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Plant endophytes promote plant growth and enhance plants\u2019 resistance to diseases, pests, and environmental stresses. In addition, they enhance the synthesis of important secondary metabolites in plants and improve the potential applicability of plants in agriculture, medicine, food, and horticulture. In this review, we summarize the recent progress in understanding the interaction between endophytes and plants and summarize the construction of synthetic microbial communities (SynComs) and metaomics analysis of the interaction between endophytes and plants. The application and development prospects of endophytes in agriculture, medicine, and other industries are also discussed to provide a reference for further study of the interaction between endophytes and plants and further development and utilization of endophytes.<\/jats:p>","DOI":"10.3390\/ijms24021153","type":"journal-article","created":{"date-parts":[[2023,1,9]],"date-time":"2023-01-09T02:09:39Z","timestamp":1673230179000},"page":"1153","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":95,"title":["Functional Endophytes Regulating Plant Secondary Metabolism: Current Status, Prospects and Applications"],"prefix":"10.3390","volume":"24","author":[{"given":"Zhaogao","family":"Li","sequence":"first","affiliation":[{"name":"Department of Cell Biology, Zunyi Medical University, Zunyi 563099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keyi","family":"Xiong","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Zunyi Medical University, Zunyi 563099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weie","family":"Wen","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Zunyi Medical University, Zunyi 563099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Zunyi Medical University, Zunyi 563099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3695-2997","authenticated-orcid":false,"given":"Delin","family":"Xu","sequence":"additional","affiliation":[{"name":"Engineering Research Center of Key Technology Development for Guizhou Provincial Dendrobium Nobile Industry, Zunyi Medical University, Zunyi 563099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1111\/1462-2920.12631","article-title":"The soil resistome: A critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria","volume":"17","author":"Nesme","year":"2015","journal-title":"Environ. 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