High-throughput measurement of recombinant genes in vivo using molecular barcodes

As recombinant microbes are gaining increased interest for deployment to host-associated or environmental sites, a significant challenge is testing the activity of different strain designs in high throughput. This is because many of these host-associated or environmental settings (i.e. whole animals or soil) are expensive to operate and have large intrinsic length scales. One characteristic of interest is the expression of a heterologous gene, as this is likely to be environment-specific. To measure the expression of heterologous genes in high-throughput using a small number of experimental systems, we propose adding molecular barcodes to the transcript of interest. In this work, we generated and pooled E. coli strains expressing barcoded GFP constructs for 30 E. coli promoters. We then exposed this pool to a panel of culture conditions (oxygen level, media composition, growth phase) and host-associated settings (mouse gut site), allowing us to determine how the expression of recombinant genes in the gut correlates with their expression in monoculture settings.