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The Human Oral Microbiome
Open accessAbstract
The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible ( www.homd.org ). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria , Bacteroidetes , Chlamydiae , Chloroflexi , Euryarchaeota , Firmicutes , Fusobacteria , Proteobacteria , Spirochaetes , SR1, Synergistetes , Tenericutes , and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.
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“It is estimated that about 50% of oral bacterial species are resistant to cultivation (Dewhirst et al., 2010)”
From Microbial colonisation associated with conventional and self-ligating brackets: a systematic review (2022) · cites this paper as Dewhirst et al., 2010
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In the citing paper
“These species are known to play roles in dental biofilm maturation and oral inflammatory conditions [35,36].”
From Severity-dependent alterations in oral microbiota and antibiotic resistance in children with dental fluorosis (2026) · cites this paper as [36]
Experimental — accuracy not yet measuredIn the citing paper
“Other core members with greater than 1% abundance across at least 80% of samples from 1 or more sites, included those from the family Pasteurellaceae, those from the genera Gemella, Veillonella, Prevotella, Fusobacterium, Porphyromonas, Neisseria, Capnocytophaga, Corynebacterium, and Actinomyces, and those from the orders Lactobacillales and Lachnospiraceae.160”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [160]
In the citing paper
“Moreover, the Human Microbiome Project found that the main genus among intraoral sites, at greater than 10% abundance and present in more than 75% of samples, was Streptococcus, specifically Streptococcus oralis, S mitis, and Streptococcus peroris.”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [160]
In the citing paper
“The oral cavity houses the second largest microbiota in the human body and can include bacteria, fungi, viruses, and archaea (Dewhirst et al., 2010).”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Dewhirst et al., 2010
In the citing paper
“Most of above mentioned microbiota can be found in human oral cavity (Dewhirst et al., 2010)”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Dewhirst et al., 2010
In the citing paper
“Culture-independent sequencing of the bacterial 16S ribosome has suggested an estimated 50–100 billion bacteria in the mouth, comprised of nearly 700 identified bacterial species[170,171].”
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 [171]
In the citing paper
“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 [171]
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Metadata
- Authors
- Dewhirst, F. E., Chen, T., Izard, J., Paster, B. J., Tanner, A. C. R., Yu, W.-H., Lakshmanan, A., & Wade, W. G.
- Affiliations
- Harvard University (US)
- The Forsyth Institute (US)
- King's College London (GB)
- Venue
- Journal of Bacteriology
- Publisher
- American Society for Microbiology
- Published
- 2010-10
- Volume
- 192
- Issue
- 19
- Pages
- 5002-5017
- ISSN
- 0021-9193 (ISSN-L)
- 1098-5530
- PMC
- PMC2944498
- OpenAlex
- W2121748291
- Cited by
- 3,352
- References
- 75
- Citations by year
- 2026: 188 · 2025: 232 · 2024: 250 · 2023: 290 · 2022: 276 · 2021: 327 · 2020: 325 · 2019: 246 · 2018: 193 · 2017: 211 · 2016: 152 · 2015: 174 · 2014: 183 · 2013: 106 · 2012: 108
- FWCI
- 111.50
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Bacteriology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Lincoln (University of Nebraska) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Funders
- National Institute of Dental and Craniofacial Research (DE017106, DE-015847, U01DE016937, DE-016937, R01DE015847, R37DE016937, R21DE017106, R01DE016937)
- Topics
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- oral microbiota, 16S rRNA gene sequences, bacterial diversity, bacterial phylogeny, novel bacterial taxa, bacterial abundance
- MeSH terms
- Bacteria, Chlamydia, Humans, Molecular Sequence Data, Mouth, Phylogeny, RNA, Ribosomal, 16S, Spirochaetales, Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Fusobacteria, Metagenome
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