Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes
The virome, composed of viruses inhabiting diverse ecosystems, significantly influences microbial community dynamics and host health. The phenol-chloroform DNA extraction protocol for viromes, though effective, is time-intensive and requires the use of multiple toxic chemicals. This study introduces...
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PeerJ Inc.
2025-01-01
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| author | Michael Shamash Saniya Kapoor Corinne F. Maurice |
| author_facet | Michael Shamash Saniya Kapoor Corinne F. Maurice |
| author_sort | Michael Shamash |
| collection | DOAJ |
| description | The virome, composed of viruses inhabiting diverse ecosystems, significantly influences microbial community dynamics and host health. The phenol-chloroform DNA extraction protocol for viromes, though effective, is time-intensive and requires the use of multiple toxic chemicals. This study introduces a streamlined, scalable protocol for DNA extraction using a commercially-available kit as an alternative, assessing its performance against the phenol-chloroform method across human fecal, mouse fecal, and soil samples. No significant differences in virome diversity or community composition were seen between methods. Most viral operational taxonomic units (vOTUs) were common to both methods, with only a small percentage unique to either approach. Alpha- and beta-diversity analyses showed no significant impact of the extraction method on virome composition, confirming the kit’s efficacy and versatility on sample types beyond those officially supported by the manufacturer. While the kit approach offers benefits like reduced toxicity and increased throughput, it has limitations such as higher costs and potential issues reliably capturing low-abundance taxa. This protocol provides a viable option for large-scale virome studies, although the phenol-chloroform approach may still be preferable for specific sample types. |
| format | Article |
| id | doaj-art-463244459ace4c339e5dadb65d42c3cd |
| institution | Kabale University |
| issn | 2167-8359 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj-art-463244459ace4c339e5dadb65d42c3cd2025-01-16T15:05:14ZengPeerJ Inc.PeerJ2167-83592025-01-0113e1878510.7717/peerj.18785Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromesMichael Shamash0Saniya Kapoor1Corinne F. Maurice2Department of Microbiology & Immunology, McGill University, Montreal, QC, CanadaDepartment of Microbiology & Immunology, McGill University, Montreal, QC, CanadaDepartment of Microbiology & Immunology, McGill University, Montreal, QC, CanadaThe virome, composed of viruses inhabiting diverse ecosystems, significantly influences microbial community dynamics and host health. The phenol-chloroform DNA extraction protocol for viromes, though effective, is time-intensive and requires the use of multiple toxic chemicals. This study introduces a streamlined, scalable protocol for DNA extraction using a commercially-available kit as an alternative, assessing its performance against the phenol-chloroform method across human fecal, mouse fecal, and soil samples. No significant differences in virome diversity or community composition were seen between methods. Most viral operational taxonomic units (vOTUs) were common to both methods, with only a small percentage unique to either approach. Alpha- and beta-diversity analyses showed no significant impact of the extraction method on virome composition, confirming the kit’s efficacy and versatility on sample types beyond those officially supported by the manufacturer. While the kit approach offers benefits like reduced toxicity and increased throughput, it has limitations such as higher costs and potential issues reliably capturing low-abundance taxa. This protocol provides a viable option for large-scale virome studies, although the phenol-chloroform approach may still be preferable for specific sample types.https://peerj.com/articles/18785.pdfViromeDNA extractionBacteriophageHuman gut microbiotaSoil |
| spellingShingle | Michael Shamash Saniya Kapoor Corinne F. Maurice Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes PeerJ Virome DNA extraction Bacteriophage Human gut microbiota Soil |
| title | Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes |
| title_full | Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes |
| title_fullStr | Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes |
| title_full_unstemmed | Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes |
| title_short | Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes |
| title_sort | benchmarking of a time saving and scalable protocol for the extraction of dna from diverse viromes |
| topic | Virome DNA extraction Bacteriophage Human gut microbiota Soil |
| url | https://peerj.com/articles/18785.pdf |
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