis:

Analysis ID AN002860 AN002861
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak intensity (area) Peak intensity (area)

Chromatography:

Chromatography ID:CH002118
Chromatography Summary:UHPLC reverse phase C18 chromatography
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:40
Flow Gradient:2% B, 0-1 min; 2% to 15% B, 1-3 min; 15% to 50% B, 3-6 min; 50% to 98% B, 6-7.5 min; 98% B, 7.5-11.5 min; 98% to 2% B, 11.5-11.6 min; 2% B, 11.6-15 min
Flow Rate:0.4 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS002653
Analysis ID:AN002860
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:fullscan XCMS Online for data processing
Ion Mode:POSITIVE
  
MS ID:MS002654
Analysis ID:AN002861
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:fullscan XCMS Online for data processing
Ion Mode:NEGATIVE
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