The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead
Open accessAbstract
Studies of the roles of microbial communities in the development of inflammatory bowel disease (IBD) have reached an important milestone. A decade of genome-wide association studies and other genetic analyses have linked IBD with loci that implicate an aberrant immune response to the intestinal microbiota. More recently, profiling studies of the intestinal microbiome have associated the pathogenesis of IBD with characteristic shifts in the composition of the intestinal microbiota, reinforcing the view that IBD results from altered interactions between intestinal microbes and the mucosal immune system. Enhanced technologies can increase our understanding of the interactions between the host and its resident microbiota and their respective roles in IBD from both a large-scale pathway view and at the metabolic level. We review important microbiome studies of patients with IBD and describe what we have learned about the mechanisms of intestinal microbiota dysfunction. We describe the recent progress in microbiome research from exploratory 16S-based studies, reporting associations of specific organisms with a disease, to more recent studies that have taken a more nuanced view, addressing the function of the microbiota by metagenomic and metabolomic methods. Finally, we propose study designs and methodologies for future investigations of the microbiome in patients with inflammatory gut and autoimmune diseases in general.
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Studies of faecal and gut mucosal-associated microbiota have demonstrated quantitative and qualitative changes in composition and function associated with IBD, with a shift towards an inflammatory-promoting microbiome.
“Studies of faecal and gut mucosal-associated microbiota have demonstrated quantitative and qualitative changes in composition and function associated with IBD, with a shift towards an inflammatory-promoting microbiome [32] .”
From Intestinal microbiota in health and disease: Role of bifidobacteria in gut homeostasis (2014) · cites this paper as [32]
Advanced molecular techniques have demonstrated fundamental differences in microbial composition and function in IBD patients.
“Advanced molecular techniques have demonstrated fundamental differences in both microbial composition and function in patients with IBD.56–58”
From Update on Fecal Microbiota Transplantation 2015: Indications, Methodologies, Mechanisms, and Outlook (2015) · cites this paper as [56]
Multiple lines of evidence point towards central roles of gut microbiome perturbations in the pathogenesis of IBD.
“Multiple lines of evidence point towards central roles of gut microbiome perturbations in the pathogenesis of IBD.”
From Interaction between microbiota and immunity in health and disease (2020) · cites this paper as [149]
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- Authors
- Kostic, A. D., Xavier, R. J., & Gevers, D.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Xavier, Ramnik J.
- Venue
- Gastroenterology
- Publisher
- Elsevier BV
- Published
- 2014-05
- Volume
- 146
- Issue
- 6
- Pages
- 1489-1499
- ISSN
- 0016-5085 (ISSN-L)
- PMC
- PMC4034132
- OpenAlex
- W2152751713
- Cited by
- 1,789
- References
- 123
- Citations by year
- 2026: 81 · 2025: 121 · 2024: 151 · 2023: 136 · 2022: 216 · 2021: 181 · 2020: 163 · 2019: 189 · 2018: 129 · 2017: 159 · 2016: 116 · 2015: 111 · 2014: 34 · 2013: 1
- FWCI
- 13.20
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Gastroenterology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Crohn's and Colitis Foundation of America
- National Institutes of Health (U54 DE023798, R01 DK092405)
- 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 › Medicine › Epidemiology › Microscopic Colitis
- Keywords
- inflammatory bowel disease, gut microbiota, host-microbe interactions, mucosal immunity, dysbiosis, 16S rRNA gene profiling, metagenomics, metabolomics, autoimmune disease
- MeSH terms
- Animals, Anti-Inflammatory Agents, Bacteria, Humans, Intestines, Risk Factors, Inflammatory Bowel Diseases, Immunity, Mucosal, Probiotics, Metagenome, Metagenomics, Microbiota
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