Meslier, Victoria;
Menozzi, Elisa;
David, Aymeric;
Morabito, Christian;
Lucas Del Pozo, Sara;
Famechon, Alexandre;
North, Janet;
... Almeida, Mathieu; + view all
(2023)
Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics.
Biomolecules
, 13
(10)
, Article 1505. 10.3390/biom13101505.
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Abstract
Recent attention has highlighted the importance of oral microbiota in human health and disease, e.g., in Parkinson’s disease, notably using shotgun metagenomics. One key aspect for efficient shotgun metagenomic analysis relies on optimal microbial sampling and DNA extraction, generally implementing commercial solutions developed to improve sample collection and preservation, and provide high DNA quality and quantity for downstream analysis. As metagenomic studies are today performed on a large number of samples, the next evolution to increase study throughput is with DNA extraction automation. In this study, we proposed a semi-automated DNA extraction protocol for human salivary samples collected with a commercial kit, and compared the outcomes with the DNA extraction recommended by the manufacturer. While similar DNA yields were observed between the protocols, our semi-automated DNA protocol generated significantly higher DNA fragment sizes. Moreover, we showed that the oral microbiome composition was equivalent between DNA extraction methods, even at the species level. This study demonstrates that our semi-automated protocol is suitable for shotgun metagenomic analysis, while allowing for improved sample treatment logistics with reduced technical variability and without compromising the structure of the oral microbiome.
| Type: | Article |
|---|---|
| Title: | Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.3390/biom13101505 |
| Publisher version: | https://doi.org/10.3390/biom13101505 |
| Language: | English |
| Additional information: | Copyright © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
| Keywords: | DNA extraction; automation; oral microbiome; shotgun metagenomics |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Medicine UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Medicine > Inst for Liver and Digestive Hlth |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10179748 |
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