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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000547 |
| Study Title | Intergenerational murine gut microbiome variation |
| Study Type | Intergenerational |
| Study 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 | Rogers |
| First Name | Geraint |
| Address | SAHMRI, North Terrace, Adelaide, SA 5000, Australia |
| Geraint.rogers@sahmri.com | |
| Phone | N/A |
| Submit Date | 2016-12-22 |
| Num Groups | 4 |
| Total Subjects | 82 |
| Raw Data File Type(s) | raw(Waters) |
| Analysis Type Detail | LC-MS |
| Release Date | 2018-02-07 |
| Release Version | 1 |
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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. |
