The human oral microbiome database: a web accessible resource for investigating oral microbe taxonomic and genomic information
Open accessAbstract
The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD--taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites. Database URL: http://www.homd.org.
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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.
“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 [170]
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“[18] Chen T, Yu W-H, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE.”
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- Authors
- Chen, T., Yu, W.-H., Izard, J., Baranova, O. V., Lakshmanan, A., & Dewhirst, F. E.
- Affiliations
- The Forsyth Institute (US)
- Harvard University (US)
- Corresponding author
- Chen, T.
- Venue
- Database
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-07-06
- Volume
- 2010
- Issue
- 0
- Pages
- baq013-baq013
- ISSN
- 1758-0463 (ISSN-L)
- PMC
- PMC2911848
- OpenAlex
- W2115699469
- Cited by
- 1,162
- References
- 51
- Citations by year
- 2026: 70 · 2025: 74 · 2024: 78 · 2023: 94 · 2022: 82 · 2021: 112 · 2020: 104 · 2019: 106 · 2018: 92 · 2017: 73 · 2016: 70 · 2015: 58 · 2014: 53 · 2013: 28 · 2012: 37
- FWCI
- 35.21
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc
- Locations
- Database (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Lincoln (University of Nebraska) (submittedVersion)
- Funders
- National Institute of Dental and Craniofacial Research (DE017106, U01DE016937, DE-016937, R21DE017106)
- 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, oral bacteria, 16S rRNA gene, bacterial taxonomy, bacterial genomes, Human Microbiome Project
- MeSH terms
- Bacteria, Computers, Humans, Mouth, Phenotype, RNA, Bacterial, RNA, Ribosomal, 16S, Software, Sequence Alignment, Genome, Bacterial, Internet, Databases, Genetic, Metagenome, Metagenomics
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