From coarse-grained metabolic rules to fine-grained control of microbial communities

Over the past decade, microbial ecology has revealed remarkable coarse-grained regularities in community assembly and metabolic function. Across diverse systems, distinct taxonomic compositions can converge on similar functional outputs, and simple physiological principles can predict steady-state outcomes. These findings suggest that complex microbiomes may, in some regimes, be governed by emergent simplicity and therefore be predictable. Yet many of the traits we want to understand or engineer seem to depend on fine-grained dynamics that may be transient, strain-specific, and history dependent. Here, we argue that bridging the gap between coarse-grained metabolic rules and fine-grained metabolic complexity is essential for a predictive and engineering-oriented microbiome ecology. While progress is limited by the lack of (or insufficient) temporal, spatial, and chemical resolution, we highlight both conceptual advances and emerging technologies that may help fill that gap by providing temporal, spatial, single-cell resolved, dynamic, quantitative measurements.