Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease
Numerous studies have accelerated the knowledge expansion on the role of gut microbiota in inflammatory bowel disease (IBD). However, the precise mechanisms behind host-microbe cross-talk remain largely undefined, due to the complexity of the human intestinal ecosystem and multiple external factors....
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2025-12-01
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| Series: | Gut Microbes |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/19490976.2025.2476570 |
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| author | Fengyuan Su Meng Su Wenting Wei Jiayun Wu Leyan Chen Xiqiao Sun Moyan Liu Shiqiang Sun Ren Mao Arno R. Bourgonje Shixian Hu |
| author_facet | Fengyuan Su Meng Su Wenting Wei Jiayun Wu Leyan Chen Xiqiao Sun Moyan Liu Shiqiang Sun Ren Mao Arno R. Bourgonje Shixian Hu |
| author_sort | Fengyuan Su |
| collection | DOAJ |
| description | Numerous studies have accelerated the knowledge expansion on the role of gut microbiota in inflammatory bowel disease (IBD). However, the precise mechanisms behind host-microbe cross-talk remain largely undefined, due to the complexity of the human intestinal ecosystem and multiple external factors. In this review, we introduce the interactome concept to systematically summarize how intestinal dysbiosis is involved in IBD pathogenesis in terms of microbial composition, functionality, genomic structure, transcriptional activity, and downstream proteins and metabolites. Meanwhile, this review also aims to present an updated overview of the relevant mechanisms, high-throughput multi-omics methodologies, different types of multi-omics cohort resources, and computational methods used to understand host-microbiota interactions in the context of IBD. Finally, we discuss the challenges pertaining to the integration of multi-omics data in order to reveal host-microbiota cross-talk and offer insights into relevant future research directions. |
| format | Article |
| id | doaj-art-830493fd2ebb4464928491b0429b75ea |
| institution | OA Journals |
| issn | 1949-0976 1949-0984 |
| language | English |
| publishDate | 2025-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Gut Microbes |
| spelling | doaj-art-830493fd2ebb4464928491b0429b75ea2025-08-20T02:34:39ZengTaylor & Francis GroupGut Microbes1949-09761949-09842025-12-0117110.1080/19490976.2025.2476570Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel diseaseFengyuan Su0Meng Su1Wenting Wei2Jiayun Wu3Leyan Chen4Xiqiao Sun5Moyan Liu6Shiqiang Sun7Ren Mao8Arno R. Bourgonje9Shixian Hu10Institute of Precision Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, ChinaThe First Clinical Medical School, Nanfang Hospital of Southern Medical University, Guangzhou, ChinaZhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, ChinaZhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, ChinaZhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, ChinaZhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, ChinaAmsterdam UMC location Academic Medical Center, Department of Experimental Vascular Medicine, Amsterdam, The NetherlandsDepartment of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The NetherlandsDepartment of Gastroenterology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, ChinaDepartment of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The NetherlandsInstitute of Precision Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, ChinaNumerous studies have accelerated the knowledge expansion on the role of gut microbiota in inflammatory bowel disease (IBD). However, the precise mechanisms behind host-microbe cross-talk remain largely undefined, due to the complexity of the human intestinal ecosystem and multiple external factors. In this review, we introduce the interactome concept to systematically summarize how intestinal dysbiosis is involved in IBD pathogenesis in terms of microbial composition, functionality, genomic structure, transcriptional activity, and downstream proteins and metabolites. Meanwhile, this review also aims to present an updated overview of the relevant mechanisms, high-throughput multi-omics methodologies, different types of multi-omics cohort resources, and computational methods used to understand host-microbiota interactions in the context of IBD. Finally, we discuss the challenges pertaining to the integration of multi-omics data in order to reveal host-microbiota cross-talk and offer insights into relevant future research directions.https://www.tandfonline.com/doi/10.1080/19490976.2025.2476570IBDgut microbiomehost-microbiota interactomemulti-omicsmethodologies |
| spellingShingle | Fengyuan Su Meng Su Wenting Wei Jiayun Wu Leyan Chen Xiqiao Sun Moyan Liu Shiqiang Sun Ren Mao Arno R. Bourgonje Shixian Hu Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease Gut Microbes IBD gut microbiome host-microbiota interactome multi-omics methodologies |
| title | Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease |
| title_full | Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease |
| title_fullStr | Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease |
| title_full_unstemmed | Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease |
| title_short | Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease |
| title_sort | integrating multi omics data to reveal the host microbiota interactome in inflammatory bowel disease |
| topic | IBD gut microbiome host-microbiota interactome multi-omics methodologies |
| url | https://www.tandfonline.com/doi/10.1080/19490976.2025.2476570 |
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