Summary of Study ST002342

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001504. The data can be accessed directly via it's Project DOI: 10.21228/M88X2F This work is supported by NIH grant, U2C- DK119886.


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 IDST002342
Study TitleThe gut microbiome has sexually dimorphic effects on bone tissue energy metabolism and multiscale bone quality in C57BL/6J mice
Study SummaryMale and female germ-free and conventional were euthanized at 20 weeks of age, and various tissues were obtained to assess differences in bone properties associated with microbiome status and sex. For metabolomic analyses, the humeri was obtained, bone marrow was flushed using PBS, and subchondral bone metabolites were extracted using a methanol:acetone precipitation approach. Next, samples were injected, ionized, and data was acquired using LC-MS. Data was processed and converted using MSConvert and XCMS. Following this step, metabolic phenotypes of mice that differ by microbiome status and sex were investigated using MetaboAnalyst. Differences in metabolism were related to lipid, energy, and amino acid metabolism. Specifically, females, both conventional and germ-free, had dysregulated lipid metabolism, whereas, males, both conventional and germ-free had dysregulated amino acid metabolism. Other differences detected between male and female mice that differ by germ-free status corresponded to differences in bone strength, bone marrow adiposity, and osteocyte density.
Montana State University
DepartmentMechanical & Industrial Engineering, Chemistry & Biochemistry
Last NameWelhaven
First NameHope
AddressCulbertson Hall, 100
Submit Date2022-10-19
Num Groups4
Total Subjects33
Num Males17
Num Females16
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-11-28
Release Version1
Hope Welhaven Hope Welhaven application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR001504
Project DOI:doi: 10.21228/M88X2F
Project Title:Welhaven_Vahidi_JBMR
Project Summary:C57BL/6J male and female germ-free and conventional mice were housed at Montana State University and then used to study differences in bone associated with microbiome status and sex.
Institute:Montana State University
Last Name:Welhaven
First Name:Hope
Address:Culbertson Hall, 100
Funding Source:National Science Foundation (CMMI 1554708, CMMI 2120239) and the National Institutes of Health (NIAMS R01AR073964, NIGMS P20GM103474, NIH R03AG068680


Subject ID:SU002431
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57Bl/6
Age Or Age Range:20 weeks (at euthanasia)
Gender:Male and female
Animal Animal Supplier:Jackson Labratories
Animal Light Cycle:Standard light dark cycle
Animal Feed:PicoLab Rodent Diet 20, 20% protein


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

mb_sample_id local_sample_id Sex Microbiome Status
SA235201H33Female Control
SA235202H34Female Control
SA235203H35Female Control
SA235204H32Female Control
SA235205H27Female Control
SA235206H30Female Control
SA235207H29Female Control
SA235208H28Female Control
SA235209H36Female Control
SA235210H31Female Control
SA235211H18Female Germ-Free
SA235212H20Female Germ-Free
SA235213H3Female Germ-Free
SA235214H1Female Germ-Free
SA235215H19Female Germ-Free
SA235216H2Female Germ-Free
SA235217H5Male Control
SA235218H6Male Control
SA235219H4Male Control
SA235220H13Male Control
SA235221H7Male Control
SA235222H8Male Control
SA235223H11Male Control
SA235224H12Male Control
SA235225H9Male Control
SA235226H10Male Control
SA235227H17Male Germ-Free
SA235228H15Male Germ-Free
SA235229H14Male Germ-Free
SA235230H16Male Germ-Free
SA235231H21Male Germ-Free
SA235232H22Male Germ-Free
SA235233H23Male Germ-Free
Showing results 1 to 33 of 33


Collection ID:CO002424
Collection Summary:Samples were collected following mouse euthanasia. The humerus was obtained and bone marrow was flushed using PBS. Next, metabolites were extracted using methanol:acetone.
Sample Type:Bone


Treatment ID:TR002443
Treatment Summary:All C57Bl/6J mice (male, female, germ-free, conventional) were housed at Montana State University. During this time, mice were kept on a light/dark cycle and fed a standard chow diet ad libitum. Upon 20 weeks of age, mice were euthanized. No additional factors such as injury, diet, or exercise occurred. Mice were employed to analyze differences in bone at macro and micro levels that are associated with the microbiome and sex.

Sample Preparation:

Sampleprep ID:SP002437
Sampleprep Summary:Once euthanized, tissues were dissected and harvested for various techniques. For metabolomics, humeri samples underwent homogenization/crushing, extracted with methanol:acetone, and were then subjected to rounds of vortexing and centrifugation. Once metabolites were isolated, samples were dried via vacuum concentration and resuspended with acetonitrile:water for LC-MS analysis.

Combined analysis:

Analysis ID AN003826
Analysis type MS
Chromatography type HILIC
Chromatography system Agilent 1290
Column Cogent Diamond Hydride (150 × 2.1mm,4um)
MS instrument type Single quadrupole
MS instrument name Agilent 6538 QTOF
Units Peak Intensity


Chromatography ID:CH002831
Chromatography Summary:Samples were analyzed using an Agilent 1290 UPLC coupled to an Agilent 6538 QTOF. All samples were run in normal phase using a Cogent Diamond Hydride HILIC column (150 x 2.1 mm; 100Å pore size on a 4µm particle size). Solvents: 0.1% formic acid in water (A), 0.1% formic acid in acetonitrile (B). Elution gradient: 100 to 25% solvent B over 17 minutes, 0 to 70% solvent A over 20 minutes, at 21 minutes, B increases from 25% to 100% till 25 minutes while A decreases from 70% to 0% till 25 minutes. The last 4 minutes act as a wash. Total run time = 25 minute method (per sample)
Instrument Name:Agilent 1290
Column Name:Cogent Diamond Hydride (150 × 2.1mm,4um)
Flow Gradient:100 to 25% solvent B over 17 minutes, 0 to 70% solvent A over 20 minutes, at 21 minutes, B increases from 25% to 100% till 25 minutes while A decreases from 70% to 0% till 25 minutes. The last 4 minutes act as a wash.
Flow Rate:0.400 mL/min
Injection Temperature:4C
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Analytical Time:25 minutes
Chromatography Type:HILIC


MS ID:MS003568
Analysis ID:AN003826
Instrument Name:Agilent 6538 QTOF
Instrument Type:Single quadrupole
MS Comments:Data was acquired in positive mode following a 25-minute method. Following injection and acquisition, .d files were converted to .mzMLs using MSConvert (Threshold peak filter value = 1000; Peak picking = true, 1-1; 32-bit, no z-lib compression). Once .mzMLs were avaiable, XCMS was used (parameters reflected run parameters = positive mode, feature detection 15 ppm, adducts = [M+H]+, [M+Na]+