Summary of Study ST003206

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 PR001999. The data can be accessed directly via it's Project DOI: 10.21228/M8BB26 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 IDST003206
Study TitleDynamics of Gut Metabolome and Microbiome Maturation during Early Life - untargeted GC, LECO tof MS
Study SummaryEarly-life gut microbiome-metabolome crosstalk has a pivotal role in the maintenance of host physiology. However, our understanding on early-life gut microbiome-metabolome maturation trajectories in humans remains limited. This study aims to explore the longitudinal patterns of gut metabolites during early life, and how they are related to gut microbiota composition in birth cohort samples of n = 670 children collected at 2.5 (n=272), 6 (n=232), 14 (n=289), and 30 months (n=157) of age. Factor analysis showed that breastfeeding has an effect on several metabolites including secondary bile acids. We found that the prevalent gut microbial abundances were associated with metabolite levels, especially in the 2.5 months-olds. We also demonstrated that the prevalent early colonizers Bacteroides, Escherichia and Bifidobacterium abundances associated with microbial metabolites bile acids especially in the breastfed infants. Taken together, our results suggests that as the microbiome matures during the early-life there is an association with the metabolome composition in an analogous fashion to how the genome information mature during early life.
Institute
University of Turku
Last NameIsokääntä
First NameHeidi
AddressItäharjunkatu 37
Emailheidi.kunnasranta@utu.fi
Phone0408250762
Submit Date2024-04-16
Raw Data AvailableYes
Raw Data File Type(s)abf
Analysis Type DetailOther
Release Date2025-01-02
Release Version1
Heidi Isokääntä Heidi Isokääntä
https://dx.doi.org/10.21228/M8BB26
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001999
Project DOI:doi: 10.21228/M8BB26
Project Title:Dynamics of Gut Metabolome and Microbiome Maturation during Early Life
Project Type:Multi part study
Project Summary:Early-life gut microbiome-metabolome crosstalk has a pivotal role in the maintenance of host physiology. However, our understanding on early-life gut microbiome-metabolome maturation trajectories in humans remains limited. This study aims to explore the longitudinal patterns of gut metabolites during early life, and how they are related to gut microbiota composition in birth cohort samples of n = 670 children collected at 2.5 (n=272), 6 (n=232), 14 (n=289), and 30 months (n=157) of age. Factor analysis showed that breastfeeding has an effect on several metabolites including secondary bile acids. We found that the prevalent gut microbial abundances were associated with metabolite levels, especially in the 2.5 months-olds. We also demonstrated that the prevalent early colonizers Bacteroides, Escherichia and Bifidobacterium abundances associated with microbial metabolites bile acids especially in the breastfed infants. Taken together, our results suggests that as the microbiome matures during the early-life there is an association with the metabolome composition in an analogous fashion to how the genome information mature during early life.
Institute:University of Turku
Department:Biomedical faculty
Laboratory:Medical microbiology and metabolomics
Last Name:Isokääntä
First Name:Heidi
Address:Itäharjunkatu 37
Email:heidi.kunnasranta@utu.fi
Phone:+358408250762
Project Comments:Multi part study: Short chain fatty acid (SCFA) data (targeted GC), Bile acid data (targeted LCMS) and GC-tof (untargeted Leco) data uploaded as zip files. Method details in attached pdf.

Subject:

Subject ID:SU003325
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 Timepoint (months) Sample source Deliverymode breastfeedingstatus
SA348922157_1414 feces NA BREASTFno
SA348923603_1414 feces NA BREASTFno
SA348924406_1414 feces NA BREASTFno
SA348925263_1414 feces section BREASTFNA
SA348926604_1414 feces section BREASTFNA
SA348927510_1414 feces section BREASTFNA
SA34892849_1414 feces section BREASTFno
SA348929552_1414 feces section BREASTFno
SA348930422_1414 feces section BREASTFno
SA34893124_1414 feces section BREASTFno
SA348932113_1414 feces section BREASTFno
SA3489336_1414 feces section BREASTFno
SA348934538_1414 feces section BREASTFno
SA348935354_1414 feces section BREASTFno
SA348936576_1414 feces section BREASTFno
SA348937348_1414 feces section BREASTFno
SA348938331_1414 feces section BREASTFno
SA348939562_1414 feces section BREASTFno
SA348940398_1414 feces section BREASTFno
SA34894140_1414 feces section BREASTFno
SA348942236_1414 feces section BREASTFno
SA348943570_1414 feces section BREASTFno
SA348944567_1414 feces section BREASTFno
SA348945509_1414 feces section BREASTFno
SA348946395_1414 feces section BREASTFno
SA348947274_1414 feces section BREASTFno
SA348948486_1414 feces section BREASTFno
SA348949615_1414 feces section BREASTFno
SA348950614_1414 feces section BREASTFno
SA348951443_1414 feces section BREASTFno
SA348952180_1414 feces section BREASTFno
SA34895389_1414 feces section BREASTFno
SA34895473_1414 feces section BREASTFno
SA34895572_1414 feces section BREASTFno
SA348956610_1414 feces section BREASTFno
SA348957616_1414 feces section BREASTFno
SA348958608_1414 feces section BREASTFno
SA34895944_1414 feces section BREASTFno
SA34896025_1414 feces section BREASTFyes
SA348961162_1414 feces section BREASTFyes
SA348962534_1414 feces section BREASTFyes
SA348963165_1414 feces section BREASTFyes
SA348964586_1414 feces vaginal BREASTFNA
SA348965280_1414 feces vaginal BREASTFNA
SA3489667_1414 feces vaginal BREASTFNA
SA348967469_1414 feces vaginal BREASTFNA
SA34896845_1414 feces vaginal BREASTFno
SA348969386_1414 feces vaginal BREASTFno
SA348970389_1414 feces vaginal BREASTFno
SA348971388_1414 feces vaginal BREASTFno
SA348972385_1414 feces vaginal BREASTFno
SA348973435_1414 feces vaginal BREASTFno
SA348974379_1414 feces vaginal BREASTFno
SA348975381_1414 feces vaginal BREASTFno
SA348976382_1414 feces vaginal BREASTFno
SA348977384_1414 feces vaginal BREASTFno
SA348978383_1414 feces vaginal BREASTFno
SA348979392_1414 feces vaginal BREASTFno
SA348980397_1414 feces vaginal BREASTFno
SA348981409_1414 feces vaginal BREASTFno
SA348982440_1414 feces vaginal BREASTFno
SA348983414_1414 feces vaginal BREASTFno
SA348984417_1414 feces vaginal BREASTFno
SA348985421_1414 feces vaginal BREASTFno
SA348986420_1414 feces vaginal BREASTFno
SA348987423_1414 feces vaginal BREASTFno
SA348988404_1414 feces vaginal BREASTFno
SA348989396_1414 feces vaginal BREASTFno
SA348990437_1414 feces vaginal BREASTFno
SA348991378_1414 feces vaginal BREASTFno
SA348992431_1414 feces vaginal BREASTFno
SA348993424_1414 feces vaginal BREASTFno
SA348994441_1414 feces vaginal BREASTFno
SA348995394_1414 feces vaginal BREASTFno
SA348996340_1414 feces vaginal BREASTFno
SA348997291_1414 feces vaginal BREASTFno
SA348998277_1414 feces vaginal BREASTFno
SA348999264_1414 feces vaginal BREASTFno
SA349000261_1414 feces vaginal BREASTFno
SA349001295_1414 feces vaginal BREASTFno
SA34900230_1414 feces vaginal BREASTFno
SA349003311_1414 feces vaginal BREASTFno
SA349004310_1414 feces vaginal BREASTFno
SA349005304_1414 feces vaginal BREASTFno
SA349006248_1414 feces vaginal BREASTFno
SA349007242_1414 feces vaginal BREASTFno
SA349008197_1414 feces vaginal BREASTFno
SA349009192_1414 feces vaginal BREASTFno
SA349010191_1414 feces vaginal BREASTFno
SA349011166_1414 feces vaginal BREASTFno
SA349012204_1414 feces vaginal BREASTFno
SA349013206_1414 feces vaginal BREASTFno
SA34901422_1414 feces vaginal BREASTFno
SA349015218_1414 feces vaginal BREASTFno
SA349016214_1414 feces vaginal BREASTFno
SA349017314_1414 feces vaginal BREASTFno
SA349018316_1414 feces vaginal BREASTFno
SA349019359_1414 feces vaginal BREASTFno
SA349020357_1414 feces vaginal BREASTFno
SA349021356_1414 feces vaginal BREASTFno
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Collection:

Collection ID:CO003318
Collection Summary:The fecal samples were collected from the children by the parents according to written and oral instructions at 2.5, 6, 14 and 30 months postpartum. The samples were collected in plastic tubes, and parents were instructed to store the sample in a refrigerator, and bring the sample to the laboratory within 24 h. The sample collection time was reported.
Sample Type:Feces

Treatment:

Treatment ID:TR003334
Treatment Summary:No treatment. The samples were kept in -80 degrees until metabolome preprosessing.

Sample Preparation:

Sampleprep ID:SP003332
Sampleprep Summary:Only samples frozen within 24 h of sample collection were included in the metabolome analyses. The order of the samples was randomized before sample preparation. Two aliquots (50 mg) of each fecal sample were weighed. An aliquot was freeze-dried prior to extraction to determine the dry weight. The second aliquot was homogenized by adding homogenizer beads and 20 μL of water for each mg of dry weight in the fecal sample, followed by samples freezing to at least -70 °C and homogenizing them for five minutes using a bead beater.
Sampleprep Protocol Filename:Methods_Aatsinki.pdf

Combined analysis:

Analysis ID AN005258
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890B
Column Agilent DB-5MS (20 m x 0.18 mm, 0.18 um)
MS Type EI
MS instrument type GC-TOF
MS instrument name LECO Pegasus BT system
Ion Mode POSITIVE
Units ng/ml

Chromatography:

Chromatography ID:CH003979
Chromatography Summary:Gas chromatographic (GC) separation was carried out on an Agilent 7890B GC system equipped with an Agilent DB-5MS (20 m x 0.18 mm (0.18 μm)) column. A sample volume of 1 μl was injected into a split/splitless inlet at 250°C using splitless mode. The system was guarded by a retention gap column of deactivated silica (internal dimensions 1.7 m, 0.18 mm, PreColumn FS, Ultimate Plus Deact; Agilent Technologies, CA, USA). Helium was used as carrier gas at a flow rate of 1.2 ml/min for 16 min followed by 2 mL/min for 5.75 min. The temperature programme started at 50°C (5 min), then a gradient of 20°C/min up to 270°C was applied and then finally a gradient of 40°/min to 300°C, where it was held stable for 7 min. The mass spectrometry was carried out on a LECO Pegasus BT system (LECO).
Methods Filename:Methods_Aatsinki.pdf
Instrument Name:Agilent 7890B
Column Name:Agilent DB-5MS (20 m x 0.18 mm, 0.18 um)
Column Temperature:50 - 300
Flow Gradient:-
Flow Rate:-
Solvent A:NA
Solvent B:NA
Chromatography Type:GC

MS:

MS ID:MS004989
Analysis ID:AN005258
Instrument Name:LECO Pegasus BT system
Instrument Type:GC-TOF
MS Type:EI
MS Comments:The mass spectrometry was carried out on a LECO Pegasus BT system (LECO). The acquisition delay was 420 sec. The acquisition rate was 16 spectra/sec. The mass range was 50 – 500 m/z and the extraction frequency was 30 kHz. The ion source was held at 250 °C and the transferline heater temperature was 230 °C. ChromaTOF software (version 5.51) was used for data aquisition. The samples were run in 9 batches, each consisting of 100 samples and a calibration curve. In order to monitor the run a blank, a QC and a standard sample with a known concentration run between every 10 samples. Between every batch the septum and liner on the GC were replaced, the precolumn was cut if necessary and the instrument was tuned. The retention index was determined with ChromaTOF using the reference method function. For every batch a reference file was created. The reference file contained the spectras and approximate retention times of the alkanes from C10 to C30 as determined manually). A reference method was implemented for every sample in order to determine the exact retention time of the alkanes. Text files with the names and retention times of the alkanes were then exported and converted to the correct format for MSDIAL using an in-house R script. The samples were exported from ChromaTOF using the netCDF format. After this they were converted to abf files using the abfConverter software (Reifycs). Untargeted data processing was carried out using MSDIAL (version 4.7). The minimum peak height was set to an amplitude of 1000, the sigma window value was 0.7 and the EI spectra cut off was 10. The identification was carried out using retention index with the help of the GCMS DBPublic-kovatsRI-VS3 library provided on the MSDIAL webpage. A separate RI file was used for each sample. The RI tolerance was 20 and the m/z tolerance was 0.5 Da. the EI similarly cut off was 70 %. The identification score cut off was 70 % and retention information was used for scoring. Alignment was carried out using the RI with an RI tolerance of 10. The EI similarity tolerance was 60 %. The RI factor was 0.7 and the EI similarity factor was 0.5. The results were exported as peak areas and further processed with excel. In excel the results were normalized using heptadecanoic acid as internal standard and the features with a coefficient of variance of less than 30 % in QC samples were selected. Further filtering was carried out to remove alkanes and duplicate features. The IDs of the features which passed the CV check were further checked using the Golm Metabolome Database.
Ion Mode:POSITIVE
Analysis Protocol File:Methods_Aatsinki.pdf
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