High-throughput chemical genomic screening: a step-by-step workflow from plate to phenotype

Abstract

Chemical genomic screening is a powerful systems biology approach for linking gene function to phenotype under diverse chemical and environmental stressors. However, its broader use in microbial research has been limited by the lack of standardized, reproducible workflows. Our study introduces a scalable, end-to-end protocol that integrates experimental, imaging, and computational steps into a cohesive framework for high-throughput screening across a range of microbial species. This enables researchers to generate consistent, high-quality phenotypic data suitable for large-scale analyses. The protocol supports systematic exploration of gene-environment interactions, microbial stress responses, and antimicrobial resistance. Its adaptability and troubleshooting guidance make it especially useful for groups working in microbiome research, synthetic biology, and microbial community studies. By bridging benchwork and computational analysis, this workflow expands the technical toolkit available to microbial systems biologists. Our work contributes to the development of robust methods for functional genomics and supports the core mission of mSystems to advance microbial systems biology.