Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Artículo científico |
| Language: | en |
| Published: |
International journal of molecular sciences
2025
|
| Subjects: | |
| Online Access: | https://pubmed.ncbi.nlm.nih.gov/41373768/ |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1868266114431057921 |
|---|---|
| author | Sobolev, Andrey Sibiryakina, Daria Chevokina, Elizaveta Slonova, Darya Yurikova, Daria Kozlova, Svetlana Trofimova, Anna Zubarev, Vasiliy Kiselev, Alexander Konovalova, Olga Sutormin, Dmitry Isaev, Artem |
| author_facet | Sobolev, Andrey Sibiryakina, Daria Chevokina, Elizaveta Slonova, Darya Yurikova, Daria Kozlova, Svetlana Trofimova, Anna Zubarev, Vasiliy Kiselev, Alexander Konovalova, Olga Sutormin, Dmitry Isaev, Artem Sobolev, Andrey Sibiryakina, Daria Chevokina, Elizaveta Slonova, Darya Yurikova, Daria Kozlova, Svetlana Trofimova, Anna Zubarev, Vasiliy Kiselev, Alexander Konovalova, Olga Sutormin, Dmitry Isaev, Artem |
| collection | PubMed - marine biology |
| contents | Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples. Sobolev, Andrey Sibiryakina, Daria Chevokina, Elizaveta Slonova, Darya Yurikova, Daria Kozlova, Svetlana Trofimova, Anna Zubarev, Vasiliy Kiselev, Alexander Konovalova, Olga Sutormin, Dmitry Isaev, Artem Metagenomics Animals RNA, Ribosomal, 16S Cost-Benefit Analysis Feces Benchmarking Metagenome DNA, Bacterial Reproducibility of Results Geologic Sediments DNA Gastrointestinal Microbiome 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 () 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. |
| format | Artículo científico |
| id | pubmed_41373768 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | International journal of molecular sciences |
| record_format | pubmed |
| spellingShingle | Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples. Sobolev, Andrey Sibiryakina, Daria Chevokina, Elizaveta Slonova, Darya Yurikova, Daria Kozlova, Svetlana Trofimova, Anna Zubarev, Vasiliy Kiselev, Alexander Konovalova, Olga Sutormin, Dmitry Isaev, Artem Metagenomics Animals RNA, Ribosomal, 16S Cost-Benefit Analysis Feces Benchmarking Metagenome DNA, Bacterial Reproducibility of Results Geologic Sediments DNA Gastrointestinal Microbiome Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples. Sobolev, Andrey Sibiryakina, Daria Chevokina, Elizaveta Slonova, Darya Yurikova, Daria Kozlova, Svetlana Trofimova, Anna Zubarev, Vasiliy Kiselev, Alexander Konovalova, Olga Sutormin, Dmitry Isaev, Artem Metagenomics Animals RNA, Ribosomal, 16S Cost-Benefit Analysis Feces Benchmarking Metagenome DNA, Bacterial Reproducibility of Results Geologic Sediments DNA Gastrointestinal Microbiome 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 () 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. |
| title | Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples. |
| topic | Metagenomics Animals RNA, Ribosomal, 16S Cost-Benefit Analysis Feces Benchmarking Metagenome DNA, Bacterial Reproducibility of Results Geologic Sediments DNA Gastrointestinal Microbiome |
| url | https://pubmed.ncbi.nlm.nih.gov/41373768/ |