Dissecting the human microbiome with single-cell genomics

doi:10.1186/s13073-017-0448-7

Review

. 2017 Jun 14;9(1):56.

doi: 10.1186/s13073-017-0448-7.

Dissecting the human microbiome with single-cell genomics

Andrew C Tolonen¹, Ramnik J Xavier^{2

3

4

5}

Affiliations

¹ Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA. atolonen@broadinstitute.org.
² Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA. xavier@molbio.mgh.harvard.edu.
³ Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA. xavier@molbio.mgh.harvard.edu.
⁴ Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA. xavier@molbio.mgh.harvard.edu.
⁵ Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, 02139, USA. xavier@molbio.mgh.harvard.edu.

PMID: 28615076
PMCID: PMC5471897
DOI: 10.1186/s13073-017-0448-7

Review

Dissecting the human microbiome with single-cell genomics

Andrew C Tolonen et al. Genome Med. 2017.

. 2017 Jun 14;9(1):56.

doi: 10.1186/s13073-017-0448-7.

Authors

Andrew C Tolonen¹, Ramnik J Xavier^{2

3

4

5}

Affiliations

¹ Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA. atolonen@broadinstitute.org.
² Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA. xavier@molbio.mgh.harvard.edu.
³ Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA. xavier@molbio.mgh.harvard.edu.
⁴ Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA. xavier@molbio.mgh.harvard.edu.
⁵ Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, 02139, USA. xavier@molbio.mgh.harvard.edu.

PMID: 28615076
PMCID: PMC5471897
DOI: 10.1186/s13073-017-0448-7

Abstract

Recent advances in genome sequencing of single microbial cells enable the assignment of functional roles to members of the human microbiome that cannot currently be cultured. This approach can reveal the genomic basis of phenotypic variation between closely related strains and can be applied to the targeted study of immunogenic bacteria in disease.

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Figures

**Fig. 1**
Overview of steps for single-cell sequencing of microbial genomes. Experimental steps include (*upper half*) isolation and lysis of single cells with subsequent amplification of their genomes, followed by (*lower half*) high-throughput sequencing, genome assembly and genome analysis. *FACS* fluorescence-activated cell sorting, *MDA* multiple displacement amplification, *PCR* polymerase chain reaction

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References

1. Blainey PC. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev. 2013;37:407–27. doi: 10.1111/1574-6976.12015. - DOI - PMC - PubMed
1. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, et al. Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol. 2006;24:680–6. doi: 10.1038/nbt1214. - DOI - PubMed
1. Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW. Whole genome amplification and de novo assembly of single bacterial cells. PloS One. 2009;4 doi: 10.1371/journal.pone.0006864. - DOI - PMC - PubMed
1. Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, et al. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME J. 2016;10:427–36. doi: 10.1038/ismej.2015.124. - DOI - PMC - PubMed
1. Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat Biotechnol. 2016;34:64–9. doi: 10.1038/nbt.3416. - DOI - PMC - PubMed

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[1] Blainey PC. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev. 2013;37:407–27. doi: 10.1111/1574-6976.12015. - DOI - PMC - PubMed

[2] Blainey PC. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev. 2013;37:407–27. doi: 10.1111/1574-6976.12015. - DOI - PMC - PubMed

[3] Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, et al. Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol. 2006;24:680–6. doi: 10.1038/nbt1214. - DOI - PubMed

[4] Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, et al. Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol. 2006;24:680–6. doi: 10.1038/nbt1214. - DOI - PubMed

[5] Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW. Whole genome amplification and de novo assembly of single bacterial cells. PloS One. 2009;4 doi: 10.1371/journal.pone.0006864. - DOI - PMC - PubMed

[6] Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW. Whole genome amplification and de novo assembly of single bacterial cells. PloS One. 2009;4 doi: 10.1371/journal.pone.0006864. - DOI - PMC - PubMed

[7] Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, et al. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME J. 2016;10:427–36. doi: 10.1038/ismej.2015.124. - DOI - PMC - PubMed

[8] Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, et al. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME J. 2016;10:427–36. doi: 10.1038/ismej.2015.124. - DOI - PMC - PubMed

[9] Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat Biotechnol. 2016;34:64–9. doi: 10.1038/nbt.3416. - DOI - PMC - PubMed

[10] Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat Biotechnol. 2016;34:64–9. doi: 10.1038/nbt.3416. - DOI - PMC - PubMed

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Dissecting the human microbiome with single-cell genomics

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Dissecting the human microbiome with single-cell genomics

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