Engineering Microbial Communities: Bottom-Up Strategies for Assembly and Resource-Based Control

Abstract

Achieving precise control over microbial community composition is critical for applications ranging from bioremediation to human health but remains challenging due to the complexity of microbial interactions and resource variability. This work presents a framework for the bottom-up engineering of microbial communities by leveraging resource dynamics and temporal niches in fluctuating environments.
This approach assembles and maintains microbial "dream teams" - small, defined communities with desired properties—using serial dilution experiments. By treating resource concentrations as dynamic "control knobs," it enables stable coexistence and precise tuning of species abundances. Theoretical models, informed by experimental data from natural and synthetic microcosms, incorporate ecological and metabolic parameters, including species-specific time lags and dilution factors, to identify resource combinations that maximize community stability and diversity.
I will also describe how to engineer a multi-cycle resource strategy to overcome resource limitations and dramatically increase microbial diversity. By systematically varying resource ratios across growth-dilution cycles, this strategy creates additional temporal niches that allow for the coexistence of a larger number of species than traditional methods. Numerical simulations demonstrate that multi-cycle strategies significantly enhance species diversity, approaching the theoretical upper bound of 2^n-1 species coexisting on n resources.