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Cultivating the uncultured
Open accessAbstract
The recent application of molecular phylogeny to environmental samples has resulted in the discovery of an abundance of unique and previously unrecognized microorganisms. The vast majority of this microbial diversity has proved refractory to cultivation. Here, we describe a universal method that provides access to this immense reservoir of untapped microbial diversity. This technique combines encapsulation of cells in gel microdroplets for massively parallel microbial cultivation under low nutrient flux conditions, followed by flow cytometry to detect microdroplets containing microcolonies. The ability to grow and study previously uncultured organisms in pure culture will enhance our understanding of microbial physiology and metabolic adaptation and will provide new sources of microbial metabolites. We show that this technology can be applied to samples from several different environments, including seawater and soil.
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“Another method, which has had success for culturing marine bacteria, is the microdroplet encapsulation technique (Zengler et al., 2002).”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Zengler et al., 2002
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Metadata
- Authors
- Zengler, K., Toledo, G., Rappé, M., Elkins, J., Mathur, E. J., Short, J. M., & Keller, M.
- Affiliations
- Oregon State University (US)
- Corresponding author
- Keller, Martin
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2002-11-18
- Volume
- 99
- Issue
- 24
- Pages
- 15681-15686
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC137776
- OpenAlex
- W1931874932
- Cited by
- 796
- References
- 29
- Citations by year
- 2026: 12 · 2025: 16 · 2024: 17 · 2023: 16 · 2022: 27 · 2021: 34 · 2020: 35 · 2019: 37 · 2018: 40 · 2017: 29 · 2016: 33 · 2015: 35 · 2014: 45 · 2013: 51 · 2012: 31
- FWCI
- 32.03
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- University of Ghana
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Chemical Engineering › Fluid Flow and Transfer Processes › Innovative Microfluidic and Catalytic Techniques Innovation
- Keywords
- unculturable microorganisms, microbial cultivation, encapsulation, microcolonies, flow cytometry, microbial diversity, seawater, soil, microbial metabolites, microbial physiology
- MeSH terms
- Bacteria, Bacteriological Techniques, Drug Compounding, Flow Cytometry, Fresh Water, Gels, Ghana, Kenya, Particle Size, Phylogeny, RNA, Ribosomal, RNA, Ribosomal, 16S, Seawater, Soil Microbiology, Species Specificity, Water Microbiology, Polymerase Chain Reaction
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