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Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics.
Meslier, Victoria; Menozzi, Elisa; David, Aymeric; Morabito, Christian; Lucas Del Pozo, Sara; Famechon, Alexandre; North, Janet; Quinquis, Benoit; Koletsi, Sofia; Macnaughtan, Jane; Mezabrovschi, Roxana; Ehrlich, S Dusko; Schapira, Anthony H V; Almeida, Mathieu.
Afiliação
  • Meslier V; MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
  • Menozzi E; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
  • David A; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
  • Morabito C; Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK.
  • Lucas Del Pozo S; MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
  • Famechon A; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
  • North J; MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
  • Quinquis B; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
  • Koletsi S; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
  • Macnaughtan J; Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK.
  • Mezabrovschi R; MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
  • Ehrlich SD; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
  • Schapira AHV; Research Department of Hematology, Cancer Institute, University College London (UCL), London WC1E 6BT, UK.
  • Almeida M; MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Biomolecules ; 13(10)2023 10 11.
Article em En | MEDLINE | ID: mdl-37892187
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.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: DNA / Microbiota Limite: Humans Idioma: En Ano de publicação: 2023 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: DNA / Microbiota Limite: Humans Idioma: En Ano de publicação: 2023 Tipo de documento: Article