The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies
Abstract The capability to understand and construct synthetic microbiomes is crucial in biotechnological innovation and application. Tetrabromobisphenol A (TBBPA) is an emerging pollutant, and the understanding of its biodegradation is very limited. Here, a top-down approach was applied for the enri...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | npj Biofilms and Microbiomes |
| Online Access: | https://doi.org/10.1038/s41522-025-00777-9 |
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| author | Tong Wu Sheng-Zhi Guo Yi Zhang Xi-Ze Zhao Cong-Guo Ran Feng-Lan Liu Run-Hua Wang De-Feng Li Hai-Zhen Zhu Cheng-Ying Jiang Xi-Hui Shen Shuang-Jiang Liu |
| author_facet | Tong Wu Sheng-Zhi Guo Yi Zhang Xi-Ze Zhao Cong-Guo Ran Feng-Lan Liu Run-Hua Wang De-Feng Li Hai-Zhen Zhu Cheng-Ying Jiang Xi-Hui Shen Shuang-Jiang Liu |
| author_sort | Tong Wu |
| collection | DOAJ |
| description | Abstract The capability to understand and construct synthetic microbiomes is crucial in biotechnological innovation and application. Tetrabromobisphenol A (TBBPA) is an emerging pollutant, and the understanding of its biodegradation is very limited. Here, a top-down approach was applied for the enrichment of TBBPA-degrading microbiomes from natural microbiomes. Ten keystone taxa correlated to TBBPA degradation and their co-occurrence interactions were identified by the dissection of the degrading microbiomes. Those keystone taxa were targeted and cultivated, and the genomic information was obtained by genome sequencing of strains and metagenomic binning. The keystone bacterial strains showed efficient degradation of TBBPA, and L-amino acids were important co-metabolic substrates to promote the degradation. Guided by this knowledge, a bottom-up approach was applied to design and construct a simplified synthetic consortium SynCon2, that consisted of four strains. The SynCon2 demonstrated efficient TBBPA degradation activity and soil bioremediation. Our study demonstrates the importance of the application of multiple tools in understanding the functions of microbiomes and provides an integrated top-down and bottom-up strategy for the construction of synthetic microbiomes with various applications. |
| format | Article |
| id | doaj-art-7152f5b63ecd4d52adc08040c7b9747d |
| institution | Kabale University |
| issn | 2055-5008 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Biofilms and Microbiomes |
| spelling | doaj-art-7152f5b63ecd4d52adc08040c7b9747d2025-08-20T03:45:48ZengNature Portfolionpj Biofilms and Microbiomes2055-50082025-07-0111111210.1038/s41522-025-00777-9The engineering of TBBPA-degrading synthetic microbiomes with integrated strategiesTong Wu0Sheng-Zhi Guo1Yi Zhang2Xi-Ze Zhao3Cong-Guo Ran4Feng-Lan Liu5Run-Hua Wang6De-Feng Li7Hai-Zhen Zhu8Cheng-Ying Jiang9Xi-Hui Shen10Shuang-Jiang Liu11State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F UniversityState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesState Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F UniversityState Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of SciencesAbstract The capability to understand and construct synthetic microbiomes is crucial in biotechnological innovation and application. Tetrabromobisphenol A (TBBPA) is an emerging pollutant, and the understanding of its biodegradation is very limited. Here, a top-down approach was applied for the enrichment of TBBPA-degrading microbiomes from natural microbiomes. Ten keystone taxa correlated to TBBPA degradation and their co-occurrence interactions were identified by the dissection of the degrading microbiomes. Those keystone taxa were targeted and cultivated, and the genomic information was obtained by genome sequencing of strains and metagenomic binning. The keystone bacterial strains showed efficient degradation of TBBPA, and L-amino acids were important co-metabolic substrates to promote the degradation. Guided by this knowledge, a bottom-up approach was applied to design and construct a simplified synthetic consortium SynCon2, that consisted of four strains. The SynCon2 demonstrated efficient TBBPA degradation activity and soil bioremediation. Our study demonstrates the importance of the application of multiple tools in understanding the functions of microbiomes and provides an integrated top-down and bottom-up strategy for the construction of synthetic microbiomes with various applications.https://doi.org/10.1038/s41522-025-00777-9 |
| spellingShingle | Tong Wu Sheng-Zhi Guo Yi Zhang Xi-Ze Zhao Cong-Guo Ran Feng-Lan Liu Run-Hua Wang De-Feng Li Hai-Zhen Zhu Cheng-Ying Jiang Xi-Hui Shen Shuang-Jiang Liu The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies npj Biofilms and Microbiomes |
| title | The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies |
| title_full | The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies |
| title_fullStr | The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies |
| title_full_unstemmed | The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies |
| title_short | The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies |
| title_sort | engineering of tbbpa degrading synthetic microbiomes with integrated strategies |
| url | https://doi.org/10.1038/s41522-025-00777-9 |
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