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Kim KS, Tiffany E, Lee JY, Oh A, Jin HS, Kim JS, Lee JS, Nam MH, Hong SJ, Park S, Koh H, Kim BS, Lee YK, Lee DW. Genome-wide multi-omics analysis reveals the nutrient-dependent metabolic features of mucin-degrading gut bacteria. Gut Microbes 2023; 15:2221811. [PMID: 37305974 DOI: 10.1080/19490976.2023.2221811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/13/2023] Open
Abstract
The prevalence and occurrence of mucin-degrading (MD) bacteria, such as Akkermansia muciniphila and Ruminococcus gnavus, is highly associated with human health and disease states. However, MD bacterial physiology and metabolism remain elusive. Here, we assessed functional modules of mucin catabolism, through a comprehensive bioinformatics-aided functional annotation, to identify 54 A. muciniphila genes and 296 R. gnavus genes. The reconstructed core metabolic pathways coincided with the growth kinetics and fermentation profiles of A. muciniphila and R. gnavus grown in the presence of mucin and its constituents. Genome-wide multi-omics analyses validated the nutrient-dependent fermentation profiles of the MD bacteria and identified their distinct mucolytic enzymes. The distinct metabolic features of the two MD bacteria induced differences in the metabolite receptor levels and inflammatory signals of the host immune cells. In addition, in vivo experiments and community-scale metabolic modeling demonstrated that different dietary intakes influenced the abundance of MD bacteria, their metabolic fluxes, and gut barrier integrity. Thus, this study provides insights into how diet-induced metabolic differences in MD bacteria determine their distinct physiological roles in the host immune response and the gut ecosystem.
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Affiliation(s)
- Kyoung Su Kim
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Eunike Tiffany
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan, Republic of Korea
| | - Ji-Young Lee
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Ara Oh
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan, Republic of Korea
| | - Hyeon-Su Jin
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Republic of Korea
| | - Myung Hee Nam
- Seoul Center, Korea Basic Science Institute, Seoul, Republic of Korea
| | - Soo-Jong Hong
- Department of Pediatrics, Childhood Asthma Atopy Center, Humidifier Disinfectant Health Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sowon Park
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hong Koh
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Bong-Soo Kim
- Department of Life Science, Hallym University, Chuncheon, Republic of Korea
| | - Yun Kyung Lee
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan, Republic of Korea
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, Republic of Korea
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