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The work integrates enzymatic reaction databases, food health-benefit information, and 3,068 public human gut microbiomes to link 775 plant phytonutrients to enzymes encoded by diverse gut microbes. In vitro assays support biotransformation across species, revealing strong interpersonal and geographic variability and altered potential in disease. Metagenomics and metatranscriptomics in mice validate microbiome-encoded enzyme links to anti-inflammatory activity, informing personalized diet design.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/gut-microbiome-mediated-transformation-of-dietary-phytonutrients-is-associated-with-health-outcomes/440886/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/gut-microbiome-mediated-transformation-of-dietary-phytonutrients-is-associated-with-health-outcomes/440886.png","ImageObject",300,407,{"name":92,"@type":93},"Lucas Martin","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-02","2026-09-29",true,{"@type":102,"interactionType":103,"userInteractionCount":14},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"How did the study link dietary phytonutrients to gut microbiome enzymes?","Question",{"text":112,"@type":113},"The researchers mapped plant-derived phytonutrients to enzymatic reactions using multiple databases and functional profiles from 3,068 human gut microbiomes, linking thousands of compounds to enzymes with Enzyme Commission (EC) numbers.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"What did the study find about phytonutrient transformation across people and regions?",{"text":117,"@type":113},"Biotransformation of phytonutrients showed high interpersonal and geographical variability, indicating that microbial enzyme repertoires and activities differ substantially between individuals and populations.",{"name":119,"@type":110,"acceptedAnswer":120},"How were microbiome-encoded enzyme associations validated for health effects?",{"text":121,"@type":113},"The team combined metagenomics and metatranscriptomics analyses in specific-pathogen-free and germ-free mice to validate associations between microbiome-encoded enzymes and the anti-inflammatory activity of common edible plants.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},440886,1790908906,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":14,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":139,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":144,"read_time":145},8796095360427,"https://ap-avatar.wpscdn.com/davatar_994ba38a5ba835b3df7d355c54d3ed8d","nature microbiology  \nArticle [https://doi.org/10.1038/s41564-025-02197-z](https://doi.org/10.1038/s41564-025-02197-z)  \nGut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes  \nReceived: 27 January 2025  \nAccepted: 21 October 2025  \n\n| Published online: 3 December 2025 |\n| --- |\n|  Check for updates |\n\nLu Zhang1,9, Andrea Marfil-Sánchez  1,9, Ting-Hao Kuo2, Bastian Seelbinder  1, Loes van Dam  3, Ana Depetris-Chauvin1, Leonie Johanna Jahn  3,  \nMortenO. A. Sommer  3, Michael Zimmermann  2, Yueqiong Ni  1,4,5 & Gianni Panagiotou  1,5,6,7,8   \nFood, especially plant-based diet, has complex chemical diversity. However, large-scale phytonutrient-metabolizing activities of gut bacteria are largely unknown. Here we integrated and systematically analysed multiple databases containing information on enzymatic reactions and food health benefits, and 3,068 global public human microbiomes. Transformation of 775 phytonutrients from edible plants was associated with enzymes encoded by diverse gut microbes. In vitro assays validated the biotransformation activity of gut species, for example, Eubacterium ramulus. The biotransformation of phytonutrients demonstrated high interpersonal and geographical variability. Machine learning models based on 2,486 public case–control microbiomes, using the abundances of enzymes associated with modification of phytonutrients present in health-associated foods, discriminated the health status of individuals in multiple disease contexts, suggesting altered biotransformation potential in disease. We validated the association of microbiome-encoded enzymes with the anti-inflammatory activity of common edible plants by combining metagenomicsand metatranscriptomics analysis in specific-pathogen-free and germ-free mice. These findings have implications for designing precise, personalized diets to guide an individual towards a healthy state.  \nDefinitions of nutritious diets continuously evolve along with understanding of how foods, essential nutrients and other dietary components influence health and disease1. Adopting dietary patterns emphasizing plant-based foods, including fruits, vegetables, whole grains, legumes, seeds and nuts, rather than a conventional Western diet2, can enhance health3,4 and environmental sustainability5. However, the appealing concept of universally applicable dietary strategies to prevent or treat disease is undercut by the heterogeneous responses to identical foods6–8. One primary source of variability is the gut microbiome7, as its composition contributes to responses to foods (for example, glycaemic index9) and its metabolic output altered  \nby diets impacts physiological homeostasis and metabolic disease progression10–12, emphasizing the need to consider microbiome in personalized dietary recommendations.  \nPrevious dietary research was predominantly based on 150 macronutrients, such as fat, protein and carbohydrate13, and on correlating overall dietary patterns, including red meat, fish and vegetable consumption, with health outcomes14 rather than from a biochemical standpoint. Yet human food has vast chemical diversity, comprising >26,000 mainly plant-derived distinct small molecules13, many bioactive and, additionally, subject to biotransformation by the gut microbiota’s enormous enzymatic repository15.  \nA full list of affiliations appears at the end of the paper. [e-mail:](e-mail: bernard_ni@sjtu.edu.cn)[ bernard_ni@sjtu.edu.cn](e-mail: bernard_ni@sjtu.edu.cn); [gianni.panagiotou@leibniz-hki.de](gianni.panagiotou@leibniz-hki.de)  \nNature Microbiology | Volume 11 | January 2026 | 94–110 94  \nCompared with research on gut microbial metabolism of drugs15,16, research on the biotransformation of plant-derived food compounds (hereafter termed phytonutrients) by gut microbiota and its relationship to human health is only just emerging17. Phytonutrients associated with certain bacterial classes have been identified18, yet most studies hav","cbCaii5FykwivIbC","https://ap.wps.com/l/cbCaii5FykwivIbC","pdf",23595434,28,"English","# Background\n## Dietary patterns and microbiome variability\n## Limitations of prior macronutrient-focused research\n# Study approach\n## Linking phytonutrients to microbial enzymes\n## Global microbiome cohort and functional profiling\n# Results\n## Genomic linkage between gut enzymes and phytonutrients\n## Phytonutrient–enzyme mapping and filtering strategy\n## Regional and interpersonal variability in biotransformation\n## Disease-linked differences in enzyme-mediated transformations\n## Validation in mice and anti-inflammatory associations","[{\"question\":\"How did the study link dietary phytonutrients to gut microbiome enzymes?\",\"answer\":\"The researchers mapped plant-derived phytonutrients to enzymatic reactions using multiple databases and functional profiles from 3,068 human gut microbiomes, linking thousands of compounds to enzymes with Enzyme Commission (EC) numbers.\"},{\"question\":\"What did the study find about phytonutrient transformation across people and regions?\",\"answer\":\"Biotransformation of phytonutrients showed high interpersonal and geographical variability, indicating that microbial enzyme repertoires and activities differ substantially between individuals and populations.\"},{\"question\":\"How were microbiome-encoded enzyme associations validated for health effects?\",\"answer\":\"The team combined metagenomics and metatranscriptomics analyses in specific-pathogen-free and germ-free mice to validate associations between microbiome-encoded enzymes and the anti-inflammatory activity of common edible plants.\"}]","Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes | PDF",1790693806,71]