ArticleScientific reports2018
Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers, 7 of them syntheses that pooled it.
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Who cites it
99 citing papers in PubMed, 7 syntheses or guidelines pooled it.
- Salivary microbial meta-analysis reveals gender differences in oral microbiota, core microbiota, and molecular markers.Frontiers in cellular and infection microbiology · 2026Pooled it
- Effects of Nut Intake on Gut Microbiome Composition and Gut Function in Adults: A Systematic Review and Meta-analysis.Advances in nutrition (Bethesda, Md.) · 2025Pooled it
- Meta-analysis identifies common gut microbiota associated with multiple sclerosis.Genome medicine · 2024Pooled it
- A systematic review exploring the association between the human gut microbiota and brain connectivity in health and disease.Molecular psychiatry · 2023Pooled it
- The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives.Drugs · 2021Pooled it
- Characterization of the Oral and Gut Microbiota in Patients with Psoriatic Diseases: A Systematic Review.Acta dermato-venereologica · 2021Pooled it
- Gut Microbiota, Probiotics and Psychological States and Behaviors after Bariatric Surgery-A Systematic Review of Their Interrelation.Nutrients · 2020Pooled it
- Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.PloS one · 2021Trial
- Trial
- Systematic quantification and removal of host DNA contamination in 16S rRNA gene sequencing.Quantitative biology (Beijing, China) · 2026Article
- Optimized approaches to profile low biomass DNA and RNA virome in the upper respiratory tract of beef cattle.Animal microbiome · 2026Article
- Machine learning-assisted analysis of saliva-containing mixtures using a saliva-specific multi-CpG-microhaplotype marker system.International journal of legal medicine · 2026Article
- Article
- Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.Biology · 2026Review
- The impact of DNA extraction methods on species quantification and apparent community composition of in vitro oral biofilms.FEMS microbiology letters · 2026Article
- The association between tongue features and tongue coating microbiota and gastrointestinal cancer: a systematic review and meta-analysis.Journal of oral microbiology · 2026Review
- Oral Microbiome in Oral Cancer Research from Sampling to Analysis: Strategies, Challenges, and Recommendations.Cancers · 2025Review
- Profiling the Bacterial Microbiome Across Peri-Implant Conditions.Journal of clinical periodontology · 2025Article
- Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.Molecular ecology resources · 2025Article
- Creating unity: linking 16S rRNA gene sequence information to the core taxonomy of genomes.Environmental microbiome · 2025Article
39 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amplification and sequencing of 16S amplicons are widely used for profiling the structure of oral microbiota. However, it remains not clear whether and to what degree DNA extraction and targeted 16S rRNA hypervariable regions influence the analysis. Based on a mock community consisting of five oral bacterial species in equal abundance, we compared the 16S amplicon sequencing results on the Illumina MiSeq platform from six frequently employed DNA extraction procedures and three pairs of widely used 16S rRNA hypervariable primers targeting different 16S rRNA regions. Technical reproducibility of selected 16S regions was also assessed. DNA extraction method exerted considerable influence on the observed bacterial diversity while hypervariable regions had a relatively minor effect. Protocols with beads added to the enzyme-mediated DNA extraction reaction produced more accurate bacterial community structure than those without either beads or enzymes. Hypervariable regions targeting V3-V4 and V4-V5 seemed to produce more reproducible results than V1-V3. Neither sequencing batch nor change of operator affected the reproducibility of bacterial diversity profiles. Therefore, DNA extraction strategy and 16S rDNA hypervariable regions both influenced the results of oral microbiota biodiversity profiling, thus should be carefully considered in study design and data interpretation.
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