Comparative analysis of microbial communities in different oral ecological niches of preschool children

doi:10.7518/hxkq.2025.2025285

Abstract

Abstract:

Objective This study aims to investigate the structural differences, dominant bacterial genera, and potential functions of microbial communities in different oral ecological niches (dorsal tongue, tooth surface, and buccal mucosa) of preschool children to clarify the influence of local microenvironments on microbial colonization and provide a theoretical basis for the microbiota-targeted regulation of pediatric oral diseases. Methods A total of 105 plaque samples were collected from the dorsal tongue, tooth surface, and buccal mucosa of 35 healthy preschool children (aged 4-6 years). High-throughput sequencing of the 16S rRNA gene was performed to analyze the microbial community structure and alpha/beta diversity. Principal coordinate analysis, UPGMA clustering, and LEfSe analysis were used to identify niche-specific dominant genera. PICRUSt2 was applied to predict the potential metabolic functional profiles across niches. Results Spatial hete-rogeneity in microbial composition and structure was observed across the three oral niches. Species richness was significantly higher on the tooth surface and buccal mucosa than on the dorsal tongue. The dominant phyla included Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Fusobacteria, and Patescibacteria. At the genus level, Actinomyces and Corynebacterium were enriched on the tooth surface, Veillonella was enriched on the dorsal tongue, and Streptococcus was predominant on the buccal mucosa. Beta diversity and clustering analyses confirmed distinct microbial community structures among the niches. LEfSe analysis identified several niche-specific genera. PICRUSt2 functional prediction revealed significant differences in amino acid metabolism, carbohydrate metabolism, cell motility, translation, signal transduction, immune system, infectious disea-ses, and membrane transport (P<0.05). Conclusion The dorsal tongue, tooth surface, and buccal mucosa in preschool children harbor distinct microbial communities with different taxonomic composition, diversity, and functional potential. The findings suggest that local microenvironmental factors shape oral microbiota and may contribute to the early onset of oral diseases. This study provides foundational data and theoretical insights for early microbiome-based risk assessment and personalized oral health interventions in children.

Key words: preschool children, oral microbiota, ecological niches, 16S rRNA sequencing, microbial diversity, functional prediction

CLC Number:

R780.2

Liu Jiajia, Sun Yuhui, Wu Juefei, Tang Shuai, Ding Gang. Comparative analysis of microbial communities in different oral ecological niches of preschool children[J]. West China Journal of Stomatology, 2026, 44(2): 197-205.

Figures/Tables 7

Fig 1

Fig 2

Fig 3

Fig 4

Fig 5

Fig 6

Fig 7

References 38

[1]	Tuganbaev T, Yoshida K, Honda K. The effects of oral microbiota on health[J]. Science, 2022, 376(6596): 934-936.
[2]	Mark Welch JL, Ramírez-Puebla ST, Borisy GG. Oral microbiome geography: micron-scale habitat and niche[J]. Cell Host Microbe, 2020, 28(2): 160-168.
[3]	Mason MR, Chambers S, Dabdoub SM, et al. Characteri-zing oral microbial communities across dentition states and colonization niches[J]. Microbiome, 2018, 6(1): 67.
[4]	Ward TL, Dominguez-Bello MG, Heisel T, et al. Deve-lopment of the human mycobiome over the first month of life and across body sites[J]. mSystems, 2018, 3(3): e00140-17.
[5]	Xiao J, Fiscella KA, Gill SR. Oral microbiome: possible harbinger for children's health[J]. Int J Oral Sci, 2020, 12(1): 12.
[6]	Liu HH, Chen HW, Liao Y, et al. Comparative analyses of the subgingival microbiome in chronic periodontitis patients with and without gingival erosive oral lichen planus based on 16S rRNA gene sequencing[J]. Biomed Res Int, 2021, 2021: 9995225.
[7]	Chen BY, Lin WZ, Li YL, et al. Roles of oral microbiota and oral-gut microbial transmission in hypertension[J]. J Adv Res, 2023, 43: 147-161.
[8]	Segata N, Haake SK, Mannon P, et al. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples[J]. Genome Biol, 2012, 13(6): R42.
[9]	Yang F, Teng F, Zhang YF, et al. Single-tooth resolved, whole-mouth prediction of early childhood caries via spatiotemporal variations of plaque microbiota[J]. Cell Host Microbe, 2025, 33(6): 1019-1032.e6.
[10]	Weng L, Cui Y, Jian W, et al. Inter-kingdom interactions and environmental influences on the oral microbiome in severe early childhood caries[J]. Microbiol Spectr, 2025, 13(6): e0251824.
[11]	Teng F, Yang F, Huang S, et al. Prediction of early childhood caries via spatial-temporal variations of oral microbiota[J]. Cell Host Microbe, 2015, 18(3): 296-306.
[12]	Grier A, Myers JA, O’Connor TG, et al. Oral microbiota composition predicts early childhood caries onset[J]. J Dent Res, 2021, 100(6): 599-607.
[13]	Proctor DM, Shelef KM, Gonzalez A, et al. Microbial biogeography and ecology of the mouth and implications for periodontal diseases[J]. Periodontol 2000, 2020, 82(1): 26-41.
[14]	Duran-Pinedo AE. Metatranscriptomic analyses of the oral microbiome[J]. Periodontol 2000, 2021, 85(1): 28-45.
[15]	张洋洋, 何金枝, 周学东, 等. 人颊黏膜微生物群落年龄相关性演替研究[J]. 华西口腔医学杂志, 2014, 32(2): 177-181.
	Zhang YY, He JZ, Zhou XD, et al. Human buccal mucosa microbiota succession across age[J]. West China J Stomatol, 2014, 32(2): 177-181.
[16]	AlHarbi SG, Almushayt AS, Bamashmous S, et al. The oral microbiome of children in health and disease—a li-terature review[J]. Front Oral Health, 2024, 5: 1477004.
[17]	Opydo-Szymaczek J, Torlińska-Walkowiak N, Maćko-wiak K, et al. Supragingival plaque microbiota and ca-ries risk factors among children with mixed dentition[J]. BMC Oral Heal, 2025, 25: 791.
[18]	Lee E, Park S, Um S, et al. Microbiome of saliva and plaque in children according to age and dental caries experience[J]. Diagnostics (Basel), 2021, 11(8): 1324.
[19]	Rajasekaran JJ, Krishnamurthy HK, Bosco J, et al. Oral microbiome: a review of its impact on oral and systemic health[J]. Microorganisms, 2024, 12(9): 1797.
[20]	Yang XX, He LD, Yan SQ, et al. The impact of caries status on supragingival plaque and salivary microbiome in children with mixed dentition: a cross-sectional survey[J]. BMC Oral Heal, 2021, 21: 319.
[21]	Giacomini JJ, Torres-Morales J, Dewhirst FE, et al. Spatial ecology of the Neisseriaceae family in the human oral cavity[J]. Microbiol Spectr, 2025, 13(5): e0327524.
[22]	Tsai CY, Tang CY, Tan TS, et al. Subgingival microbiota in individuals with severe chronic periodontitis[J]. J Microbiol Immunol Infect, 2018, 51(2): 226-234.
[23]	Chaple-Gil AM, Santiesteban-Velázquez M, Urbizo Vélez JJ. Association between oral microbiota dysbiosis and the risk of dementia: a systematic review[J]. Dent J, 2025, 13(6): 227.
[24]	Ho TE, Yang YM, Gu WJ, et al. Construction of an early childhood caries risk prediction model based on the oral microbiome: a nested case‒control study[J]. BMC Oral Heal, 2025, 25: 923.
[25]	Qudeimat MA, Alyahya A, Karched M, et al. Dental plaque microbiota profiles of children with caries-free and caries-active dentition[J]. J Dent, 2021, 104: 103539.
[26]	Tynior W, Kłósek M, Salatino S, et al. Metagenomic analysis of the buccal microbiome by nanopore sequen-cing reveals structural differences in the microbiome of a patient with molar incisor hypomineralization (MIH) compared to a healthy child: case study[J]. Int J Mol Sci, 2024, 25(23): 13143.
[27]	Sato-Suzuki Y, Washio J, Wicaksono DP, et al. Nitrite-producing oral microbiome in adults and children[J]. Sci Rep, 2020, 10: 16652.
[28]	Wicaksono DP, Washio J, Abiko Y, et al. Nitrite production from nitrate and its link with lactate metabolism in oral Veillonella spp[J]. Appl Environ Microbiol, 2020, 86(20): e01255-20.
[29]	Ma SY, Zhou QN, Cai S, et al. A comparative study of microbial changes in dental plaque before and after single- and multiappointment treatments in patients with severe early childhood caries[J]. BMC Oral Heal, 2024, 24: 695.
[30]	Borisy GG, Valm AM. Spatial scale in analysis of the dental plaque microbiome[J]. Periodontol 2000, 2021, 86(1): 97-112.
[31]	Stephen AS, Dhadwal N, Nagala V, et al. Interdental and subgingival microbiota May affect the tongue microbial ecology and oral malodour in health, gingivitis and pe-riodontitis[J]. J Periodontal Res, 2021, 56(6): 1174-1184.
[32]	Zeng X, Ma Q, Huang CX, et al. Diagnostic potential of salivary microbiota in persistent pulmonary nodules: identifying biomarkers and functional pathways using 16S rRNA sequencing and machine learning[J]. J Transl Med, 2024, 22: 1079.
[33]	Luo SS, Shao RR, Hong Y, et al. Identifying the oral microbiome of adolescents with and without dental fluorosis based on full-length 16S rRNA gene sequencing[J]. Front Microbiol, 2024, 15: 1296753.
[34]	Jaber Y, Sarusi-Portuguez A, Netanely Y, et al. Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner[J]. NPJ Biofilms Microbiomes, 2024, 10(1): 142.
[35]	Cantalupo P, Diacou A, Park S, et al. Single-cell RNA-seq reveals a resolving immune phenotype in the oral mucosa[J]. iScience, 2024, 27(9): 110735.
[36]	Samaranayake L, Matsubara VH. Normal oral flora and the oral ecosystem[J]. Dent Clin N Am, 2017, 61(2): 199-215.
[37]	Martínez-Porchas M, Villalpando-Canchola E, Vargas-Albores F. Significant loss of sensitivity and specificity in the taxonomic classification occurs when short 16S rRNA gene sequences are used[J]. Heliyon, 2016, 2(9): e00170.
[38]	Na HS, Song YR, Yu Y, et al. Comparative analysis of primers used for 16S rRNA gene sequencing in oral microbiome studies[J]. MPs, 2023, 6(4): 71.