通过对来自人类口腔的罕见且不可培养的TM7微生物进行单细胞遗传分析来剖析生物“暗物质”。
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth.
作者信息
Marcy Yann, Ouverney Cleber, Bik Elisabeth M, Lösekann Tina, Ivanova Natalia, Martin Hector Garcia, Szeto Ernest, Platt Darren, Hugenholtz Philip, Relman David A, Quake Stephen R
机构信息
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
出版信息
Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11889-94. doi: 10.1073/pnas.0704662104. Epub 2007 Jul 9.
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.
摘要
我们开发了一种微流控装置，该装置能够分离单个微生物细胞并进行基因组扩增，从而无需培养即可对复杂微生物生态系统进行生物体水平的基因组分析。该装置用于对人类龈下裂隙进行定向调查，并分离出具有杆状形态的细菌。几个分离出的微生物具有16S rRNA序列，将它们归入候选门TM7，该门没有已培养或测序的成员。对单个TM7细胞进行基因组扩增使我们能够对1000多个基因进行测序和组装，从而深入了解该门成员的生理学特性。这种方法能够对微生物群落中任何未培养的少数成员进行单细胞遗传分析。
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2
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Mol Microbiol. 2006 Nov;62(3):680-94. doi: 10.1111/j.1365-2958.2006.05414.x. Epub 2006 Sep 25.
3
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities.两个强化生物除磷（EBPR）污泥群落的宏基因组分析。
Nat Biotechnol. 2006 Oct;24(10):1263-9. doi: 10.1038/nbt1247. Epub 2006 Sep 24.
4
An experimental metagenome data management and analysis system.一个实验性宏基因组数据管理与分析系统。
Bioinformatics. 2006 Jul 15;22(14):e359-67. doi: 10.1093/bioinformatics/btl217.
5
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6
Rapid quantitative profiling of complex microbial populations.复杂微生物群体的快速定量分析
Nucleic Acids Res. 2006 Jan 10;34(1):e5. doi: 10.1093/nar/gnj007.
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8
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9
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