ArticleScientific reports2024
Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses.
Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Impact of Electronic Cigarette Use on the Oral Microbiota: A Systematic Review.Journal of clinical periodontology · 2026Pooled it
- Tildrakizumab for the prophylaxis of graft-versus-host disease after allogeneic hematopoietic stem cell transplantation.Blood advances · 2026Trial
- Single-cell detection and quantification of the microbiota by MicFLY.Cell host & microbe · 2026Article
- Maternal Microbiome in Gestational Diabetes Mellitus: Mechanisms, Biomarkers, and Therapeutic Perspectives.Life (Basel, Switzerland) · 2026Review
- Firmicutes/Bacteroidetes ratio of the gut microbiota and its association with abdominal obesity and insulin resistance (METS-IR) in Korean adults.Scientific reports · 2026Article
- A Green and Practical Magnetic Ionic Liquid-Based Microextraction of DNA Using a Low-Cost 3D-Printed Open-Source Apparatus.ACS omega · 2026Article
- Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.Nutrients · 2026Article
- Comparative performance of traditional and commercial DNA extraction methods for fish gut microbiota analysis.Molecular biology reports · 2026Article
- Integrating intestinal microbiome and urinary metabolome data to predict secondary infection in critically ill patients.Critical care (London, England) · 2026Article
- The interplay of sleep characteristics with health factors and gut microbiome.Nature communications · 2026Article
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- Nanopore sequencing of the Tunisian gut microbiome: effect of the DNA extraction methods.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- The role of the gut-lung axis in persistent inflammation and disease progression in chronic obstructive pulmonary disease: mechanistic evidence and therapeutic implications.Frontiers in immunology · 2026Review
- Early-life microbiome trajectories as biomarkers to predict health outcomes.Microbiome research reports · 2026Review
- Article
- Defining reference values for the gut microbiota in a Southern European population.Frontiers in cellular and infection microbiology · 2026Article
- Toward reproducible pig gut microbiome profiling through standardized methodologies.ISME communications · 2026Article
- Reinventing malaria control: hierarchical intervention strategies for African settings based on the microbiota-barrier-innate immunity axis.Frontiers in immunology · 2026Review
- Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Metagenomics enables parallel detection of 176 clinically relevant targets from faecal samples.Frontiers in cellular and infection microbiology · 2026Article
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
The lack of standardization in the methods of DNA extraction from fecal samples represents the major source of experimental variation in the microbiome research field. In this study, we aimed to compare the metagenomic profiles and microbiome-phenotype associations obtained by applying two commercially available DNA extraction kits: the AllPrep DNA/RNA Mini Kit (APK) and the QIAamp Fast DNA Stool Mini Kit (FSK). Using metagenomic sequencing data available from 745 paired fecal samples from two independent population cohorts, Lifelines-DEEP (LLD, n = 292) and the 500 Functional Genomics project (500FG, n = 453), we confirmed significant differences in DNA yield and the recovered microbial communities between protocols, with the APK method resulting in a higher DNA concentration and microbial diversity. Further, we observed a massive difference in bacterial relative abundances at species-level between the APK and the FSK protocols, with > 75% of species differentially abundant between protocols in both cohorts. Specifically, comparison with a standard mock community revealed that the APK method provided higher accuracy in the recovery of microbial relative abundances, with the absence of a bead-beating step in the FSK protocol causing an underrepresentation of gram-positive bacteria. This heterogeneity in the recovered microbial composition led to remarkable differences in the association with anthropometric and lifestyle phenotypes. The results of this study further reinforce that the choice of DNA extraction method impacts the metagenomic profile of human gut microbiota and highlight the importance of harmonizing protocols in microbiome studies.
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