Guided assembly of multispecies positive biofilms targeting undesirable bacteria

Abstract

The use of synthetic microbial communities (SynComs) engineered to form positive biofilms that prevent the settlement of harmful bacteria is emerging as a promising strategy in biotechnology, particularly in reducing reliance on chemical antimicrobials. Despite this potential, the rationale for selecting specific strains in SynComs and the mechanisms underlying their antagonistic effects remains insufficiently understood. In this study, we present a bottom-up approach integrating live-cell imaging with high-throughput analysis of multi-strain biofilms across diverse scenarios. Through this method, we identified beneficial strains based on their superior ability to exclude undesirable bacteria and form mixed biofilms. Notably, our findings revealed that competitive strains against undesirable bacteria could also exclude other beneficial strains, emphasising the need for compatibility control in SynComs design. SynComs composed of B. velezensis and Pediococcus spp. demonstrated enhanced pathogen exclusion compared to single strains. Temporal analysis of biofilm interactions, supported by mathematical models, showed that pathogen exclusion was primarily driven by nutritional competition (Jameson effect) with additional specific interference mechanisms (prey-predator Lotka-Volterra model). Furthermore, pre-establishing SynComs to surfaces significantly increased pathogen inhibition, indicating a distinct biofilm-associated exclusion effect. These insights offer a framework for rational SynCom design and deepen our understanding of the mechanisms underpinning positive biofilm applications.