ArticleScientific reports2023
Benchmarking DNA isolation methods for marine metagenomics.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- Taxonomy bias in metagenome-assembled genome recovery.Microbial genomics · 2026Article
- The effects of feeding guild, seasonality, and warming on the gut microbiomes of Antarctic echinoderms.BMC microbiology · 2026Article
- Environmental Adaptation Strategies of Deep-Sea Fungi.Journal of fungi (Basel, Switzerland) · 2026Review
- Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.ISME communications · 2026Article
- Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples.International journal of molecular sciences · 2025Article
- Microbial community characterization in Red Sea-derived samples using a field-deployable DNA extraction system and nanopore sequencing.Environmental microbiome · 2025Article
- Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing.bioRxiv : the preprint server for biology · 2025Article
- Comparative evaluation of sequencing technologies and primer sets for mouse gut microbiota profiling.Frontiers in microbiology · 2025Article
- Efficient recovery and DNA extraction for algae-associated microbial communities.Frontiers in plant science · 2025Article
- Evaluation of DNA Extraction Methods for Microbial Community Profiling in Deadwood Decomposition.MicrobiologyOpen · 2024Article
- Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics.International journal of molecular sciences · 2024Article
- Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.Access microbiology · 2024Article
- Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach.Frontiers in microbiology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.