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.
Study ID | ST002247 |
Study Title | Microbiota and Health Study (Dhaka, Bangladesh) |
Study 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 |
rxavier@broadinstitute.org | |
Phone | 617717084 |
Submit Date | 2022-08-08 |
Analysis Type Detail | LC-MS |
Release Date | 2022-11-01 |
Release Version | 1 |
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 |
Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
mb_sample_id | local_sample_id | host_age |
---|---|---|
SA214822 | 9981 | - |
SA214823 | 9978 | - |
SA214824 | 9888 | - |
SA214825 | 9971 | - |
SA214826 | 9975 | - |
SA214827 | 9989 | - |
SA214828 | 9539 | - |
SA214829 | 9956 | - |
SA214830 | 10002 | - |
SA214831 | 10007 | - |
SA214832 | 10004 | - |
SA214833 | 9900 | - |
SA214834 | 10009 | - |
SA214835 | 9958 | - |
SA214836 | 8736 | - |
SA214837 | 9813 | - |
SA214838 | 9995 | - |
SA214839 | 10001 | - |
SA214840 | 9959 | - |
SA214841 | 9916 | - |
SA214842 | 9945 | 0 months |
SA214843 | 9946 | 0 months |
SA214844 | 9583 | 0 months |
SA214845 | 9953 | 0 months |
SA214846 | 9952 | 0 months |
SA214847 | 9929 | 0 months |
SA214848 | 9922 | 0 months |
SA214849 | 9948 | 0 months |
SA214850 | 9944 | 0 months |
SA214851 | 9934 | 0 months |
SA214852 | 9935 | 0 months |
SA214853 | 9585 | 0 months |
SA214854 | 9927 | 0 months |
SA214855 | 9937 | 0 months |
SA214856 | 9951 | 0 months |
SA214857 | 9941 | 0 months |
SA214858 | 9921 | 0 months |
SA214859 | 9923 | 0 months |
SA214860 | 9924 | 0 months |
SA214861 | 9933 | 0 months |
SA214862 | 9584 | 0 months |
SA214863 | 9926 | 0 months |
SA214864 | 9928 | 0 months |
SA214865 | 9932 | 0 months |
SA214866 | 9950 | 0 months |
SA214867 | 9940 | 0 months |
SA214868 | 9947 | 0 months |
SA214869 | 9954 | 0 months |
SA214870 | 9949 | 0 months |
SA214871 | 9942 | 0 months |
SA214872 | 9920 | 0 months |
SA214873 | 9943 | 0 months |
SA214874 | 9938 | 0 months |
SA214875 | 9931 | 0 months |
SA214876 | 9939 | 0 months |
SA214877 | 9936 | 0 months |
SA214878 | 9925 | 0 months |
SA214879 | 9930 | 0 months |
SA214880 | 9582 | 0 months |
SA214881 | 9955 | 0 months |
SA215096 | 9972 | 102 days |
SA214882 | 8596 | 10 months |
SA214883 | 8582 | 10 months |
SA214884 | 8656 | 10 months |
SA214885 | 8867 | 10 months |
SA214886 | 8611 | 10 months |
SA214887 | 8693 | 10 months |
SA214888 | 8586 | 10 months |
SA214889 | 8665 | 10 months |
SA214890 | 8569 | 10 months |
SA214891 | 8823 | 10 months |
SA214892 | 8620 | 10 months |
SA214893 | 8559 | 10 months |
SA214894 | 8603 | 10 months |
SA214895 | 8858 | 10 months |
SA214896 | 8812 | 10 months |
SA214897 | 8788 | 10 months |
SA214898 | 8618 | 10 months |
SA214899 | 8659 | 10 months |
SA214900 | 8633 | 10 months |
SA214901 | 8856 | 10 months |
SA214902 | 8805 | 10 months |
SA214903 | 8829 | 10 months |
SA214904 | 8685 | 10 months |
SA214905 | 8816 | 10 months |
SA214906 | 8612 | 10 months |
SA214907 | 8852 | 10 months |
SA214908 | 8658 | 10 months |
SA214909 | 8583 | 10 months |
SA214910 | 8695 | 10 months |
SA214911 | 8798 | 10 months |
SA214912 | 8828 | 10 months |
SA214913 | 8868 | 10 months |
SA214914 | 8654 | 10 months |
SA214915 | 8700 | 10 months |
SA214916 | 8824 | 10 months |
SA214917 | 8557 | 10 months |
SA214918 | 8635 | 10 months |
SA214919 | 8861 | 10 months |
SA214920 | 8640 | 10 months |
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 |