Significance Traditional genetic modulation approaches are typically restricted to binary perturbations, single-sided titrations (either graded up- or down-regulation), or individual gene expression modulation. Here, we utilize a library approach that is able to simultaneously modulate gene expression in a metabolism-wide manner. This library, when coupled with next-generation sequencing, allows for the identification of gene perturbations that would have been missed by classic approaches. For the examples tested, this library identified targets that improved growth on alternative carbon sources as well as improved production of betaxanthins.