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. 2012 Jan;6(1):1-10.
doi: 10.1038/ismej.2011.71. Epub 2011 Jun 30.

Saliva microbiomes distinguish caries-active from healthy human populations

Fang Yang  1 , Xiaowei Zeng, Kang Ning, Kuan-Liang Liu, Chien-Chi Lo, Wei Wang, Jie Chen, Dongmei Wang, Ranran Huang, Xingzhi Chang, Patrick S Chain, Gary Xie, Junqi Ling, Jian Xu
Affiliations

Saliva microbiomes distinguish caries-active from healthy human populations

Fang Yang et al. ISME J. 2012 Jan.

Abstract

The etiology of dental caries remains elusive because of our limited understanding of the complex oral microbiomes. The current methodologies have been limited by insufficient depth and breadth of microbial sampling, paucity of data for diseased hosts particularly at the population level, inconsistency of sampled sites and the inability to distinguish the underlying microbial factors. By cross-validating 16S rRNA gene amplicon-based and whole-genome-based deep-sequencing technologies, we report the most in-depth, comprehensive and collaborated view to date of the adult saliva microbiomes in pilot populations of 19 caries-active and 26 healthy human hosts. We found that: first, saliva microbiomes in human population were featured by a vast phylogenetic diversity yet a minimal organismal core; second, caries microbiomes were significantly more variable in community structure whereas the healthy ones were relatively conserved; third, abundance changes of certain taxa such as overabundance of Prevotella Genus distinguished caries microbiota from healthy ones, and furthermore, caries-active and normal individuals carried different arrays of Prevotella species; and finally, no 'caries-specific' operational taxonomic units (OTUs) were detected, yet 147 OTUs were 'caries associated', that is, differentially distributed yet present in both healthy and caries-active populations. These findings underscored the necessity of species- and strain-level resolution for caries prognosis, and were consistent with the ecological hypothesis where the shifts in community structure, instead of the presence or absence of particular groups of microbes, underlie the cariogenesis.

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Figures

Figure 1
Figure 1
Phylogenetic diversity of the saliva microbiomes among individuals and between the healthy (H) and caries-active (C) pilot populations. (a) The number of OTUs in each sample. (b) Rarefaction curves for healthy and caries-active populations. A given number of sequences (1000 or 5000) were randomly sampled from each data set. The average number of OTUs in each sample was then calculated (mean±s.e.m. shown). Samples from the two host populations displayed similar phylogenetic diversity at 97% identity level. (c) Shared and distinct OTUs among individuals in the healthy and caries-active individuals. The x axis is the number of samples included in the data set. The y axis is the number of OTUs, representing the means of 100 iterations. Error bars represent s.d. Among healthy hosts, 0.53% of the total OTUs were shared (0.08% were shared among caries-active individuals).
Figure 2
Figure 2
Community structures of healthy (H) and caries-active (C) microbiomes. (a) Pair-wise UniFrac distances within and across the host populations. Colors indicate the degree of similarity in bacterial-community structure. (b) Hosts from the healthy population harbored a more similar bacterial-community structure than those from the caries-active population (***P<0.01).
Figure 3
Figure 3
Comparisons of bacterial taxonomy profiles of the caries-active (C) and healthy (H) host populations based on HOMD. The taxonomy assignment was based on HOMD Database. Comparisons were performed at each of the taxonomical levels of Phylum, Class, Order, Family and Genus. The most frequently detected taxa (above 1% of relative abundance) in each level are shown. Means of the relative abundance for each taxon at each taxonomical level between the healthy and caries-active host-populations are compared (*P<0.1; **P<0.05; mean±s.e.m.).
Figure 4
Figure 4
Structure of the Prevotella communities in the caries-active (C) and healthy (H) host populations. Means of the fraction of each Prevotella species in the total Prevotella community in each sample are compared between the two host populations (*P<0.1; **P<0.05; mean±s.e.m.).
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