Research Article: The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries

Date Published: July 5, 2017

Publisher: Public Library of Science

Author(s): Apoena Aguiar Ribeiro, Maria Andrea Azcarate-Peril, Maria Belen Cadenas, Natasha Butz, Bruce J. Paster, Tsute Chen, Eric Bair, Roland R. Arnold, Marcelle Nascimento.


Dental caries is the most prevalent disease in humans globally. Efforts to control it have been invigorated by an increasing knowledge of the oral microbiome composition. This study aimed to evaluate the bacterial diversity in occlusal biofilms and its relationship with clinical surface diagnosis and dietary habits. Anamneses were recorded from thirteen 12-year-old children. Biofilm samples collected from occlusal surfaces of 46 permanent second molars were analyzed by 16S rRNA amplicon sequencing combined with the BLASTN-based search algorithm for species identification. The overall mean decayed, missing and filled surfaces modified index [DMFSm Index, including active white spot lesions (AWSL)] value was 8.77±7.47. Biofilm communities were highly polymicrobial collectively, representing 10 bacterial phyla, 25 classes, 29 orders, 58 families, 107 genera, 723 species. Streptococcus sp_Oral_Taxon_065, Corynebacterium matruchotii, Actinomyces viscosus, Actinomyces sp_Oral_Taxon_175, Actinomyces sp_Oral_Taxon_178, Actinomyces sp_Oral_Taxon_877, Prevotella nigrescens, Dialister micraerophilus, Eubacterium_XI G 1 infirmum were more abundant among surfaces with AWSL, and Streptococcus gordonii, Streptococcus sp._Oral_Taxon_058, Enterobacter sp._str._638 Streptococcus australis, Yersinia mollaretii, Enterobacter cloacae, Streptococcus sp._Oral_Taxon_71, Streptococcus sp._Oral_Taxon_F11, Centipeda sp._Oral_Taxon_D18 were more abundant among sound surfaces. Streptococcus mutans was detected on all surfaces in all patients, while Streptococcus sobrinus was detected only in three patients (mean relative abundances 7.1% and 0.6%, respectively). Neither species differentiated healthy from diseased sites. Diets of nine of the subjects were scored as high in fermentable carbohydrates (≧2X/day between meals). A direct association between relative abundances of bacteria and carbohydrate consumption was observed among 18 species. High consumption of fermentable carbohydrates and sound surfaces were associated with a reduction in bacterial diversity. PCoA plots displayed differences in bacterial community profiles between sound and diseased surfaces. Our study showed that, in addition to mutans streptococci, other species may be associated with the initiation of dental caries on occlusal surfaces, and that biofilm diversity of tooth surfaces is influenced by carbohydrate consumption and a surface’s health status.

Partial Text

Dental caries remains the most common chronic disease among children aged between 5 and 17 years in the US, as well as in the world [1,2]. Recent data from CDC showed that in the US the prevalence of untreated cavities among children remains high with 19.5% in children 2–5 years of age and 22.9% in children 6–19 years of age [3]. Caries is a biofilm-mediated disease with a diverse composition of the biofilm associated with initiation and progression [4]. Different oral structures and tissues, such as tongue, teeth and gingiva, are colonized by distinct microbial communities [5,6]. Hence, to gather full information on the healthy and disease-associated oral microbiome, microbial samples should be obtained from clinically defined, discrete sites [7]. Few studies, however, have applied specific sampling for accurate characterization of the different oral microniches [6,8–10]. Moreover, most oral microbiologic studies were based on pooled samples [11–14], rather than characterizing potential differences in microbial composition between teeth and discrete sites on teeth that could influence interpretation of results.

Dental caries continues to be a major public health problem worldwide. It has been shown that the human oral microbiota plays an important role in the health status of the host as the oral cavity contains hundreds of different bacterial species [33]. Cultivation-independent molecular methods, primarily using 16S rRNA gene-based cloning studies, identified approximately 700 species or phylotypes [34,35]. In the present study, by combining 16S rRNA amplicon sequencing and a BLASTN-based search algorithm, we were able to identify collectively 723 species and demonstrated a high bacterial diversity in biofilms collected from the occlusal surface. Considering all teeth, 25 species showed relative abundances higher than 1%. The threshold of relative abundance ≧ 0.1 was chosen because it represented more than 98% of the total sample by each patient, and the results were not influenced if less than 2% of the remaining species were considered in the analyses.




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