ArticleMicrobial genomics2024
Nanopore and Illumina sequencing reveal different viral populations from human gut samples.
Article in Microbial genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny.Current protocols · 2026Article
- Oxford Nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing.Microbiology spectrum · 2026Article
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- Protein structure-informed bacteriophage genome annotation with Phold.Nucleic acids research · 2026Article
- Limited consensus of marine viral diversity observed across techniques.Environmental microbiome · 2025Article
- The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.European respiratory review : an official journal of the European Respiratory Society · 2025Review
- Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.bioRxiv : the preprint server for biology · 2025Article
- Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.Viruses · 2025Article
- Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses.Environmental microbiology · 2025Article
- Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners.Microbiome · 2024Article
- How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies.Microbial genomics · 2024Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.