Summary of Study ST001832

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.

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 IDST001832
Study TitleQuantitative bile acids study on blood serum and ceacal content of rat models (part I)
Study Typeblood serum and caecum content
Study SummaryBile acids 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 Date2021-06-15
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

Select appropriate tab below to view additional metadata details:

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:SU001909
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
SA1703411024041020Caecum DIO
SA1703501024041673Caecum DIO
SA1703511024039031Caecum DIO
SA1703521024039045Caecum DIO
SA1703531024039050Caecum DIO
SA1703661024040931Caecum DIO
SA1703961024041499Caecum DIO
SA1704011024040999Caecum DIO
SA1704041024041015Caecum DIO
SA1703721024040946Caecum DIO_AB
SA1703821024040951Caecum DIO_AB
SA1703871024038632Caecum DIO_AB
SA1703891024035907Caecum DIO_AB
SA1703901024040965Caecum DIO_AB
SA1703971024040984Caecum DIO_AB
SA1703461024041034Caecum DIO_FMT_RYGB
SA1703471024041635Caecum DIO_FMT_RYGB
SA1703481024041640Caecum DIO_FMT_RYGB
SA1703541024041049Caecum DIO_FMT_RYGB
SA1703551024041654Caecum DIO_FMT_RYGB
SA1703561024041669Caecum DIO_FMT_RYGB
SA1703921024035931Caecum DIO_FMT_RYGB
SA1703941024040970Caecum DIO_FMT_RYGB
SA1703981024041514Caecum DIO_FMT_RYGB
SA1704021024041001Caecum DIO_FMT_RYGB
SA1703491024039079Caecum DIO_PF_FMT
SA1703571024039083Caecum DIO_PF_FMT
SA1703581024039098Caecum DIO_PF_FMT
SA1703591024039109Caecum DIO_PF_FMT
SA1703601024039113Caecum DIO_PF_FMT
SA1703881024035896Caecum FMT_lean
SA1703931024035945Caecum FMT_lean
SA1703951024035964Caecum FMT_lean
SA1703991024041529Caecum FMT_lean
SA1704001024041533Caecum FMT_lean
SA1703371024039132Caecum Lean
SA1703611024039147Caecum Lean
SA1703621024039151Caecum Lean
SA1703711024038481Caecum Lean
SA1703731024038496Caecum Lean
SA1703761024038526Caecum Lean
SA1703771024038531Caecum Lean
SA1703911024035926Caecum Lean
SA1704031024039128Caecum Lean
SA1703691024038462Caecum Lean_AB
SA1703701024038477Caecum Lean_AB
SA1703741024038507Caecum Lean_AB
SA1703751024038511Caecum Lean_AB
SA1703851024038613Caecum Lean_AB
SA1703861024038628Caecum Lean_AB
SA1703421024041586Caecum RYGB_AB
SA1703441024041591Caecum RYGB_AB
SA1703451024041621Caecum RYGB_AB
SA1703631024041053Caecum RYGB_AB
SA1703641024041072Caecum RYGB_AB
SA1703681024041102Caecum RYGB_AB
SA1703811024038579Caecum RYGB_AB
SA1703831024038583Caecum RYGB_AB
SA1703841024038609Caecum RYGB_AB
SA1703381024041548Caecum RYGB_Donor
SA1703391024041552Caecum RYGB_Donor
SA1703401024041567Caecum RYGB_Donor
SA1703431024041571Caecum RYGB_Donor
SA1703651024041087Caecum RYGB_Donor
SA1703671024041091Caecum RYGB_Donor
SA1703781024038545Caecum RYGB_Donor
SA1703791024038550Caecum RYGB_Donor
SA1703801024038564Caecum RYGB_Donor
SA1704091024038458Serum DIO
SA1704181024033195Serum DIO
SA1704191024033206Serum DIO
SA1704201024033211Serum DIO
SA1704211024033225Serum DIO
SA1704311024038375Serum DIO
SA1704621024035363Serum DIO
SA1704641024035378Serum DIO
SA1704701024038443Serum DIO
SA1704361024038380Serum DIO_AB
SA1704461024038394Serum DIO_AB
SA1704511024035261Serum DIO_AB
SA1704531024035281Serum DIO_AB
SA1704541024038405Serum DIO_AB
SA1704631024038424Serum DIO_AB
SA1704131024032366Serum DIO_FMT_RYGB
SA1704141024033157Serum DIO_FMT_RYGB
SA1704151024033161Serum DIO_FMT_RYGB
SA1704221024032371Serum DIO_FMT_RYGB
SA1704571024035311Serum DIO_FMT_RYGB
SA1704591024038410Serum DIO_FMT_RYGB
SA1704651024035382Serum DIO_FMT_RYGB
SA1704681024038439Serum DIO_FMT_RYGB
SA1704161024033230Serum DIO_PF_FMT
SA1704171024033244Serum DIO_PF_FMT
SA1704231024033259Serum DIO_PF_FMT
SA1704241024033282Serum DIO_PF_FMT
SA1704521024035276Serum FMT_lean
SA1704581024035325Serum FMT_lean
SA1704601024035330Serum FMT_lean
SA1704611024035359Serum FMT_lean
SA1704661024035397Serum FMT_lean
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Collection:

Collection ID:CO001902
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:TR001922
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 body weight-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:SP001915
Sampleprep Summary: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 To approximately 100 mg of sample four steel balls of size M rae added in Eppendorf tubes. Then add for each mg of sample 5 µL of extracting agent. Shake the samples for 10 minutes at 30 Hz in the tissue slicer and centrifuge for 2 minutes at 14000 rpm. The supernatant is used for targeted analytics as described in the kit manufactures manual. Kit measurement The analysis was performed using the validated Bile Acid Kit (Biocrates Life Sciences, Inssbruck, Austria) as described in Pham et al. 2017 [1]. Data processing is carried out with the provided quantitation method Kit (Biocrates Life Sciences AG, Innsbruck, Austria). 1 Pham HT, Arnhard K, Asad YJ, Deng L, Felder TK, St John-Williams L, et al. Inter-Laboratory Robustness of Next-Generation Bile Acid Study in Mice and Humans: International Ring Trial Involving 12 Laboratories. The Journal of Applied Laboratory Medicine 2019;1:129-42.

Combined analysis:

Analysis ID AN002974
Analysis type MS
Chromatography type Reversed phase
Chromatography system UPLC (Waters Acquity, Waters Corporation, Milford, USA)
Column none
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap
Ion Mode NEGATIVE
Units µM

Chromatography:

Chromatography ID:CH002203
Instrument Name:UPLC (Waters Acquity, Waters Corporation, Milford, USA)
Column Name:none
Chromatography Type:Reversed phase

MS:

MS ID:MS002764
Analysis ID:AN002974
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
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