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Genomic sequencing of uncultured microorganisms from single cells

Nature Reviews Microbiology volume 10, pages 631–640 (2012)Cite this article

Subjects

Key Points

  • Genomic sequencing from a single cell became feasible with the introduction of the multiple displacement amplification (MDA) method, which generates micrograms of amplified DNA.

  • Methods have improved over the past 10 years to isolate single cells, amplify the DNA by MDA for use in sequencing, and assemble genomes from those single cells.

  • A vast range of novel microorganisms will now be amenable to genomic sequencing directly from single cells, eliminating the need to develop culture methods in order to obtain sufficient DNA template.

  • Single-cell sequencing is increasingly being used in combination with metagenomic sequencing to assemble individual genomes and analyse complex microbial communities.

Abstract

Sequencing DNA from single cells has opened new windows onto the microbial world. It is becoming routine to sequence bacterial species directly from environmental samples or clinical specimens without the need to develop cultivation methods. Recent technical improvements often allow nearly complete genome assembly from these otherwise inaccessible species. New bioinformatics methods are also improving genome assembly from single cells. The use of single-cell sequencing in combination with metagenomic analysis is also emerging as a powerful new strategy to analyse bacterial communities. Here, the technical developments that have enabled single-cell sequencing, as well as some of the most exciting applications of this approach from the past few years, are reviewed.

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Figure 1: Comparison of DNA amplification reactions and cellular DNA replication.
Figure 2: Isolation of single microbial cells.
Figure 3: Metagenomics and single-cell sequencing.
Figure 4: Combined use of metagenomic and single-cell approaches.

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Acknowledgements

The author gratefully acknowledges C. Dupont for suggestions on metagenomics and marine communities.

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  1. J. Craig Venter Institute, La Jolla, 92121, California, USA

    Roger S. Lasken

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FURTHER INFORMATION

HMP MDA sequencing

Glossary

Global Ocean Sampling study

(GOS study). A global circumnavigation aboard the sailing yacht, Sorcerer II, conducted by the J. Craig Venter Institute (La Jolla, USA), with the aim of providing a comprehensive genomic survey of microbial (bacterial, archaeal and viral) life in the world's oceans.

Klenow fragment

The large fragment of Escherichia coli DNA polymerase I; this fragment has a processivity of ∼10 nucleotides.

Bar-coded DNA libraries

Mixed DNA libraries that are created by the addition of short DNA sequences (bar-codes) onto the DNA templates. Multiple DNA sets (for example, from different bacteria) are each tagged with a unique bar-code and then pooled for use in a single sequencing run. The sequences obtained can be separated back into the individual sets based on the bar-codes.

Chemolithoautotrophic

Pertaining to an organism: deriving energy from a chemical reaction (chemotrophic) using inorganic substrates such as nitrate, ferrous iron or sulphur as electron donors (lithotrophic), and using CO2 as the sole carbon source (autotrophic).

Pelagic

Relating to or occurring in the water column.

Mesopelagic

Typically between 200m and 1,000m below the ocean surface.

CARD–FISH

(Catalysed reporter deposition–fluorescence in situ hybridization). A method for increasing the sensitivity of FISH, for example, by using horseradish peroxidase-labelled oligonucleotide probes. The horseradish peroxidase catalyses the deposition of tyramine molecules, which results in amplification of the fluorescent signal at the site of probe hybridization.

Phycobiliproteins

Water-soluble proteins that are present in cyanobacteria and certain algae and capture light energy, which is passed on to chlorophylls during photosynthesis. Phycobiliproteins are complexes consisting of proteins and covalently bound phycobilins that act as chromophores (capturing light).

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Lasken, R. Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol 10, 631–640 (2012). https://doi.org/10.1038/nrmicro2857

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