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Engineering bacteria for diagnostic and therapeutic applications


Our ability to generate bacterial strains with unique and increasingly complex functions has rapidly expanded in recent times. The capacity for DNA synthesis is increasing and costing less; new tools are being developed for fast, large-scale genetic manipulation; and more tested genetic parts are available for use, as is the knowledge of how to use them effectively. These advances promise to unlock an exciting array of 'smart' bacteria for clinical use but will also challenge scientists to better optimize preclinical testing regimes for early identification and validation of promising strains and strategies. Here, we review recent advances in the development and testing of engineered bacterial diagnostics and therapeutics. We highlight new technologies that will assist the development of more complex, robust and reliable engineered bacteria for future clinical applications, and we discuss approaches to more efficiently evaluate engineered strains throughout their preclinical development.

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Figure 1: Examples of strategies for bacterial therapeutic delivery.
Figure 2: Examples of recently developed synthetic circuits.
Figure 3: Bacterial sensing through one-component and two-component systems.
Figure 4: Control, biosafety and biocontainment strategies for therapeutic bacteria.


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The authors thank A. Naydich for critical review of the manuscript. D.T.R. is supported by a Human Frontier Science Program Long-Term Fellowship and a National Health and Medical Research Council (NHMRC) RG Menzies Early Career Fellowship from the Menzies Foundation through the Australian NHMRC.

Author information




D.T.R. researched data for the article and wrote the article. D.T.R. and P.A.S. substantially contributed to the discussion of content and reviewed and edited the manuscript before submission.

Corresponding author

Correspondence to Pamela A. Silver.

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The authors declare no competing financial interests.

Supplementary information

Supplementary information S1 (table)

Completed, Active and Proposed clinical trials involving engineered live bacteria as therapeutics. (DOCX 30 kb)

Supplementary information S2 (table)

Examples of pre-clinical studies testing therapeutic engineered bacteria in animal disease models. (DOCX 27 kb)

PowerPoint slides



An inactive form of a drug that requires activation, often by enzymatic cleavage, before adopting its therapeutic form.

Toll-like receptor

(TLR). A class of membrane receptors used by the innate immune system to recognize microbial molecules.


The spread of cancer cells from the original tumour to secondary sites around the body.


Inflammation of the colon.

Trefoil factors

(TFFs). A family of peptides that are expressed at mucous membranes, including the gastrointestinal mucosa, and may have a protective role.


Enzymes that catalyse the excision, insertion, inversion or translocation of DNA between sites of specific DNA sequence.

Memory circuit

A genetic circuit that is designed to encode an extended response, or memory, following a transient cellular event.


The combined resources required by a cell to operate a given synthetic genetic pathway.

Quorum sensing

A common mechanism by which bacteria naturally sense the local population density of their own or other bacterial species to enable density- dependent cellular responses. Bacteria produce and sense a specific quorum sensing molecule. Constant secretion ensures that concentrations only reach threshold levels and change downstream transcriptional profiles when many bacteria are present in the population.

Kill switches

Circuits used as safety mechanisms to prevent incorrect activity of an engineered bacterial strain, usually by attempting to kill it or to prevent engineered functions.


Live microorganisms that are beneficial to health.

Genetic firewalls

Changes to the underlying genetic code of an organism in an attempt to prevent the possibility of effective genetic exchange between the engineered strain and other bacteria in the environment.

Log reduction

Measure of reduced bacterial growth based on the logarithm (base 10). Every additional log reduction therefore corresponds to tenfold lower growth or survival.

Logic gates

Circuits that use Boolean logic to activate an output only when a given combination of inputs is present.

State machines

Devices able to exist in one ofseveral unique states depending on the history of its inputs.

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Riglar, D., Silver, P. Engineering bacteria for diagnostic and therapeutic applications. Nat Rev Microbiol 16, 214–225 (2018).

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