Microbiome Engineering
Industrial Biotechnology Challenge:

Streamline industrial process development.

Enable more robust biomanufacturing processes.

Engineer microbiomes to enable production in non-conventional industrial conditions.

  • Technical Achievement: Engineer microbiomes that enable production at ambient or near-ambient temperatures and pressures.
  • Technical Achievement: Engineer microbiomes that maintain their function at low or high pH.
  • Technical Achievement: Engineer microbiomes that continue functioning in high salt concentrations to reduce the need for dilution or desalination in industrial processes.

Engineer microbiomes to reduce the need for aeration industrial processes.

  • Technical Achievement: Design collections of gas-generating or gas-consuming microbes that grow/die in response to gas concentrations.
  • Technical Achievement: Engineer ‘universal buffer’ strains that can prevent the buildup of toxic chemicals (e.g., waste products, pH changes) in growth media.

Increase biomanufacturing process flexibility and adaptability, to shorten process development timeline for novel products and proof-of-concept translation into industrial workflows.

Develop “modular” microbiomes that specialize in classes of metabolic functions for “plug and play” pathway engineering, so each species or strain is optimized for one step of the process.

  • Technical Achievement: Create computational models that optimize microbiome composition based on the guilds needed for a given application.
  • Technical Achievement: Produce libraries of strains with unique, but well-catalogued metabolic requirements and enzyme reaction capabilities, so communities can be developed based on available nutrients.

Enable parallel processing (i.e., production of multiple outputs simultaneously) within a single microbiome (see also: Distributed Metabolism).

  • Technical Achievement: Design microbiomes to synthesize products that are easily separated to high purity using simple industrial processes (e.g., phase separations, column separation).
  • Technical Achievement: Engineer microbiomes with distributed metabolic pathways to prevent accumulation of toxic intermediates and lost production capacity.

Design methods to analyze and improve performance of industrial microbiomes over time.

  • Technical Achievement: Couple product synthesis to an easily detectable readout (e.g., fluorescence, luminescence, colored dye) so production can be monitored continuously or near-continuously.
  • Technical Achievement: Identify and add or remove microbes that are present in industrial fermentations at a background level to improve or modulate performance.


  1. Roberts, A. D., Finnigan, W., Wolde-Michael, E., Kelly, P., Blaker, J. J., Hay, S., Breitling, R., Takano, E., & Scrutton, N. S. (2019). Synthetic biology for fibers, adhesives, and active camouflage materials in protection and aerospace. MRS Communications, 9(02), 486–504. https://doi.org/10.1557/mrc.2019.35
  2. Jones, S. W., Fast, A. G., Carlson, E. D., Wiedel, C. A., Au, J., Antoniewicz, M. R., Papoutsakis, E. T., & Tracy, B. P. (2016). CO2 fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion. Nature Communications, 7(1), 12800. https://doi.org/10.1038/ncomms12800
Last updated: October 1, 2020 Back