References
-
Bahadır, E. B. & Sezgintürk, M. K. Applications of commercial biosensors in clinical, food, environmental, and biothreat/biowarfare analyses. Anal. Biochem. 478, 107–120 (2015).
-
Clark, L. C. Jr & Lyons, C. Electrode systems for continuous monitoring in cardiovascular surgery. Ann. N. Y. Acad. Sci. 102, 29–45 (1962).
-
Azimi, S., Farahani, A., Docoslis, A. & Vahdatifar, S. Developing an integrated microfluidic and miniaturized electrochemical biosensor for point of care determination of glucose in human plasma samples. Anal. Bioanal. Chem. 413, 1441–1452 (2021).
-
Zeng, N. & Xiang, J. Detection of KRAS G12D point mutation level by anchor-like DNA electrochemical biosensor. Talanta 198, 111–117 (2019).
-
Lim, J. Y. & Lee, S. S. Sensitive detection of microRNA using QCM biosensors: sandwich hybridization and signal amplification by TiO2 nanoparticles. Anal. Methods 12, 5103–5109 (2020).
-
Geng, H. et al. Noble metal nanoparticle biosensors: from fundamental studies toward point-of-care diagnostics. Acc. Chem. Res. 55, 593–604 (2022).
-
Bhardwaj, T., Ramana, L. N. & Sharma, T. K. Current advancements and future road map to develop ASSURED microfluidic biosensors for infectious and non-infectious diseases. Biosensors 12, 357 (2022).
-
Justino, C. I., Duarte, A. C. & Rocha-Santos, T. A. Recent progress in biosensors for environmental monitoring: a review. Sensors 17, 2918 (2017).
-
McConnell, E. M., Nguyen, J. & Li, Y. Aptamer-based biosensors for environmental monitoring. Front. Chem. 8, 434 (2020).
-
Li, J., Jiang, J., Su, Y., Liang, Y. & Zhang, C. A novel cloth-based supersandwich electrochemical aptasensor for direct, sensitive detection of pathogens. Anal. Chim. Acta 1188, 339176 (2021).
-
Lv, M. et al. Engineering nanomaterials-based biosensors for food safety detection. Biosens. Bioelectron. 106, 122–128 (2018).
-
Lee, I., Probst, D., Klonoff, D. & Sode, K. Continuous glucose monitoring systems-Current status and future perspectives of the flagship technologies in biosensor research. Biosens. Bioelectron. 181, 113054 (2021).
-
Alharthi, S. D., Bijukumar, D., Prasad, S., Khan, A. M. & Mathew, M. T. Evolution in biosensors for cancers biomarkers detection: a review. J. Bio- Tribo-Corros. 7, 42 (2021).
-
Sassolas, A., Prieto-Simón, B. & Marty, J.-L. Biosensors for pesticide detection: new trends. Am. J. Anal. Chem. 3, 210–232 (2012).
-
Zhang, W., Asiri, A. M., Liu, D., Du, D. & Lin, Y. Nanomaterial-based biosensors for environmental and biological monitoring of organophosphorus pesticides and nerve agents. Trends Anal. Chem. 54, 1–10 (2014).
-
Jain, S. et al. Development of an antibody functionalized carbon nanotube biosensor for foodborne bacterial pathogens. J. Biosens. Bioelectron. 11, 002 (2012).
-
Li, Y., Liu, X. & Lin, Z. Recent developments and applications of surface plasmon resonance biosensors for the detection of mycotoxins in foodstuffs. Food Chem. 132, 1549–1554 (2012).
-
d’Oelsnitz, S., Love, J. D., Diaz, D. J. & Ellington, A. D. GroovDB: a database of ligand-inducible transcription factors. ACS Synth. Biol. 11, 3534–3537 (2022).
-
Liu, J. & Lu, Y. A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. J. Am. Chem. Soc. 125, 6642–6643 (2003).
-
Jiang, P. & Guo, Z. Fluorescent detection of zinc in biological systems: recent development on the design of chemosensors and biosensors. Coord. Chem. Rev. 248, 205–229 (2004).
-
McNerney, M. P. et al. Point-of-care biomarker quantification enabled by sample-specific calibration. Sci. Adv. 5, eaax4473 (2019).
-
Hui, C., Guo, Y., Liu, L. & Yi, J. Recent advances in bacterial biosensing and bioremediation of cadmium pollution: a mini-review. World J. Microbiol. Biotechnol. 38, 9 (2022).
-
Jo, H. et al. Electrochemical aptasensor of cardiac troponin I for the early diagnosis of acute myocardial infarction. Anal. Chem. 87, 9869–9875 (2015).
-
Bezerra, G. et al. Electrochemical aptasensor for the detection of HER2 in human serum to assist in the diagnosis of early stage breast cancer. Anal. Bioanal. Chem. 411, 6667–6676 (2019).
-
Javier, D. J., Nitin, N., Levy, M., Ellington, A. & Richards-Kortum, R. Aptamer-targeted gold nanoparticles as molecular-specific contrast agents for reflectance imaging. Bioconjugate Chem. 19, 1309–1312 (2008).
-
Valero, J. et al. A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry. Proc. Natl Acad. Sci. USA 118, e2112942118 (2021).
-
Tombelli, S., Minunni, M., Luzi, E. & Mascini, M. Aptamer-based biosensors for the detection of HIV-1 Tat protein. Bioelectrochemistry 67, 135–141 (2005).
-
Yu, X., Chen, F., Wang, R. & Li, Y. Whole-bacterium SELEX of DNA aptamers for rapid detection of E. coli O157:H7 using a QCM sensor. J. Biotechnol. 266, 39–49 (2018).
-
Duan, N. et al. Selection and characterization of aptamers against Salmonella typhimurium using whole-bacterium systemic evolution of ligands by exponential enrichment (SELEX). J. Agric. Food Chem. 61, 3229–3234 (2013).
-
Gupta, N., Renugopalakrishnan, V., Liepmann, D., Paulmurugan, R. & Malhotra, B. D. Cell-based biosensors: recent trends, challenges and future perspectives. Biosens. Bioelectron. 141, 111435 (2019).
-
Riglar, D. T. & Silver, P. A. Engineering bacteria for diagnostic and therapeutic applications. Nat. Rev. Microbiol. 16, 214–225 (2018).
-
Inda, M. E. & Lu, T. K. Microbes as biosensors. Annu. Rev. Microbiol. 74, 337–359 (2020). This review discusses considerations and capabilities for using bacteria as biosensors.
-
Chiang, A. J. & Hasty, J. Design of synthetic bacterial biosensors. Curr. Opin. Microbiol. 76, 102380 (2023).
-
Pham, H. L., Ling, H. & Chang, M. W. Design and fabrication of field-deployable microbial biosensing devices. Curr. Opin. Biotechnol. 76, 102731 (2022).
-
Armstrong, A. & Isalan, M. Engineering bacterial theranostics: from logic gates to in vivo applications. Front. Bioeng. Biotechnol. 12, 1437301 (2024). This review describes recent advances in bacterial theranostics.
-
Richard, H. T. & Foster, J. W. Acid resistance in Escherichia coli. Adv. Appl. Microbiol. 52, 167–186 (2003).
-
Winkler, J. D., Garcia, C., Olson, M., Callaway, E. & Kao, K. C. Evolved osmotolerant Escherichia coli mutants frequently exhibit defective N-acetylglucosamine catabolism and point mutations in cell shape-regulating protein MreB. Appl. Environ. Microbiol. 80, 3729–3740 (2014).
-
Chien, T. et al. Enhancing the tropism of bacteria via genetically programmed biosensors. Nat. Biomed. Eng. 6, 94–104 (2022).
-
Jiao, C. et al. RNA recording in single bacterial cells using reprogrammed tracrRNAs. Nat. Biotechnol. 41, 1107–1116 (2023).
-
Schmidt, F., Cherepkova, M. Y. & Platt, R. J. Transcriptional recording by CRISPR spacer acquisition from RNA. Nature 562, 380–385 (2018).
-
Parker, M. L., Rubien, J., McCormick, D. & Li, G.-W. Molecular time capsules enable transcriptomic recording in living cells. Preprint at bioRxiv https://doi.org/10.1101/2023.10.12.562053 (2023).
-
Schmidt, F. et al. Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science 376, eabm6038 (2022).
-
Shen, H. et al. Engineered microbial systems for advanced drug delivery. Adv. Drug Deliv. Rev. 187, 114364 (2022).
-
Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).
-
Zhang, J. Y., Bender, A. T., Boyle, D. S., Drain, P. K. & Posner, J. D. Current state of commercial point-of-care nucleic acid tests for infectious diseases. Analyst 146, 2449–2462 (2021).
-
Kumar, K. R., Cowley, M. J. & Davis, R. L. Next-generation sequencing and emerging technologies. Semin. Thromb. Hemost. 50, 1026–1038 (2024).
-
Valentin, T. et al. Prospective evaluation of three rapid molecular tests for seasonal influenza in patients presenting at an emergency unit. J. Clin. Virol. 111, 29–32 (2019).
-
Leber, A. L. et al. Multicenter evaluation of BioFire FilmArray meningitis/encephalitis panel for detection of bacteria, viruses, and yeast in cerebrospinal fluid specimens. J. Clin. Microbiol. 54, 2251–2261 (2016).
-
Land, K. J., Boeras, D. I., Chen, X.-S., Ramsay, A. R. & Peeling, R. W. Reassured diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes. Nat. Microbiol. 4, 46–54 (2019). This perspective lays out the REASSURED criteria for ideal point-of-care diagnostic tests.
-
Makarova, K. S. et al. An updated evolutionary classification of CRISPR–Cas systems. Nat. Rev. Microbiol. 13, 722–736 (2015).
-
Kaminski, M. M., Abudayyeh, O. O., Gootenberg, J. S., Zhang, F. & Collins, J. J. CRISPR-based diagnostics. Nat. Biomed. Eng. 5, 643–656 (2021). This review examines in vitro CRISPR–Cas-based diagnostic devices.
-
Singh, S. et al. Crispr-Cas based biosensing: a fast-expanding molecular diagnostic tool. Microchem. J. 200, 110421 (2024).
-
Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl Acad. Sci. USA 109, E2579–E2586 (2012).
-
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).
-
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas Systems. Science 339, 819–823 (2013).
-
Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).
-
Gootenberg, J. S. et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356, 438–442 (2017).
-
Chen, J. S. et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360, 436–439 (2018).
-
Hadi, R., Poddar, A., Sonnaila, S., Bhavaraju, V. S. M. & Agrawal, S. Advancing CRISPR-based solutions for COVID-19 diagnosis and therapeutics. Cells 13, 1794 (2024).
-
Joung, J. et al. Detection of SARS-CoV-2 with SHERLOCK one-pot testing. N. Engl. J. Med. 383, 1492–1494 (2020).
-
Broughton, J. P. et al. CRISPR–Cas12-based detection of SARS-CoV-2. Nat. Biotechnol. 38, 870–874 (2020).
-
Cooper, R. M. et al. Engineered bacteria detect tumor DNA. Science 381, 682–686 (2023). This article reports A. baylyi as DNA biosensor using a deletion-of-repressor approach, showing that it can detect donor DNA cassettes spontaneously released from tumour cells in the mouse colon.
-
Cheng, Y.-Y. et al. Programming bacteria for multiplexed DNA detection. Nat. Commun. 14, 2001 (2023). This article reports on B. subtilis as DNA biosensor using both a deletion-of-repressor and deletion-of-toxin approach, demonstrating that it can detect target bacteria spiked into unpurified cecal contents.
-
Nou, X. A. & Voigt, C. A. Sentinel cells programmed to respond to environmental DNA including human sequences. Nat. Chem. 20, 211–220 (2024). This article reports B. subtilis as DNA biosensor using a deletion-of-terminator approach, showing that it can detect multiple targets using an AND gate.
-
Tellechea-Luzardo, J., Stiebritz, M. T. & Carbonell, P. Transcription factor-based biosensors for screening and dynamic regulation. Front. Bioeng. Biotechnol. 11, 1118702 (2023).
-
Vaaben, T. H., Vazquez-Uribe, R. & Sommer, M. O. A. Characterization of eight bacterial biosensors for microbial diagnostic and therapeutic applications. ACS Synth. Biol. 11, 4184–4192 (2022).
-
Charbonneau, M. R., Isabella, V. M., Li, N. & Kurtz, C. B. Developing a new class of engineered live bacterial therapeutics to treat human diseases. Nat. Commun. 11, 1738 (2020).
-
Hahn, J. et al. Bacterial therapies at the interface of synthetic biology and nanomedicine. Nat. Rev. Bioeng. 2, 120–135 (2024).
-
Graham, G. et al. Genome-scale transcriptional dynamics and environmental biosensing. Proc. Natl Acad. Sci. USA 117, 3301–3306 (2020).
-
Courbet, A., Endy, D., Renard, E., Molina, F. & Bonnet, J. Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates. Sci. Transl. Med. 7, 289ra83 (2015).
-
Amrofell, M. B., Rottinghaus, A. G. & Moon, T. S. Engineering microbial diagnostics and therapeutics with smart control. Curr. Opin. Biotechnol. 66, 11–17 (2020).
-
Wang, B., Kitney, R. I., Joly, N. & Buck, M. Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat. Commun. 2, 508 (2011).
-
Kitada, T., DiAndreth, B., Teague, B. & Weiss, R. Programming gene and engineered-cell therapies with synthetic biology. Science 359, eaad1067 (2018).
-
Bulter, T. et al. Design of artificial cell-cell communication using gene and metabolic networks. Proc. Natl Acad. Sci. 101, 2299–2304 (2004).
-
Wan, X. et al. Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals. Nat. Chem. Biol. 15, 540–548 (2019).
-
Stricker, J. et al. A fast, robust and tunable synthetic gene oscillator. Nature 456, 516–519 (2008).
-
Becskei, A., Séraphin, B. & Serrano, L. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J. 20, 2528–2535 (2001).
-
Müller, M. et al. Designed cell consortia as fragrance-programmable analog-to-digital converters. Nat. Chem. Biol. 13, 309–316 (2017).
-
Kotula, J. W. et al. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc. Natl Acad. Sci. 111, 4838–4843 (2014).
-
Riglar, D. T. et al. Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation. Nat. Biotechnol. 35, 653–658 (2017).
-
Naydich, A. D. et al. Synthetic gene circuits enable systems-level biosensor trigger discovery at the host-microbe interface. mSystems 4, e00125–19 (2019).
-
Nakamura, M. et al. Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells. Nat. Commun. 10, 194 (2019).
-
Xie, M. & Fussenegger, M. Designing cell function: assembly of synthetic gene circuits for cell biology applications. Nat. Rev. Mol. Cell Biol. 19, 507–525 (2018).
-
Bradley, R. W., Buck, M. & Wang, B. Tools and principles for microbial gene circuit engineering. J. Mol. Biol. 428, 862–888 (2016).
-
Munkler, L. P. et al. Genetic heterogeneity of engineered Escherichia coli Nissle 1917 strains during scale-up simulation. Metab. Eng. 85, 159–166 (2024).
-
Phaneuf, P. V. et al. Escherichia coli data-driven strain design using aggregated adaptive Laboratory evolution mutational data. ACS Synth. Biol. 10, 3379–3395 (2021).
-
Meyer, A. J., Segall-Shapiro, T. H., Glassey, E., Zhang, J. & Voigt, C. A. Escherichia coli “marionette” strains with 12 highly optimized small-molecule sensors. Nat. Chem. Biol. 15, 196–204 (2019).
-
Sandberg, T. E., Salazar, M. J., Weng, L. L., Palsson, B. O. & Feist, A. M. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab. Eng. 56, 1–16 (2019).
-
Miller, C. A., Ho, J. M. & Bennett, M. R. Strategies for improving small-molecule biosensors in bacteria. Biosensors 12, 64 (2022).
-
Li, S. et al. Directed evolution of TetR for constructing sensitive and broad-spectrum tetracycline antibiotics whole-cell biosensor. J. Hazard. Mater. 460, 132311 (2023).
-
Chang, H.-J. et al. Programmable receptors enable bacterial biosensors to detect pathological biomarkers in clinical samples. Nat. Commun. 12, 5216 (2021).
-
Chiang, A. J. et al. Evolved microbial diversity enables combinatoric biosensing in complex environments. Preprint at bioRxiv https://doi.org/10.1101/2025.03.24.645055 (2025).
-
Danino, T. et al. Programmable probiotics for detection of cancer in urine. Sci. Transl. Med. 7, 289ra84 (2015).
-
Gurbatri, C. R., Arpaia, N. & Danino, T. Engineering bacteria as interactive cancer therapies. Science 378, 858–864 (2022).
-
Li, S. et al. Oral delivery of bacteria: basic principles and biomedical applications. J. Control. Release 327, 801–833 (2020).
-
Drees, J. J., Mertensotto, M. J., Augustin, L. B., Schottel, J. L. & Saltzman, D. A. Vasculature disruption enhances bacterial targeting of autochthonous tumors. J. Cancer 6, 843–848 (2015).
-
Din, M. O. et al. Synchronized cycles of bacterial lysis for in vivo delivery. Nature 536, 81–85 (2016).
-
Chien, T., Doshi, A. & Danino, T. Advances in bacterial cancer therapies using synthetic biology. Curr. Opin. Syst. Biol. 5, 1–8 (2017).
-
Gurbatri, C. R. et al. Engineering tumor-colonizing E. coli Nissle 1917 for detection and treatment of colorectal neoplasia. Nat. Commun. 15, 646 (2024).
-
Mimee, M. et al. An ingestible bacterial-electronic system to monitor gastrointestinal health. Science 360, 915–918 (2018).
-
Daeffler, K. N.-M. et al. Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation. Mol. Syst. Biol. 13, 923 (2017).
-
Zou, Z.-P., Du, Y., Fang, T.-T., Zhou, Y. & Ye, B.-C. Biomarker-responsive engineered probiotic diagnoses, records, and ameliorates inflammatory bowel disease in mice. Cell Host Microbe 31, 199–212.e5 (2023).
-
Leventhal, D. S. et al. Immunotherapy with engineered bacteria by targeting the sting pathway for anti-tumor immunity. Nat. Commun. 11, 2739 (2020).
-
Mao, N., Cubillos-Ruiz, A., Cameron, D. E. & Collins, J. J. Probiotic strains detect and suppress cholera in mice. Sci. Transl. Med. 10, eaao2586 (2018).
-
Renella, G. & Giagnoni, L. Light dazzles from the black box: whole-cell biosensors are ready to inform on fundamental soil biological processes. Chem. Biol. Technol. Agric. 3, 8 (2016).
-
Moraskie, M. et al. Microbial whole-cell biosensors: current applications, challenges, and future perspectives. Biosens. Bioelectron. 191, 113359 (2021).
-
Chen, S., Chen, X., Su, H., Guo, M. & Liu, H. Advances in synthetic-biology-based whole-cell biosensors: Principles, genetic modules, and applications in food safety. Int. J. Mol. Sci. 24, 7989 (2023).
-
Liu, C. et al. Engineering whole-cell microbial biosensors: design principles and applications in monitoring and treatment of heavy metals and organic pollutants. Biotechnol. Adv. 60, 108019 (2022).
-
Muñoz-Martín, M. A., Mateo, P., Leganés, F. & Fernández-Piñas, F. A battery of bioreporters of nitrogen bioavailability in aquatic ecosystems based on cyanobacteria. Sci. Total. Environ. 475, 169–179 (2014).
-
Cardemil, C. V., Smulski, D. R., LaRossa, R. A. & Vollmer, A. C. Bioluminescent Escherichia coli strains for the quantitative detection of phosphate and ammonia in coastal and suburban watersheds. DNA Cell Biol. 29, 519–531 (2010).
-
Kang, Y. et al. Enhancing the copper-sensing capability of Escherichia coli-based whole-cell bioreporters by genetic engineering. Appl. Microbiol. Biotechnol. 102, 1513–1521 (2018).
-
Liu, P., Huang, Q. & Chen, W. Construction and application of a zinc-specific biosensor for assessing the immobilization and bioavailability of zinc in different soils. Environ. Pollut. 164, 66–72 (2012).
-
Jia, X., Zhao, T., Liu, Y., Bu, R. & Wu, K. Gene circuit engineering to improve the performance of a whole-cell lead biosensor. FEMS Microbiol. Lett. 365, fny157 (2018).
-
Wang, B., Barahona, M. & Buck, M. A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals. Biosens. Bioelectron. 40, 368–376 (2013).
-
Whangsuk, W., Thiengmag, S., Dubbs, J., Mongkolsuk, S. & Loprasert, S. Specific detection of the pesticide chlorpyrifos by a sensitive genetic-based whole cell biosensor. Anal. Biochem. 493, 11–13 (2016).
-
Chong, H. & Ching, C. B. Development of colorimetric-based whole-cell biosensor for organophosphorus compounds by engineering transcription regulator DmpR. ACS Synth. Biol. 5, 1290–1298 (2016).
-
Riangrungroj, P., Bever, C. S., Hammock, B. D. & Polizzi, K. M. A label-free optical whole-cell Escherichia coli biosensor for the detection of pyrethroid insecticide exposure. Sci. Rep. 9, 12466 (2019).
-
Tecon, R. et al. Development of a multistrain bacterial bioreporter platform for the monitoring of hydrocarbon contaminants in marine environments. Environ. Sci. Technol. 44, 1049–1055 (2010).
-
Hernández-Śanchez, V., Molina, L., Ramos, J. L. & Segura, A. New family of biosensors for monitoring BTX in aquatic and edaphic environments. Microb. Biotechnol. 9, 858–867 (2016).
-
Song, Y. et al. A whole-cell bioreporter approach for the genotoxicity assessment of bioavailability of toxic compounds in contaminated soil in China. Environ. Pollut. 195, 178–184 (2014).
-
Kutraite, I. & Malys, N. Development and application of whole-cell biosensors for the detection of gallic acid. ACS Synth. Biol. 12, 533–543 (2023).
-
Wu, W. et al. Genetically assembled fluorescent biosensor for in situ detection of bio-synthesized alkanes. Sci. Rep. 5, 10907 (2015).
-
Renda, B. A., Dasgupta, A., Leon, D. & Barrick, J. E. Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution. J. Bacteriol. 197, 872–881 (2015).
-
Dubnau, D. & Blokesch, M. Mechanisms of DNA uptake by naturally competent bacteria. Annu. Rev. Genet. 53, 217–237 (2019). This review describes DNA uptake by naturally competent bacteria.
-
Cooper, R. M., Tsimring, L. & Hasty, J. Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance. eLife 6, e25950 (2017).
-
Ghahfarokhi, S. M. A. T. & Peña-Castillo, L. BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble. NAR Genom. Bioinform. 7, lqaf016 (2025).
-
Larson, M. H. et al. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat. Protoc. 8, 2180–2196 (2013).
-
Cooper, R. M. & Hasty, J. CRISPR-Cas inhibits natural transformation through altruistic group defense and self-sacrifice. Preprint at bioRxiv https://doi.org/10.1101/2021.09.16.460680 (2021).
-
Li, S.-Y. et al. CRISPR-Cas12a-assisted nucleic acid detection. Cell Discov. 4, 20 (2018).
-
Li, L. et al. HOLMESv2: a CRISPR-Cas12b-assisted platform for nucleic acid detection and DNA methylation quantitation. ACS Synth. Biol. 8, 2228–2237 (2019).
-
Palmen, R., Buijsman, P. & Hellingwerf, K. J. Physiological regulation of competence induction for natural transformation in Acinetobacter calcoaceticus. Arch. Microbiol. 162, 344–351 (1994).
-
Suárez, G. A., Renda, B. A., Dasgupta, A. & Barrick, J. E. Reduced mutation rate and increased transformability of transposon-free Acinetobacter baylyi ADP1-ISx. Appl. Environ. Microbiol. 83, e01025-17 (2017).
-
Halvorsen, E. M., Williams, J. J., Bhimani, A. J., Billings, E. A. & Hergenrother, P. J. Txe, an endoribonuclease of the enterococcal Axe–Txe toxin–antitoxin system, cleaves mRNA and inhibits protein synthesis. Microbiology 157, 387–397 (2011).
-
Cooper, R. M. & Hasty, J. One-Day construction of multiplex arrays to harness natural CRISPR-CAS systems. ACS Synth. Biol. 9, 1129–1137 (2020).
-
Zhang, J. et al. The international cancer genome consortium data portal. Nat. Biotechnol. 37, 367–369 (2019).
-
Lau, C.H., Huang, S. & Zhu, H. Amplification-free nucleic acids detection with next-generation CRISPR/dx systems. Crit. Rev. Biotechnol. 45, 859–866 (2025).
-
Grinstein, J. D. Sherlock biosciences acquires sense biodetection to commercialize disposable CRISPR-based diagnostics. Genet. Eng. Biotechnol. News 5, 124–127 (2023).
-
Zhou, W. et al. A CRISPR–Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection. Nat. Commun. 9, 5012 (2018).
-
Zhang, Y. et al. Paired design of dCas9 as a systematic platform for the detection of featured nucleic acid sequences in pathogenic strains. ACS Synth. Biol. 6, 211–216 (2017).
-
Pardee, K. et al. Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165, 1255–1266 (2016).
-
Yuan, C. et al. Universal and naked-eye gene detection platform based on the clustered regularly interspaced short palindromic repeats/Cas12a/13a system. Anal. Chem. 92, 4029–4037 (2020).
-
Gootenberg, J. S. et al. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360, 439–444 (2018).
-
Teng, F. et al. CDetection: CRISPR-Cas12b-based DNA detection with sub-attomolar sensitivity and single-base specificity. Genome Biol. 20, 132 (2019).
-
Azhar, M. et al. Rapid and accurate nucleobase detection using FnCas9 and its application in COVID-19 diagnosis. Biosens. Bioelectron. 183, 113207 (2021).
-
Zhou, S. et al. Endonuclease-assisted PAM-free recombinase polymerase amplification coupling with CRISPR/Cas12a (E-PfRPA/Cas) for sensitive detection of DNA methylation. ACS Sens. 7, 3032–3040 (2022).
-
Karvelis, T. et al. PAM recognition by miniature CRISPR-Cas12f nucleases triggers programmable double-stranded DNA target cleavage. Nucleic Acids Res. 48, 5016–5023 (2020).
-
Lee, Y. et al. Fabrication of ultrasensitive electrochemical biosensor for dengue fever viral RNA based on CRISPR/Cpf1 reaction. Sens. Actuators B Chem. 326, 128677 (2021).
-
LeMieux, J. CRISPR comes of age—as a diagnostic: hailed for its gene editing power, Sherlock Bioscience’s COVID-19 diagnostic is the first CRISPR technology to gain FDA approval. Clinical OMICs 7, 10–12 (2020).
-
Guglielmi, G. First CRISPR test for the coronavirus approved in the United States. Nature https://doi.org/10.1038/d41586-020-01402-9 (2020).
-
Myhrvold, C. et al. Field-deployable viral diagnostics using CRISPR-Cas13. Science 360, 444–448 (2018).
-
Saiki, R. K. et al. Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230, 1350–1354 (1985).
-
Wang, D.-G., Brewster, J. D., Paul, M. & Tomasula, P. M. Two methods for increased specificity and sensitivity in loop-mediated isothermal amplification. Molecules 20, 6048–6059 (2015).
-
Piepenburg, O., Williams, C. H., Stemple, D. L. & Armes, N. A. DNA detection using recombination proteins. PLoS Biol. 4, e204 (2006).
-
Godeux, A.-S. et al. Interbacterial transfer of carbapenem resistance and large antibiotic resistance islands by natural transformation in pathogenic Acinetobacter. mBio 13, e02631-21 (2022).
-
Nielsen, K. M., Smalla, K. & van Elsas, J. D. Natural transformation of Acinetobacter sp. strain BD413 with cell lysates of Acinetobacter sp., Pseudomonas fluorescens, and Burkholderia cepacia in soil microcosms. Appl. Environ. Microbiol. 66, 206–212 (2000).
-
Zhang, X. et al. Stress-induced, highly efficient, donor cell-dependent cell-to-cell natural transformation in Bacillus subtilis. J. Bacteriol. 200, e002670-18 (2018).
-
Cowley, L. A. et al. Evolution via recombination: cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae. PLoS Genet. 14, e1007410 (2018).
-
Siguenza, N. et al. Engineered bacterial therapeutics for detecting and treating CRC. Trends Cancer 10, 588–597 (2024).
-
Redenti, A. et al. Probiotic neoantigen delivery vectors for precision cancer immunotherapy. Nature 635, 453–461 (2024).
-
Guo, F. et al. Live attenuated bacterium limits cancer resistance to CAR-T therapy by remodeling the tumor microenvironment. J. Immunother. Cancer 10, e003760 (2022).
-
Abedi, M. H. et al. Ultrasound-controllable engineered bacteria for cancer immunotherapy. Nat. Commun. 13, 1585 (2022).
-
Hurt, R. C. et al. Genomically mined acoustic reporter genes for real-time in vivo monitoring of tumors and tumor-homing bacteria. Nat. Biotechnol. 41, 919–931 (2023).
-
Ma, Y., Manna, A. & Moon, T. S. Advances in engineering genetic circuits for microbial biocontainment. Curr. Opin. Syst. Biol. 36, 100483 (2023).
-
Low, K. B. et al. Lipid A mutant Salmonella with suppressed virulence and TNFα induction retain tumor-targeting in vivo. Nat. Biotechnol. 17, 37–41 (1999).
-
Clairmont, C. et al. Biodistribution and genetic stability of the novel antitumor agent VNP20009, a genetically modified strain of Salmonella typhimuvium. J. Infect. Dis. 181, 1996–2002 (2000).
-
Pawelek, J. M., Low, K. B. & Bermudes, D. Bacteria as tumour-targeting vectors. Lancet Oncol. 4, 548–556 (2003).
-
Ecological fitness, genomic islands and bacterial pathogenicity. EMBO Rep. 2, 376–381 (2001)
-
Hacker, J., Hentschel, U. & Dobrindt, U. Prokaryotic chromosomes and disease. Science 301, 790–793 (2003).
-
Hoffman, R. M. Tumor-seeking Salmonella amino acid auxotrophs. Curr. Opin. Biotechnol. 22, 917–923 (2011).
-
Chan, C. T., Lee, J. W., Cameron, D. E., Bashor, C. J. & Collins, J. J. ‘Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment. Nat. Chem. Biol. 12, 82–86 (2016).
-
Cui, L. & Bikard, D. Consequences of Cas9 cleavage in the chromosome of Escherichia coli. Nucleic Acids Res. 44, 4243–4251 (2016).
-
Richter, F. et al. Engineering of temperature- and light-switchable Cas9 variants. Nucleic Acids Res. 44, 10003–10014 (2013).
-
Foo, G. W. et al. Intein-based thermoregulated meganucleases for containment of genetic material. Nucleic Acids Res. 52, 2066–2077 (2024).
-
Rovner, A. J. et al. Recoded organisms engineered to depend on synthetic amino acids. Nature 518, 89–93 (2015).
-
Ma, N. J. & Isaacs, F. J. Genomic recoding broadly obstructs the propagation of horizontally transferred genetic elements. Cell Syst. 3, 199–207 (2016).
-
Zürcher, J. F. et al. Refactored genetic codes enable bidirectional genetic isolation. Science 378, 516–523 (2022).
-
Nia, L. H. & Claesen, J. Engineered cancer targeting microbes and encapsulation devices for human gut microbiome applications. Biochemistry 61, 2841–2848 (2022).
-
Yamanaka, Y., Watanabe, H., Yamauchi, E., Miyake, Y. & Yamamoto, K. Measurement of the promoter activity in Escherichia coli by using a luciferase reporter. Bio-protocol 10, e3500 (2020).
-
Nordgård, L. et al. Lack of detectable DNA uptake by bacterial gut isolates grown in vitro and by Acinetobacter baylyi colonizing rodents in vivo. Environ. Biosafety Res. 6, 149–160 (2007).
-
Paz, E. D. la et al. A self-powered ingestible wireless biosensing system for real-time in situ monitoring of gastrointestinal tract metabolites. Nat. Commun. 13, 7405 (2022).
-
Recorbet, G., Picard, C., Normand, P. & Simonet, P. Kinetics of the persistence of chromosomal DNA from genetically engineered Escherichia coli introduced into soil. Appl. Environ. Microbiol. 59, 4289–4294 (1993).
-
Alarcon, C. M. et al. Application of DNA- and protein-based detection methods in agricultural biotechnology. J. Agric. Food Chem. 67, 1019–1028 (2019).
-
Martzy, R. et al. Challenges and perspectives in the application of isothermal DNA amplification methods for food and water analysis. Anal. Bioanal. Chem. 411, 1695–1702 (2019).
-
Pawlowski, J., Bonin, A., Boyer, F., Cordier, T. & Taberlet, P. Environmental DNA for biomonitoring. Mol. Ecol. 30, 2931–2936 (2021).
-
Gettings, K. B., Tillmar, A., Sturk-Andreaggi, K. & Marshall, C. Review of SNP assays for disaster victim identification: cost, time, and performance information for decision-makers. J. Forensic Sci. 69, 1546–1557 (2024).
-
Vasala, A., Hytönen, V. P. & Laitinen, O. H. Modern Tools for rapid diagnostics of antimicrobial resistance. Front. Cell. Infect. Microbiol. 10, 308 (2020).
-
Belkum, A. van et al. Developmental roadmap for antimicrobial susceptibility testing systems. Nat. Rev. Microbiol. 17, 51–62 (2019).
-
Misra, S. K. in Next Generation Biomanufacturing Technologies (eds Rathinam, N. K. & Sani, R. K.) 141–154 (ACS Publications, 2019).
-
Süntar, I., Çetinkaya, S., Haydarŏglu, Ü. S. & Habtemariam, S. Bioproduction process of natural products and biopharmaceuticals: biotechnological aspects. Biotechnol. Adv. 50, 107768 (2021).
-
Tang, Q. et al. Current sampling methods for gut microbiota: a call for more precise devices. Front. Cell. Infect. Microbiol. 10, 151 (2020).
-
Levitan, O. et al. The gut microbiome–does stool represent right? Heliyon 9, e13602 (2023).
-
Opgenorth, P. et al. Lessons from two design-build-test-learn cycles of dodecanol production in Escherichia coli aided by machine learning. ACS Synth. Biol. 8, 1337–1351 (2019).
-
Carbonell, P. et al. An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals. Commun. Biol. 1, 66 (2018).
-
Miskovic, L. et al. A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models. Biotechnol. Biofuels 10, 166 (2017).
