Increase the diversity of outputs or products.

Engineer ‘one-pot’ microbiomes that robustly produce multiple end-products from untreated or variable inputs.

• Technical Achievement: Engineer microbiomes made of bacteria with different carbon source preferences, so they can degrade complex mixtures of carbon sources and more efficiently utilize substrates without releasing carbon dioxide.
• Technical Achievement: Engineer microbiomes that utilize a single input precursor, but can produce multiple high-purity products depending on the species substituted into a community.

Use microbiomes to expand the types of chemicals that can be synthesized.

• Technical Achievement: Design microbiomes that have individual species capable of metabolizing or sequestering toxic intermediates to facilitate continued production.
• Technical Achievement: Engineer microbiomes that can capture and scrub compounds (e.g., sulfur species, carbon dioxide) that inhibit other industrial processes.

Increase manufacturing efficiency by reducing the need for energy- or chemical-intensive processes, and making processes more malleable and modular.

Engineer microbiomes that can sense environmental or nutrient changes to regulate specific processes.

• Technical Achievement: Engineer auto-inductive signal networks within a microbiome, so multiple gene or protein expression programs can be triggered without the need for exogenous inducers
• Technical Achievement: Use optogenetically engineered microbiomes to reduce the cost of chemical inducers, but maintain tighter control over cell processes than could be accomplished using environmental signals.

Engineer microbiomes to secrete desired products from cells to enable rapid, low-cost separation of products from growth media.

• Technical Achievement: Engineer microbiomes that “package” high-value chemicals in secretable liposomes or other extracellular structures.
• Technical Achievement: Engineer synchronized microbiome lysis, so products are periodically released from the intracellular compartment without complex secretion systems or extraction methods.

Engineer microbiome communities that can mitigate contamination between batches or during batch production, to allow for wider use of non-aseptic fermentation facilities.

• Technical Achievement: Engineer microbiomes that can be added to equipment post-processing to consume residual waste and nutritionally outcompete contaminants.
• Technical Achievement: Engineer microbiome biofilms that produce antimicrobial compounds (e.g., antibiotics, antibacterial peptides) in the presence of contaminating microbes.

Optimize processes for handling more diverse bio-based inputs to reduce pretreatment and waste disposal costs.

Engineer microbiomes that can accept waste as an alternative feedstock (e.g., fruit/vegetable/plant waste biomass, animal byproducts) to utilize unused carbon and other compounds.

• Technical Achievement: Engineer ecological succession, so waste and microbial strains containing sensitive intellectual property are destroyed by a generic ‘degradation’ strain.
• Technical Achievement: Design microbiomes that can utilize greenhouse gases (e.g., carbon dioxide, carbon monoxide, methane) produced or generated by industrial processes.
• Technical Achievement: Create microbiomes that degrade waste into simple precursors (e.g., sugar monomers, organic acids, amines, terpenes) that can be used to synthesize higher value products such as adhesives and polymers in remote environments.¹Roberts, 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. View Publication

Engineer microbiomes that can utilize process byproducts and low-value intermediate compounds as a feedstock.

• Technical Achievement: Engineer strains to preferentially uptake process byproducts, instead of the inputs that will be converted into value-added products by main production strains in the microbiome.
• Technical Achievement: Engineer microbiomes that simultaneously consume low-value metabolic intermediates (e.g., acetate, formate) that may be toxic in high concentrations but can be converted to higher value intermediates or products.
• Technical Achievement: Engineer microbiomes that can fix recaptured carbon dioxide or hydrogen gas generated by fermentative processes into usable compounds like acetone.²Jones, 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. View Publication

Footnotes

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