Programming bacteria for multiplexed DNA detection

DNA is a universal and programmable signal of living organisms. Here we developed cell-based DNA sensors by engineering the naturally competent bacterium Bacillus subtilis ( B. subtilis ) to detect specific DNA sequences in the environment. The DNA sensor strains can identify diverse bacterial species including major human pathogens with high specificity and sensitivity. Multiplexed detection of genomic DNA from different species in complex samples can be achieved by coupling the sensing mechanism to orthogonal fluorescent reporters. We also demonstrate that the DNA sensors can detect the presence of species in the complex samples without requiring DNA extraction. The modularity of the living cell-based DNA sensing mechanism and simple detection procedure could enable programmable DNA sensing for broad applications. ### Competing Interest Statement O.S.V., Y.Y.C. and Z.C. are inventors on a provisional patent application filed by the Wisconsin Alumni Research Foundation (WARF) with the US Patent and Trademark Office, which describes and claims concepts disclosed herein (Application No. 63/290,442 Filing Date: 12/16/2021). All other authors declare no conflict of interest.