Summary of Study ST002320

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 PR001486. The data can be accessed directly via it's Project DOI: 10.21228/M8N999 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 IDST002320
Study TitleUntargeted Fecal Metabolomic Analyses Across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions
Study SummaryThe metabolome is a central determinant of human phenotypes and includes the plethora of small molecules produced by host and microbiome, or taken up from exogenous sources. However, studies of the metabolome have so far focused predominantly on urban, industrialized populations. Through an untargeted metabolomic analysis of 90 fecal samples from human individuals from Africa and the Americas—the birthplace and the last continental expansion of our species, respectively—we characterized a shared human fecal metabolome. The majority of detected metabolite features were ubiquitous across populations, despite any geographic, dietary, or behavioral differences. Such shared metabolite features included hyocholic acid and cholesterol. However, any characterization of the shared human fecal metabolome is insufficient without exploring the influence of industrialization. Here, we show chemical differences along an industrialization gradient, where the degree of industrialization correlates with metabolomic changes. We identified differential metabolite features like amino acid-conjugated bile acids and urobilin as major metabolic correlates of these behavioral shifts. Additionally, co-analyses with over 5,000 publicly available human fecal samples and co-occurrence probability analyses with the gut microbiome highlight connections between the human fecal metabolome and gut microbiome. Our results indicate that industrialization significantly influences the human fecal metabolome, but diverse human lifestyles and behavior still maintain a shared human fecal metabolome. This study represents the first characterization of the shared human fecal metabolome through untargeted analyses of populations along an industrialization gradient.
Institute
University of Oklahoma
Last NameHaffner
First NameJacob
Address101 David L. Boren Blvd, Norman, OK, 73019
Emailjacob.haffner@ou.edu
Phone405-325-7381
Submit Date2022-10-07
Num Groups6
Total Subjects90
Num Males29
Num Females47
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2022-10-25
Release Version1
Jacob Haffner Jacob Haffner
https://dx.doi.org/10.21228/M8N999
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001486
Project DOI:doi: 10.21228/M8N999
Project Title:Untargeted Fecal Metabolomic Analyses Across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions
Project Summary:The metabolome is a central determinant of human phenotypes and includes the plethora of small molecules produced by host and microbiome, or taken up from exogenous sources. However, studies of the metabolome have so far focused predominantly on urban, industrialized populations. Through an untargeted metabolomic analysis of 90 fecal samples from human individuals from Africa and the Americas—the birthplace and the last continental expansion of our species, respectively—we characterized a shared human fecal metabolome. The majority of detected metabolite features were ubiquitous across populations, despite any geographic, dietary, or behavioral differences. Such shared metabolite features included hyocholic acid and cholesterol. However, any characterization of the shared human fecal metabolome is insufficient without exploring the influence of industrialization. Here, we show chemical differences along an industrialization gradient, where the degree of industrialization correlates with metabolomic changes. We identified differential metabolite features like amino acid-conjugated bile acids and urobilin as major metabolic correlates of these behavioral shifts. Additionally, co-analyses with over 5,000 publicly available human fecal samples and co-occurrence probability analyses with the gut microbiome highlight connections between the human fecal metabolome and gut microbiome. Our results indicate that industrialization significantly influences the human fecal metabolome, but diverse human lifestyles and behavior still maintain a shared human fecal metabolome. This study represents the first characterization of the shared human fecal metabolome through untargeted analyses of populations along an industrialization gradient.
Institute:University of Oklahoma, Department of Anthropology
Laboratory:Laboratories of Molecular Anthropology and Microbiome Research
Last Name:Haffner
First Name:Jacob
Address:101 David L. Boren Blvd., Norman, Oklahoma, 73019, USA
Email:jacob.haffner@ou.edu
Phone:405-325-7381

Subject:

Subject ID:SU002406
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:5-77
Weight Or Weight Range:NA
Height Or Height Range:NA
Gender:Male and female
Human Lifestyle Factors:Urban industrial; Rural industrial; Rural traditional; Isolated traditional
Human Alcohol Drug Use:NA
Human Nutrition:NA
Human Inclusion Criteria:NA
Human Exclusion Criteria:NA

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Population Industrialization_Category Sex Age Time_Kept_on_Ice_before_Frozen
SA227282TM09_02Boulkiemd� Rural Traditional F 32 Within 1 day
SA227283TM17_02Boulkiemd� Rural Traditional F 35 Within 1 day
SA227284TM20_03Boulkiemd� Rural Traditional F 37 Within 1 day
SA227285TM25_03Boulkiemd� Rural Traditional F 38 Within 1 day
SA227286TM11_04Boulkiemd� Rural Traditional F 40 Within 1 day
SA227287TM23_02Boulkiemd� Rural Traditional F 51 Within 1 day
SA227288TM22_03Boulkiemd� Rural Traditional M 29 Within 1 day
SA227289TM13_01Boulkiemd� Rural Traditional M 53 Within 1 day
SA227290TM10_01Boulkiemd� Rural Traditional M 55 Within 1 day
SA227291TM01_01Boulkiemd� Rural Traditional M 55 Within 1 day
SA227292TM29_01Boulkiemd� Rural Traditional M 73 Within 1 day
SA227293GU2Guayabo Rural Industrial F 19 Within 4 days
SA227294GU19Guayabo Rural Industrial F 24 Within 4 days
SA227295GU4Guayabo Rural Industrial F 40 Within 4 days
SA227296GU13Guayabo Rural Industrial F 41 Within 4 days
SA227297GU17Guayabo Rural Industrial F 51 Within 4 days
SA227298GU1Guayabo Rural Industrial F 52 Within 4 days
SA227299GU10Guayabo Rural Industrial F 58 Within 4 days
SA227300GU20Guayabo Rural Industrial F 63 Within 4 days
SA227301GU12Guayabo Rural Industrial NA 16 Within 4 days
SA227302GU6Guayabo Rural Industrial NA 6 Within 4 days
SA227303GU11Guayabo Rural Industrial NA 7 Within 4 days
SA227304GU7Guayabo Rural Industrial NA 9 Within 4 days
SA227305SM02Matses Isolated Traditional F 25 Within 4 days
SA227306SM39Matses Isolated Traditional F 40 Within 4 days
SA227307SM29Matses Isolated Traditional F 50 Within 4 days
SA227308SM28Matses Isolated Traditional F 52 Within 4 days
SA227309SM33Matses Isolated Traditional F 5 Within 4 days
SA227310SM10Matses Isolated Traditional F 6 Within 4 days
SA227311SM03Matses Isolated Traditional M 10 Within 4 days
SA227312SM37Matses Isolated Traditional M 12 Within 4 days
SA227313SM01Matses Isolated Traditional M 30 Within 4 days
SA227314SM41Matses Isolated Traditional M 6 Within 4 days
SA227315SM23Matses Isolated Traditional M 7 Within 4 days
SA227316NO23Norman Urban Industrial F 26 Within 1 day
SA227317NO12Norman Urban Industrial F 27 Within 1 day
SA227318NO08Norman Urban Industrial F 32 Within 1 day
SA227319NO07Norman Urban Industrial F 32 Within 1 day
SA227320NO19Norman Urban Industrial F 32 Within 1 day
SA227321NO09Norman Urban Industrial F 34 Within 1 day
SA227322NO02Norman Urban Industrial F 37 Within 1 day
SA227323NO21Norman Urban Industrial M 23 Within 1 day
SA227324NO01Norman Urban Industrial M 23 Within 1 day
SA227325NO04Norman Urban Industrial M 26 Within 1 day
SA227326NO20Norman Urban Industrial M 26 Within 1 day
SA227327NO11Norman Urban Industrial M 26 Within 1 day
SA227328NO22Norman Urban Industrial M 26 Within 1 day
SA227329NO06Norman Urban Industrial M 28 Within 1 day
SA227330NO05Norman Urban Industrial M 28 Within 1 day
SA227331NO13Norman Urban Industrial M 35 Within 1 day
SA227332NO03Norman Urban Industrial M 40 Within 1 day
SA227333NO10Norman Urban Industrial M 41 Within 1 day
SA2273346TMTambo de Mora Rural Industrial F 31 Within 4 days
SA22733526TMTambo de Mora Rural Industrial F 36 Within 4 days
SA22733616TMTambo de Mora Rural Industrial F 38 Within 4 days
SA2273374TMTambo de Mora Rural Industrial F 40 Within 4 days
SA2273382TMTambo de Mora Rural Industrial F 40 Within 4 days
SA2273391TMTambo de Mora Rural Industrial F 61 Within 4 days
SA22734014TMTambo de Mora Rural Industrial F 77 Within 4 days
SA22734111TMTambo de Mora Rural Industrial M 39 Within 4 days
SA22734218TMTambo de Mora Rural Industrial NA 13 Within 4 days
SA22734327TMTambo de Mora Rural Industrial NA 13 Within 4 days
SA22734431TMTambo de Mora Rural Industrial NA 28 Within 4 days
SA2273453TMTambo de Mora Rural Industrial NA 5 Within 4 days
SA22734617TMTambo de Mora Rural Industrial NA 7 Within 4 days
SA22734710TMTambo de Mora Rural Industrial NA 8 Within 4 days
SA227348HCO61Tunapuco Rural Traditional F 20 Within 4 days
SA227349HCO67Tunapuco Rural Traditional F 26 Within 4 days
SA227350HCO14Tunapuco Rural Traditional F 34 Within 4 days
SA227351HCO12Tunapuco Rural Traditional F 35 Within 4 days
SA227352HCO01Tunapuco Rural Traditional F 36 Within 4 days
SA227353HCO74Tunapuco Rural Traditional F 36 Within 4 days
SA227354HCO70Tunapuco Rural Traditional F 40 Within 4 days
SA227355HCO53Tunapuco Rural Traditional F 44 Within 4 days
SA227356HCO72Tunapuco Rural Traditional F 5 Within 4 days
SA227357HCO15Tunapuco Rural Traditional F 63 Within 4 days
SA227358HCO63Tunapuco Rural Traditional F 6 Within 4 days
SA227359HCO17Tunapuco Rural Traditional F 7 Within 4 days
SA227360HCO13Tunapuco Rural Traditional F 9 Within 4 days
SA227361HCO10Tunapuco Rural Traditional M 10 Within 4 days
SA227362HCO21Tunapuco Rural Traditional M 10 Within 4 days
SA227363HCO66Tunapuco Rural Traditional M 11 Within 4 days
SA227364HCO18Tunapuco Rural Traditional M 11 Within 4 days
SA227365HCO11Tunapuco Rural Traditional M 36 Within 4 days
SA227366HCO03Tunapuco Rural Traditional M 6 Within 4 days
SA227367HCO68Tunapuco Rural Traditional M 7 Within 4 days
SA227368HCO16Tunapuco Rural Traditional NA 11 Within 4 days
SA227369HCO09Tunapuco Rural Traditional NA 13 Within 4 days
SA227370HCO41Tunapuco Rural Traditional NA 54 Within 4 days
SA227371HCO69Tunapuco Rural Traditional NA 9 Within 4 days
Showing results 1 to 90 of 90

Collection:

Collection ID:CO002399
Collection Summary:Fecal material was deposited into polypropylene containers and then put on ice. Samples were kept in ice while in the field until arriving at research facilities equipped with freezers. The Norman samples were kept in ice after collection and frozen at the laboratory within 24 hours. The Peruvian samples were secured similarly to the Norman samples. After collection, samples were stored on ice for four days until arriving at Lima, Peru. Samples were frozen and sent to the laboratory in Norman, Oklahoma. Boulkiemdé samples were collected similarly to Norman and Peruvian samples. After collection, Boulkiemdé samples were frozen at -20 °C within 24 hours and kept frozen overnight. Samples were thawed the following evening to extract DNA, refrozen at -20 °C, and kept frozen until shipped to the laboratory in Norman, Oklahoma. Upon arrival, 2 g of fecal material was extracted from each sample for anaerobic culturing. Following this 2 g aliquoting, samples were frozen at -80 °C until use for this project. The Norman, Tunapuco, and Matses samples had previously been aliquoted and underwent 16S rRNA gene sequencing for an earlier study.
Sample Type:Feces
Collection Location:United States; Peru; Burkina Faso
Volumeoramount Collected:Variable; 50mg used for experimental analyses
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002418
Treatment Summary:The sample preparation protocol used for this project was adapted from a global metabolite extraction protocol with proven success (Want et al. 2013). Samples were thawed and 500 μl of chilled LC-MS grade water (Fisher Scientific) was added to 50 mg of fecal material. Next, a TissueLyzer homogenized samples at 25 Hz for three minutes. Following homogenization, chilled LC-grade methanol (Fisher Scientific) spiked with 4 μM sulfachloropyridazine as the internal standard (IS) was added, bringing the total concentration to 50% methanol. The TissueLyzer homogenized samples again at 25 Hz for three minutes, followed by overnight incubation at 4 °C. The next day, samples were centrifuged at 16,000 x g at 4 °C for ten minutes. Aqueous supernatant was then removed and dried using a SpeedVac vacuum concentrator. Dried extracts were frozen at -80 °C until the day of MS analysis. Immediately prior to MS analysis, extracts were resuspended in 150 μl chilled LC-MS methanol:water (1:1) spiked with 1 μg/ml sulfadimethoxine as a second IS. After resuspension, samples were diluted to a 1:10 ratio. Diluted samples were sonicated using a Fisher Scientific Ultrasonic Cleaning Bath at maximum power for ten minutes. Supernatants were spun briefly to remove any particulates, then loaded into a 96-well plate for MS analysis. One well contained only 150 μl of the resuspension solution to serve as blank control.

Sample Preparation:

Sampleprep ID:SP002412
Sampleprep Summary:The sample preparation protocol used for this project was adapted from a global metabolite extraction protocol with proven success (Want et al. 2013). Samples were thawed and 500 μl of chilled LC-MS grade water (Fisher Scientific) was added to 50 mg of fecal material. Next, a TissueLyzer homogenized samples at 25 Hz for three minutes. Following homogenization, chilled LC-grade methanol (Fisher Scientific) spiked with 4 μM sulfachloropyridazine as the internal standard (IS) was added, bringing the total concentration to 50% methanol. The TissueLyzer homogenized samples again at 25 Hz for three minutes, followed by overnight incubation at 4 °C. The next day, samples were centrifuged at 16,000 x g at 4 °C for ten minutes. Aqueous supernatant was then removed and dried using a SpeedVac vacuum concentrator. Dried extracts were frozen at -80 °C until the day of MS analysis. Immediately prior to MS analysis, extracts were resuspended in 150 μl chilled LC-MS methanol:water (1:1) spiked with 1 μg/ml sulfadimethoxine as a second IS. After resuspension, samples were diluted to a 1:10 ratio. Diluted samples were sonicated using a Fisher Scientific Ultrasonic Cleaning Bath at maximum power for ten minutes. Supernatants were spun briefly to remove any particulates, then loaded into a 96-well plate for MS analysis. One well contained only 150 μl of the resuspension solution to serve as blank control.
Extract Storage:On ice

Combined analysis:

Analysis ID AN003787
Analysis type MS
Chromatography type Reversed phase
Chromatography system ThermoFisher Scientific Vanquish Flex Binary LC System
Column Kinetex C18 core-shell (50 x 2.1mm,1.7um,100Å)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE
Units Peak area

Chromatography:

Chromatography ID:CH002801
Methods Filename:C18_RP_Pos_QEPlus_20180403_12.5mint_ddMS2_Chrom.txt
Instrument Name:ThermoFisher Scientific Vanquish Flex Binary LC System
Column Name:Kinetex C18 core-shell (50 x 2.1mm,1.7um,100Å)
Column Temperature:40
Flow Gradient:12.5 min runtime gradient
Internal Standard:Sulfadimethoxine
Sample Injection:5 uL randomized order
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS003530
Analysis ID:AN003787
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:LC was performed on a ThermoFisher Scientific Vanquish Flex Binary LC System with a Kinetex C18 core-shell column (50 x 2.1 mm, 1.7 μM particle size, 100 Å pore size). LC column was kept at 40 °C and the sample compartment was held at 10 °C. The LC System was coupled to a ThermoFisher Scientific Q Exactive Plus Hybrid Quadrupole-Orbitrap Mass Spectrometer for MS/MS analysis. For the LC mobile phase, Solvent A was LC-MS grade water (Fisher Scientific) with 0.1% formic acid and Solvent B was LC-MS grade acetonitrile (Fisher Scientific) with 0.1% formic acid. Elution gradient started at 5% Solvent B for one minute, increased to 100% Solvent B until minute nine, held at 100% Solvent B for two minutes, dropped to 5% Solvent B over 30 seconds, and 5% Solvent B for one minute as re-equilibration. Samples were injected in random order with an injection volume of 5 μl. After elution, electrospray ionization was conducted with spray voltage of 3.8 kV, auxiliary gas flow rate of 10, auxiliary gas temperature at 350 °C, sheath gas flow rate at 35, and sweep gas flow at 0. Capillary temperature was 320 °C and S-lens RF was 50 V. MS1 scan range was 100-1,500 m/z, MS1 resolution was set to 35,000 and MS1 AGC target to 1e6. MS1 data were obtained in positive mode and MS2 data were obtained using data-dependent acquisition. In each cycle, 5 MS/MS scans of the most abundant ion were recorded. Both MS1 and MS2 injection times were set at 100 ms. MS2 resolutions were set to 17,500, MS2 AGC target was set to 5e5, and the inclusion window to 2 m/z. MS/MS was conducted at an apex trigger of 2-8 seconds and an exclusion window of 10 seconds. MS/MS collision energy gradually increased from 20-40%.
Ion Mode:POSITIVE
Capillary Temperature:320°C
Ionization:ESI
Analysis Protocol File:C18_RP_Pos_QEPlus_20180403_12.5mint_ddMS2_MS.txt
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