Abstract
The oral cavity is one of the most important and complicated habitats in our body and supports diverse microbial communities. In this study, we aimed to determine the bacterial diversity and composition of various oral micro-niches. Samples were collected from supragingival plaque, saliva, and tongue coating from 10 preschool children (30 samples total). 16S rRNA gene pyrosequencing dataset generated 314,639 clean reads with an average of 10,488 ± 2,787 reads per sample. The phyla Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria were predominant, accounting for more than 90% of the total sequences. We found the highest α diversity, microbial richness, and evenness in plaque, compared with saliva and tongue coating. Plaque was also distinguished from saliva and tongue coating by phylogenetic distances (weighted UniFrac). Taxa with different relative abundances were further identified, confirming the existence of microbial differences across the three niches. Core microbiomes were defined of each niche; however, only a small proportion of operational taxonomic units (8.07%) were shared by the three niches. Coaggregation between Actinomyces spp. and Streptococcus spp. and other correlations among periodontal pathogens, such as Prevotella, Fusobacteria, Capnocytophaga, and Tannerella, were shown by a co-occurrence network. In summary, our study provides a framework of oral microbial communities in the population of preschool children as a baseline for further studies of oral diseases related to microbes.
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References
Abusleme, L., Dupuy, A.K., Dutzan, N., Silva, N., Burleson, J.A., Strausbaugh, L.D., Gamonal, J., and Diaz, P.I. 2013. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J. 7, 1016–1025.
Avila, M., Ojcius, D.M., and Yilmaz, O. 2009. The oral microbiota: living with a permanent guest. DNA Cell Biol. 28, 405–411.
Belda-Ferre, P., Alcaraz, L.D., Cabrera-Rubio, R., Romero, H., Simon-Soro, A., Pignatelli, M., and Mira, A. 2012. The oral metagenome in health and disease. ISME J. 6, 46–56.
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Pena, A.G., Goodrich, J.K., Gordon, J.I., et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336.
Chen, T., Yu, W.H., Izard, J., Baranova, O.V., Lakshmanan, A., and Dewhirst, F.E. 2010. The Human oral microbiome database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database 7, baq013.
Crielaard, W., Zaura, E., Schuller, A.A., Huse, S.M., Montijn, R.C., and Keijser, B.J.F. 2011. Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med. Genomics 4, 1–13.
Dewhirst, F.E., Chen, T., Izard, J., Paster, B.J., Tanner, A.C., Yu, W.H., Lakshmanan, A., and Wade, W.G. 2010. The human oral microbiome. J. Bacteriol. 192, 5002–5017.
Donaldson, A.C., McKenzie, D., Riggio, M.P., Hodge, P.J., Rolph, H., Flanagan, A., and Bagg, J. 2005. Microbiological culture analysis of the tongue anaerobic microflora in subjects with and without halitosis. Oral Dis. 11 Suppl. 1, 61–63.
Fabian, T.K., Fejerdy, P., and Csermely, P. 2008. Salivary genomics, transcriptomics and proteomics: the emerging concept of the oral ecosystem and their use in the early diagnosis of cancer and other diseases. Curr. Genomics 9, 11–21.
Gevers, D., Knight, R., Petrosino, J.F., Huang, K., McGuire, A.L., Birren, B.W., Nelson, K.E., White, O., Methe, B.A., and Huttenhower, C. 2012. The human microbiome project: a community resource for the healthy human microbiome. PLoS Biol. 10, e1001377.
Group, N.H.W., Peterson, J., Garges, S., Giovanni, M., McInnes, P., Wang, L., Schloss, J.A., Bonazzi, V., McEwen, J.E., Wetterstrand, K.A., et al. 2009. The NIH human microbiome project. Genome Res. 19, 2317–2323.
He, X.S. and Shi, W.Y. 2009. Oral microbiology: past, present and future. IJOS 1, 47–58.
Human Microbiome Project, C. 2012a. A framework for human microbiome research. Nature 486, 215–221.
Human Microbiome Project, C. 2012b. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214.
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., and Crielaard, W. 2008. Pyrosequencing analysis of the oral microflora of healthy adults. J. Dent. Res. 87, 1016–1020.
Kolenbrander, P.E., Andersen, R.N., Blehert, D.S., Egland, P.G., Foster, J.S., and Palmer, R.J., 2002. Communication among oral bacteria. Microbiol. Mol. Biol. Rev. 66, 486–505.
Langille, M.G., Zaneveld, J., Caporaso, J.G., McDonald, D., Knights, D., Reyes, J.A., Clemente, J.C., Burkepile, D.E., Vega Thurber, R.L., Knight, R., et al. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814–821.
Ling, Z.X., Kong, J.M., Jia, P., Wei, C.C., Wang, Y.Z., Pan, Z.W., Huang, W.J., Li, L.J., Chen, H., and Xiang, C. 2010. Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing. Microb. Ecol. 60, 677–690.
Marsh, P.D. 2004. Dental plaque as a microbial biofilm. Caries Res. 38, 204–211.
Qin, J.J., Li, R.Q., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65.
Sender, R., Fuchs, S., and Milo, R. 2016. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell 164, 337–340.
Shaw, F.L., Mulholland, F., Le Gall, G., Porcelli, I., Hart, D.J., Pearson, B.M., and Van Vliet, A.H. 2012. Selenium-dependent biogenesis of formate dehydrogenase in Campylobacter jejuni is controlled by the fdhTU accessory genes. J. Bacteriol. 194, 3814–3823.
Simon-Soro, A., Tomas, I., Cabrera-Rubio, R., Catalan, M.D., Nyvad, B., and Mira, A. 2013. Microbial geography of the oral cavity. J. Dent. Res. 92, 616–621.
Takahashi, N. and Yamada, T. 1999. Glucose and lactate metabolism by Actinomyces naeslundii. Crit. Rev. Oral Biol. Med. 10, 487–503.
Tenovuo, J. 2002. Antimicrobial agents in saliva–protection for the whole body. J. Dent. Res. 81, 807–809.
Turnbaugh, P.J., Ley, R.E., Hamady, M., Fraser-Liggett, C.M., Knight, R., and Gordon, J.I. 2007. The human microbiome project. Nature 449, 804–810.
Viorica Chetruş, I.R.I. 2013. Dental plaque–classification, formation, and identification. IJMD 3, 139–143.
Xiao, C., Ran, S., Huang, Z., and Liang, J. 2016. Bacterial diversity and community structure of supragingival plaques in adults with dental health or caries revealed by 16S pyrosequencing. Front. Microbiol. 7, 1145.
Xin, B.C., Luo, A.H., Qin, J., Paster, B.J., Xu, Y.L., Li, Y.L., and Yang, D.Q. 2013. Microbial diversity in the oral cavity of healthy chinese han children. Oral Dis. 19, 401–405.
Xu, H., Hao, W., Zhou, Q., Wang, W., Xia, Z., Liu, C., Chen, X., Qin, M., and Chen, F. 2014. Plaque bacterial microbiome diversity in children younger than 30 months with or without caries prior to eruption of second primary molars. PLoS One 9, e89269.
Xu, X., He, J.Z., Xue, J., Wang, Y., Li, K., Zhang, K.K., Guo, Q., Liu, X.H., Zhou, Y., Cheng, L., et al. 2015. Oral cavity contains distinct niches with dynamic microbial communities. Environ. Microbiol. 17, 699–710.
Yang, F., Huang, S., He, T., Catrenich, C., Teng, F., Bo, C., Chen, J., Liu, J., Li, J., Song, Y., et al. 2013. Microbial basis of oral malodor development in humans. J. Dent. Res. 92, 1106–1112.
Yang, F., Zeng, X., Ning, K., Liu, K.L., Lo, C.C., Wang, W., Chen, J., Wang, D., Huang, R., Chang, X., et al. 2012. Saliva microbiomes distinguish caries-active from healthy human populations. ISME J. 6, 1–10.
Zhang, Z., Geng, J., Tang, X., Fan, H., Xu, J., Wen, X., Ma, Z.S., and Shi, P. 2014. Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota. ISME J. 8, 881–893.
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This work was supported by grants from the National Natural Science Foundation of China (81300880), Academic Collaboration Fund (T.X.), and International S & T Cooperation Program of China (2014DFA31520).
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Ren, W., Zhang, Q., Liu, X. et al. Exploring the oral microflora of preschool children. J Microbiol. 55, 531–537 (2017). https://doi.org/10.1007/s12275-017-6474-8
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DOI: https://doi.org/10.1007/s12275-017-6474-8