Probing and manipulating the gut microbiome with chemistry and chemical tools
The human gut microbiome represents an extended “second genome” harbouring about 1015 microbes containing >100 times the number of genes as the host. States of health and disease are largely mediated by host–microbial metabolic interplay, and the microbiome composition also underlies the differen...
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| Format: | Article |
| Language: | English |
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Cambridge University Press
2025-01-01
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| Series: | Gut Microbiome |
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| Online Access: | https://www.cambridge.org/core/product/identifier/S2632289725000040/type/journal_article |
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| author | Pavan K. Mantravadi Basavaraj S. Kovi Sabbasani Rajasekhara Reddy Ganesh Pandian Namasivayam Karunakaran Kalesh Anutthaman Parthasarathy |
| author_facet | Pavan K. Mantravadi Basavaraj S. Kovi Sabbasani Rajasekhara Reddy Ganesh Pandian Namasivayam Karunakaran Kalesh Anutthaman Parthasarathy |
| author_sort | Pavan K. Mantravadi |
| collection | DOAJ |
| description | The human gut microbiome represents an extended “second genome” harbouring about 1015 microbes containing >100 times the number of genes as the host. States of health and disease are largely mediated by host–microbial metabolic interplay, and the microbiome composition also underlies the differential responses to chemotherapeutic agents between people. Chemical information will be the key to tackle this complexity and discover specific gut microbiome metabolism for creating more personalised interventions. Additionally, rising antibiotic resistance and growing awareness of gut microbiome effects are creating a need for non-microbicidal therapeutic interventions. We classify chemical interventions for the gut microbiome into categories like molecular decoys, bacterial conjugation inhibitors, colonisation resistance-stimulating molecules, “prebiotics” to promote the growth of beneficial microbes, and inhibitors of specific gut microbial enzymes. Moreover, small molecule probes, including click chemistry probes, artificial substrates for assaying gut bacterial enzymes and receptor agonists/antagonists, which engage host receptors interacting with the microbiome, are some other promising developments in the expanding chemical toolkit for probing and modulating the gut microbiome. This review explicitly excludes “biologics” such as probiotics, bacteriophages, and CRISPR to concentrate on chemistry and chemical tools like chemoproteomics in the gut-microbiome context. |
| format | Article |
| id | doaj-art-a2a3f70a43434ecc97e13e1e9b350c63 |
| institution | Kabale University |
| issn | 2632-2897 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Cambridge University Press |
| record_format | Article |
| series | Gut Microbiome |
| spelling | doaj-art-a2a3f70a43434ecc97e13e1e9b350c632025-08-20T03:53:39ZengCambridge University PressGut Microbiome2632-28972025-01-01610.1017/gmb.2025.4Probing and manipulating the gut microbiome with chemistry and chemical toolsPavan K. Mantravadi0Basavaraj S. Kovi1Sabbasani Rajasekhara Reddy2Ganesh Pandian Namasivayam3Karunakaran Kalesh4Anutthaman Parthasarathy5https://orcid.org/0000-0003-1830-5948CMC and Analytical, Cytokinetics, South San Francisco, CA, USAInstitute for Integrated Cell-Material Sciences (ICeMS), Kyoto University, Kyoto, JapanDepartment of Chemistry, School of Advanced Sciences, Vellore Institute of Technology (VIT), Vellore, IndiaInstitute for Integrated Cell-Material Sciences (ICeMS), Kyoto University, Kyoto, JapanSchool of Health and Life Sciences, Teesside University, Middlesbrough, UK National Horizons Centre, Darlington, UKThe School of Chemistry and Biosciences, University of Bradford, Bradford, UKThe human gut microbiome represents an extended “second genome” harbouring about 1015 microbes containing >100 times the number of genes as the host. States of health and disease are largely mediated by host–microbial metabolic interplay, and the microbiome composition also underlies the differential responses to chemotherapeutic agents between people. Chemical information will be the key to tackle this complexity and discover specific gut microbiome metabolism for creating more personalised interventions. Additionally, rising antibiotic resistance and growing awareness of gut microbiome effects are creating a need for non-microbicidal therapeutic interventions. We classify chemical interventions for the gut microbiome into categories like molecular decoys, bacterial conjugation inhibitors, colonisation resistance-stimulating molecules, “prebiotics” to promote the growth of beneficial microbes, and inhibitors of specific gut microbial enzymes. Moreover, small molecule probes, including click chemistry probes, artificial substrates for assaying gut bacterial enzymes and receptor agonists/antagonists, which engage host receptors interacting with the microbiome, are some other promising developments in the expanding chemical toolkit for probing and modulating the gut microbiome. This review explicitly excludes “biologics” such as probiotics, bacteriophages, and CRISPR to concentrate on chemistry and chemical tools like chemoproteomics in the gut-microbiome context.https://www.cambridge.org/core/product/identifier/S2632289725000040/type/journal_articlegut microbiomechemistryprebioticsconjugation inhibitorschemical probes |
| spellingShingle | Pavan K. Mantravadi Basavaraj S. Kovi Sabbasani Rajasekhara Reddy Ganesh Pandian Namasivayam Karunakaran Kalesh Anutthaman Parthasarathy Probing and manipulating the gut microbiome with chemistry and chemical tools Gut Microbiome gut microbiome chemistry prebiotics conjugation inhibitors chemical probes |
| title | Probing and manipulating the gut microbiome with chemistry and chemical tools |
| title_full | Probing and manipulating the gut microbiome with chemistry and chemical tools |
| title_fullStr | Probing and manipulating the gut microbiome with chemistry and chemical tools |
| title_full_unstemmed | Probing and manipulating the gut microbiome with chemistry and chemical tools |
| title_short | Probing and manipulating the gut microbiome with chemistry and chemical tools |
| title_sort | probing and manipulating the gut microbiome with chemistry and chemical tools |
| topic | gut microbiome chemistry prebiotics conjugation inhibitors chemical probes |
| url | https://www.cambridge.org/core/product/identifier/S2632289725000040/type/journal_article |
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