Metabolomic analysis in inflammatory bowel disease: A systematic review
Abstract
Background and Aims: The inflammatory bowel diseases [IBD], Crohn’s disease and ulcerative colitis, are chronic, idiopathic gastrointestinal diseases. Although their precise aetiology is unknown, it is thought to involve a complex interaction between genetic predisposition and an abnormal host immune response to environmental exposures, probably microbial. Microbial dysbiosis has frequently been documented in IBD. Metabolomics [the study of small molecular intermediates and end products of metabolism in biological samples] provides a unique opportunity to characterize disease-associated metabolic changes and may be of particular use in quantifying gut microbial metabolism. Numerous metabolomic studies have been undertaken in IBD populations, identifying consistent alterations in a range of molecules across several biological matrices. This systematic review aims to summarize these findings. Methods: A comprehensive, systematic search was carried out using Medline and Embase. All studies were reviewed by two authors independently using predefined exclusion criteria. Sixty-four relevant papers were assessed for quality and included in the review. Results: Consistent metabolic perturbations were identified, including increases in levels of branched chain amino acids and lipid classes across stool, serum, plasma and tissue biopsy samples, and reduced levels of microbially modified metabolites in both urine [such as hippurate] and stool [such as secondary bile acids] samples. Conclusions: This review provides a summary of metabolomic research in IBD to date, highlighting underlying themes of perturbed gut microbial metabolism and mammalian–microbial co-metabolism associated with disease status.
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BA metabolism is defective in patients with IBD, indicated by increased levels of primary BAs and/or their conjugated forms and decreased levels of secondary BAs.
“BA metabolism is defective in patients with IBD, as indicated by increased levels of primary BAs (PBAs) and/or their conjugated forms, accompanied by decreased levels of second BAs (SBAs) (Lavelle and Sokol, 2020; Biagioli et al., 2021; Gallagher et al., 2021).”
From Bacteroides dorei BDX-01 alleviates DSS-induced experimental colitis in mice by regulating intestinal bile salt hydrolase activity and the FXR-NLRP3 signaling pathway (2023) · cites this paper as Gallagher et al., 2021
The Stool metabolomics studies section (p. 15) reports increased primary or conjugated bile acids alongside decreased secondary bile acids in dysbiotic Crohn’s disease samples. But it also reports two studies finding lower levels of both primary and secondary bile acids in IBD patients than controls, so the claimed pattern is not supported as a general finding across patients with IBD. (LLM, conf=0.88)
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- Authors
- Gallagher, K., Catesson, A., Griffin, J. L., Holmes, E., & Williams, H. R. T.
- Affiliations
- Imperial College London (GB)
- Murdoch University (AU)
- Imperial College Healthcare NHS Trust (GB)
- Corresponding author
- Gallagher, Kate
- Venue
- Journal of Crohn's and Colitis
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-11-11
- Volume
- 15
- Issue
- 5
- Pages
- 813-826
- ISSN
- 1873-9946 (ISSN-L)
- 1876-4479
- OpenAlex
- W3102377839
- Cited by
- 133
- References
- 155
- Citations by year
- 2026: 18 · 2025: 27 · 2024: 29 · 2023: 27 · 2022: 20 · 2021: 12
- FWCI
- 1.41
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Journal of Crohn s and Colitis (publishedVersion)
- PubMed (publishedVersion)
- Murdoch University Research Portal (submittedVersion)
- Spiral (Imperial College London) (submittedVersion)
- Funders
- National Institute for Health Research Imperial Biomedical Research Centre
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- inflammatory bowel disease, Crohn's disease
- MeSH terms
- Gastrointestinal Microbiome, Humans, Inflammatory Bowel Diseases, Metabolomics, Dysbiosis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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