The DOI matches its Crossref record; 44 of the 44 references it cites were found in a registry or an index.
Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis
Open accessAbstract
A major limitation for better understanding the role of the human gut virome in health and disease is the lack of validated methods that allow high throughput virome analysis. To overcome this, we evaluated the quantitative effect of homogenisation, centrifugation, filtration, chloroform treatment and random amplification on a mock-virome (containing nine highly diverse viruses) and a bacterial mock-community (containing four faecal bacterial species) using quantitative PCR and next-generation sequencing. This resulted in an optimised protocol that was able to recover all viruses present in the mock-virome and strongly alters the ratio of viral versus bacterial and 16S rRNA genetic material in favour of viruses (from 43.2% to 96.7% viral reads and from 47.6% to 0.19% bacterial reads). Furthermore, our study indicated that most of the currently used virome protocols, using small filter pores and/or stringent centrifugation conditions may have largely overlooked large viruses present in viromes. We propose NetoVIR (N ovel e nrichment t echnique o f VIR omes), which allows for a fast, reproducible and high throughput sample preparation for viral metagenomics studies, introducing minimal bias. This procedure is optimised mainly for faecal samples, but with appropriate concentration steps can also be used for other sample types with lower initial viral loads.
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Cites
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Cited by
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
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Microbial Ecology along the Gastrointestinal Tract
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Phages and their potential to modulate the microbiome and immunity
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Virus Metagenomics in Farm Animals: A Systematic Review
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Metadata
- Authors
- Conceição-Neto, N., Zeller, M., Lefrère, H., De Bruyn, P., Beller, L., Deboutte, W., Yinda, C. K., Lavigne, R., Maes, P., Ranst, M. V., Heylen, E., & Matthijnssens, J.
- Venue
- Scientific Reports
- Published
- 2015-11-12
- Volume
- 5
- Issue
- 1
- Pages
- 16532-16532
- ISSN
- 2045-2322 (ISSN-L)
- OpenAlex
- W2410580207
- Cited by
- 363
- References
- 44
- FWCI
- 15.15
- Type
- journal article
- Language
- en
- Open access
- gold
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- Conceição-Neto, N., Zeller, M., Lefrère, H., De Bruyn, P., Beller, L., Deboutte, W., Yinda, C. K., Lavigne, R., Maes, P., Ranst, M. V., Heylen, E., & Matthijnssens, J. (2015). Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Scientific Reports. https://doi.org/10.1038/srep16532
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
