The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery

@article{1549527,
   author = {Fiedorová, Kristýna and Radvanský, Matěj and Němcová, Eva and Grombiříková, Hana and Bosák, Juraj and Černochová, Michaela and Lexa, Matej and Šmajs, David and Freiberger, Tomáš},
   article_location = {Lausanne},
   article_number = {821},
   doi = {http://dx.doi.org/10.3389/fmicb.2019.00821},
   keywords = {gut microbiome; gut microbiota; gut mycobiome; gut mycobiota; fungal microbiota; DNA extraction method; 16S rDNA; ITS rDNA},
   language = {eng},
   issn = {1664-302X},
   journal = {Frontiers in Microbiology},
   title = {The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery},
   url = {https://www.frontiersin.org/articles/10.3389/fmicb.2019.00821/full},
   volume = {10},
   year = {2019}
}

TY  - JOUR
ID  - 1549527
AU  - Fiedorová, Kristýna - Radvanský, Matěj - Němcová, Eva - Grombiříková, Hana - Bosák, Juraj - Černochová, Michaela - Lexa, Matej - Šmajs, David - Freiberger, Tomáš
PY  - 2019
TI  - The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery
JF  - Frontiers in Microbiology
VL  - 10
IS  - 821
SP  - 1-11
EP  - 1-11
PB  - Frontiers Media SA
SN  - 1664302X
KW  - gut microbiome
KW  - gut microbiota
KW  - gut mycobiome
KW  - gut mycobiota
KW  - fungal microbiota
KW  - DNA extraction method
KW  - 16S rDNA
KW  - ITS rDNA
UR  - https://www.frontiersin.org/articles/10.3389/fmicb.2019.00821/full
L2  - https://www.frontiersin.org/articles/10.3389/fmicb.2019.00821/full
N2  - 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 (QlAamp DNA Stool Mini Kit, PureLink (TM) Microbiome DNA Purification Kit, ZR Fecal DNA MiniPrep((TM)) Kit, NucleoSpir (R) 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.
ER  - 

FIEDOROVÁ, Kristýna, Matěj RADVANSKÝ, Eva NĚMCOVÁ, Hana GROMBIŘÍKOVÁ, Juraj BOSÁK, Michaela ČERNOCHOVÁ, Matej LEXA, David ŠMAJS a Tomáš FREIBERGER. The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery. \textit{Frontiers in Microbiology}. Lausanne: Frontiers Media SA, roč.~10, č.~821, s.~1-11. ISSN~1664-302X. doi:10.3389/fmicb.2019.00821. 2019.