Summary of Study ST002510

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 IDST002510
Study TitleStrain supernatants: Strain diversity of Eggerthella lenta metabolites in defined media
Study TypeUntargeted LC-MS
Study SummaryThis dataset contains untargeted metabolomics analysis of supernatants from stationary phase of a collection of 30 strains of Eggerthella lenta grown in defined EDM1 media.
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:SU002610
Subject Type:Bacteria
Subject Species:Eggerthella lenta
Taxonomy ID:84112
Genotype Strain:various (see sample table)


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

mb_sample_id local_sample_id Strain Strain name Condition PlateNum
SA252743Ctrl_B3_1Ctrl Ctrl_B3 GL_Ctrl_B3 1
SA252744Ctrl_B3_2Ctrl Ctrl_B3 GL_Ctrl_B3 2
SA252745Ctrl_B3_3Ctrl Ctrl_B3 GL_Ctrl_B3 3
SA252746Ctrl_D9_2Ctrl Ctrl_D9 GL_Ctrl_D9 2
SA252747Ctrl_F5_1Ctrl Ctrl_F5 GL_Ctrl_F5 1
SA252748Ctrl_F5_2Ctrl Ctrl_F5 GL_Ctrl_F5 2
SA252749Ctrl_F5_3Ctrl Ctrl_F5 GL_Ctrl_F5 3
SA252750Ctrl_G12_1Ctrl Ctrl_G12 GL_Ctrl_G12 1
SA252751Ctrl_G12_2Ctrl Ctrl_G12 GL_Ctrl_G12 2
SA252752Ctrl_G12_3Ctrl Ctrl_G12 GL_Ctrl_G12 3
SA252753PTJ0086_1PTJ0086 Eggerthella_lenta_1160AFAABroad GL 1
SA252754PTJ0086_2PTJ0086 Eggerthella_lenta_1160AFAABroad GL 2
SA252755PTJ0086_3PTJ0086 Eggerthella_lenta_1160AFAABroad GL 3
SA252756PTJ0087_1PTJ0087 Eggerthella_lenta_1356FAA GL 1
SA252757PTJ0087_2PTJ0087 Eggerthella_lenta_1356FAA GL 2
SA252758PTJ0087_3PTJ0087 Eggerthella_lenta_1356FAA GL 3
SA252759PTJ0089_1PTJ0089 Eggerthella_lenta_11C GL 1
SA252760PTJ0089_3PTJ0089 Eggerthella_lenta_11C GL 3
SA252761PTJ0090_1PTJ0090 Eggerthella_lenta_14A GL 1
SA252762PTJ0090_3PTJ0090 Eggerthella_lenta_14A GL 3
SA252763PTJ0092_1PTJ0092 Eggerthella_lenta_22C GL 1
SA252764PTJ0092_2PTJ0092 Eggerthella_lenta_22C GL 2
SA252765PTJ0092_3PTJ0092 Eggerthella_lenta_22C GL 3
SA252766PTJ0093_1PTJ0093 Eggerthella_lenta_28B GL 1
SA252767PTJ0093_2PTJ0093 Eggerthella_lenta_28B GL 2
SA252768PTJ0093_3PTJ0093 Eggerthella_lenta_28B GL 3
SA252769PTJ0109_1PTJ0109 Eggerthella_lenta_DSM11767 GL 1
SA252770PTJ0109_2PTJ0109 Eggerthella_lenta_DSM11767 GL 2
SA252771PTJ0109_3PTJ0109 Eggerthella_lenta_DSM11767 GL 3
SA252772PTJ0110_1PTJ0110 Eggerthella_lenta_DSM11863 GL 1
SA252773PTJ0110_2PTJ0110 Eggerthella_lenta_DSM11863 GL 2
SA252774PTJ0110_3PTJ0110 Eggerthella_lenta_DSM11863 GL 3
SA252775PTJ0111_1PTJ0111 Eggerthella_lenta_DSM15644 GL 1
SA252776PTJ0111_2PTJ0111 Eggerthella_lenta_DSM15644 GL 2
SA252777PTJ0111_3PTJ0111 Eggerthella_lenta_DSM15644 GL 3
SA252778PTJ0112_1PTJ0112 Eggerthella_sinensis_DSM16107 GL 1
SA252779PTJ0112_2PTJ0112 Eggerthella_sinensis_DSM16107 GL 2
SA252780PTJ0112_3PTJ0112 Eggerthella_sinensis_DSM16107 GL 3
SA252781PTJ0166_1PTJ0166 Eggerthella_lenta_UCSF2243 GL 1
SA252782PTJ0166_2PTJ0166 Eggerthella_lenta_UCSF2243 GL 2
SA252783PTJ0166_3PTJ0166 Eggerthella_lenta_UCSF2243 GL 3
SA252784PTJ0169_1PTJ0169 Eggerthella_lenta_Valencia GL 1
SA252785PTJ0169_2PTJ0169 Eggerthella_lenta_Valencia GL 2
SA252786PTJ0169_3PTJ0169 Eggerthella_lenta_Valencia GL 3
SA252787PTJ0170_1PTJ0170 Eggerthella_lenta_AN51LG GL 1
SA252788PTJ0170_2PTJ0170 Eggerthella_lenta_AN51LG GL 2
SA252789PTJ0170_3PTJ0170 Eggerthella_lenta_AN51LG GL 3
SA252790PTJ0171_1PTJ0171 Eggerthella_lenta_MR1n12 GL 1
SA252791PTJ0171_2PTJ0171 Eggerthella_lenta_MR1n12 GL 2
SA252792PTJ0171_3PTJ0171 Eggerthella_lenta_MR1n12 GL 3
SA252793PTJ0173_2PTJ0173 Eggerthella_lenta_326I6NA GL 2
SA252794PTJ0173_3PTJ0173 Eggerthella_lenta_326I6NA GL 3
SA252795PTJ0174_1PTJ0174 Eggerthella_lenta_AB8n2 GL 1
SA252796PTJ0174_3PTJ0174 Eggerthella_lenta_AB8n2 GL 3
SA252797PTJ0175_1PTJ0175 Eggerthella_lenta_AB12n2 GL 1
SA252798PTJ0175_2PTJ0175 Eggerthella_lenta_AB12n2 GL 2
SA252799PTJ0175_3PTJ0175 Eggerthella_lenta_AB12n2 GL 3
SA252800PTJ0176_1PTJ0176 Eggerthella_lenta_CC82BHI2 GL 1
SA252801PTJ0176_2PTJ0176 Eggerthella_lenta_CC82BHI2 GL 2
SA252802PTJ0176_3PTJ0176 Eggerthella_lenta_CC82BHI2 GL 3
SA252803PTJ0177_1PTJ0177 Eggerthella_lenta_RC46F GL 1
SA252804PTJ0177_2PTJ0177 Eggerthella_lenta_RC46F GL 2
SA252805PTJ0177_3PTJ0177 Eggerthella_lenta_RC46F GL 3
SA252806PTJ0178_1PTJ0178 Eggerthella_lenta_CC75D52 GL 1
SA252807PTJ0178_2PTJ0178 Eggerthella_lenta_CC75D52 GL 2
SA252808PTJ0178_3PTJ0178 Eggerthella_lenta_CC75D52 GL 3
SA252809PTJ0179_1PTJ0179 Eggerthella_lenta_CC86D54 GL 1
SA252810PTJ0179_2PTJ0179 Eggerthella_lenta_CC86D54 GL 2
SA252811PTJ0179_3PTJ0179 Eggerthella_lenta_CC86D54 GL 3
SA252812PTJ0180_1PTJ0180 Eggerthella_lenta_W1BHI6 GL 1
SA252813PTJ0180_2PTJ0180 Eggerthella_lenta_W1BHI6 GL 2
SA252814PTJ0180_3PTJ0180 Eggerthella_lenta_W1BHI6 GL 3
SA252815PTJ0237_1PTJ0237 Eggerthella_lenta_A2 GL 1
SA252816PTJ0237_2PTJ0237 Eggerthella_lenta_A2 GL 2
SA252817PTJ0237_3PTJ0237 Eggerthella_lenta_A2 GL 3
SA252818PTJ0240_1PTJ0240 Eggerthella_lenta_ATCC25559 GL 1
SA252819PTJ0240_2PTJ0240 Eggerthella_lenta_ATCC25559 GL 2
SA252820PTJ0240_3PTJ0240 Eggerthella_lenta_ATCC25559 GL 3
SA252821PTJ0261_1PTJ0261 Eggerthella_lenta_DSM2243D GL 1
SA252822PTJ0261_2PTJ0261 Eggerthella_lenta_DSM2243D GL 2
SA252823PTJ0261_3PTJ0261 Eggerthella_lenta_DSM2243D GL 3
SA252824PTJ0289_1PTJ0289 Eggerthella_lenta_ELUC2 GL 1
SA252825PTJ0289_2PTJ0289 Eggerthella_lenta_ELUC2 GL 2
SA252826PTJ0289_3PTJ0289 Eggerthella_lenta_ELUC2 GL 3
SA252827PTJ0290_1PTJ0290 Eggerthella_lenta_ELUC5 GL 1
SA252828PTJ0290_2PTJ0290 Eggerthella_lenta_ELUC5 GL 2
SA252829PTJ0290_3PTJ0290 Eggerthella_lenta_ELUC5 GL 3
SA252830PTJ0295_1PTJ0295 Eggerthella_lenta_RJX1627 GL 1
SA252831PTJ0295_2PTJ0295 Eggerthella_lenta_RJX1627 GL 2
SA252832PTJ0295_3PTJ0295 Eggerthella_lenta_RJX1627 GL 3
SA252833PTJ0296_1PTJ0296 Eggerthella_lenta_RJX1626 GL 1
SA252834PTJ0296_2PTJ0296 Eggerthella_lenta_RJX1626 GL 2
SA252835PTJ0296_3PTJ0296 Eggerthella_lenta_RJX1626 GL 3
SA252836PTJ0297_1PTJ0297 Eggerthella_lenta_SECOmt75m2 GL 1
SA252837PTJ0297_2PTJ0297 Eggerthella_lenta_SECOmt75m2 GL 2
SA252838PTJ0297_3PTJ0297 Eggerthella_lenta_SECOmt75m2 GL 3
SA252687PTJ0181_3- - - -
SA252688PTJ0181_2- - - -
SA252689PTJ0174_2- - - -
SA252690PTJ0182_1- - - -
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Collection ID:CO002603
Collection Summary:For the comparative strain metabolomics experiment, 96-well polypropylene deep well plates were prepared with 800μL of fresh media in each well. Starter cultures and inocula for 29 isolates of Eggerthella lenta and 1 isolate of Eggerthella sinensis [26] were prepared as described above for growth assays, except without final dilution, and 80 μL was used to inoculate wells, leaving a blank well in between every culture well to prevent cross-contamination. After 72 hours, OD600 measurements were taken, plates were centrifuged, and supernatants were collected. 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:single time point (72 hours)
Storage Conditions:-80℃


Treatment ID:TR002622
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:SP002616
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 AN004133 AN004134
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:CH003062
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:MS003880
Analysis ID:AN004133
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:MS003881
Analysis ID:AN004134
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.