Microbiome Engineering
Distributed Metabolism Goal:

Engineer microbiomes to transform recalcitrant materials into useful products.

Current State-of-the-Art

Both natural (e.g., lignin, cellulose, lignocellulose) and non-natural (e.g., plastics, other polymers) recalcitrant materials are difficult to degrade into usable precursor molecules for other chemical processes.1Ragauskas, A. J., & Yoo, C. G. (Eds.). (2019). Advancements in Biomass Recalcitrance: The Use of Lignin for the Production of Fuels and Chemicals. Frontiers Media SA. View Publication Microorganisms have been engineered to degrade several non-natural compounds in the laboratory but they tend to be non-model organisms with underdeveloped tool-sets to facilitate their engineering to use produced precursors for biosynthesis.2Henske, J. K., Wilken, St. E., Solomon, K. V., Smallwood, C. R., Shutthanandan, V., Evans, J. E., Theodorou, M. K., & O’Malley, M. A. (2018). Metabolic characterization of anaerobic fungi provides a path forward for bioprocessing of crude lignocellulose. Biotechnology and Bioengineering, 115(4), 874–884. View Publication,3Minty, J. J., Singer, M. E., Scholz, S. A., Bae, C.-H., Ahn, J.-H., Foster, C. E., Liao, J. C., & Lin, X. N. (2013). Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proceedings of the National Academy of Sciences, 110(36), 14592–14597. View Publication We currently have poor control over the degradation products that are produced, which can make biosynthesis with the liberated precursors suboptimal. There are many natural organisms that have been shown to degrade non-natural compounds when exposed to them over time, including chlorinated alkenes and polychlorinated biphenyls.4Bedard, D. L. (2008). A Case Study for Microbial Biodegradation: Anaerobic Bacterial Reductive Dechlorination of Polychlorinated Biphenyls—From Sediment to Defined Medium. Annual Review of Microbiology, 62(1), 253–270. View Publication Finally, much of the work on engineering the breakdown of non-natural products has been performed using single microorganisms, not in microbiomes.

Breakthrough Capabilities & Milestones

Engineer communities metabolically tailored to capture and degrade recalcitrant materials.

Engineer parallel degradation of inputs using normally incompatible chemistries (e.g., combine anaerobic and aerobic processes).

Engineer microbiomes that specialize in nutrient recapture and recycling to minimize inputs and create self sufficient environments.

Footnotes

  1. Ragauskas, A. J., & Yoo, C. G. (Eds.). (2019). Advancements in Biomass Recalcitrance: The Use of Lignin for the Production of Fuels and Chemicals. Frontiers Media SA. https://doi.org/10.3389/978-2-88945-706-9
  2. Henske, J. K., Wilken, St. E., Solomon, K. V., Smallwood, C. R., Shutthanandan, V., Evans, J. E., Theodorou, M. K., & O’Malley, M. A. (2018). Metabolic characterization of anaerobic fungi provides a path forward for bioprocessing of crude lignocellulose. Biotechnology and Bioengineering, 115(4), 874–884. https://doi.org/10.1002/bit.26515
  3. Minty, J. J., Singer, M. E., Scholz, S. A., Bae, C.-H., Ahn, J.-H., Foster, C. E., Liao, J. C., & Lin, X. N. (2013). Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proceedings of the National Academy of Sciences, 110(36), 14592–14597. https://doi.org/10.1073/pnas.1218447110
  4. Bedard, D. L. (2008). A Case Study for Microbial Biodegradation: Anaerobic Bacterial Reductive Dechlorination of Polychlorinated Biphenyls—From Sediment to Defined Medium. Annual Review of Microbiology, 62(1), 253–270. https://doi.org/10.1146/annurev.micro.62.081307.162733
Last updated: October 1, 2020 Back