Next Article in Journal
Magnetic Fields and Cancer: Epidemiology, Cellular Biology, and Theranostics
Previous Article in Journal
Genome Editing Using CRISPR-Cas9 and Autoimmune Diseases: A Comprehensive Review
Article

Determination of the Optimal Bacterial DNA Extraction Method to Explore the Urinary Microbiota

1
Laboratoire de Biologie des Tumeurs Solides, Département de Pathologie et Oncobiologie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France
2
Laboratoire de Bactériologie, CHU Montpellier, Université de Montpellier, 34295 Montpellier, France
3
UMR MIVEGEC, IRD-CNRS-Université de Montpellier, 34394 Montpellier, France
4
Institut Régional du Cancer de Montpellier, ICM, 34298 Montpellier, France
*
Author to whom correspondence should be addressed.
Academic Editor: Grzegorz Wegrzyn
Int. J. Mol. Sci. 2022, 23(3), 1336; https://doi.org/10.3390/ijms23031336
Received: 24 December 2021 / Revised: 21 January 2022 / Accepted: 22 January 2022 / Published: 25 January 2022
(This article belongs to the Section Molecular Microbiology)
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. View Full-Text
Keywords: microbiota; DNA extraction; NGS microbiota; DNA extraction; NGS
Show Figures

Figure 1

MDPI and ACS Style

Vendrell, J.A.; Henry, S.; Cabello-Aguilar, S.; Heckendorn, E.; Godreuil, S.; Solassol, J. Determination of the Optimal Bacterial DNA Extraction Method to Explore the Urinary Microbiota. Int. J. Mol. Sci. 2022, 23, 1336. https://doi.org/10.3390/ijms23031336

AMA Style

Vendrell JA, Henry S, Cabello-Aguilar S, Heckendorn E, Godreuil S, Solassol J. Determination of the Optimal Bacterial DNA Extraction Method to Explore the Urinary Microbiota. International Journal of Molecular Sciences. 2022; 23(3):1336. https://doi.org/10.3390/ijms23031336

Chicago/Turabian Style

Vendrell, Julie A., Steven Henry, Simon Cabello-Aguilar, Elise Heckendorn, Sylvain Godreuil, and Jérôme Solassol. 2022. "Determination of the Optimal Bacterial DNA Extraction Method to Explore the Urinary Microbiota" International Journal of Molecular Sciences 23, no. 3: 1336. https://doi.org/10.3390/ijms23031336

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop