| VÍDEŇSKÁ, Petra, Kristýna ŠMERKOVÁ, Barbora ZWINSOVÁ, Vlad POPOVICI, Lenka MICENKOVÁ, Karel SEDLAR and Eva BUDINSKÁ. Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform. Scientific reports. LONDON: NATURE PUBLISHING GROUP, 2019, vol. 9, SEP 2019, p. 1-14. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-019-49520-3. |
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@article{1639936,
author = {Vídeňská, Petra and Šmerková, Kristýna and Zwinsová, Barbora and Popovici, Vlad and Micenková, Lenka and Sedlar, Karel and Budinská, Eva},
article_location = {LONDON},
article_number = {SEP 2019},
doi = {http://dx.doi.org/10.1038/s41598-019-49520-3},
keywords = {GUT MICROBIOME; EXTRACTION METHODS; FECAL DNA; COLLECTION; QUANTIFICATION; DIVERSITY; DYSBIOSIS; REVEALS; AGE},
language = {eng},
issn = {2045-2322},
journal = {Scientific reports},
title = {Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform},
url = {http://dx.doi.org/10.1038/s41598-019-49520-3},
volume = {9},
year = {2019}
}
TY - JOUR
ID - 1639936
AU - Vídeňská, Petra - Šmerková, Kristýna - Zwinsová, Barbora - Popovici, Vlad - Micenková, Lenka - Sedlar, Karel - Budinská, Eva
PY - 2019
TI - Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform
JF - Scientific reports
VL - 9
IS - SEP 2019
SP - 1-14
EP - 1-14
PB - NATURE PUBLISHING GROUP
SN - 20452322
KW - GUT MICROBIOME
KW - EXTRACTION METHODS
KW - FECAL DNA
KW - COLLECTION
KW - QUANTIFICATION
KW - DIVERSITY
KW - DYSBIOSIS
KW - REVEALS
KW - AGE
UR - http://dx.doi.org/10.1038/s41598-019-49520-3
L2 - http://dx.doi.org/10.1038/s41598-019-49520-3
N2 - Many studies correlate changes in human gut microbiome with the onset of various diseases, mostly by 16S rRNA gene sequencing. Setting up the optimal sampling and DNA isolation procedures is crucial for robustness and reproducibility of the results. We performed a systematic comparison of several sampling and DNA isolation kits, quantified their effect on bacterial gDNA quality and the bacterial composition estimates at all taxonomic levels. Sixteen volunteers tested three sampling kits. All samples were consequently processed by two DNA isolation kits. We found that the choice of both stool sampling and DNA isolation kits have an effect on bacterial composition with respect to Gram-positivity, however the isolation kit had a stronger effect than the sampling kit. The proportion of bacteria affected by isolation and sampling kits was larger at higher taxa levels compared to lower taxa levels. The PowerLyzer PowerSoil DNA Isolation Kit outperformed the QIAamp DNA Stool Mini Kit mainly due to better lysis of Gram-positive bacteria while keeping the values of all the other assessed parameters within a reasonable range. The presented effects need to be taken into account when comparing results across multiple studies or computing ratios between Gram-positive and Gram-negative bacteria.
ER -
VÍDEŇSKÁ, Petra, Kristýna ŠMERKOVÁ, Barbora ZWINSOVÁ, Vlad POPOVICI, Lenka MICENKOVÁ, Karel SEDLAR and Eva BUDINSKÁ. Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform. \textit{Scientific reports}. LONDON: NATURE PUBLISHING GROUP, 2019, vol.~9, SEP 2019, p.~1-14. ISSN~2045-2322. Available from: https://dx.doi.org/10.1038/s41598-019-49520-3.
|
