Cited by 796Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesInnovative Microfluidic and Catalytic Techniques Innovation

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Cultivating the uncultured

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Zengler, Karsten, Toledo, Gerardo, Rappé, Michael, Elkins, James, Mathur, Eric J., Short, Jay M., Keller, Martin·2002·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.252630999PMC PMC137776

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Abstract

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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Phylogenetic identification and in situ detection of individual microbial cells without cultivation
Amann, R., Ludwig, W., & SCHLEIFER, K. H. (1995) · Microbiological Reviews · doi:10.1128/mr.59.1.143-169.1995 · Cited by 9,218
A Molecular View of Microbial Diversity and the Biosphere
Pace, N. R. (1997) · Science · doi:10.1126/science.276.5313.734 · Cited by 2,797
Gram-Negative Mesophilic Sulfate-Reducing Bacteria
Widdel, F., & Bak, F. (1992) · Springer eBooks · doi:10.1007/978-1-4757-2191-1_21 · Cited by 1,567
Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea
Béjà, O., Aravind, L., Koonin, E. V., Suzuki, M. T., Hadd, A. G., Nguyen, L. P., Jovanovich, S. B., Gates, C. M., Feldman, R. A., Spudich, J. L., et al. (2000) · Science · doi:10.1126/science.289.5486.1902 · Cited by 1,532
Isolating "Uncultivable" Microorganisms in Pure Culture in a Simulated Natural Environment
Kaeberlein, T., Lewis, K., & Epstein, S. S. (2002) · Science · doi:10.1126/science.1070633 · Cited by 1,258
Microbial Ecology of the Oceans
Kirchman, D. L. (2008) · Wiley eBooks · doi:10.1002/9780470281840 · Cited by 1,137
Survival and viability of nonculturableEscherichia coli andVibrio cholerae in the estuarine and marine environment
Xu, H. S., Roberts, N. C., Singleton, F. L., Attwell, R. W., Grimes, D. J., & Colwell, R. R. (1982) · Microbial Ecology · doi:10.1007/bf02010671 · Cited by 1,095
Cultivation of the ubiquitous SAR11 marine bacterioplankton clade
Rappé, M. S., Connon, S. A., Vergin, K. L., & Giovannoni, S. J. (2002) · Nature · doi:10.1038/nature00917 · Cited by 1,020
Self-citation
High-Throughput Methods for Culturing Microorganisms in Very-Low-Nutrient Media Yield Diverse New Marine Isolates
Connon, S. A., & Giovannoni, S. J. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.8.3878-3885.2002 · Cited by 742
Improved Culturability of Soil Bacteria and Isolation in Pure Culture of Novel Members of the Divisions Acidobacteria , Actinobacteria , Proteobacteria , and Verrucomicrobia
Janssen, P. H., Yates, P. S., Grinton, B. E., Taylor, P., & Sait, M. L. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.5.2391-2396.2002 · Cited by 729

Show all 29 references

Research works printed but not linked: 4

Vobis G. (1992) in The Prokaryotes, eds. Balows, A., Trüper, H. G., Dworkin, M., Harder, W. & Schleifer, K.-H. (Springer, New York), Vol. 2, pp. 1029–1060.
Powell K. T. & Weaver, J. C. (1990) Bio/Technology8,333-337.1366534
Tanner M. A., Everett, C. L., Coleman, W. J., Yang, M. M. & Youvan, D. C. (2000) Bio/Technology8,1-16.
Robertson D. E., Mathur, E. J., Swanson, R. V., Marrs, B. L. & Short, J. M. (1996) SIM News46,3-8.

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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
ORCID: Zengler, Karsten
Toledo, Gerardo
Rappé, Michael
Elkins, James
Short, Jay M.
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
DOI: 10.1073/pnas.252630999
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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