The DOI matches its Crossref record; 158 of the 158 references it cites were found in a registry or an index.
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, 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
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Cites
Preferred Reporting Items for Systematic Reviews and Meta-Analyses: the PRISMA statement
Moher, D., Liberati, A., Tetzlaff, J., Altman, D. G., & for the PRISMA Group (2009) · BMJ · doi:10.1136/bmj.b2535 · Cited by 83,823
Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement
Moher, D., Liberati, A., Tetzlaff, J., Altman, D. G., & The PRISMA Group (2009) · PLoS Medicine · doi:10.1371/journal.pmed.1000097 · Cited by 64,042
Preferred reporting items for systematic reviews and meta-analyses: the PRISMA Statement.
(2009) · PubMed Central · Cited by 44,859
Principal component analysis: A review and recent developments
Jolliffe, I. T., & Cadima, J. (2016) · Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences · doi:10.1098/rsta.2015.0202 · Cited by 10,117
den Besten, G., van Eunen, K., Groen, A. K., Venema, K., Reijngoud, D.-J., & Bakker, B. M. (2013) · Journal of Lipid Research · doi:10.1194/jlr.r036012 · Cited by 5,048
Host-gut microbiota metabolic interactions
Nicholson, J. K., Holmes, E., Kinross, J., Burcelin, R., Gibson, G., Jia, W., & Pettersson, S. (2012) · Science · doi:10.1126/science.1223813 · Cited by 4,760
Self-citationWhiting, P., Rutjes, A. W., Reitsma, J. B., Bossuyt, P. M., & Kleijnen, J. (2003) · BMC Medical Research Methodology · doi:10.1186/1471-2288-3-25 · Cited by 3,592
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
Lloyd-Price, J., Arze, C., Ananthakrishnan, A. N., Schirmer, M., Avila-Pacheco, J., Poon, T. W., Andrews, E., Ajami, N. J., Bonham, K. S., Brislawn, C. J., et al. (2019) · Nature · doi:10.1038/s41586-019-1237-9 · Cited by 3,143
Gut microbiota functions: metabolism of nutrients and other food components
Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I., & Tuohy, K. (2018) · European Journal of Nutrition · doi:10.1007/s00394-017-1445-8 · Cited by 2,878
Bile salt biotransformations by human intestinal bacteria
Ridlon, J. M., Kang, D.-J., & Hylemon, P. B. (2006) · Journal of Lipid Research · doi:10.1194/jlr.r500013-jlr200 · Cited by 2,829
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Research works printed but not linked: 2
- Qi, 2020, High, Genomics
- Machiels, 2014, A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis, Gut, 63, 1275, 10.1136/gutjnl-2013-304833 · DOI · Paper page
Cited by
Sorted by citations
Items 101–133 of 133
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Rey, A. I., Higueras, C., Olmeda, P., Sainz, Á., Gálvez, B. G., & Larrosa, M. (2025) · Animals · doi:10.3390/ani15131927 · Cited by 1
The event of multiomics in metagenomics
Mallick, H., Bardhan, M., Dagli, C. S., Liu, Z., & Gao, J. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-22376-1.00010-6 · Cited by 2
Бакулин, И. Г., Akishina, Y. A., Lyamina, S., & Maev, I. V. (2025) · Russian Journal of Evidence-Based Gastroenterology · doi:10.17116/dokgastro20251403144 · Cited by 1
Zou, Y., Yang, Z., Liu, J., Sheng, M., Wang, Z., & Xu, W. (2026) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2026.122266 · Cited by 1
Plasma Bacterial Metabolites in Crohn’s Disease Pathogenesis and Complications
Deskur, A., Ambrożkiewicz, F., Samborowska, E., Błogowski, W., Sulikowski, T., Białek, A., Zawada, I., Dąbkowski, K., Mitrus, J., Karczmarski, J., et al. (2024) · Nutrients · doi:10.3390/nu17010074 · Cited by 1
Multi-omics empowered deep phenotyping of ulcerative colitisPreprint
Janker, L., Schuster, D., Bortel, P., Hagn, G., Brunmair, J., Meier, S. M., Mader, J. C., Slany, A., Bileck, A., Madl, C., et al. (2022) · medRxiv · doi:10.1101/2022.05.25.22275502 · Cited by 1
Tien, N. T. N., Choi, E. J., Thu, N. Q., Yu, S. J., Nguyen, D. N., Kim, D. H., Long, N. P., & Lee, H. S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.13.593901 · Cited by 1
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Tsonev, N. (2022) · American Journal of Biomedical Science & Research · doi:10.34297/ajbsr.2022.17.002356
Zhu, J.-W., Wang, H., Aisikaer, M., Wenjun, Z. H. O. U., Yang, T., & Aximujiang, K. (2024) · Pharmacological Research - Natural Products · doi:10.1016/j.prenap.2024.100029
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Mendez, H., & Rijkers, G. T. (2025) · Exploration of Immunology · doi:10.37349/ei.2025.1003191 · Cited by 1
Huang, L., Zhang, L., Lotfi, A., Jarmusch, A. K., Lee, I., Kim, A., Morton, J. T., & Aksenov, A. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.26.649581
Detman, A., Schiro, G., Filip, R., Samborowska, E., Karczmarski, J., Jakubowska, K., Jarmakiewicz-Czaja, S., Williams, A., Hickman, N., Laubitz, D., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.29.656803 · Cited by 1
Qu, X., Zhao, L., & Kang, C. (2025) · Medicine · doi:10.1097/md.0000000000042773 · Cited by 1
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Enaud, R., Rivière, P., Poullenot, F., & Lamireau, T. (2025) · Perfectionnement en Pédiatrie · doi:10.1016/j.perped.2025.10.005
Welz, L., Laabs, B., Harris, D. M. M., Schuchardt, S., Tran, F., Waschina, S., Frey, N., Franke, A., Verstockt, B., Vermeire, S., et al. (2025) · medRxiv · doi:10.64898/2025.12.10.25341951
Li, H., Zhu, Z., Wang, X., Du, M., Wei, R., Wang, C., Miao, J., & Cheng, L. (2026) · Genes & Diseases · doi:10.1016/j.gendis.2026.102070
Kim, D. J., Lee, Y. J., Choi, J.-W., Lee, H. S., Lee, W. S., Park, H., Choi, E., Park, H., Lee, J.-H., Lee, J.-H., et al. (2026) · Scientific Reports · doi:10.1038/s41598-026-38818-8 · Cited by 1
Decanoic acid in Crohn’s disease-associated complications: Antifibrotic effect mediated by PPARγ
Cejudo-Garcés, A., Patel, J., Jarén, A. C., Boscá-Watts, M. M., Calatayud, S., Barrachina, M. D., Ortiz‐Masiá, D., & Cosín‐Roger, J. (2026) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2026.119294
Antonelli, E., Dell’Era, A., Maconi, G., & Bassotti, G. (2026) · Metabolites · doi:10.3390/metabo16040238
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Khan, S., Li, Y. C., & Rodriguez‐Palacios, A. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1844649
Andersen, J. H. M., Verbiest, A., Hvistendahl, M., Vanuytsel, T., & Jeppesen, P. B. (2026) · Intestinal failure. · doi:10.1016/j.intf.2026.100373
Xu, H., Huang, G., Zhang, L., Liu, W., Wu, Q., Chen, M., Zhao, D., Zhang, Y., & Xu, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.25.734643
Leng, L., Chen, J. K., 左金蘭, Chen, Z., Cao, K., Zhang, L., Li, C., Hu, L., Zhou, T., Liu, Q., et al. (2026) · Journal of Applied Microbiology · doi:10.1093/jambio/lxag150
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Wei, W., Yan, P., Wang, F., Wang, Q., Li, C., Bai, X., Zhang, Y., Bao, Y., Li, J., & Yu, K. (2026) · Frontiers in Nutrition · doi:10.3389/fnut.2026.1942104
Meng, X.-W., Tian, C., Zhu, Y.-J., & Zheng, D.-P. (2026) · Microorganisms · doi:10.3390/microorganisms14092108
Krynicka, P., Piotrowska, A. H., & Kłopocka, M. (2026) · Metabolites · doi:10.3390/metabo16090696
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Yu, Y., Wang, J., Yuan, Q., Yu, L., & Zhang, C. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1977691
Metadata
- 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
- Health Sciences › Medicine › Gastroenterology › 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
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