Engineer microbiomes to transform recalcitrant materials into useful products.

Microbiome Engineering

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.¹ 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.²^,³ 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.⁴ 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.

Develop tools to identify partner microbes for a given feedstock composition.

For a known compound, design a microbiome to degrade it and experimentally demonstrate partial degradation of the compound.

Develop retro biodegradation programs that can rationally design microbiomes to break down a non-natural compound with high efficiency.

Bottleneck/Challenge: We do not have computational programs that can model the available metabolism in a community, or even in individual organisms, which will be necessary to predict the metabolism that is needed to completely mineralize a compound.

Potential Solution: Utilize black box machine learning models to better understand metabolic inputs and outputs at the microbiome level, rather than tracking specific metabolites as they move within a community.

Engineer dynamic community stability.

Bottleneck/Challenge: As inputs are consumed and exhausted, the need for intermediate transformations and their microbes may diminish. Current approaches to community stability rely on mutualistic exchange between all members which destabilizes the community and its function as the importance of individual members diminishes.

Potential Solution: Engineer universal degradation communities that autonomously enhance/suppress growth of individual species to enable efficient compound degradation.

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

Identify organisms that independently break down different components of a compound (e.g., one organism can perform one step aerobically, a second organism can perform a downstream step anaerobically).

Engineer microbiomes that can create and maintain distinct microenvironments (e.g., anaerobic reaction vesicles, acidic microcompartments).

Design microenvironment-generating microbiomes, in combination with paired degradation organisms, to enable near simultaneous degradation by each organism (i.e., it does not require diffusion between layers).

Create a physical linkage, or another close connection, between otherwise incompatible species that makes them dependent on each other for survival.

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

Design methods to identify ‘usable’ metabolites from bioreactor waste products.

Demonstrate process to “reuse” materials from completed biosynthesis (i.e., whatever is left after the product is extracted from the bioreactor) as a feedstock for a new biosynthesis run.

Create methods to recycle dead biomass.

Engineer complex microbiomes that are self-sustaining ecosystems that recycle dead cell biomass, and are capable of transforming inputs to products.

Bottleneck/Challenge: Ability to engineer needed inter-kingdom interactions is unprecedented. The dynamics of predator-prey interactions will lead to emergent bistability, which may be difficult to control.

Potential Solution: Engineer microbial/bacterial apoptosis. Create a predator-prey system for recycling and maintaining stability by including microbes from all kingdoms (e.g., protists eat dead bacteria, dying protists release enzymes to break down their bodies to sustain the next generation of microbes in the community).

Footnotes

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
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
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
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