The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00209775%3A_____%2F19%3AN0000005" target="_blank" >RIV/00209775:_____/19:N0000005 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14110/19:00110423
Result on the web
<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6479168/pdf/fmicb-10-00821.pdf" target="_blank" >https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6479168/pdf/fmicb-10-00821.pdf</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3389/fmicb.2019.00821" target="_blank" >10.3389/fmicb.2019.00821</a>
Alternative languages
Result language
angličtina
Original language name
The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery
Original language description
Our understanding of human gut microbiota in health and disease depends on accurate and reproducible microbial data acquisition. The critical step in this process is to apply an appropriate methodology to extract microbial DNA, since biases introduced during the DNA extraction process may result in inaccurate microbial representation. In this study, we attempted to find a DNA extraction protocol which could be effectively used to analyze both the bacterial and fungal community. We evaluated the effect of five DNA extraction methods (QIAamp DNA Stool Mini Kit, PureLinkTM Microbiome DNA Purification Kit, ZR Fecal DNA MiniPrepTM Kit, NucleoSpin® DNA Stool Kit, and IHMS protocol Q) on bacterial and fungal gut microbiome recovery using (i) a defined system of germ-free mice feces spiked with bacterial or fungal strains, and (ii) non-spiked human feces. In our experimental setup, we confirmed that the examined methods significantly differed in efficiency and quality, which affected the identified stool microbiome composition. In addition, our results indicated that fungal DNA extraction might be prone to be affected by reagent/kit contamination, and thus an appropriate blank control should be included in mycobiome research. Overall, standardized IHMS protocol Q, recommended by the International Human Microbiome Consortium, performed the best when considering all the parameters analyzed, and thus could be applied not only in bacterial, but also in fungal microbiome research.
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
10606 - Microbiology
Result continuities
Project
—
Continuities
V - Vyzkumna aktivita podporovana z jinych verejnych zdroju
Others
Publication year
2019
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Frontiers in microbiology
ISSN
1664-302X
e-ISSN
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Volume of the periodical
10
Issue of the periodical within the volume
April 2019
Country of publishing house
CH - SWITZERLAND
Number of pages
11
Pages from-to
821
UT code for WoS article
000464958900001
EID of the result in the Scopus database
2-s2.0-85067103238