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

    3 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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