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Data from: An <i>in vitro</i> model of the small intestinal microbiota provides key insights into interindividual variability in structure and function

Published by Agricultural Research Service | Department of Agriculture | Catalog Last Checked: August 03, 2026 at 05:01 PM | Dataset Last Updated: June 26, 2026
Although known to play a vital role in nutrient digestion and absorption and immune function, the small intestinal microbiota (SIM) is often overlooked due to difficulty accessing the anatomical site and known variability between donors. In this study, an in vitro model of the SIM was designed and used to develop the microbiota of four unique donors. Shotgun sequencing was used to determine community structure and genomic representation. Short chain fatty acid (SCFA) analysis, bile acid quantification, and untargeted metabolomics were combined to determine community function. Combining the results of metagenomics and metabolomics revealed that despite variation in taxonomic structure there was a core set of genes shared among the communities that correlated with a relatively consistent metabolomic signature.

Resources

10 resources available

  • Table S1-Composition of MBHI and PJ.xlsx

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  • Table S2-Metagenomic structural profiles.xlsx

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  • Table S3- Spearman rho and q values for structure over time.xlsx

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  • Table S4-Bile acid concentrations and Spearmans data.xlsx

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  • Table S5- Humann pathways and taxa associated.xlsx

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  • Table S6- Levels of SCFAs and Spearmans data.xlsx

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  • Table S7 - untargeted metabolomics with ChEBI classifications and q values.xlsx

    XLSX
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  • Table S8- all humann pathways with stats.xlsx

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  • Table S9- MAGs assembled and MicroTraits.xlsx

    XLSX
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  • Supplemental Table legends.docx

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Complete Metadata
@type dcat:Dataset
accessLevel public
bureauCode 
[
  "005:18"
]
contactPoint 
{
  "fn": "Narrowe, Adrienne B.",
  "hasEmail": "mailto:adrienne.narrowe@usda.gov"
}
description <p dir="ltr">Although known to play a vital role in nutrient digestion and absorption and immune function, the small intestinal microbiota (SIM) is often overlooked due to difficulty accessing the anatomical site and known variability between donors. In this study, an <i>in vitro</i><i> </i>model of the SIM was designed and used to develop the microbiota of four unique donors. Shotgun sequencing was used to determine community structure and genomic representation. Short chain fatty acid (SCFA) analysis, bile acid quantification, and untargeted metabolomics were combined to determine community function. Combining the results of metagenomics and metabolomics revealed that despite variation in taxonomic structure there was a core set of genes shared among the communities that correlated with a relatively consistent metabolomic signature.</p>
distribution 
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    "@type": "dcat:Distribution",
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]
identifier 10.15482/USDA.ADC/32328621.v1
keyword 
[
  "Small intestinal microbiota",
  "bile acids",
  "gut microbiota",
  "in vitro culturing",
  "metagenomics",
  "untargeted metabolomics"
]
license https://creativecommons.org/publicdomain/zero/1.0/
modified 2026-06-26
programCode 
[
  "005:040"
]
publisher 
{
  "name": "Agricultural Research Service",
  "@type": "org:Organization"
}
temporal 2023-01-03/2023-01-31
title Data from: An <i>in vitro</i> model of the small intestinal microbiota provides key insights into interindividual variability in structure and function

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