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Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes

Alexandra L. McCully, McKenna Loop Yao, Kara K. Brower, Polly M. Fordyce, Alfred M. Spormann
doi: https://doi.org/10.1101/2022.10.23.513397
Alexandra L. McCully
1Department of Civil and Environmental Engineering, Stanford University, CA
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McKenna Loop Yao
2Department of Chemical Engineering, Stanford University, CA
3Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA
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Kara K. Brower
4Department of Bioengineering, Stanford University, Stanford, CA
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Polly M. Fordyce
4Department of Bioengineering, Stanford University, Stanford, CA
5Department of Genetics, Stanford University, Stanford, CA
6ChEM-H Institute, Stanford University, Stanford, CA
7Chan Zuckerberg Biohub, San Francisco, CA
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Alfred M. Spormann
1Department of Civil and Environmental Engineering, Stanford University, CA
2Department of Chemical Engineering, Stanford University, CA
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  • For correspondence: spormann@stanford.edu
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Abstract

Our understanding of in situ microbial physiology is primarily based on physiological characterization of fast-growing and readily-isolatable microbes. Microbial enrichments to obtain novel isolates with slower growth rates or physiologies adapted to low nutrient environments are plagued by intrinsic biases for fastest-growing species when using standard laboratory isolation protocols. New cultivation tools to minimize these biases and enrich for less well-studied taxa are needed. In this study, we developed a high-throughput bacterial enrichment platform based on single cell encapsulation and growth within double emulsions (GrowMiDE). We showed that GrowMiDE can cultivate many different microorganisms and enrich for novel taxa that are never observed in traditional batch enrichments. For example, preventing dominance of the enrichment by fast-growing microbes due to nutrient privatization within the double emulsion droplets allowed cultivation of novel Negativicutes and Methanobacteria from stool samples in rich media enrichment cultures. In competition experiments between growth rate and growth yield specialist strains, GrowMiDE enrichments prevented competition for shared nutrient pools and enriched for slower-growing but more efficient strains. Finally, we demonstrated the compatibility of GrowMiDE with commercial fluorescence-activated cell sorting (FACS) to obtain isolates from GrowMiDE enrichments. Together, GrowMiDE + DE-FACS is a promising new high-throughput enrichment platform that can be easily applied to diverse microbial enrichments or screens.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Competing Interest Statement: The authors declare no conflict of interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted October 23, 2022.
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Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes
Alexandra L. McCully, McKenna Loop Yao, Kara K. Brower, Polly M. Fordyce, Alfred M. Spormann
bioRxiv 2022.10.23.513397; doi: https://doi.org/10.1101/2022.10.23.513397
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Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes
Alexandra L. McCully, McKenna Loop Yao, Kara K. Brower, Polly M. Fordyce, Alfred M. Spormann
bioRxiv 2022.10.23.513397; doi: https://doi.org/10.1101/2022.10.23.513397

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