The study presents a framework for engineering natural microbiomes to enhance bioremediation capabilities. By combining top-down and bottom-up approaches, the researchers developed a method to construct function-enhanced synthetic microbiomes. They demonstrated that applying herbicides and inoculating with herbicide-degraders can drive the convergence of different natural microbiomes toward functional microbiomes, particularly in enhancing the bioremediation of herbicide-contaminated soils. The team developed SuperCC, a metabolic modeling pipeline, to document metabolic interactions within microbiomes and simulate their performances. Using SuperCC, they identified 18 keystone species from natural microbiomes and constructed bioremediation-enhanced synthetic microbiomes. The results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes. The framework has wide-ranging applications, from bioremediation to biosynthesis of industrial products.The study presents a framework for engineering natural microbiomes to enhance bioremediation capabilities. By combining top-down and bottom-up approaches, the researchers developed a method to construct function-enhanced synthetic microbiomes. They demonstrated that applying herbicides and inoculating with herbicide-degraders can drive the convergence of different natural microbiomes toward functional microbiomes, particularly in enhancing the bioremediation of herbicide-contaminated soils. The team developed SuperCC, a metabolic modeling pipeline, to document metabolic interactions within microbiomes and simulate their performances. Using SuperCC, they identified 18 keystone species from natural microbiomes and constructed bioremediation-enhanced synthetic microbiomes. The results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes. The framework has wide-ranging applications, from bioremediation to biosynthesis of industrial products.