Publication detail

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

VÍDEŇSKÁ, P. ŠMERKOVÁ, K. ZWINSOVÁ, B. POPOVICI, V. MICENKOVÁ, L. SEDLÁŘ, K. BUDINSKÁ, E.

Original Title

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

Type

journal article in Web of Science

Language

English

Original Abstract

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.

Keywords

16S rRNA; metagenomics; microbiome

Authors

VÍDEŇSKÁ, P.; ŠMERKOVÁ, K.; ZWINSOVÁ, B.; POPOVICI, V.; MICENKOVÁ, L.; SEDLÁŘ, K.; BUDINSKÁ, E.

Released

25. 9. 2019

Publisher

Springer Nature

ISBN

2045-2322

Periodical

Scientific Reports

Year of study

2019

Number

9

State

United Kingdom of Great Britain and Northern Ireland

Pages from

1

Pages to

14

Pages count

14

URL

https://www.nature.com/articles/s41598-019-49520-3

Full text in the Digital Library

http://hdl.handle.net/11012/181131

BibTex

@article{BUT158865,
  author="Petra {Vídeňská} and Kristýna {Šmerková} and Barbora {Zwinsová} and Vlad {Popovici} and Lenka {Micenková} and Karel {Sedlář} and Eva {Budinská}",
  title="Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform",
  journal="Scientific Reports",
  year="2019",
  volume="2019",
  number="9",
  pages="1--14",
  doi="10.1038/s41598-019-49520-3",
  issn="2045-2322",
  url="https://www.nature.com/articles/s41598-019-49520-3"
}