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Data and references

Explore our research references and the availability of underlying data.

Data availability

Our figures are presented in Engineering.docx and Manuscript.pdf. Our public data record does not yet include replicate-level spreadsheets, instrument exports, complete plasmid sequence files, sequencing chromatograms, image-analysis files, or dated notebook records. Those materials are needed to independently reproduce our summary values and resolve the discrepancies listed on the Methods and Results pages.

We retain the original experimental figures and explain each assay and its interpretation in the accompanying captions. Website preparation did not generate additional experimental observations.

Source files

  • Engineering summary and figures: LZU-CHINA research documentation.
  • Manuscript and figures: LZU-CHINA research documentation.
  • Related project context: LZU-CHINA project documentation.

Research references

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  2. Stecher B, Robbiani R, Walker AW, et al. Salmonella enterica serovar Typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biology. 2007;5:e244.
  3. Bäumler AJ, Sperandio V. Interactions between the microbiota and pathogenic bacteria in the gut. Nature. 2016;535:85–93.
  4. Buffie CG, Pamer EG. Microbiota-mediated colonization resistance against intestinal pathogens. Nature Reviews Immunology. 2013;13:790–801.
  5. Alverdy JC, Chang EB. The re-emerging role of the intestinal microflora in surgical infections and gut-derived sepsis. Surgical Clinics of North America. 2005;85:65–84.
  6. Courbet A, Endy D, Renard E, et al. Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates. Science Translational Medicine. 2015;7:289ra83.
  7. Riglar DT, Giessen TW, Baym M, et al. Engineered bacteria can function in the mammalian gut long term as live diagnostics of inflammation. Science. 2017;356:970–975.
  8. Sassone-Corsi M, Nuccio SP, Liu H, et al. Microcins mediate competition among Enterobacteriaceae in the inflamed gut. Nature. 2016;540:280–283.
  9. Ozdemir T, Fedorec AJ, Danino T, et al. Synthetic biology and engineered live biotherapeutics: towards targeted treatment and diagnostics. Cell Host & Microbe. 2018;24:180–192.
  10. Sonnenborn U. Escherichia coli strain Nissle 1917—from bench to bedside and back: history of a special probiotic. Microbial Ecology in Health and Disease. 2016;27:30372.
  11. Hwang IY, Koh E, Wong A, et al. Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa infection in animal models. Nature Communications. 2017;8:15028.
  12. Xavier KB, Bassler BL. Interference with AI-2-mediated bacterial cell-cell communication. Nature. 2005;437:750–753.
  13. Roy V, Fernandes R, Tsao CY, et al. Cross species quorum sensing and the lsr operon of Escherichia coli. ACS Chemical Biology. 2010;5:223–232.
  14. Hensel M, Hinsley AP, Nikolaus T, et al. The genetic basis of tetrathionate respiration in Salmonella typhimurium. Molecular Microbiology. 1999;32:275–287.
  15. Daeffler KNM, Galley JD, Sheth RU, et al. Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation. Molecular Systems Biology. 2017;13:923.
  16. Shis DL, Bennett MR. Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants. PNAS. 2013;110:5028–5033.
  17. Han TC, Bennett MR. Synthetic split intein T7 RNA polymerase for transcriptional AND-logic. Nucleic Acids Research. 2014;42:12322–12329.
  18. Forkus B, Ritter S, Vlysidis M, et al. Antimicrobial probiotics reduce Salmonella enterica in poultry. Scientific Reports. 2017;7:2415.
  19. Gerdes K, Poulsen LK, Thisted T, et al. The Hok/Sok killer system from plasmid R1. Molecular Microbiology. 1990;4:1807–1818.
  20. Stirling F, Bitzan L, O’Keefe S, et al. Rational design of spendable microbial containment switches based on toxin-antitoxin modules. Molecular Cell. 2017;68:186–197.
  21. Rivera-Chávez F, Zhang LF, Faber F, et al. Depletion of butyrate-producing Clostridia from the gut microbiota drives an aerobic luminal expansion of Salmonella. Cell Host & Microbe. 2016;19:443–454.
  22. Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nature Biotechnology. 2009;27:946–950.
  23. Chan CTY, Lee JW, Cameron DE, et al. ‘Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment. Nature Chemical Biology. 2016;12:82–86.
  24. Rottinghaus AG, Ferreiro A, Fishbein SRS, et al. Genetically stable CRISPR-based kill switches for engineered microbes. Nature Communications. 2022;13:672.
  25. Steenackers H, Hermans K, Vanderleyden J, et al. Salmonella biofilms: an overview on occurrence, structure, regulation and eradication. Food Research International. 2012;45:502–531.
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  27. Danino T, Prindle A, Kwong GA, et al. Programmable probiotics for detection of cancer in urine. Science Translational Medicine. 2015;7:289ra84.
  28. Charbonneau MR, Isabella VM, Li N, et al. Developing a new class of engineered live biotherapeutics for human disease. Journal of Molecular Biology. 2020;432:4335–4354.
  29. Geller LT, Barzily-Rokni M, Danino T, et al. Potential of engineered bacteria in disease diagnostics and therapeutics. Trends in Biotechnology. 2020;38:1239–1250.
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  31. Chen Y, Wu H, Shen Z, et al. Engineering synthetic microbial systems for biomedical applications. Nature Reviews Bioengineering. 2023;1:258–275.

Bibliographic verification against the original publications remains pending.