Targeted genomics of flow cytometrically sorted cultured and uncultured microbial groups

Sophie Mazard, Martin Ostrowski, Ross Holland, Mikhail V. Zubkov, David J. Scanlan

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

2 Citations (Scopus)


High throughput sequencing of genetic material recovered from environmental samples (i.e., metagenomics) is becoming the method of choice for either medical or environmental genomic studies. However, the large amount of data and complexity of the sequenced "biomes" present challenges for teasing meaningful results out of the mass. Here, we describe a targeted genomic pipeline which uses fluorescence-activated cell sorting (FACS) in combination with multiple displacement amplification (MDA) of nucleic acids that allows to dissect a complex system into its component parts to facilitate high-quality single-cell, or targeted population, genomic reconstructions of microbial communities. This pipeline is presented with methods for collecting, concentrating, and preserving cells from aquatic and marine environments suitable for flow cytometric processing at a later date.

Original languageEnglish
Title of host publicationEnvironmental Microbiology
Subtitle of host publicationMethods and Protocols
EditorsIan T. Paulsen, Andrew J. Holmes
Place of PublicationTotowa, NJ
PublisherHumana Press
Number of pages10
ISBN (Electronic)9781627037129
ISBN (Print)9781627037112
Publication statusPublished - 2014

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Cyanobacteria
  • Flow-cytometry
  • Genomics
  • Marine Synechococcus
  • Metagenomics
  • Population genomics
  • Single cell genomics
  • Whole-genome amplification

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