Metagenomics in the diagnosis and monitoring of inflammatory bowel diseases
DOI:
https://doi.org/10.62305/biosana.v5i3.625Keywords:
Keywords: metagenomics, gastrointestinal microbiome, inflammatory bowel diseases, clinical diagnosis.Abstract
Inflammatory bowel disease (IBD) is a chronic disorder characterized by inflammation in structures of the digestive system. In this context, metagenomics has become established as a useful tool in the diagnosis and monitoring of IBD, since it is responsible for studying the sequencing of microbial DNA in a community, determining its microbial lineages and genes, as well as protein components in both the community of microorganisms and their metabolic network. Objective: To evaluate the best available scientific evidence on the role of metagenomics in inflammatory bowel diseases. Method: A bibliographic review was conducted during the period 2012-2025 using the PRISMA method. Results: Most studies show frequent modifications in the intestinal microbiota of patients with IBD. In bacterial communities, there was a reduction in Faecalibacterium prausnitzii and an increase in adherent-invasive Escherichia coli, while other investigations indicated a close relationship between metagenomic profiles and their usefulness in the prognosis and clinical monitoring of the disease. Conclusion: Metagenomics has allowed a significant understanding of IBD, which has identified specific traits such as: dysbiosis, modification of metabolic pathways and diagnostic biomarkers of IBD.
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Bakir B, Hacilar H, Jabeer A, Nalbantoglu O, Aran O, Yousef M. Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods. PeerJ. 2022;10. doi: 10.7717/PEERJ.13205
Cai J, Sun L, Gonzalez FJ. Gut microbiota-derived bile acids in intestinal immunity, inflammation, and tumorigenesis. Cell Host Microbe. 2022;30(3):289–300. doi: 10.1016/J.CHOM.2022.02.004
Mak WY, Zhao M, Ng SC, Burisch J. The epidemiology of inflammatory bowel disease: East meets west. J Gastroenterol Hepatol. 2020;35(3):380–9. doi: 10.1111/JGH.14872
Lee JWJ, Plichta D, Hogstrom L, Borren NZ, Lau H, Gregory SM, et al. Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. Cell Host Microbe. 2021;29(8):1294-1304.e4. doi: 10.1016/J.CHOM.2021.06.019
Vitetta L, Oldfield D, Sali A. Inflammatory Bowel Diseases and the Efficacy of Probiotics as Functional Foods. Front Biosci (Elite Ed). 2024;16(2). doi: 10.31083/J.FBE1602013
Sairenji T, Collins KL, Evans D V. An Update on Inflammatory Bowel Disease. Prim Care. 2017;44(4):673–92. doi: 10.1016/J.POP.2017.07.010
Serrano-Gómez G, Mayorga L, Oyarzun I, Roca J, Borruel N, Casellas F, et al. Dysbiosis and relapse-related microbiome in inflammatory bowel disease: A shotgun metagenomic approach. Comput Struct Biotechnol J. 2021;19:6481–9. doi: 10.1016/J.CSBJ.2021.11.037
Li M, Yang L, Mu C, Sun Y, Gu Y, Chen D, et al. Gut microbial metabolome in inflammatory bowel disease: From association to therapeutic perspectives. Comput Struct Biotechnol J. 2022;20:2402–14. doi: 10.1016/J.CSBJ.2022.03.038
Singh N, Bernstein CN. Environmental risk factors for inflammatory bowel disease. United Eur Gastroenterol J. 2022;10(10):1047–53. doi: 10.1002/UEG2.12319
Gonczi L, Bessissow T, Lakatos PL. Disease monitoring strategies in inflammatory bowel diseases: What do we mean by “tight control”? World J Gastroenterol. 2019;25(41):6172. doi: 10.3748/WJG.V25.I41.6172
Peterson DA, Frank DN, Pace NR, Gordon JI. Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe. 2008;3(6):417–27. doi: 10.1016/J.CHOM.2008.05.001
Bekkers M, Stojkovic B, Kaiko GE. Mining the Microbiome and Microbiota-Derived Molecules in Inflammatory Bowel Disease. Int J Mol Sci. 2021;22(20). doi: 10.3390/IJMS222011243
Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, et al. Metagenomic assembly through the lens of validation: Recent advances in assessing and improving the quality of genomes assembled from metagenomes. Brief Bioinform. 2018;20(4):1140–50.
Ning L, Zhou YL, Sun H, Zhang Y, Shen C, Wang Z, et al. Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts. Nat Commun. 2023;14(1). doi: 10.1038/S41467-023-42788-0
Zhou Y, Xu Z, He Y, Yang Y, Liu L, Lin Q, et al. Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction. mSystems. 2018;3(1). doi: 10.1128/MSYSTEMS.00188-17,
Ma Y, Zhang Y, Xiang J, Xiang S, Zhao Y, Xiao M, et al. Metagenome Analysis of Intestinal Bacteria in Healthy People, Patients With Inflammatory Bowel Disease and Colorectal Cancer. Front Cell Infect Microbiol. 2021;11. doi: 10.3389/FCIMB.2021.599734,
Xu X, Ocansey D, Hang S, Wang B, Amoah S, Yi C, et al. The gut metagenomics and metabolomics signature in patients with inflammatory bowel disease. Gut Pathog. 2022;14(1). doi: 10.1186/S13099-022-00499-9,
Erickson A, Cantarel B, Lamendella R, Darzi Y, Mongodin E, Pan C, et al. Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn’s Disease. PLoS One. 2012;7(11). doi: 10.1371/JOURNAL.PONE.0049138,
Norman J, Handley S, Baldridge M, Droit L, Liu C, Keller B, et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015;160(3):447–60. doi: 10.1016/j.cell.2015.01.002
Pérez V, García R, Vázquez J, Nos P, Beltrán B, Latorre A, et al. Study of the viral and microbial communities associated with Crohn’s disease: A metagenomic approach. Clin Transl Gastroenterol. 2013;4(6). doi: 10.1038/CTG.2013.9,
Pérez V, García R, Nos P, Beltrán B, Moret I, Moya A. Metagenomic analysis of Crohn’s disease patients identifies changes in the virome and microbiome related to disease status and therapy, and detects potential interactions and biomarkers. Inflamm Bowel Dis. 2015;21(11):2515–32. doi: 10.1097/MIB.0000000000000549,
Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569(7758):655–62. doi: 10.1038/S41586-019-1237-9
Elmassry M, Sugihara K, Chankhamjon P, Kim Y, Camacho F, Wang S, et al. A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. Cell Host Microbe. 2025;33(2):218-234.e12. doi: 10.1016/J.CHOM.2025.01.002
Lewis J, Daniel S, Li H, Hao F, Patterson A, Hecht A, et al. Surgery for Crohn’s Disease Is Associated With a Dysbiotic Microbiome and Metabolome: Results From Two Prospective Cohorts. CMGH. 2024;18(3). doi: 10.1016/j.jcmgh.2024.05.005
Rojas M, Romero T, Fernández J, Ramírez H, Avilés M, Castro M, et al. Modulation of faecal metagenome in Crohn’s disease: Role of microRNAs as biomarkers. World J Gastroenterol. 2018;24(46):5223–33. doi: 10.3748/WJG.V24.I46.5223,
Gonzalez C, Mills R, Zhu Q, Sauceda C, Knight R, Dulai P, et al. Location-specific signatures of Crohn’s disease at a multi-omics scale. Microbiome. 2022;10(1). doi: 10.1186/S40168-022-01331-X,
Coretti L, Natale A, Cuomo M, Florio E, Keller S, Lembo F, et al. The Interplay between Defensins and Microbiota in Crohn’s Disease. Mediators Inflamm. 2017;2017. doi: 10.1155/2017/8392523,
Frank D, St. Amand A, Feldman R, Boedeker E, Harpaz N, Pace N. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007;104(34):13780–5. doi: 10.1073/PNAS.0706625104,
Kostic A, Xavier R, Gevers D. The microbiome in inflammatory bowel disease: Current status and the future ahead. Gastroenterology. 2014;146(6):1489–99. doi: 10.1053/j.gastro.2014.02.009
Coretti L, Paparo L, Riccio M, Amato F, Cuomo M, Natale A, et al. Gut microbiota features in young children with autism spectrum disorders. Front Microbiol. 2018;9. doi: 10.3389/FMICB.2018.03146,
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