Abstract
The pathogenesis of inflammatory bowel disease is related to the imbalance of microbial community composition. A reduction in the diversity of the intestinal microbiota as well as specific taxonomic and functional shifts have been reported in inflammatory bowel diseases and may play a central role in the inflammatory process. The aim was to review recent developments in the structural and functional changes observed in the gastrointestinal microbiome in patients with inflammatory bowel diseases and to survey the use of machine learning to discover the microbiome in inflammatory bowel disease. We start by highlighting the relationship between gut microbiome disorder with inflammatory bowel disease including different studies that confirmed this association, then, we provide an overview of the use of Machine Learning in analyzing the microbiome in inflammatory bowel diseases.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Wright, E.K., Kamm, M.A., Teo, S.M., Inouye, M., Wagner, J., Kirkwood, C.D.: Recent advances in characterizing the gastrointestinal microbiome in Crohn’s disease: a systematic review. Inflamm. Bowel Dis. 21(6), 1219–1228 (2015). https://doi.org/10.1097/MIB.0000000000000382
Tefas, C., Ciobanu, L., Tantău, M., Moraru, C., Socaciu, C.: The potential of metabolic and lipid profiling in inflammatory bowel diseases: a pilot study. Bosnian J. Basic Med. Sci. 20(2), 262–270 (2020). https://doi.org/10.17305/bjbms.2019.423
Di Paola, M., et al.: Comparative immunophenotyping of Saccharomyces cerevisiae and Candida spp. strains from Crohn’s disease patients and their interactions with the gut microbiome. J. Trans. Autoimmunity 3, 100036 (2020). https://doi.org/10.1016/j.jtauto.2020.100036
Dong, L.N., Wang, M., Guo, J., Wang, J.P.: Role of intestinal microbiota and metabolites in inflammatory bowel disease. Chin. Med. J. 132(13), 1610–1614 (2019). https://doi.org/10.1097/CM9.0000000000000290
Rubbens, P., Props, R., Kerckhof, F.M., Boon, N., Waegeman, W.: Cytometric fingerprints of gut microbiota predict Crohn’s disease state. ISME J. 15(1), 354–358 (2021). https://doi.org/10.1038/s41396-020-00762-4
Glassner, K.L., Abraham, B.P., Quigley, E.M.M.: The microbiome and inflammatory bowel disease. J. Allergy Clin. Immunol. 145(1), 16–27 (2020). https://doi.org/10.1016/j.jaci.2019.11.003
Roda, G., et al.: Crohn’s disease. Nature reviews. Disease Primers 6(1), 22 (2020). https://doi.org/10.1038/s41572-020-0156-2
Braun, T., et al.: Individualized dynamics in the gut microbiota precede Crohn’s disease flares. Am. J. Gastroenterol. 114(7), 1142–1151 (2019). https://doi.org/10.14309/ajg.0000000000000136
He, M., Li, C., Tang, W., Kang, Y., Zuo, Y., Wang, Y.: Machine learning gene expression predicting model for ustekinumab response in patients with Crohn’s disease. Immun., Inflamm. Disease 9(4), 1529–1540 (2021). https://doi.org/10.1002/iid3.506
Choi, Y.I., et al.: Development of machine learning model to predict the 5-year risk of starting biologic agents in patients with inflammatory bowel disease (IBD): K-CDM network study. J. Clin. Med. 9(11), 3427 (2020). https://doi.org/10.3390/jcm9113427
Kraszewski, S., Szczurek, W., Szymczak, J., Reguła, M., Neubauer, K.: Machine learning prediction model for inflammatory bowel disease based on laboratory markers. working model in a discovery cohort study. J. Clin. Med. 10(20), 4745 (2021). https://doi.org/10.3390/jcm10204745
Gubatan, J., Levitte, S., Patel, A., Balabanis, T., Wei, M.T., Sinha, S.R.: Artificial intelligence applications in inflammatory bowel disease: emerging technologies and future directions. World J. Gastroenterol. 27(17), 1920–1935 (2021). https://doi.org/10.3748/wjg.v27.i17.1920
Xu, C., Zhou, M., Xie, Z., Li, M., Zhu, X., Zhu, H.: LightCUD: a program for diagnosing IBD based on human gut microbiome data. BioData Mining 14, 1–13 (2021)
McDonnell, M., et al.: High incidence of glucocorticoid-induced hyperglycaemia in inflammatory bowel disease: metabolic and clinical predictors identified by machine learning. BMJ Open Gastroenterol. 7(1), e000532 (2020). https://doi.org/10.1136/bmjgast-2020-000532
Clooney, A.G., et al.: Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study. Gut 70(3), 499–510 (2021). https://doi.org/10.1136/gutjnl-2020-321106
Sarrabayrouse, G., et al.: Fungal and bacterial loads: noninvasive inflammatory bowel disease biomarkers for the clinical setting. mSystems 6(2), e01277–20 (2021). https://doi.org/10.1128/mSystems.01277-20
LaPierre, N., Ju, C. J., Zhou, G., Wang, W.: MetaPheno: a critical evaluation of deep learning and machine learning in metagenome-based disease prediction. Methods (San Diego, Calif.) 166, 74–82 (2019). https://doi.org/10.1016/j.ymeth.2019.03.003
Reiman, D., Metwally, A.A., Sun, J., Dai, Y.: PopPhy-CNN: a phylogenetic tree embedded architecture for convolutional neural networks to predict host phenotype from metagenomic data. IEEE J. Biomed. Health Inform. 24(10), 2993–3001 (2020). https://doi.org/10.1109/JBHI.2020.2993761
Pasolli, E., Truong, D.T., Malik, F., Waldron, L., Segata, N.: Machine learning meta-analysis of large metagenomic datasets: tools and biological insights. PLoS Comput. Biol. 12(7), e1004977 (2016). https://doi.org/10.1371/journal.pcbi.1004977
Nguyen, T.H., Prifti, E., Chevaleyre, Y., Sokolovska, N., Zucker, J.D.: Disease classification in metagenomics with 2D embeddings and deep learning (2018). arXiv preprint arXiv:1806.09046
Rahman, M.A., Rangwala, H.: RegMIL: phenotype classification from metagenomic data. In: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 145–154 (2018)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2024 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this paper
Cite this paper
En Najih, N., Moussa, P.A. (2024). Machine Learning for the Analysis of Human Microbiome in Inflammatory Bowel Diseases: Literature Review. In: Tabaa, M., Badir, H., Bellatreche, L., Boulmakoul, A., Lbath, A., Monteiro, F. (eds) New Technologies, Artificial Intelligence and Smart Data. INTIS INTIS 2022 2023. Communications in Computer and Information Science, vol 1728. Springer, Cham. https://doi.org/10.1007/978-3-031-47366-1_1
Download citation
DOI: https://doi.org/10.1007/978-3-031-47366-1_1
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-47365-4
Online ISBN: 978-3-031-47366-1
eBook Packages: Computer ScienceComputer Science (R0)