Summary of Study ST001837

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 PR001157. The data can be accessed directly via it's Project DOI: 10.21228/M8510S This work is supported by NIH grant, U2C- DK119886.

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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 IDST001837
Study TitleQuantitative total hexose study on blood serum and ceacal content of rat models
Study Typeblood serum and caecum content
Study SummaryLipids were analyzed in blood serum and cecal content in rat models
Institute
Helmholtz Centre for Environmental Research
DepartmentDepartment of Molecular Systems biology
LaboratoryFunctional Metabolomics
Last NameRolle-Kampczyk
First NameUlrike
AddressPermoserstrasse 15, 04318 Leipzig, Germany
Emailulrike.rolle-kampczyk@ufz.de
Phone0049 341 235 1537
Submit Date2021-06-21
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2021-07-02
Release Version1
Ulrike Rolle-Kampczyk Ulrike Rolle-Kampczyk
https://dx.doi.org/10.21228/M8510S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001157
Project DOI:doi: 10.21228/M8510S
Project Title:Fecal Transplant from Roux-Y-Gastric-Bypass rat model into a diet induced obesity rat model
Project Summary:Investigating alterations in the intestinal microbiome metabolome and host blood metabolome in a diet induced obesity (DIO) rat model after fecal transplant from rats, which underwent Roux-Y-Gastric-Bypass surgery (RYGB). Experimental groups for rat experiments. 1)Rats in the ‘RYGB_Donor group’ underwent RYGB surgery. Postoperatively, animals received a two-choice diet, consisting of a SC and HFD. Once the animals recovered and achieved a stabilized weight reduction at 4 weeks postoperatively, body weight and food intake were recorded daily. 2)Rats allocated into the ‘RYGB_AB group’ were handled the same as animals in the ‘RYGB_donor group’. From postoperative week 4 onwards, animals received an antibiotic treatment (AB) consisting of ampicillin (1 g/l; Ratiopharm), vancomycin (0.5 g/l; Ratiopharm), neomycin (1 g/l; Bela-pharm), and metronidazole (1 g/l; CP-Pharma), provided freshly every day via drinking water.[19, 20] All antibiotics were given for the time period indicated in each figure.[21] 3)Rats in the ‘Lean group’ served as healthy, age-matched controls, constantly kept under SC. 4)Rats in the ‘Lean_AB group’ received the same antibiotic treatment as animals in the RYGB_AB group, serving as a control for antibiotic-specific side effects. All antibiotics were given for the time periods indicated in each figure. 5)Rats in the ‘DIO group’ received no surgery, but were otherwise handled like RYGB litter mates. 6)Rats in the ‘DIO_FMT_RYGB group’ received fecal RYGB_Donor microbiota transplantation once per week, but were otherwise handled like DIO litter mates. For fecal transplantation experiments, 100 mg of fresh stool from body weight-stabilized RYGB donors were re-suspended in 1 ml of PBS, homogenized carefully and administered via oral gavage with 200 μl of the suspension. 7)Rats in the ‘FMT_Lean group’ were handled like DIO litter mates, but were orally gavaged with 200 μl of filtrate received from lean donors, and served as a control for fecal transplantation and specificity of effect size(s) as a function of the donor microbiota. 8)Rats in the ‘DIO_PF_FMT group’ were handled like DIO litter mates, but pair-fed to the SC/HFD food intake of ‘FMT_Lean littermates, serving as a control for effects secondary to reduced caloric intake.
Institute:Helmholtz Centre for Environmental Research - UFZ
Last Name:Haange
First Name:Sven
Address:Permoserstrasse 1, Leipzig, Saxony, 04318, Germany
Email:sven.haange@ufz.de
Phone:0049 341 2351099

Subject:

Subject ID:SU001914
Subject Type:Mammal
Subject Species:Rattus norvegicus
Taxonomy ID:10116

Factors:

Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)

mb_sample_id local_sample_id Tissue Sample treatment
SA1708291024038893Caecum DIO
SA1708301024038923Caecum DIO
SA1708311024041378Caecum DIO
SA1708321024038919Caecum DIO
SA1708331024041363Caecum DIO
SA1708341024038904Caecum DIO
SA1708351024038651Caecum DIO
SA1708361024041295Caecum DIO
SA1708371024041276Caecum DIO
SA1708381024041219Caecum DIO
SA1708391024041238Caecum DIO_AB
SA1708401024041261Caecum DIO_AB
SA1708411024035756Caecum DIO_AB
SA1708421024041223Caecum DIO_AB
SA1708431024041242Caecum DIO_AB
SA1708441024035775Caecum DIO_AB
SA1708451024038889Caecum DIO_FMT_RYGB
SA1708461024038841Caecum DIO_FMT_RYGB
SA1708471024038874Caecum DIO_FMT_RYGB
SA1708481024038860Caecum DIO_FMT_RYGB
SA1708491024041257Caecum DIO_FMT_RYGB
SA1708501024041382Caecum DIO_FMT_RYGB
SA1708511024038666Caecum DIO_FMT_RYGB
SA1708521024038671Caecum DIO_FMT_RYGB
SA1708531024041325Caecum DIO_FMT_RYGB
SA1708541024041281Caecum DIO_FMT_RYGB
SA1708551024038981Caecum DIO_PF_FMT
SA1708561024038938Caecum DIO_PF_FMT
SA1708571024038942Caecum DIO_PF_FMT
SA1708581024038961Caecum DIO_PF_FMT
SA1708591024038957Caecum DIO_PF_FMT
SA1708601024038976Caecum DIO_PF_FMT
SA1708611024041408Caecum FMT_lean
SA1708621024041397Caecum FMT_lean
SA1708631024041359Caecum FMT_lean
SA1708641024041330Caecum FMT_lean
SA1708651024041344Caecum FMT_lean
SA1708661024035761Caecum FMT_lean
SA1708671024038768Caecum Lean
SA1708681024041306Caecum Lean
SA1708691024041311Caecum Lean
SA1708701024038753Caecum Lean
SA1708711024039026Caecum Lean
SA1708721024039011Caecum Lean
SA1708731024038791Caecum Lean
SA1708741024038995Caecum Lean
SA1708751024038802Caecum Lean
SA1708761024039007Caecum Lean
SA1708771024032797Caecum Lean_AB
SA1708781024032782Caecum Lean_AB
SA1708791024038787Caecum Lean_AB
SA1708801024038749Caecum Lean_AB
SA1708811024038772Caecum Lean_AB
SA1708821024038734Caecum Lean_AB
SA1708831024032759Caecum RYGB_AB
SA1708841024038720Caecum RYGB_AB
SA1708851024038685Caecum RYGB_AB
SA1708861024032763Caecum RYGB_AB
SA1708871024032778Caecum RYGB_AB
SA1708881024038690Caecum RYGB_AB
SA1708891024041465Caecum RYGB_AB
SA1708901024041484Caecum RYGB_AB
SA1708911024041446Caecum RYGB_AB
SA1708921024032744Caecum RYGB_Donor
SA1708931024041427Caecum RYGB_Donor
SA1708941024041412Caecum RYGB_Donor
SA1708951024041451Caecum RYGB_Donor
SA1708961024038836Caecum RYGB_Donor
SA1708971024038701Caecum RYGB_Donor
SA1708981024038715Caecum RYGB_Donor
SA1708991024041431Caecum RYGB_Donor
SA1709001024038821Caecum RYGB_Donor
SA1709011024033074Plasma DIO
SA1709021024033093Plasma DIO
SA1709031024033060Plasma DIO
SA1709041024033089Plasma DIO
SA1709051024033041Plasma DIO_FMT_RYGB
SA1709061024033055Plasma DIO_FMT_RYGB
SA1709071024033021Plasma DIO_FMT_RYGB
SA1709081024033036Plasma DIO_FMT_RYGB
SA1709091024035794Plasma DIO_PF_FMT
SA1709101024033104Plasma DIO_PF_FMT
SA1709111024033119Plasma DIO_PF_FMT
SA1709121024035805Plasma DIO_PF_FMT
SA1709131024035810Plasma DIO_PF_FMT
SA1709141024035780Plasma DIO_PF_FMT
SA1709151024035858Plasma Lean
SA1709161024035839Plasma Lean
SA1709171024035843Plasma Lean
SA1709181024035824Plasma Lean
SA1709191024033017Plasma RYGB_AB
SA1709201024032991Plasma RYGB_AB
SA1709211024032971Plasma RYGB_AB
SA1709221024032986Plasma RYGB_Donor
SA1709231024032948Plasma RYGB_Donor
SA1709241024032933Plasma RYGB_Donor
SA1709251024032952Plasma RYGB_Donor
SA1709261024041174Serum DIO
SA1709271024041155Serum DIO
SA1709281024032623Serum DIO
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Collection:

Collection ID:CO001907
Collection Summary:Animals were sacrificed, blood and cecum tissue were removed, snap frozen in liquid nitrogen and stored at -80°C until further analysis
Sample Type:Cecum

Treatment:

Treatment ID:TR001927
Treatment Summary:RYGB surgery was performed on age-matched (8-10-weeks old) male Wistar IGS rats. After four weeks of recovery, animals were put on an antibiotic cocktail consisting of ampicillin (1 g/l; Ratiopharm), vancomycin (0.5 g/l; Ratiopharm), neomycin (1 g/l; Bela-pharm), and metronidazole (1 g/l; CP-Pharma), provided freshly every day via drinking water. The parallel FMT group received fecal RYGB microbiota transplantation once per week, but were otherwise handled like DIO littermates. For fecal transplantation experiments, 100 mg of fresh stool from bodyweight-stabilized RYGB donors was re-suspended in 1 ml of PBS, homogenized carefully and administered via oral gavage with 200 μl of the suspension.

Sample Preparation:

Sampleprep ID:SP001920
Sampleprep Summary:Sample preparation for MetIDQ p180 Kit measurement Solvents: Acetonitril (Merck KGaA, Darmstadt, Germany hypergrade for LC-MS) Water MiliQ, Extracting agent - ACN / H2O (1:1) Equipment 4 steel balls size M Eppendorf Tubes 2mL Tissue slicer (Rettberg, Germany) Centrifuge (Sigma) Work steps Approximately 100mg of caecum sample and 4 steel balls of size M into each tube. Per mg of sample 5µL of extracting agent was added. Shake the samples for 10 minutes at 30 Hz in the tissue slicer and centrifuge for 2 minutes at 14000 rpm. 10 µL supernatant was used for the targeted analytics. Blood serum samples 10 µL were used for analysis Kit reparation The analysis was performed using the validated MetIDQ p180 Kit and described in Siskos et al. [1]. Data processing was carried out with the provided quantitation method Kit (Biocrates Life Sciences AG, Innsbruck, Austria). 1 Siskos AP, Jain P, Römisch-Margl W, Bennett M, Achaintre D, Asad Y, et al. Interlaboratory Reproducibility of a Targeted Metabolomics Platform for Analysis of Human Serum and Plasma. Anal Chem 2017;89:656-65.

Combined analysis:

Analysis ID AN002979
Analysis type MS
Chromatography type Reversed phase
Chromatography system UPLC (Waters Acquity, Waters Corporation, Milford, USA)
Column Agilent Zorbax Eclipse XDB C18 (100 x 3.0mm,3.5um)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap
Ion Mode NEGATIVE
Units µM

Chromatography:

Chromatography ID:CH002208
Chromatography Summary:LC - Instrument Parameters AbsoluteIDQ® p180 Kit (Biocrates Life Science AG, Innsbruck, Austria) System: UPLC (Waters Acquity, Waters Corporation, Milford, USA) Column: Agilent, Zorbax Eclipse XDB C18, 3.0 x 100 mm, 3.5 μM, Agilent Waldbronn, Germany Precolumn: Security Guard, Phenomenex, C18, 4 x 3 mm; Phenomenex, Aschaffenburg, Germany Materials: Water MiliQ, Methanol (Merck KGaA, Darmstadt, Germany, hypergrade for LC-MS) Acetonitril (Merck KGaA, Darmstadt, Germany hypergrade for LC-MS) Ammonium Acetate (Honeywell - Fluka, Seelze, Germany) Formic Acid (Honeywell, Fluka, Seelze, Germany) Running Solvent: 5mM ammonium acetat in methanol LC: A: 2mL Formic acid in MilliQ water B: 1mL Formic Acid in Acetonitrile Gradient Table LC Time (min) Flow Rate (mL/min) %A %B Curve Initial 0.500 100.0 0.0 Initial 0.50 0.500 100.0 0.0 6 4.00 0.500 30.0 70.0 6 5.30 0.500 30.0 70.0 6 5.40 0.500 100.0 0.0 6 7.30 0.500 100.0 0.0 6
Methods Filename:LC_parameters.pdf
Instrument Name:UPLC (Waters Acquity, Waters Corporation, Milford, USA)
Column Name:Agilent Zorbax Eclipse XDB C18 (100 x 3.0mm,3.5um)
Flow Gradient:FIA Time (min) Flow Rate (mL/min) %A %B Curve Initial 0.030 0.0 100.0 Initial 1.60 0.030 0.0 100.0 6 2.40 0.200 0.0 100.0 6 2.80 0.200 0.0 100.0 6 3.00 0.030 0.0 100.0 6
Flow Rate:0.03ml/min
Solvent A:100% methanol; 5mM ammonium acetate
Solvent B:50% methanol/50% water; 5mM ammonium acetate
Chromatography Type:Reversed phase

MS:

MS ID:MS002769
Analysis ID:AN002979
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Analyst version 1.6 Software from SCIEX. For Validation METIDQ Software version Boron from Biocrates
Ion Mode:NEGATIVE
Analysis Protocol File:MS_parameters_1.pdf
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