| Added by | pcoopman |
|---|---|
| Group name | EquipePC |
| Item Type | Journal Article |
| Title | Determination of the Optimal Bacterial DNA Extraction Method to Explore the Urinary Microbiota |
| Creator | Vendrell et al. |
| Author | Julie A. Vendrell |
| Author | Steven Henry |
| Author | Simon Cabello-Aguilar |
| Author | Elise Heckendorn |
| Author | Sylvain Godreuil |
| Author | Jérôme Solassol |
| Abstract | Recent advances in molecular biology have been successfully applied to the exploration of microbiota from various fluids. However, the urinary microbiota remains poorly explored, as its analysis requires specific technical considerations. Indeed, urine is a low microbial biomass environment, in which the representativity of each bacterium must be respected to obtain accurate data. Thus, sensitive extraction methods must be used to obtain good quality DNA while preserving the proportions between species. To address this, we compared the efficiency of five extraction methods on artificial urine samples spiked with low amounts of four bacteria species. The quality of the DNA obtained was further evaluated by different molecular biology approaches, including quantitative PCR and amplicon-based next-generation sequencing (NGS). Although two extraction methods allowed DNA of sufficient quality for NGS analysis to be obtained, one kit extracted a larger amount of DNA, which is more suitable for the detection of low-abundant bacteria. Results from the subsequent assessment of this kit on 29 human clinical samples correlated well with results obtained using conventional bacterial urine culture. We hope that our work will make investigators aware of the importance of challenging and adapting their practice in terms of the molecular biology approaches used for the exploration of microbiota. |
| Publication | International Journal of Molecular Sciences |
| Volume | 23 |
| Issue | 3 |
| Pages | 1336 |
| Date | 2022-01-25 |
| Journal Abbr | Int J Mol Sci |
| Language | eng |
| DOI | 10.3390/ijms23031336 |
| ISSN | 1422-0067 |
| Library Catalog | PubMed |
| Extra | PMID: 35163261 PMCID: PMC8835916 |
| Tags | Bacteria, Biomass, clinic, DNA extraction, DNA, Bacterial, first-last-corresponding, Humans, Male, Microbiota, NGS, Urine |
| Date Added | 2023/11/15 - 16:25:40 |
| Date Modified | 2023/11/15 - 16:26:25 |
| Notes and Attachments | PubMed entry (Attachment) Texte intégral (Attachment) |
Institut de Recherche en Cancérologie de
