Abstract
Understanding the development of the oral microbiota in healthy children is of great importance to oral and general health. However, limited data exist on a healthy maturation of the oral microbial ecosystem in children. Moreover, the data are biased by mislabeling “caries-free” populations. Therefore, we aimed to characterize the healthy salivary and dental plaque microbiome in young children. Caries-free (ICDAS [International Caries Detection and Assessment System] score 0) children (n = 119) and their primary caregivers were followed from 1 until 4 y of child age. Salivary and dental plaque samples were collected from the children at 3 time points (T1, ~1 y old; T2, ~2.5 y old; and T3, ~4 y old). Only saliva samples were collected from the caregivers. Bacterial V4 16S ribosomal DNA amplicons were sequenced using Illumina MiSeq. The reads were denoised and mapped to the zero-radius operational taxonomic units (zOTUs). Taxonomy was assigned using HOMD. The microbial profiles of children showed significant differences (P = 0.0001) over time. Various taxa increased, including Fusobacterium, Actinomyces, and Corynebacterium, while others showed significant decreases (e.g., Alloprevotella and Capnocytophaga) in their relative abundances over time. Microbial diversity and child-caregiver similarity increased most between 1 and 2.5 y of age while still not reaching the complexity of the caregivers at 4 y of age. The microbiome at 1 y of age differed the most from those at later time points. A single zOTU (Streptococcus) was present in all samples (n = 925) of the study. A large variation in the proportion of shared zOTUs was observed within an individual child over time (2% to 42% of zOTUs in saliva; 2.5% to 38% in dental plaque). These findings indicate that the oral ecosystem of caries-free toddlers is highly heterogeneous and dynamic with substantial changes in microbial composition over time and only few taxa persisting across the 3 y of the study. The salivary microbiome of 4-y-old children is still distinct from that of their caregivers.
| Original language | English |
|---|---|
| Pages (from-to) | 159-167 |
| Number of pages | 9 |
| Journal | Journal of Dental Research |
| Volume | 99 |
| Issue number | 2 |
| Early online date | 26 Nov 2019 |
| DOIs | |
| Publication status | Published - 1 Feb 2020 |
Bibliographical note
Funding Information:Kahharova D. 1 Brandt B.W. 1 Buijs M.J. 1 https://orcid.org/0000-0003-2050-3978 Peters M. 2 Jackson R. 3 Eckert G. 3 Katz B. 3 Keels M.A. 4 Levy S.M. 5 Fontana M. 2 * Zaura E. 1 * 1 Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, the Netherlands 2 University of Michigan, Ann Arbor, MI, USA 3 Indiana University, Indianapolis, IN, USA 4 Duke University, Durham, NC, USA 5 University of Iowa, Iowa City, IA, USA D. Kahharova, Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Gustav Mahlerlaan 3004, 1081 LA Amsterdam, the Netherlands. Email: [email protected] * Authors contributing equally as co–senior authors 11 2019 0022034519889015 © International & American Associations for Dental Research 2019 2019 International & American Associations for Dental Research This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License ( http://www.creativecommons.org/licenses/by-nc/4.0/ ) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages ( https://us.sagepub.com/en-us/nam/open-access-at-sage ). Understanding the development of the oral microbiota in healthy children is of great importance to oral and general health. However, limited data exist on a healthy maturation of the oral microbial ecosystem in children. Moreover, the data are biased by mislabeling “caries-free” populations. Therefore, we aimed to characterize the healthy salivary and dental plaque microbiome in young children. Caries-free (ICDAS [International Caries Detection and Assessment System] score 0) children ( n = 119) and their primary caregivers were followed from 1 until 4 y of child age. Salivary and dental plaque samples were collected from the children at 3 time points (T1, ~1 y old; T2, ~2.5 y old; and T3, ~4 y old). Only saliva samples were collected from the caregivers. Bacterial V4 16S ribosomal DNA amplicons were sequenced using Illumina MiSeq. The reads were denoised and mapped to the zero-radius operational taxonomic units (zOTUs). Taxonomy was assigned using HOMD. The microbial profiles of children showed significant differences ( P = 0.0001) over time. Various taxa increased, including Fusobacterium, Actinomyces , and Corynebacterium , while others showed significant decreases (e.g., Alloprevotella and Capnocytophaga ) in their relative abundances over time. Microbial diversity and child-caregiver similarity increased most between 1 and 2.5 y of age while still not reaching the complexity of the caregivers at 4 y of age. The microbiome at 1 y of age differed the most from those at later time points. A single zOTU ( Streptococcus ) was present in all samples ( n = 925) of the study. A large variation in the proportion of shared zOTUs was observed within an individual child over time (2% to 42% of zOTUs in saliva; 2.5% to 38% in dental plaque). These findings indicate that the oral ecosystem of caries-free toddlers is highly heterogeneous and dynamic with substantial changes in microbial composition over time and only few taxa persisting across the 3 y of the study. The salivary microbiome of 4-y-old children is still distinct from that of their caregivers. saliva plaque caries-free children caregiver 16S rRNA gene amplicon sequencing fungal qPCR national institutes of health https://doi.org/10.13039/100000002 2UL1-TR000433 national institutes of health https://doi.org/10.13039/100000002 5U01DE021412 national institutes of health https://doi.org/10.13039/100000002 UL1-TR000006 national institutes of health https://doi.org/10.13039/100000002 UL1-TR000442 colgate-palmolive company https://doi.org/10.13039/100004368 school of dentistry, university of michigan https://doi.org/10.13039/100008115 delta dental foundation https://doi.org/10.13039/100002050 edited-state corrected-proof We thank the members of the Caries Risk Grant Group who contributed in data acquisition: Emily Yanca, Susan Flannagan, Barcey Levy, Jeanette Daly, John Warren, Justine Kolker, Alex Kemper, Dennis Clements, Jennifer Talbert, Fredrica Gallack, Brenda Pattison, Beth Patterson, Anderson Hara, Sue Kelly, Jen Tran, Sharon Gwinn, Lorena Galvez, and Lisa Robinson. D. Kahharova was supported by Stichting Bevordering Tandheelkundige Kennis with NTvT Onderzoeksbeurs 2017 and by the ACTA Research Institute. A supplemental appendix to this article is available online. This study was supported by National Health Institute (NIH) grant 5U01DE021412, NIH CTSA grants (UL1-TR000442 [University of Iowa], 2UL1-TR000433 [University of Michigan], and UL1-TR000006 [Indiana University]), Colgate, the University of Michigan, School of Dentistry, and a Consortium of Delta Dental Plans (Delta Dental of Iowa, Delta Dental of Wisconsin, the Renaissance Health Service Corporation for Delta Dental of Michigan). The authors declare no potential conflicts of interest with respect to the authorship and/or publication of this article. ORCID iD M. Peters https://orcid.org/0000-0003-2050-3978
Publisher Copyright:
© International & American Associations for Dental Research 2019.
Funding
Kahharova D. 1 Brandt B.W. 1 Buijs M.J. 1 https://orcid.org/0000-0003-2050-3978 Peters M. 2 Jackson R. 3 Eckert G. 3 Katz B. 3 Keels M.A. 4 Levy S.M. 5 Fontana M. 2 * Zaura E. 1 * 1 Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam and University of Amsterdam, the Netherlands 2 University of Michigan, Ann Arbor, MI, USA 3 Indiana University, Indianapolis, IN, USA 4 Duke University, Durham, NC, USA 5 University of Iowa, Iowa City, IA, USA D. Kahharova, Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), Gustav Mahlerlaan 3004, 1081 LA Amsterdam, the Netherlands. Email: [email protected] * Authors contributing equally as co–senior authors 11 2019 0022034519889015 © International & American Associations for Dental Research 2019 2019 International & American Associations for Dental Research This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License ( http://www.creativecommons.org/licenses/by-nc/4.0/ ) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages ( https://us.sagepub.com/en-us/nam/open-access-at-sage ). Understanding the development of the oral microbiota in healthy children is of great importance to oral and general health. However, limited data exist on a healthy maturation of the oral microbial ecosystem in children. Moreover, the data are biased by mislabeling “caries-free” populations. Therefore, we aimed to characterize the healthy salivary and dental plaque microbiome in young children. Caries-free (ICDAS [International Caries Detection and Assessment System] score 0) children ( n = 119) and their primary caregivers were followed from 1 until 4 y of child age. Salivary and dental plaque samples were collected from the children at 3 time points (T1, ~1 y old; T2, ~2.5 y old; and T3, ~4 y old). Only saliva samples were collected from the caregivers. Bacterial V4 16S ribosomal DNA amplicons were sequenced using Illumina MiSeq. The reads were denoised and mapped to the zero-radius operational taxonomic units (zOTUs). Taxonomy was assigned using HOMD. The microbial profiles of children showed significant differences ( P = 0.0001) over time. Various taxa increased, including Fusobacterium, Actinomyces , and Corynebacterium , while others showed significant decreases (e.g., Alloprevotella and Capnocytophaga ) in their relative abundances over time. Microbial diversity and child-caregiver similarity increased most between 1 and 2.5 y of age while still not reaching the complexity of the caregivers at 4 y of age. The microbiome at 1 y of age differed the most from those at later time points. A single zOTU ( Streptococcus ) was present in all samples ( n = 925) of the study. A large variation in the proportion of shared zOTUs was observed within an individual child over time (2% to 42% of zOTUs in saliva; 2.5% to 38% in dental plaque). These findings indicate that the oral ecosystem of caries-free toddlers is highly heterogeneous and dynamic with substantial changes in microbial composition over time and only few taxa persisting across the 3 y of the study. The salivary microbiome of 4-y-old children is still distinct from that of their caregivers. saliva plaque caries-free children caregiver 16S rRNA gene amplicon sequencing fungal qPCR national institutes of health https://doi.org/10.13039/100000002 2UL1-TR000433 national institutes of health https://doi.org/10.13039/100000002 5U01DE021412 national institutes of health https://doi.org/10.13039/100000002 UL1-TR000006 national institutes of health https://doi.org/10.13039/100000002 UL1-TR000442 colgate-palmolive company https://doi.org/10.13039/100004368 school of dentistry, university of michigan https://doi.org/10.13039/100008115 delta dental foundation https://doi.org/10.13039/100002050 edited-state corrected-proof We thank the members of the Caries Risk Grant Group who contributed in data acquisition: Emily Yanca, Susan Flannagan, Barcey Levy, Jeanette Daly, John Warren, Justine Kolker, Alex Kemper, Dennis Clements, Jennifer Talbert, Fredrica Gallack, Brenda Pattison, Beth Patterson, Anderson Hara, Sue Kelly, Jen Tran, Sharon Gwinn, Lorena Galvez, and Lisa Robinson. D. Kahharova was supported by Stichting Bevordering Tandheelkundige Kennis with NTvT Onderzoeksbeurs 2017 and by the ACTA Research Institute. A supplemental appendix to this article is available online. This study was supported by National Health Institute (NIH) grant 5U01DE021412, NIH CTSA grants (UL1-TR000442 [University of Iowa], 2UL1-TR000433 [University of Michigan], and UL1-TR000006 [Indiana University]), Colgate, the University of Michigan, School of Dentistry, and a Consortium of Delta Dental Plans (Delta Dental of Iowa, Delta Dental of Wisconsin, the Renaissance Health Service Corporation for Delta Dental of Michigan). The authors declare no potential conflicts of interest with respect to the authorship and/or publication of this article. ORCID iD M. Peters https://orcid.org/0000-0003-2050-3978
| Funders | Funder number |
|---|---|
| ACTA Research Institute | |
| NIH CTSA | UL1-TR000442 |
| Renaissance Health Service Corporation | |
| Stichting bevordering tandheelkundige kennis | |
| National Institutes of Health | 5U01DE021412 |
| Foundation for the National Institutes of Health | |
| Delta | |
| National Center for Advancing Translational Sciences | UL1TR000433 |
| Indiana University | |
| University of Michigan | |
| School of Dentistry, Nihon University | |
| University of Iowa | UL1-TR000006 |
Keywords
- 16S rRNA gene amplicon sequencing
- caregiver
- caries-free children
- fungal qPCR
- plaque
- saliva