An Integrated Miniaturized Metabologenomics Workflow for High-Throughput Actinomycetes Prioritization
- 1University of Fribourg, Fribourg, Switzerland
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.
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BibTeX
@misc{ouchene2026integrated,
title = {{An Integrated Miniaturized Metabologenomics Workflow for High-Throughput Actinomycetes Prioritization}},
author = {R. Ouchene and L. Falquet and L. Poirel and P.-M. Allard},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.28.762431},
url = {https://www.biorxiv.org/content/10.64898/2026.10.28.762431v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - An Integrated Miniaturized Metabologenomics Workflow for High-Throughput Actinomycetes Prioritization
AU - R. Ouchene
AU - L. Falquet
AU - L. Poirel
AU - P.-M. Allard
PY - 2026
DA - 2026/10/28
PB - bioRxiv
DO - 10.64898/2026.10.28.762431
UR - https://www.biorxiv.org/content/10.64898/2026.10.28.762431v1
AB - 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.
ER -