Comparing the effectiveness of different DNA extraction methods in MX-80 bentonite
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F46747885%3A24620%2F24%3A00012904" target="_blank" >RIV/46747885:24620/24:00012904 - isvavai.cz</a>
Result on the web
<a href="https://doi.org/10.1111/1758-2229.70047" target="_blank" >https://doi.org/10.1111/1758-2229.70047</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1111/1758-2229.70047" target="_blank" >10.1111/1758-2229.70047</a>
Alternative languages
Result language
angličtina
Original language name
Comparing the effectiveness of different DNA extraction methods in MX-80 bentonite
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10511 - Environmental sciences (social aspects to be 5.7)
Result continuities
Project
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Continuities
R - Projekt Ramcoveho programu EK
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Environmental Microbiology Reports
ISSN
1758-2229
e-ISSN
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Volume of the periodical
16
Issue of the periodical within the volume
6
Country of publishing house
US - UNITED STATES
Number of pages
15
Pages from-to
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UT code for WoS article
001369987200001
EID of the result in the Scopus database
2-s2.0-85210549495