{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002247","ANALYSIS_ID":"AN003673","VERSION":"1","CREATED_ON":"August 9, 2022, 8:17 am"},

"PROJECT":{"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"},

"STUDY":{"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","EMAIL":"rxavier@broadinstitute.org","PHONE":"617717084"},

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"Additional sample data":{"sample_name":"R25_18m","sample_title":"Stool sample collected at the age of 18 months from subject R25","visit":"V12"}
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{
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},
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"Additional sample data":{"sample_name":"R36_DS1","sample_title":"Stool sample collected during a diarrheal episode at the age of 332 days from subject R36","visit":"DS"}
},
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"Factors":{"host_age":"10 months"},
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},
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"Subject ID":"R36",
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},
{
"Subject ID":"R36",
"Sample ID":"9995",
"Factors":{"host_age":"-"},
"Additional sample data":{"sample_name":"R36_DS4","sample_title":"-","visit":"DS"}
},
{
"Subject ID":"R36",
"Sample ID":"9050",
"Factors":{"host_age":"15 months"},
"Additional sample data":{"sample_name":"R36_15m","sample_title":"Stool sample collected at the age of 15 months from subject R36","visit":"V11"}
},
{
"Subject ID":"R36",
"Sample ID":"9993",
"Factors":{"host_age":"446 days"},
"Additional sample data":{"sample_name":"R36_DS2","sample_title":"Stool sample collected during a diarrheal episode at the age of 446 days from subject R36","visit":"DS"}
},
{
"Subject ID":"R36",
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"Factors":{"host_age":"2 months"},
"Additional sample data":{"sample_name":"R36_2m","sample_title":"Stool sample collected at the age of 2 months from subject R36","visit":"V5"}
},
{
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"Sample ID":"8532",
"Factors":{"host_age":"6 months"},
"Additional sample data":{"sample_name":"R36_6m","sample_title":"Stool sample collected at the age of 6 months from subject R36","visit":"V7"}
},
{
"Subject ID":"R237",
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"Factors":{"host_age":"15 months"},
"Additional sample data":{"sample_name":"R237_15m","sample_title":"Stool sample collected at the age of 15 months from subject R237","visit":"V11"}
},
{
"Subject ID":"R237",
"Sample ID":"9832",
"Factors":{"host_age":"2 months"},
"Additional sample data":{"sample_name":"R237_2m","sample_title":"Stool sample collected at the age of 2 months from subject R237","visit":"V5"}
},
{
"Subject ID":"R237",
"Sample ID":"9225",
"Factors":{"host_age":"24 months"},
"Additional sample data":{"sample_name":"R237_24m","sample_title":"Stool sample collected at the age of 24 months from subject R237","visit":"V13"}
},
{
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"Sample ID":"9563",
"Factors":{"host_age":"2 months"},
"Additional sample data":{"sample_name":"R101_2m","sample_title":"Stool sample collected at the age of 2 months from subject R101","visit":"V5"}
},
{
"Subject ID":"R101",
"Sample ID":"9277",
"Factors":{"host_age":"24 months"},
"Additional sample data":{"sample_name":"R101_24m","sample_title":"Stool sample collected at the age of 24 months from subject R101","visit":"V13"}
},
{
"Subject ID":"R275",
"Sample ID":"8514",
"Factors":{"host_age":"6 months"},
"Additional sample data":{"sample_name":"R275_6m","sample_title":"Stool sample collected at the age of 6 months from subject R275","visit":"V7"}
},
{
"Subject ID":"R275",
"Sample ID":"9021",
"Factors":{"host_age":"18 months"},
"Additional sample data":{"sample_name":"R275_18m","sample_title":"Stool sample collected at the age of 18 months from subject R275","visit":"V12"}
},
{
"Subject ID":"R275",
"Sample ID":"9390",
"Factors":{"host_age":"24 months"},
"Additional sample data":{"sample_name":"R275_24m","sample_title":"Stool sample collected at the age of 24 months from subject R275","visit":"V13"}
},
{
"Subject ID":"R275",
"Sample ID":"9863",
"Factors":{"host_age":"2 months"},
"Additional sample data":{"sample_name":"R275_2m","sample_title":"Stool sample collected at the age of 2 months from subject R275","visit":"V5"}
},
{
"Subject ID":"R31",
"Sample ID":"9916",
"Factors":{"host_age":"-"},
"Additional sample data":{"sample_name":"R31_","sample_title":"-","visit":"-"}
},
{
"Subject ID":"R19",
"Sample ID":"9060",
"Factors":{"host_age":"15 months"},
"Additional sample data":{"sample_name":"R19_15m","sample_title":"Stool sample collected at the age of 15 months from subject R19","visit":"V11"}
},
{
"Subject ID":"R19",
"Sample ID":"9182",
"Factors":{"host_age":"18 months"},
"Additional sample data":{"sample_name":"R19_18m","sample_title":"Stool sample collected at the age of 18 months from subject R19","visit":"V12"}
},
{
"Subject ID":"R19",
"Sample ID":"9227",
"Factors":{"host_age":"24 months"},
"Additional sample data":{"sample_name":"R19_24m","sample_title":"Stool sample collected at the age of 24 months from subject R19","visit":"V13"}
},
{
"Subject ID":"R19",
"Sample ID":"8547",
"Factors":{"host_age":"6 months"},
"Additional sample data":{"sample_name":"R19_6m","sample_title":"Stool sample collected at the age of 6 months from subject R19","visit":"V7"}
},
{
"Subject ID":"R19",
"Sample ID":"8866",
"Factors":{"host_age":"10 months"},
"Additional sample data":{"sample_name":"R19_10m","sample_title":"Stool sample collected at the age of 10 months from subject R19","visit":"V9"}
},
{
"Subject ID":"R19",
"Sample ID":"9833",
"Factors":{"host_age":"2 months"},
"Additional sample data":{"sample_name":"R19_2m","sample_title":"Stool sample collected at the age of 2 months from subject R19","visit":"V5"}
}
],
"COLLECTION":{"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_SUMMARY":"NA"},

"SAMPLEPREP":{"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."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Shimadzu Nexera X2","COLUMN_NAME":"Waters Acquity T3 (150 x 2.1 mm, 1.7 um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","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.","MS_RESULTS_FILE":"ST002247_AN003673_Results.txt UNITS:Abundances Has m/z:Yes Has RT:Yes RT units:Minutes"},

"MS_METABOLITE_DATA":{
"Units":"Abundances",

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}

}