The trajectory of microbial single-cell sequencing

Abstract

Over the past decade, it has become nearly routine to sequence genomes of individual microbial cells directly isolated from environmental samples ranging from deep-sea hydrothermal vents to insect guts, providing a powerful complement to shotgun metagenomics in microbial community studies. In this review, we address the technical aspects and challenges of single-cell genome sequencing and discuss some of the scientific endeavors that it has enabled. Specifically, we highlight newly added leaves and branches in the genomic tree of bacterial and archaeal life and illustrate the unique and exciting advantages that single-cell genomics offers over metagenomics, both now and in the near future.

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Figure 1: Single-cell sequencing and analysis workflow for standard (untargeted) and targeted single-cell sequencing approaches.
Figure 2: Timeline of scientific milestones in single-cell microbial sequencing.
Figure 3: Single-cell sequencing links all DNA-containing elements within a cell and can also reveal tight physical associations between cells.
Figure 4: Bacterial and archaeal SSU-rRNA-gene-based phylogenetic tree.

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Acknowledgements

This work was conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, under contract no. DE-AC02-05CH11231. T.W. and D.F.R.D. were also supported under the LBNL Microbes to Biomes LDRD entitled “Tackling microbial-mediated plant carbon decomposition using function-driven genomics.”

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T.W., D.F.R.D. and F.S. constructed the figures and wrote the article.

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Correspondence to Tanja Woyke.

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Woyke, T., Doud, D. & Schulz, F. The trajectory of microbial single-cell sequencing. Nat Methods 14, 1045–1054 (2017). https://doi.org/10.1038/nmeth.4469

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