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Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation

Nature Biotechnology volume 35, pages 653658 (2017) | Download Citation


Bacteria can be engineered to function as diagnostics or therapeutics in the mammalian gut but commercial translation of technologies to accomplish this has been hindered by the susceptibility of synthetic genetic circuits to mutation and unpredictable function during extended gut colonization. Here, we report stable, engineered bacterial strains that maintain their function for 6 months in the mouse gut. We engineered a commensal murine Escherichia coli strain to detect tetrathionate, which is produced during inflammation. Using our engineered diagnostic strain, which retains memory of exposure in the gut for analysis by fecal testing, we detected tetrathionate in both infection-induced and genetic mouse models of inflammation over 6 months. The synthetic genetic circuits in the engineered strain were genetically stable and functioned as intended over time. The durable performance of these strains confirms the potential of engineered bacteria as living diagnostics.

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We thank A. Graveline and L. Bry for discussions and assistance with mouse experiments and A. Verdegaal for experimental assistance. S. typhimurium TT22470 was a gift from J. Roth. We thank Dana-Farber/Harvard Cancer Center in Boston for the use of the Rodent Histopathology Core, which provided histology preparation service. Dana-Farber/Harvard Cancer Center is supported in part by a NCI Cancer Center Support Grant # NIH 5 P30 CA06516. D.T.R. was supported by a Human Frontier Science Program Long-Term Fellowship and an NHMRC/RG Menzies Early Career Fellowship from the Menzies Foundation through the Australian National Health and Medical Research Council. T.W.G. was supported by a Leopoldina Research Fellowship (LPDS 2014-05) from the German National Academy of Sciences Leopoldina. The research was funded by Defense Advanced Research Projects Agency Grant HR0011-15-C-0094 (P.A.S.) and the Wyss Institute for Biologically Inspired Engineering.

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Author notes

    • S Jordan Kerns
    •  & Jonathan W Kotula

    Present addresses: Emulate Inc., Boston, Massachusetts, USA (S.J.K.) and SynLogic, Cambridge, Massachusetts, USA (J.W.K.).


  1. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.

    • David T Riglar
    • , Tobias W Giessen
    • , Michael Baym
    • , S Jordan Kerns
    • , Matthew J Niederhuber
    • , Jonathan W Kotula
    •  & Pamela A Silver
  2. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA.

    • David T Riglar
    • , Tobias W Giessen
    • , S Jordan Kerns
    • , Matthew J Niederhuber
    • , Jonathan W Kotula
    • , Jeffrey C Way
    •  & Pamela A Silver
  3. Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.

    • Michael Baym
  4. Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA.

    • Roderick T Bronson
  5. Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.

    • Georg K Gerber


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D.T.R., T.W.G., M.B., S.J.K., G.K.G., J.C.W. and P.A.S. designed experiments. D.T.R. and M.J.N. performed and analyzed in vitro characterization. D.T.R. performed and analyzed all mouse experiments. T.W.G. performed and analyzed tetrathionate mass spectrometry. M.B. performed and analyzed whole genome sequencing. S.J.K. and J.W.K. generated strains and collected preliminary data for the study. R.T.B. performed all histology scoring. D.T.R. and P.A.S. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Pamela A Silver.

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