Ecologically inspired assembly of a Bacillales synthetic community for lignin degradation

Lignin remains a major bottleneck in biomass valorization due to its heterogeneous and recalcitrant structure. Traditionally, lignin degradation has been developed using a single-microorganism or single-enzyme approach, with efforts focused on identifying ligninolytic activities of individual bacteria or fungi. Here, we establish a framework for designing lignin-degrading synthetic microbial communities (SynComs) by integrating top-down ecological filtering with bottom-up trait-based selection. This approach enables the selection of bacteria with ligninolytic capacity while retaining community members that form strong biofilms and contribute indirectly to overall community function. Proteomic profiling uncovered lignin-driven functional reprogramming of the SynCom, highlighting strain-specific enzymatic specializations that collectively enable lignin depolymerization. Our work highlights the potential of SynComs for lignin degradation and shows how rationally designed, functionally partitioned communities can enhance lignin conversion.