title: Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers.
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.
authors.affiliation: Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Spencer
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.|Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland.
authors.forename: Manu V
authors.initials: MV
authors.lastname: Tamminen
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
authors.forename: Sarah P
authors.initials: SP
authors.lastname: Preheim
authors.affiliation: School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
authors.forename: Mira T
authors.initials: MT
authors.lastname: Guo
authors.affiliation: Department of Physics, Harvard University, Cambridge, MA, USA.
authors.forename: Adrian W
authors.initials: AW
authors.lastname: Briggs
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
authors.forename: Ilana L
authors.initials: IL
authors.lastname: Brito
authors.affiliation: School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.|Department of Physics, Harvard University, Cambridge, MA, USA.
authors.forename: David
authors.initials: D
authors.lastname: A Weitz
authors.affiliation: Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland.
authors.forename: Leena K
authors.initials: LK
authors.lastname: Pitkänen
authors.affiliation: AbVitro Inc., Boston, MA, USA.
authors.forename: Francois
authors.initials: F
authors.lastname: Vigneault
authors.affiliation: Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland.
authors.forename: Marko P
authors.initials: MP
authors.lastname: Juhani Virta
authors.affiliation: Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.|Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.|Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.|The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.|The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Alm
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001426:Bacterial Proteins / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D060106:Lakes / Q000382:microbiology*; D056186:Metagenomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S