Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling

Engineering natural microbiomes for biotechnological applications remains challenging due to limited knowledge of metabolic interactions and a lack of practical engineering principles and tools. This study presents a combined top-down and bottom-up framework to engineer natural microbiomes into function-enhanced synthetic microbiomes for enhanced bioremediation of herbicide-contaminated soils. Herbicide application together with inoculation of herbicide degraders drove convergent succession of different natural microbiomes toward functional communities with increased degradation capacity. A metabolic engineering and modeling pipeline, SuperCC, was developed to document metabolic interactions and simulate microbiome performance. Using SuperCC, function-enhanced synthetic microbiomes were constructed from 18 keystone species identified from natural communities. The results underscore the importance of metabolic interactions in shaping microbiome functions and offer practical guidance for engineering natural microbiomes.

Zhepu Ruan, Kai Chen, Weimiao Cao, Lei Meng, Bingang Yang, Mengjun Xu, Youwen Xing, Pengfa Li, Shiri Freilich, Chen Chen, Yanzheng Gao, Jiandong Jiang, Xihui Xu