Microbial biotechnology meets ecological theory: a unified framework to design industrial microbial consortia

Abstract

Microbial biotechnology and ecological theory are increasingly converging, driven by the recognition that microbial function emerges from community interactions and environmental context. Traditional reductionist approaches, focused on single strains, often fail to capture the complexity and emergent behaviors of multispecies systems underpinning bioproduction, bioremediation, and food fermentation. This review presents a framework for integrating ecological principles into microbial biotechnology to enable the rational design of industrial consortia. Here, I argue that industrial microbiomes provide an ideal intermediate between simplified laboratory models and natural ecosystems, being tractable, moderately complex, and ecologically realistic. Understanding context dependence, ecosystem-informed design, and evolutionary dynamics is essential for engineering stable, resilient, and high-performing communities. Using agri-food microbiomes as examples, this review illustrates how ecological and evolutionary concepts can guide the design of synthetic consortia with predictable functionality. By combining ecological theory with engineering strategies, microbial biotechnology can move from descriptive empiricism toward predictive, theory-driven design.