Dynamics of the human gut microbiome in inflammatory bowel disease
Open accessAbstract
Inflammatory bowel disease (IBD) is characterized by flares of inflammation with a periodic need for increased medication and sometimes even surgery. The aetiology of IBD is partly attributed to a deregulated immune response to gut microbiome dysbiosis. Cross-sectional studies have revealed microbial signatures for different IBD subtypes, including ulcerative colitis, colonic Crohn's disease and ileal Crohn's disease. Although IBD is dynamic, microbiome studies have primarily focused on single time points or a few individuals. Here, we dissect the long-term dynamic behaviour of the gut microbiome in IBD and differentiate this from normal variation. Microbiomes of IBD subjects fluctuate more than those of healthy individuals, based on deviation from a newly defined healthy plane (HP). Ileal Crohn's disease subjects deviated most from the HP, especially subjects with surgical resection. Intriguingly, the microbiomes of some IBD subjects periodically visited the HP then deviated away from it. Inflammation was not directly correlated with distance to the healthy plane, but there was some correlation between observed dramatic fluctuations in the gut microbiome and intensified medication due to a flare of the disease. These results will help guide therapies that will redirect the gut microbiome towards a healthy state and maintain remission in IBD.
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To avoid confounding by colitis and PPI use, patients with PFS ≥12 months versus PFS <12 months on monotherapy or combination therapy who did not develop colitis and did not use PPIs were compared, while also averaging over the effects of irAEs that were not colitis, previous antibiotics use, previous therapy and cancer center.
“To avoid confounding by colitis and PPI use, which individually has considerable effects on the gut microbiome19,20, we compared patients with PFS ≥12 months versus patients with PFS <12 months on monotherapy (Extended Data Fig. 8 and Supplementary Table 7) or combination therapy (Extended Data Fig. 9 and Supplementary Table 8) who did not develop colitis and did not use PPIs, while also averaging”
From Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma (2024) · cites this paper as [19]
IrAEs, including colitis, were assessed using the CTCAE version 5.
“IrAEs, including colitis, were assessed using the CTCAE version 5 (19).”
From Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma (2024) · cites this paper as [19]
Microbiomes of IBD patients tend to display greater instability and reduced diversity compared to healthy subjects.
“The microbiomes of IBD patients tend to display greater instability and reduced diversity compared to healthy subjects (Halfvarson et al., 2017).”
From Viral Infections, the Microbiome, and Probiotics (2021) · cites this paper as Halfvarson et al., 2017
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- Authors
- Halfvarson, J., Brislawn, C. J., Lamendella, R., Vázquez-Baeza, Y., Walters, W. A., Bramer, L. M., D'Amato, M., Bonfiglio, F., McDonald, D., Gonzalez, A., McClure, E. E., Dunklebarger, M. F., Knight, R., & Jansson, J. K.
- Affiliations
- Örebro University (SE)
- Pacific Northwest National Laboratory (US)
- Juniata College (US)
- Karolinska Institutet (SE)
- University of California San Diego (US)
- Corresponding author
- Jansson, Janet K.
- ORCID
- Venue
- Nature Microbiology
- Published
- 2017-02-13
- Volume
- 2
- Issue
- 5
- Pages
- 17004-17004
- ISSN
- 2058-5276 (ISSN-L)
- PMC
- PMC5319707
- OpenAlex
- W2588997555
- Cited by
- 1,204
- References
- 37
- Citations by year
- 2026: 91 · 2025: 131 · 2024: 145 · 2023: 144 · 2022: 150 · 2021: 178 · 2020: 136 · 2019: 119 · 2018: 76 · 2017: 31
- FWCI
- 40.41
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Microbiology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation
- Howard Hughes Medical Institute
- Hospital Research Foundation
- Universitetssjukhuset Örebro
- National Institutes of Health
- National Institute of Dental and Craniofacial Research (U54DE023798)
- Division of Undergraduate Education
- Pacific Northwest National Laboratory (DE-AC05-76RLO 1830)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Inflammatory Bowel Disease
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- gut microbiome dynamics, inflammatory bowel disease, Crohn's disease, ulcerative colitis, dysbiosis, ileal Crohn's disease, surgical resection, disease flares, remission
- MeSH terms
- Gastrointestinal Microbiome, Adult, Colitis, Ulcerative, Crohn Disease, Cross-Sectional Studies, Feces, Female, Humans, Inflammation, Male, Phenotype, Inflammatory Bowel Diseases, Leukocyte L1 Antigen Complex, Dysbiosis
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