Summary of Study ST003470

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 IDST003470
Study TitleGut Microbiota Regulates Stress Responsivity via the Circadian System - Mice Amygdala
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 Date2024-09-03
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

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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:SU003598
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
SA383085ABX_90Amygadala ABX ZT11
SA383086ABX_62Amygadala ABX ZT11
SA383087ABX_64Amygadala ABX ZT11
SA383088ABX_65Amygadala ABX ZT11
SA383089ABX_87Amygadala ABX ZT11
SA383090ABX_88Amygadala ABX ZT11
SA383091ABX_89Amygadala ABX ZT11
SA383092ABX_63Amygadala ABX ZT11
SA383093ABX_119Amygadala ABX ZT17
SA383094ABX_108Amygadala ABX ZT17
SA383095ABX_107Amygadala ABX ZT17
SA383096ABX_106Amygadala ABX ZT17
SA383097ABX_105Amygadala ABX ZT17
SA383098ABX_121Amygadala ABX ZT17
SA383099ABX_109Amygadala ABX ZT23
SA383100ABX_114Amygadala ABX ZT23
SA383101ABX_116Amygadala ABX ZT23
SA383102ABX_115Amygadala ABX ZT23
SA383103ABX_112Amygadala ABX ZT23
SA383104ABX_113Amygadala ABX ZT23
SA383105ABX_111Amygadala ABX ZT23
SA383106ABX_110Amygadala ABX ZT23
SA383107ABX_72Amygadala ABX ZT5
SA383108ABX_73Amygadala ABX ZT5
SA383109ABX_74Amygadala ABX ZT5
SA383110ABX_75Amygadala ABX ZT5
SA383111ABX_76Amygadala ABX ZT5
SA383112ABX_77Amygadala ABX ZT5
SA383113ABX_84Amygadala ABX ZT5
SA383114ABX_86Amygadala ABX ZT5
SA383115CV_20Amygadala CV ZT11
SA383116CV_19Amygadala CV ZT11
SA383117CV_18Amygadala CV ZT11
SA383118CV_17Amygadala CV ZT11
SA383119CV_16Amygadala CV ZT11
SA383120CV_101Amygadala CV ZT11
SA383121CV_102Amygadala CV ZT11
SA383122CV_68Amygadala CV ZT17
SA383123CV_67Amygadala CV ZT17
SA383124CV_70Amygadala CV ZT17
SA383125CV_71Amygadala CV ZT17
SA383126CV_122Amygadala CV ZT17
SA383127CV_123Amygadala CV ZT17
SA383128CV_69Amygadala CV ZT17
SA383129CV_66Amygadala CV ZT17
SA383130CV_83Amygadala CV ZT23
SA383131CV_79Amygadala CV ZT23
SA383132CV_118Amygadala CV ZT23
SA383133CV_117Amygadala CV ZT23
SA383134CV_82Amygadala CV ZT23
SA383135CV_81Amygadala CV ZT23
SA383136CV_80Amygadala CV ZT23
SA383137CV_78Amygadala CV ZT23
SA383138CV_13Amygadala CV ZT5
SA383139CV_6Amygadala CV ZT5
SA383140CV_7Amygadala CV ZT5
SA383141CV_9Amygadala CV ZT5
SA383142CV_10Amygadala CV ZT5
SA383143CV_11Amygadala CV ZT5
SA383144CV_12Amygadala CV ZT5
SA383145CV_8Amygadala CV ZT5
SA383146GF_43Amygadala GF ZT11
SA383147GF_47Amygadala GF ZT11
SA383148GF_45Amygadala GF ZT11
SA383149GF_36Amygadala GF ZT11
SA383150GF_42Amygadala GF ZT11
SA383151GF_41Amygadala GF ZT11
SA383152GF_32Amygadala GF ZT11
SA383153GF_48Amygadala GF ZT11
SA383154GF_94Amygadala GF ZT17
SA383155GF_92Amygadala GF ZT17
SA383156GF_93Amygadala GF ZT17
SA383157GF_91Amygadala GF ZT17
SA383158GF_95Amygadala GF ZT17
SA383159GF_96Amygadala GF ZT17
SA383160GF_97Amygadala GF ZT17
SA383161GF_98Amygadala GF ZT17
SA383162GF_55Amygadala GF ZT23
SA383163GF_57Amygadala GF ZT23
SA383164GF_54Amygadala GF ZT23
SA383165GF_56Amygadala GF ZT23
SA383166GF_59Amygadala GF ZT23
SA383167GF_60Amygadala GF ZT23
SA383168GF_61Amygadala GF ZT23
SA383169GF_53Amygadala GF ZT23
SA383170GF_24Amygadala GF ZT5
SA383171GF_52Amygadala GF ZT5
SA383172GF_51Amygadala GF ZT5
SA383173GF_25Amygadala GF ZT5
SA383174GF_28Amygadala GF ZT5
SA383175GF_26Amygadala GF ZT5
SA383176GF_49Amygadala GF ZT5
Showing results 1 to 92 of 92

Collection:

Collection ID:CO003591
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:TR003607
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:SP003605
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 AN005705
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:CH004327
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:MS005429
Analysis ID:AN005705
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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