Diversity of the microbiota communities found in the various regions of the intestinal tract in healthy individuals and inflammatory bowel diseases

Samuel Adefisoye Lawal; Athalia Voisin; Hana Olof; Michael Bording-Jorgensen; Heather Armstrong

doi:10.3389/fimmu.2023.1242242

Diversity of the microbiota communities found in the various regions of the intestinal tract in healthy individuals and inflammatory bowel diseases

Front Immunol. 2023 Nov 2:14:1242242. doi: 10.3389/fimmu.2023.1242242. eCollection 2023.

Authors

Samuel Adefisoye Lawal^{1

2

3}, Athalia Voisin^{1

2

3}, Hana Olof^{2

3

4}, Michael Bording-Jorgensen⁵, Heather Armstrong^{1

2

3

4

5

6}

Affiliations

¹ Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.
² Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada.
³ IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada.
⁴ Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.
⁵ Department of Pediatrics, University of Alberta, Edmonton, AB, Canada.
⁶ Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada.

Abstract

The severe and chronic inflammatory bowel diseases (IBD), Crohn disease and ulcerative colitis, are characterized by persistent inflammation and gut damage. There is an increasing recognition that the gut microbiota plays a pivotal role in IBD development and progression. However, studies of the complete microbiota composition (bacteria, fungi, viruses) from precise locations within the gut remain limited. In particular, studies have focused primarily on the bacteriome, with available methods limiting evaluation of the mycobiome (fungi) and virome (virus). Furthermore, while the different segments of the small and large intestine display different functions (e.g., digestion, absorption, fermentation) and varying microenvironment features (e.g., pH, metabolites), little is known about the biogeography of the microbiota in different segments of the intestinal tract or how this differs in IBD. Here, we highlight evidence of the differing microbiota communities of the intestinal sub-organs in healthy and IBD, along with method summaries to improve future studies.

Keywords: IBD; bacteriome; dysbiosis; microbiome; mycobiome; virome.

Publication types

Review
Research Support, Non-U.S. Gov't

MeSH terms

Colitis, Ulcerative* / microbiology
Crohn Disease* / microbiology
Gastrointestinal Microbiome*
Humans
Inflammatory Bowel Diseases* / microbiology
Microbiota*
Viruses*

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The funders had no role in study design, collection, or interpretation of data. The following grants were used to fund the project: Canada Research Chair (HA; CRC-2021-00172), Manitoba Medical Services Foundation grant (HA; #2021-03), and Weston Family Foundation (HA; Transformation of Research). HO was funded by a Mitacs scholarship and Mindel and Tom Olenick scholarship. SL was funded by a Rady Faculty of Health Sciences graduate studentship. MB-J was supported by a Mitacs Fellowship. AV was funded by a CGS-M scholarship.