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The gut microbiota and its biogeography

Nature Reviews Microbiology volume 22, pages 105–118 (2024)Cite this article

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Abstract

Biogeography is the study of species distribution and diversity within an ecosystem and is at the core of how we understand ecosystem dynamics and interactions at the macroscale. In gut microbial communities, a historical reliance on bulk sequencing to probe community composition and dynamics has overlooked critical processes whereby microscale interactions affect systems-level microbiota function and the relationship with the host. In recent years, higher-resolution sequencing and novel single-cell level data have uncovered an incredible heterogeneity in microbial composition and have enabled a more nuanced spatial understanding of the gut microbiota. In an era when spatial transcriptomics and single-cell imaging and analysis have become key tools in mammalian cell and tissue biology, many of these techniques are now being applied to the microbiota. This fresh approach to intestinal biogeography has given important insights that span temporal and spatial scales, from the discovery of mucus encapsulation of the microbiota to the quantification of bacterial species throughout the gut. In this Review, we highlight emerging knowledge surrounding gut biogeography enabled by the observation and quantification of heterogeneity across multiple scales.

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Fig. 1: Regional biogeographical features of the gastrointestinal tract at the scale of the whole gut.
Fig. 2: Biogeographical features across the transverse axis of the gut.
Fig. 3: Mucus layer depletion in inflammatory bowel disease and inflammation.

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Acknowledgements

The authors acknowledge that this work was completed on the traditional, ancestral and unceded territory of the xʷməθkʷəy̕əm (Musqueam) people. The authors encourage the reader to learn about the history of the land they work on at Native Land Digital (www.native-land.ca). They thank K. Ng, M. Orozco-Hidalgo, F. Papazotos, J. Burkhardt, H. Ghezzi and M. Hunter for their feedback and guidance in shaping this Review. G.M. acknowledges support from Natural Sciences and Engineering Research Council of Canada, Canada Graduate Scholarships.

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  1. Department of Biology, Concordia University, Montreal, Quebec, Canada

    Giselle McCallum

  2. Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada

    Giselle McCallum & Carolina Tropini

  3. School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada

    Carolina Tropini

  4. Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada

    Carolina Tropini

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McCallum, G., Tropini, C. The gut microbiota and its biogeography. Nat Rev Microbiol 22, 105–118 (2024). https://doi.org/10.1038/s41579-023-00969-0

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