ArticleScientific reports2019
Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers, 3 of them syntheses that pooled it.
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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.
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Who cites it
47 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- A systematic review of gut microbiota composition in observational studies of major depressive disorder, bipolar disorder and schizophrenia.Molecular psychiatry · 2022Pooled it
- Systematic Review of the Effects of Exercise and Physical Activity on the Gut Microbiome of Older Adults.Nutrients · 2022Pooled it
- The effects of dairy and dairy derivatives on the gut microbiota: a systematic literature review.Gut microbes · 2020Pooled it
- Quercetin alleviates CClBiochemistry and biophysics reports · 2026Article
- Metagenomic Profiling Reveals Extensive Bacterial Diversity in Chicken Manure and Associated Contaminated Wastewater.International journal of molecular sciences · 2026Article
- The Barrier-Microbiota-Inflammation Axis in Colorectal Cancer: Mechanisms and Emerging Diagnostic & Therapeutic Strategies.Cancers · 2026Review
- Interaction between the breast tumor microenvironment and gut microbiome.Gut microbes · 2025Review
- Pharmacomicrobiomics.Clinical pharmacology and therapeutics · 2025Review
- Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples.International journal of molecular sciences · 2025Article
- Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?Poultry science · 2025Review
- Comparison of Fecal DNA Extraction Kits for the Giant Panda (Ecology and evolution · 2025Article
- Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level.Frontiers in bioinformatics · 2025Article
- Advancements in analytical methods for studying the human gut microbiome.Journal of biological methods · 2025Review
- Sampling frequency matters: mapping of the healthy infants' gut microbiome during the first year of life.Current research in microbial sciences · 2025Article
- A Comparison of Three Automated Nucleic Acid Extraction Systems for Human Stool Samples.Microorganisms · 2024Article
- Impact of intrapartum antibiotic prophylaxis on the oral and fecal bacteriomes of children in the first week of life.Scientific reports · 2024Article
- Optimization of the Method for Isolating Bacterial DNA from the Aboveground Part of Lettuce.International journal of molecular sciences · 2024Article
- Protective effect of gut microbiota restored by fecal microbiota transplantation in a sepsis model in juvenile mice.Frontiers in immunology · 2024Article
- Impact of antibiotic prophylaxis on gut microbiota in colorectal surgery: insights from an Eastern European stewardship study.Frontiers in cellular and infection microbiology · 2024Article
- Benchmarking DNA isolation methods for marine metagenomics.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many studies correlate changes in human gut microbiome with the onset of various diseases, mostly by 16S rRNA gene sequencing. Setting up the optimal sampling and DNA isolation procedures is crucial for robustness and reproducibility of the results. We performed a systematic comparison of several sampling and DNA isolation kits, quantified their effect on bacterial gDNA quality and the bacterial composition estimates at all taxonomic levels. Sixteen volunteers tested three sampling kits. All samples were consequently processed by two DNA isolation kits. We found that the choice of both stool sampling and DNA isolation kits have an effect on bacterial composition with respect to Gram-positivity, however the isolation kit had a stronger effect than the sampling kit. The proportion of bacteria affected by isolation and sampling kits was larger at higher taxa levels compared to lower taxa levels. The PowerLyzer PowerSoil DNA Isolation Kit outperformed the QIAamp DNA Stool Mini Kit mainly due to better lysis of Gram-positive bacteria while keeping the values of all the other assessed parameters within a reasonable range. The presented effects need to be taken into account when comparing results across multiple studies or computing ratios between Gram-positive and Gram-negative bacteria.
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