Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

Yann Marcy; Cleber Ouverney; Elisabeth M. Bik; Tina Lösekann; Natalia Ivanova; Hector Garcia Martin; Ernest Szeto; Darren Platt; Philip Hugenholtz; David A. Relman; Stephen R. Quake

doi:10.1073/pnas.0704662104

Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

Yann Marcy, Cleber Ouverney, Elisabeth M. Bik, Tina Lösekann, Natalia Ivanova, Hector Garcia Martin, Ernest Szeto, Darren Platt, Philip Hugenholtz, David A. Relman, Stephen R. Quake

Microbiology

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504 Scopus citations

Abstract

We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community.

Original language	English (US)
Pages (from-to)	11889-11894
Number of pages	6
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	104
Issue number	29
DOIs	https://doi.org/10.1073/pnas.0704662104
State	Published - Jul 17 2007

Keywords

Environmental microbiology
Metagenomics
Microfluidics
Single-cell analysis

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10.1073/pnas.0704662104

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Marcy, Y., Ouverney, C., Bik, E. M., Lösekann, T., Ivanova, N., Martin, H. G., Szeto, E., Platt, D., Hugenholtz, P., Relman, D. A., & Quake, S. R. (2007). Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences of the United States of America, 104(29), 11889-11894. https://doi.org/10.1073/pnas.0704662104

Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. / Marcy, Yann; Ouverney, Cleber; Bik, Elisabeth M. et al.
In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 29, 17.07.2007, p. 11889-11894.

Research output: Contribution to journal › Article › peer-review

Marcy, Y, Ouverney, C, Bik, EM, Lösekann, T, Ivanova, N, Martin, HG, Szeto, E, Platt, D, Hugenholtz, P, Relman, DA & Quake, SR 2007, 'Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth', Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 29, pp. 11889-11894. https://doi.org/10.1073/pnas.0704662104

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AU - Lösekann, Tina

AU - Ivanova, Natalia

AU - Martin, Hector Garcia

AU - Szeto, Ernest

AU - Platt, Darren

AU - Hugenholtz, Philip

AU - Relman, David A.

AU - Quake, Stephen R.

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AB - We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community.

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KW - Microfluidics

KW - Single-cell analysis

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Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

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