Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles

Ramunas Stepanauskas (), Elizabeth A. Fergusson, Joseph Brown, Nicole J. Poulton, Ben Tupper, Jessica M. Labonté, Eric D. Becraft, Julia M. Brown, Maria G. Pachiadaki, Tadas Povilaitis, Brian P. Thompson, Corianna J. Mascena, Wendy K. Bellows and Arvydas Lubys
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Ramunas Stepanauskas: Bigelow Laboratory for Ocean Sciences
Elizabeth A. Fergusson: Bigelow Laboratory for Ocean Sciences
Joseph Brown: Bigelow Laboratory for Ocean Sciences
Nicole J. Poulton: Bigelow Laboratory for Ocean Sciences
Ben Tupper: Bigelow Laboratory for Ocean Sciences
Jessica M. Labonté: Bigelow Laboratory for Ocean Sciences
Eric D. Becraft: Bigelow Laboratory for Ocean Sciences
Julia M. Brown: Bigelow Laboratory for Ocean Sciences
Maria G. Pachiadaki: Bigelow Laboratory for Ocean Sciences
Tadas Povilaitis: Thermo Fisher Scientific Baltics
Brian P. Thompson: Bigelow Laboratory for Ocean Sciences
Corianna J. Mascena: Bigelow Laboratory for Ocean Sciences
Wendy K. Bellows: Bigelow Laboratory for Ocean Sciences
Arvydas Lubys: Thermo Fisher Scientific Baltics

Nature Communications, 2017, vol. 8, issue 1, 1-10

Abstract: Abstract Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils. By integrating WGA-X with calibrated index-cell sorting and high-throughput genomic sequencing, we are able to analyze genomic sequences and cell sizes of hundreds of individual, uncultured bacteria, archaea, protists, and viral particles, obtained directly from marine and soil samples, in a single experiment. This approach may find diverse applications in microbiology and in biomedical and forensic studies of humans and other multicellular organisms.

Date: 2017
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DOI: 10.1038/s41467-017-00128-z

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