biostudies-literatureTaketani MNIBIB NIH HHSU.S. Department of Health & Human Services | NIH | National Institute of General Medical SciencesUnited States Department of Defense | Defense Advanced Research Projects AgencyU.S. Department of DefenseUnited States Department of Defense | United States Navy | ONR | Office of Naval Research GlobalNIGMS NIH HHSNational Science FoundationU.S. Department of Health & Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering962-969https://www.ebi.ac.uk/biostudies/studies/S-EPMC8922546biostudies-literatureUnknown38(8)Bacteroides thetaiotaomicron is a human-associated bacterium that holds promise for delivery of therapies in the gut microbiome¹. Therapeutic bacteria would benefit from the ability to turn on different programs of gene expression in response to conditions inside and outside of the gut; however, the availability of regulatory parts, and methods to combine them, have been limited in B. thetaiotaomicron^2-5. We report implementation of Cello circuit design automation software⁶ for this species. First, we characterize a set of genome-integrated NOT/NOR gates based on single guide RNAs (CRISPR-dCas9) to inform a Bt user constraint file (UCF) for Cello. Then, logic circuits are designed to integrate sensors that respond to bile acid and anhydrotetracycline (aTc),Nature biotechnologyGenetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron.PMC8922546CCF-1807575P50 GM098792N00014-13-1-0074P50-GM098792R01 EB021908FA8750-17-C-0229R01EB021908Zhang JHuang YJVoigt CATaketani MTriassi AJGriffith LGZhang SfalseGenetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron.Bacteroides thetaiotaomicron is a human-associated bacterium that holds promise for delivery of therapies in the gut microbiome¹. Therapeutic bacteria would benefit from the ability to turn on different programs of gene expression in response to conditions inside and outside of the gut; however, the availability of regulatory parts, and methods to combine them, have been limited in B. thetaiotaomicron^2-5. We report implementation of Cello circuit design automation software⁶ for this species. First, we characterize a set of genome-integrated NOT/NOR gates based on single guide RNAs (CRISPR-dCas9) to inform a Bt user constraint file (UCF) for Cello. Then, logic circuits are designed to integrate sensors that respond to bile acid and anhydrotetracycline (aTc),2020-01-01T00:00:00Z2020 Aug2025-05-29T21:04:25.224Z2025-05-29T21:04:25.224ZS-EPMC89225463223133410.1038/s41587-020-0468-5