{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T17:02:27Z","timestamp":1787763747129,"version":"build-2784847793"},"reference-count":61,"publisher":"MDPI AG","issue":"23","license":[{"start":{"date-parts":[[2025,11,30]],"date-time":"2025-11-30T00:00:00Z","timestamp":1764460800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012190","name":"Ministry of Science and Higher Education","doi-asserted-by":"publisher","award":["075-10-2021-114"],"award-info":[{"award-number":["075-10-2021-114"]}],"id":[{"id":"10.13039\/501100012190","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["22-14-00004"],"award-info":[{"award-number":["22-14-00004"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>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 (\u201ckitome\u201d and \u201csplashome\u201d) 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.<\/jats:p>","DOI":"10.3390\/ijms262311616","type":"journal-article","created":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T08:13:49Z","timestamp":1764576829000},"page":"11616","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2941-5325","authenticated-orcid":false,"given":"Andrey","family":"Sobolev","sequence":"first","affiliation":[{"name":"The Center for Bio- and Medical Technologies, Moscow 121205, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daria","family":"Sibiryakina","sequence":"additional","affiliation":[{"name":"The Center for Bio- and Medical Technologies, Moscow 121205, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizaveta","family":"Chevokina","sequence":"additional","affiliation":[{"name":"The Center for Bio- and Medical Technologies, Moscow 121205, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2465-0193","authenticated-orcid":false,"given":"Darya","family":"Slonova","sequence":"additional","affiliation":[{"name":"The Center for Bio- and Medical Technologies, Moscow 121205, Russia"},{"name":"Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow 123098, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daria","family":"Yurikova","sequence":"additional","affiliation":[{"name":"Marine Research Center of Lomonosov Moscow State University, Moscow 119607, Russia"},{"name":"Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2251-0354","authenticated-orcid":false,"given":"Svetlana","family":"Kozlova","sequence":"additional","affiliation":[{"name":"The Center for Bio- and Medical Technologies, Moscow 121205, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Trofimova","sequence":"additional","affiliation":[{"name":"The Center for Bio- and Medical Technologies, Moscow 121205, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0204-6191","authenticated-orcid":false,"given":"Vasiliy","family":"Zubarev","sequence":"additional","affiliation":[{"name":"The Center for Bio- and Medical Technologies, Moscow 121205, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-5737-1480","authenticated-orcid":false,"given":"Alexander","family":"Kiselev","sequence":"additional","affiliation":[{"name":"Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9023-7938","authenticated-orcid":false,"given":"Olga","family":"Konovalova","sequence":"additional","affiliation":[{"name":"Marine Research Center of Lomonosov Moscow State University, Moscow 119607, Russia"},{"name":"Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitry","family":"Sutormin","sequence":"additional","affiliation":[{"name":"The Center for Bio- and Medical Technologies, Moscow 121205, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9593-2745","authenticated-orcid":false,"given":"Artem","family":"Isaev","sequence":"additional","affiliation":[{"name":"The Center for Bio- and Medical Technologies, Moscow 121205, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5970","DOI":"10.1073\/pnas.1521291113","article-title":"Scaling Laws Predict Global Microbial Diversity","volume":"113","author":"Locey","year":"2016","journal-title":"Proc. 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