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Review
. 2024 Dec 2;12(12):2482.
doi: 10.3390/microorganisms12122482.

Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology

Yanhua Han  1   2 , Jinling He  1   2 , Minghui Li  1   2 , Yunjuan Peng  3 , Hui Jiang  1   2 , Jiangchao Zhao  3 , Ying Li  1   2 , Feilong Deng  1   2
Affiliations
Review

Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology

Yanhua Han et al. Microorganisms. .

Abstract

Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio's high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, such as the human gut and soil, which provides broader context for further exploration. Key studies are discussed to highlight HiFi sequencing's ability to recover complete and coherent microbial genomes from complex microbiomes, showcasing its superior accuracy and continuity compared to other sequencing technologies. Additionally, we explore the potential applications of HiFi sequencing in quantitative microbial analysis, as well as the detection of single nucleotide variations (SNVs) and structural variations (SVs). PacBio HiFi sequencing is establishing a new benchmark in metagenomics, with the potential to significantly enhance our understanding of microbial ecology and drive forward advancements in both environmental and clinical applications.

Keywords: PacBio HiFi; high-fidelity sequencing; long-read sequencing; metagenomics; taxonomic resolution.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Potential application of shotgun metagenomics.
Figure 2
Figure 2
A comparison of metagenomic and culturomic approaches in microbial research.
Figure 3
Figure 3
Schematic diagram of the advantages of long reads.
See this image and copyright information in PMC

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