Engineering microbial consortia for controllable outputs

Lindemann, Stephen R.; Bernstein, Hans C.; Song, Hyun-Seob; Fredrickson, Jim K.; Fields, Matthew W.; Shou, Wenying; Johnson, David R.; Beliaev, Alexander S.

doi:10.1038/ismej.2016.26

Engineering microbial consortia for controllable outputs

Journal Article · Thu Mar 10 23:00:00 EST 2016 · The ISME Journal

DOI:https://doi.org/10.1038/ismej.2016.26· OSTI ID:1324901

Lindemann, Stephen R.; ; Song, Hyun-Seob; Fredrickson, Jim K.; ; Shou, Wenying; Johnson, David R.; Beliaev, Alexander S.

Much research has been invested into engineering microorganisms to perform desired biotransformations; nonetheless, these efforts frequently fall short of expected results due to the unforeseen effects of biofeedback regulation and functional incompatibility. In nature, metabolic function is compartmentalized into diverse organisms assembled into resilient consortia, in which the division of labor is thought to lead to increased community efficiency and productivity. Here, we consider whether and how consortia can be designed to perform bioprocesses of interest beyond the metabolic flexibility limitations of a single organism. Advances in post-genomic analysis of microbial consortia and application of high-resolution global measurements now offer the promise of systems-level understanding of how microbial consortia adapt to changes in environmental variables and inputs of carbon and energy. We argue that when combined with appropriate modeling framework that predictive knowledge generates testable hypotheses and orthogonal synthetic biology tools, such understanding can dramatically improve our ability to control the fate and functioning of consortia. In this article, we articulate our collective perspective on the current and future state of microbial community engineering and control while placing specific emphasis on ecological principles that promote control over community function and emergent properties.

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (US)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1324901

Report Number(s):: PNNL-SA-110327; KP1601010

Journal Information:: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 9 Vol. 10; ISSN 1751-7362

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

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Metabolite toxicity slows local diversity loss during expansion of a microbial cross-feeding community Goldschmidt, Felix; Regoes, Roland R.; Johnson, David R. The ISME Journal, Vol. 12, Issue 1 https://doi.org/10.1038/ismej.2017.147	journal	September 2017
Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems Pacheco, Alan R.; Moel, Mauricio; Segrè, Daniel Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-018-07946-9	journal	January 2019
Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates Lilja, Elin E.; Johnson, David R. The ISME Journal, Vol. 10, Issue 7 https://doi.org/10.1038/ismej.2015.243	journal	January 2016
Community-intrinsic properties enhance keratin degradation from bacterial consortia Nasipuri, Poonam; Herschend, Jakob; Brejnrod, Asker D. PLOS ONE, Vol. 15, Issue 1 https://doi.org/10.1371/journal.pone.0228108	journal	January 2020
Characterization of an autotrophic bioreactor microbial consortium degrading thiocyanate Watts, Mathew Paul; Spurr, Liam Patrick; Gan, Han Ming Applied Microbiology and Biotechnology, Vol. 101, Issue 14 https://doi.org/10.1007/s00253-017-8313-6	journal	May 2017
Analysis of productivity and stability of synthetic microbial communities Di, Sihao; Yang, Aidong Journal of The Royal Society Interface, Vol. 16, Issue 150 https://doi.org/10.1098/rsif.2018.0859	journal	January 2019
Ecological interactions and coexistence are predicted by gene expression similarity in freshwater green algae Narwani, Anita; Bentlage, Bastian; Alexandrou, Markos A. Journal of Ecology, Vol. 105, Issue 3 https://doi.org/10.1111/1365-2745.12759	journal	April 2017
A Clostridium Group IV Species Dominates and Suppresses a Mixed Culture Fermentation by Tolerance to Medium Chain Fatty Acids Products Andersen, Stephen J.; De Groof, Vicky; Khor, Way Cern Frontiers in Bioengineering and Biotechnology, Vol. 5 https://doi.org/10.3389/fbioe.2017.00008	journal	February 2017
Toxicity drives facilitation between 4 bacterial species Piccardi, Philippe; Vessman, Björn; Mitri, Sara Proceedings of the National Academy of Sciences, Vol. 116, Issue 32 https://doi.org/10.1073/pnas.1906172116	journal	July 2019
Design Principles of Microbial Communities: From Understanding to Engineering Song, Hyun-Seob Current Genomics, Vol. 19, Issue 8 https://doi.org/10.2174/138920291908181005100741	journal	October 2018
A three-species microbial consortium for power generation Liu, Yue; Ding, Mingzhu; Ling, Wei Energy & Environmental Science, Vol. 10, Issue 7 https://doi.org/10.1039/c6ee03705d	journal	January 2017
Understanding the evolution of interspecies interactions in microbial communities Gorter, Florien A.; Manhart, Michael; Ackermann, Martin Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 375, Issue 1798 https://doi.org/10.1098/rstb.2019.0256	journal	March 2020
Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia Ben Said, Sami; Or, Dani ETH Zurich https://doi.org/10.3929/ethz-b-000190284	text	January 2017

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