Summary of Study ST002513

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 PR001620. The data can be accessed directly via it's Project DOI: 10.21228/M89B04 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 IDST002513
Study TitleGnotobiotic mice: Metabolites in serum of germ-free mice colonized with strains of gut bacterium Eggerthella lenta
Study TypeUntargeted LC-MS
Study SummaryThis dataset contains untargeted metabolomics analysis of serum of gnotobiotic mice either colonized with different strains of Eggerthella lenta for 2 weeks, or germ-free controls.
Institute
University of California, San Francisco
Last NameNoecker
First NameCecilia
Address513 Parnassus Ave HSW1501, San Francisco, CA 94143
Emailcecilia.noecker@ucsf.edu
Phone415-502-3264
Submit Date2023-03-21
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-04-10
Release Version1
Cecilia Noecker Cecilia Noecker
https://dx.doi.org/10.21228/M89B04
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001620
Project DOI:doi: 10.21228/M89B04
Project Title:Systems biology illuminates the alternative metabolic niche of the human gut bacterium Eggerthella lenta
Project Type:Untargeted LC-MS
Project Summary:Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem.
Institute:University of California, San Francisco
Department:Microbiology and Immunology
Laboratory:Peter Turnbaugh
Last Name:Noecker
First Name:Cecilia
Address:513 Parnassus Ave HSW1501, San Francisco, CA 94143
Email:cecilia.noecker@ucsf.edu
Phone:415-502-3264
Funding Source:This work was supported by the National Institutes of Health (2R01HL122593; 1R01AT011117; 1R01DK114034 to P.J.T., F32GM140808 to C.N.). P.J.T. is a Chan Zuckerberg Biohub Investigator and held an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund.
Publications:https://doi.org/10.1101/2022.09.19.508335

Subject:

Subject ID:SU002613
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6J
Age Or Age Range:6-10 weeks
Gender:Male
Animal Animal Supplier:University of California, San Francisco Gnotobiotics core facility
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id SampleType Group
SA252972Serum_El15644_6- -
SA252973Serum_El15644_21Serum El15644
SA252974Serum_El15644_14Serum El15644
SA252975Serum_El15644_22Serum El15644
SA252976Serum_El15644_7Serum El15644
SA252977Serum_El15644_23Serum El15644
SA252978Serum_El2243_5Serum El2243
SA252979Serum_El2243_25Serum El2243
SA252980Serum_El2243_4Serum El2243
SA252981Serum_El2243_24Serum El2243
SA252982Serum_El2243_12Serum El2243
SA252983Serum_El2243_13Serum El2243
SA252984Serum_ElAB12n2_29Serum ElAB12n2
SA252985Serum_ElAB12n2_30Serum ElAB12n2
SA252986Serum_ElAB12n2_28Serum ElAB12n2
SA252987Serum_ElAB12n2_18Serum ElAB12n2
SA252988Serum_GF_27Serum GF
SA252989Serum_GF_3Serum GF
SA252990Serum_GF_26Serum GF
SA252991Serum_GF_1Serum GF
SA252992Serum_GF_2Serum GF
Showing results 1 to 21 of 21

Collection:

Collection ID:CO002606
Collection Summary:Sample collection was performed as described in doi.org/10.1016/j.chom.2021.11.001 . Briefly, C57BL/6J mice (males, ages 4-8 weeks) were obtained from the University of California, San Francisco Gnotobiotics core facility (gnotobiotics.ucsf.edu) and housed in Iso positive cages (Tecniplast). Mice were colonized via oral gavage with E. lenta monocultures (109 CFU/mL, 200 μl gavage, n=6 E. lenta DSM 2243, n=5 E. lenta DSM 15644, n=4 E. lenta AB12n2) or control media (n=5 GF). Colonization was confirmed via anaerobic culturing and/or qPCR for an E. lenta specific marker (elnmrk1) [10,26]. Mice were colonized for 2 weeks prior to sacrifice and sample collection. Serum samples were collected.
Sample Type:Blood (serum)
Collection Frequency:single time point (2 weeks after colonization)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002625
Treatment Summary:Mice were colonized via oral gavage with E. lenta monocultures (109 CFU/mL, 200 μl gavage, n=6 E. lenta DSM 2243, n=5 E. lenta DSM 15644, n=4 E. lenta AB12n2) or control media (n=5 GF). Colonization was confirmed via anaerobic culturing and/or qPCR for an E. lenta specific marker (elnmrk1). Mice were colonized for 2 weeks prior to sacrifice and sample collection. Samples were collected of ileal, cecal, and colonic contents, as well as serum.

Sample Preparation:

Sampleprep ID:SP002619
Sampleprep Summary:Serum samples were first thawed on wet ice. 20 μL of serum was extracted with 4 volumes of methanol, containing stable isotope labeled internal standards. Samples were homogenized by vortexing for 20 seconds and placed in a -20oC for 1 hour to maximize protein precipitation. After freezer incubation, samples were centrifuged at 4oC at 18,407 rcf for 5 minutes. Supernatant was removed and dried under vacuum via centrivap (Labconco Corp.). Dried samples were then resuspended in 30 μL of 80% acetonitrile in water containing exogenous standard CUDA at 60 ng/mL. Samples were maintained at 4oC prior to prompt analysis.

Combined analysis:

Analysis ID AN004138 AN004139
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units relative ion counts relative ion counts

Chromatography:

Chromatography ID:CH003065
Chromatography Summary:Samples, pools, and blanks were promptly added to a Thermo Vanquish Autosampler at 4°C in a Vanquish UHPLC (Thermo Fisher Scientific, Waltham, MA). Chromatographic separation was performed using an ACQUITY Bridged Ethylene Hybrid (BEH) Amide column 2.1 x 150 mm, 1.7-micron particle size, (Waters Corp. Milford, MA), using chromatographic conditions published elsewhere (HILIC method described in the Supplementary Methods of doi.org/10.1038/s41586-021-03707-9).
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:40
Flow Gradient:The gradient profile was held at 100% B for 2 minutes, from 100% B to 70% B in 5 minutes, holding at 70% B for 0.7 minute, from 70% B to 40% B for 1.3 minutes, holding at 40% B for 0.5 minutes, from 40% B to 30% B for 0.75 minutes, before returning to 100% B for 2.5 minutes and holding at 100% B for 4 minutes.
Flow Rate:400 μL per minute
Solvent A:100% water; 0.125% formic acid; 10 mM ammonium formate, pH 3
Solvent B:95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate
Chromatography Type:HILIC

MS:

MS ID:MS003885
Analysis ID:AN004138
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Full MS-ddMS2 data was collected, an inclusion list was used to prioritize MS2 selection of metabolites from our in-house ‘local’ library, when additional scan bandwidth was available MS2 was collected in a data-dependent manner. Mass range was 60-900 mz, resolution was 60k (MS1) and 15k (MS2), centroid data was collected, loop count was 4, isolation window was 1.5 Da. Metabolomics data was processed using MS-DIAL v4.60. Features were excluded from analysis if peak height was not at least 5-fold greater in one or more samples compared to the procedural blank average.
Ion Mode:POSITIVE
  
MS ID:MS003886
Analysis ID:AN004139
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Full MS-ddMS2 data was collected, an inclusion list was used to prioritize MS2 selection of metabolites from our in-house ‘local’ library, when additional scan bandwidth was available MS2 was collected in a data-dependent manner. Mass range was 60-900 mz, resolution was 60k (MS1) and 15k (MS2), centroid data was collected, loop count was 4, isolation window was 1.5 Da. Metabolomics data was processed using MS-DIAL v4.60. Features were excluded from analysis if peak height was not at least 5-fold greater in one or more samples compared to the procedural blank average.
Ion Mode:NEGATIVE
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