Abstract
Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing’s profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.
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Acknowledgements
We thank D. M. Portik, for important feedback and kindly authorizing the use of Fig. 3. We also thank A. F. Pomerantz and K. D. Curry for their helpful feedback. This work was supported by the National Institute of Allergy and Infectious Diseases (grant nos. 1U19AI144297 and P01-AI152999) and by the National Science Foundation (grant nos. EF-2126387 and IIS-2239114). Y.F. and T.T. were supported in part by the National Institutes of Health NIAID award P01-AI152999. T.T. was also supported by the National Science Foundation grants EF-2126387, IIS-2239114 and CNS-1338099.
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F.J.S. has received research funding from Illumina, PacBio, Genentech and Oxford Nanopore. V.K.M. is an employee of Genentech. The remaining authors declare no competing interests.
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Agustinho, D.P., Fu, Y., Menon, V.K. et al. Unveiling microbial diversity: harnessing long-read sequencing technology. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02262-1
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DOI: https://doi.org/10.1038/s41592-024-02262-1
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