1887

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Volume 10, Issue 4

Nanopore and Illumina sequencing reveal different viral populations from human gut samples Open Access

Abstract

The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): human virome , Illumina , microbiome , Nanopore and viromics
Funding
This study was supported by the:
  • Medical Research Council (Award MR/T030062/1)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BB/W015706/1)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BB/CCG1860/1)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR13636)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR13635)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR13634)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BB/X011011/1)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR13633)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR13631)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BB/X011054/1)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR10356)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR10355)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BB/R012490/1)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/731 000PR10353)
    • Principle Award Recipient: NotApplicable
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-05-16
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Nanopore and Illumina sequencing reveal different viral populations from human gut samples
M Gen 10, 001236 (2024); https://doi.org/10.1099/mgen.0.001236
/content/journal/mgen/10.1099/mgen.0.001236
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