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Increasing attention has been directed toward plant-derived foods and medicines, which interact with gut microbiota and modulate host physiological responses through microbial metabolism, leading to the formation of bioactive metabolites that influence host signaling pathways and therapeutic response. The review, based on relevant articles from major international databases using specific terms with a focus on microbiome-mediated interactions and molecular mechanisms, highlights the role of microbiome and diagnostic methods through the analysis of specific composition and changes in microbiota, as well as the importance of microbiomes in relation to the treatment of chronic diseases, given their complex influence on drug metabolism. The microbiome influences the response to medications and resistance to therapy, being also involved in the metabolism of plant-derived foods and medicines through complex microbial interactions, while the importance of modern diagnostic approaches supports the use of microbiome analysis to improve diagnosis, monitoring, and personalized medical strategies.<\/jats:p>","DOI":"10.3390\/molecules31122191","type":"journal-article","created":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T08:19:52Z","timestamp":1782202792000},"page":"2191","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Plant-Derived Foods and Medicines as Modulators of the Gut Microbiome: Molecular Interactions and Implications for Disease and Therapy"],"prefix":"10.3390","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-3442-7107","authenticated-orcid":false,"given":"Gabriela","family":"Mitea","sequence":"first","affiliation":[{"name":"Department of Pharmacology, Faculty of Pharmacy, Ovidius University of Constanta, 900470 Constanta, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8876-1901","authenticated-orcid":false,"given":"Verginica","family":"Schr\u00f6der","sequence":"additional","affiliation":[{"name":"Department of Cellular and Molecular Biology, Faculty of Pharmacy, Ovidius University of Constanta, 900470 Constanta, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marius Daniel","family":"Radu","sequence":"additional","affiliation":[{"name":"Faculty of Natural and Agricultural Sciences, Ovidius University of Constanta, 900470 Constanta, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7863-7138","authenticated-orcid":false,"given":"Hora\u021biu","family":"Mire\u0219an","sequence":"additional","affiliation":[{"name":"Department of Toxicology, Faculty of Pharmacy, Ovidius University of Constanta, 900470 Constanta, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-1589-573X","authenticated-orcid":false,"given":"Irina Mihaela","family":"Iancu","sequence":"additional","affiliation":[{"name":"Department of Toxicology, Faculty of Pharmacy, Ovidius University of Constanta, 900470 Constanta, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,22]]},"reference":[{"key":"ref_1","unstructured":"Basile, E.J., Shukla, K., Launico, M.V., and Sheer, A.J. 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