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

Author:

Cook Ryan1ORCID,Telatin Andrea1ORCID,Hsieh Shen-Yuan1ORCID,Newberry Fiona2ORCID,Tariq Mohammad A.3ORCID,Baker Dave J.1ORCID,Carding Simon R.41ORCID,Adriaenssens Evelien M.1ORCID

Affiliation:

1. Quadram Institute Bioscience, Norwich, NR4 7UQ, UK

2. Department of Biosciences, Nottingham Trent University, Nottingham, NG11 8NS, UK

3. Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne, NE1 8ST, UK

4. Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK

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.

Funder

Biotechnology and Biological Sciences Research Council

Medical Research Council

Publisher

Microbiology Society

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