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Updated: Jun 24, 2025
Prospecting Microbial Strains for Bioremediation and Probiotics Development for Metaorganism Research and Preservation
Published on: October 31, 2019
Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling
Zhepu Ruan1,2, Kai Chen1, Weimiao Cao1
1Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
Scientists engineered functional microbiomes for enhanced bioremediation. They developed a framework and metabolic modeling tool (SuperCC) to guide microbiome engineering using keystone species, improving herbicide-contaminated soil cleanup.
Area of Science:
- Microbiome Engineering
- Synthetic Biology
- Environmental Biotechnology
Background:
- Engineering natural microbiomes for biotechnology is difficult due to unknown metabolic interactions and lack of practical tools.
- Current methods lack systematic approaches for creating functional synthetic microbiomes from natural ones.
Purpose of the Study:
- To develop a framework for engineering natural microbiomes into function-enhanced synthetic microbiomes.
- To create a metabolic modeling pipeline for analyzing microbiome interactions and predicting performance.
- To construct synthetic microbiomes for enhanced bioremediation applications.
Main Methods:
- A combinatory top-down and bottom-up framework was applied.
- Herbicide application and specific inoculations induced convergent microbiome succession.
- A metabolic modeling pipeline, SuperCC, was developed to document interactions and simulate microbiome performance.
- Synthetic microbiomes were constructed using 18 identified keystone species.
Main Results:
- Herbicide application and degrader inoculation led to functional microbiome development, enhancing bioremediation.
- The SuperCC pipeline successfully documented metabolic interactions and predicted microbiome functions.
- Constructed synthetic microbiomes demonstrated enhanced bioremediation capabilities for herbicide-contaminated soils.
- The study identified key metabolic interactions crucial for shaping microbiome functions.
Conclusions:
- Metabolic interactions are critical determinants of microbiome functions.
- The developed framework and SuperCC pipeline offer practical guidance for engineering natural microbiomes.
- This approach enables the creation of synthetic microbiomes with enhanced biotechnological applications, such as bioremediation.
