{
  "abstract": "Antibiotic resistance is a growing global health threat, while the discovery of new antimicrobial agents remains constrained by labor-intensive cultivation, extraction, and screening workflows. We developed a miniaturized, high-throughput metabologenomics workflow integrating Duetz system-based microfermentation, extraction-free UHPLC-HRMS/MS profiling, antibacterial screening, and genome mining. A collection of 80 soil-derived actinomycetes was screened against clinically relevant pathogens, identifying seven isolates active against methicillin-resistant Staphylococcus aureus (MRSA), Enterococcus faecium, or both. All isolates were cultivated in Duetz system-based microfermentation plates, and cell-free culture filtrates were analyzed directly by UHPLC-HRMS/MS without solvent extraction. Compared with a conventional workflow, the approach reduced culture-medium consumption by approximately 99%, decreased recurring consumable costs by approximately 96%, and reduced the time required to obtain LC-MS-ready samples from typically 5 days to approximately 20 min. Integration of antibacterial, metabolomic, and genomic datasets supported the annotation of diverse metabolite families, including actinomycins, polyether ionophores, ansamycins, angucyclines, hydroxamate siderophores, ectoines, tambromycin-associated metabolites, and putative lydicamycin metabolites. Selected annotations were validated using commercial standards. Overall, this study demonstrates that integrating miniaturized Duetz system-based cultivation, extraction-free metabolomics, antibacterial screening, and genome mining provides a scalable, robust, and cost-effective platform for high-throughput strain prioritization and natural product discovery.",
  "abstract_shown": true,
  "affiliations": [
    "University of Fribourg, Fribourg, Switzerland"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "R. Ouchene"
    },
    {
      "name": "L. Falquet"
    },
    {
      "name": "L. Poirel"
    },
    {
      "name": "P.-M. Allard"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6syw36gtqab35.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.28.762431",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.28.762431v1.full",
  "id": "6syw36gtqab35",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.28.762431v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "microbiology"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.28.762431v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-28",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/6syw36gtqab35.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:30:31Z",
      "native_id": "10.64898/2026.10.28.762431",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.28.762431v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:microbiology",
      "subfield": "microbiology"
    }
  ],
  "title": "An Integrated Miniaturized Metabologenomics Workflow for High-Throughput Actinomycetes Prioritization",
  "title_text": "An Integrated Miniaturized Metabologenomics Workflow for High-Throughput Actinomycetes Prioritization",
  "type": "preprint",
  "updated_at": "2026-10-31T00:20:54Z",
  "url": "https://research.draconitic.com/paper/6syw36gtqab35",
  "venue": "bioRxiv",
  "versions": []
}