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Synthetic extremophiles via species-specific formulations improve microbial therapeutics

Nature Materials volume 23, pages 1436–1443 (2024)Cite this article

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Abstract

Microorganisms typically used to produce food and pharmaceuticals are now being explored as medicines and agricultural supplements. However, maintaining high viability from manufacturing until use remains an important challenge, requiring sophisticated cold chains and packaging. Here we report synthetic extremophiles of industrially relevant gram-negative bacteria (Escherichia coli Nissle 1917, Ensifer meliloti), gram-positive bacteria (Lactobacillus plantarum) and yeast (Saccharomyces boulardii). We develop a high-throughput pipeline to define species-specific materials that enable survival through drying, elevated temperatures, organic solvents and ionizing radiation. Using this pipeline, we enhance the stability of E. coli Nissle 1917 by more than four orders of magnitude over commercial formulations and demonstrate its capacity to remain viable while undergoing tableting and pharmaceutical processing. We further show, in live animals and plants, that synthetic extremophiles remain functional against enteric pathogens and as nitrogen-fixing plant supplements even after exposure to elevated temperatures. This synthetic, material-based stabilization enhances our capacity to apply microorganisms in extreme environments on Earth and potentially during exploratory space travel.

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Fig. 1: Survey of commercially available dry formulations of microbial probiotics.
Fig. 2: Development and validation of high-throughput pipeline for dry stabilized microbial materials.
Fig. 3: Application of pipeline to make E. coli Nissle 1917 into a synthetic extremophile.
Fig. 4: Synthetic extremophiles withstand harsh processing manufacturing processes.
Fig. 5: Synthetic extremophiles remain effective microbial therapeutics despite extreme temperature and radiation exposure.

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Data availability

Data generated or analysed during this study are included in the Supplementary Information. Further data are available from the corresponding author upon request. Source data are provided with this paper.

Code availability

The customized code used for liquid handling and image analysis is available from the corresponding author upon request.

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Acknowledgements

We thank R. Langer for providing guidance, feedback and experimental facilities; B. Fields and C. Voigt for the enteric pathogen cultures; M. Ericsson at the HMS Electron Microscopy Core for the transmission electron microscopy characterization; and A. Hupalowska for creating the illustration in Fig. 4a. Illustrations in Figs. 2a and 5a,b,e and Supplementary Figs. 15 and 16 were created partially with BioRender.com. This work was supported in part by the Translational Research Institute for Space Health through Cooperative Agreement NNX16AO69A through grants awarded to G.T. and M.J.; G.T. was supported in part by the Department of Mechanical Engineering, Massachusetts Institute of Technology (MIT) and the Karl van Tassel (1925) Career Development Professorship, MIT. Part of this material is based on research sponsored by 711 Human Performance Wing (HPW) and Defense Advanced Research Projects Agency (DARPA) under agreement number FA8650-21-2-7120 awarded to G.T. The US Government is authorized to reproduce and distribute reprints for governmental purposes notwithstanding any copyright notation thereon. The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of 711 Human Performance Wing (HPW) and Defense Advanced Research Projects Agency (DARPA) or the US Government.

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Authors and Affiliations

  1. Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Miguel Jimenez, Emily Kolaya, Husna Ellis, Alfred Dao, Niora Fabian, Joshua Jenkins, Christina Karavasili & Giovanni Traverso

  2. Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Miguel Jimenez, Johanna L’Heureux, Gary W. Liu & Zachary Villaverde

  3. David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA

    Miguel Jimenez, Johanna L’Heureux, Gary W. Liu, Zachary Villaverde, Niora Fabian, Nina Fitzgerald, Christina Karavasili, James D. Byrne & Giovanni Traverso

  4. Division of Gastroenterology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

    Miguel Jimenez, Kyle B. Martin, Christina Karavasili, Benjamin Muller, James D. Byrne & Giovanni Traverso

  5. Department of Biomedical Engineering, Boston University, Boston, MA, USA

    Miguel Jimenez

  6. Department of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, MA, USA

    Margaret Yang & Qinhao Cao

  7. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Afeefah Khazi-Syed

  8. Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA

    Niora Fabian

  9. Department of Biomedical Engineering, University of Iowa, Iowa City, IA, USA

    James D. Byrne

  10. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Giovanni Traverso

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Contributions

M.J. and G.T. conceived and designed the research; M.J. designed the high-throughput pipelines; J.L., Z.V., A.K.-S. and Q.C. established the calibration curves for microbial quantification; M.J. and J.L. designed and performed the commercial probiotics survey; M.J. and J.L. performed the initial material stabilizer evaluations and validations; M.J. and E.K. performed the material stabilizer optimization and validations; M.J. and E.K. designed and performed the synthetic extremophile pharmaceutical manufacturing and viability evaluation; M.J. and J.D.B. designed and performed the ionizing radiation experiment; M.J., J.L. and K.B.M. designed, performed and optimized the plant nodulation assay; G.W.L., H.E. and A.D. designed and performed the in vitro pathogen assays; M.J., G.W.L. and N. Fabian designed the in vivo intestinal pathogen model; M.J., G.W.L., N. Fabian, J.J., N. Fitzgerald and A.D. performed the in vivo pathogen assay; M.Y. performed the blinded quantification of pathogen load; C.K. performed the compendial and non-compendial tests on the bacterial tablets; B.M. performed scanning electron microscopy of the microbial materials; M.J., J.L. and E.K. performed formal analysis of the data; M.J. and G.T. wrote the manuscript; M.J., J.L., E.K. and G.T. edited the manuscript; M.J. and G.T. supervised and managed project progress and personnel; and M.J. and G.T. supervised and managed funding of the project.

Corresponding author

Correspondence to Giovanni Traverso.

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Competing interests

M.J., G.T., J.L. and E.K. are co-inventors on patent application 18/477,970 (filed 29 September 2023 by MIT), which describes the microbial-stabilizing materials and processes reported here. M.J. and G.T. consult for VitaKey. The other authors declare no competing interests.

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Jimenez, M., L’Heureux, J., Kolaya, E. et al. Synthetic extremophiles via species-specific formulations improve microbial therapeutics. Nat. Mater. 23, 1436–1443 (2024). https://doi.org/10.1038/s41563-024-01937-6

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