Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison
Open accessAbstract
OBJECTIVES: The human oral microbiome is potentially related to diverse health conditions and high-throughput technology provides the possibility of surveying microbial community structure at high resolution. We compared two oral microbiome survey methods: broad-based microbiome identification by 16S rRNA gene sequencing and targeted characterization of microbes by custom DNA microarray. METHODS: Oral wash samples were collected from 20 individuals at Memorial Sloan-Kettering Cancer Center. 16S rRNA gene survey was performed by 454 pyrosequencing of the V3-V5 region (450 bp). Targeted identification by DNA microarray was carried out with the Human Oral Microbe Identification Microarray (HOMIM). Correlations and relative abundance were compared at phylum and genus level, between 16S rRNA sequence read ratio and HOMIM hybridization intensity. RESULTS: The major phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were identified with high correlation by the two methods (r = 0.70∼0.86). 16S rRNA gene pyrosequencing identified 77 genera and HOMIM identified 49, with 37 genera detected by both methods; more than 98% of classified bacteria were assigned in these 37 genera. Concordance by the two assays (presence/absence) and correlations were high for common genera (Streptococcus, Veillonella, Leptotrichia, Prevotella, and Haemophilus; Correlation = 0.70-0.84). CONCLUSION: Microbiome community profiles assessed by 16S rRNA pyrosequencing and HOMIM were highly correlated at the phylum level and, when comparing the more commonly detected taxa, also at the genus level. Both methods are currently suitable for high-throughput epidemiologic investigations relating identified and more common oral microbial taxa to disease risk; yet, pyrosequencing may provide a broader spectrum of taxa identification, a distinct sequence-read record, and greater detection sensitivity.
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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 [177]
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- Authors
- Ahn, J., Yang, L., Paster, B. J., Ganly, I., Morris, L., Pei, Z., & Hayes, R. B.
- Affiliations
- New York University (US)
- Harvard University (US)
- Memorial Sloan Kettering Cancer Center (US)
- Corresponding author
- Ahn, Jiyoung
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-07-29
- Volume
- 6
- Issue
- 7
- Pages
- e22788
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3146496
- OpenAlex
- W2032525833
- Cited by
- 183
- References
- 14
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 5 · 2023: 6 · 2022: 13 · 2021: 9 · 2020: 11 · 2019: 12 · 2018: 11 · 2017: 15 · 2016: 21 · 2015: 19 · 2014: 21 · 2013: 16 · 2012: 17
- FWCI
- 22.12
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- National Institutes of Health
- National Cancer Institute (R01CA159036, UH3CA140233)
- National Institute of Allergy and Infectious Diseases (R01AI063477)
- Topics
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- oral microbiota, 16S rRNA pyrosequencing, DNA microarrays, method comparison, microbial community analysis, Streptococcus, Veillonella, Prevotella, Haemophilus, Leptotrichia, cancer patients
- MeSH terms
- Adult, Aged, Aged, 80 and over, Bacteria, Female, Humans, Male, Middle Aged, Mouth, RNA, Bacterial, RNA, Ribosomal, 16S, Biomarkers, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Metagenome, Young Adult, DNA Barcoding, Taxonomic
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