The effect of DNA extraction methodology on gut microbiota research applications

Research output: Contribution to journalArticlepeer-review

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The effect of DNA extraction methodology on gut microbiota research applications. / Gerasimidis, Konstantinos; Bertz, Martin; Quince, Christopher; Brunner, Katja; Bruce, Alanna; Combet, Emilie; Calus, Szymon; Loman, Nick; Ijaz, Umer Zeeshan.

In: BMC Research Notes, Vol. 9, 365, 26.07.2016.

Research output: Contribution to journalArticlepeer-review

Harvard

Gerasimidis, K, Bertz, M, Quince, C, Brunner, K, Bruce, A, Combet, E, Calus, S, Loman, N & Ijaz, UZ 2016, 'The effect of DNA extraction methodology on gut microbiota research applications', BMC Research Notes, vol. 9, 365. https://doi.org/10.1186/s13104-016-2171-7

APA

Gerasimidis, K., Bertz, M., Quince, C., Brunner, K., Bruce, A., Combet, E., Calus, S., Loman, N., & Ijaz, U. Z. (2016). The effect of DNA extraction methodology on gut microbiota research applications. BMC Research Notes, 9, [365]. https://doi.org/10.1186/s13104-016-2171-7

Vancouver

Gerasimidis K, Bertz M, Quince C, Brunner K, Bruce A, Combet E et al. The effect of DNA extraction methodology on gut microbiota research applications. BMC Research Notes. 2016 Jul 26;9. 365. https://doi.org/10.1186/s13104-016-2171-7

Author

Gerasimidis, Konstantinos ; Bertz, Martin ; Quince, Christopher ; Brunner, Katja ; Bruce, Alanna ; Combet, Emilie ; Calus, Szymon ; Loman, Nick ; Ijaz, Umer Zeeshan. / The effect of DNA extraction methodology on gut microbiota research applications. In: BMC Research Notes. 2016 ; Vol. 9.

Bibtex

@article{ae54c302b4394d40a1d145930cac1a94,
title = "The effect of DNA extraction methodology on gut microbiota research applications",
abstract = "BACKGROUND: The effect that traditional and modern DNA extraction methods have on applications to study the role of gut microbiota in health and disease is a topic of current interest. Genomic DNA was extracted from three faecal samples and one probiotic capsule using three popular methods; chaotropic (CHAO) method, phenol/chloroform (PHEC) extraction, proprietary kit (QIAG). The performance of each of these methods on DNA yield and quality, microbiota composition using quantitative PCR, deep sequencing of the 16S rRNA gene, and sequencing analysis pipeline was evaluated.RESULTS: The CHAO yielded the highest and the QIAG kit the lowest amount of double-stranded DNA, but the purity of isolated nucleic acids was better for the latter method. The CHAO method yielded a higher concentration of bacterial taxa per mass (g) of faeces. Sequencing coverage was higher in CHAO method but a higher proportion of the initial sequencing reads were retained for assignments to operational taxonomic unit (OTU) in the QIAG kit compared to the other methods. The QIAG kit appeared to have longer trimmed reads and shorter regions of worse quality than the other two methods. A distinct separation of α-diversity indices between different DNA extraction methods was not observed. When compositional dissimilarities between samples were explored, a strong separation was observed according to sample type. The effect of the extraction method was either marginal (Bray-Curtis distance) or none (unweighted Unifrac distance). Taxon membership and abundance in each sample was independent of the DNA extraction method used.CONCLUSIONS: We have benchmarked several DNA extraction methods commonly used in gut microbiota research and their differences depended on the downstream applications intended for use. Caution should be paid when the intention is to pool and analyse samples or data from studies which have used different DNA extraction methods.",
keywords = "Journal Article",
author = "Konstantinos Gerasimidis and Martin Bertz and Christopher Quince and Katja Brunner and Alanna Bruce and Emilie Combet and Szymon Calus and Nick Loman and Ijaz, {Umer Zeeshan}",
year = "2016",
month = jul,
day = "26",
doi = "10.1186/s13104-016-2171-7",
language = "English",
volume = "9",
journal = "BMC Research Notes",
issn = "1756-0500",
publisher = "Springer",

}

RIS

TY - JOUR

T1 - The effect of DNA extraction methodology on gut microbiota research applications

AU - Gerasimidis, Konstantinos

AU - Bertz, Martin

AU - Quince, Christopher

AU - Brunner, Katja

AU - Bruce, Alanna

AU - Combet, Emilie

AU - Calus, Szymon

AU - Loman, Nick

AU - Ijaz, Umer Zeeshan

PY - 2016/7/26

Y1 - 2016/7/26

N2 - BACKGROUND: The effect that traditional and modern DNA extraction methods have on applications to study the role of gut microbiota in health and disease is a topic of current interest. Genomic DNA was extracted from three faecal samples and one probiotic capsule using three popular methods; chaotropic (CHAO) method, phenol/chloroform (PHEC) extraction, proprietary kit (QIAG). The performance of each of these methods on DNA yield and quality, microbiota composition using quantitative PCR, deep sequencing of the 16S rRNA gene, and sequencing analysis pipeline was evaluated.RESULTS: The CHAO yielded the highest and the QIAG kit the lowest amount of double-stranded DNA, but the purity of isolated nucleic acids was better for the latter method. The CHAO method yielded a higher concentration of bacterial taxa per mass (g) of faeces. Sequencing coverage was higher in CHAO method but a higher proportion of the initial sequencing reads were retained for assignments to operational taxonomic unit (OTU) in the QIAG kit compared to the other methods. The QIAG kit appeared to have longer trimmed reads and shorter regions of worse quality than the other two methods. A distinct separation of α-diversity indices between different DNA extraction methods was not observed. When compositional dissimilarities between samples were explored, a strong separation was observed according to sample type. The effect of the extraction method was either marginal (Bray-Curtis distance) or none (unweighted Unifrac distance). Taxon membership and abundance in each sample was independent of the DNA extraction method used.CONCLUSIONS: We have benchmarked several DNA extraction methods commonly used in gut microbiota research and their differences depended on the downstream applications intended for use. Caution should be paid when the intention is to pool and analyse samples or data from studies which have used different DNA extraction methods.

AB - BACKGROUND: The effect that traditional and modern DNA extraction methods have on applications to study the role of gut microbiota in health and disease is a topic of current interest. Genomic DNA was extracted from three faecal samples and one probiotic capsule using three popular methods; chaotropic (CHAO) method, phenol/chloroform (PHEC) extraction, proprietary kit (QIAG). The performance of each of these methods on DNA yield and quality, microbiota composition using quantitative PCR, deep sequencing of the 16S rRNA gene, and sequencing analysis pipeline was evaluated.RESULTS: The CHAO yielded the highest and the QIAG kit the lowest amount of double-stranded DNA, but the purity of isolated nucleic acids was better for the latter method. The CHAO method yielded a higher concentration of bacterial taxa per mass (g) of faeces. Sequencing coverage was higher in CHAO method but a higher proportion of the initial sequencing reads were retained for assignments to operational taxonomic unit (OTU) in the QIAG kit compared to the other methods. The QIAG kit appeared to have longer trimmed reads and shorter regions of worse quality than the other two methods. A distinct separation of α-diversity indices between different DNA extraction methods was not observed. When compositional dissimilarities between samples were explored, a strong separation was observed according to sample type. The effect of the extraction method was either marginal (Bray-Curtis distance) or none (unweighted Unifrac distance). Taxon membership and abundance in each sample was independent of the DNA extraction method used.CONCLUSIONS: We have benchmarked several DNA extraction methods commonly used in gut microbiota research and their differences depended on the downstream applications intended for use. Caution should be paid when the intention is to pool and analyse samples or data from studies which have used different DNA extraction methods.

KW - Journal Article

U2 - 10.1186/s13104-016-2171-7

DO - 10.1186/s13104-016-2171-7

M3 - Article

C2 - 27456340

VL - 9

JO - BMC Research Notes

JF - BMC Research Notes

SN - 1756-0500

M1 - 365

ER -