Functional potential and applications of Ureibacillus massiliensis based on whole-genome sequencing analysis
Abstract Background Ureibacillus massiliensis (U. massiliensis), a Gram-positive bacterium belonging to the phylum Bacillota, has undergone two significant taxonomic revisions before being classified under the Ureibacillus. Although previous studies have highlighted its promising applications in ind...
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BMC
2025-08-01
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| Series: | BMC Microbiology |
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| Online Access: | https://doi.org/10.1186/s12866-025-04225-8 |
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| author | Shiyao He Qi Ding Wenting Wu Yun Zhang Yan Kang Yang Meng Sirui Zhu Jinyuan Wu |
| author_facet | Shiyao He Qi Ding Wenting Wu Yun Zhang Yan Kang Yang Meng Sirui Zhu Jinyuan Wu |
| author_sort | Shiyao He |
| collection | DOAJ |
| description | Abstract Background Ureibacillus massiliensis (U. massiliensis), a Gram-positive bacterium belonging to the phylum Bacillota, has undergone two significant taxonomic revisions before being classified under the Ureibacillus. Although previous studies have highlighted its promising applications in industrial production and environmental remediation, the lack of genomic information has limited the research on its functional mechanisms and industrial development. Result This study successfully isolated and identified a novel strain of U. massiliensis through whole-genome sequencing, constructing a complete genomic map of the species. Orthologous gene cluster (OGs) analysis and genetic recombination analysis revealed the phylogenetic position of the newly isolated strain B05, highlighting deficiencies in the current classification of Lysinibacillus and Ureibacillus, as well as the limitations of traditional taxonomic approaches that rely on single phenotypic or genic characteristics. These findings provide new molecular insights into the accurate delineation of these two genera. In terms of pathogenicity, the isolated strain harbors 239 virulence factors, primarily associated with gastric and brain infections, along with four major antibiotic resistance genes involved in resistance to teicoplanin and vancomycin. Functional annotation revealed that the strain predominantly carries genes related to carbohydrate enzyme activity, with over 50% being glycosyl transferase genes. A significant number of genes are also involved in critical processes such as amino acid transport and metabolism, and transcription, while very few are associated with chromatin structure, dynamics, or the cytoskeleton. Additionally, we found that the strain possesses robust metabolic capabilities for carbohydrate compounds, including the ability to convert ginsenoside Rb1 into Rd, showcasing its potential applications in biotransformation. In terms of microplastic degradation, U. massiliensis can accelerate the degradation process by producing specific P450 enzymes that assist in the further metabolism of initial oxidation products. It may also synergize with other microorganisms to enhance overall degradation efficiency. Conclusion This study successfully isolated and identified a novel strain of U. massiliensis through whole-genome sequencing, constructing a complete genomic map of the species and clarifying its phylogenetic position. Based on functional annotation and virulence factor prediction, the study further delineated the potential functions of the strain, comprehensively evaluating its potential pathogenic risks as well as its application value in biotransformation and microplastic degradation. These findings lay a foundation for the further development of microbial resources and provide new insights for the production and application of U. massiliensis. |
| format | Article |
| id | doaj-art-4b7b052f88824c31bcb3f4d3b5bc96b3 |
| institution | Kabale University |
| issn | 1471-2180 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj-art-4b7b052f88824c31bcb3f4d3b5bc96b32025-08-20T03:46:04ZengBMCBMC Microbiology1471-21802025-08-0125111310.1186/s12866-025-04225-8Functional potential and applications of Ureibacillus massiliensis based on whole-genome sequencing analysisShiyao He0Qi Ding1Wenting Wu2Yun Zhang3Yan Kang4Yang Meng5Sirui Zhu6Jinyuan Wu7Nanchang Key Laboratory for Quality Evaluation of Medical Devices, Jiangxi Medical Device Testing CenterNanchang Key Laboratory for Quality Evaluation of Medical Devices, Jiangxi Medical Device Testing CenterNanchang Key Laboratory for Quality Evaluation of Medical Devices, Jiangxi Medical Device Testing CenterNanchang Key Laboratory for Quality Evaluation of Medical Devices, Jiangxi Medical Device Testing CenterNanchang Key Laboratory for Quality Evaluation of Medical Devices, Jiangxi Medical Device Testing CenterNanchang Key Laboratory for Quality Evaluation of Medical Devices, Jiangxi Medical Device Testing CenterNanchang Key Laboratory for Quality Evaluation of Medical Devices, Jiangxi Medical Device Testing CenterCollege of Bioscience and Bioengineering, Jiangxi Agricultural UniversityAbstract Background Ureibacillus massiliensis (U. massiliensis), a Gram-positive bacterium belonging to the phylum Bacillota, has undergone two significant taxonomic revisions before being classified under the Ureibacillus. Although previous studies have highlighted its promising applications in industrial production and environmental remediation, the lack of genomic information has limited the research on its functional mechanisms and industrial development. Result This study successfully isolated and identified a novel strain of U. massiliensis through whole-genome sequencing, constructing a complete genomic map of the species. Orthologous gene cluster (OGs) analysis and genetic recombination analysis revealed the phylogenetic position of the newly isolated strain B05, highlighting deficiencies in the current classification of Lysinibacillus and Ureibacillus, as well as the limitations of traditional taxonomic approaches that rely on single phenotypic or genic characteristics. These findings provide new molecular insights into the accurate delineation of these two genera. In terms of pathogenicity, the isolated strain harbors 239 virulence factors, primarily associated with gastric and brain infections, along with four major antibiotic resistance genes involved in resistance to teicoplanin and vancomycin. Functional annotation revealed that the strain predominantly carries genes related to carbohydrate enzyme activity, with over 50% being glycosyl transferase genes. A significant number of genes are also involved in critical processes such as amino acid transport and metabolism, and transcription, while very few are associated with chromatin structure, dynamics, or the cytoskeleton. Additionally, we found that the strain possesses robust metabolic capabilities for carbohydrate compounds, including the ability to convert ginsenoside Rb1 into Rd, showcasing its potential applications in biotransformation. In terms of microplastic degradation, U. massiliensis can accelerate the degradation process by producing specific P450 enzymes that assist in the further metabolism of initial oxidation products. It may also synergize with other microorganisms to enhance overall degradation efficiency. Conclusion This study successfully isolated and identified a novel strain of U. massiliensis through whole-genome sequencing, constructing a complete genomic map of the species and clarifying its phylogenetic position. Based on functional annotation and virulence factor prediction, the study further delineated the potential functions of the strain, comprehensively evaluating its potential pathogenic risks as well as its application value in biotransformation and microplastic degradation. These findings lay a foundation for the further development of microbial resources and provide new insights for the production and application of U. massiliensis.https://doi.org/10.1186/s12866-025-04225-8Ureibacillus massiliensisPhylogenetic positionPathogenicityBiotransformationMicroplastic degradation |
| spellingShingle | Shiyao He Qi Ding Wenting Wu Yun Zhang Yan Kang Yang Meng Sirui Zhu Jinyuan Wu Functional potential and applications of Ureibacillus massiliensis based on whole-genome sequencing analysis BMC Microbiology Ureibacillus massiliensis Phylogenetic position Pathogenicity Biotransformation Microplastic degradation |
| title | Functional potential and applications of Ureibacillus massiliensis based on whole-genome sequencing analysis |
| title_full | Functional potential and applications of Ureibacillus massiliensis based on whole-genome sequencing analysis |
| title_fullStr | Functional potential and applications of Ureibacillus massiliensis based on whole-genome sequencing analysis |
| title_full_unstemmed | Functional potential and applications of Ureibacillus massiliensis based on whole-genome sequencing analysis |
| title_short | Functional potential and applications of Ureibacillus massiliensis based on whole-genome sequencing analysis |
| title_sort | functional potential and applications of ureibacillus massiliensis based on whole genome sequencing analysis |
| topic | Ureibacillus massiliensis Phylogenetic position Pathogenicity Biotransformation Microplastic degradation |
| url | https://doi.org/10.1186/s12866-025-04225-8 |
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