@misc{10481/99173,
year = {2024},
month = {11},
url = {https://hdl.handle.net/10481/99173},
abstract = {Approaches to DNA extraction play a crucial role in determining the variability
of results obtained through 16S rRNA amplicon sequencing. Particularly,
clay-rich samples can impede the efficiency of various standard cultivationindependent
techniques. We conducted an inter-laboratory comparison
study to thoroughly assess the efficacy of two published DNA extraction
methods (kit-based and phenol-chloroform-based) specifically designed for
bentonite samples. To this end, we spiked Wyoming MX 80 bentonite with
two different mock communities and compared the obtained DNA yield and
purity, the presence of contaminants and the community profile. Our findings
suggest that both methods are equally viable, with the best choice
depending on the specific requirements of the downstream analysis. However,
it is crucial to maintain consistency in the chosen method, as comparing
results becomes challenging, particularly in the presence of bentonite. In
summary, our study emphasizes the significance of standardized DNA
extraction methods and underscores the importance of validating these
methods using appropriate controls when studying microbial communities
with 16S rRNA amplicon sequencing, particularly in environments characterized
by low biomass and clay-rich compositions. Additionally, slight modifications
to one of the extraction methods can substantially enhance its
efficiency.},
organization = {European Union’s Horizon
2020 Research and Innovation Programme
(2014-2018) under grant agreement No. 847593},
organization = {SÚRAO
(SO2020-017)},
publisher = {Wiley Online Library},
title = {Comparing the effectiveness of different DNA extraction methods in MX-80 bentonite},
doi = {10.1111/1758-2229.70047},
author = {Mijnendonckx, Kristel and Smolders, Carla and Bartak, Deepa and Le Duc, Trung and Morales Hidalgo, Mar and Povedano-Priego, Cristina and Jroundi, Fadwa and L. Merroun, Mohamed and Leys, Natalie and Cerna, Katerina},
}