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They exhibit a broad host range and high pathogenicity, leading to yield losses, reduced quality, and plant mortality. Current control measures rely primarily on chemical pesticides, with few sustainable biological options available. This study compared rhizosphere microbial diversity between healthy and diseased\n                    <jats:italic>Lonicera macranthoides<\/jats:italic>\n                    , revealing increased pathogenic fungi abundance (\n                    <jats:italic>Fusarium<\/jats:italic>\n                    ,\n                    <jats:italic>Plectosphaerella<\/jats:italic>\n                    ,\n                    <jats:italic>p<\/jats:italic>\n                    \u2009&lt;\u20090.01) and reduced beneficial fungi abundance (\n                    <jats:italic>Trichoderma<\/jats:italic>\n                    ) along with significantly lower Chao1 and Shannon diversity indices (\n                    <jats:italic>p<\/jats:italic>\n                    \u2009&lt;\u20090.05). An endophytic\n                    <jats:italic>Bacillus velezensis<\/jats:italic>\n                    strain, NS13, was isolated from healthy roots. Plate confrontation assays showed strong inhibition of\n                    <jats:italic>Fusarium oxysporum<\/jats:italic>\n                    from\n                    <jats:italic>L. macranthoides<\/jats:italic>\n                    and other\n                    <jats:italic>Fusarium<\/jats:italic>\n                    species (\n                    <jats:italic>Fusarium solani<\/jats:italic>\n                    ,\n                    <jats:italic>Fusarium graminearum<\/jats:italic>\n                    ,\n                    <jats:italic>Fusarium fujikuroi<\/jats:italic>\n                    ). The 3.95\u00a0Mb genome encoded 4,060 proteins, including 96 biocontrol-related genes. AntiSMASH identified 15 biosynthetic gene clusters, including antifungal (fengycin, surfactin), antibacterial (bacillaene, difficidin), and other bioactive metabolites (bacilysin, bacillibactin), alongside seven potentially novel clusters. The presence of these BGCs was further corroborated by LC-MS\/MS metabolomic profiling, which detected multiple corresponding antifungal metabolites, including cyclic dipeptides, fatty acid amides (e.g., erucamide), and oleanolic acid. These results demonstrate soil microbial dysbiosis in\n                    <jats:italic>L. macranthoides<\/jats:italic>\n                    affected by root rot and confirm the broad-spectrum anti-\n                    <jats:italic>Fusarium<\/jats:italic>\n                    potential of NS13, highlighting its promise as a biocontrol resource against\n                    <jats:italic>Fusarium<\/jats:italic>\n                    pathogens in medicinal plants. The findings provide both theoretical insights and practical guidance for developing sustainable biocontrol strategies against\n                    <jats:italic>Fusarium<\/jats:italic>\n                    and other soil-borne pathogens, benefiting both the scientific community and agricultural practitioners.\n                  <\/jats:p>","DOI":"10.1186\/s12866-025-04551-x","type":"journal-article","created":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T15:33:10Z","timestamp":1767627190000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Integrated genomic and metabolomic analysis reveals the biocontrol potential of endophytic Bacillus velezensis NS13 against Fusarium species in Lonicera macranthoides"],"prefix":"10.1186","volume":"26","author":[{"given":"Junpeng","family":"Qi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhong","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheng\u2019e","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Zhuo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuqi","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meisen","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongxu","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yin","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fengming","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,1,5]]},"reference":[{"key":"4551_CR1","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1111\/mpp.12289","volume":"17","author":"JJ Coleman","year":"2016","unstructured":"Coleman JJ. 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