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Demkina A, Slonova D, Mamontov V, Konovalova O, Yurikova D, Rogozhin V, Belova V, Korostin D, Sutormin D, Severinov K, Isaev A. Benchmarking DNA isolation methods for marine metagenomics. Sci Rep 2023; 13:22138. [PMID: 38092853 PMCID: PMC10719357 DOI: 10.1038/s41598-023-48804-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Metagenomics is a powerful tool to study marine microbial communities. However, obtaining high-quality environmental DNA suitable for downstream sequencing applications is a challenging task. The quality and quantity of isolated DNA heavily depend on the choice of purification procedure and the type of sample. Selection of an appropriate DNA isolation method for a new type of material often entails a lengthy trial and error process. Further, each DNA purification approach introduces biases and thus affects the composition of the studied community. To account for these problems and biases, we systematically investigated efficiency of DNA purification from three types of samples (water, sea sediment, and digestive tract of a model invertebrate Magallana gigas) with eight commercially available DNA isolation kits. For each kit-sample combination we measured the quantity of purified DNA, extent of DNA fragmentation, the presence of PCR-inhibiting contaminants, admixture of eukaryotic DNA, alpha-diversity, and reproducibility of the resulting community composition based on 16S rRNA amplicons sequencing. Additionally, we determined a "kitome", e.g., a set of contaminating taxa inherent for each type of purification kit used. The resulting matrix of evaluated parameters allows one to select the best DNA purification procedure for a given type of sample.
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Affiliation(s)
- Alina Demkina
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Darya Slonova
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Viktor Mamontov
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga Konovalova
- Marine Research Center of Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Daria Yurikova
- Marine Research Center of Lomonosov Moscow State University, Moscow, Russia
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Rogozhin
- Marine Research Center of Lomonosov Moscow State University, Moscow, Russia
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | - Vera Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry Sutormin
- Skolkovo Institute of Science and Technology, Moscow, Russia.
| | | | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow, Russia.
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