Summary of Study ST001813

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 PR001146. The data can be accessed directly via it's Project DOI: 10.21228/M8K69N 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 IDST001813
Study TitleAssociations between the gut microbiome and metabolome in early life
Study TypeUntargeted and semi-targeted metabolomics analysis
Study SummaryThe 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
DepartmentNutrition
LaboratoryMetabolomics and Exposome Laboratory at UNC CH Nutrition Research Institute
Last NameSumner
First NameSusan
Address500 Laureate Way, Kannapolis, NC, 28081, USA
Emailsusan_sumner@unc.edu
Phone919-541-6861
Submit Date2021-05-26
Total Subjects440
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2021-07-14
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8K69N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001146
Project DOI:doi: 10.21228/M8K69N
Project Title:Associations between the gut microbiome and metabolome in early life
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
Last Name:Karagas
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

Subject:

Subject ID:SU001890
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 Timepoint Sample Type
SA168318S_271_1Y12M Sample
SA168319S_272_1Y12M Sample
SA168320S_268_1Y12M Sample
SA168321S_267_1Y12M Sample
SA168322S_26512M Sample
SA168323S_273_1Y12M Sample
SA168324S_27412M Sample
SA168325S_278_1Y12M Sample
SA168326S_27612M Sample
SA168327S_275_1Y12M Sample
SA168328S_274_1Y12M Sample
SA168329S_264_1Y12M Sample
SA168330S_260_1Y12M Sample
SA168331S_255_1Y12M Sample
SA168332S_256_1Y12M Sample
SA168333S_254_1Y12M Sample
SA168334S_252_1Y12M Sample
SA168335S_251_1Y12M Sample
SA168336S_258_1Y12M Sample
SA168337S_259_1Y12M Sample
SA168338S_27912M Sample
SA168339S_26012M Sample
SA168340S_26_1Y12M Sample
SA168341S_2612M Sample
SA168342S_263_1Y12M Sample
SA168343S_28_1Y12M Sample
SA168344S_3_1Y12M Sample
SA168345S_30_1Y12M Sample
SA168346S_299_1Y12M Sample
SA168347S_298_1Y12M Sample
SA168348S_297_1Y12M Sample
SA168349S_300_1Y12M Sample
SA168350S_30112M Sample
SA168351S_306_1Y12M Sample
SA168352S_304_1Y12M Sample
SA168353S_303_1Y12M Sample
SA168354S_302_1Y12M Sample
SA168355S_293_1Y12M Sample
SA168356S_292_1Y12M Sample
SA168357S_284_1Y12M Sample
SA168358S_283_1Y12M Sample
SA168359S_282_1Y12M Sample
SA168360S_28112M Sample
SA168361S_285_1Y12M Sample
SA168362S_288_1Y12M Sample
SA168363S_29212M Sample
SA168364S_290_1Y12M Sample
SA168365S_2912M Sample
SA168366S_28912M Sample
SA168367S_249_1Y12M Sample
SA168368S_245_1Y12M Sample
SA168369S_213_1Y12M Sample
SA168370S_21412M Sample
SA168371S_212_R_1Y12M Sample
SA168372S_210_1Y12M Sample
SA168373S_209_1Y12M Sample
SA168374S_214_1Y12M Sample
SA168375S_21512M Sample
SA168376S_218_1Y12M Sample
SA168377S_217_1Y12M Sample
SA168378S_216_1Y12M Sample
SA168379S_21612M Sample
SA168380S_208_1Y12M Sample
SA168381S_20812M Sample
SA168382S_20_1Y12M Sample
SA168383S_201_1Y12M Sample
SA168384S_2_1Y12M Sample
SA168385S_199_1Y12M Sample
SA168386S_198_1Y12M Sample
SA168387S_20312M Sample
SA168388S_203_1Y12M Sample
SA168389S_207_1Y12M Sample
SA168390S_20712M Sample
SA168391S_205_1Y12M Sample
SA168392S_204_1Y12M Sample
SA168393S_22_R_1Y12M Sample
SA168394S_221_1Y12M Sample
SA168395S_24_1Y12M Sample
SA168396S_24012M Sample
SA168397S_239_1Y12M Sample
SA168398S_23812M Sample
SA168399S_237_1Y12M Sample
SA168400S_240_1Y12M Sample
SA168401S_241_1Y12M Sample
SA168402S_30712M Sample
SA168403S_244_1Y12M Sample
SA168404S_24412M Sample
SA168405S_242_1Y12M Sample
SA168406S_236_1Y12M Sample
SA168407S_235_1Y12M Sample
SA168408S_226_1Y12M Sample
SA168409S_224_1Y12M Sample
SA168410S_223_1Y12M Sample
SA168411S_222_1Y12M Sample
SA168412S_227_1Y12M Sample
SA168413S_230_1Y12M Sample
SA168414S_23512M Sample
SA168415S_234_1Y12M Sample
SA168416S_232_1Y12M Sample
SA168417S_231_1Y12M Sample
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Collection:

Collection ID:CO001883
Collection Summary:Feces collected from 6W and 1Y infants in the New Hampshire Birth Cohort
Sample Type:Feces

Treatment:

Treatment ID:TR001903
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP001896
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:

Analysis ID:AN002939
Laboratory Name:Metabolomics and Exposome Laboratory at UNC Nutrition Research Institute
Analysis Type:NMR
Acquisition Date:June 05, 2018-August 31, 2021
Software Version:TopSpin 3.5
Operator Name:Wimal Pathmasiri
Detector Type:NMR
Data Format:fid, 1r
Num Factors:3
Num Metabolites:36
Units:uM

NMR:

NMR ID:NM000206
Analysis ID:AN002939
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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