{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001813","ANALYSIS_ID":"AN002939","VERSION":"1","CREATED_ON":"June 3, 2021, 9:48 am"},

"PROJECT":{"PROJECT_TYPE":"Metabolomics Analysis","PROJECT_SUMMARY":"Broad spectrum NMR metabolomics data was acquired from feces collected from infants at age 6 weeks (n=158) and 1 year (n=282) of life who are enrolled in the New Hampshire Birth Cohort. NMR binned data (untargeted) and relative concentration data (semi-targeted) were integrated with these subject’s microbiome data using statistical and machine learning-based methods to characterize the taxa-function relationship in early life.","INSTITUTE":"Dartmouth College","DEPARTMENT":"Department of Epidemiology","FIRST_NAME":"Margaret","ADDRESS":"One Medical Center Road, 7927 HB, Rubin Building, Lebanon, NH 03756, USA","EMAIL":"Margaret.Karagas@Dartmouth.edu","PHONE":"603-653-9010","FUNDING_SOURCE":"National Institutes of Health (grants NLM R01LM012723, NIGMS P20GM104416, NCI P30CA023108, NCI R21CA253408, NLM K01LM012426, NIH UG3 OD023275, NIEHS P01ES022832 and EPA RD-83544201)","PROJECT_COMMENTS":"For further details, contact Margaret Karagass for information on the New Hampshire Birth Cohort Study","PROJECT_TITLE":"Associations between the gut microbiome and metabolome in early life","LAST_NAME":"Karagas"},

"STUDY":{"STUDY_TITLE":"Associations between the gut microbiome and metabolome in early life","STUDY_SUMMARY":"The infant intestinal microbiome plays an important role in metabolism and immune development with impacts on lifelong health. The linkage between the taxonomic composition of the microbiome and its metabolic phenotype is undefined and complicated by redundancies in the taxon-function relationship within microbial communities. To inform a more mechanistic understanding of the relationship between the microbiome and health, we performed an integrative statistical and machine learning-based analysis of microbe taxonomic structure and metabolic function (using untargeted (binned) NMR and relative concentration data) in order to characterize the taxa-function relationship in early life.","INSTITUTE":"University of North Carolina at Chapel Hill","DEPARTMENT":"Nutrition","LABORATORY":"Metabolomics and Exposome Laboratory at UNC CH Nutrition Research Institute","LAST_NAME":"Sumner","FIRST_NAME":"Susan","ADDRESS":"500 Laureate Way, Kannapolis, NC, 28081, USA","EMAIL":"susan_sumner@unc.edu","TOTAL_SUBJECTS":"440","STUDY_TYPE":"Untargeted and semi-targeted metabolomics analysis","PHONE":"919-541-6861"},

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"COLLECTION":{"COLLECTION_SUMMARY":"Feces collected from 6W and 1Y infants in the New Hampshire Birth Cohort","SAMPLE_TYPE":"Feces"},

"TREATMENT":{"TREATMENT_SUMMARY":"None"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"De-identified stool aliquots were shipped on dry ice and immediately stored at -80 °C for metabolomics analysis. Samples were randomized into batches. For each batch, samples were thawed and ~150mg of stool was transferred to MagNA Lyser tubes after recording the weight, Samples were then homogenized with 50% acetonitrile in water by using the Omni Bead Disruptor (Omni International, GA, USA). Homogenized samples were centrifuged at 16000 rcf and the supernatant was separated into another tube. An aliquot (1000 uL, 100 mg equivalent of fecal mass) was transferred into Eppendorf tube and lyophilized overnight. The dried extract was reconstituted in 700 uL of NMR master mix (containing 0.2M phosphate, 0.5 mM DSS-d6, and 0.2% sodium azide), vortexed on a multitube vortexer at speed 5 for 2 min and centrifuged at 16000 rcf for 5 min. A 600 µl aliquot of the supernatant was transferred into a pre-labeled 5mm NMR tube for data acquisition on a 700 MHz spectrometer. Additionally, study pooled samples (created from randomly selected study samples) and batch pooled quality control (QC) samples were generated from supernatants of study samples and aliquots of supernatants were dried and reconstituted similar to study samples described above, and used for QC purposes.","SAMPLEPREP_PROTOCOL_FILENAME":"1.Fecal_Metabolomics_Microbiome_Study_Procedures","PROCESSING_STORAGE_CONDITIONS":"4℃","EXTRACT_STORAGE":"-80℃","SAMPLE_RESUSPENSION":"In phosphate buffer containing D2O"},

"ANALYSIS":{"DATA_FORMAT":"fid, 1r"},

"NM":{"INSTRUMENT_NAME":"Avance III 700 MHz NMR Spectrometer","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","FIELD_FREQUENCY_LOCK":"3015 Hz, D2O","STANDARD_CONCENTRATION":"0.5 mM","SPECTROMETER_FREQUENCY":"700 MHz","NMR_PROBE":"CP QCI/HPCN","NMR_SOLVENT":"90% H2O, 10% D2O","NMR_TUBE_SIZE":"5 mm","SHIMMING_METHOD":"topshim","PULSE_SEQUENCE":"noesygppr1d","WATER_SUPPRESSION":"pre-saturation","PULSE_WIDTH":"14.59 us","POWER_LEVEL":"12.3 Watts","RECEIVER_GAIN":"36","OFFSET_FREQUENCY":"3290.61 Hz","PRESATURATION_POWER_LEVEL":"0.0000964 Watts","CHEMICAL_SHIFT_REF_CPD":"DSS-d6","TEMPERATURE":"25 C","NUMBER_OF_SCANS":"64","DUMMY_SCANS":"4","ACQUISITION_TIME":"3.9 seconds","RELAXATION_DELAY":"2 seconds","SPECTRAL_WIDTH":"12 ppm","NUM_DATA_POINTS_ACQUIRED":"65536","REAL_DATA_POINTS":"32768","LINE_BROADENING":"0.5 Hz","ZERO_FILLING":"Yes","APODIZATION":"Lorentzian","BASELINE_CORRECTION_METHOD":"Polynomial","CHEMICAL_SHIFT_REF_STD":"DSS-d6","BINNED_INCREMENT":"0.04ppm","BINNED_DATA_EXCLUDED_RANGE":"4.79 - 4.85 ppm (Water region)"},

"NMR_METABOLITE_DATA":{
"Units":"uM",

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Compound":"284"},{"Metabolite":"Fucose","CAS Registry":"2438-80-4","HMDB Accession Number":"HMDB00174","KEGG Compound ID":"C01019","PubChem Compound":"17106"},{"Metabolite":"Fumarate","CAS Registry":"110-17-8","HMDB Accession Number":"HMDB00134","KEGG Compound ID":"C00122","PubChem Compound":"723"},{"Metabolite":"Glucose","CAS Registry":"50-99-7","HMDB Accession Number":"HMDB00122","KEGG Compound ID":"C00031","PubChem Compound":"5793"},{"Metabolite":"Glutamate","CAS Registry":"56-86-0","HMDB Accession Number":"HMDB00148","KEGG Compound ID":"C00025","PubChem Compound":"33032"},{"Metabolite":"Glycerol","CAS Registry":"56-81-5","HMDB Accession Number":"HMDB00131","KEGG Compound ID":"C00116","PubChem Compound":"753"},{"Metabolite":"Glycine","CAS Registry":"56-40-6","HMDB Accession Number":"HMDB00123","KEGG Compound ID":"C00037","PubChem Compound":"750"},{"Metabolite":"Histidine","CAS Registry":"71-00-1","HMDB Accession Number":"HMDB00177","KEGG Compound ID":"C00135","PubChem Compound":"6274"},{"Metabolite":"Inosine","CAS Registry":"58-63-9","HMDB Accession Number":"HMDB00195","KEGG Compound ID":"C00294","PubChem Compound":"6021"},{"Metabolite":"Isobutyrate","CAS Registry":"79-31-2","HMDB Accession Number":"HMDB01873","KEGG Compound ID":"C02632","PubChem Compound":"6590"},{"Metabolite":"Isoleucine","CAS Registry":"73-32-5","HMDB Accession Number":"HMDB00172","KEGG Compound ID":"C00407","PubChem Compound":"6306"},{"Metabolite":"Lactate","CAS Registry":"79-33-4","HMDB Accession Number":"HMDB00190","KEGG Compound ID":"C00186","PubChem Compound":"107689"},{"Metabolite":"Leucine","CAS Registry":"61-90-5","HMDB Accession Number":"HMDB00687","KEGG Compound ID":"C00123","PubChem Compound":"6106"},{"Metabolite":"Lysine","CAS Registry":"56-87-1","HMDB Accession Number":"HMDB00182","KEGG Compound ID":"C00047","PubChem Compound":"5962"},{"Metabolite":"Malonate","CAS Registry":"141-82-2","HMDB Accession Number":"HMDB00691","KEGG Compound ID":"C00383","PubChem Compound":"867"},{"Metabolite":"Maltose","CAS Registry":"69-79-4","HMDB Accession Number":"HMDB00163","KEGG Compound ID":"C00208","PubChem Compound":"439186"},{"Metabolite":"Methionine","CAS Registry":"63-68-3","HMDB Accession Number":"HMDB00696","KEGG Compound ID":"C00073","PubChem Compound":"6137"},{"Metabolite":"Nicotinate","CAS Registry":"59-67-6","HMDB Accession Number":"HMDB01488","KEGG Compound ID":"C00253","PubChem Compound":"938"},{"Metabolite":"Phenylalanine","CAS Registry":"63-91-2","HMDB Accession Number":"HMDB00159","KEGG Compound ID":"C00079","PubChem Compound":"6140"},{"Metabolite":"Proline","CAS Registry":"147-85-3","HMDB Accession Number":"HMDB00162","KEGG Compound ID":"C00148","PubChem Compound":"145742"},{"Metabolite":"Propionate","CAS Registry":"79-09-4","HMDB Accession Number":"HMDB00237","KEGG Compound ID":"C00163","PubChem Compound":"1032"},{"Metabolite":"Propylene glycol","CAS Registry":"57-55-6","HMDB Accession Number":"HMDB01881","KEGG Compound ID":"C00583","PubChem Compound":"1030"},{"Metabolite":"Succinate","CAS Registry":"110-15-6","HMDB Accession Number":"HMDB00254","KEGG Compound ID":"C00042","PubChem Compound":"1110"},{"Metabolite":"Threonine","CAS Registry":"72-19-5","HMDB Accession Number":"HMDB00167","KEGG Compound ID":"C00188","PubChem Compound":"6288"},{"Metabolite":"Tryptophan","CAS Registry":"73-22-3","HMDB Accession Number":"HMDB00929","KEGG Compound ID":"C00078","PubChem Compound":"6305"},{"Metabolite":"Tyrosine","CAS Registry":"60-18-4","HMDB Accession Number":"HMDB00158","KEGG Compound ID":"C00082","PubChem Compound":"6057"},{"Metabolite":"Uracil","CAS Registry":"66-22-8","HMDB Accession Number":"HMDB00300","KEGG Compound ID":"C00106","PubChem Compound":"1174"},{"Metabolite":"Uridine","CAS Registry":"58-96-8","HMDB Accession Number":"HMDB00296","KEGG Compound ID":"C00299","PubChem Compound":"6029"},{"Metabolite":"Valine","CAS Registry":"72-18-4","HMDB Accession Number":"HMDB00883","KEGG Compound ID":"C00183","PubChem Compound":"6287"},{"Metabolite":"pi-Methylhistidine","CAS Registry":"368-16-1","HMDB Accession Number":"HMDB00479","KEGG Compound ID":"C01152","PubChem Compound":"64969"}]
}

}