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.

Basic information

Original name

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

Authors

VÍDEŇSKÁ, Petra (203 Czech Republic, belonging to the institution), Kristýna ŠMERKOVÁ (203 Czech Republic, belonging to the institution), Barbora ZWINSOVÁ (203 Czech Republic, belonging to the institution), Vlad POPOVICI (642 Romania, belonging to the institution), Lenka MICENKOVÁ (703 Slovakia, belonging to the institution), Karel SEDLAR and Eva BUDINSKÁ (703 Slovakia, guarantor, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10511 Environmental sciences

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.998

RIV identification code

RIV/00216224:14310/19:00113377

Organization unit

Faculty of Science

DOI

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

UT WoS

000487586600028

Keywords in English

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

Abstract

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.

Links

EF15_003/0000469, research and development project

Name: Cetocoen Plus

EF16_013/0001761, research and development project

Name: RECETOX RI

LM2015051, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX RI)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

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.

@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.

Detailed Information on Publication Record