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Single-Cell Genomics of Microbial Dark Matter

Part of the Methods in Molecular Biology book series (MIMB,volume 1849)


Single-cell genomics allows bypassing the culturing step and to directly access environmental microbes one cell at a time. The method has been successfully applied to explore archaeal and bacterial candidate phyla, referred to as microbial dark matter. Here I summarize the single-cell genomics workflow, including sample preparation and preservation, high-throughput fluorescence-activated cell sorting, cell lysis and amplification of environmental samples. Furthermore I describe phylogenetic screening based on 16S rRNA genes and suggest a suitable library preparation and sequencing approach.

Key words

  • Single-cell genomics
  • Microbial dark matter
  • Fluorescence-activated cell sorting
  • FACS
  • Multiple genome amplification
  • 16S rRNA gene
  • ILLUMINA Nextera XT libraries
  • Biofilm
  • Sludge
  • Sediment

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  • DOI: 10.1007/978-1-4939-8728-3_7
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The work was conducted at the Australian Centre for Ecogenomics (ACE) at UQ, and was supported by the ARC Discovery Project DP160103811. I would like to thank the ACE team for support, especially Dr. Michael Nefedov and Alexander Baker.

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Correspondence to Christian Rinke .

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Rinke, C. (2018). Single-Cell Genomics of Microbial Dark Matter. In: Beiko, R., Hsiao, W., Parkinson, J. (eds) Microbiome Analysis. Methods in Molecular Biology, vol 1849. Humana Press, New York, NY.

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