Open-Source High-Throughput Phenomics of Bacterial Promoter-Reporter Strains

Open-source electronics are becoming more prevalent in biological sciences, enabling novel and unique means of data acquisition. Here, we present 3D-printed, open-source tools to acquire fluorescence phenotypes with high temporal resolution. Printed fluorescence imaging boxes (PFIboxes) cost approximately 200 US dollars to assemble, can be placed in incubators or hypoxic chambers, and accurately read high-density colony arrays of microorganisms. We demonstrate the utility of PFIboxes using a time course gene expression approach, examining global Escherichia coli promoter activity using a fluorescent reporter library across a diverse panel of 15 antibiotics, each at several concentrations. Many secondary and indirect effects were observed when E. coli was challenged with various drugs, including increased gene expression in carbon metabolism processes. Further, kinetic data acquisition enabled non-destructive time course gene expression, clustering of which revealed patterns of co-expression. In all, PFIboxes provide an open solution to gene expression, for about 2 US dollars per treatment condition, including technical replicates. [Display omitted] •Open-source 3D-printed tool for acquiring fluorescence of microbial colony arrays•PFIboxes are inexpensive and can be placed in incubators•Full phenomics platform when used with fluorescent reporter libraries•Enables non-destructive, temporally resolved gene expression studies We developed an open-source, 3D-printed phenomics platform to study gene expression in microorganisms. The platform is non-destructive and quantifies fluorescence from high-density colony arrays with high temporal resolution. Here, we demonstrate this platform by exposing Escherichia coli to a panel of antibiotics, exploring time-resolved gene expression using a promoter-reporter library.