Summary of Study ST002247

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 PR001435. The data can be accessed directly via it's Project DOI: 10.21228/M87D7V 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 IDST002247
Study TitleMicrobiota and Health Study (Dhaka, Bangladesh)
Study SummaryThe Microbiota and Health Study (clinicaltrials.gov: NCT02361164) was a longitudinal, community-based cohort study in Nandipara, a peri-urban community of Dhaka, Bangladesh conducted from April 2013 to October 2016. 267 newborns born to healthy mothers were followed from birth to two years of age. Fecal samples were collected at birth, during subsequent scheduled visits, and when possible during illness episodes. Active surveillance of diarrheal and respiratory infections was conducted by a community-based team of nurses supervised by a physician. Fecal samples of 222 participants were analyzed by metabolomic profiling.
Institute
Broad Institute of MIT and Harvard
Last NameXavier
First NameRamnik
Address415 Main Street
Emailrxavier@broadinstitute.org
Phone617717084
Submit Date2022-08-08
Analysis Type DetailLC-MS
Release Date2022-11-01
Release Version1
Ramnik Xavier Ramnik Xavier
https://dx.doi.org/10.21228/M87D7V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001435
Project DOI:doi: 10.21228/M87D7V
Project Title:Microbiota and Health Study (Dhaka, Bangladesh)
Project Type:Metabolomic profiling of human fecal samples
Project Summary:The Microbiota and Health Study (clinicaltrials.gov: NCT02361164) was a longitudinal, community-based cohort study in Nandipara, a peri-urban community of Dhaka, Bangladesh conducted from April 2013 to October 2016. 267 newborns born to healthy mothers were followed from birth to two years of age. Fecal samples were collected at birth, during subsequent scheduled visits, and when possible during illness episodes. Active surveillance of diarrheal and respiratory infections was conducted by a community-based team of nurses supervised by a physician. Fecal samples of 222 participants were analyzed by metabolomic profiling.
Institute:Broad Institute of MIT and Harvard
Last Name:Xavier
First Name:Ramnik
Address:415 Main Street
Email:rxavier@broadinstitute.org
Phone:6177147080
Funding Source:Generation of metabolomics data was supported by a grant from Nestle
Contributors:Tommi Vatanen, Qi Yan Ang, Léa Siegwald, Shafiqul Alam Sarker, Caroline I. Le Roy, Stéphane Duboux, Omar Delannoy-Bruno, Catherine Ngom-Bru, Claire L. Boulangé, Martin Stražar, Julian Avila-Pacheco, Amy Deik, Kerry Pierce, Kevin Bullock, Courtney Dennis, Shamima Sultana, Sharika Sayed, Mahbubar Rahman, Tahmeed Ahmed, Clary B. Clish, Hera Vlamakis, Damian R. Plichta, Olga Sakwinska, Ramnik J. Xavier

Subject:

Subject ID:SU002333
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 host_age
SA2148229981-
SA2148239978-
SA2148249888-
SA2148259971-
SA2148269975-
SA2148279989-
SA2148289539-
SA2148299956-
SA21483010002-
SA21483110007-
SA21483210004-
SA2148339900-
SA21483410009-
SA2148359958-
SA2148368736-
SA2148379813-
SA2148389995-
SA21483910001-
SA2148409959-
SA2148419916-
SA21484299450 months
SA21484399460 months
SA21484495830 months
SA21484599530 months
SA21484699520 months
SA21484799290 months
SA21484899220 months
SA21484999480 months
SA21485099440 months
SA21485199340 months
SA21485299350 months
SA21485395850 months
SA21485499270 months
SA21485599370 months
SA21485699510 months
SA21485799410 months
SA21485899210 months
SA21485999230 months
SA21486099240 months
SA21486199330 months
SA21486295840 months
SA21486399260 months
SA21486499280 months
SA21486599320 months
SA21486699500 months
SA21486799400 months
SA21486899470 months
SA21486999540 months
SA21487099490 months
SA21487199420 months
SA21487299200 months
SA21487399430 months
SA21487499380 months
SA21487599310 months
SA21487699390 months
SA21487799360 months
SA21487899250 months
SA21487999300 months
SA21488095820 months
SA21488199550 months
SA2150969972102 days
SA214882859610 months
SA214883858210 months
SA214884865610 months
SA214885886710 months
SA214886861110 months
SA214887869310 months
SA214888858610 months
SA214889866510 months
SA214890856910 months
SA214891882310 months
SA214892862010 months
SA214893855910 months
SA214894860310 months
SA214895885810 months
SA214896881210 months
SA214897878810 months
SA214898861810 months
SA214899865910 months
SA214900863310 months
SA214901885610 months
SA214902880510 months
SA214903882910 months
SA214904868510 months
SA214905881610 months
SA214906861210 months
SA214907885210 months
SA214908865810 months
SA214909858310 months
SA214910869510 months
SA214911879810 months
SA214912882810 months
SA214913886810 months
SA214914865410 months
SA214915870010 months
SA214916882410 months
SA214917855710 months
SA214918863510 months
SA214919886110 months
SA214920864010 months
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Collection:

Collection ID:CO002326
Collection Summary:Fecal samples were collected at birth (between 0 and 10 days post-delivery, median = 1 day, time point labeled as “birth”), during subsequent scheduled visits, and when possible during illness episodes. Stool samples were initially stored at -20°C at the International Centre for Diarrhoeal Disease Research (Bangladesh) and subsequently transferred to -80°C for shipment on dry ice to Nestlé Research where they were stored at -80°C until analysis.
Sample Type:Feces

Treatment:

Treatment ID:TR002345
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP002339
Sampleprep Summary:Stool samples were homogenized in 10 μL of water per milligram stool sample weight using a bead mill (TissueLyser II; Qiagen) and the aqueous homogenates were aliquoted for metabolite profiling analyses. LC-MS samples were prepared for four profiling methods as follows: HILIC-pos: Metabolites were extracted by adding 90 μL 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) to a 10 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C8-pos: Lipids were extracted by adding 190 μL of isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL) to a 10 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, ambient temperature) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. HILIC-neg: Metabolites were extracted by adding 120 μL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA) to a 30 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C18-neg: Metabolites were extracted by adding 90 μL of methanol containing PGE2-d4 as an internal standard (Cayman Chemical Co.; Ann Arbor, MI) to a 30 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis.

Combined analysis:

Analysis ID AN003670 AN003671 AN003672 AN003673
Analysis type MS MS MS MS
Chromatography type HILIC Reversed phase HILIC Reversed phase
Chromatography system Shimadzu Nexera X2 Shimadzu Nexera X2 Shimadzu Nexera X2 Shimadzu Nexera X2
Column Waters Atlantis HILIC (150 x 2mm,3um) Waters Acquity BEH C8 (100 x 2.1mm,1.7um) Phenomenex Luna NH2 (150 x 2.1mm,3um) Waters Acquity T3 (150 x 2.1 mm,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 Plus Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE NEGATIVE
Units Abundances Abundances Unitless Abundances Abundances

Chromatography:

Chromatography ID:CH002720
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Atlantis HILIC (150 x 2mm,3um)
Chromatography Type:HILIC
  
Chromatography ID:CH002721
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002722
Instrument Name:Shimadzu Nexera X2
Column Name:Phenomenex Luna NH2 (150 x 2.1mm,3um)
Chromatography Type:HILIC
  
Chromatography ID:CH002723
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity T3 (150 x 2.1 mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003421
Analysis ID:AN003670
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:MS003422
Analysis ID:AN003671
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:MS003423
Analysis ID:AN003672
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:MS003424
Analysis ID:AN003673
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
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