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
Access options
Subscribe to Nature+
Get immediate online access to Nature and 55 other Nature journal
$29.99
monthly
Subscribe to Journal
Get full journal access for 1 year
$99.00
only $8.25 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Buy article
Get time limited or full article access on ReadCube.
$32.00
All prices are NET prices.
References
Timmis, K. et al. Microb. Biotechnol. 10, 984–987 (2017).
Cavicchioli, R. et al. Nat. Rev. Microbiol. 17, 569–586 (2019).
Gilbert, J. A. et al. Nat. Med. 24, 392–400 (2018).
Ling, L. L. et al. Nature 517, 455–459 (2015).
Lu, H. et al. Nature 604, 662–667 (2022).
Gilbert, J. A. & Neufeld, J. D. PLoS Biol. 12, e1002020 (2014).
Bernhardsgrütter, I., Stoffel, G. M., Miller, T. E. & Erb, T. J. Curr. Opin. Biotechnol. 67, 80–87 (2021).
Lander, E. S. et al. Nature 409, 860–921 (2001).
Venter, J. C. et al. Science 291, 1304–1351 (2001).
Koren, S. & Phillippy, A. M. Curr. Opin. Microbiol. 23, 110–120 (2015).
Loman, N. J., Quick, J. & Simpson, J. T. Nat. Methods 12, 733–735 (2015).
Lewis, W. H., Tahon, G., Geesink, P., Sousa, D. Z. & Ettema, T. J. G. Nat. Rev. Microbiol. 19, 225–240 (2021).
Lee, K. S. et al. Nat. Protoc. 16, 634–676 (2021).
Imachi, H. et al. Nature 577, 519–525 (2020).
Spang, A. et al. Nature 521, 173–179 (2015).
Tyson, G. W. et al. Nature 428, 37–43 (2004).
Teeling, H., Meyerdierks, A., Bauer, M., Amann, R. & Glöckner, F. O. Environ. Microbiol. 6, 938–947 (2004).
Sharon, I. et al. Genome Res. 23, 111–120 (2013).
Albertsen, M. et al. Nat. Biotechnol. 31, 533–538 (2013).
Hug, L. A. et al. Nat. Microbiol. 1, 16048 (2016).
Louca, S., Mazel, F., Doebeli, M. & Parfrey, L. W. PLoS Biol. 17, e3000106 (2019).
Larsen, B. B. et al. Q. Rev. Biol. 92, 229–265 (2017).
Parks, D. H. et al. Nucleic Acids Res. 50(D1), D785–D794 (2022).
Singleton, C. M. et al. Nat. Commun. 12, 2009 (2021).
Sereika, M. et al. Nat. Methods 19, 823–826 (2022).
Kolmogorov, M. et al. Nat. Methods 17, 1103–1110 (2020).
Bickhart, D. M. et al. Nat. Biotechnol. 40, 711–719 (2022).
Feng, X., Cheng, H., Portik, D. & Li, H. Nat. Methods 19, 671–674 (2022).
Bowers, R. M. et al. Nat. Biotechnol. 35, 725–731 (2017).
Chen, L.-X., Anantharaman, K., Shaiber, A., Eren, A. M. & Banfield, J. F. Genome Res. 30, 315–333 (2020).
Lieberman-Aiden, E. et al. Science 326, 289–293 (2009).
Tourancheau, A., Mead, E. A., Zhang, X. S. & Fang, G. Nat. Methods 18, 491–498 (2021).
NIH HMP Working Group. et al. Genome Res. 19, 2317–2323 (2009).
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
Ley, R. Nature 606, 435 (2022).
Lewin, H. A. et al. Proc. Natl Acad. Sci. USA 119, e2115635118 (2022).
Wu, D. et al. Nature 462, 1056–1060 (2009).
Rinke, C. et al. Nature 499, 431–437 (2013).
Nayfach, S. et al. Nat. Biotechnol. 39, 499–509 (2021).
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
Corresponding author
Ethics declarations
Competing interests
The author declares no competing interests.
Rights and permissions
About this article
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
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41592-022-01726-6