Bacterial diversity in the oral cavity of 10 healthy individuals
Open accessAbstract
The composition of the oral microbiota from 10 individuals with healthy oral tissues was determined using culture-independent techniques. From each individual, 26 specimens, each from different oral sites at a single point in time, were collected and pooled. An 11th pool was constructed using portions of the subgingival specimens from all 10 individuals. The 16S ribosomal RNA gene was amplified using broad-range bacterial primers, and clone libraries from the individual and subgingival pools were constructed. From a total of 11,368 high-quality, nonchimeric, near full-length sequences, 247 species-level phylotypes (using a 99% sequence identity threshold) and 9 bacterial phyla were identified. At least 15 bacterial genera were conserved among all 10 individuals, with significant interindividual differences at the species and strain level. Comparisons of these oral bacterial sequences with near full-length sequences found previously in the large intestines and feces of other healthy individuals suggest that the mouth and intestinal tract harbor distinct sets of bacteria. Co-occurrence analysis showed significant segregation of taxa when community membership was examined at the level of genus, but not at the level of species, suggesting that ecologically significant, competitive interactions are more apparent at a broader taxonomic level than species. This study is one of the more comprehensive, high-resolution analyses of bacterial diversity within the healthy human mouth to date, and highlights the value of tools from macroecology for enhancing our understanding of bacterial ecology in human health.
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Up to 80% of oral bacteria are dominated by about 200 species in the Phyla Firmicutes and Proteobacteria, with contributions from Bacteroidetes, Actinobacteria and Fusobacteria totaling upwards of 95% of all identified oral microbiota.
“Up to 80% of oral bacteria are dominated by about 200 species in the Phyla Firmicutes (esp. Streptococcus, Veillonella, Granulicatella, Gemella spp.) and Proteobacteria (esp. Neisseria, Haemophilus spp.), with contributions from Bacteroidetes, Actinobacteria and Fusobacteria totaling upwards of 95% of all identified oral microbiota (Figure 2)[171–177].”
From Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health (2017) · cites this paper as [175]
The bacterial taxa found in this study are similar to those in the Human Oral Microbiome Database and those typically reported in other studies of mainstream human subjects.
“The bacterial taxa found in this study are similar to those represented in the Human Oral Microbiome Database (HOMD), as well as those typically reported in other studies of mainstream human subjects [17,18].”
From Analysis of the Effects of Dietary Pattern on the Oral Microbiome of Elite Endurance Athletes (2019) · cites this paper as [17]
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- Authors
- Bik, E. M., Long, C. D., Armitage, G. C., Loomer, P., Emerson, J., Mongodin, E. F., Nelson, K. E., Gill, S. R., Fraser-Liggett, C. M., & Relman, D. A.
- Affiliations
- Stanford Medicine (US)
- University of California, San Francisco (US)
- J. Craig Venter Institute (US)
- University of Maryland, Baltimore (US)
- University at Buffalo, State University of New York (US)
- Institute For Genome Sciences, University of Maryland School of Medicine , Baltimore, MD ,
- VA Palo Alto Health Care System (US)
- Corresponding author
- Relman, David A
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-03-25
- Volume
- 4
- Issue
- 8
- Pages
- 962-974
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- PMC
- PMC2941673
- OpenAlex
- W1981959283
- Cited by
- 651
- References
- 43
- Citations by year
- 2026: 13 · 2025: 27 · 2024: 43 · 2023: 47 · 2022: 48 · 2021: 52 · 2020: 41 · 2019: 47 · 2018: 48 · 2017: 39 · 2016: 43 · 2015: 48 · 2014: 51 · 2013: 39 · 2012: 32
- FWCI
- 38.58
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- The ISME Journal (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (NIH-R01, DP1OD000964)
- National Institute of Dental and Craniofacial Research (R01DE014868, R01DE013541, R01-DE13541)
- 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, bacterial diversity, subgingival bacteria, 16S rRNA gene, bacterial phylotypes, interindividual variability, bacterial co-occurrence, bacterial community structure
- MeSH terms
- Adult, Aged, Bacteria, DNA, Bacterial, DNA, Ribosomal, Female, Health Status, Humans, Male, Middle Aged, Molecular Sequence Data, Mouth, Phylogeny, RNA, Ribosomal, 16S, Biodiversity
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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