Summary of Study ST001040

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 PR000696. The data can be accessed directly via it's Project DOI: 10.21228/M8Q96S 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 IDST001040
Study TitleMaternal gut microbiome, pregnancy exposure to environmental contaminants, and child health outcomes: A pilot study exploring potential effect modifications by diet
Study TypeCHEAR Pilot Study
Study SummaryUsing specimens collected as part of a pilot RCT of a diet intervention in pregnancy, we propose to ship our time 2 blood and urine samples (collected post-diet intervention or usual care at 36 weeks gestation) to: 1) Assess biomarker confirmation of the diet intervention effect via: (a) carotenoids and/or other antioxidants (which have been shown to be a good marker of fruit and vegetable intake); and (b) untargeted metabolomics. 2) Assess pregnancy exposure to metals and/or other environmental contaminants. 3) Combine the biomarker data proposed here in aims 1 and 2 with the data being analyzed at MSU (diet survey data and butyrate composition of stool) to explore potential bi-directional effects on gut microbiome, environmental contaminants, and dietary factors.
Institute
Icahn School of Medicine at Mount Sinai
DepartmentDepartment of Environmental Medicine and Public Health
LaboratoryMount Sinai CHEAR Untargeted Laboratory Hub
Last NameWalker
First NameDouglas
AddressAtran Building RM AB3-39, 1428 Madison Ave
Emaildouglas.walker@mssm.edu
Phone212-241-4392
Submit Date2018-08-21
Total Subjects26
Raw Data AvailableYes
Raw Data File Type(s)d
Chear StudyYes
Analysis Type DetailLC-MS
Release Date2024-12-31
Release Version1
Douglas Walker Douglas Walker
https://dx.doi.org/10.21228/M8Q96S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000696
Project DOI:doi: 10.21228/M8Q96S
Project Title:Pregnancy Eating and Postpartum Diapers (PEAPOD)
Project Type:Pilot Study
Project Summary:This was a pilot study (n=27), to assess the feasibility, acceptability, and preliminary efficacy of implementing a randomized controlled trial of a diet intervention in pregnancy designed to test the effect of maternal diet on the maternal and infant gut microbiome. Our specific aims were to: 1) test feasibility of enrollment and implementation; 2) assess acceptability of weekly food deliveries; and 3) estimate the preliminary effect size of the intervention relative to the usual care group on (a) maternal gut butyrate composition measured in three maternal stool samples collected at two time points during pregnancy (pre- and post-diet intervention phase) and also collected at 6 weeks postpartum; and (b) infant gut butyrate composition measured in infant stool samples collected at 6 weeks of age. The overall goal of PEAPOD was to gather pilot data to effectively refine the intervention so that it can be tested in a larger, longer study using a factorial design. For this pilot, we employed a 2-arm RCT with a total sample size of 27 mother-child pairs. We enrolled women in mid-pregnancy who were intending to breastfeed, randomized them to the diet intervention (n=13) or to a usual care group (n=14) and followed them to 6 weeks postpartum. Data collection included surveys of detailed maternal dietary information, as well as collection of maternal blood, urine, and stool at three time points (25 and 36 weeks gestation, and 6 weeks postpartum), and an infant stool sample at 6 weeks of age along with information about infant feeding practices. The diet intervention was initiated at 32 weeks gestation and continued until birth of the baby; thus the 25 week gestation biospecimens are pre-intervention and the 36 week gestation biospecimens are after 4 weeks of receiving the diet intervention. We chose to collect the second set of biospecimens at 36 weeks gestation to avoid missing post-intervention samples in instances where women delivered preterm. We partnered with the hospital catering service and the diet intervention including either legumes (e.g. minestrone with white beans) or whole grains (e.g. beef barley), and 5 pieces of fresh fruit (e.g. apples, oranges). In addition, in the first week, participants received a collection of non-perishable high fiber foods (whole wheat breakfast cereal, oatmeal, dried fruit, and canned beans) as well as upscale olive oil and vinegar from a local store along with recipes for salad dressing, side dishes, and some general information about the health benefits of the Mediterranean diet. We anticipated that participants would likely share the food with their families but our intent was to provide enough supplementary food to increase the fiber consumption of the pregnant women.
Institute:Michigan State University
Department:Department of Epidemiology and Biostatistics
Last Name:Kerver
First Name:Jean
Address:314 Munson Professional Building, MSU/CHM Research, 1105 Sixth Street, Traverse City, MI 49684
Email:kerverje@msu.edu
Phone:231-392-8227
Contributors:Jean Kerver, Sarah Comstock, Joseph Gardiner, Robert Wright, Lauren Petrick, Douglas Walker

Subject:

Subject ID:SU001079
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 Sample Type/Matrix
SA070037LQC_1Pooled quality control sample
SA070038LQC_5Pooled quality control sample
SA070039LQC_4Pooled quality control sample
SA070040LQC_2Pooled quality control sample
SA070041LQC_3Pooled quality control sample
SA070045TCPP22urine
SA070046TCPP21urine
SA070047TCPP20urine
SA070048TCPP19urine
SA070049TCPP23urine
SA070050TCPP28urine
SA070051TCPP18urine
SA070052TCPP29urine
SA070053TCPP27urine
SA070054TCPP26urine
SA070055TCPP25urine
SA070056TCPP24urine
SA070057TCPP12urine
SA070058TCPP4urine
SA070059TCPP5urine
SA070060TCPP3urine
SA070061TCPP2urine
SA070062TCPP1urine
SA070063TCPP6urine
SA070064TCPP8urine
SA070065TCPP15urine
SA070066TCPP16urine
SA070067TCPP13urine
SA070068TCPP11urine
SA070069TCPP10urine
SA070070TCPP17urine
SA070042matrix_3Water matrix blank
SA070043matrix_2Water matrix blank
SA070044matrix_1Water matrix blank
Showing results 1 to 34 of 34

Collection:

Collection ID:CO001073
Collection Summary:For this pilot, we employed a 2-arm RCT with a total sample size of 27 mother-child pairs. We enrolled women in mid-pregnancy who were intending to breastfeed, randomized them to the diet intervention (n=13) or to a usual care group (n=14) and followed them to 6 weeks postpartum. Data collection included surveys of detailed maternal dietary information, as well as collection of maternal blood, urine, and stool at three time points (25 and 36 weeks gestation, and 6 weeks postpartum), and an infant stool sample at 6 weeks of age along with information about infant feeding practices. The diet intervention was initiated at 32 weeks gestation and continued until birth of the baby; thus the 25 week gestation biospecimens are pre-intervention and the 36 week gestation biospecimens are after 4 weeks of receiving the diet intervention. We chose to collect the second set of biospecimens at 36 weeks gestation to avoid missing post-intervention samples in instances where women delivered preterm.
Sample Type:Urine

Treatment:

Treatment ID:TR001093
Treatment Summary:We enrolled women in mid-pregnancy who were intending to breastfeed, randomized them to the diet intervention (n=13) or to a usual care group (n=14) and followed them to 6 weeks postpartum. We partnered with the hospital catering service and the diet intervention consisted of weekly food delivery of 3 large prepared salads (without dressing), 2 quarts of soup including either legumes (e.g. minestrone with white beans) or whole grains (e.g. beef barley), and 5 pieces of fresh fruit (e.g. apples, oranges). In addition, in the first week, participants received a collection of non-perishable high fiber foods (whole wheat breakfast cereal, oatmeal, dried fruit, and canned beans) as well as upscale olive oil and vinegar from a local store along with recipes for salad dressing, side dishes, and some general information about the health benefits of the Mediterranean diet.

Sample Preparation:

Sampleprep ID:SP001086
Sampleprep Summary:Urine samples were thawed on ice, vortexed, and specific gravity (SpG) was measured. Samples were diluted with LC-MS grade water to the lowest measured SpG with ultrapure water. Aliquots of 20 μL of the diluted urine were prepared for analysis with the LC-HRMS. A third 20 μL aliquot from each sample was combined for use as a pooled quality control sample (‘LQC’). When aliquoting was complete, the LQC sample was re-aliquoted into 20μL samples. All aliquots were returned to -80°C until analysis. Extraction was performed immediately prior to LC-HRMS analysis. All sample aliquots were thawed on ice, combined with 180uL of acetonitrile containing internal standards. Samples were then centrifuged and 80μL of supernatant transferred to an LC vial for analysis. Following the same protocol matrix blank (replacing the urine with H2O) and multiple LQCs were extracted.
Processing Storage Conditions:On ice

Combined analysis:

Analysis ID AN001702 AN001703
Analysis type MS MS
Chromatography type HILIC Reversed phase
Chromatography system Agilent 1290 Infinity II Agilent 1290 Infinity II
Column SeQuant ZIC-pHILIC (100 x 2.1mm,3.5um) Agilent Zorbax Eclipse Plus C18 (50 x 2.1mm, 1.8 um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6550 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE
Units Peak Intensity Peak Intensity

Chromatography:

Chromatography ID:CH001200
Chromatography Summary:Sample extracts were analyzed using an ultra-high performance liquid chromatography (UHPLC) 1290 Infinity II system (including 0.3 µm inline filter, Agilent Technologies, Santa Clara, USA) with 1260 Infinity II isocratic pump (including 1:100 splitter) coupled to a 6550 iFunnel quadrupole-time time of flight (Q-TOF) mass spectrometer with a dual AJS electrospray ionization source (Agilent Technologies, Santa Clara, USA). Samples were maintained at 5C in the autosampler module. For polar metabolites separation, 2 uL of sample was injected onto a HILIC SeQuant® ZIC®-HILIC column (100 mm × 2.1 mm, 100 Å, 3.5 µm particle size, Merck, Darmstadt, Germany) with a guard fitting (14 mm × 1 mm, 5.0 µm particle size, Merck, Darmstadt, Germany) maintained at 25C. Separation occurred using Mobile phase A consisted of water with 0.1% formic acid and Mobile phase B consisted of Acetonitrile with 0.1% formic acid at a flow rate of 0.3 ml/min as described in Table 1. Data was acquired with a mass range of 40-1200 m/z. Solvent gradients were as follows: 95% solvent B, hold for 1.5 min; linear decrease to 40% solvent B at 12 minutes; hold for 2 min, linear decrease to 25% solvent B at 14.2 min, hold for 2.8 min; increase to 95% solvent B at 18 min, hold for 7 min.
Instrument Name:Agilent 1290 Infinity II
Column Name:SeQuant ZIC-pHILIC (100 x 2.1mm,3.5um)
Column Temperature:25C
Flow Rate:0.3 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Analytical Time:25 min
Chromatography Type:HILIC
  
Chromatography ID:CH001201
Chromatography Summary:Sample extracts were analyzed using an ultra-high performance liquid chromatography (UHPLC) 1290 Infinity II system (including 0.3 µm inline filter, Agilent Technologies, Santa Clara, USA) with 1260 Infinity II isocratic pump (including 1:100 splitter) coupled to a 6550 iFunnel quadrupole-time time of flight (Q-TOF) mass spectrometer with a dual AJS electrospray ionization source (Agilent Technologies, Santa Clara, USA). Samples were maintained at 5C in the autosampler module. For nonpolar metabolites separation, 2 uL of sample sandwiched between 10 uL of water was injected onto a Zorbax Eclipse Plus C18, RRHD column (50 mm × 2.1 mm, 1.8 µm particle size, Agilent Technologies, Santa Clara, USA) coupled to a guard column (5 mm × 2 mm, 1.8 µm Agilent Technologies, Santa Clara, USA) maintained at 50C. Separation occurred using Mobile phase A consisted of water with 0.1% formic acid and Mobile phase B consisted of 2-propanol:ACN (90:10, v/v) with 0.1% formic acid at a flow rate of 0.4 ml/min as described in Table 2. Data was acquired with a mass range of 50-1200 m/z. Solvent gradients were as follows: 5% solvent B; linear increase to 98% solvent B at 13.5 min, hold for 1.5 min; decrease to 5% solvent B at 15.5 min, hold for 3.5 min.
Instrument Name:Agilent 1290 Infinity II
Column Name:Agilent Zorbax Eclipse Plus C18 (50 x 2.1mm, 1.8 um)
Column Temperature:50C
Flow Rate:0.4 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:90% isopropanol/10% acetonitrile; 0.1% formic acid
Analytical Time:19 min
Chromatography Type:Reversed phase

MS:

MS ID:MS001576
Analysis ID:AN001702
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Temperature:250C
Capillary Voltage:3000
  
MS ID:MS001577
Analysis ID:AN001703
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Temperature:250C
Capillary Voltage:-3000
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