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Gastroenterology

A multi-omic trip through the human gut

Nature Metabolism volume 5, pages 720–721 (2023)Cite this article

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Most of human microbiome research has focused on analysing faecal samples, which represent the final stop of the digestive journey. Two recent articles use a novel sampling approach to capture luminal content at different points during digestion and reveal that the analysis of faecal samples tells only a fraction of the story.

The sampling capsule used in these studies can collect small amounts of luminal content through the action of its one-way valve, which only opens when the capsule’s coating dissolves (dependent on pH). Although it can vary depending on the individual, the pH of the human gut is lower in the duodenum, increases towards the ileum and then drops again upon the transition to the colon3. The authors of both papers take advantage of this pH transition by having each of 15 healthy volunteers ingest four separate capsules designed to sample three locations in the small intestine and one in the ascending colon. The luminal contents contained in these four devices were then analysed using multi-omics with the aim of comparing differences between the four devices, as well as with the faecal sample that marks the end of each capsular adventure. The article by Shalon et al., published in Nature, provides a more general overview of the sampling approach and a broad analysis of the metagenome, metabolome, virome and proteome in the sampled material1, whereas the Folz et al. paper, published in Nature Metabolism, takes a deeper dive into the diverse metabolomic data in which thousands of biomolecules were detected throughout the gastrointestinal tract (many of which remain unknown)2, making both articles nicely complementary.

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Fig. 1: Sampling approach.

References

  1. Shalon, D. et al. Nature https://doi.org/10.1038/s41586-023-05989-7 (2023).

  2. Folz, J. et al. Nat. Metab. https://doi.org/10.1038/s42255-023-00777-z (2023).

  3. Evans, D.F., Pye, G., Bramley, R., Clark, A.G., Dyson, T.J., Hardcastle, J.D. 1988. Gut 29, 1035–1041 (1988).

  4. Devkota, S. et al. Nature 487, 104–108 (2012).

  5. da Silva, R.R., Dorrestein, P.C. & Quinn, R.A. Proc. Natl Acad. Sci. 112, 12549–12550 (2015).

  6. Hofmann, A.F. & Hagey L.R. J. Lipid Res. 55, 1553–1595 (2014).

  7. Quinn, R.A. Nature 579, 123–129 (2020).

  8. Lucas, L.N. mSystems 6, e0080521 (2021).

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA

    Robert A. Quinn, Christian Martin & Douglas V. Guzior

  2. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA

    Douglas V. Guzior

Authors
  1. Robert A. Quinn
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  2. Christian Martin
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  3. Douglas V. Guzior
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Correspondence to Robert A. Quinn.

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The authors declare no competing interests.

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Quinn, R.A., Martin, C. & Guzior, D.V. A multi-omic trip through the human gut. Nat Metab 5, 720–721 (2023). https://doi.org/10.1038/s42255-023-00773-3

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