Open AccessImproved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles
Author(s) -
Ramûnas Stepanauskas,
Elizabeth A. Fergusson,
Joseph Brown,
Nicole Poulton,
Ben Tupper,
Jessica Labonté,
Eric D. Becraft,
Julia Brown,
Maria Pachiadaki,
Tadas Povilaitis,
Brian Thompson,
Corianna J. Mascena,
Wendy K. Bellows,
Arvydas Lubys
Publication year - 2017
Publication title -
nature communications
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.559
H-Index - 365
ISSN - 2041-1723
DOI - 10.1038/s41467-017-00128-z
Subject(s) - archaea , biology , genome , microorganism , multiple displacement amplification , computational biology , genomics , bacteria , single cell sequencing , metagenomics , gene , genetics , polymerase chain reaction , mutation , dna extraction , exome sequencing
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.