Summary of study ST001192

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 PR000804. The data can be accessed directly via it's Project DOI: 10.21228/M8RM32 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 IDST001192
Study TitleA library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research
Study TypeStool metabolite profiling
Study SummaryFecal microbiota transplantation (FMT) is used in the treatment of microbiome-associated diseases such as Clostridium difficile infections. In order to develop synthetic therapeutics and customized disease treatments we will need to understand the bacterial communities in the stool samples used in such treatments. For this purpose, a microbiome library was generated using human stool obtained from healthy human FMT recruited by OpenBiome, a non-profit organization that provides fecal microbiome therapeutics. In addition to characterizing the bacterial populations and obtaining bacterial isolates from FMT samples, we conducted metabolite profiling with the goal of: (1) generating a library of metabolites in FMT samples, (2) Identifying metabolites associated with defined bacterial populations, and (3) identifying microbial metabolites with immunoregulatory functions. We conducted metabolite profiling on a subset consisting of 180 stool samples from 84 donors using four nontargeted liquid chromatography mass spectrometry (LC-MS) methods. Generated data were processed, isotopes removed, and adducts and fragments clustered. The identity of known metabolites was determined based on matching retention times of neat standards run in parallel with the study.
Institute
Broad Institute of MIT and Harvard
Last NameAvila-Pacheco
First NameJulian
Address415 Main Street
Emailjravilap@broadinstitute.org
Phone617-714-8264
Submit Date2019-06-10
Total Subjects84
Raw Data AvailableYes
Raw Data File Type(s).xlsx
Analysis Type DetailLC-MS
Release Date2019-07-17
Release Version1
Julian Avila-Pacheco Julian Avila-Pacheco
https://dx.doi.org/10.21228/M8RM32
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000804
Project DOI:doi: 10.21228/M8RM32
Project Title:A large library of gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome studies
Project Type:Metabolite profiling of human stool from a healthy cohort
Project Summary:Here, we present the Broad Institute-OpenBiome Microbiome Library (BIO-ML), a comprehensive collection of 7,758 gut bacterial isolates with 3,632 paired genome sequences, and densely sampled multi-omic time series from many individual humans. Our longitudinal data reveal (1) that microbial species maintain stable population sizes within and across humans, (2) that commonly used ‘omic survey methods are more reliable when using averages over multiple days of sampling, (3) that variation of gut metabolites within people over time is driven by amino acid levels, while differences across people are driven by differences in bile acids, and (4) that functional evolution and genomic diversification can be used to infer eco-evolutionary dynamics and in vivo selection pressures for strains within individual people. The BIO-ML is a unique resource that will enable hypothesis-driven microbiome research and the rational design of microbial therapeutics.
Institute:Broad Institute of MIT and Harvard
Department:Metabolomics Platform
Last Name:Avila-Pacheco
First Name:Julian
Address:415 Main Street, Rm 7175, Cambridge, MA, 02142, USA
Email:jravilap@broadinstitute.org
Phone:6177148264
Contributors:Mathilde Poyet, Mathieu Groussin, Sean M Gibbons, Julian Avila-Pacheco, Xiaogang Jiang, Sean M Kearney, Allison R Perrotta, Shijie Zhao, Tammi Lieberman, P K Swanson, Mark Smith, Shane Roesemann, Jessica E Alexander, Scott A. Rich, Jonathan Livny, Hera Vlamakis, Clary Clish, Kevin Bullock, Amy Deik, Justin Scott, Kerry Pierce, Ramnik Xavier, Eric J Alm

Subject:

Subject ID:SU001259
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Diet
SA082724bj-0001-
SA082725bi-0026-
SA082726bi-0001-
SA082727aa-0163-
SA082728bj-0032-
SA082729bj-0095-
SA082730bj-0056-
SA082731av-0107-
SA082732bj-0014-
SA082733au-0002-
SA082734ao-0090-
SA082735ao-0085-
SA082736ao-0049-
SA082737ar-0039-
SA082738as-0033-
SA082739bj-0110-
SA082740at-0044-
SA082741at-0004-
SA082742av-0006-
SA082743bk-0002-
SA082744ce-0001-
SA082745bw-0033-
SA082746bw-0001-
SA082747ce-0007-
SA082748ct-0001-
SA082749cu-0009-
SA082750cu-0001-
SA082751ct-0005-
SA082752bv-0001-
SA082753bt-0039-
SA082754bm-0013-
SA082755bm-0002-
SA082756bl-0009-
SA082757bn-0002-
SA082758bn-0038-
SA082759bt-0001-
SA082760bp-0002-
SA082761ao-0025-
SA082762bj-0004-
SA082763ah-0028-
SA082764ah-0002-
SA082765ai-0002-
SA082766aj-0001-
SA082767ak-0010-
SA082768ak-0001-
SA082769ag-0005-
SA082770ag-0001-
SA082771ac-0002-
SA082772ab-0140-
SA082773ad-0002-
SA082774ad-0005-
SA082775ao-0004-
SA082776af-0003-
SA082777al-0002-
SA082778af-0060-
SA082779an-0082-
SA082780an-0013-
SA082781an-0030-
SA082782an-0001-
SA082783an-0025-
SA082784ao-0001-
SA082785an-0004-
SA082786an-0002-
SA082787ch-0008Omnivore
SA082788cj-0004Omnivore
SA082789cl-0001Omnivore
SA082790cm-0001Omnivore
SA082791cm-0022Omnivore
SA082792cl-0134Omnivore
SA082793cl-0068Omnivore
SA082794cl-0018Omnivore
SA082795cl-0004Omnivore
SA082796cf-0037Omnivore
SA082797ca-0012Omnivore
SA082798cb-0001Omnivore
SA082799ca-0001Omnivore
SA082800bz-0033Omnivore
SA082801ax-0001Omnivore
SA082802cb-0051Omnivore
SA082803cc-0002Omnivore
SA082804cf-0001Omnivore
SA082805cn-0002Omnivore
SA082806ae-0003Omnivore
SA082807ae-0007Omnivore
SA082808cd-0050Omnivore
SA082809cg-0001Omnivore
SA082810cp-0009Omnivore
SA082811df-0030Omnivore
SA082812dg-0001Omnivore
SA082813df-0001Omnivore
SA082814de-0031Omnivore
SA082815dc-0028Omnivore
SA082816de-0001Omnivore
SA082817dg-0008Omnivore
SA082818dh-0001Omnivore
SA082819dk-0001Omnivore
SA082820dk-0003Omnivore
SA082821di-0009Omnivore
SA082822di-0001Omnivore
SA082823dh-0010Omnivore
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Collection:

Collection ID:CO001253
Collection Summary:Stool samples were obtained from OpenBiome (https://www.openbiome.org/), a non-profit stool bank, under a protocol approved by the institutional review boards at MIT and the Broad Institute (IRB protocol ID #1603506899)
Sample Type:Stool
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001274
Treatment Summary:Subjects were healthy people screened by OpenBiome to minimize the potential for carrying pathogens, with ages between 19-45 years and with BMI between 17.5-29.8 at initial sampling.

Sample Preparation:

Sampleprep ID:SP001267
Sampleprep Summary:Raw stool were diluted 1:10 in 12.5% glycerol buffer and 0.9% NaCl, homogenized and filtered through a 330um filter. HILIC-pos: LC-MS samples were prepared from homogenate(10 μL) via protein precipitation with the addition of nine volumes of 74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (valine-d8, Isotec; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA). The samples are centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were injected directly. HILIC-neg: Stool homogenates (30μL) were extracted using 120 μL of 80% methanol (VWR) containing 0.05 ng/μL inosine-15N4, 0.05 ng/μL thymine-d4, and 0.1 ng/μL glycocholate-d4 as internal standards (Cambridge Isotope Laboratories). The samples were centrifuged (10 min, 9,000 x g, 4ºC) and the supernatants (10 μL) were injected directly. C18-neg: Stool homogenates (30 μL) were extracted using 90 μL of methanol containing PGE2-d4 as an internal standard (Cayman Chemical Co.; Ann Arbor, MI) and centrifuged (10 min, 9,000 x g, 4°C). C8-pos: Lipids were extracted from homogenates (10 μL) using 190 μL of isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL). After centrifugation (10 min, 9,000 x g, ambient temperature), supernatants (10 μL) were injected directly

Combined analysis:

Analysis ID AN001984 AN001985 AN001986 AN001987
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Shimadzu Nexera X2 Waters Acquity Shimadzu Nexera X2 Shimadzu Nexera X2
Column Waters Atlantis HILIC (150 x 2 mm) Phenomenex Luna NH2 (150 x 2mm) Waters Acquity BEH C18 (150 x 2mm, 1.7um) Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE NEGATIVE NEGATIVE POSITIVE
Units abundance abundance Abundance Abundance

Chromatography:

Chromatography ID:CH001432
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Atlantis HILIC (150 x 2 mm)
Solvent A:10 mM ammonium formate and 0.1% formic acid in water
Solvent B:acetonitrile with 0.1% formic acid
Chromatography Type:HILIC
  
Chromatography ID:CH001433
Instrument Name:Waters Acquity
Column Name:Phenomenex Luna NH2 (150 x 2mm)
Solvent A:20 mM ammonium acetate and 20 mM ammonium hydroxide (Sigma-Aldrich) in water (VWR)
Solvent B:10 mM ammonium hydroxide in 75:25 v/v acetonitrile/methanol (VWR)
Chromatography Type:HILIC
  
Chromatography ID:CH001434
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C18 (150 x 2mm, 1.7um)
Solvent A:0.1% formic acid in water
Solvent B:acetonitrile with 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH001435
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
Solvent A:95:5:0.1 vol/vol/vol 10 mM ammonium acetate/methanol/acetic acid
Solvent B:99.9:0.1 vol/vol methanol/acetic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS001837
Analysis ID:AN001984
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:MS001838
Analysis ID:AN001985
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:NEGATIVE
  
MS ID:MS001839
Analysis ID:AN001986
Instrument Name:Thermo Q Exactive 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:NEGATIVE
  
MS ID:MS001840
Analysis ID:AN001987
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
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