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Pyrosequencing analysis of the Oral Microflora of healthy adults
Abstract
A good definition of commensal microflora and an understanding of its relation to health are essential in preventing and combating disease. We hypothesized that the species richness of human oral microflora is underestimated. Saliva and supragingival plaque were sampled from 71 and 98 healthy adults, respectively. Amplicons from the V6 hypervariable region of the small-subunit ribosomal RNA gene were generated by PCR, pooled into saliva and plaque pools, and sequenced by means of the Genome Sequencer 20 system at 454 Life Sciences. Data were evaluated by taxonomic and rarefaction analyses. The 197,600 sequences generated yielded about 29,000 unique sequences, representing 22 taxonomic phyla. Grouping the sequences in operational taxonomic units (6%) yielded 3621 and 6888 species-level phylotypes in saliva and plaque, respectively. This work gives a radically new insight into the diversity of human oral microflora, which, with an estimated number of 19,000 phylotypes, is considerably higher than previously reported.
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“The reduction in pathogenic periodontal bacteria in biofilms by mechanical instrumentation [13] through nonsurgical periodontal treatment has been shown to have limited long-term benefits [14,15].”
From A Cross-Talk between Diet and the Oral Microbiome: Balance of Nutrition on Inflammation and Immune System’s Response during Periodontitis (2022) · cites this paper as [15]
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“The microbial diversity of various ecosystems such as deep mines [8], soil [9], deep marine biospheres [10], tidal flats [11], and human microflora [12] were analyzed by employing pyrosequencing technique.”
MethodSengupta, D., Kang, D., Anaya-Bergman, C., Wyant, T., Ghosh, A., Miyazaki, H., & Lewis, J. (2014) · Infection and Immunity · doi:10.1128/iai.01361-13 · Cited by 16
Khalid, G. S., Hamrah, M. H., Ghafary, E. S., Hosseini, S., & Almasi, F. (2021) · Drug Design Development and Therapy · doi:10.2147/dddt.s290021 · Cited by 15
“In the oral cavity, the number of phylotypes was estimated to exceed 19,000.(6) It is composed of proteins, hydrated Correspondence: Elaha Somaya Ghafary Department of Periodontics, Kabul Medical University, Kabul, Afghanistan Tel/Fax +93776665337 Email elaha.”
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“More than 1000 bacterial species have been identified in the oral cavity (Keijser et al., 2008; Kuramitsu et al., 2007).”
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Amplification of Oral Streptococcal DNA from Human Incisors and Bite Marks
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Functional Intestinal Metagenomics
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Host–Pathogen Interactions in Tuberculosis
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Morella, N. M., & Koskella, B. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.01114 · Cited by 12
Draft Genome Sequence of Veillonella parvula HSIVP1, Isolated from the Human Small Intestine
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Perturbation of the indigenous rat oral microbiome by ciprofloxacin dosing
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“The human oral cavity harbors between 700 and 19,000 operative taxonomic units (16, 19, 45), among which streptococci are the most abundant microorganisms, contributing about 80% of the total microbial population in the dental biofilm (5, 31).”
BackgroundComparison of the oral microbiome of siblings using next‐generation sequencing: a pilot study
Lee, H., Lee, J. H., Kim, S., Song, J. S., Kim, B., Kim, Y., & Lee, J. H. (2016) · Oral Diseases · doi:10.1111/odi.12491 · Cited by 11
The Human Microbiome of Local Body Sites and Their Unique Biology
Aagaard, K. M., Luna, R. A., & Versalovic, J. A. (2015) · Elsevier eBooks · doi:10.1016/b978-1-4557-4801-3.00002-3 · Cited by 12
Genomic Alphabets of Saliva as a Biomarker in Oral Cancer
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Human Decomposition Ecology at the University of Tennessee Anthropology Research Facility
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Commensal Neisseria and Antimicrobial-Resistant Gonorrhea
Wadsworth, C. B., Goytia, M., & Shafer, W. M. (2025) · Annual Review of Microbiology · doi:10.1146/annurev-micro-022024-024306 · Cited by 10
Salivary biomarkers in cancer - A narrative review
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Analysis of the microbial community diversity in various regions of the healthy oral cavity
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“This distribution aligns with previous studies highlighting the dominance of these phyla in different oral niches [1, 22, 23].”
ResultA Transcriptome—Targeting EcoChip for Assessing Functional Mycodiversity
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“In recent studies, it exhibited an enormous diversity of fungal genotypes in soil samples [12] as well as a strikingly high bacterial diversity, for instance, in deep sea and oral microflora samples [13,14].”
BackgroundImpact of different oral treatments on the composition of the supragingival plaque microbiome
Rabe, A., Salazar, M. G., Michalik, S., Kocher, T., Below, H., Völker, U., & Welk, A. (2022) · Journal of Oral Microbiology · doi:10.1080/20002297.2022.2138251 · Cited by 10
Proteomic snapshot of saliva samples predicts new pathways implicated in SARS-CoV-2 pathogenesis
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“Indeed, previous metagenomic studies have detected more than 10,000 taxa in saliva [3–6].”
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Salivary Diagnostics and the Oral Microbiome
Kerr, J., & Tribble, G. D. (2015) · Springer eBooks · doi:10.1007/978-3-662-45399-5_5 · Cited by 10
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MethodSampling Modification Effects in the Subgingival Microbiome Profile of Healthy Children
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“The number of microorganisms that colonize in the oral cavity may be more than 19,000 phylotypes (Keijser et al., 2008).”
BackgroundApplication of nanoparticles in oral hygiene
(2016) · Biomaterials and Tissue Engineering Bulletin · doi:10.33263/bteb314.035049 · Cited by 10
The Influence of Orthodontic Treatment on Oral Microbiology
Lucchese, A., & Bondemark, L. (2021) · Wiley eBooks · doi:10.1002/9781119608912.ch10 · Cited by 12
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“Therefore, delineating the symbiotic interactions between the host and its resident oral microbiota is imperative if we are to unravel the complexities underlying the pathogenesis of oral disease [1,2].”
BackgroundFrumento, D., & Ţălu, Ş. (2025) · Applied Sciences · doi:10.3390/app15063157 · Cited by 9
Lim, S., Lee, T., Kim, E., Park, J.-H., Lee, Y., Bae, K., & Kum, K. (2011) · The Journal of Korean Academy of Conservative Dentistry · doi:10.5395/jkacd.2011.36.6.498 · Cited by 9
A pilot study: microbiological conditions of the oral cavity in minipigs for peri-implantitis models
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VMG II transport medium stabilises oral microbiome samples for Next-Generation Sequencing
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Progress of Nanomaterials in Preventative and Restorative Dentistry
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Oral Biofilm Sampling for Microbiome Analysis in Healthy Children
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The Plaque Microbiota Community of Giant Panda (Ailuropoda melanoleuca) Cubs With Dental Caries
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“For these reasons, without anesthesia, we obtained 350,420 high-quality sequences with an average of 43,802 sequences per sample, which was much higher than reported in previous human studies and animal studies (Keijser et al., 2008; Ling et al., 2010; Sturgeon et al., 2014).”
ResultIndividual growth detection of bacterial species in an in vitro oral polymicrobial biofilm model
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“Several multinational projects on the human microbiome have been launched, which, together with studies of 16S rRNA amplicons, have provided new insights into the human intestinal [26] [27] [28] , oral [29] , and vaginal flora [30] .”
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“In addition, our findings on the relative abundance of bacteria in OLP were different from previously reported studies, suggesting that further research on the salivary microbiome of OLP is needed.”
ResultHuang, Z., & Cheng, Y. (2024) · BMC Microbiology · doi:10.1186/s12866-024-03322-4 · Cited by 8
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Lactobacillus rhamnosus LRB mediated inhibition of oral streptococci
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Droplet-based microsystems as novel assessment tools for oral microbial dynamics
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Microbiome Ecosystem Ecology: Unseen Majority in an Anthropogenic Ecosystem
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“) in saliva of healthy subjects and they were less frequent in dental plaque of the same subjects (Keijser et al., 2008).”
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How will next-generation sequencing contribute to the knowledge concerning Helicobacter pylori?
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“Recently, researchers have developed a pyrosequencing method for determining oral microbiota and concluded that these microbiota may include many uncultivable species (29).”
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“In contrast, the diversity of bacterial species is the lowest in mucosal flora, followed by saliva and dental plaque (Keijser et al. 2008).”
Gao, P., Yuan, H., Mei, Z., Yin, X., Zeng, Y., Liu, Z., Yang, X., Xue, J., Liu, Z., Jiang, Y., et al. (2025) · Cell Reports Medicine · doi:10.1016/j.xcrm.2025.102431 · Cited by 6
“7 Specifically, poor oral health indicators, including teeth lost after age 20, a high number of missing and filled teeth, teeth lost without denture use, infrequent tooth brushing, and a high oral health risk score (Figure S1), were significantly associated with a higher risk of ESCC (Table S2).”
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Dysbiosis of Oral Microbiota and Its Effect on Epithelial-Mesenchymal Transition: a Review
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Metadata
- Authors
- Keijser, B. J. F., Zaura, E., Huse, S. M., van der Vossen, J. M. B. M., Schuren, F. H. J., Montijn, R. C., ten Cate, J. M., & Crielaard, W.
- Affiliations
- Marine Biological Laboratory (US)
- TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Microbial Genomics Group, Zeist, The Netherlands;
- Venue
- Journal of Dental Research
- Publisher
- SAGE Publications
- Published
- 2008-11
- Volume
- 87
- Issue
- 11
- Pages
- 1016-1020
- ISSN
- 0022-0345 (ISSN-L)
- 1544-0591
- OpenAlex
- W2103805072
- Cited by
- 669
- References
- 27
- Citations by year
- 2026: 6 · 2025: 14 · 2024: 33 · 2023: 16 · 2022: 39 · 2021: 26 · 2020: 30 · 2019: 24 · 2018: 47 · 2017: 45 · 2016: 41 · 2015: 42 · 2014: 49 · 2013: 50 · 2012: 65
- FWCI
- 53.33
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Dental Research (publishedVersion)
- PubMed (publishedVersion)
- UvA-DARE (University of Amsterdam) (publishedVersion)
- UvA-DARE (University of Amsterdam) (submittedVersion)
- VU Research Portal (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Topics
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- oral microbiota, species richness, saliva, supragingival plaque, 16S rRNA gene, operational taxonomic units, phylotypes, microbial diversity, healthy adults
- MeSH terms
- Adult, Dental Plaque, DNA, Bacterial, Humans, RNA, Bacterial, RNA, Ribosomal, 16S, Saliva, Bacterial Typing Techniques, Sequence Analysis, DNA
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