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Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts

Nature volume 553, pages 8690 (04 January 2018) | Download Citation


The mammalian microbiome has many important roles in health and disease1,2, and genetic engineering is enabling the development of microbial therapeutics and diagnostics3,4,5,6,7. A key determinant of the activity of both natural and engineered microorganisms in vivo is their location within the host organism8,9. However, existing methods for imaging cellular location and function, primarily based on optical reporter genes, have limited deep tissue performance owing to light scattering or require radioactive tracers10,11,12. Here we introduce acoustic reporter genes, which are genetic constructs that allow bacterial gene expression to be visualized in vivo using ultrasound, a widely available inexpensive technique with deep tissue penetration and high spatial resolution13,14,15. These constructs are based on gas vesicles, a unique class of gas-filled protein nanostructures that are expressed primarily in water-dwelling photosynthetic organisms as a means to regulate buoyancy16,17. Heterologous expression of engineered gene clusters encoding gas vesicles allows Escherichia coli and Salmonella typhimurium to be imaged noninvasively at volumetric densities below 0.01% with a resolution of less than 100 μm. We demonstrate the imaging of engineered cells in vivo in proof-of-concept models of gastrointestinal and tumour localization, and develop acoustically distinct reporters that enable multiplexed imaging of cellular populations. This technology equips microbial cells with a means to be visualized deep inside mammalian hosts, facilitating the study of the mammalian microbiome and the development of diagnostic and therapeutic cellular agents.

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We thank F. S. Foster, D. Maresca, A. Mukherjee, M. Din, T. Danino, J. Willmann and S. K. Mazmanian for discussions, and A. McDowall for assistance with electron microscopy. This research was supported by the National Institutes of Health grant R01-EB018975, the Canadian Institute of Health Research grant MOP 136842 and the Pew Scholarship in the Biomedical Sciences. A.L. is supported by the NSF graduate research fellowship (award 1144469) and the Biotechnology Leaders Program. A.F. is supported by the NSERC graduate fellowship. S.P.N. was supported by the Caltech Summer Undergraduate Research Fellowship. Research in the Shapiro laboratory is also supported by the Heritage Medical Research Institute, the Burroughs Wellcome Career Award at the Scientific Interface and the David and Lucile Packard Fellowship for Science and Engineering.

Author information


  1. Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA

    • Raymond W. Bourdeau
    • , Audrey Lee-Gosselin
    • , Suchita P. Nety
    •  & Mikhail G. Shapiro
  2. Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA

    • Anupama Lakshmanan
    • , Arash Farhadi
    •  & Sripriya Ravindra Kumar


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R.W.B. and M.G.S. conceived and designed the study. R.W.B., A.L., A.L.-G., A.F. and S.P.N. prepared genetic constructs in E. coli. R.W.B., A.L., A.L.-G., S.P.N. and A.F. conducted in vitro ultrasound experiments. A.L.-G. and R.W.B. performed in vivo ultrasound experiments. A.L., A.F. and A.L.-G. conducted metabolic burden experiments in Nissle 1917 cells. R.W.B. and S.R.K. prepared genetic constructs in S. typhimurium. R.W.B. and A.L. obtained TEM images. R.W.B., A.L.-G. and M.G.S. analysed ultrasound data. R.W.B. and M.G.S. wrote the manuscript with input from all authors. M.G.S. supervised the research.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Mikhail G. Shapiro.

Reviewer Information Nature thanks C. Caskey, O. Couture, P. Silver and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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    Supplementary Information

    This file contains Supplementary Notes 1–5, Plasmid Sequences for ARG1 and ARG2 constructs, Supplementary References and Supplementary Table 1.

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