Figure 3.

Schematic diagram for the combined framework of top‐down and bottom‐up approaches for environmental use. (i) Preliminary microbial community with a degrading capability of interest is derived from a seeding microbiome by one or several top‐down DBTL cycle(s), in which enrichment, artificial selection, or directed evolution could be applied. (ii) Mechanistic insights of this top‐down engineered microbiome can be identified by meta‐omics (metagenomics, metatranscriptomics, metaproteomics, or metabolomics), which is incorporated into mathematical modeling to predict interactions among the members. (iii) Based on the mechanistic insights, microorganisms of interest can be isolated by enrichment or high‐throughput single‐cell sorting and then used for further bottom‐up microbiome engineering. (iv) Bottom‐up design‐build‐test‐learn (DBTL) cycle(s) would be conducted, guided by mechanistic insights, to engineer a new bottom‐up microbiome with higher degrading efficiency and assessed in its effectiveness in the intended application.