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Volume 26
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10.3390/ijms262311616
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples

by
Andrey Sobolev
1,†,
Daria Sibiryakina
1,†,
Elizaveta Chevokina
1,
Darya Slonova
1,2,
Daria Yurikova
3,4,
Svetlana Kozlova
1,
Anna Trofimova
1,
Vasiliy Zubarev
1,
Alexander Kiselev
4,
Olga Konovalova
3,5,
Dmitry Sutormin
1,* and
Artem Isaev
1,*
1
The Center for Bio- and Medical Technologies, Moscow 121205, Russia
2
Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow 123098, Russia
3
Marine Research Center of Lomonosov Moscow State University, Moscow 119607, Russia
4
Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia
5
Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2025, 26(23), 11616; https://doi.org/10.3390/ijms262311616
Submission received: 24 October 2025 / Revised: 26 November 2025 / Accepted: 27 November 2025 / Published: 30 November 2025
(This article belongs to the Special Issue Molecular Tools in Environmental Microbiology)
Versions Notes

Abstract

Extraction of high-quality microbial DNA remains a critical bottleneck in metagenomic research. Environmental samples often produce fragmented DNA and are prone to contaminations that interfere with downstream sequencing, while widely used commercial kits can be prohibitively expensive. Therefore, systematic evaluation of cost-effective alternatives is essential to support large-scale metagenomic studies. In this work, we benchmarked eight commercial DNA extraction kits from Magen, SkyGen, and Sileks against Qiagen reference kits. Four representative sample types were analyzed: freshwater, seafloor sediments, Pacific oyster (Magallana gigas) gut microbiome, and mammalian feces. DNA yield, integrity, purity, PCR inhibitor content, and eukaryotic DNA admixture were assessed. Microbial community composition, alpha diversity, reproducibility, and contamination (“kitome” and “splashome”) were further evaluated using 16S rRNA amplicon sequencing. We revealed that several alternative kits performed comparably or better than the Qiagen reference standard. Magen Soil and Magen Bacterial provided high yields and reproducibility, though the latter produced more fragmented DNA. SkyGen Stool excelled with host-associated samples, while Sileks Soil and Metagenomic kits preserved higher diversity in sediments. Magen Microbiome consistently underperformed. This study identifies multiple cost-effective DNA extraction strategies and provides practical guidance for selecting balanced DNA purification methods for different sample types.
Keywords: DNA purification; benchmark; 16S sequencing; metagenomics; cost-effectiveness; environmental samples DNA purification; benchmark; 16S sequencing; metagenomics; cost-effectiveness; environmental samples

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MDPI and ACS Style

Sobolev, A.; Sibiryakina, D.; Chevokina, E.; Slonova, D.; Yurikova, D.; Kozlova, S.; Trofimova, A.; Zubarev, V.; Kiselev, A.; Konovalova, O.; et al. Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples. Int. J. Mol. Sci. 2025, 26, 11616. https://doi.org/10.3390/ijms262311616

AMA Style

Sobolev A, Sibiryakina D, Chevokina E, Slonova D, Yurikova D, Kozlova S, Trofimova A, Zubarev V, Kiselev A, Konovalova O, et al. Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples. International Journal of Molecular Sciences. 2025; 26(23):11616. https://doi.org/10.3390/ijms262311616

Chicago/Turabian Style

Sobolev, Andrey, Daria Sibiryakina, Elizaveta Chevokina, Darya Slonova, Daria Yurikova, Svetlana Kozlova, Anna Trofimova, Vasiliy Zubarev, Alexander Kiselev, Olga Konovalova, and et al. 2025. "Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples" International Journal of Molecular Sciences 26, no. 23: 11616. https://doi.org/10.3390/ijms262311616

APA Style

Sobolev, A., Sibiryakina, D., Chevokina, E., Slonova, D., Yurikova, D., Kozlova, S., Trofimova, A., Zubarev, V., Kiselev, A., Konovalova, O., Sutormin, D., & Isaev, A. (2025). Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples. International Journal of Molecular Sciences, 26(23), 11616. https://doi.org/10.3390/ijms262311616

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