Dental caries is caused by the release of organic acids from fermentative bacteria, which results in the dissolution of hydroxyapatite matrices of enamel and dentine. While low environmental pH is proposed to cause a shift in the consortium of oral bacteria, favouring the development of caries, the impact of this variable has been overlooked in microbial population studies. This study aimed to detail the zonal composition of the microbiota associated with carious dentine lesions with reference to pH. We used 454 sequencing of the 16S rRNA gene (V3–V4 region) to compare microbial communities in layers ranging in pH from 4.5–7.8 from 25 teeth with advanced dentine caries. Pyrosequencing of the amplicons yielded 449,762 sequences. Nine phyla, 97 genera and 409 species were identified from the quality-filtered, de-noised and chimera-free sequences. Among the microbiota associated with dentinal caries, the most abundant taxa included Lactobacillus sp., Prevotella sp., Atopobium sp., Olsenella sp. and Actinomyces sp. We found a disparity between microbial communities localised at acidic versus neutral pH strata. Acidic conditions were associated with low diversity microbial populations, with Lactobacillus species including L. fermentum, L. rhamnosus and L. crispatus, being prominent. In comparison, the distinctive species of a more diverse flora associated with neutral pH regions of carious lesions included Alloprevotella tanerrae, Leptothrix sp., Sphingomonas sp. and Streptococcus anginosus. While certain bacteria were affected by the pH gradient, we also found that ∼60% of the taxa associated with caries were present across the investigated pH range, representing a substantial core. We demonstrated that some bacterial species implicated in caries progression show selective clustering with respect to pH gradient, providing a basis for specific therapeutic strategies.

Mature biofilm and planktonic cells of Streptococcus mutans cultured in a neutral pH environment were subjected to comparative proteome analysis. Of the 242 protein spots identified, 48 were significantly altered in their level of expression (P<0?050) or were unique to planktonic or biofilm-grown cells. Among these were four hypothetical proteins as well as proteins known to be associated with the maintenance of competence or found to possess a cin-box-like element upstream of their coding gene. Most notable among the non-responsive genes were those encoding the molecular chaperones DnaK, GroEL and GroES, which are considered to be up-regulated by sessile growth. Analysis of the rest of the proteome indicated that a number of cellular functions associated with carbon uptake and cell division were down-regulated. The data obtained were consistent with the hypothesis that a reduction in the general growth rate of mature biofilms of S. mutans in a neutral pH environment is associated with the maintenance of transformation without the concomitant stress response observed during the transient state of competence in bacterial batch cultures.

Children’s oral health is in a dire state, with dental decay (caries) being one of the most common chronic diseases. While the role of bacteria in the oral microbiome and dental caries is established, the contribution of fungi is relatively unknown. We assessed the oral mycobiome in childhood (n = 17), to determine if the composition of fungi varies between children with and without caries. Oral mycobiome composition was assessed by using Illumina MiSeq to sequence the ITS2 region, which was amplified from dental plaque. This revealed that the oral mycobiome in the investigated children contained 46 fungal species. Candida albicans was the most abundant species and was ubiquitous in all samples, indicating this species may not be involved in caries development as previously suggested. While the overall diversity of fungi was similar, independent of caries status (p > 0.05), we found caries influenced the abundance of specific fungi. Children without caries had a significantly higher abundance of 17 species compared to children with caries, which had three enriched species (p < 0.001). While the differentially abundant species between health and caries may be specific to an Australian population, our findings indicate the mycobiome plays a role in oral health.

BackgroundPeriodontal disease is highly prevalent amongst domestic cats, causing pain, gingival bleeding, reduced food intake, loss of teeth and possibly impacts on overall systemic health. Diet has been suggested to play a role in the development of periodontal disease in cats. There is a complete lack of information about how diet (composition and texture) affects the feline oral microbiome, the composition of which may influence oral health and the development of periodontal disease. We undertook a pilot study to assess if lifelong feeding of dry extruded kibble or wet (canned and/or fresh meat combinations) diets to cats (n = 10) with variable oral health affected the microbiome.ResultsOral microbiome composition was assessed by amplifying the V1-V3 region of the 16S gene from supragingival dental plaque DNA extracts. These amplicons were sequenced using Illumina technology. This deep sequencing revealed the feline oral microbiome to be diverse, containing 411 bacterial species from 14 phyla. We found that diet had a significant influence on the overall diversity and abundance of specific bacteria in the oral environment. Cats fed a dry diet exclusively had higher bacterial diversity in their oral microbiome than wet-food diet cats (p < 0.001). Amongst this higher diversity, cats on dry-food diets had a higher abundance of Porphyromonas spp. (p < 0.01) and Treponema spp. (p < 0.01).ConclusionsWhile we observed differences in the oral microbiome between cats on the two diets assessed, the relationship between these differences and gingival health was unclear. Our preliminary results indicate that further analysis of the influence of dietary constituents and texture on the feline oral microbiome is required to reveal the relationship between diet, the oral microbiome and gingival health in cats.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0169-y) contains supplementary material, which is available to authorized users.