ArticleJournal of advanced research2023
Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome.
Article in Journal of advanced research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 44 citations in OpenAlex.
- Disrupted Gut Viral-Bacterial Ecology of Patients With Liver Cirrhosis.Liver international : official journal of the International Association for the Study of the Liver · 2026Article
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- Article
- Combined NGS and proteomics improves viral diagnostics in wildlife: coronaviruses confirmed in hedgehogs.Frontiers in cellular and infection microbiology · 2026Article
- A comparison of methods for the optimal recovery of the human fecal virome.ISME communications · 2026Article
- DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.bioRxiv : the preprint server for biology · 2025Article
- CLAE: A High-Fidelity Nanopore Sequencing Strategy for Read-Level Viral Variant Detection and Environmental RNA Virus Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Shotgun metagenomics on indoor air for surveillance of respiratory, enteric, and skin viruses in a Belgian daycare setting, January to December 2022.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2025Article
- Biases and complementarity in gut viromes obtained from bulk and virus-like particle-enriched metagenomic sequencing.Microbiology spectrum · 2025Article
- Characteristics of the gut virome in patients with premalignant colorectal adenoma.Journal of translational medicine · 2025Article
- Advances in Wastewater-Based Epidemiology for Pandemic Surveillance: Methodological Frameworks and Future Perspectives.Microorganisms · 2025Review
- The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures.Genome medicine · 2025Article
- Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.Viruses · 2025Article
- The gut and circulating virome: emerging players in aging and longevity.Frontiers in aging · 2025Review
- Metagenomic insights into viral dynamics and funcation in Baijiu.Current research in food science · 2025Article
- A metagenome-wide study of the gut virome in chronic kidney disease.Theranostics · 2025Article
- Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.mSystems · 2024Article
- Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics.Food and environmental virology · 2024Article
- Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis.Journal of translational medicine · 2024Article
- Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia.mSphere · 2024Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
introductionViruses in the human gut have been linked to health and disease. Deciphering the gut virome is dependent on metagenomic sequencing of the virus-like particles (VLPs) purified from the fecal specimens. A major limitation of conventional viral metagenomic sequencing is the low recoverability of viral genomes from the metagenomic dataset.
objectivesTo develop an optimal method for viral amplification and metagenomic sequencing for maximizing the recovery of viral genomes.
methodsWe performed parallel virus enrichment and DNA extraction to generate ∼ 30 viral DNA samples from each of 5 fresh fecal specimens and conducted the experiments including 1) optimizing the cycle number for high-fidelity enzyme-based PCR amplification, 2) evaluating the reproducibility of the optimally whole viral metagenomic experimental process, 3) evaluating the reliability of multiple displacement amplification (MDA), 4) testing the capability of long-read sequencing for improving viral metagenomic assembly, and 5) comparing the differences between viral metagenomic and bulk metagenomic approaches.
resultsOur results revealed that the optimal cycle number for PCR amplification is 15. We verified the reliability of MDA and the effectiveness of long-read sequencing. Based on our optimized results, we generated 151 high-quality viruses using the dataset combined from short-read and long-read sequencing. Genomic analysis of these viruses found that most (60.3%) of them were previously unknown and showed a remarkable diversity of viral functions, especially the existence of 206 viral auxiliary metabolic genes. Finally, we uncovered significant differences in the efficiency and coverage of viral identification between viral metagenomic and bulk metagenomic approaches.
conclusionsOur study demonstrates the potential of optimized experiment and sequencing strategies in uncovering viral genomes from fecal specimens, which will facilitate future research about the genome-level characterization of complex viral communities.
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