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Hydrogel-based biocontainment of bacteria for continuous sensing and computation


Genetically modified microorganisms (GMMs) can enable a wide range of important applications including environmental sensing and responsive engineered living materials. However, containment of GMMs to prevent environmental escape and satisfy regulatory requirements is a bottleneck for real-world use. While current biochemical strategies restrict unwanted growth of GMMs in the environment, there is a need for deployable physical containment technologies to achieve redundant, multi-layered and robust containment. We developed a hydrogel-based encapsulation system that incorporates a biocompatible multilayer tough shell and an alginate-based core. This deployable physical containment strategy (DEPCOS) allows no detectable GMM escape, bacteria to be protected against environmental insults including antibiotics and low pH, controllable lifespan and easy retrieval of genomically recoded bacteria. To highlight the versatility of DEPCOS, we demonstrated that robustly encapsulated cells can execute useful functions, including performing cell–cell communication with other encapsulated bacteria and sensing heavy metals in water samples from the Charles River.

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Fig. 1: Schematic of the DEPCOS platform.
Fig. 2: Cell encapsulation in tough hydrogel capsules.
Fig. 3: Tough hydrogel shell provides robust biocontainment.
Fig. 4: Combining chemical and physical containment strategies for optimal biocontainment and protection.
Fig. 5: Sensing, recording and communication capabilities of encapsulated bacterial cells.

Data availability

Data supporting this study are presented in the main text and Supplementary Information, and are available from the corresponding authors upon request. Source data are provided with this paper.


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We thank F. Farzadfard for proving the SCRIBE strains and M. Mimee for providing the heme sensing strain. We thank S. Lin, N. Roquet, R. Citorik and S. Lemire for useful discussions. T.K.L. is grateful for funding received from the National Institutes of Health (NIH) New Innovator Award (no. 1DP2OD008435), NIH National Centers for Systems Biology (no. 1P50GM098792), the US Office of Naval Research (no. N00014-13-1-0424) and the Defense Advanced Research Projects Agency (no. HR0011-15-C-0091). X.Z. is grateful for funding received from the NIH (no. 1R01HL153857-01), the National Science Foundation (no. EFMA-1935291) and the US Army Research Office through the Institute for Soldier Nanotechnologies at MIT (no. W911NF-13-D-0001). C.F.-N. holds a Presidential Professorship at the University of Pennsylvania, is a recipient of the Langer Prize by the AIChE Foundation and acknowledges funding from the Institute for Diabetes, Obesity, and Metabolism, the Penn Mental Health AIDS Research Center of the University of Pennsylvania, the National Institute of General Medical Sciences of the NIH (no. R35GM138201), and the Defense Threat Reduction Agency (no. HDTRA11810041 and HDTRA1-21-1-0014). T.-C.T. gratefully acknowledge the support from The Abdul Latif Jameel Water and Food Systems Laboratory (J-WAFS) Graduate Student Fellowship.

Author information

Authors and Affiliations



T.-C.T., E.T., X.L., X.Z. and T.K.L. conceived and designed the research. T.-C.T., E.T., X.L. and H.Y. performed encapsulation and mechanical testing experiments. T.-C.T. and E.T. performed genetic circuit experiments. T.-C.T., E.T. and A.J.R. performed GRO experiments. T.-C.T. and E.T. performed river water experiments. T.-C.T., E.T., X.L., K.Y., A.J.R., C.F.-N., F.J.I., X.Z. and T.K.L. analyzed the data and wrote the manuscript.

Corresponding authors

Correspondence to Tzu-Chieh Tang, Xuanhe Zhao or Timothy K. Lu.

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Competing interests

T.-C.T., E.T., X.L., H.Y., X.Z. and T.K.L. have filed a patent application based on the hydrogel encapsulation technologies with the US Patent and Trademark Office. T.K.L. is a cofounder of Senti Biosciences, Synlogic, Engine Biosciences, Tango Therapeutics, Corvium, BiomX, Eligo Biosciences, Bota.Bio, Avendesora and NE47Bio. T.K.L. also holds financial interests in, Armata, IndieBio, MedicusTek, Quark Biosciences, Personal Genomics, Thryve, Lexent Bio, MitoLab, Vulcan, Serotiny, Avendesora and Pulmobiotics.

Additional information

Peer review information Nature Chemical Biology thanks Keekyoung Kim, Minglin Ma and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Responses of encapsulated bacterial cells to external stimuli.

(a) Left: Schematic of GFP expression under the control of an aTc-inducible promoter. Center: Flow cytometry analysis of GFP expression in liquid culture and in hydrogel beads. Samples prepared in triplicate, data represent the mean ±1 s.d. based on analyses of 30000 events. The percentage data were calculated by dividing the numbers of GFP ON cells with the total cell counts. The fold-change data were derived from the mean of fluorescence. Right: Confocal microscopy images of beads encapsulating the aTc-sensing E. coli strain with and without 200 ng/mL aTc. (b) Left: A heme sensing strain which sense heme and generate bioluminescence as an output. The heme released from blood is transported into the cell by ChuA. Middle: Cells retrieved from beads showed a significant increase in luciferase activity. Right: The resulting bioluminescence can be detected with high sensitivity from intact beads. Samples prepared in triplicate, data represent the mean ±1 s.d.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–18 and Tables 1 and 2.

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Source Data Fig. 3

Statistical source data and loading curves.

Source Data Fig. 4

Statistical source data.

Source Data Fig. 5

Statistical source data.

Source Data Extended Data Fig. 1

Statistical source data.

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Tang, TC., Tham, E., Liu, X. et al. Hydrogel-based biocontainment of bacteria for continuous sensing and computation. Nat Chem Biol 17, 724–731 (2021).

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