Summary of Study ST002509

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 PR001620. The data can be accessed directly via it's Project DOI: 10.21228/M89B04 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 IDST002509
Study TitleTime course 1: Growth of Eggerthella lenta in defined media
Study TypeUntargeted LC-MS
Study SummaryThis dataset contains untargeted metabolomics analysis of supernatants from 3 strains of Eggerthella lenta grown in defined EDM1 media with varying acetate concentrations.
University of California, San Francisco
Last NameNoecker
First NameCecilia
Address513 Parnassus Ave HSW1501, San Francisco, CA 94143
Submit Date2023-03-17
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-04-04
Release Version1
Cecilia Noecker Cecilia Noecker application/zip

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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
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.


Subject ID:SU002609
Subject Type:Bacteria
Subject Species:Eggerthella lenta
Taxonomy ID:84112
Genotype Strain:DSM 2243, Valencia, AB8n2


Subject type: Bacteria; Subject species: Eggerthella lenta (Factor headings shown in green)

mb_sample_id local_sample_id Strain AcetateConcentration_mM Time
SA2524382243_0_TP1_1_R22243 0 16.5
SA2524392243_0_TP1_1_R32243 0 16.5
SA2524402243_0_TP1_1_R12243 0 16.5
SA2524412243_0_TP2_1_R32243 0 21.5
SA2524422243_0_TP2_1_R22243 0 21.5
SA2524432243_0_TP2_1_R12243 0 21.5
SA2524442243_0_TP3_1_R32243 0 26
SA2524452243_0_TP3_1_R22243 0 26
SA2524462243_0_TP3_1_R12243 0 26
SA2524472243_0_TP4_1_R32243 0 30
SA2524482243_0_TP4_1_R22243 0 30
SA2524492243_0_TP4_1_R12243 0 30
SA2524502243_0_TP5_1_R32243 0 42
SA2524512243_0_TP5_1_R22243 0 42
SA2524522243_0_TP5_1_R12243 0 42
SA2524532243_0_TP6_1_R32243 0 50
SA2524542243_0_TP6_1_R22243 0 50
SA2524552243_0_TP6_1_R12243 0 50
SA2524562243_10Add_TP1_1_R32243 10Add 16.5
SA2524572243_10Add_TP1_1_R22243 10Add 16.5
SA2524582243_10Add_TP1_1_R12243 10Add 16.5
SA2524592243_10Add_TP2_1_R32243 10Add 21.5
SA2524602243_10Add_TP2_1_R22243 10Add 21.5
SA2524612243_10Add_TP2_1_R12243 10Add 21.5
SA2524622243_10Add_TP3_1_R12243 10Add 26
SA2524632243_10Add_TP3_1_R32243 10Add 26
SA2524642243_10Add_TP3_1_R22243 10Add 26
SA2524652243_10Add_TP4_1_R12243 10Add 30
SA2524662243_10Add_TP4_1_R22243 10Add 30
SA2524672243_10Add_TP4_1_R32243 10Add 30
SA2524682243_10Add_TP5_1_R22243 10Add 42
SA2524692243_10Add_TP5_1_R32243 10Add 42
SA2524702243_10Add_TP5_1_R12243 10Add 42
SA2524712243_10Add_TP6_1_R32243 10Add 50
SA2524722243_10Add_TP6_1_R22243 10Add 50
SA2524732243_10Add_TP6_1_R12243 10Add 50
SA2524742243_10_TP1_1_R32243 10 16.5
SA2524752243_10_TP1_1_R12243 10 16.5
SA2524762243_10_TP1_1_R22243 10 16.5
SA2524772243_10_TP2_1_R22243 10 21.5
SA2524782243_10_TP2_1_R12243 10 21.5
SA2524792243_10_TP2_1_R32243 10 21.5
SA2524802243_10_TP3_1_R22243 10 26
SA2524812243_10_TP3_1_R32243 10 26
SA2524822243_10_TP3_1_R12243 10 26
SA2524832243_10_TP4_1_R32243 10 30
SA2524842243_10_TP4_1_R12243 10 30
SA2524852243_10_TP4_1_R22243 10 30
SA2524862243_10_TP5_1_R22243 10 42
SA2524872243_10_TP5_1_R12243 10 42
SA2524882243_10_TP5_1_R32243 10 42
SA2524892243_10_TP6_1_R32243 10 50
SA2524902243_10_TP6_1_R12243 10 50
SA2524912243_10_TP6_1_R22243 10 50
SA2524922243_1_TP1_1_R22243 1 16.5
SA2524932243_1_TP1_1_R12243 1 16.5
SA2524942243_1_TP1_1_R32243 1 16.5
SA2524952243_1_TP2_1_R12243 1 21.5
SA2524962243_1_TP2_1_R22243 1 21.5
SA2524972243_1_TP2_1_R32243 1 21.5
SA2524982243_1_TP3_1_R22243 1 26
SA2524992243_1_TP3_1_R32243 1 26
SA2525002243_1_TP3_1_R12243 1 26
SA2525012243_1_TP4_1_R12243 1 30
SA2525022243_1_TP4_1_R22243 1 30
SA2525032243_1_TP5_1_R22243 1 42
SA2525042243_1_TP5_1_R12243 1 42
SA2525052243_1_TP5_1_R32243 1 42
SA2525062243_1_TP6_1_R22243 1 50
SA2525072243_1_TP6_1_R32243 1 50
SA2525082243_1_TP6_1_R12243 1 50
SA252509AB8_0_TP1_1_R3AB8 0 16.5
SA252510AB8_0_TP1_1_R2AB8 0 16.5
SA252511AB8_0_TP1_1_R1AB8 0 16.5
SA252512AB8_0_TP2_1_R1AB8 0 21.5
SA252513AB8_0_TP2_1_R3AB8 0 21.5
SA252514AB8_0_TP2_1_R2AB8 0 21.5
SA252515AB8_0_TP3_1_R1AB8 0 26
SA252516AB8_0_TP3_1_R2AB8 0 26
SA252517AB8_0_TP4_1_R2AB8 0 30
SA252518AB8_0_TP4_1_R3AB8 0 30
SA252519AB8_0_TP4_1_R1AB8 0 30
SA252520AB8_0_TP5_1_R2AB8 0 42
SA252521AB8_0_TP5_1_R3AB8 0 42
SA252522AB8_0_TP5_1_R1AB8 0 42
SA252523AB8_0_TP6_1_R2AB8 0 50
SA252524AB8_0_TP6_1_R3AB8 0 50
SA252525AB8_0_TP6_1_R1AB8 0 50
SA252526AB8_10_TP1_1_R3AB8 10 16.5
SA252527AB8_10_TP1_1_R1AB8 10 16.5
SA252528AB8_10_TP1_1_R2AB8 10 16.5
SA252529AB8_10_TP2_1_R1AB8 10 21.5
SA252530AB8_10_TP2_1_R2AB8 10 21.5
SA252531AB8_10_TP2_1_R3AB8 10 21.5
SA252532AB8_10_TP3_1_R1AB8 10 26
SA252533AB8_10_TP3_1_R2AB8 10 26
SA252534AB8_10_TP3_1_R3AB8 10 26
SA252535AB8_10_TP4_1_R3AB8 10 30
SA252536AB8_10_TP4_1_R2AB8 10 30
SA252537AB8_10_TP4_1_R1AB8 10 30
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Collection ID:CO002602
Collection Summary:Time course experiments were conducted in tubes in the anaerobic chamber in a 37°C incubator. For all metabolomics experiments, three independent culture replicates were included for each condition, with an equal number of uninoculated control tubes. Starter cultures and inocula were prepared as described above for growth assays. 5mLs of defined media was added to VWR glass culture tubes (53283-800) with screw caps. The PBS-washed inoculum was added to culture tubes to obtain an approximate starting OD600 of 0.001. A preliminary growth assay was conducted to define time points spanning the exponential growth phase in the tested conditions. At each time point, OD600 measurements of all inoculated tubes were first measured using a Hach DR1900 spectrophotometer, with a paired control tube to normalize for the background. 100 μL from each tube were then transferred into a 96-well microplate, which was sealed and removed from the anaerobic chamber. Plates were centrifuged at 1,928 rcf at 4°C for 8 minutes, after which supernatants were collected into fresh polypropylene tubes or plates, sealed, and flash-frozen in liquid nitrogen.
Sample Type:Bacterial culture supernatant
Collection Frequency:at time points specified in study design table over 50 hours (full growth phase)
Storage Conditions:-80℃


Treatment ID:TR002621
Treatment Summary:For growth and metabolomics experiments, glycerol stocks of the 3 E. lenta strains were first streaked on BHI+ agar plates and incubated at 37°C for 2-3 days. Individual colonies were inoculated into 3-4 mL liquid BHI+ and incubated at 37°C for 40-48 hours, or until approximately early stationary phase. Culture optical density (600 nm wavelength absorbance, OD600) was measured using a Hach DR1900 spectrophotometer. 1 mL samples of BHI starter cultures were then centrifuged at 1,568 rcf for 4 minutes in a microcentrifuge (ThermoScientific mySpin 12) in the anaerobic chamber and resuspended in 1 mL sterile phosphate-buffered saline (PBS). The resulting suspension was vortexed and diluted to an approximate OD600 of 0.1, and used as inoculum into defined experimental conditions. Varying media conditions were prepared separately and all allowed to fully reduce in the anaerobic chamber prior to inoculation.

Sample Preparation:

Sampleprep ID:SP002615
Sampleprep Summary:Bacterial culture supernatant and sterile media, used in culture, were thawed on wet ice. Once thawed, samples were homogenized by inversion five times. Extracellular culture supernatant samples were prepared as follows: 20 μL of culture supernatant were extracted using 80 μL of a chilled extraction solvent at −20°C (1:1 acetonitrile:methanol, 5% water containing stable isotope-labeled internal standards). Samples were homogenized via pipette action, incubated for 1 hour at −20°C, centrifuged at 4°C at 6000 rcf for 5 min. The supernatant was transferred to a new plate and immediately sealed and kept at 4°C prior to prompt analysis via LC-MS/MS.

Combined analysis:

Analysis ID AN004131 AN004132
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 instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Units relative ion counts relative ion counts


Chromatography ID:CH003061
Chromatography Summary:Samples, sterile media, 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
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 ID:MS003878
Analysis ID:AN004131
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
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.
MS ID:MS003879
Analysis ID:AN004132
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
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.