Abstract
Information on how the oral microbiome develops during early childhood and how external factors influence this ecological process is scarce. We used high-throughput sequencing to characterize bacterial composition in saliva samples collected at 3, 6, 12, 24 months and 7 years of age in 90 longitudinally followed children, for whom clinical, dietary and health data were collected. Bacterial composition patterns changed through time, starting with “early colonizers”, including Streptococcus and Veillonella; other bacterial genera such as Neisseria settled after 1 or 2 years of age. Dental caries development was associated with diverging microbial composition through time. Streptococcus cristatus appeared to be associated with increased risk of developing tooth decay and its role as potential biomarker of the disease should be studied with species-specific probes. Infants born by C-section had initially skewed bacterial content compared with vaginally delivered infants, but this was recovered with age. Shorter breastfeeding habits and antibiotic treatment during the first 2 years of age were associated with a distinct bacterial composition at later age. The findings presented describe oral microbiota development as an ecological succession where altered colonization pattern during the first year of life may have long-term consequences for child´s oral and systemic health.
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References
Gomez A, Nelson KE. The oral microbiome of children: development, disease, and implications beyond oral health. Microb Ecol. 2017;73:492–503.
Sampaio-Maia B, Monteiro-Silva F. Acquisition and maturation of oral microbiome throughout childhood: an update. Dent Res J (Isfahan). 2014;11:291–301.
Cephas KD, Kim J, Mathai RA, Barry KA, Dowd SE, Meline BS, et al. Comparative analysis of salivary bacterial microbiome diversity in edentulous infants and their mothers or primary care givers using pyrosequencing. PLoS One. 2011;6:e23503.
Lif Holgerson P, Öhman C, Rönnlund A, Johansson I, Könönen E, Könönen E, et al. Maturation of oral microbiota in children with or without dental caries. PLoS One. 2015;10:e0128534.
Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, et al. Temporal variability is a personalized feature of the human microbiome. Genome Biol. 2014;15:531.
Teng F, Yang F, Huang S, Bo C, Xu ZZ, Amir A, et al. Prediction of early childhood caries via spatial-temporal variations of oral microbiota. Cell Host Microbe. 2015;18:296–306.
Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J. The placenta harbors a unique microbiome. Sci Transl Med. 2014;6:237–65.
Zaura E, Nicu EA, Krom BP, Keijser BJF. Acquiring and maintaining a normal oral microbiome: current perspective. Front Cell Infect Microbiol. 2014;4:85.
Hesselmar B, Sjöberg F, Saalman R, Åberg N, Adlerberth I, Wold AE. Pacifier cleaning practices and risk of allergy development. Pediatrics. 2013;131:1829–37.
Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, et al. Cohabiting family members share microbiota with one another and with their dogs. Elife. 2013;2:e00458.
Jakobsson HE, Abrahamsson TR, Jenmalm MC, Harris K, Quince C, Jernberg C, et al. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section. Gut. 2014;63:559–66.
Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics. 2006;118:511–21.
Boix-Amorós A, Collado MC, Mira A. Relationship between milk microbiota, bacterial load, macronutrients, and human cells during lactation. Front Microbiol. 2016;7:492.
Fernández L, Langa S, Martín V, Maldonado A, Jiménez E, Martín R, et al. The human milk microbiota: Origin and potential roles in health and disease. Pharmacol Res. 2013;69:1–10.
Fitzstevens JL, Smith KC, Hagadorn JI, Caimano MJ, Matson AP, Brownell EA. Systematic review of the human milk microbiota. Nutr Clin Pract. 2016;32:354–64.
Rodriguez JM. The origin of human milk bacteria: is there a bacterial entero-mammary pathway during late pregnancy and lactation? Adv Nutr Int Rev J. 2014;5:779–84.
Carlsson J, Grahnen H, Jonsson G, Wikner S. Early establishment of Streptococcus salivarius in the mouths of infants. J Dent Res. 1970;49:415–8.
Danielsson Niemi L, Hernell O, Johansson I. Human milk compounds inhibiting adhesion of mutans Streptococci to host ligand-coated hydroxyapatite in vitro. Caries Res. 2009;43:171–8.
Sheedy JR, Wettenhall REH, Scalon D, Gooley PR, Lewis DP, MCGregor N, et al. Increased D-lactic acid intestinal bacteria in patients with chronic fatigue syndrome. Vivo (Brooklyn). 2009;23:621–8.
Aimutis WR. Bioactive properties of milk proteins with particular focus on anticariogenesis. J Nutr. 2004;134:989S–95S.
Wernersson J, Danielsson Niemi L, Einarson S, Hernell O, Johansson I. Effects of human milk on adhesion of Streptococcus mutans to saliva-coated hydroxyapatite in vitro. Caries Res. 2006;40:412–7.
Reynolds LA, Finlay BB. Early life factors that affect allergy development. Nat Rev Immunol. 2017;17:518–28. https://doi.org/10.1038/nri.2017.39
Ajslev TA, Andersen CS, Gamborg M, Sørensen TIA, Jess T. Childhood overweight after establishment of the gut microbiota: the role of delivery mode, pre-pregnancy weight and early administration of antibiotics. Int J Obes. 2011;35:522–9.
Petersen PE. The World Oral Health Report 2003: continuous improvement of oral health in the 21st century—the approach of the WHO Global Oral Health Programme. Community Dent Oral Epidemiol. 2003;31:3–24.
Selwitz RH, Ismail AI, Pitts NB. Dental caries. Lancet. 2007;369:51–9.
Kanasi E, Dewhirst FE, Chalmers NI, Kent R, Moore A, Hughes CV, et al. Clonal analysis of the microbiota of severe early childhood caries. Caries Res. 2010;44:485–97.
Tanner ACR, Mathney JMJ, Kent RL, Chalmers NI, Hughes CV, Loo CY, et al. Cultivable anaerobic microbiota of severe early childhood caries. J Clin Microbiol. 2011;49:1464–74.
Nelun Barfod M, Magnussnon K, Lexner MO, Blomqvist S, Dahlén G, Twetman S. Oral microflora in infants delivered vaginally and by caesarean section. Int J Paediatr Dent. 2011;21:401–6.
Abiko Y. Passive immunization against dental caries and periodontal disease: development of recombinant and human monoclonal antibodies. Crit Rev Oral Biol Med. 2000;11:140–58.
Mathews MJ, Mathews EH, Mathews GE. Oral health and coronary heart disease. BMC Oral Health. 2016;16:122.
Scannapieco FA, Bush RB, Paju S. Associations between periodontal disease and risk for atherosclerosis, cardiovascular disease, and stroke. A systematic review. Ann Periodontol. 2003;8:38–53.
Demmer RT, Desvarieux M. Periodontal infections and cardiovascular disease. JADA. 2006;137:14–20.
Fong IW. Emerging relations between infectious diseases and coronary artery disease and atherosclerosis. CMAJ. 2000;163:49–56.
Huang X, Schulte RM, Burne RA, Nascimento MM. Characterization of the arginolytic microflora provides insights into pH homeostasis in human oral biofilms. Caries Res. 2015;49:165–76.
López-López A, Camelo-Castillo A, Ferrer MD, Simon-Soro Á, Mira A. Health-associated niche inhabitants as oral probiotics: the case of Streptococcus dentisani. Front Microbiol. 2017;8:379.
Nyvad B, Crielaard W, Mira A, Takahashi N, Beighton D. Dental caries from a molecular microbiological perspective. Caries Res. 2013;47:89–102.
Abrahamsson TR, Jakobsson T, Björkstén B, Oldaeus G, Jenmalm MC. No effect of probiotics on respiratory allergies: a seven-year follow-up of a randomized controlled trial in infancy. Pediatr Allergy Immunol. 2013;24:556–61.
Abrahamsson TR, Jakobsson T, Böttcher MF, Fredrikson M, Jenmalm MC, Björkstén B, et al. Probiotics in prevention of IgE-associated eczema: a double-blind, randomized, placebo-controlled trial. J Allergy Clin Immunol. 2007;119:1174–80.
Stensson M, Koch G, Coric S, Abrahamsson TR, Jenmalm MC, Birkhed D, et al. Oral administration of Lactobacillus reuteri during the first year of life reduces caries prevalence in the primary dentition at 9 years of age. Caries Res. 2014;48:111–7.
Alm A, Wendt LK, Koch G, Birkhed D. Prevalence of approximal caries in posterior teeth in 15-year-old Swedish teenagers in relation to their caries experience at 3 years of age. Caries Res. 2007;41:392–8.
Koch G. Effect of sodium fluoride in dentifrice and mouthwash on incidence of dental caries in schoolchildren. Odontol Rev. 1967;18:38–43.
Sipos R, Székely AJ, Palatinszky M, Révész S, Márialiget K, Nikolausz M. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiol Ecol. 2007;60:341–50.
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.
Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27:863–4.
Edgar RC. UNCROSS: filtering of high-frequency cross-talk in 16S amplicon reads. bioRxiv. 2016. https://doi.org/10.1101/088666
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9.
Chen T, Yu W-H, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE. The human oral microbiome database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxf). 2010;2010:baq013.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42:D633–42.
Oksanen J. Vegan: community ecology. R Package Version. 2018;2:4–6.
Dray S, Dufour AB. The ade4 package: implementing the duality diagram for ecologists. J Stat Softw. 2007;22:1–20.
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60.
Azad MB, Konya T, Maughan H, Guttman DS, Field CJ, Chari RS, et al. Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. Can Med Assoc J. 2013;185:385–94.
Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P, et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe. 2015;17:690–703.
Abrahamsson T, Jakobsson HE, Andersson AF, Bjorksten B, Engstrand L, Jenmalm M. Reply: gut microbiota diversity and atopic disease: does breast-feeding play a role? J Allergy Clin Immunol. 2013;1:248–9.
Könönen E. Development of oral bacterial flora in young children. Ann Med. 2000;32:107–12.
Nelson-Filho P, Borba IG, Mesquita KSF de, Silva RAB, Queiroz AM de, Silva LAB, et al. Dynamics of microbial colonization of the oral cavity in newborns. Braz Dent J. 2013;24:415–9.
Lif Holgerson P, Harnevik L, Hernell O, Tanner ACR, Johansson I. Mode of birth delivery affects oral microbiota in infants. J Dent Res. 2011;90:1183–8.
Hyde MJ, Modi N. The long-term effects of birth by caesarean section: the case for a randomised controlled trial. Early Hum Dev. 2012;88:943–9.
Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA. 2010;107:11971–5.
Amarasekare P, Possingham H. Patch dynamics and metapopulation theory: the case of successional species. J Theor Biol. 2001;209:333–44.
Luo AH, Yang DQ, Xin BC, Paster BJ, Qin J. Microbial profiles in saliva from children with and without caries in mixed dentition. Oral Dis. 2012;18:595–601.
Hunt KM, Foster JA, Forney LJ, Schütte UME, Beck DL, Abdo Z, et al. Characterization of the diversity and temporal stability of bacterial communities in human milk. PLoS One. 2011;6:e21313.
Cabrera-Rubio R, Collado MC, Laitinen K, Salminen S, Isolauri E, Mira A. The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery. Am J Clin Nutr. 2012;96:544–51.
Jost T, Lacroix C, Braegger CP, Rochat F, Chassard C. Vertical mother–neonate transfer of maternal gut bacteria via breastfeeding. Environ Microbiol. 2014;16:2891–904.
Jost T, Lacroix C, Braegger C, Chassard C. Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health. Nutr Rev. 2015;73:426–37.
Martin DH, Zozaya M, Lillis R, Miller J, Ferris MJ. The microbiota of the human genitourinary tract: trying to see the forest through the trees. Trans Am Clin Climatol Assoc. 2012;123:242–56.
Soto A, Martín V, Jiménez E, Mader I, Rodríguez JM, Fernández L. Lactobacilli and Bifidobacteria in human breast milk: influence of antibiotherapy and other host and clinical factors. J Pediatr Gastroenterol Nutr. 2014;59:78–88.
Marcobal A, Barboza M, Froehlich JW, Block DE, German JB, Lebrilla CB, et al. Consumption of human milk oligosaccharides by gut-related microbes. J Agric Food Chem. 2010;58:5334–40.
Sprockett D, Fukami T, Relman DA. Role of priority effects in the early-life assembly of the gut microbiota. Nat Rev Gastroenterol Hepatol. 2018;15:197–205. https://doi.org/10.1038/nrgastro.2017.173
Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol. 2005;43:5721–32.
Mysak J, Podzimek S, Sommerova P, Lyuya-Mi Y, Bartova J, Janatova T, et al. Porphyromonas gingivalis: Major periodontopathic pathogen overview. J Immunol Res. 2014;2014:476068.
Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, et al. Bacterial diversity in the oral cavity of ten healthy individuals. ISME J. 2010;4:962–74.
Holgerson PL, Vestman NR, Claesson R, Ohman C, Domellöf M, Tanner ACR, et al. Oral microbial profile discriminates breast-fed from formula-fed infants. J Pediatr Gastroenterol Nutr. 2013;56:127–36.
Aas JA, Griffen AL, Dardis SR, Lee AM, Olsen I, Dewhirst FE, et al. Bacteria of dental caries in primary and permanent teeth in children and young adults. J Clin Microbiol. 2008;46:1407–17.
Alcaraz LD, Belda-Ferre P, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, et al. Identifying a healthy oral microbiome through metagenomics. Clin Microbiol Infect. 2012;18:54–57.
Kolenbrander PE, Palmer RJ, Rickard AH, Jakubovics NS, Chalmers NI, Diaz PI. 2006. Bacterial interactions and successions during plaque development. Periodontol. 2000 42:47–79.
Yasukawa T, Ohmori M, Sato S. 2010. The relationship between physiologic halitosis and periodontopathic bacteria of the tongue and gingival sulcus. Odontology 98:44–51.
Badet C, Thebaud NB. 2008. Ecology of lactobacilli in the oral cavity: a review of literature. Open Microbiol. J. 2:38–48.
Bradshaw DJ, Marsh PD. 1998. Analysis of pH-driven disruption of oral microbial communities in vitro. Caries Res. 32:456–62.
Zaura E, Brandt BW, Teixeira de Mattos MJ, Buijs MJ, Caspers MPM, Rashid M-U, et al. Same exposure but two radically different responses to antibiotics: resilience of the salivary microbiome versus long-term microbial shifts in feces. MBio. 2015;6:e01693–15.
Simón-Soro Á, Belda-Ferre P, Cabrera-Rubio R, Alcaraz LD, Mira A. A tissue-dependent hypothesis of dental caries. Caries Res. 2013;47:591–600.
Mira A. Oral microbiome studies: potential diagnostic and therapeutic implications. Adv Dent Res. 2018;29(1):71–7. https://doi.org/10.1177/0022034517737024
Law V, Seow WK, Townsend G. Factors influencing oral colonization of mutans streptococci in young children. Aust Dent J. 2007;52:93–100.
Wan AKL, Seow WK, Purdie DM, Bird PS, Walsh LJ, Tudehope DI. Oral colonization of Streptococcus mutans in six-month-old predentate infants. J Dent Res. 2001a;80:2060–5.
Wan AKL, Seow WK, Walsh LJ, Bird P, Tudehope DI, Purdie DM. Association of Streptococcus mutans infection and oral developmental nodules in pre-dentate infants. J Dent Res. 2001b;80:1945–8.
Gruner D, Paris S, Schwendicke F. Probiotics for managing caries and periodontitis: systematic review and meta-analysis. J Dent. 2016;48:16–25.
Zbinden A, Bostanci N, Belibasakis GN. The novel species Streptococcus tigurinus and its association with oral infection. Virulence. 2015;6:177–82.
Gross EL, Leys EJ, Gasparovich SR, Firestone ND, Schwartzbaum JA, Janies DA, et al. Bacterial 16S sequence analysis of severe caries in young permanent teeth. J Clin Microbiol. 2010;48:4121–8.
Burton JP, Wescombe PA, Moore CJ, Chilcott CN, Tagg JR. Safety assessment of the oral cavity probiotic Streptococcus salivarius K12. Appl Environ Microbiol. 2006;72:3050–3.
Martín V, Mañes-Lázaro R, Miguel Rodríguez J, Maldonado-Barragá A. Streptococcus lactarius sp. nov., isolated from breast milk of healthy women. Int J Syst Evol Microbiol. 2011;61:1048–52.
Caufield PW, Dasanayake AP, Li Y, Pan Y, Hsu J, Hardin JM. Natural history of Streptococcus sanguinis in the oral cavity of infants: evidence for a discrete window of infectivity. Infect Immun. 2000;68:4018–23.
Coffey J, Shlossman M. Multiplex real‐time PCR detection and relative quantification of periodontal pathogens. Clin Exp Dent Res. 2016;2(3):185-92. https://doi.org/10.1002/cre2.37
Ho M-H, Lamont RJ, Xie H. Identification of Streptococcus cristatus peptides that repress expression of virulence genes in Porphyromonas gingivalis. Sci Rep. 2017;7:1413 https://doi.org/10.1038/s41598-017-01551-4
Wang BY, Wu J, Lamont RJ, Lin X, Xie H. Negative correlation of distributions of Streptococcus cristatus and Porphyromonas gingivalis in subgingival plaque. J Clin Microbiol. 2009;47:3902–6. https://doi.org/10.1128/JCM.00072-09
Mira A, Artacho A, Camelo-Castillo A, Garcia-Esteban S, Simon-Soro A. Salivary immune and metabolic marker analysis (SIMMA): a diagnostic test to predict caries risk. Diagnostics. 2017;7:38.
Young DA, Featherstone JDB. Implementing caries risk assessment and clinical interventions. Dent Clin North Am. 2010;54:495–505.
Kanasi E, Johansson I, Lu SC, Kressin NR, Nunn ME, Kent R, et al. Microbial risk markers for childhood caries in pediatricians’ offices. J Dent Res. 2010;89:378–83.
Simón-Soro Á, D’Auria G, Collado MC, Džunková M, Culshaw S, Mira A. Revealing microbial recognition by specific antibodies. BMC Microbiol. 2015;15:132.
Belda-Ferre P, Williamson J, Simón-Soro Á, Artacho A, Jensen ON, Mira A. The human oral metaproteome reveals potentialbiomarkers for caries disease. Proteomics. 2015;15:3497–507.
Van Best N, Hornef MW, Savelkoul PHM, Penders J. On the origin of species: factors shaping the establishment of infant’s gut microbiota. Birth Defects Res Part C Embryo Today Rev. 2015;105:240–51.
Acknowledgements
We would like to acknowledge the technical assistance performed by Ann-Marie Fornander and Camilla Janefjord. We would also like to thank Alba Boix-Amorós and Sandra Garcia-Esteban for their great assistance in the laboratory work.
Funding
A.M.: Spanish Ministry of Economy and Competitiveness (grant no. BIO2015-68711-R). M.S.: The Research Council for the South-East Sweden (grant no: 79001). M.C.J.: The Swedish Research Council (2016-01698); the Swedish Heart and Lung Foundation (20140321); the Medical Research Council of Southeast Sweden (FORSS-573471); the Cancer and Allergy Foundation. M.C.C.: European Research Council (ERC-starting grant 639226).
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Dzidic, M., Collado, M.C., Abrahamsson, T. et al. Oral microbiome development during childhood: an ecological succession influenced by postnatal factors and associated with tooth decay. ISME J 12, 2292–2306 (2018). https://doi.org/10.1038/s41396-018-0204-z
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DOI: https://doi.org/10.1038/s41396-018-0204-z
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