Decoding Multicellularity in Streptomyces: Single-Cell Technologies Reveal the Link between Phenotypic Heterogeneity and Secondary Metabolite Production

Abstract

Streptomyces species are among the most prolific natural sources of antibiotics and other bioactive secondary metabolites, supporting major therapeutic advances, including streptomycin and ivermectin. In addition to their ecological role as saprophytic decomposers, they remain central to modern medicine and agriculture, with nearly two-thirds of clinically used antibiotics originating directly or indirectly from this genus. Recent progress in genome sequencing, CRISPR-Cas9 editing, and synthetic biology has expanded our ability to modify Streptomyces genomes, activate silent biosynthetic gene clusters, remove competing pathways, and increase metabolite output. Yet, industrial use of these bacteria continues to be difficult due to their complex multicellular life cycle and pronounced phenotypic heterogeneity. Even genetically identical cells display differences in germination, growth, and metabolic activity, leading to inconsistent fermentation performance and variable yields. More recent studies have shown that this heterogeneity is not simply a technical barrier but a beneficial ecological strategy that improves survival in changing environments. These findings underscore the need to understand the spatial and temporal diversity that shapes Streptomyces biology. New single-cell technologies, including microfluidics and Raman spectroscopy, now allow direct observation of developmental processes, spatial mapping of metabolite production, and high-resolution screening of superior producer strains. This review summarises current advances in engineering Streptomyces and examines how single-cell approaches are transforming our understanding of their variability. By combining genetic tools with precise phenotypic analysis, researchers are moving toward more consistent and scalable production systems for valuable natural products.