Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Comment
  • Published:

Long-read metagenomics paves the way toward a complete microbial tree of life

Nature Methods volume 20, pages 30–31 (2023)Cite this article

Subjects

Long-read sequencing has made closed microbial genomes a routine task, and the dramatic increase in quality and quantity now paves the way to a complete microbial tree of life through genome-centric metagenomics.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

References

  1. Timmis, K. et al. Microb. Biotechnol. 10, 984–987 (2017).

    Article  Google Scholar 

  2. Cavicchioli, R. et al. Nat. Rev. Microbiol. 17, 569–586 (2019).

    Article  CAS  Google Scholar 

  3. Gilbert, J. A. et al. Nat. Med. 24, 392–400 (2018).

    Article  CAS  Google Scholar 

  4. Ling, L. L. et al. Nature 517, 455–459 (2015).

    Article  CAS  Google Scholar 

  5. Lu, H. et al. Nature 604, 662–667 (2022).

    Article  CAS  Google Scholar 

  6. Gilbert, J. A. & Neufeld, J. D. PLoS Biol. 12, e1002020 (2014).

    Article  Google Scholar 

  7. Bernhardsgrütter, I., Stoffel, G. M., Miller, T. E. & Erb, T. J. Curr. Opin. Biotechnol. 67, 80–87 (2021).

    Article  Google Scholar 

  8. Lander, E. S. et al. Nature 409, 860–921 (2001).

    Article  CAS  Google Scholar 

  9. Venter, J. C. et al. Science 291, 1304–1351 (2001).

    Article  CAS  Google Scholar 

  10. Koren, S. & Phillippy, A. M. Curr. Opin. Microbiol. 23, 110–120 (2015).

    Article  CAS  Google Scholar 

  11. Loman, N. J., Quick, J. & Simpson, J. T. Nat. Methods 12, 733–735 (2015).

    Article  CAS  Google Scholar 

  12. Lewis, W. H., Tahon, G., Geesink, P., Sousa, D. Z. & Ettema, T. J. G. Nat. Rev. Microbiol. 19, 225–240 (2021).

    Article  CAS  Google Scholar 

  13. Lee, K. S. et al. Nat. Protoc. 16, 634–676 (2021).

    Article  CAS  Google Scholar 

  14. Imachi, H. et al. Nature 577, 519–525 (2020).

    Article  CAS  Google Scholar 

  15. Spang, A. et al. Nature 521, 173–179 (2015).

    Article  CAS  Google Scholar 

  16. Tyson, G. W. et al. Nature 428, 37–43 (2004).

    Article  CAS  Google Scholar 

  17. Teeling, H., Meyerdierks, A., Bauer, M., Amann, R. & Glöckner, F. O. Environ. Microbiol. 6, 938–947 (2004).

    Article  CAS  Google Scholar 

  18. Sharon, I. et al. Genome Res. 23, 111–120 (2013).

    Article  CAS  Google Scholar 

  19. Albertsen, M. et al. Nat. Biotechnol. 31, 533–538 (2013).

    Article  CAS  Google Scholar 

  20. Hug, L. A. et al. Nat. Microbiol. 1, 16048 (2016).

    Article  CAS  Google Scholar 

  21. Louca, S., Mazel, F., Doebeli, M. & Parfrey, L. W. PLoS Biol. 17, e3000106 (2019).

    Article  CAS  Google Scholar 

  22. Larsen, B. B. et al. Q. Rev. Biol. 92, 229–265 (2017).

    Article  Google Scholar 

  23. Parks, D. H. et al. Nucleic Acids Res. 50(D1), D785–D794 (2022).

    Article  CAS  Google Scholar 

  24. Singleton, C. M. et al. Nat. Commun. 12, 2009 (2021).

    Article  CAS  Google Scholar 

  25. Sereika, M. et al. Nat. Methods 19, 823–826 (2022).

    Article  CAS  Google Scholar 

  26. Kolmogorov, M. et al. Nat. Methods 17, 1103–1110 (2020).

    Article  CAS  Google Scholar 

  27. Bickhart, D. M. et al. Nat. Biotechnol. 40, 711–719 (2022).

    Article  CAS  Google Scholar 

  28. Feng, X., Cheng, H., Portik, D. & Li, H. Nat. Methods 19, 671–674 (2022).

    Article  CAS  Google Scholar 

  29. Bowers, R. M. et al. Nat. Biotechnol. 35, 725–731 (2017).

    Article  CAS  Google Scholar 

  30. Chen, L.-X., Anantharaman, K., Shaiber, A., Eren, A. M. & Banfield, J. F. Genome Res. 30, 315–333 (2020).

    Article  CAS  Google Scholar 

  31. Lieberman-Aiden, E. et al. Science 326, 289–293 (2009).

    Article  CAS  Google Scholar 

  32. Tourancheau, A., Mead, E. A., Zhang, X. S. & Fang, G. Nat. Methods 18, 491–498 (2021).

    Article  CAS  Google Scholar 

  33. NIH HMP Working Group. et al. Genome Res. 19, 2317–2323 (2009).

    Article  Google Scholar 

  34. Ehrlich, S. D. & the MetaHIT Consortium. in Metagenomics of the Human Body (ed. Nelson, K.) 307–316 (Springer, 2011); https://doi.org/10.1007/978-1-4419-7089-3_15

  35. Ley, R. Nature 606, 435 (2022).

    Article  CAS  Google Scholar 

  36. Lewin, H. A. et al. Proc. Natl Acad. Sci. USA 119, e2115635118 (2022).

  37. Wu, D. et al. Nature 462, 1056–1060 (2009).

    Article  CAS  Google Scholar 

  38. Rinke, C. et al. Nature 499, 431–437 (2013).

    Article  CAS  Google Scholar 

  39. Nayfach, S. et al. Nat. Biotechnol. 39, 499–509 (2021).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by research grants from Villum Fonden (15510) and the Poul Due Jensen Foundation (Microflora Danica).

Author information

Authors and Affiliations

  1. Center for Microbial Communities, Aalborg University, Aalborg, Denmark

    Mads Albertsen

Authors
  1. Mads Albertsen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mads Albertsen.

Ethics declarations

Competing interests

The author declares no competing interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Albertsen, M. Long-read metagenomics paves the way toward a complete microbial tree of life. Nat Methods 20, 30–31 (2023). https://doi.org/10.1038/s41592-022-01726-6

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41592-022-01726-6

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research