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

Simple item page
dc.contributor.authorVídeňská, Petracs
dc.contributor.authorŠmerková, Kristýnacs
dc.contributor.authorZwinsová, Barboracs
dc.contributor.authorPopovici, Vladcs
dc.contributor.authorMicenková, Lenkacs
dc.contributor.authorSedlář, Karelcs
dc.contributor.authorBudinská, Evacs
dc.coverage.issue9cs
dc.coverage.volume2019cs
dc.date.issued2019-09-25cs
dc.description.abstractMany 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.en
dc.formattextcs
dc.format.extent1-14cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationScientific Reports. 2019, vol. 2019, issue 9, p. 1-14.en
dc.identifier.doi10.1038/s41598-019-49520-3cs
dc.identifier.issn2045-2322cs
dc.identifier.orcid0000-0002-8269-4020cs
dc.identifier.other158865cs
dc.identifier.researcheridK-1120-2014cs
dc.identifier.scopus56309904900cs
dc.identifier.urihttp://hdl.handle.net/11012/181131
dc.language.isoencs
dc.publisherSpringer Naturecs
dc.relation.ispartofScientific Reportscs
dc.relation.urihttps://www.nature.com/articles/s41598-019-49520-3cs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/2045-2322/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subject16S rRNAen
dc.subjectmetagenomicsen
dc.subjectmicrobiomeen
dc.titleStool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platformen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-158865en
sync.item.dbtypeVAVen
sync.item.insts2025.02.03 15:39:41en
sync.item.modts2025.01.17 19:36:34en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
s41598019495203.pdf
Size:
4.57 MB
Format:
Adobe Portable Document Format
Description:
s41598019495203.pdf
Download
Collections
Ústav biomedicínského inženýrství