ArticleMethods and protocols2023
Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies.
Article in Methods and protocols, 2023. 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, 35 citations in OpenAlex.
- From culture-based to 16S sequencing approaches: oral microbiota changes in aging, frailty, and oral hypofunction - a systematic review.BMC oral health · 2026Pooled it
- Community succession and functional trait reorganization in a continuous aerobic denitrification reactor under repeated hydraulic retention time reductions.Bioprocess and biosystems engineering · 2026Article
- Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis.Microbiology spectrum · 2026Article
- Exploring the oral microbiome: from traditional techniques to advanced omics and databases.Antonie van Leeuwenhoek · 2026Review
- Detection to Disruption: A Comprehensive Review of Bacterial Biofilms and Therapeutic Advances.Antibiotics (Basel, Switzerland) · 2026Review
- [Comparative analysis of microbial communities in different oral ecological niches of preschool children].Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology · 2026Article
- Optimizing primer selection for microbial diversity studies in freshwater lakes: a comprehensive evaluation of 16S rRNA, 18S rRNA, and ITS gene regions.FEMS microbiology ecology · 2026Article
- Association Between Continuous Consumption of Yogurt Fermented withJournal of clinical medicine · 2026Article
- Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling.Journal of oral microbiology · 2026Article
- Longitudinal Analysis of Vulvovaginal Bacteriome Following Use of Water- and Silicone-Based Personal Lubricants: Stability, Spatial Specificity, and Clinical Implications.Microorganisms · 2025Article
- DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study.mSystems · 2025Article
- Prokaryotic communities profile from metagenomic libraries of the brown rock sea cucumber (Microbiology resource announcements · 2025Article
- Microbiome Shifts in Peri-Implantitis: Longitudinal Characterization of Dysbiosis and Resolution.International dental journal · 2025Article
- Oral Microbiota Dysbiosis in Male HIV Patients: Comparative Analysis of Candidiasis and HPV-Associated Lesions.Microorganisms · 2025Article
- Characteristics of Subgingival Plaque Microbiome in Japanese Older Adults With Healthy Gingiva.Journal of clinical periodontology · 2025Article
- Role of gut microbiota and its functional products in prenatal alcohol-induced anxiety-like behavior.Progress in neuro-psychopharmacology & biological psychiatry · 2025Article
- The Skin Microbiome Profile of Contact Sports Athletes-Focus on Sexual Dimorphism and Athlete-Non-Athlete Differences.Sports (Basel, Switzerland) · 2025Article
- Tier-based standards for FAIR sequence data and metadata sharing in microbiome research.Nucleic acids research · 2025Article
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Culturable Human Microorganisms and the Impact of Transportation Conditions on Cultivability.Microorganisms · 2025Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Recent advances in genomic technologies have enabled more in-depth study of the oral microbiome. In this study, we compared the amplicons generated by primers targeting different sites of the 16S rRNA gene found in the Human Oral Microbiome Database (HOMD). Six sets of primer targeting V1-V2, V1-V3, V3-V4, V4-V5, V5-V7 and V6-V8 regions of 16S rRNA were tested via in silico simulation. Primers targeting the V1-V2, V3-V4, and V4-V5 regions generated more than 90% of the original input sequences. Primers targeting the V1-V2 and V1-V3 regions exhibited a low number of mismatches and unclassified sequences at the taxonomic level, but there were notable discrepancies at the species level. Phylogenetic tree comparisons showed primers targeting the V1-V2 and V3-V4 regions showed performances similar to primers targeting the whole 16s RNA region in terms of separating total oral microbiomes and periodontopathogens. In an analysis of clinical oral samples, V1-V2 primers showed superior performance for identifying more taxa and had better resolution sensitivity for
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