Abstract: Engineered microbial organisms for altering gene expression are provided. In some embodiments, the engineered microbial organism comprises: one or more heterologous polynucleotide sequence comprising a phenotype coding sequence operably linked to a promoter; a heterologous polynucleotide sequence comprising an inducible promoter operably linked to a polynucleotide encoding a Cas nuclease; and a heterologous polynucleotide sequence comprising a guide RNA (gRNA) that targets the phenotype coding sequence.