Tools
ToolsCook, Ryan, Telatin, Andrea, Hsieh, Shen Yuan, Newberry, Fiona, Tariq, Mohammad A., Baker, Dave J., Carding, Simon R. and Adriaenssens, Evelien M. (2024) Nanopore and Illumina sequencing reveal different viral populations from human gut samples. Microbial Genomics, 10 (4). ISSN 2057-5858
Preview |
PDF (Cook_etal_2024_mgen001236)
- Published Version
Available under License Creative Commons Attribution. Download (2MB) | Preview |
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.
| Item Type: | Article |
|---|---|
| Additional Information: | Data Summary: All reads used in this study are available on European Nucleotide Archive (ENA) within the project PRJEB47625. The assemblies are available on Zenodo via https://zenodo.org/records/10650983. Funding Information: This research was supported by the BBSRC Institute Strategic Programme Grant Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/731 000PR10353, BBS/E/F/000PR10355 and BBS/E/F/000PR10356 (S.R.C., E.M.A); and by the BBSRC Institute Strategic Programme Food Microbiome and Health BB/X011054/1 and its constituent projects BBS/E/F/000PR13631 and BBS/E/F/000PR13633 (R.C, S.R.C, E.M.A); and by the BBSRC Institute Strategic Programme Microbes and Food Safety BB/X011011/1 and its constituent projects BBS/E/F/000PR13634, BBS/E/ F/000PR13635 and BBS/E/F/000PR13636 (E.M.A); and the BBSRC Core Capability Grant BB/CCG1860/1 (D.B). R.C and E.M.A were supported by the BBSRC grant Bacteriophages in Gut Health BB/W015706/1. F.N was supported by an Invest in ME Research and UEA-Faculty of Health and Medicine PhD studentship and a Ramsey Award from SOLVE M.E. We gratefully acknowledge CLIMB-BIG-DATA infrastructure (MR/T030062/1) support for high-performance computing. |
| Uncontrolled Keywords: | human virome,illumina,microbiome,nanopore,viromics,epidemiology,microbiology,molecular biology,genetics ,/dk/atira/pure/subjectarea/asjc/2700/2713 |
| Faculty \ School: | Faculty of Medicine and Health Sciences > Norwich Medical School Faculty of Science > School of Biological Sciences |
| UEA Research Groups: | Faculty of Medicine and Health Sciences > Research Centres > Norwich Institute for Healthy Aging Faculty of Medicine and Health Sciences > Research Groups > Gastroenterology and Gut Biology |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 23 Oct 2024 15:30 |
| Last Modified: | 23 Oct 2024 15:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97154 |
| DOI: | 10.1099/mgen.0.001236 |
Downloads
Downloads per month over past year
Actions (login required)
 |
View Item |