Application of high-throughput sequencing in understanding human oral microbiome related with health and disease
Open accessAbstract
The oral microbiome is one of most diversity habitat in the human body and they are closely related with oral health and disease. As the technique developing, high-throughput sequencing has become a popular approach applied for oral microbial analysis. Oral bacterial profiles have been studied to explore the relationship between microbial diversity and oral diseases such as caries and periodontal disease. This review describes the application of high-throughput sequencing for characterization of oral microbiota and analyzing the changes of the microbiome in the states of health or disease. Deep understanding the knowledge of microbiota will pave the way for more effective prevent dentistry and contribute to the development of personalized dental medicine.
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An ever-growing number of specific microbial taxa have been associated with both oral and systemic diseases.
“Amid this complexity, an ever-growing number of specific microbial taxa have been associated with both oral and systemic diseases[181,182].”
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 [181]
Local variation in site-specific core microbial members speaks to heterogeneity of influences bacterial communities experience, including host factors such as age, diet, geography and oral health.
“Local variation in site-specific “core” microbial members speaks to the heterogeneity of influences bacterial communities experience, including host factors such as age, diet, geography and oral health[180–182].”
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 [181]
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Cites
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066 · see citing works
Metagenomic Analysis of the Human Distal Gut Microbiome
Gill, S. R., Pop, M., DeBoy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M., & Nelson, K. E. (2006) · Science · doi:10.1126/science.1124234 · Cited by 4,699 · see citing works
Role of Streptococcus mutans in human dental decay
Loesche, W. J. (1986) · Microbiological Reviews · doi:10.1128/mr.50.4.353-380.1986 · Cited by 3,363 · see citing works
Defining the normal bacterial flora of the oral cavity
Aas, J. A., Paster, B. J., Stokes, L. N., Olsen, I., & Dewhirst, F. E. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.11.5721-5732.2005 · Cited by 3,092 · see citing works
The global burden of oral diseases and risks to oral health.
(2005) · Europe PMC (PubMed Central) · Cited by 2,619 · see citing works
Occlusal Caries: Biological Approach for Its Diagnosis and Management
Carvalho, J. C., Dige, I., Mačhiulskienė, V., Qvist, V., Bakhshandeh, A., Parolo, C. C. F., & Maltz, M. (2016) · Caries Research · doi:10.1159/000448662 · Cited by 2,159 · see citing works
Biology, immunology, and cariogenicity of Streptococcus mutans
Hamada, S., & Slade, H. D. (1980) · Microbiological Reviews · doi:10.1128/mr.44.2.331-384.1980 · Cited by 1,907 · see citing works
Role of Streptococcus mutans in human dental decay.
Loeshe, W. J. (1986) · Medical Entomology and Zoology · Cited by 1,346 · see citing works
Defining the healthy “core microbiome” of oral microbial communities
Zaura, E., Keijser, B. J., Huse, S. M., & Crielaard, W. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-259 · Cited by 1,323 · see citing works
Beyond the Venn diagram: the hunt for a core microbiome
Shade, A. L., & Handelsman, J. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02585.x · Cited by 1,243 · see citing works
Aetiology of root canal treatment failure: why well‐treated teeth can fail
Siqueira, J. F., Jr. (2001) · International Endodontic Journal · doi:10.1046/j.1365-2591.2001.00396.x · Cited by 1,068 · see citing works
Griffen, A. L., Beall, C. J., Campbell, J. H., Firestone, N. D., Kumar, P., Yang, Z. K., Podar, M., & Leys, E. J. (2011) · The ISME Journal · doi:10.1038/ismej.2011.191 · Cited by 1,006 · see citing works
The breadth of bacterial diversity in the human periodontal pocket and other oral sites
Paster, B. J., Olsen, I., Aas, J. A., & Dewhirst, F. E. (2006) · Periodontology 2000 · doi:10.1111/j.1600-0757.2006.00174.x · Cited by 862 · see citing works
Ashimoto, A., Chen, C., Bakker, I., & Slots, J. (1996) · Oral Microbiology and Immunology · doi:10.1111/j.1399-302x.1996.tb00180.x · Cited by 850 · see citing works
Pyrosequencing Sheds Light on DNA SequencingPreprint
Ronaghi, M. (2001) · Genome Research · doi:10.1101/gr.11.1.3 · Cited by 845 · see citing works
`Ome Sweet `Omics--A Genealogical Treasury of Words
Lederberg, J., & McCray, A. T. (2001) · The Scientist (Philadelphia, Pa. Online)/The Scientist · Cited by 727 · see citing works
Clercq, E. D. (1987) · Springer eBooks · doi:10.1007/978-94-009-3353-8 · Cited by 671 · see citing works
Pyrosequencing analysis of the oral microflora of healthy adults
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. (2008) · Journal of Dental Research · doi:10.1177/154405910808701104 · Cited by 669 · cited 1× · see citing works
“At species level, it had been estimated that the number of species–level phylotypes were between 500 and 10000 (Keijser et al., 2008; Lazarevic et al., 2009), and each oral niches harbored 266 “species-level” phylotypes on average (Zaura et al., 2009).”
BackgroundBacterial diversity in the oral cavity of 10 healthy individuals
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. (2010) · The ISME Journal · doi:10.1038/ismej.2010.30 · Cited by 651 · see citing works
A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters
Huse, S. M., Ye, Y., Zhou, Y., & Fodor, A. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034242 · Cited by 572 · see citing works
The development and impact of 454 sequencing
Rothberg, J. M., & Leamon, J. H. (2008) · Nature Biotechnology · doi:10.1038/nbt1485 · Cited by 529 · see citing works
The oral microbiome in health and disease and the potential impact on personalized dental medicine
Zarco, M., Vess, T., & Ginsburg, G. (2011) · Oral Diseases · doi:10.1111/j.1601-0825.2011.01851.x · Cited by 509 · see citing works
Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
Liu, B., Faller, L. L., Klitgord, N., Mazumdar, V., Ghodsi, M., Sommer, D. D., Gibbons, T. R., Treangen, T. J., Chang, Y.-C., Li, S., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037919 · Cited by 411 · see citing works
Endodontic infections: Concepts, paradigms, and perspectives
Siqueira, J. F., Jr. (2002) · Oral Surgery Oral Medicine Oral Pathology Oral Radiology and Endodontology · doi:10.1067/moe.2002.126163 · Cited by 375 · see citing works
Saliva microbiomes distinguish caries-active from healthy human populations
Yang, F., Zeng, X., Ning, K., Liu, K.-L., Lo, C., Wang, W., Chen, J., Wang, D., Huang, R., Chang, X., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2011.71 · Cited by 363 · see citing works
Comparative analyses of the bacterial microbiota of the human nostril and oropharynx
Lemon, K. P., Klepac-Ceraj, V., Schiffer, H. K., Brodie, E. L., Lynch, S. V., & Kolter, R. (2010) · mBio · doi:10.1128/mbio.00129-10 · Cited by 322 · see citing works
Crielaard, W., Zaura, E., Schuller, A. A., Huse, S. M., Montijn, R. C., & Keijser, B. J. F. (2011) · BMC Medical Genomics · doi:10.1186/1755-8794-4-22 · Cited by 320 · see citing works
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing
Lazarević, V., Whiteson, K., Huse, S. M., Hernández, D., Farinelli, L., Østerås, M., Schrenzel, J., & François, P. (2009) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2009.09.012 · Cited by 313 · see citing works
Analysis of Oral Microbiota in Children with Dental Caries by PCR-DGGE and Barcoded Pyrosequencing
Ling, Z., Kong, J., Jia, P., Wei, C., Wang, Y., Pan, Z., Huang, W., Li, L., Chen, H., & Xiang, C. (2010) · Microbial Ecology · doi:10.1007/s00248-010-9712-8 · Cited by 268 · see citing works
Self-citationWang, J., Qi, J., Zhao, H., He, S. C., Zhang, Y., Wei, S., & Zhao, F. (2013) · Scientific Reports · doi:10.1038/srep01843 · Cited by 241 · see citing works
Study of inter- and intra-individual variations in the salivary microbiota
Lazarević, V., Whiteson, K., Hernández, D., François, P., & Schrenzel, J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-523 · Cited by 236 · see citing works
Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing
Hasan, N. A., Young, B. A., Minard-Smith, A. T., Saeed, K., Li, H., Heizer, E. M., McMillan, N. J., Isom, R., Abdullah, A., Bornman, D. M., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097699 · Cited by 207 · see citing works
CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome
Griffen, A. L., Beall, C. J., Firestone, N. D., Gross, E. L., DiFranco, J. M., Hardman, J., Vriesendorp, B., Faust, R. A., Janies, D. A., & Leys, E. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019051 · Cited by 182 · see citing works
Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients
Li, Y., He, J., He, Z., Zhou, Y., Yuan, M., Xu, X., Sun, F., Liu, C., Li, J., Xie, W., et al. (2014) · The ISME Journal · doi:10.1038/ismej.2014.28 · Cited by 180 · see citing works
Cephas, K., Kim, J., Mathai, R. A., Barry, K. A., Dowd, S. E., Meline, B. S., & Swanson, K. S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023503 · Cited by 156 · see citing works
Pyrosequencing Analysis of Oral Microbiota Shifting in Various Caries States in Childhood
Jiang, W. H., Ling, Z., Lin, X., Chen, Y., Zhang, J., Yu, J., Xiang, C., & Chen, H. (2014) · Microbial Ecology · doi:10.1007/s00248-014-0372-y · Cited by 151 · see citing works
Self-citationComparing the Bacterial Diversity of Acute and Chronic Dental Root Canal Infections
dos Santos, A. L., Siqueira, J. F., Jr., Rôças, I. N., Jesus, E. C., Rosado, A. S., & Tiedje, J. M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028088 · Cited by 148 · see citing works
Xu, H., Hao, W., Zhou, Q., Wang, W., Xia, Z., Liu, C., Chen, X., Qin, M., & Chen, F. (2014) · PLoS ONE · doi:10.1371/journal.pone.0089269 · Cited by 143 · see citing works
Jünemann, S., Prior, K., Szczepanowski, R., Harks, I., Ehmke, B., Goesmann, A., Stoye, J., & Harmsen, D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0041606 · Cited by 140 · see citing works
Microbial Analysis in Primary and Persistent Endodontic Infections by Using Pyrosequencing
Hong, B., Lee, T.-K., Lim, S.-M., Chang, S. W., Park, J., Han, S. H., Zhu, Q., Safavi, K. E., FOUAD, A. F., & Kum, K. (2013) · Journal of Endodontics · doi:10.1016/j.joen.2013.05.001 · Cited by 140 · see citing works
Pyrosequencing Analysis of the Apical Root Canal Microbiota
Siqueira, J. F., Jr., Alves, F. R. F., & Rôças, I. N. (2011) · Journal of Endodontics · doi:10.1016/j.joen.2011.08.012 · Cited by 135 · see citing works
Mutans Streptococci and Lactobacilli in Breast-Fed Children with Rampant Caries
Matee, M. I., Mikx, F. H. M., Maselle, S. Y., & Helderman, W. H. V. P. (2009) · Caries Research · doi:10.1159/000261440 · Cited by 121 · see citing works
Hutchins, T. L., Vivanti, G., Mateljevic, N., et al. (2012) · Springer eBooks · doi:10.1007/978-1-4419-1698-3_100856 · Cited by 118 · see citing works
Rogers, Y.-H., & Venter, J. C. (2005) · Nature · doi:10.1038/437326a · Cited by 116 · see citing works
Analyzing Endodontic Infections by Deep Coverage Pyrosequencing
Li, L., Hsiao, W., Nandakumar, R., Barbuto, S., Mongodin, E. F., Paster, B. J., Fraser, C. M., & FOUAD, A. F. (2010) · Journal of Dental Research · doi:10.1177/0022034510370026 · Cited by 116 · see citing works
Oral Microbiome of Deep and Shallow Dental Pockets In Chronic Periodontitis
Ge, X., Rodriguez, R., Trinh, M., Gunsolley, J. C., & Xu, P. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065520 · Cited by 115 · see citing works
The Personal Human Oral Microbiome Obscures the Effects of Treatment on Periodontal Disease
Schwarzberg, K., Le, R., Bharti, B., Lindsay, S. P., Casaburi, G., Salvatore, F., Saber, M. H., Alonaizan, F. A., Slots, J., Gottlieb, R. A., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0086708 · Cited by 102 · see citing works
Pyrosequencing Analysis of Oral Microbiota in Children with Severe Early Childhood Dental Caries
Jiang, W. H., Zhang, J., & Chen, H. (2013) · Current Microbiology · doi:10.1007/s00284-013-0393-7 · Cited by 84 · see citing works
Self-citationDiversity and site-specificity of the oral microflora in the elderly
Preza, D., Olsen, I., Willumsen, T., Grinde, B., & Paster, B. J. (2009) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-009-0743-3 · Cited by 83 · see citing works
The next-generation sequencing technology: A technology review and future perspective
Zhou, X., Ren, L., Li, Y., Zhang, M., Yu, Y., & Yu, J. M. (2010) · Science China Life Sciences · doi:10.1007/s11427-010-0023-6 · Cited by 80 · see citing works
Identification of the Microbiota in Carious Dentin Lesions Using 16S rRNA Gene Sequencing
Obata, J., Takeshita, T., Shibata, Y., Yamanaka, W., Unemori, M., Akamine, A., & Yamashita, Y. (2014) · PLoS ONE · doi:10.1371/journal.pone.0103712 · Cited by 76 · see citing works
Bowden, G. H. (1997) · Community Dentistry And Oral Epidemiology · doi:10.1111/j.1600-0528.1997.tb00902.x · Cited by 75 · see citing works
Kashket, S., Zhang, J., & van Houte, J. (1996) · Journal of Dental Research · doi:10.1177/00220345960750111101 · Cited by 67 · see citing works
Pyrosequencing Analysis of the Salivary Microbiota of Healthy Chinese Children and Adults
Ling, Z., Liu, X., Wang, Y., Li, L., & Xiang, C. (2012) · Microbial Ecology · doi:10.1007/s00248-012-0123-x · Cited by 67 · see citing works
Relationship of children’s salivary microbiota with their caries status: a pyrosequencing study
Gomar‐Vercher, S., Cabrera‐Rubio, R., Mira, Á., & Almerich‐Silla, J. M. (2014) · Clinical Oral Investigations · doi:10.1007/s00784-014-1200-y · Cited by 55 · see citing works
Bacterial Flora of Dental Periradicular Lesions Analyzed by the 454-Pyrosequencing Technology
Saber, M. H., Schwarzberg, K., Alonaizan, F. A., Kelley, S. T., Sedghizadeh, P. P., Furlan, M., Levy, T. A., Simon, J. H., & Slots, J. (2012) · Journal of Endodontics · doi:10.1016/j.joen.2012.06.037 · Cited by 46 · see citing works
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 · see citing works
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Burcham, Z. M., Garneau, N. L., Comstock, S. S., Tucker, R. M., Knight, R., Metcalf, J. L., Scientists, G. O. T. L. C., Miranda, A., Reinhart, B., Meyers, D., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-59016-0 · Cited by 183 · see citing works
Koch, C. D., Gladwin, M. T., Freeman, B. A., Lundberg, J. O., Weitzberg, E., & Morris, A. (2017) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2016.12.015 · Cited by 186 · see citing works
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Shang, Q., Gao, Y., Qin, T., Wang, S., Shi, Y., & Chen, T. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00017 · Cited by 39 · see citing works
- Authors
- Chen, H., & Jiang, W.
- Affiliations
- Zhejiang University (CN)
- Corresponding author
- Chen, Hui
- ORCID
- Venue
- Frontiers in Microbiology
- Publisher
- Frontiers Media SA
- Published
- 2014-10-13
- Volume
- 5
- Pages
- 508-508
- ISSN
- 1664-302X (ISSN-L)
- PMC
- PMC4195358
- OpenAlex
- W2155553719
- Cited by
- 317
- References
- 57
- Citations by year
- 2026: 7 · 2025: 24 · 2024: 19 · 2023: 30 · 2022: 45 · 2021: 45 · 2020: 53 · 2019: 47 · 2018: 17 · 2017: 12 · 2016: 12 · 2015: 6
- FWCI
- 1.68
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Frontiers in Microbiology (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)
- Topics
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- oral microbiota, next-generation sequencing, oral health, oral diseases, dental caries, periodontal disease, microbial diversity, preventive dentistry
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