Cultivating the uncultured

Zengler, Karsten; Toledo, Gerardo; Rappé, Michael; Elkins, James; Mathur, Eric J.; Short, Jay M.; Keller, Martin

doi:10.1073/pnas.252630999

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

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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Microdroplet encapsulation technique has had success for culturing marine bacteria.
“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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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 › Engineering › Biomedical Engineering › 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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