Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling

Engineering natural microbiomes for biotechnological applications is challenging due to largely unknown metabolic interactions and a lack of practical principles and tools. This study presents a combined top-down and bottom-up framework to engineer natural microbiomes for enhanced bioremediation. Herbicide application and herbicide-degrader inoculation drive convergent succession of different natural microbiomes toward functional microbiomes. A metabolic engineering pipeline, SuperCC, documents metabolic interactions and simulates microbiome performance. Using SuperCC, bioremediation-enhanced synthetic microbiomes are constructed based on 18 keystone species. The results highlight the importance of metabolic interactions in shaping microbiome functions and provide 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