ArticleScientific reports2023
Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome.
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 27 papers.
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Who cites it
27 citing papers in PubMed, 38 citations in OpenAlex.
- Early risk stratification of late-onset sepsis in very preterm infants by intestinal microbiota profiling: a multicenter case-control validation study.Gut microbes · 2026Article
- Analytic attributes of the 16S rRNA gene sequencing methodology for human gut microbiota characterization.Applied microbiology and biotechnology · 2026Article
- Gut Microbiome Dysbiosis in Metabolic Syndrome: Current Evidence and Emerging Perspectives.Nutrients · 2026Review
- Probiotic-Induced Gut Microbiota Modulation: A Comparative Analysis Using 16S rRNA V3-V4 and Targeted Sequencing.Microorganisms · 2026Article
- A Scalable and Cost-Effective In-Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment.Molecular ecology resources · 2026Article
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- Genomics of host-microbiome interactions in humans.Nature reviews. Genetics · 2026Review
- Comparative modulation of the gut microbiota by date-derived products and refined sugar: a 16S rRNA gene taxonomic profile in healthy rats.Frontiers in microbiology · 2026Article
- Microbiota-mediated mechanisms of natural products in atherosclerosis: focus on metabolic and inflammatory pathways.Frontiers in endocrinology · 2026Review
- Toward reproducible pig gut microbiome profiling through standardized methodologies.ISME communications · 2026Article
- Gut Microbiome Dysbiosis in COVID-19: A Systematic Review and Meta-Analysis of Diversity Indices, Taxa Alterations, and Mortality Risk.Microorganisms · 2025Review
- Molecular Mechanisms and Therapeutic Perspectives of Gut Microbiota, Autophagy, and Apoptosis in Cholangiocarcinoma Pathophysiology.International journal of molecular sciences · 2025Review
- Associations Between the Gut Microbiome and Outcomes in Autologous Stem Cell Transplantation: A Systematic Review.Microorganisms · 2025Review
- Toward standardized methods in canine vaginal microbiome research: evaluation of storage, host DNA depletion, and database selection.Microbiology spectrum · 2025Article
- Effect of a Gluten-Free Diet on the Intestinal Microbiota of Women with Celiac Disease.Antibiotics (Basel, Switzerland) · 2025Article
- Gut Microbiota and Hepatocellular Carcinoma: Metabolic Products and Immunotherapy Modulation.Cancer medicine · 2025Review
- Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.Phenomics (Cham, Switzerland) · 2025Article
- From Dysbiosis to Hepatic Inflammation: A Narrative Review on the Diet-Microbiota-Liver Axis in Steatotic Liver Disease.Microorganisms · 2025Review
- Comparison between metatranscriptomics and viral metagenomics, 16S, and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response.Frontiers in microbiology · 2025Article
- Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies.Frontiers in microbiology · 2025Article
Corrections and comments
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Authors and funding
13 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to compare DNA extraction protocols for 16S sequencing. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) upstream DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and 16S sequenced. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates. SPD improved overall efficiency of three of the four tested protocols compared with their commercial version, in terms of DNA extraction yield, sample alpha-diversity, and recovery of Gram-positive bacteria. The best overall performance was obtained for the S-DQ protocol, SPD combined with the DNeasy PowerLyser PowerSoil protocol from QIAGEN. Based on this evaluation, we strongly believe that the use of such stool preprocessing device improves both the standardization and the quality of the DNA extraction in the human gut microbiome studies.
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