Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers.

ISME J
Authors
Keywords
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.

Year of Publication
2016
Journal
ISME J
Volume
10
Issue
2
Pages
427-36
Date Published
2016 Feb
ISSN
1751-7370
URL
DOI
10.1038/ismej.2015.124
PubMed ID
26394010
PubMed Central ID
PMC4737934
Links
Grant list
P30 ES002109 / ES / NIEHS NIH HHS / United States
P30-ES002109 / ES / NIEHS NIH HHS / United States