The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00209775%3A_____%2F19%3AN0000005" target="_blank" >RIV/00209775:_____/19:N0000005 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216224:14110/19:00110423

Výsledek na webu

<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6479168/pdf/fmicb-10-00821.pdf" target="_blank" >https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6479168/pdf/fmicb-10-00821.pdf</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3389/fmicb.2019.00821" target="_blank" >10.3389/fmicb.2019.00821</a>

Jazyk výsledku

angličtina

Název v původním jazyce

The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery

Popis výsledku v původním jazyce

Our understanding of human gut microbiota in health and disease depends on accurate and reproducible microbial data acquisition. The critical step in this process is to apply an appropriate methodology to extract microbial DNA, since biases introduced during the DNA extraction process may result in inaccurate microbial representation. In this study, we attempted to find a DNA extraction protocol which could be effectively used to analyze both the bacterial and fungal community. We evaluated the effect of five DNA extraction methods (QIAamp DNA Stool Mini Kit, PureLinkTM Microbiome DNA Purification Kit, ZR Fecal DNA MiniPrepTM Kit, NucleoSpin® DNA Stool Kit, and IHMS protocol Q) on bacterial and fungal gut microbiome recovery using (i) a defined system of germ-free mice feces spiked with bacterial or fungal strains, and (ii) non-spiked human feces. In our experimental setup, we confirmed that the examined methods significantly differed in efficiency and quality, which affected the identified stool microbiome composition. In addition, our results indicated that fungal DNA extraction might be prone to be affected by reagent/kit contamination, and thus an appropriate blank control should be included in mycobiome research. Overall, standardized IHMS protocol Q, recommended by the International Human Microbiome Consortium, performed the best when considering all the parameters analyzed, and thus could be applied not only in bacterial, but also in fungal microbiome research.

Název v anglickém jazyce

The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery

Popis výsledku anglicky

Our understanding of human gut microbiota in health and disease depends on accurate and reproducible microbial data acquisition. The critical step in this process is to apply an appropriate methodology to extract microbial DNA, since biases introduced during the DNA extraction process may result in inaccurate microbial representation. In this study, we attempted to find a DNA extraction protocol which could be effectively used to analyze both the bacterial and fungal community. We evaluated the effect of five DNA extraction methods (QIAamp DNA Stool Mini Kit, PureLinkTM Microbiome DNA Purification Kit, ZR Fecal DNA MiniPrepTM Kit, NucleoSpin® DNA Stool Kit, and IHMS protocol Q) on bacterial and fungal gut microbiome recovery using (i) a defined system of germ-free mice feces spiked with bacterial or fungal strains, and (ii) non-spiked human feces. In our experimental setup, we confirmed that the examined methods significantly differed in efficiency and quality, which affected the identified stool microbiome composition. In addition, our results indicated that fungal DNA extraction might be prone to be affected by reagent/kit contamination, and thus an appropriate blank control should be included in mycobiome research. Overall, standardized IHMS protocol Q, recommended by the International Human Microbiome Consortium, performed the best when considering all the parameters analyzed, and thus could be applied not only in bacterial, but also in fungal microbiome research.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10606 - Microbiology

Projekt

—

Návaznosti

V - Vyzkumna aktivita podporovana z jinych verejnych zdroju

Rok uplatnění

2019

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Frontiers in microbiology

ISSN

1664-302X

e-ISSN

—

Svazek periodika

10

Číslo periodika v rámci svazku

April 2019

Stát vydavatele periodika

CH - Švýcarská konfederace

Počet stran výsledku

11

Strana od-do

821

Kód UT WoS článku

000464958900001

EID výsledku v databázi Scopus

2-s2.0-85067103238