ArticleJournal of microbiological methods2009
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.
Article in Journal of microbiological methods, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 157 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
157 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Using next-generation sequencing to detect oral microbiome change following periodontal interventions: A systematic review.Oral diseases · 2021Pooled it
- Oral microbiome diversity and composition before and after chemotherapy treatment in pediatric oncology patients.BMC oral health · 2025Trial
- Variations of Tongue Coating Microbiota in Patients with Gastric Cancer.BioMed research international · 2015Trial
- Trial
- Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.PloS one · 2012Trial
- Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.Environment & health (Washington, D.C.) · 2025Review
- Forest Soil pH and Dissolved Organic Matter Aromaticity Are Distinct Drivers for Soil Microbial Community and Carbon Metabolism Potential.Microbial ecology · 2025Article
- Oral Microbiome: A Review of Its Impact on Oral and Systemic Health.Microorganisms · 2024Review
- Estimating postmortem interval based on oral microbial community succession in rat cadavers.Heliyon · 2024Article
- Full-length 16S rRNA gene sequencing by PacBio improves taxonomic resolution in human microbiome samples.BMC genomics · 2024Article
- The Impact of ProbioticLife (Basel, Switzerland) · 2024Review
- Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing.mSystems · 2023Article
- Sonication versus the conventional method for evaluation of the dental microbiome: a prospective pilot study.BMC oral health · 2022Article
- The lung microbiome in HIV-positive patients with active pulmonary tuberculosis.Scientific reports · 2022Article
- Oral Microbiota during Childhood and Its Role in Chemotherapy-Induced Oral Mucositis in Children with Cancer.Pathogens (Basel, Switzerland) · 2022Review
- A ribosomal operon database and MegaBLAST settings for strain-level resolution of microbiomes.FEMS microbes · 2022Article
- Diversity of the gut, vaginal and oral microbiome among pregnant women in South Africa with and without pre-eclampsia.Frontiers in global women's health · 2022Article
- Oral Fungal Infections: Past, Present, and Future.Frontiers in oral health · 2022Review
- The Microbiome in Periodontitis and Diabetes.Frontiers in oral health · 2022Review
- Insights into the Oral Bacterial Microbiota of Sows.Microorganisms · 2021Article
97 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
To date, metagenomic studies have relied on the utilization and analysis of reads obtained using 454 pyrosequencing to replace conventional Sanger sequencing. After extensively scanning the 16S ribosomal RNA (rRNA) gene, we identified the V5 hypervariable region as a short region providing reliable identification of bacterial sequences available in public databases such as the Human Oral Microbiome Database. We amplified samples from the oral cavity of three healthy individuals using primers covering an approximately 82-base segment of the V5 loop, and sequenced using the Illumina technology in a single orientation. We identified 135 genera or higher taxonomic ranks from the resulting 1,373,824 sequences. While the abundances of the most common phyla (Firmicutes, Proteobacteria, Actinobacteria, Fusobacteria and TM7) are largely comparable to previous studies, Bacteroidetes were less present. Potential sources for this difference include classification bias in this region of the 16S rRNA gene, human sample variation, sample preparation and primer bias. Using an Illumina sequencing approach, we achieved a much greater depth of coverage than previous oral microbiota studies, allowing us to identify several taxa not yet discovered in these types of samples, and to assess that at least 30,000 additional reads would be required to identify only one additional phylotype. The evolution of high-throughput sequencing technologies, and their subsequent improvements in read length enable the utilization of different platforms for studying communities of complex flora. Access to large amounts of data is already leading to a better representation of sample diversity at a reasonable cost.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.