{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T13:56:44Z","timestamp":1790863004486,"version":"4.1.0"},"reference-count":36,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82370785"],"award-info":[{"award-number":["82370785"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007129","name":"Natural Science Foundation of Shandong Province","doi-asserted-by":"publisher","award":["ZR2022QC169"],"award-info":[{"award-number":["ZR2022QC169"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2022M711915"],"award-info":[{"award-number":["2022M711915"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Microbial natural products are vital for drug discovery, yet pervasive genomic fragmentation and data volume hinder the translation of metagenomic biosynthetic gene clusters (BGCs) into therapeutic leads. We present\n                      <jats:italic toggle=\"yes\">metasynBGC<\/jats:italic>\n                      , a target-oriented framework that employs a \u201cfunction-first\u201d logic using experimentally validated gene cluster families (GCFs) as evolutionary templates and functional beacons. This dual-path strategy enables (i) template-guided reconstruction of fragmented BGCs via conserved biosynthetic synteny, and (ii) high-resolution prioritization of complete BGCs based on therapeutic potential. Applying\n                      <jats:italic toggle=\"yes\">metasynBGC<\/jats:italic>\n                      to large-scale public metagenome-assembled genome (MAG) data sets, we uncovered hidden biosynthetic potential, including BGC0001089_plus, a novel bacillaene-like variant containing an additional functional\n                      <jats:italic toggle=\"yes\">pksF<\/jats:italic>\n                      gene. Simultaneously, bioactivity-prioritized mining of nonribosomal peptide synthetase (NRPS) BGCs, coupled with deep learning and chemical synthesis, yielded six novel compounds. These molecules exhibited diverse\n                      <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                      cytotoxic profiles across seven cancer cell lines, with\n                      <jats:inline-formula>\n                        <jats:alternatives>\n                          <jats:inline-graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"spectrum.01098-26.im001.tif\"\/>\n                          <mml:math xmlns:mml=\"http:\/\/www.w3.org\/1998\/Math\/MathML\" display=\"inline\" overflow=\"scroll\">\n                            <mml:msub>\n                              <mml:mrow>\n                                <mml:mi>I<\/mml:mi>\n                                <mml:mi>C<\/mml:mi>\n                              <\/mml:mrow>\n                              <mml:mrow>\n                                <mml:mn>50<\/mml:mn>\n                              <\/mml:mrow>\n                            <\/mml:msub>\n                          <\/mml:math>\n                        <\/jats:alternatives>\n                      <\/jats:inline-formula>\n                      values as low as 38.04 \u00b5M. Compounds D and E showed potent activity and pronounced cell-line selectivity. By transforming microbial \u201cdark matter\u201d into an actionable reservoir of therapeutic leads,\n                      <jats:italic toggle=\"yes\">metasynBGC<\/jats:italic>\n                      provides a practical target-oriented strategy for linking metagenomic BGC mining with downstream experimental validation. The scripts used in this study are publicly available at\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/Shirly-Yang\/metasynBGC\" xlink:type=\"simple\">https:\/\/github.com\/Shirly-Yang\/metasynBGC<\/jats:ext-link>\n                      .\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        The vast chemical diversity hidden within metagenomic data remains largely inaccessible because biosynthetic gene clusters (BGCs) are often highly fragmented. Our study introduces\n                        <jats:italic toggle=\"yes\">metasynBGC<\/jats:italic>\n                        , a target-oriented framework designed to bridge these gaps by using well-characterized BGCs within gene cluster families (GCFs) as templates to reconstruct incomplete biosynthetic pathways. Unlike traditional methods,\n                        <jats:italic toggle=\"yes\">metasynBGC<\/jats:italic>\n                        integrates a dual-path discovery engine: it performs priority-driven mining to precisely locate naturally intact clusters while reconstructing fragmented ones using representative BGC members as guides. We demonstrate its efficacy by identifying and synthesizing novel compounds with notable cytotoxic activity, providing a validated \u201csequence-to-molecule\u201d pipeline. This work offers a scalable framework for the systematic discovery of therapeutic candidates from uncultivated microbes and expands our capacity to interpret genomic \u201cdark matter.\u201d By enabling the functional validation of complex molecules from fragmented data,\n                        <jats:italic toggle=\"yes\">metasynBGC<\/jats:italic>\n                        facilitates the translation of metagenomic data sets into promising leads for therapeutic development.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01098-26","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T13:00:54Z","timestamp":1790859654000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["GCF-anchored and target-oriented mining of metagenomic BGC space for bioactive product discovery"],"prefix":"10.1128","author":[{"given":"Xiao","family":"Yang","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0207yh398","id-type":"ROR","asserted-by":"publisher"}],"name":"Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University","place":["Jinan, China"]},{"name":"State Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-3048-2820","authenticated-orcid":true,"given":"Jiacheng","family":"Wu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0207yh398","id-type":"ROR","asserted-by":"publisher"}],"name":"Microbiome-X, School of Public Health, Cheeloo College of Medicine, Shandong University","place":["Jinan, China"]},{"name":"State Key Laboratory of Quantitative Synthetic 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