Summary of Study ST001913

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 PR000319. The data can be accessed directly via it's Project DOI: 10.21228/M8H029 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 IDST001913
Study TitleStool metabolomics in the New Hampshire Birth Cohort Study
Study TypeUntargeted and semi-targeted metabolomics analysis
Study SummaryThis is a study of data collected from fecal samples from larger New Hampshire Birth Cohort Study (NHBCS). 1H NMR metabolomic profiling of 524 infant stool samples collected at 6 week - 3 year age was performed and spectra were binned (untargeted metabolomics). A set of host-microbiome co-metabolites were library matched in individual sample spectra and their relative concentrations were determined. This study investigated associations of the functional metabolic response of the microbial milieu of the infant gut with environmental and other factors.
Institute
University of North Carolina at Chapel Hill
DepartmentNutrition
LaboratoryMetabolomics and Exposome Laboratory, Nutrition Research Institute, UNC Chapel Hill
Last NameSumner
First NameSusan
Address500 Laureate Way, Kannapolis, NC 28081
Emailsusan_sumner@unc.edu
Phone(919) 622-4456
Submit Date2021-08-09
Num Groups2
Total Subjects524
Study CommentsThe number of groups includes the QC samples, Total samples = 572
Raw Data AvailableYes
Analysis Type DetailNMR
Release Date2023-01-31
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8H029
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000319
Project DOI:doi: 10.21228/M8H029
Project Title:Metabolomics Changes in the feces of infants exposed to arsenic
Project Summary:Exposure to arsenic (As) during the vulnerable window of fetal development and early childhood has shown significant clinical effects. In highly exposed populations, altered immunity is one of the most affected pathways and can lead to an elevated risk of infection and a pre-disposition to allergy/atopy. Since well water in the New Hampshire region has been determined to be a potential source of As exposure, this study includes mother-infant dyads living in the area, who obtain household water from private wells. This study seeks to determine if in utero and early life As exposure is related to increase occurrence of childhood: infections, allergy and atopy, and diminished vaccine response. It has been observed that the microbiome is an important mediator of immune impairment due to As exposure. Therefore, we will further investigate the relation between in utero and early life As exposure on the development of the infant intestinal microbiome in the first year of life. For this study fecal samples, from infants at risk of As exposure, were collected at 6 weeks and 12 months of age. Metabolomics data will allow for a more complete picture of the relationships between the microbiome, As exposure and immune function.
Institute:Dartmouth College
Department:Department of Epidemiology
Last Name:Margaret
First Name:Karagas
Address:One Medical Center Road, 7927 HB, Rubin Building, Lebanon, NH 03756
Email:Margaret.Karagas@Dartmouth.edu
Phone:603-653-9010

Subject:

Subject ID:SU001991
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 Sample type
SA177030BD3_P1Batch-QC
SA177031BD2_P4Batch-QC
SA177032BD3_P2Batch-QC
SA177033BD3_P3Batch-QC
SA177034BD3_P4Batch-QC
SA177035BD2_P2Batch-QC
SA177036BD2_P1Batch-QC
SA177037BD1_P1Batch-QC
SA177038BD1_P2Batch-QC
SA177039BD1_P3Batch-QC
SA177040BD1_P4Batch-QC
SA177041BD4_P1Batch-QC
SA177042BD2_P3Batch-QC
SA177043BD6_P2Batch-QC
SA177044BD5_P4Batch-QC
SA177045BD6_P3Batch-QC
SA177046BD6_P4Batch-QC
SA177047BD4_P2Batch-QC
SA177048BD5_P3Batch-QC
SA177049BD6_P1Batch-QC
SA177050BD4_P4Batch-QC
SA177051BD5_P1Batch-QC
SA177052BD4_P3Batch-QC
SA177053BD5_P2Batch-QC
SA177054S_440Sample
SA177055S_441Sample
SA177056S_44Sample
SA177057S_438Sample
SA177058S_442Sample
SA177059S_437Sample
SA177060S_439Sample
SA177061S_449Sample
SA177062S_448Sample
SA177063S_436Sample
SA177064S_447Sample
SA177065S_446Sample
SA177066S_444Sample
SA177067S_445Sample
SA177068S_443Sample
SA177069S_420Sample
SA177070S_423Sample
SA177071S_425Sample
SA177072S_422Sample
SA177073S_421Sample
SA177074S_42Sample
SA177075S_45Sample
SA177076S_426Sample
SA177077S_427Sample
SA177078S_433Sample
SA177079S_434Sample
SA177080S_431Sample
SA177081S_430Sample
SA177082S_428Sample
SA177083S_429Sample
SA177084S_435Sample
SA177085S_461Sample
SA177086S_47Sample
SA177087S_470Sample
SA177088S_469Sample
SA177089S_468Sample
SA177090S_466Sample
SA177091S_467Sample
SA177092S_471Sample
SA177093S_472Sample
SA177094S_477Sample
SA177095S_478Sample
SA177096S_476Sample
SA177097S_475Sample
SA177098S_473Sample
SA177099S_474Sample
SA177100S_465Sample
SA177101S_464Sample
SA177102S_455Sample
SA177103S_456Sample
SA177104S_454Sample
SA177105S_453Sample
SA177106S_451Sample
SA177107S_452Sample
SA177108S_457Sample
SA177109S_458Sample
SA177110S_419Sample
SA177111S_463Sample
SA177112S_460Sample
SA177113S_46Sample
SA177114S_459Sample
SA177115S_450Sample
SA177116S_407Sample
SA177117S_38Sample
SA177118S_380Sample
SA177119S_379Sample
SA177120S_378Sample
SA177121S_376Sample
SA177122S_377Sample
SA177123S_381Sample
SA177124S_382Sample
SA177125S_387Sample
SA177126S_388Sample
SA177127S_386Sample
SA177128S_385Sample
SA177129S_383Sample
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Collection:

Collection ID:CO001984
Collection Summary:Infant stool samples were collected at home using provided diapers, sealed in a separate polyethylene bag and frozen in a home freezer or kept chilled until transport. Samples were transported in a cooler with ice packs and brought to the routine 6-week post-partum visit within 24 hours of collection. Stool samples remained frozen until processing where they were thawed at 4 °C. Using sterile applicators, 0.5–1 g of stool was aliquoted into trace element-free cryovial tubes and then frozen at −80 °C in a biorepository
Sample Type:Feces
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002003
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP001997
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. Dartmouth-Fecal Metabolomics_NMR_Batch2 Procedures
Processing Storage Conditions:4℃
Extraction Method:50% Acetonitrile in Water
Extract Storage:-80℃
Sample Resuspension:In phosphate buffer containing D2O

Analysis:

Analysis ID:AN003111
Laboratory Name:Metabolomics and Exposome Lab at UNC Nutrition Research Institute
Analysis Type:NMR
Software Version:TopSpin 3.5
Operator Name:Wimal Pathmasiri
Detector Type:NMR
Data Format:fid, 1r
Results File:4a._Dartmouth-Fecal_Metabolomics_NMR_Normalized_Binned_Data.txt
Units:ppm

NMR:

NMR ID:NM000214
Analysis ID:AN003111
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)
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