Original Article

The ISME Journal (2016) 10, 427–436; doi:10.1038/ismej.2015.124; published online 22 September 2015

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers
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Sarah J Spencer1,10, Manu V Tamminen2,3,10, Sarah P Preheim2, Mira T Guo4, Adrian W Briggs5, Ilana L Brito2, David A Weitz4,5, Leena K Pitkänen3, Francois Vigneault6, Marko PJuhani Virta3 and Eric J Alm1,2,7,8,9

  1. 1Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
  2. 2Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
  3. 3Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
  4. 4School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
  5. 5Department of Physics, Harvard University, Cambridge, MA, USA
  6. 6AbVitro Inc., Boston, MA, USA
  7. 7Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
  8. 8The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
  9. 9The Broad Institute of MIT and Harvard, Cambridge, MA, USA

Correspondence: EJ Alm, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA E-mail: ejalm@mit.edu; MV Tamminen, Department of Food and Environmental Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland. E-mail: mvtammin@mit.edu

10These authors contributed equally to this work.

Received 18 December 2014; Revised 18 June 2015; Accepted 24 June 2015
Advance online publication 22 September 2015

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Abstract

Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.