Fig. 1: Experimental design and general scheme of synthetic microbiome construction.

The workflow of synthetic microbiome construction is based on a balanced combination of top-down and bottom-up strategies. The workflow starts from engineering natural microbiomes by herbicide application and/or herbicide-degrader inoculation to obtain the functional microbiomes. In the top-down phase, three different soils were treated with alternative combinations of two herbicides (BO and DBHB, representing complex and simple pollutants, respectively) and three kinds of inoculants (single-strain and synergistic or competitive consortia), resulting in 320 soil samples for testing degradation capability and tracing dynamic microbiome successions. Then, potential keystone species were identified by exploring strain abundance shifts combined with strain isolation. The keystones were then used to construct simplified microbiomes to substitute for the complex functional microbiomes. In the bottom-up phase, a newly developed microbiome modeling framework, SuperCC, was used to simulate the performances of simplified microbiomes with different combinations of keystones to optimize the combination of keystones. The synthetic microbiome with an optimal keystone combination was used for further testing and application. Beyond the microbiome simulation, a new computational strategy for synthetic cell design based on learning metabolic interactions of synthetic microbiomes was also provided by SuperCC. BO, bromoxynil octanoate; DBHB, 3,5-dibromo-4-hydroxybenzoate.