The future is now: single-cell genomics of bacteria and archaea


  • Paul C. Blainey

    Corresponding author
    1. Department of Biological Engineering, MIT, Cambridge, MA, USA
    • Broad Institute of Harvard and MIT, Cambridge, MA, USA
    Search for more papers by this author

Correspondence: Paul C. Blainey, 7 Cambridge Center, Cambridge, MA 02142, USA. Tel.: +1 650 714 7320;



Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation are driving considerable progress in single-cell genomics. Here, the spectrum of applications for single-cell genomics, key advances in the development of the field, and emerging methodology for single-cell genome sequencing are reviewed by example with attention to the diversity of approaches and their unique characteristics. Experimental strategies transcending specific methodologies are identified and organized as a road map for future studies in single-cell genomics of environmental microorganisms. Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology.