Table 4.

Accomplishments and perspectives of microbiome engineering strategies.

Approach	Strategy	What we have done	What we can do
Bottom‐up engineering	With naturally occurring strains	Successfully applied for construction of the microbiome to degrade specific compounds in the lab and practical bioremediation	Maintaining long‐term stability and coexistence of the members
	With engineered strains	Synthetic consortia were constructed by the DOL approach, such as dividing the pollutant mineralization pathway into different strains	Maintaining long‐term stability and enhancing metabolite‐exchange efficiency. Mathematical models proposed by Lingchong You et al. can help guide the engineering of metabolic pathways by the DOL approach 54 . Developing population control techniques for GMO restriction
Top‐down engineering	Enrichment	Successfully applied for construction of microbiomes to degrade specific compounds in the lab and practical bioremediation	Optimization of imposed perturbations, including various environmental conditions, and dilution factors guiding the top‐down engineering process with the ecological models and mathematical models, such as bottleneck, resource shift, and species knock‐in 107 . If possible, using artificial selection and directed evolution before enrichment
	Artificial selection	After dozens of selection cycles, the late generations are more efficient than the seeding microbiome
	Directed evolution	Only in theory