Summary of Study ST003471

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 PR002130. The data can be accessed directly via it's Project DOI: 10.21228/M89525 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 IDST003471
Study TitleGut Microbiota Regulates Stress Responsivity via the Circadian System - Mice Hippocampus
Study SummaryStress and circadian systems are interconnected through the hypothalamic-pituitary-adrenal (HPA) axis to maintain appropriate responses to external stimuli. Yet, the mechanisms of how such signals are orchestrated remains unknown. We now uncover the gut microbiota as a regulator of HPA-axis rhythmic function. Additionally, microbiota depletion markedly disturbs the brain transcriptome and metabolome in key stress response pathways in the hippocampus and amygdala across the day. This is coupled with a dysregulation of the master circadian pacemaker in the brain that resulted in perturbed glucocorticoid rhythmicity. The resulting hyper-activation of the HPA-axis at the sleep/wake transition drives time-of-day-specific impairments of the stress response and altered stress-sensitive behaviors. Finally, using microbiota transplantation we confirm that diurnal oscillations of gut microbes underlie altered glucocorticoid secretion and identify L. reuteri as a candidate strain for such effects. Together, our data offers compelling evidence that the microbiota regulates stress responsiveness in a circadian manner and is necessary to respond adaptively to psychological stressors throughout the day.
Institute
University College Cork
DepartmentAnatomy & Neuroscience
LaboratoryMicrobiome Gut Brain Axis
Last NameJohn
First NameCryan
Address4th Floor, Block E, Food Science Building, University College Cork, College Road, Cork, Ireland.
Emailj.cryan@ucc.ie
Phone+353 (0)21 4903500
Submit Date2024-09-06
Analysis Type DetailLC-MS
Release Date2024-09-27
Release Version1
Cryan John Cryan John
https://dx.doi.org/10.21228/M89525
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002130
Project DOI:doi: 10.21228/M89525
Project Title:Gut Microbiota Regulates Stress Responsivity via the Circadian System
Project Summary:Metabolomics of adult mice Amygdala and Hippocampus. Samples collected from conventional, antibiotic-treated and germ-free mice across 4 timepoints of the day. The goal of the project is to investigate the role of the gut microbiota on the circadian patterns of metabolites in the brain. Results indicated that metabolites involved in glutamate metabolism are altered across the day depending on microbial status.
Institute:University College Cork
Department:Anatomy & Neuroscience
Laboratory:Microbiome Gut Brain Axis
Last Name:John
First Name:Cryan
Address:College Road, Cork, County Cork, T12 XF62, Ireland
Email:gabriel.tofani@ucc.ie
Phone:+353 (0)21 4903500
Funding Source:Saks Kavanaugh

Subject:

Subject ID:SU003599
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Age Or Age Range:8-14 weeks
Gender:Male
Animal Animal Supplier:Taconic Biosciences
Animal Light Cycle:12h Light/Dark

Factors:

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

mb_sample_id local_sample_id Sample source Treatment Zeitgeber_time
SA383177ABX_90Hippocampus ABX ZT11
SA383178ABX_62Hippocampus ABX ZT11
SA383179ABX_64Hippocampus ABX ZT11
SA383180ABX_65Hippocampus ABX ZT11
SA383181ABX_87Hippocampus ABX ZT11
SA383182ABX_88Hippocampus ABX ZT11
SA383183ABX_89Hippocampus ABX ZT11
SA383184ABX_63Hippocampus ABX ZT11
SA383185ABX_121Hippocampus ABX ZT17
SA383186ABX_119Hippocampus ABX ZT17
SA383187ABX_108Hippocampus ABX ZT17
SA383188ABX_107Hippocampus ABX ZT17
SA383189ABX_106Hippocampus ABX ZT17
SA383190ABX_105Hippocampus ABX ZT17
SA383191ABX_104Hippocampus ABX ZT17
SA383192ABX_114Hippocampus ABX ZT23
SA383193ABX_116Hippocampus ABX ZT23
SA383194ABX_115Hippocampus ABX ZT23
SA383195ABX_109Hippocampus ABX ZT23
SA383196ABX_113Hippocampus ABX ZT23
SA383197ABX_112Hippocampus ABX ZT23
SA383198ABX_110Hippocampus ABX ZT23
SA383199ABX_111Hippocampus ABX ZT23
SA383200ABX_75Hippocampus ABX ZT5
SA383201ABX_72Hippocampus ABX ZT5
SA383202ABX_73Hippocampus ABX ZT5
SA383203ABX_74Hippocampus ABX ZT5
SA383204ABX_77Hippocampus ABX ZT5
SA383205ABX_76Hippocampus ABX ZT5
SA383206ABX_84Hippocampus ABX ZT5
SA383207ABX_86Hippocampus ABX ZT5
SA383208CV_20Hippocampus CV ZT11
SA383209CV_19Hippocampus CV ZT11
SA383210CV_18Hippocampus CV ZT11
SA383211CV_17Hippocampus CV ZT11
SA383212CV_16Hippocampus CV ZT11
SA383213CV_101Hippocampus CV ZT11
SA383214CV_102Hippocampus CV ZT11
SA383215CV_68Hippocampus CV ZT17
SA383216CV_67Hippocampus CV ZT17
SA383217CV_70Hippocampus CV ZT17
SA383218CV_71Hippocampus CV ZT17
SA383219CV_122Hippocampus CV ZT17
SA383220CV_123Hippocampus CV ZT17
SA383221CV_69Hippocampus CV ZT17
SA383222CV_66Hippocampus CV ZT17
SA383223CV_83Hippocampus CV ZT23
SA383224CV_79Hippocampus CV ZT23
SA383225CV_118Hippocampus CV ZT23
SA383226CV_117Hippocampus CV ZT23
SA383227CV_82Hippocampus CV ZT23
SA383228CV_81Hippocampus CV ZT23
SA383229CV_80Hippocampus CV ZT23
SA383230CV_78Hippocampus CV ZT23
SA383231CV_13Hippocampus CV ZT5
SA383232CV_6Hippocampus CV ZT5
SA383233CV_7Hippocampus CV ZT5
SA383234CV_9Hippocampus CV ZT5
SA383235CV_12Hippocampus CV ZT5
SA383236CV_10Hippocampus CV ZT5
SA383237CV_11Hippocampus CV ZT5
SA383238CV_8Hippocampus CV ZT5
SA383239GF_43Hippocampus GF ZT11
SA383240GF_47Hippocampus GF ZT11
SA383241GF_45Hippocampus GF ZT11
SA383242GF_36Hippocampus GF ZT11
SA383243GF_42Hippocampus GF ZT11
SA383244GF_41Hippocampus GF ZT11
SA383245GF_32Hippocampus GF ZT11
SA383246GF_48Hippocampus GF ZT11
SA383247GF_94Hippocampus GF ZT17
SA383248GF_92Hippocampus GF ZT17
SA383249GF_93Hippocampus GF ZT17
SA383250GF_91Hippocampus GF ZT17
SA383251GF_95Hippocampus GF ZT17
SA383252GF_96Hippocampus GF ZT17
SA383253GF_97Hippocampus GF ZT17
SA383254GF_98Hippocampus GF ZT17
SA383255GF_54Hippocampus GF ZT23
SA383256GF_57Hippocampus GF ZT23
SA383257GF_55Hippocampus GF ZT23
SA383258GF_56Hippocampus GF ZT23
SA383259GF_59Hippocampus GF ZT23
SA383260GF_60Hippocampus GF ZT23
SA383261GF_61Hippocampus GF ZT23
SA383262GF_53Hippocampus GF ZT23
SA383263GF_25Hippocampus GF ZT5
SA383264GF_52Hippocampus GF ZT5
SA383265GF_24Hippocampus GF ZT5
SA383266GF_51Hippocampus GF ZT5
SA383267GF_26Hippocampus GF ZT5
SA383268GF_27Hippocampus GF ZT5
SA383269GF_28Hippocampus GF ZT5
SA383270GF_49Hippocampus GF ZT5
Showing results 1 to 94 of 94

Collection:

Collection ID:CO003592
Collection Summary:Mice were transferred to a cull room and immediately decapitated. Tissues were then harvested, stored in PCR-grade tubes and flash-frozen in dry ice. Samples were stored in -80°C until further analysis.
Sample Type:Brain

Treatment:

Treatment ID:TR003608
Treatment Summary:Treatment = Conventional (Controls) - CV, Germ-Free - GF, Antibiotic Treated - ABX. Timepoints = ZT (Zeitgeber) 5, 11, 17 and 23. Group_ID = Treatment + Timepoint (eg. GF_ZT5, GF_ZT11) Details on antibiotic treatment: Mice received antibiotic treatment in ad libitum drinking water for a period of 14 days. The antibiotic cocktail consisted of ampicillin sodium salt (1g/L), gentamicin sulfate (1g/L), vancomycin hydrochloride (0.5g/L) and imipenem (0.25g/L) (Discovery Fine Chemicals). Water containing antibiotics was replaced every two days for the duration of the treatment and prepared freshly every time. Cages were randomly assigned to either vehicle or antibiotic treatment.

Sample Preparation:

Sampleprep ID:SP003606
Sampleprep Summary:1. Add pre-weighted sample and stainless steel beads in an extraction tube. 2. Add MeOH/Water (1:2) 3. Place the ET-1s into the pre-cooled Bead-beater and homogenize for 4 x 30 sec at 30 Hz. 4. Ultrasonicate the samples for 5 mins 5. Centrifuge the samples for 5 minutes at 18000 RCF and 4 °C and collect the supernatant in a Phree filter. 6. Repeat step 2-5 7. Centrifuge the Phree filters for 5 minutes at 1800 RCF and 4 °C. 8. Collect the filtrate and transfer it to a new extraction tube, 9. Dry the extracts under nitrogen gas. 10. Reconstitute 20 x the initial sample weight with Eluent Mix (10% Eluent B in Eluent A) and shake @ 1000 for 3.5 min therafter vortex for 10 sec. 11. Transfer 100 ul of the liquid to a filter plate and centrifuge them for 2 mins at 1800 RCF and 4 °C. 12. Collect the filtrate and dilute five times in eluent A.

Combined analysis:

Analysis ID AN005706
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Ion Mode NEGATIVE
Units Peak area

Chromatography:

Chromatography ID:CH004328
Chromatography Summary:Thermo Scientific Vanquish LC coupled to a Q Exactive HF Hybrid Quadrupole-Orbitrap
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
Column Temperature:30°C
Flow Gradient:0.0 min 0% B, 2.0 min 0% B, 4.0 min 35% B, 6.0 min 90% B, 14.0 min 90% B, 14.1 min 0% B, 15.0 min 0% B
Flow Rate:300 µl/min
Solvent A:100% water; 10 mM ammonium formate; 0.1% formic acid
Solvent B:100% methanol; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS005430
Analysis ID:AN005706
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metabolomics processing was performed untargeted using Compound Discoverer 3.3 (Thermo Scientific) and Skyline 22.2 (MacCoss Lab Software) for peak picking and feature grouping, followed by a in-house annotation and curation pipeline written in MatLab (2022b, MathWorks). Identification of compounds were performed at four levels; Level 1: identification by retention times (compared against in-house authentic standards), accurate mass (with an accepted deviation of 3ppm), and MS/MS spectra, Level 2a: identification by retention times (compared against in-house authentic standards), accurate mass (with an accepted deviation of 3ppm). Level 2b: identification by accurate mass (with an accepted deviation of 3ppm), and MS/MS spectra, Level 3: identification by accurate mass alone (with an accepted deviation of 3ppm).
Ion Mode:NEGATIVE
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