Unveiling Microbial Diversity: Harnessing Long-Read Sequencing Technology

Authors

Daniel P Agustinho
Yilei Fu
Vipin K Menon
Ginger A Metcalf
Todd J Treangen
Fritz J Sedlazeck

Language

English

Publication Date

6-1-2024

Journal

Nature Methods

DOI

10.1038/s41592-024-02262-1

PMID

38689099

PMCID

PMC11955098

PubMedCentral® Posted Date

3-30-2025

PubMedCentral® Full Text Version

Author MSS

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.

Keywords

Humans, Computational Biology, High-Throughput Nucleotide Sequencing, Metagenome, Metagenomics, Microbiota, Sequence Analysis, DNA

Published Open-Access

yes

Recommended Citation

Agustinho, Daniel P; Fu, Yilei; Menon, Vipin K; et al., "Unveiling Microbial Diversity: Harnessing Long-Read Sequencing Technology" (2024). Faculty and Staff Publications. 5107.
https://digitalcommons.library.tmc.edu/baylor_docs/5107