Stool sampling and DNA isolation kits affect DNA quality and
bacterial composition following 16S rRNA gene sequencing using
MiSeq Illumina platform

J 2019

Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform

VÍDEŇSKÁ, Petra, Kristýna ŠMERKOVÁ, Barbora ZWINSOVÁ, Vlad POPOVICI, Lenka MICENKOVÁ et. al.

Základní údaje

Originální název

Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform

Autoři

VÍDEŇSKÁ, Petra (203 Česká republika, domácí), Kristýna ŠMERKOVÁ (203 Česká republika, domácí), Barbora ZWINSOVÁ (203 Česká republika, domácí), Vlad POPOVICI (642 Rumunsko, domácí), Lenka MICENKOVÁ (703 Slovensko, domácí), Karel SEDLAR a Eva BUDINSKÁ (703 Slovensko, garant, domácí)

Vydání

Scientific reports, LONDON, NATURE PUBLISHING GROUP, 2019, 2045-2322

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10511 Environmental sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.998

Kód RIV

RIV/00216224:14310/19:00113377

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1038/s41598-019-49520-3

UT WoS

000487586600028

Klíčová slova anglicky

GUT MICROBIOME; EXTRACTION METHODS; FECAL DNA; COLLECTION; QUANTIFICATION; DIVERSITY; DYSBIOSIS; REVEALS; AGE

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 15. 4. 2020 21:37, Mgr. Marie Šípková, DiS.

Anotace

V originále

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.

Návaznosti

EF15_003/0000469, projekt VaV

Název: Cetocoen Plus

EF16_013/0001761, projekt VaV

Název: RECETOX RI

LM2015051, projekt VaV

Název: Centrum pro výzkum toxických látek v prostředí (Akronym: RECETOX RI)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Výzkumná infrastruktura RECETOX

Citovat

VÍDEŇSKÁ, Petra, Kristýna ŠMERKOVÁ, Barbora ZWINSOVÁ, Vlad POPOVICI, Lenka MICENKOVÁ, Karel SEDLAR a 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, roč. 9, SEP 2019, s. 1-14. ISSN 2045-2322. Dostupné z: https://dx.doi.org/10.1038/s41598-019-49520-3.

@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 a 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, roč.~9, SEP 2019, s.~1-14. ISSN~2045-2322. Dostupné z: https://dx.doi.org/10.1038/s41598-019-49520-3.

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