Microbiome Engineering
Distributed Metabolism Goal:

Produce natural and non-natural compounds using multi-species microbiomes.

Current State-of-the-Art

Current efforts to use microbiomes for biosynthesis have focused on using consortia to improve production efficiency or to produce compounds that are difficult to synthesize using a single strain. Different strains or species have been co-cultured to optimize substrate utilization. Multiple species that are naturally well-suited to convert the molecule of interest can be co-cultured to identify optimal species compositions to achieve high titers. Mutualistic interactions can be engineered in synthetic multi-species consortia to increase fermentation efficiency.1Mee, M. T., Collins, J. J., Church, G. M., & Wang, H. H. (2014). Syntrophic exchange in synthetic microbial communities. Proceedings of the National Academy of Sciences, 111(20), E2149–E2156. View Publication,2Wang, E.-X., Ding, M.-Z., Ma, Q., Dong, X.-T., & Yuan, Y.-J. (2016). Reorganization of a synthetic microbial consortium for one-step vitamin C fermentation. Microbial Cell Factories, 15(1), 21. View Publication,3Wang, E.-X., Liu, Y., Ma, Q., Dong, X.-T., Ding, M.-Z., & Yuan, Y.-J. (2019). Synthetic cell–cell communication in a three-species consortium for one-step vitamin C fermentation. Biotechnology Letters, 41(8–9), 951–961. View Publication Co-cultures of different species can also be used to convert multiple substrates into the desired products through different metabolic routes. This strategy was used to demonstrate complete conversion of glucose and xylose to ethanol.4Fu, N., Peiris, P., Markham, J., & Bavor, J. (2009). A novel co-culture process with Zymomonas mobilis and Pichia stipitis for efficient ethanol production on glucose/xylose mixtures. Enzyme and Microbial Technology, 45(3), 210–217. View Publication Similarly, when multiple sugars are available for fermentation, mixtures of “specialist” strains that ferment only one of each type of sugar can outperform individual strains that ferment multiple sugars.5Eiteman, M. A., Lee, S. A., & Altman, E. (2008). A co-fermentation strategy to consume sugar mixtures effectively. Journal of Biological Engineering, 2(1), 3. View Publication Microbial co-cultures have been demonstrated to use carbon dioxide and synthesis gas (syngas) to produce alcohols and other metabolites, while single cultures would only be capable of producing acetate.6Haas, T., Krause, R., Weber, R., Demler, M., & Schmid, G. (2018). Technical photosynthesis involving CO2 electrolysis and fermentation. Nature Catalysis, 1(1), 32–39. View Publication,7Molitor, B., Mishra, A., & Angenent, L. T. (2019). Power-to-protein: Converting renewable electric power and carbon dioxide into single cell protein with a two-stage bioprocess. Energy & Environmental Science, 12(12), 3515–3521. View Publication,8Richter, H., Molitor, B., Diender, M., Sousa, D. Z., & Angenent, L. T. (2016). A Narrow pH Range Supports Butanol, Hexanol, and Octanol Production from Syngas in a Continuous Co-culture of Clostridium ljungdahlii and Clostridium kluyveri with In-Line Product Extraction. Frontiers in Microbiology, 7. View Publication

Another approach relies on consortia where biosynthetic reactions are distributed among naturally-occurring or engineered specialist organisms that are best-suited to perform select reactions within a metabolic pathway. Consortia have been engineered where engineered strains remove the metabolic byproducts generated by a primary producer strain.9Bernstein, H. C., Paulson, S. D., & Carlson, R. P. (2012). Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. Journal of Biotechnology, 157(1), 159–166. View Publication There are also several examples of production pathways split between different strains. Using this strategy, compounds previously too burdensome or toxic for using a single strain could be produced.10Bernstein, H. C., Paulson, S. D., & Carlson, R. P. (2012). Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. Journal of Biotechnology, 157(1), 159–166. View Publication,11Jones, J. A., Vernacchio, V. R., Collins, S. M., Shirke, A. N., Xiu, Y., Englaender, J. A., Cress, B. F., McCutcheon, C. C., Linhardt, R. J., Gross, R. A., & Koffas, M. A. G. (2017). Complete Biosynthesis of Anthocyanins Using E. coli Polycultures. MBio, 8(3), mBio.00621-17, e00621-17. View Publication,12Zhou, K., Qiao, K., Edgar, S., & Stephanopoulos, G. (2015). Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nature Biotechnology, 33(4), 377–383. View Publication Quorum sensing regulation and division of labor have also been reported to engineer time-controlled expression of portions of the pathway and improve production.13Jones, J. A., Vernacchio, V. R., Sinkoe, A. L., Collins, S. M., Ibrahim, M. H. A., Lachance, D. M., Hahn, J., & Koffas, M. A. G. (2016). Experimental and computational optimization of an Escherichia coli co-culture for the efficient production of flavonoids. Metabolic Engineering, 35, 55–63. View Publication

Most current work has used a limited selection of model organisms (e.g., Escherichia coli, Saccharomyces cerevisiae, Bacillus subtilis) with well-established genetic tools. Significant advances in microbiome engineering will require expanding these models to include microbes from across the tree of life, including Archaea.

Breakthrough Capabilities & Milestones

Distributed compound biosynthesis using multiple microbial species.

Compound biosynthesis using community members that support a primary production strain.

Rapid design of engineered microbiomes that functionally complement existing natural microbiomes.

Footnotes

  1. Mee, M. T., Collins, J. J., Church, G. M., & Wang, H. H. (2014). Syntrophic exchange in synthetic microbial communities. Proceedings of the National Academy of Sciences, 111(20), E2149–E2156. https://doi.org/10.1073/pnas.1405641111
  2. Wang, E.-X., Ding, M.-Z., Ma, Q., Dong, X.-T., & Yuan, Y.-J. (2016). Reorganization of a synthetic microbial consortium for one-step vitamin C fermentation. Microbial Cell Factories, 15(1), 21. https://doi.org/10.1186/s12934-016-0418-6
  3. Wang, E.-X., Liu, Y., Ma, Q., Dong, X.-T., Ding, M.-Z., & Yuan, Y.-J. (2019). Synthetic cell–cell communication in a three-species consortium for one-step vitamin C fermentation. Biotechnology Letters, 41(8–9), 951–961. https://doi.org/10.1007/s10529-019-02705-2
  4. Fu, N., Peiris, P., Markham, J., & Bavor, J. (2009). A novel co-culture process with Zymomonas mobilis and Pichia stipitis for efficient ethanol production on glucose/xylose mixtures. Enzyme and Microbial Technology, 45(3), 210–217. https://doi.org/10.1016/j.enzmictec.2009.04.006
  5. Eiteman, M. A., Lee, S. A., & Altman, E. (2008). A co-fermentation strategy to consume sugar mixtures effectively. Journal of Biological Engineering, 2(1), 3. https://doi.org/10.1186/1754-1611-2-3
  6. ]Haas, T., Krause, R., Weber, R., Demler, M., & Schmid, G. (2018). Technical photosynthesis involving CO2 electrolysis and fermentation. Nature Catalysis, 1(1), 32–39. https://doi.org/10.1038/s41929-017-0005-1
  7. Molitor, B., Mishra, A., & Angenent, L. T. (2019). Power-to-protein: Converting renewable electric power and carbon dioxide into single cell protein with a two-stage bioprocess. Energy & Environmental Science, 12(12), 3515–3521. https://doi.org/10.1039/C9EE02381J
  8. Richter, H., Molitor, B., Diender, M., Sousa, D. Z., & Angenent, L. T. (2016). A Narrow pH Range Supports Butanol, Hexanol, and Octanol Production from Syngas in a Continuous Co-culture of Clostridium ljungdahlii and Clostridium kluyveri with In-Line Product Extraction. Frontiers in Microbiology, 7. https://doi.org/10.3389/fmicb.2016.01773
  9. Bernstein, H. C., Paulson, S. D., & Carlson, R. P. (2012). Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. Journal of Biotechnology, 157(1), 159–166. https://doi.org/10.1016/j.jbiotec.2011.10.001
  10. Bernstein, H. C., Paulson, S. D., & Carlson, R. P. (2012). Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. Journal of Biotechnology, 157(1), 159–166. https://doi.org/10.1016/j.jbiotec.2011.10.001
  11. Jones, J. A., Vernacchio, V. R., Collins, S. M., Shirke, A. N., Xiu, Y., Englaender, J. A., Cress, B. F., McCutcheon, C. C., Linhardt, R. J., Gross, R. A., & Koffas, M. A. G. (2017). Complete Biosynthesis of Anthocyanins Using E. coli Polycultures. MBio, 8(3), mBio.00621-17, e00621-17. https://doi.org/10.1128/mBio.00621-17
  12. Zhou, K., Qiao, K., Edgar, S., & Stephanopoulos, G. (2015). Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nature Biotechnology, 33(4), 377–383. https://doi.org/10.1038/nbt.3095
  13. Jones, J. A., Vernacchio, V. R., Sinkoe, A. L., Collins, S. M., Ibrahim, M. H. A., Lachance, D. M., Hahn, J., & Koffas, M. A. G. (2016). Experimental and computational optimization of an Escherichia coli co-culture for the efficient production of flavonoids. Metabolic Engineering, 35, 55–63. https://doi.org/10.1016/j.ymben.2016.01.006
  14. Claassens, N. J., Cotton, C. A. R., Kopljar, D., & Bar-Even, A. (2019). Making quantitative sense of electromicrobial production. Nature Catalysis, 2(5), 437–447. https://doi.org/10.1038/s41929-019-0272-0
  15. Kracke, F., Vassilev, I., & Kömer, J. O. (2015). Microbial electron transport and energy conservation – the foundation for optimizing bioelectrochemical systems. Frontiers in Microbiology, 6. https://doi.org/10.3389/fmicb.2015.00575
Last updated: October 1, 2020 Back