ArticleJournal of oral microbiology2014
Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing.
Article in Journal of oral microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 70 citations in OpenAlex.
- The impact of DNA extraction methods on species quantification and apparent community composition of in vitro oral biofilms.FEMS microbiology letters · 2026Article
- A dual-loop chemostat to investigate multi-species biofilms on implant surfaces under adjustable flow conditions.Frontiers in microbiology · 2026Article
- Impact of DNA Extraction and 16S rRNA Gene Amplification Strategy on Microbiota Profiling of Faecal Samples.International journal of molecular sciences · 2025Article
- State-of-the-art approaches in the investigation of human seminal bacteriome using metagenomic methods.Frontiers in reproductive health · 2025Review
- Aggregatibacter is inversely associated with inflammatory mediators in sputa of patients with chronic airway diseases and reduces inflammation in vitro.Respiratory research · 2024Article
- Metrological evaluation of DNA extraction method effects on the bacterial microbiome and resistome in sputum.mSystems · 2024Article
- Improved DNA Extraction and Amplification Strategy for 16S rRNA Gene Amplicon-Based Microbiome Studies.International journal of molecular sciences · 2024Article
- Microparticles as Viral RNA Carriers from Stool for Stable and Sensitive Surveillance.Diagnostics (Basel, Switzerland) · 2023Article
- Sonication versus the conventional method for evaluation of the dental microbiome: a prospective pilot study.BMC oral health · 2022Article
- Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting.Periodontology 2000 · 2021Review
- Fish gill microbiome from India's largest Brahmaputra River-a trans-border biodiversity hotspot region.Environmental monitoring and assessment · 2021Article
- Contamination Scenario Matters when Using Viral and Bacterial Human-Associated Genetic Markers as Indicators of a Health Risk in Untreated Sewage-Impacted Recreational Waters.Environmental science & technology · 2020Article
- Establishment and Stability of the Murine Oral Microbiome.Journal of dental research · 2020Article
- Profiling of Oral Bacterial Communities.Journal of dental research · 2020Review
- Evaluation of a Highly Efficient DNA Extraction Method forMicroorganisms · 2020Article
- The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles.Methods and protocols · 2020Article
- Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens.BMC microbiology · 2020Article
- Rapid, Inexpensive Measurement of Synthetic Bacterial Community Composition by Sanger Sequencing of Amplicon Mixtures.iScience · 2020Article
- Performance evaluation of a new custom, multi-component DNA isolation method optimized for use in shotgun metagenomic sequencing-based aerosol microbiome research.Environmental microbiome · 2020Article
- Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods.Computational and structural biotechnology journal · 2020Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
BACKGROUND AND
objectiveThe advent of next-generation sequencing has significantly facilitated characterization of the oral microbiome. Despite great efforts in streamlining the processes of sequencing and data curation, upstream steps required for amplicon library generation could still influence 16S rRNA gene-based microbial profiles. Among upstream processes, DNA extraction is a critical step that could represent a great source of bias. Accounting for bias introduced by extraction procedures is important when comparing studies that use different methods. Identifying the method that best portrays communities is also desirable. Accordingly, the aim of this study was to evaluate bias introduced by different DNA extraction procedures on oral microbiome profiles.
designFour DNA extraction methods were tested on mock communities consisting of seven representative oral bacteria. Additionally, supragingival plaque samples were collected from seven individuals and divided equally to test two commonly used DNA extraction procedures. Amplicon libraries of the 16S rRNA gene were generated and sequenced via 454-pyrosequencing.
resultsEvaluation of mock communities revealed that DNA yield and bacterial species representation varied with DNA extraction methods. Despite producing the lowest yield of DNA, a method that included bead beating was the only protocol capable of detecting all seven species in the mock community. Comparison of the performance of two commonly used methods (crude lysis and a chemical/enzymatic lysis+column-based DNA isolation) on plaque samples showed no effect of extraction protocols on taxa prevalence but global community structure and relative abundance of individual taxa were affected. At the phylum level, the latter method improved the recovery of Actinobacteria, Bacteroidetes, and Spirochaetes over crude lysis.
conclusionDNA extraction distorts microbial profiles in simulated and clinical oral samples, reinforcing the importance of careful selection of a DNA extraction protocol to improve species recovery and facilitate data comparison across oral microbiology studies.
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