Summary of Study ST000547

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 PR000401. The data can be accessed directly via it's Project DOI: 10.21228/M8701F This work is supported by NIH grant, U2C- DK119886.

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Study IDST000547
Study TitleIntergenerational murine gut microbiome variation
Study TypeIntergenerational
Study SummaryInbred mice are used to investigate many aspects of human physiology, including susceptibility to disease and response to therapies. Despite increasing evidence that the composition and function of the murine intestinal microbiota can substantially influence a broad range of experimental outcomes, relatively little is known about microbiome dynamics within experimental mouse populations. We investigated changes in the intestinal microbiome between C57BL/6J mice spanning six generations (assessed at generations 1, 2, 3 and 6), following their introduction to a stringently controlled facility. Faecal microbiota composition and function were assessed by 16S rRNA gene amplicon sequencing and liquid chromatography mass spectrometry, respectively. Significant divergence of the intestinal microbiota between founder and second generation mice, as well as continuing inter-generational variance, was observed. Bacterial taxa whose relative abundance changed significantly included Akkermansia, Turicibacter and Bifidobacterium (p< 0.05), all of which are recognised as having the potential to substantially influence host physiology. Shifts in microbiota composition were mirrored by corresponding differences in the faecal metabolome (r=0.57, p=0.0001), with notable differences in levels of tryptophan pathway metabolites and amino acids, including glutamine, glutamate and aspartate. The magnitude of these changes in the intestinal microbiota and metabolome characteristics during acclimation were on a scale with those observed between populations housed in separate facilities, which differed in regards to husbandry, barrier conditions and dietary intake. The microbiome variance reported here has major implications for experimental reproducibility, and as a consequence, experimental design and the interpretation of research outcomes across as wide range of contexts.
Institute
South Australian Health and Medical Research Institute
DepartmentInfection and Immunity Theme
Last NameRogers
First NameGeraint
AddressSAHMRI, North Terrace, Adelaide, SA 5000, Australia
EmailGeraint.rogers@sahmri.com
PhoneN/A
Submit Date2016-12-22
Num Groups4
Total Subjects82
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2018-02-07
Release Version1
Geraint Rogers Geraint Rogers
https://dx.doi.org/10.21228/M8701F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000401
Project DOI:doi: 10.21228/M8701F
Project Title:Intergenerational murine gut microbiome variation
Project Type:untargeted metabolomics
Project Summary:Inbred mice are used to investigate many aspects of human physiology, including susceptibility to disease and response to therapies. Despite increasing evidence that the composition and function of the murine intestinal microbiota can substantially influence a broad range of experimental outcomes, relatively little is known about microbiome dynamics within experimental mouse populations. We investigated changes in the intestinal microbiome between C57BL/6J mice spanning six generations (assessed at generations 1, 2, 3 and 6), following their introduction to a stringently controlled facility. Faecal microbiota composition and function were assessed by 16S rRNA gene amplicon sequencing and liquid chromatography mass spectrometry, respectively. Significant divergence of the intestinal microbiota between founder and second generation mice, as well as continuing inter-generational variance, was observed. Bacterial taxa whose relative abundance changed significantly included Akkermansia, Turicibacter and Bifidobacterium (p< 0.05), all of which are recognised as having the potential to substantially influence host physiology. Shifts in microbiota composition were mirrored by corresponding differences in the faecal metabolome (r=0.57, p=0.0001), with notable differences in levels of tryptophan pathway metabolites and amino acids, including glutamine, glutamate and aspartate. The magnitude of these changes in the intestinal microbiota and metabolome characteristics during acclimation were on a scale with those observed between populations housed in separate facilities, which differed in regards to husbandry, barrier conditions and dietary intake. The microbiome variance reported here has major implications for experimental reproducibility, and as a consequence, experimental design and the interpretation of research outcomes across as wide range of contexts.
Institute:South Australian Health and Medical Research Institute
Department:Infection and Immunity Theme
Last Name:Choo
First Name:Jocelyn
Address:SAHMRI, North Terrace, Adelaide, SA 5000, Australia
Email:Jocelyn.choo@sahmri.com
Phone:N/A

Subject:

Subject ID:SU000569
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Generation Gender
SA028158SG161st Gen F
SA028159SG141st Gen F
SA028160SG131st Gen F
SA028161SG171st Gen F
SA028162SG181st Gen F
SA028163SG11st Gen F
SA028164SG191st Gen F
SA028165SG121st Gen F
SA028166SG151st Gen F
SA028167SG41st Gen F
SA028168SG31st Gen F
SA028169SG21st Gen F
SA028170SG111st Gen M
SA028171SG1091st Gen M
SA028172SG1121st Gen M
SA028173SG1111st Gen M
SA028174SG1101st Gen M
SA028175SG1081st Gen M
SA028176SG51st Gen M
SA028177SG101st Gen M
SA028178SG81st Gen M
SA028179SG91st Gen M
SA028180SG61st Gen M
SA028181SG71st Gen M
SA028182SG1632nd Gen F
SA028183SG1662nd Gen F
SA028184SG1682nd Gen F
SA028185SG1622nd Gen F
SA028186SG1672nd Gen F
SA028187SG1582nd Gen F
SA028188SG1602nd Gen F
SA028189SG1562nd Gen F
SA028190SG1592nd Gen M
SA028191SG1612nd Gen M
SA028192SG1572nd Gen M
SA028193SG1702nd Gen M
SA028194SG1913rd Gen F
SA028195SG1903rd Gen F
SA028196SG1873rd Gen F
SA028197SG1843rd Gen F
SA028198SG1833rd Gen F
SA028199SG1773rd Gen F
SA028200SG1883rd Gen F
SA028201SG1743rd Gen F
SA028202SG1713rd Gen F
SA028203SG1763rd Gen F
SA028204SG1723rd Gen F
SA028205SG1653rd Gen F
SA028206SG1753rd Gen F
SA028207SG1863rd Gen M
SA028208SG1893rd Gen M
SA028209SG1923rd Gen M
SA028210SG1733rd Gen M
SA028211SG1783rd Gen M
SA028212SG1853rd Gen M
SA028213SG1643rd Gen M
SA028214SG1793rd Gen M
SA028215SG1693rd Gen M
SA028216SG1803rd Gen M
SA028217SG1823rd Gen M
SA028218SG1813rd Gen M
SA028219SG2226th Gen F
SA028220SG2216th Gen F
SA028221SG2236th Gen F
SA028222SG2256th Gen F
SA028223SG2316th Gen F
SA028224SG2246th Gen F
SA028225SG2366th Gen F
SA028226SG2376th Gen F
SA028227SG2386th Gen F
SA028228SG2326th Gen F
SA028229SG2356th Gen F
SA028230SG2346th Gen F
SA028231SG2336th Gen F
SA028232SG2146th Gen M
SA028233SG2036th Gen M
SA028234SG2026th Gen M
SA028235SG2046th Gen M
SA028236SG2056th Gen M
SA028237SG2076th Gen M
SA028238SG2066th Gen M
SA028239SG2086th Gen M
Showing results 1 to 82 of 82

Collection:

Collection ID:CO000563
Collection Summary:Fresh faecal pellets were collected homogenised in PBS, centrifuged. Supernatant was extracted using SPE.
Sample Type:Faeces
Volumeoramount Collected:one faecal pellet
Storage Conditions:-80C
Collection Vials:1.5mL Eppendorff
Storage Vials:1.5mL Eppendorff
Collection Tube Temp:4C

Treatment:

Treatment ID:TR000583
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP000576
Sampleprep Summary:Faeces were homogenised in PBS , equivelent of 125 µg faecal supernatant was extracted using solid phase extraction prior to UPLC-MS analysis.
Processing Method:Homogenisation, SPE extraction
Processing Storage Conditions:-80C
Extraction Method:Faecal pellets were dispersed in 1 mL PBS by vortexing. Suspensions were then centrifuged at 13000 x g for 5 mins and the supernatant collected for analysis.
Extract Enrichment:A 50 µL aliquot was placed in a pre-washed (1 mL acetonitrile) and equilibrated (1 mL 0.1% TFA aqueous) Oasis HLB 10 mg SPE cartridge (Waters Corporation, Milford, MA, USA). The sample was washed with 1 mL 0.1% TFA and eluted with 1 mL 0.1% TFA in 70% acetonitrile.
Extract Storage:The eluent was lyophilized overnight in a RVC 2-33CD plus rotational vacuum concentrator (Martin Christ Gefriertrocknungsanlagen GmbH, Osterode am Harz, Germany) operated at 10 mBar and room temperature.
Sample Resuspension:Samples were reconstituted in 50 µL 0.1% FA, vortexed and centrifuged at 16 000 x g for 15 min. The supernatant was transferred into LC-MS-grade glass vials (avoiding the pellet) and stored at 6°C until use.

Combined analysis:

Analysis ID AN000834 AN000835
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters Acquity BEH C18 (150 x 2.1mm,1.7um) Waters Acquity BEH C18 (150 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Waters Synapt G1 Waters Synapt G1
Ion Mode POSITIVE NEGATIVE
Units Normalised Intensity Normalised Intensity

Chromatography:

Chromatography ID:CH000596
Chromatography Summary:RP C18 +ve and -ve Ion
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (150 x 2.1mm,1.7um)
Column Temperature:45C
Flow Rate:400 µL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Weak Wash Solvent Name:Water
Weak Wash Volume:600 µL
Strong Wash Solvent Name:Acetonitrile
Strong Wash Volume:200 µL
Target Sample Temperature:6C
Sample Loop Size:20 µL
Randomization Order:Random
Chromatography Type:Reversed phase

MS:

MS ID:MS000735
Analysis ID:AN000834
Instrument Name:Waters Synapt G1
Instrument Type:QTOF
MS Type:ESI
MS Comments:Every 3rd injection was a PBQC sample
Ion Mode:POSITIVE
Capillary Voltage:2.8 kV
Collision Energy:Trap CE 6, Transfer CE 4
Collision Gas:Nitrogen
Source Temperature:120 C
Desolvation Gas Flow:900 L/h
Desolvation Temperature:450 C
  
MS ID:MS000736
Analysis ID:AN000835
Instrument Name:Waters Synapt G1
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:2.8 kV
Collision Energy:Trap CE 6, Transfer CE 4
Collision Gas:Nitrogen
Source Temperature:120 C
Desolvation Gas Flow:900 L/h
Desolvation Temperature:450 C
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