Wu Tong, Guo Sheng-Zhi, Zhang Yi, Zhao Xi-Ze, Ran Cong-Guo, Liu Feng-Lan, Wang Run-Hua, Li De-Feng, Zhu Hai-Zhen, Jiang Cheng-Ying, Shen Xi-Hui, Liu Shuang-Jiang
State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, P. R. China.
NPJ Biofilms Microbiomes. 2025 Jul 19;11(1):139. doi: 10.1038/s41522-025-00777-9.
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.
理解和构建合成微生物群落的能力在生物技术创新与应用中至关重要。四溴双酚A（TBBPA）是一种新兴污染物，目前对其生物降解的了解非常有限。在此，采用自上而下的方法从天然微生物群落中富集降解TBBPA的微生物群落。通过剖析降解微生物群落，确定了与TBBPA降解相关的10个关键分类群及其共生相互作用。针对这些关键分类群进行靶向培养，并通过菌株基因组测序和宏基因组分箱获得基因组信息。关键细菌菌株表现出高效的TBBPA降解能力，L-氨基酸是促进降解的重要共代谢底物。基于这一认识，采用自下而上的方法设计并构建了一个由四种菌株组成的简化合成菌群SynCon2。SynCon2表现出高效的TBBPA降解活性和土壤生物修复能力。我们的研究证明了应用多种工具理解微生物群落功能的重要性，并为构建具有各种应用的合成微生物群落提供了一种自上而下和自下而上相结合的策略。
