Ecologically Informed Design of Synthetic Microbial Community Enables Robust Degradation and Engraftment for Antibiotic Removal in Wastewater

Conventional biological wastewater treatment often fails to remove emerging contaminants (ECs) because specialized degraders are absent. We developed a function-ecology-integrated framework for designing synthetic microbial communities (SynComs) by combining metagenome-guided identification of degradation potential, quorum-sensing functionality screening, and keystone-based selection from genome-scale metabolic models (GSMMs). Applied to sulfamethoxazole (SMX) degradation, this approach identified five strains with stable catabolic potential and high ecological coherence. GSMM simulations predicted SynCom5 (three species) and SynCom11 (four species) would achieve the highest SMX uptake fluxes (30.7 and 31.7 mmol gDW –1 h –1, respectively), driven by complementary amino acid cross-feeding and a high ratio of metabolic interaction potential to resource overlap. Experimentally, both SynComs removed >90% of SMX within 72 h, with SynCom11 selected for bioaugmentation. In activated sludge microcosms, SynCom11 achieved 91.3% SMX removal over 7 days, compared to 25.8% in controls, and successfully engrafted 2 of its 4 members. This approach avoids high-concentration selective pressure, minimizing resistance risks, and demonstrates that embedding an ecologically informed design within catabolic function enables robust, scalable bioaugmentation for ECs.