Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease
Microbial biochemistry is central to the pathophysiology of inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary for diagnosis and management. Here, we systematically analyzed the chemical, ecological, and epidemiological p...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Springer Science and Business Media LLC
2024
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| Online Access: | https://hdl.handle.net/1721.1/153816 |
| _version_ | 1824458361369788416 |
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| author | Bhosle, Amrisha Bae, Sena Zhang, Yancong Chun, Eunyoung Avila-Pacheco, Julian Geistlinger, Ludwig Pishchany, Gleb Glickman, Jonathan N Michaud, Monia Waldron, Levi Clish, Clary B Xavier, Ramnik J Vlamakis, Hera Franzosa, Eric A Garrett, Wendy S Huttenhower, Curtis |
| author2 | Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics |
| author_facet | Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics Bhosle, Amrisha Bae, Sena Zhang, Yancong Chun, Eunyoung Avila-Pacheco, Julian Geistlinger, Ludwig Pishchany, Gleb Glickman, Jonathan N Michaud, Monia Waldron, Levi Clish, Clary B Xavier, Ramnik J Vlamakis, Hera Franzosa, Eric A Garrett, Wendy S Huttenhower, Curtis |
| author_sort | Bhosle, Amrisha |
| collection | MIT |
| description | Microbial biochemistry is central to the pathophysiology of inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary for diagnosis and management. Here, we systematically analyzed the chemical, ecological, and epidemiological properties of ~82k metabolic features in 546 Integrative Human Microbiome Project (iHMP/HMP2) metabolomes, using a newly developed methodology for bioactive compound prioritization from microbial communities. This suggested >1000 metabolic features as potentially bioactive in IBD and associated ~43% of prevalent, unannotated features with at least one well-characterized metabolite, thereby providing initial information for further characterization of a significant portion of the fecal metabolome. Prioritized features included known IBD-linked chemical families such as bile acids and short-chain fatty acids, and less-explored bilirubin, polyamine, and vitamin derivatives, and other microbial products. One of these, nicotinamide riboside, reduced colitis scores in DSS-treated mice. The method, MACARRoN, is generalizable with the potential to improve microbial community characterization and provide therapeutic candidates. |
| first_indexed | 2024-09-23T15:27:29Z |
| format | Article |
| id | mit-1721.1/153816 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2025-02-19T04:24:40Z |
| publishDate | 2024 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1538162025-02-04T02:07:28Z Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease Bhosle, Amrisha Bae, Sena Zhang, Yancong Chun, Eunyoung Avila-Pacheco, Julian Geistlinger, Ludwig Pishchany, Gleb Glickman, Jonathan N Michaud, Monia Waldron, Levi Clish, Clary B Xavier, Ramnik J Vlamakis, Hera Franzosa, Eric A Garrett, Wendy S Huttenhower, Curtis Massachusetts Institute of Technology. Center for Microbiome Informatics and Therapeutics Applied Mathematics Computational Theory and Mathematics General Agricultural and Biological Sciences General Immunology and Microbiology General Biochemistry, Genetics and Molecular Biology Information Systems Microbial biochemistry is central to the pathophysiology of inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary for diagnosis and management. Here, we systematically analyzed the chemical, ecological, and epidemiological properties of ~82k metabolic features in 546 Integrative Human Microbiome Project (iHMP/HMP2) metabolomes, using a newly developed methodology for bioactive compound prioritization from microbial communities. This suggested >1000 metabolic features as potentially bioactive in IBD and associated ~43% of prevalent, unannotated features with at least one well-characterized metabolite, thereby providing initial information for further characterization of a significant portion of the fecal metabolome. Prioritized features included known IBD-linked chemical families such as bile acids and short-chain fatty acids, and less-explored bilirubin, polyamine, and vitamin derivatives, and other microbial products. One of these, nicotinamide riboside, reduced colitis scores in DSS-treated mice. The method, MACARRoN, is generalizable with the potential to improve microbial community characterization and provide therapeutic candidates. 2024-03-18T16:12:00Z 2024-03-18T16:12:00Z 2024-03-11 2024-03-17T04:13:20Z Article http://purl.org/eprint/type/JournalArticle 1744-4292 https://hdl.handle.net/1721.1/153816 Bhosle, Amrisha, Bae, Sena, Zhang, Yancong, Chun, Eunyoung, Avila-Pacheco, Julian et al. 2024. "Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease." Molecular Systems Biology. en 10.1038/s44320-024-00027-8 Molecular Systems Biology Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/ The Author(s) application/pdf Springer Science and Business Media LLC EMBO Press |
| spellingShingle | Applied Mathematics Computational Theory and Mathematics General Agricultural and Biological Sciences General Immunology and Microbiology General Biochemistry, Genetics and Molecular Biology Information Systems Bhosle, Amrisha Bae, Sena Zhang, Yancong Chun, Eunyoung Avila-Pacheco, Julian Geistlinger, Ludwig Pishchany, Gleb Glickman, Jonathan N Michaud, Monia Waldron, Levi Clish, Clary B Xavier, Ramnik J Vlamakis, Hera Franzosa, Eric A Garrett, Wendy S Huttenhower, Curtis Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease |
| title | Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease |
| title_full | Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease |
| title_fullStr | Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease |
| title_full_unstemmed | Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease |
| title_short | Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease |
| title_sort | integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease |
| topic | Applied Mathematics Computational Theory and Mathematics General Agricultural and Biological Sciences General Immunology and Microbiology General Biochemistry, Genetics and Molecular Biology Information Systems |
| url | https://hdl.handle.net/1721.1/153816 |
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