Inda, M. E. & Lu, T. K. Microbes as biosensors. Annu. Rev. Microbiol. 74, 337–359 (2020).
Liu, Q. et al. A threshold-based bioluminescence detector with a CMOS-integrated photodiode array in 65 nm for a multi-diagnostic ingestible capsule. IEEE J. Solid State Circuits 58, 838–851 (2023).
Bourgonje, A. R. et al. Oxidative stress and redox-modulating therapeutics in inflammatory bowel disease. Trends Mol. Med. 26, 1034–1046 (2020).
Lee, J.-Y., Tsolis, R. M. & Bäumler, A. J. The microbiome and gut homeostasis. Science 377, eabp9960 (2022).
Million, M. et al. Increased gut redox and depletion of anaerobic and methanogenic prokaryotes in severe acute malnutrition. Sci. Rep. 6, 26051 (2016).
Pribis, J. P. et al. Gamblers: an antibiotic-induced evolvable cell subpopulation differentiated by reactive-oxygen-induced general stress response. Mol. Cell 74, 785–800.e7 (2019).
Reese, A. T. et al. Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut. eLife 7, e35987 (2018).
Rivera-Chávez, F. et al. Depletion of butyrate-producing clostridia from the gut microbiota drives an aerobic luminal expansion of Salmonella. Cell Host Microbe 19, 443–454 (2016).
Dumitrescu, L. et al. Oxidative stress and the microbiota–gut–brain axis. Oxid. Med. Cell. Longev. 2018, 2406594 (2018).
Yardeni, T. et al. Host mitochondria influence gut microbiome diversity: A role for ROS. Sci. Signal. 12, eaaw3159 (2019).
Jose, S., Bhalla, P. & Suraishkumar, G. K. Oxidative stress decreases the redox ratio and folate content in the gut microbe, Enterococcus durans (MTCC 3031). Sci. Rep. 8, 12138 (2018).
Hagan, T. et al. Antibiotics-driven gut microbiome perturbation alters immunity to vaccines in humans. Cell 178, 1313–1328.e13 (2019).
Million, M. & Raoult, D. Linking gut redox to human microbiome. Hum. Microbiome J. 10, 27–32 (2018).
Rivera-Chávez, F. & Bäumler, A. J. The pyromaniac inside you: Salmonella metabolism in the host gut. Annu. Rev. Microbiol. 69, 31–48 (2015).
Kalantar-Zadeh, K. et al. A human pilot trial of ingestible electronic capsules capable of sensing different gases in the gut. Nat. Electron. 1, 79–87 (2018).
Steiger, C. et al. Dynamic monitoring of systemic biomarkers with gastric sensors. Adv. Sci. 8, 2102861 (2021).
Archer, E. J., Robinson, A. B. & Süel, G. M. Engineered E. coli that detect and respond to gut inflammation through nitric oxide sensing. ACS Synth. Biol. 1, 451–457 (2012).
Rubens, J. R., Selvaggio, G. & Lu, T. K. Synthetic mixed-signal computation in living cells. Nat. Commun. 7, 11658 (2016).
Daeffler, K. N. et al. Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation. Mol. Syst. Biol. 13, 923 (2017).
Annese, V. et al. European evidence-based consensus: inflammatory bowel disease and malignancies. J. Crohns. Colitis 9, 945–965 (2015).
Amir, A. et al. Room-temperature, correcting for microbial blooms in fecal samples during shipping. mSystems 2, e00199–16 (2017).
Raymond, F. et al. Culture-enriched human gut microbiomes reveal core and accessory resistance genes. Microbiome 7, 56 (2019).
Zmora, N. et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell 174, 1388–1405.e21 (2018).
Jain, U. et al. Debaryomyces is enriched in Crohn’s disease intestinal tissue and impairs healing in mice. Science 371, 1154–1159 (2021).
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).
Kotula, J. W. et al. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc. Natl Acad. Sci. USA 111, 4838–4843 (2014).
Lim, B., Zimmermann, M., Barry, N. A. & Goodman, A. L. Engineered regulatory systems modulate gene expression of human commensals in the gut. Cell 169, 547–558.e15 (2017).
Mimee, M., Tucker, A. C., Voigt, C. A. & Lu, T. K. Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota. Cell Syst. 1, 62–71 (2015).
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).
Pickard, J. M. et al. Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness. Nature 514, 638–641 (2014).
Swain, P. Wireless capsule endoscopy. Gut 52 (suppl. 4), 48–50 (2003).
van der Schaar, P. J. et al. A novel ingestible electronic drug delivery and monitoring device. Gastrointest. Endosc. 78, 520–528 (2013).
Din, M. O. et al. Interfacing gene circuits with microelectronics through engineered population dynamics. Sci. Adv. 6, eaaz8344 (2020).
Mimee, M. et al. An ingestible bacterial-electronic system to monitor gastrointestinal health. Science 360, 915–918 (2018).
Bass, D. M., Prevo, M. & Waxman, D. S. Gastrointestinal safety of an extended-release, nondeformable, oral dosage form (OROS). Drug Saf. 25, 1021–1033 (2002).
Isabella, V. M. et al. Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria. Nat. Biotechnol. 36, 857–864 (2018).
Bush, M., Ghosh, T., Tucker, N., Zhang, X. & Dixon, R. Transcriptional regulation by the dedicated nitric oxide sensor, NorR: a route towards NO detoxification. Biochem. Soc. Trans. 39, 289–293 (2011).
Chen, X. J., Wang, B., Thompson, I. P. & Huang, W. E. Rational design and characterization of nitric oxide biosensors in E. coli Nissle 1917 and mini SimCells. ACS Synth. Biol. 10, 2566–2578 (2021).
Ceze, L., Nivala, J. & Strauss, K. Molecular digital data storage using DNA. Nat. Rev. Genet. 20, 456–466 (2019).
Beck, P. L. et al. Paradoxical roles of different nitric oxide synthase isoforms in colonic injury. Am. J. Physiol. 286, 137–147 (2004).
Jiminez, J. A., Uwiera, T. C., Douglas Inglis, G. & Uwiera, R. R. E. Animal models to study acute and chronic intestinal inflammation in mammals. Gut Pathog. 7, 29 (2015).
Strand-Amundsen, R. J. et al. Ischemia/reperfusion injury in porcine intestine—viability assessment. World J. Gastroenterol. 24, 2009–2023 (2018).
Lundberg, J. O. N., Lundberg, J. M., Alving, K. & Hellström, P. M. Greatly increased luminal nitric oxide in ulcerative colitis. Lancet 344, 1673–1674 (1994).
Liu, X. et al. Magnetic living hydrogels for intestinal localization, retention, and diagnosis. Adv. Funct. Mater. 31, 2010918 (2021).
Song, M. et al. In 2020 IEEE International Solid- State Circuits Conference 474–476 https://doi.org/10.1109/ISSCC19947.2020.9063083 (IEEE, 2020).
Krawczyk, K. et al. Electrogenetic cellular insulin release for real-time glycemic control in type 1 diabetic mice. Science. 368, 993–1001 (2020).
Zhao, H. et al. Autonomous push button-controlled rapid insulin release from a piezoelectrically activated subcutaneous cell implant. Sci. Adv. 8, 24 (2022).
Harimoto, T. et al. A programmable encapsulation system improves delivery of therapeutic bacteria in mice. Nat. Biotechnol. 40, 1259–1269 (2022).
Li, Z. et al. Biofilm-inspired encapsulation of probiotics for the treatment of complex infections. Adv. Mater. 30, e1803925 (2018).
Chen, W. et al. Bacteria-driven hypoxia targeting for combined biotherapy and photothermal therapy. ACS Nano 12, 5995–6005 (2018).
Cao, Z., Wang, X., Pang, Y., Cheng, S. & Liu, J. Biointerfacial self-assembly generates lipid membrane coated bacteria for enhanced oral delivery and treatment. Nat. Commun. 10, 5783 (2019).
Hu, Q. et al. Engineering nanoparticle-coated bacteria as oral DNA vaccines for cancer immunotherapy. Nano Lett. 15, 2732–2739 (2015).
Vujkovic-cvijin, I. et al. Host variables confound gut microbiota studies of human disease. Nature 587, 448–454 (2020).
Chiu, C. Y. & Miller, S. A. Clinical metagenomics. Nat. Rev. Genet. 20, 341–355 (2019).
Steiger, C. et al. Ingestible electronics for diagnostics and therapy. Nat. Rev. Mater. 4, 83–98 (2019).
Ma, Y., Selby, N. & Adib, F. Minding the billions: ultra-wideband localization for deployed RFID tags. In Proc. MobiCom ’17 https://doi.org/10.1145/3117811.3117833 (Association for Computing Machinery, 2017).
Siuti, P., Yazbek, J. & Lu, T. K. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31, 448–452 (2013).
Lloyd-Price, J., Abu-Ali, G. & Huttenhower, C. The healthy human microbiome. Genome Med. 8, 51 (2016).
Inda, M. E., Mimee, M. & Lu, T. K. Cell-based biosensors for immunology, inflammation, and allergy. J. Allerg. Clin. Immunol. 144, 645–647 (2019).
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
Reinders, C. I. et al. Rectal mucosal nitric oxide in differentiation of inflammatory bowel disease and irritable bowel syndrome. Clin. Gastroenterol. Hepatol. 3, 777–783 (2005).
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