Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples

Carsten Suhr Jacobsen; Tue Kjærgaard Nielsen; Jan Kjølhede Vester; Peter Stougaard; Jeppe Lund Nielsen; Jana Voriskova; Anne Winding; Petr Baldrian; Binbin Liu; Åsa Frostegård; Dorthe Pedersen; Alexander Tøsdal Tveit; Mette Marianne Svenning; Christoph C Tebbe; Lise Øvreås; Pia Bach Jakobsen; Steven J Blazewicz; Valerie Hubablek; Stefan Bertilsson; Lars Hestbjerg Hansen; S Craig Cary; William E Holben; Flemming Ekelund; Jacob Bælum

doi:10.1038/s41598-018-24082-y

Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples

Carsten Suhr Jacobsen, Tue Kjærgaard Nielsen, Jan Kjølhede Vester, Peter Stougaard, Jeppe Lund Nielsen, Jana Voriskova, Anne Winding, Petr Baldrian, Binbin Liu, Åsa Frostegård, Dorthe Pedersen, Alexander Tøsdal Tveit, Mette Marianne Svenning, Christoph C Tebbe, Lise Øvreås, Pia Bach Jakobsen, Steven J Blazewicz, Valerie Hubablek, Stefan Bertilsson, Lars Hestbjerg HansenS Craig Cary, William E Holben, Flemming Ekelund, Jacob Bælum

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Abstract

Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil using the same batch of kits. The inter-laboratory extraction campaign revealed large variation among the participating laboratories, but the reagent increased the number of PCR-amplified16S rRNA genes recovered from biomass naturally present in the soils by one log unit. An extensive sequencing approach demonstrated that the blocking reagent was free of contaminating DNA, and may therefore also be used in metagenomics studies that require direct sequencing.

Original language	English
Article number	5711
Journal	Scientific Reports
Volume	8
Issue number	1
Number of pages	6
ISSN	2045-2322
DOIs	https://doi.org/10.1038/s41598-018-24082-y
Publication status	Published - 9 Apr 2018

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Open Access ArticleFinal published version, 946 KBLicence: CC BY 4.0

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Jacobsen, C. S., Nielsen, T. K., Vester, J. K., Stougaard, P., Nielsen, J. L., Voriskova, J., Winding, A., Baldrian, P., Liu, B., Frostegård, Å., Pedersen, D., Tveit, A. T., Svenning, M. M., Tebbe, C. C., Øvreås, L., Jakobsen, P. B., Blazewicz, S. J., Hubablek, V., Bertilsson, S., ... Bælum, J. (2018). Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples. Scientific Reports, 8(1), Article 5711. https://doi.org/10.1038/s41598-018-24082-y

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title = "Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples",

abstract = "Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil using the same batch of kits. The inter-laboratory extraction campaign revealed large variation among the participating laboratories, but the reagent increased the number of PCR-amplified16S rRNA genes recovered from biomass naturally present in the soils by one log unit. An extensive sequencing approach demonstrated that the blocking reagent was free of contaminating DNA, and may therefore also be used in metagenomics studies that require direct sequencing.",

author = "Jacobsen, {Carsten Suhr} and Nielsen, {Tue Kj{\ae}rgaard} and Vester, {Jan Kj{\o}lhede} and Peter Stougaard and Nielsen, {Jeppe Lund} and Jana Voriskova and Anne Winding and Petr Baldrian and Binbin Liu and {\AA}sa Frosteg{\aa}rd and Dorthe Pedersen and Tveit, {Alexander T{\o}sdal} and Svenning, {Mette Marianne} and Tebbe, {Christoph C} and Lise {\O}vre{\aa}s and Jakobsen, {Pia Bach} and Blazewicz, {Steven J} and Valerie Hubablek and Stefan Bertilsson and Hansen, {Lars Hestbjerg} and Cary, {S Craig} and Holben, {William E} and Flemming Ekelund and Jacob B{\ae}lum",

year = "2018",

month = apr,

day = "9",

doi = "10.1038/s41598-018-24082-y",

language = "English",

volume = "8",

journal = "Scientific Reports",

issn = "2045-2322",

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Jacobsen, CS, Nielsen, TK, Vester, JK, Stougaard, P, Nielsen, JL, Voriskova, J, Winding, A, Baldrian, P, Liu, B, Frostegård, Å, Pedersen, D, Tveit, AT, Svenning, MM, Tebbe, CC, Øvreås, L, Jakobsen, PB, Blazewicz, SJ, Hubablek, V, Bertilsson, S, Hansen, LH, Cary, SC, Holben, WE, Ekelund, F & Bælum, J 2018, 'Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples', Scientific Reports, vol. 8, no. 1, 5711. https://doi.org/10.1038/s41598-018-24082-y

TY - JOUR

T1 - Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples

AU - Jacobsen, Carsten Suhr

AU - Nielsen, Tue Kjærgaard

AU - Vester, Jan Kjølhede

AU - Stougaard, Peter

AU - Nielsen, Jeppe Lund

AU - Voriskova, Jana

AU - Winding, Anne

AU - Baldrian, Petr

AU - Liu, Binbin

AU - Frostegård, Åsa

AU - Pedersen, Dorthe

AU - Tveit, Alexander Tøsdal

AU - Svenning, Mette Marianne

AU - Tebbe, Christoph C

AU - Øvreås, Lise

AU - Jakobsen, Pia Bach

AU - Blazewicz, Steven J

AU - Hubablek, Valerie

AU - Bertilsson, Stefan

AU - Hansen, Lars Hestbjerg

AU - Cary, S Craig

AU - Holben, William E

AU - Ekelund, Flemming

AU - Bælum, Jacob

PY - 2018/4/9

Y1 - 2018/4/9

N2 - Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil using the same batch of kits. The inter-laboratory extraction campaign revealed large variation among the participating laboratories, but the reagent increased the number of PCR-amplified16S rRNA genes recovered from biomass naturally present in the soils by one log unit. An extensive sequencing approach demonstrated that the blocking reagent was free of contaminating DNA, and may therefore also be used in metagenomics studies that require direct sequencing.

AB - Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil using the same batch of kits. The inter-laboratory extraction campaign revealed large variation among the participating laboratories, but the reagent increased the number of PCR-amplified16S rRNA genes recovered from biomass naturally present in the soils by one log unit. An extensive sequencing approach demonstrated that the blocking reagent was free of contaminating DNA, and may therefore also be used in metagenomics studies that require direct sequencing.

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U2 - 10.1038/s41598-018-24082-y

DO - 10.1038/s41598-018-24082-y

M3 - Journal article

C2 - 29632323

SN - 2045-2322

VL - 8

JO - Scientific Reports

JF - Scientific Reports

IS - 1

M1 - 5711

ER -

Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples

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