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RSS FeedsIJMS, Vol. 23, Pages 1336: Determination of the Optimal Bacterial DNA Extraction Method to Explore the Urinary Microbiota (International Journal of Molecular Sciences)

 
 

25 january 2022 11:09:27

 
IJMS, Vol. 23, Pages 1336: Determination of the Optimal Bacterial DNA Extraction Method to Explore the Urinary Microbiota (International Journal of Molecular Sciences)
 


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.


 
69 viewsCategory: Biochemistry, Biophysics, Molecular Biology
 
IJMS, Vol. 23, Pages 1335: Fabrication of Fragment Antibody–Enzyme Complex as a Sensing Element for Immunosensing (International Journal of Molecular Sciences)
IJMS, Vol. 23, Pages 1337: Genome Editing Using CRISPR-Cas9 and Autoimmune Diseases: A Comprehensive Review (International Journal of Molecular Sciences)
 
 
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