Application of Metagenomic Analyses in Dentistry as a Novel Strategy Enabling Complex Insight into Microbial Diversity of the Oral Cavity

Publications

Share / Export Citation / Email / Print / Text size:

Polish Journal of Microbiology

Polish Society of Microbiologists

Subject: Microbiology

GET ALERTS

ISSN: 1733-1331
eISSN: 2544-4646

DESCRIPTION

4
Reader(s)
14
Visit(s)
0
Comment(s)
0
Share(s)

SEARCH WITHIN CONTENT

FIND ARTICLE

Volume / Issue / page

Related articles

VOLUME 66 , ISSUE 1 (March 2017) > List of articles

Application of Metagenomic Analyses in Dentistry as a Novel Strategy Enabling Complex Insight into Microbial Diversity of the Oral Cavity

Aleksandra Burczyńska / Łukasz Dziewit / Przemysław Decewicz / Izabela Strużycka / Marta Wróblewska *

Keywords : dental caries, endodontics, metagenomics, periapical abscess, periodontitis

Citation Information : Polish Journal of Microbiology. VOLUME 66 , ISSUE 1 , ISSN (Online) 2544-4646, DOI: 10.5604/17331331.1234988, March 2017

License : (CC BY-NC-ND 4.0)

Received Date : 08-November-2016 / Accepted: 12-January-2017 / Published Online: 30-March-2017

ARTICLE

ABSTRACT

The composition of the oral microbiome in healthy individuals is complex and dynamic, and depends on many factors, such as anatomi­cal location in the oral cavity, diet, oral hygiene habits or host immune responses. It is estimated at present that worldwide about 2 billion people suffer from diseases of the oral cavity, mainly periodontal disease and dental caries. Importantly, the oral microflora involved in local infections may spread and cause systemic, even life-threatening infections. In search for etiological agents of infections in dentistry, traditional approaches are not sufficient, as about 50% of oral bacteria are not cultivable. Instead, metagenomic analyses are particularly useful for studies of the complex oral microbiome – both in healthy individuals, and in patients with oral and dental diseases. In this paper we review the current and future applications of metagenomic studies in evaluation of both the composition of the oral microbiome as well as its potential pathogenic role in infections in dentistry.

Content not available PDF Share

FIGURES & TABLES

REFERENCES

Aas J.A., A.L. Griffen, S.R. Dardis, A.M. Lee, I. Olsen, F.E. Dewhirst, E.J. Leys and Paster B.J. 2008. Bacteria of dental caries in primary and permanent teeth in children and young adults. J. Clin. Microbiol. 46(4): 1407–1417.

 

Alcaraz L.D., P. Belda-Ferre, R. Cabrera-Rubio, H. Romero, A. Simon-Soro, M. Pignatelli and A. Mira. 2012. Identifying a healthy oral microbiome through metagenomics. Clin. Microbiol. Infect. 18(Suppl. 4): 54–57.

 

Astorga B., C. Barraza, J.M. Casals, M.J. Cisterna, D. Mena, F. Morales, S. González, O. de Oliveira Jnr. and G. Moncada. 2015. Advances in the study of oral bacterial diversity associated with dental caries by genomic study. Int. J. Odontostomat. 9(3): 349–356.

 

Beighton D. 2005. The complex oral microflora of high-risk individuals and groups and its role in the caries process. Comm. Dent. Oral Epidemiol. 33(4): 248–255.

 

Belda-Ferre P., L.D. Alcaraz, R. Cabrera, H. Romero, A. Simon, M. Pignatelli and A. Mira. 2012. The oral metagenome in health and disease. ISME J. 6(1): 46–56.

 

Belibasakis G.N. and E. Mylonakis. 2015. Oral infections: clinical and biological perspectives. Virulence 6(3): 173–176.

 

Colak H., C.T. Dülgergil, M. Dalli and M.M. Hamidi. 2013. Early childhood caries update: A review of causes, diagnoses, and treatments. J. Nat. Sci. Biol. Med. 4(1): 29–38.

 

Colombo A.P., S.K. Boches, S.L. Cotton, J.M. Goodson, R. Kent, A.D. Haffajee, S.S. Socransky, H. Hasturk, T.E. Van Dyke, F. Dewhirst and others. 2009. Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. J. Periodontol. 80(9): 1421–1432.

 

Dewhirst F.E., T. Chen, J. Izard, B.J. Paster, A.C. Tanner, W.H. Yu, A. Lakshmanan and W.G. Wade. 2010. The human oral microbiome. J. Bacteriol. 192: 5002–5017.

 

Duran-Pinedo A.E. and J. Frias-Lopez. 2015. Beyond microbial community composition: functional activities of the oral microbiome in health and disease. Microbes Infect. 17: 505e516.

 

Edelstein B.L. 2006. The dental caries pandemic and disparities problem. BMC Oral Health. 6(Suppl 1): S2.

 

Gooch B.F., S.O. Griffin, S.K. Gray, W.G. Kohn, R.G. Rozier, M. Siegal, M. Fontana, D. Brunson, N. Carter, D.K. Curtis and others; Centers for Disease Control and Prevention. 2009. Preventing dental caries through school-based sealant programs: updated recommendations and reviews of evidence. J. Am. Dent. Assoc. 140(11): 1356–1365.

 

Griffen A.L., C.J. Beall, J.H. Campbell, N.D. Firestone, P.S. Kumar, Z.K. Yang, M. Podar and E.J. Leys. 2012. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J. 6: 1176–1185.

 

Gross E.L., C.J. Beall, S.R. Kutsch, N.D. Firestone, E.J. Leys and A.L. Griffen. 2012. Beyond Streptococcus mutans: dental caries onset linked to multiple species by 16S rRNA community analysis. PLoS ONE. 7(10): e47722.

 

Hajishengallis G., S. Liang, M.A. Payne, A. Hashim, R. Jotwani, M.A. Eskan, M.L. McIntosh, A. Alsam, K.L. Kirkwood, J.D. Lambris and others. 2011. Low-abundance biofilm species orchestrates inflammatory periodontal disease through the commensal microbiota and complement. Cell Host Microbe. 10: 497–506.

 

Han Y.W. and X. Wang. 2013. Mobile microbiome: oral bacteria in extra-oral infections and inflammation. J. Dent. Res. 92: 485–491.

 

He J., Y. Li, Y. Cao, J. Xue and X. Zhou. 2015. The oral microbiome diversity and its relation to human diseases. Folia Microbiol. 60: 69.

 

Hsiao W.W.L., K.L. Li, Z. Liu, C. Jones, C.M. Fraser-Liggett and A.F. Fouad. 2012. Microbial transformation from normal oral microbiota to acute endodontic infections. BMC Genomics. 13: 345.

 

Jorth P., K.H. Turner, P. Gumus, N. Nizam, N. Buduneli and M. Whiteley. 2014. Metatranscriptomics of the human oral microbiome during health and disease. mBio. 5(2): e01012–14.

 

Karpinski T.M. and A.K. Szkaradkiewicz. 2013. Microbiology of dental caries. J. Biol. Earth Sci. 3(1): M21–M24.

 

Kawamura Y. and Y. Kamiya. 2012. Metagenomic analysis permitting identification of the minority bacterial populations in the oral microbiota. J. Oral Biosci. 54: 132–137.

 

Kumar P.S., A.L. Griffen, M.L. Moeschberger and E.J. Leys. 2005. Identification of candidate periodontal pathogens and beneficial species by quantitative 16S clonal analysis. J. Clin. Microbiol. 43: 3944–3955.

 

Kuramitsu H.K. and B.Y. Wang. 2011. The whole is greater than the sum of its parts: dental plaque bacterial interactions can affect the virulence properties of cariogenic Streptococcus mutans. Am. J. Dent. 24(3): 153–154.

 

Liu B., L.L. Faller, N. Klitgord, V. Mazumdar, M. Ghodsi, D.D. Sommer, T.R. Gibbons, T.J. Treangen, Y.C. Chang, S. Li and others. 2012. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One 7: e37919.

 

Mang-de la Rosa M.R., L. Castellanos-Cosano, M.J. Romero- Perez and A. Cutando. 2014. The bacteremia of dental origin and its implications in the appearance of bacterial endocarditis. Med. Oral Patol. Oral Cir. Bucal. 19(1): e67–e73.

 

Maurer P., E. Hoffman and H. Mast. 2009. Bacterial meningitis after tooth extraction. Br. Dent. J. 206: 69–71.

 

Miller R.R., V. Montoya, J.L. Gardy, D.M. Patrick and P. Tang. 2013. Metagenomics for pathogen detection in public health. Genome Med. 5(9): 81.

 

Moodley A., N.H. Wood and S.L. Shangase. 2013. The relationship between periodontitis and diabetes: a brief review. SADJ 68(260): 262–264.

 

Munson M.A., T. Pitt-Ford, B. Chong, A. Weightman and W.G. Wade. 2002. Molecular and cultural analysis of the microflora associated with endodontic infections. J. Dent. Res. 81: 761–766.

 

Narayanan L.L. and C. Vaishnavi. 2010. Endodontic microbiology. J. Conserv. Dent. 13(4): 233–239.

 

Padmanabhan R., A.K. Mishra, D. Raoult and P.E. Fournier. 2013. Genomics and metagenomics in medical microbiology. J. Microbiol. Methods. 95(3): 415–424.

 

Pappa H. and D.C. Jones. 2005. Mediastinitis from odontogenic infection. A case report. Br. Dent. J. 198: 547–548.

 

Petersen P.E. and P.C. Baehni. 2012. Periodontal health and global public health. Periodontol. 2000. 60(1): 7–14.

 

Petersen P.E., D. Bourgeois, H. Ogawa, S. Estupinan-Day and C. Ndiaye. 2005. The global burden of oral diseases and risks to oral health. Bull. World Health Org. 83(9): 661–669.

 

Ribeiro A.C., F. Matarazzo, M. Faveri, D.M. Zezell and M.P.A. Mayer. 2011. Exploring bacterial diversity of endodontic microbiota by cloning and sequencing 16S rRNA. J. Endod. 37: 922–926.

 

Robertson D.P. 2015. Management of severe acute dental infections. Br. Med. J. 350: h1300.

 

Santos A.L., J.F.J. Siqueira, I.N. Rocas, E.C. Jesus, A.S. Rosado and J.M. Tiedje. 2011. Comparing the bacterial diversity of acute and chronic dental root canal infections. PLoS One 6: e28088.

 

Scholtz M.B., C.C. Lo and P.S. Chain. 2012. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol. 23(1): 9–15.

 

Simon-Soro A., M. Guillen-Navarro and A. Mira. 2014. Metatranscriptomics reveals overall active bacterial composition in caries lesions. J. Oral Microbiol. 6: 25443.

 

Siqueira J.F.J., I.N. Rocas, R. Souto, M. de Uzeda and A.P. Colombo. 2000. Checkerboard DNA-DNA hybridization analysis of endodontic infections. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 89: 744–748.

 

Siqueira J.F.J. and I.N. Rocas. 2009. Diversity of endodontic microbiota revisited. J. Dent. Res. 88: 969–981.

 

Siqueira J.F.J., F.R. Alves and I.N. Rocas. 2011. Pyrosequencing analysis of the apical root canal microbiota. J. Endod. 37: 1499–1503.

 

Sequeira J.F.J. and I.N. Rocas. 2013. Microbiology and treatment of acute apical abscesses. Clin. Microbiol. Rev. 26(2): 255–273.

 

Slots J. and R.J. Genco. 1984. Black-pigmented Bacteroides species, Capnocytophaga species, and Actinobacillus actinomycetemcomitans in human periodontal disease: virulence factors in colonization, survival, and tissue destruction. J. Dent. Res. 63: 412–421.

 

Struzycka I. 2014. The oral microbiome in dental caries. Pol. J. Microbiol. 63(2): 127–135.

 

Sukumar S., A.P. Roberts, F.E. Martin and C.J. Adler. 2016. Metagenomic insights into transferable antibiotic resistance in oral bacteria. J. Dent. Res. 95(9): 969–76.

 

Tanner A.C.R. 2015. Anaerobic culture to detect periodontal and caries pathogens. J. Oral. Biosci. 57(1): 18–26.

 

Tansirichaiya S., M.A. Rahman, A. Antepowicz, P. Mullany and A.P. Roberts. 2016. Detection of novel integrons in the metagenome of human saliva. PLoS One 11(6): 0157605.

 

Tavares W.L.F., L.C. Neves de Brito, R.P. Teles, M.L.A. Massara, A.P. Ribeiro Sobrinho, A.D. Haffajee, S.S. Socransky and F.R. Teles. 2011. Microbiota of deciduous endodontic infections analyzed by MDA and Checkerboard DNA-DNA hybridization. Int. Endod. J. 44(3): 225–235.

 

Turaev D. and T. Rattei. 2016. High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved. Curr. Opin. Biotechnol. 39: 174–181.

 

Wang J., J. Qi, H. Zhao, S. He, Y. Zhang, S. Wei and F. Zhao. 2013. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci. Rep. 3: 1843.

 

World Health Organization (WHO). 2012. Oral health. Fact sheet. http://www.who.int/mediacentre/factsheets/fs318/en, 2016.10.30.

 

Wu J., B.A. Peters, C. Dominianni, Y. Zhang, Z. Pei, L. Yang, Y. Ma, M.P. Purdue, E.J. Jacobs, S.M. Gapstur and others. 2016. Cigarette smoking and the oral microbiome in a large study of American adults. ISME J. 10(10): 2435–2446.

 

Xu P. and J. Gunsolley. 2014. Application of metagenomics in understanding oral health and disease. Virulence 5(3): 424–432.

 

Zarco M.F., T.J. Vess and G.S. Ginsburg. 2012. The oral micro-biome in health and disease and the potential impact on personalized dental medicine. Oral Dis. 18(2): 109–120.

 

Zehnder M. and G.N. Belibasakis. 2015. On the dynamics of root canal infections – what we understand and what we don’t. Virulence 6(3): 216–222.

 

Zhou J., N. Jiang, S. Wang, X. Hu, K. Jiao, X. He, Z. Li and J. Wang. 2016. Exploration of human salivary microbiomes – insights into the novel characteristics of microbial community structure in caries and caries-free subjects. PLoS One 11(1): e0147039.

 

EXTRA FILES

COMMENTS