Genomic analysis for the identification of bioactive compounds in Xenorhabdus stockiae strain RT25.5
Abstract Elucidating microorganism genomes holds great promise for the discovery of novel bioactive compounds with diverse applications. In this study, we investigated the complete genome of Xenorhabdus stockiae strain RT25.5, which is recognized for its symbiotic association with entomopathogenic n...
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Nature Portfolio
2025-07-01
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| Online Access: | https://doi.org/10.1038/s41598-025-08454-9 |
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| author | Wipanee Meesil Helge B. Bode Christian Rückert-Reed Yi-Ming Shi Sacha J. Pidot Paramaporn Muangpat Triwit Rattanarojpong Narisara Chantratita Sutthirat Sitthisak Apichat Vitta Aunchalee Thanwisai |
| author_facet | Wipanee Meesil Helge B. Bode Christian Rückert-Reed Yi-Ming Shi Sacha J. Pidot Paramaporn Muangpat Triwit Rattanarojpong Narisara Chantratita Sutthirat Sitthisak Apichat Vitta Aunchalee Thanwisai |
| author_sort | Wipanee Meesil |
| collection | DOAJ |
| description | Abstract Elucidating microorganism genomes holds great promise for the discovery of novel bioactive compounds with diverse applications. In this study, we investigated the complete genome of Xenorhabdus stockiae strain RT25.5, which is recognized for its symbiotic association with entomopathogenic nematodes (EPNs) and its biosynthesis of secondary metabolites relevant to the pharmaceutical industry, agriculture, and ecology. Through high-throughput genome sequencing, assembly, and annotation, followed by advanced bioinformatics analyses, we elucidated the genetic basis of its antimicrobial potential. Our analysis revealed 21 putative biosynthetic gene clusters (BGCs) associated with bioactive compound production. Notably, LC‒MS/MS analysis of the bacterial cultures confirmed the presence of diverse secondary metabolites, which aligned with the in silico predictions. Furthermore, the crude extract of X. stockiae strain RT25.5 exhibited antibacterial activity against 10 pathogenic bacterial isolates, highlighting its potential as a source of novel antimicrobial agents. This study highlights the importance of X. stockiae as a promising candidate for natural product discovery. The integration of genome mining, LC‒MS/MS, and bioassays not only advances our understanding of its biosynthetic capabilities but also paves the way for the development of novel antimicrobial agents. Future research should focus on the isolation and structural characterization of key metabolites, as well as evaluations of their mechanisms of action against multidrug-resistant pathogens. |
| format | Article |
| id | doaj-art-35d264d3afbb4d35a4cf6f6cd8f56f04 |
| institution | DOAJ |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-35d264d3afbb4d35a4cf6f6cd8f56f042025-08-20T03:03:25ZengNature PortfolioScientific Reports2045-23222025-07-0115111110.1038/s41598-025-08454-9Genomic analysis for the identification of bioactive compounds in Xenorhabdus stockiae strain RT25.5Wipanee Meesil0Helge B. Bode1Christian Rückert-Reed2Yi-Ming Shi3Sacha J. Pidot4Paramaporn Muangpat5Triwit Rattanarojpong6Narisara Chantratita7Sutthirat Sitthisak8Apichat Vitta9Aunchalee Thanwisai10Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan UniversityDepartment of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial MicrobiologyCeBiTec Centrum for Biotechnology, Bielefeld UniversityState Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of SciencesDepartment of Microbiology and Immunology, Doherty InstituteDepartment of Microbiology and Parasitology, Faculty of Medical Science, Naresuan UniversityDepartment of Microbiology, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT)Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol UniversityDepartment of Microbiology and Parasitology, Faculty of Medical Science, Naresuan UniversityDepartment of Microbiology and Parasitology, Faculty of Medical Science, Naresuan UniversityDepartment of Microbiology and Parasitology, Faculty of Medical Science, Naresuan UniversityAbstract Elucidating microorganism genomes holds great promise for the discovery of novel bioactive compounds with diverse applications. In this study, we investigated the complete genome of Xenorhabdus stockiae strain RT25.5, which is recognized for its symbiotic association with entomopathogenic nematodes (EPNs) and its biosynthesis of secondary metabolites relevant to the pharmaceutical industry, agriculture, and ecology. Through high-throughput genome sequencing, assembly, and annotation, followed by advanced bioinformatics analyses, we elucidated the genetic basis of its antimicrobial potential. Our analysis revealed 21 putative biosynthetic gene clusters (BGCs) associated with bioactive compound production. Notably, LC‒MS/MS analysis of the bacterial cultures confirmed the presence of diverse secondary metabolites, which aligned with the in silico predictions. Furthermore, the crude extract of X. stockiae strain RT25.5 exhibited antibacterial activity against 10 pathogenic bacterial isolates, highlighting its potential as a source of novel antimicrobial agents. This study highlights the importance of X. stockiae as a promising candidate for natural product discovery. The integration of genome mining, LC‒MS/MS, and bioassays not only advances our understanding of its biosynthetic capabilities but also paves the way for the development of novel antimicrobial agents. Future research should focus on the isolation and structural characterization of key metabolites, as well as evaluations of their mechanisms of action against multidrug-resistant pathogens.https://doi.org/10.1038/s41598-025-08454-9Bioactive compoundsXenorhabdus spp.Antibacterial activitySecondary metabolitesNext-generation sequencing |
| spellingShingle | Wipanee Meesil Helge B. Bode Christian Rückert-Reed Yi-Ming Shi Sacha J. Pidot Paramaporn Muangpat Triwit Rattanarojpong Narisara Chantratita Sutthirat Sitthisak Apichat Vitta Aunchalee Thanwisai Genomic analysis for the identification of bioactive compounds in Xenorhabdus stockiae strain RT25.5 Scientific Reports Bioactive compounds Xenorhabdus spp. Antibacterial activity Secondary metabolites Next-generation sequencing |
| title | Genomic analysis for the identification of bioactive compounds in Xenorhabdus stockiae strain RT25.5 |
| title_full | Genomic analysis for the identification of bioactive compounds in Xenorhabdus stockiae strain RT25.5 |
| title_fullStr | Genomic analysis for the identification of bioactive compounds in Xenorhabdus stockiae strain RT25.5 |
| title_full_unstemmed | Genomic analysis for the identification of bioactive compounds in Xenorhabdus stockiae strain RT25.5 |
| title_short | Genomic analysis for the identification of bioactive compounds in Xenorhabdus stockiae strain RT25.5 |
| title_sort | genomic analysis for the identification of bioactive compounds in xenorhabdus stockiae strain rt25 5 |
| topic | Bioactive compounds Xenorhabdus spp. Antibacterial activity Secondary metabolites Next-generation sequencing |
| url | https://doi.org/10.1038/s41598-025-08454-9 |
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