Summary of Study ST002472

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 PR001596. The data can be accessed directly via it's Project DOI: 10.21228/M8D701 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.

Study ID	ST002472
Study Title	Linking bacterial metabolites to disease-associated microbes to uncover mechanisms of host-microbial interactions in intestinal inflammation. Veillonella parvula cell and media profiling
Study Summary	Understanding the role of the gut microbiome in inflammatory and autoimmune diseases requires the identification of microbial molecular effectors and their link to host pathophysiology. Here, we present a framework to identify and characterize novel microbial metabolites in patient samples and to directly link their production to disease-associated microbes. We applied this approach to investigate the spectrum of disease severity and treatment response in ulcerative colitis (UC) using longitudinal metabolite and strain profiles combined with paired plasma profiles.
Institute	Broad Institute of MIT and Harvard
Last Name	Xavier
First Name	Ramnik
Address	415 Main Street
Email	rxavier@broadinstitute.org
Phone	617717084
Submit Date	2023-02-10
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2024-02-12
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001596
Project DOI:	doi: 10.21228/M8D701
Project Title:	Linking bacterial metabolites to disease-associated microbes to uncover mechanisms of host-microbial interactions in intestinal inflammation
Project Type:	Metabolomic profiling of human fecal and plasma samples and bacterial strains
Project Summary:	Understanding the role of the gut microbiome in inflammatory and autoimmune diseases requires the identification of microbial molecular effectors and their link to host pathophysiology. Here, we present a framework to identify and characterize novel microbial metabolites in patient samples and to directly link their production to disease-associated microbes. We applied this approach to investigate the spectrum of disease severity and treatment response in ulcerative colitis (UC) using longitudinal metabolite and strain profiles combined with paired plasma profiles.
Institute:	Broad Institute of MIT and Harvard
Last Name:	Xavier
First Name:	Ramnik
Address:	415 Main Street
Email:	rxavier@broadinstitute.org
Phone:	6177147080
Publications:	Schirmer, M., Stražar, M., Avila-Pacheco, J., Rojas-Tapias, D. F., Brown, E. M., Temple, E., Deik, A., Bullock, K., Jeanfavre, S., Pierce, K., Jin, S., Invernizzi, R., Pust, M.-M., Costliow, Z., Mack, D. R., Griffiths, A. M., Walters, T., Boyle, B. M., Kugathasan, S., … Xavier, R. J. (2024). Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell Host & Microbe. https://doi.org/10.1016/j.chom.2023.12.013
Contributors:	Melanie Schirmer, Martin Strazar, Julian Avila-Pacheco, Daniel F. Rojas-Tapias, Eric Brown, Emily Temple, Subra Kugathasan, Zach Costliow, Hera Vlamakis, Jeff Hyams, Lee Denson, Clary B. Clish, Ramnik J. Xavier

Subject:

Subject ID:	SU002562
Subject Type:	Bacteria
Subject Species:	Veillonella parvula
Taxonomy ID:	29466

Factors:

Subject type: Bacteria; Subject species: Veillonella parvula (Factor headings shown in green)

mb_sample_id	local_sample_id	Matrix	Sample Type	Tretment
SA247708	C_40	Cell_pool	QC_Titration	-
SA247709	C_80	Cell_pool	QC_Titration	-
SA247710	C_100	Cell_pool	QC_Titration	-
SA247711	C_20	Cell_pool	QC_Titration	-
SA247712	C_60	Cell_pool	QC_Titration	-
SA247699	L_C1	Cell	Experiment	Lactate
SA247700	L_C3	Cell	Experiment	Lactate
SA247701	L_C2	Cell	Experiment	Lactate
SA247702	LN_C3	Cell	Experiment	Lactate+Nitrate
SA247703	LN_C2	Cell	Experiment	Lactate+Nitrate
SA247704	LN_C1	Cell	Experiment	Lactate+Nitrate
SA247705	N_C2	Cell	Experiment	Nitrate
SA247706	N_C3	Cell	Experiment	Nitrate
SA247707	N_C1	Cell	Experiment	Nitrate
SA247713	SM_80	Media_pool	QC_Titration	-
SA247714	SM_40	Media_pool	QC_Titration	-
SA247715	SM_20	Media_pool	QC_Titration	-
SA247716	SM_60	Media_pool	QC_Titration	-
SA247717	SM_100	Media_pool	QC_Titration	-
SA247718	L_SM1	Spent Media	Experiment	Lactate
SA247719	L_SM2	Spent Media	Experiment	Lactate
SA247720	L_SM3	Spent Media	Experiment	Lactate
SA247721	LN_SM1	Spent Media	Experiment	Lactate+Nitrate
SA247722	LN_SM3	Spent Media	Experiment	Lactate+Nitrate
SA247723	LN_SM2	Spent Media	Experiment	Lactate+Nitrate
SA247724	N_SM3	Spent Media	Experiment	Nitrate
SA247725	N_SM1	Spent Media	Experiment	Nitrate
SA247726	N_SM2	Spent Media	Experiment	Nitrate
SA247727	L_UM1	Unspent Media	Experiment	Lactate
SA247728	L_UM3	Unspent Media	Experiment	Lactate
SA247729	L_UM2	Unspent Media	Experiment	Lactate
SA247730	LN_UM3	Unspent Media	Experiment	Lactate+Nitrate
SA247731	LN_UM1	Unspent Media	Experiment	Lactate+Nitrate
SA247732	LN_UM2	Unspent Media	Experiment	Lactate+Nitrate
SA247733	N_UM3	Unspent Media	Experiment	Nitrate
SA247734	N_UM2	Unspent Media	Experiment	Nitrate
SA247735	N_UM1	Unspent Media	Experiment	Nitrate

Showing results 1 to 37 of 37

Showing results 1 to 37 of 37

Collection:

Collection ID:	CO002555
Collection Summary:	The strain Veillonella parvula SKV38 xdh::cat*. Briefly, V. parvula was grown on SK agar (composition: yeast extract 10 gL-1, casitone 10 gL-1, NaCl 2 gL-1, K2HPO4 0.4 gL-1) supplemented with either DL-lactate (50 mM lactate), potassium nitrate (40 mM KNO3), or both, incubated under anaerobic conditions at 37ºC overnight and then inoculated into the respective liquid media in biological triplicates. Cells and supernatants were harvested at mid-exponential phase (OD600=0.3), after centrifugation at 10,000g for 5 min. Both cell pellets and resulting supernatants were stored at -80C until processing for metabolite extraction and metabolomic analysis. A titration of cell pools and media pools was conducted (10,20,40,60,80,100%) and used to filter the data based on the correlation of the abundance of detected features with
Sample Type:	Bacterial cells

Treatment:

Treatment ID:	TR002574
Treatment Summary:	The strain was first streaked on an agar plate with SK media (composition: yeast extract 10 gL-1, casitone 10 gL-1, NaCl 2 gL-1, K2HPO4 0.4 gL-1) supplemented with 50 mM lactate and 40 mM KNO3 (SKLN medium) and antibiotics if required. From this agar plate, a single colony was selected and inoculated in 5mL SKLN media and grown for 24 hours. Next, overnight cells from this inoculum were grown using a 1/50 inoculum of the overnight culture, on either SK, SK + 50 mM lactate (SKL), SK + 40 mM nitrate (SKN), and SKLN.

Treatment ID:

TR002574

Treatment Summary:

The strain was first streaked on an agar plate with SK media (composition: yeast extract 10 gL-1, casitone 10 gL-1, NaCl 2 gL-1, K2HPO4 0.4 gL-1) supplemented with 50 mM lactate and 40 mM KNO3 (SKLN medium) and antibiotics if required. From this agar plate, a single colony was selected and inoculated in 5mL SKLN media and grown for 24 hours. Next, overnight cells from this inoculum were grown using a 1/50 inoculum of the overnight culture, on either SK, SK + 50 mM lactate (SKL), SK + 40 mM nitrate (SKN), and SKLN.

Sample Preparation:

Sampleprep ID:	SP002568
Sampleprep Summary:	Bacterial metabolites were profiled using the HILIC-pos and C8-pos methods for mapping Veillonella metabolites present in human stool. Bacterial samples were prepared as follows: mid-exponential Veillonella cultures (OD600 = 0.3-0.4) were harvested by centrifugation at 20,000g at 4°C for 1 minute, supernatants (spent media) were aliquoted, while cell pellets were resuspended in ice-cold PBS. Cells were then spun twice at 20,000g for 1 minute and all PBS supernatant removed and discarded. Cell pellet weights were estimated and all the samples harvested were stored at -80°C until metabolite profiling was conducted. For cells profiled in the C8-pos, cell pellets were resuspended in 20 µL of H2O and metabolites extracted using 380 µL of isopropanol containing 1,2-didodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids; Alabaster, AL), 10 ul of media was extracted using 190 µL of isopropanol containing internal standards. Extracts were incubated at room temperature in the dark before centrifugation (10 min, 9,000 x g, Room Temperature). For cells profiled in the HILIC-pos mode, cell pellets were resuspended in 20 µL of H2O and metabolites extracted using180 µL HILIC extraction solution with internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA), while 10 µL of media was extracted with 90 µL of extraction solution. Extracts were cleared by centrifugation (10 min, 9,000 x g, 4C) prior to analysis.

Sampleprep ID:

SP002568

Sampleprep Summary:

Bacterial metabolites were profiled using the HILIC-pos and C8-pos methods for mapping Veillonella metabolites present in human stool. Bacterial samples were prepared as follows: mid-exponential Veillonella cultures (OD600 = 0.3-0.4) were harvested by centrifugation at 20,000g at 4°C for 1 minute, supernatants (spent media) were aliquoted, while cell pellets were resuspended in ice-cold PBS. Cells were then spun twice at 20,000g for 1 minute and all PBS supernatant removed and discarded. Cell pellet weights were estimated and all the samples harvested were stored at -80°C until metabolite profiling was conducted. For cells profiled in the C8-pos, cell pellets were resuspended in 20 µL of H2O and metabolites extracted using 380 µL of isopropanol containing 1,2-didodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids; Alabaster, AL), 10 ul of media was extracted using 190 µL of isopropanol containing internal standards. Extracts were incubated at room temperature in the dark before centrifugation (10 min, 9,000 x g, Room Temperature). For cells profiled in the HILIC-pos mode, cell pellets were resuspended in 20 µL of H2O and metabolites extracted using180 µL HILIC extraction solution with internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA), while 10 µL of media was extracted with 90 µL of extraction solution. Extracts were cleared by centrifugation (10 min, 9,000 x g, 4C) prior to analysis.

Combined analysis:

Analysis ID	AN004037	AN004038
Analysis type	MS	MS
Chromatography type	HILIC	Reversed phase
Chromatography system	Shimadzu Nexera X2	Shimadzu Nexera X2
Column	Waters Atlantis HILIC (150 x 2 mm, 3 μm)	Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Plus Orbitrap	Thermo Q Exactive Plus Orbitrap
Ion Mode	POSITIVE	POSITIVE
Units	Abundance	Abundance

Chromatography:

Chromatography ID:	CH002985
Instrument Name:	Shimadzu Nexera X2
Column Name:	Waters Atlantis HILIC (150 x 2 mm, 3 μm)
Column Temperature:	30C
Flow Gradient:	Isocratically with 5% mobile phase A for 1 minute followed by a linear gradient to 40% mobile phase B over 10 minutes
Flow Rate:	250 µL/min
Solvent A:	100% water; 10 mM ammonium formate; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	HILIC

Chromatography ID:	CH002986
Instrument Name:	Shimadzu Nexera X2
Column Name:	Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
Column Temperature:	40C
Flow Gradient:	The column was eluted at a flow rate of 450 µL/min isocratically for 1 minute at 80% mobile phase A, followed by a linear gradient to 80% mobile-phase B over 2 minutes, a linear gradient to 100% mobile phase B over 7 minutes, and then 3 minutes at 100% mobile-phase B.
Flow Rate:	450 µL/min
Solvent A:	95% water/5% methanol; 10 mM ammonium acetate; 0.1% acetic acid
Solvent B:	100% methanol; 0.1% acetic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003784
Analysis ID:	AN004037
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples.
Ion Mode:	POSITIVE

MS ID:	MS003785
Analysis ID:	AN004038
Instrument Name:	Thermo Q Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples.
Ion Mode:	POSITIVE