Saliva microbiomes distinguish caries-active from healthy human populations

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.

Microbial Basis of Oral Malodor Development in Humans

“…After the H 2 S measurement, tongue plaque was collected, and total DNA was extracted. PCR amplicon libraries of the small subunit ribosomal (16S) RNA gene V1-V3 hyper-variable region (Escherichia coli positions 5-534) were pyrosequenced according to our published protocols (Huang et al, 2011;Yang et al, 2012).…”

Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

“…Culture-independent profiling techniques have allowed detection of complex microbial communities in various body sites, including the skin, oral cavity, and gastrointestinal tract (1, 2). Recent applications of these techniques have led to increased understanding of roles of microbial communities in health and in diseases such as inflammatory bowel disease, obesity, and dental caries (3)(4)(5).…”

Altered Bacterial Profiles in Saliva from Adults with Caries Lesions: A Case-Cohort Study

“…However, being easy and inexpensive to collect, saliva is an almost ideal biological secretion for studies of the oral microbial profile in health and disease [Baum et al, 2011]. The bacterial composition of saliva in oral health has been examined in previous studies [Nasidze et al, 2009;Bik et al, 2010], but the question whether or not dental caries is characterized by detectable changes in the bacterial profile of saliva has been addressed mostly in studies of young populations [Ling et al, 2010;Crielaard et al, 2011;Luo et al, 2012;Yang et al, 2012]. Thus, the objective of this study was to analyze whether presence of dental caries in a large adult population was associated with a different salivary bacterial profile when compared to individuals without untreated caries.…”