Summary of Study ST001833

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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 IDST001833
Study TitleQuantitative bile acids study on blood serum and ceacal content of rat models (part II)
Study Typeblood serum and caecum content
Study Summaryamino acids and biogenic amines were analyzed in blood serum and cecal content in rat models
Helmholtz Centre for Environmental Research
DepartmentDepartment of Molecular Systems biology
LaboratoryFunctional Metabolomics
Last NameRolle-Kampczyk
First NameUlrike
AddressPermoserstrasse 15, 04318 Leipzig, Germany
Phone0049 341 235 1537
Submit Date2021-06-16
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 application/zip

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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
Phone:0049 341 2351099


Subject ID:SU001910
Subject Type:Mammal
Subject Species:Rattus norvegicus
Taxonomy ID:10116


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

mb_sample_id local_sample_id Tissue Sample treatment
SA1704751024038651Caecum DIO
SA1704851024038893Caecum DIO
SA1704861024038904Caecum DIO
SA1704871024038919Caecum DIO
SA1704881024038923Caecum DIO
SA1705011024041219Caecum DIO
SA1705331024041363Caecum DIO
SA1705351024041378Caecum DIO
SA1705391024041276Caecum DIO
SA1705421024041295Caecum DIO
SA1705071024041223Caecum DIO_AB
SA1705171024041238Caecum DIO_AB
SA1705221024035756Caecum DIO_AB
SA1705241024035775Caecum DIO_AB
SA1705251024041242Caecum DIO_AB
SA1705341024041261Caecum DIO_AB
SA1704801024038666Caecum DIO_FMT_RYGB
SA1704811024038841Caecum DIO_FMT_RYGB
SA1704821024038860Caecum DIO_FMT_RYGB
SA1704891024038671Caecum DIO_FMT_RYGB
SA1704901024038874Caecum DIO_FMT_RYGB
SA1704911024038889Caecum DIO_FMT_RYGB
SA1705281024041325Caecum DIO_FMT_RYGB
SA1705301024041257Caecum DIO_FMT_RYGB
SA1705361024041382Caecum DIO_FMT_RYGB
SA1705401024041281Caecum DIO_FMT_RYGB
SA1704831024038938Caecum DIO_PF_FMT
SA1704841024038942Caecum DIO_PF_FMT
SA1704921024038957Caecum DIO_PF_FMT
SA1704931024038961Caecum DIO_PF_FMT
SA1704941024038976Caecum DIO_PF_FMT
SA1704951024038981Caecum DIO_PF_FMT
SA1705231024035761Caecum FMT_lean
SA1705291024041330Caecum FMT_lean
SA1705311024041344Caecum FMT_lean
SA1705321024041359Caecum FMT_lean
SA1705371024041397Caecum FMT_lean
SA1705381024041408Caecum FMT_lean
SA1704711024039007Caecum Lean
SA1704961024039011Caecum Lean
SA1704971024039026Caecum Lean
SA1705061024038753Caecum Lean
SA1705081024038768Caecum Lean
SA1705111024038791Caecum Lean
SA1705121024038802Caecum Lean
SA1705261024041306Caecum Lean
SA1705271024041311Caecum Lean
SA1705411024038995Caecum Lean
SA1705041024038734Caecum Lean_AB
SA1705051024038749Caecum Lean_AB
SA1705091024038772Caecum Lean_AB
SA1705101024038787Caecum Lean_AB
SA1705201024032782Caecum Lean_AB
SA1705211024032797Caecum Lean_AB
SA1704761024041451Caecum RYGB_AB
SA1704781024041465Caecum RYGB_AB
SA1704791024041484Caecum RYGB_AB
SA1704981024038685Caecum RYGB_AB
SA1704991024038690Caecum RYGB_AB
SA1705031024038720Caecum RYGB_AB
SA1705161024032759Caecum RYGB_AB
SA1705181024032763Caecum RYGB_AB
SA1705191024032778Caecum RYGB_AB
SA1704721024041412Caecum RYGB_Donor
SA1704731024041427Caecum RYGB_Donor
SA1704741024041431Caecum RYGB_Donor
SA1704771024041446Caecum RYGB_Donor
SA1705001024038701Caecum RYGB_Donor
SA1705021024038715Caecum RYGB_Donor
SA1705131024038821Caecum RYGB_Donor
SA1705141024038836Caecum RYGB_Donor
SA1705151024032744Caecum RYGB_Donor
SA1705471024032638Serum DIO
SA1705571024033060Serum DIO
SA1705581024033074Serum DIO
SA1705591024033089Serum DIO
SA1705601024033093Serum DIO
SA1705741024032555Serum DIO
SA1706051024041155Serum DIO
SA1706071024041174Serum DIO
SA1706131024032623Serum DIO
SA1705791024032560Serum DIO_AB
SA1705891024032574Serum DIO_AB
SA1705941024035548Serum DIO_AB
SA1705961024035567Serum DIO_AB
SA1705971024032589Serum DIO_AB
SA1706061024032604Serum DIO_AB
SA1705521024032642Serum DIO_FMT_RYGB
SA1705531024033021Serum DIO_FMT_RYGB
SA1705541024033036Serum DIO_FMT_RYGB
SA1705611024032657Serum DIO_FMT_RYGB
SA1705621024033041Serum DIO_FMT_RYGB
SA1705631024033055Serum DIO_FMT_RYGB
SA1706001024041117Serum DIO_FMT_RYGB
SA1706021024032593Serum DIO_FMT_RYGB
SA1706081024041189Serum DIO_FMT_RYGB
SA1706111024032619Serum DIO_FMT_RYGB
SA1705551024033104Serum DIO_PF_FMT
SA1705561024033119Serum DIO_PF_FMT
SA1705641024035780Serum DIO_PF_FMT
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Collection ID:CO001903
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 ID:TR001923
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:SP001916
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 AN002975
Analysis type MS
Chromatography type Reversed phase
Chromatography system UPLC (Waters Acquity, Waters Corporation, Milford, USA)
Column Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um)
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap
Units µM


Chromatography ID:CH002204
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
Instrument Name:UPLC (Waters Acquity, Waters Corporation, Milford, USA)
Column Name:Agilent Zorbax Eclipse Plus C18 (100 x 2.1mm, 1.8 um)
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 ID:MS002765
Analysis ID:AN002975
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Comments:Analyst version 1.6 Software from SCIEX. For Validation METIDQ Software version Boron from Biocrates