https://orcid.org/0000-0001-5493-3429
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Abstract
Aim: The current study investigated the performance of 4 widely used DNA extraction kits using different types of high (stool) and low biomass samples (chyme, broncho alveolar lavage and sputum). Methods: Qiagen Powerfecal Pro DNA kit, Macherey Nucleospin Soil kit, Macherey Nucleospin Tissue Kit and MagnaPure LC DNA isolation kit III were evaluated in terms of DNA quantity, quality, diversity and composition profiles. Results: The quantity and quality of DNA varied among the four kits. The microbiota of the stool samples showed similar diversity and compositional profiles for the 4 kits. Conclusion: Despite differences in DNA quality and quantity, the 4 kits yielded similar results for stool samples, while all kits were not sensitive enough for low biomass samples.
Plain Language Summary
DNA extraction is a major factor affecting the microbial profile of various samples. Considering that different kits are commonly used such as QIAamp PowerFecal Pro DNA kit (QPFPD, QIAGEN), Macherey Nucleospin Soil (MNS, MACHEREY-NAGEL) Macherey Nucleospin Tissue (MNT, MACHEREY-NAGEL) and MagnaPure LC DNA isolation kit III (MPLCD, ROCHE), this study aimed to assess their performance using high (feces) and low-biomass samples. The kits were equally effective for feces samples but not sensitive enough for low biomass samples (chyme, bronchoalveolar lavage fluid and sputum).
Author contributions
S Gall-David, G Boudry and S Buffet-Bataillon designed and performed the experiments. S Gall-David performed the data analysis. S Gall-David and S Buffet-Bataillon wrote the manuscript. G Boudry critically edited the manuscript. All authors read and approved the final manuscript.
Acknowledgments
O Zemb, L Cauquil, A Bousleh from GeT-PlaGE platform (Toulouse, France).
Financial & competing interests disclosure
The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.
No writing assistance was utilized in the production of this manuscript.
Ethical conduct of research
The study on the patient's microbiota was carried out in accordance with national guidelines and authority regulations for research (National Commission for Data Protection and Liberties (CNIL-France) no. 1412467) and registered online on Clinical Trial (MICROPRUNG, NCT02857205, 02/08/2016, https://clinicaltrials.gov/ct2/show/NCT02857205). A written informed consent to participate was obtained from parents/care givers after approval by the Ethics Review Board of Rennes University Hospital (CPP no. 2017-A03594-49).
Data sharing statement
The authors certify that this manuscript reports original clinical trial data (MICROPRUNG, NCT02857205, 02/08/2016, https://clinicaltrials.gov/ct2/show/NCT02857205). Deidentified, individual data that underlie the results reported in this article (text, tables, figures and appendices), along with the study protocol will be available indefinitely for anyone who wants access to them. Data available at https://doi.org/10.57745/L8MRR0.