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Wang T, Holscher HD, Maslov S, Hu FB, Weiss ST, Liu YY. Predicting metabolic response to dietary intervention using deep learning. bioRxiv 2023:2023.03.14.532589. [PMID: 36993761 PMCID: PMC10054958 DOI: 10.1101/2023.03.14.532589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Due to highly personalized biological and lifestyle characteristics, different individuals may have different metabolic responses to specific foods and nutrients. In particular, the gut microbiota, a collection of trillions of microorganisms living in our gastrointestinal tract, is highly personalized and plays a key role in our metabolic responses to foods and nutrients. Accurately predicting metabolic responses to dietary interventions based on individuals' gut microbial compositions holds great promise for precision nutrition. Existing prediction methods are typically limited to traditional machine learning models. Deep learning methods dedicated to such tasks are still lacking. Here we develop a new method McMLP (Metabolic response predictor using coupled Multilayer Perceptrons) to fill in this gap. We provide clear evidence that McMLP outperforms existing methods on both synthetic data generated by the microbial consumer-resource model and real data obtained from six dietary intervention studies. Furthermore, we perform sensitivity analysis of McMLP to infer the tripartite food-microbe-metabolite interactions, which are then validated using the ground-truth (or literature evidence) for synthetic (or real) data, respectively. The presented tool has the potential to inform the design of microbiota-based personalized dietary strategies to achieve precision nutrition.
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Affiliation(s)
- Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah D. Holscher
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sergei Maslov
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Frank B. Hu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract. Although the precise etiology of IBD is largely unknown, it is widely thought that diet contributes to the development of IBD. Diet shapes the composition of the gut microbiota, which plays critical roles in intestinal homeostasis. In contrast, intestinal inflammation induces gut dysbiosis and may affect the use of dietary nutrients by host cells and the gut microbiota. The interaction of diet and the gut microbiota is perturbed in patients with IBD. Herein, we review the current knowledge of diet and gut microbiota interaction in intestinal homeostasis. We also discuss alterations of diet and gut microbiota interaction that influence the outcome and the nutritional treatment of IBD. Understanding the complex relationships between diet and the gut microbiota provides crucial insight into the pathogenesis of IBD and advances the development of new therapeutic approaches.
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Affiliation(s)
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA;
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