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  • Review Article
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Microbial engineering strategies to utilize waste feedstock for sustainable bioproduction

Nature Reviews Bioengineering volume 2, pages 155–174 (2024)Cite this article

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Abstract

The desire to move from a fossil fuel-based ‘take–make–dispose’ economy to a bio-based circular economy has generated great interest in microbial metabolic engineering for its ability to create cell factories that can produce value-added commodity chemicals via biological means. However, efforts have focused largely on optimizing bioconversion pathways to maximize target compound productivity. Conversely, improvements in feedstock utilization — particularly waste feedstocks that do not compete with food resources — have lagged behind. Although waste feedstocks are abundant, their inefficient utilization by microorganisms presents a major barrier to achieving sustainable microbial bioproduction. This Review describes efforts to develop novel microbial cell factories for valorizing one-carbon waste, horticultural waste, food waste and animal agricultural waste. We discuss state-of-the-art strategies that leverage synthetic biology and multi-omics to improve waste utilization by engineered microorganisms and provide perspectives on the future of waste feedstock valorization.

Key points

  • Waste feedstock valorization can play a key role in enabling the development of a bio-based circular economy.

  • Although advances in microbial metabolic engineering have enabled the microbial production of valuable chemicals, progress in utilizing waste feedstocks as substrates has lagged.

  • One-carbon, horticultural, food, and animal agricultural waste feedstocks can be valorized for bio-based manufacturing but face critical challenges to their efficient utilization.

  • Innovations in synthetic biology, multi-omics and other diverse disciplines have facilitated the development of strategies that can accelerate waste feedstock utilization, drawing us nearer to achieving a circular economy.

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Fig. 1: Waste feedstock utilization by engineered microorganisms for biomanufacturing.
Fig. 2: Major metabolic pathways for utilization of waste feedstock.
Fig. 3: Advanced strategies to develop microbial-based waste feedstock valorization technologies.

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Acknowledgements

This work was supported by the NUS Medicine Synthetic Biology Translational Research Program (NUHSRO/2020/077/MSC/02/SB), the Synthetic Biology R&D Program of the National Research Foundation of Singapore (SBP-P2, SBP-P7, SBP-P9) and the Industry Alignment Fund-Industry Collaboration Project (I1701E0011).

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  1. These authors contributed equally: Nikhil Aggarwal, Hoang Long Pham, Bibhuti Ranjan.

Authors and Affiliations

  1. NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore

    Nikhil Aggarwal, Hoang Long Pham, Bibhuti Ranjan, Mukesh Saini, Yuanmei Liang, Gazi Sakir Hossain, Hua Ling, Jee Loon Foo & Matthew Wook Chang

  2. Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore

    Nikhil Aggarwal, Hoang Long Pham, Bibhuti Ranjan, Mukesh Saini, Yuanmei Liang, Gazi Sakir Hossain, Hua Ling, Jee Loon Foo & Matthew Wook Chang

  3. Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore

    Hoang Long Pham, Bibhuti Ranjan, Mukesh Saini, Yuanmei Liang, Gazi Sakir Hossain, Hua Ling, Jee Loon Foo & Matthew Wook Chang

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N.A., H.L.P., B.R., L.H., J.L.F. and M.W.C. conceptualized the manuscript. N.A., B.R., H.L.P., M.S., Y.L. and G.S.H. researched and wrote the article. N.A., H.L.P., B.R., L.H., J.L.F. and M.W.C. reviewed and edited the manuscript. M.W.C. obtained funding and supervised the study.

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Aggarwal, N., Pham, H.L., Ranjan, B. et al. Microbial engineering strategies to utilize waste feedstock for sustainable bioproduction. Nat Rev Bioeng 2, 155–174 (2024). https://doi.org/10.1038/s44222-023-00129-2

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