Background Oral microbiome and salivary proteins play a critical role in the occurrence and development of caries. In this study, we used metagenomic and metaproteomic analyses to explore the microbiological and proteinic biomarkers and investigate the etiology of caries in 6-8 year old children. Our study aims to offer a better comprehension of these factors and the relationship with caries, and these findings might facilitate caries risk assessment and provide a basis for future prevention strategies. Methods Children six to eight years old living in rural isolated areas including 40 caries-active subjects and 40 caries-free subjects were recruited. Supragingival plaque and unstimulated saliva were collected for 16S rDNA pyrosequencing and isobaric tags for relative and absolute quantitation (iTRAQ) technique coupled with quantitative nano-flow liquid chromatography-tandem mass spectrometry(LC-MS/MS), respectively. Results We found 6 phyla and 13 genera predominant in all the samples, and differences in relative abundances can be observed. The Alpha diversity analysis demonstrated that the richness and diversity of the bacterial communities were similar between children with caries-free and caries-active groups; LEfSe detected differences in the bacterial community including Dialister, Selenomonas, Actinomyces, and Mogibacterium in the caries-active group (P<0.05) and Capnocytophaga, Fusobacterium, Desulfuromonadales, Haemophilus, and Porphyromonas in the caries-free group(P<0.05). The core microbiome was defined as 18 predominant genera in preschool children with caries. The results of the salivary proteome identified 9135 unique peptides and 1662 proteins group from 20 salivary samples. Two hundred fifty-eight proteins were differentially expressed between the caries-free and caries-active groups. Conclusions The diversity of the microbial community has little effect on caries but some bacteria with different relative abundance between the caries-active and caries-free group could be considered as potential biomarkers for children with caries.In addition, as a critical host factor of caries, the salivary proteins are different in caries-free and caries-active groups.

Background Oral microbiome and salivary proteins play a critical role in the occurrence and development of caries. In this study, we used metagenomic and metaproteomic analyses to explore the microbiological and proteinic biomarkers and investigate the etiology of caries in preschool children. Our study aims to offer a better comprehension of these factors and the relationship with caries, and these findings might facilitate caries risk assessment and provide a basis for future prevention strategies.Methods Children six to eight years old living in rural isolated areas with or without caries were recruited. Supragingival plaque and unstimulated saliva were collected for 16S rDNA pyrosequencing and isobaric tags for relative and absolute quantitation (iTRAQ)technique coupled with quantitative nano-flow liquid chromatography-tandem mass spectrometry(LC-MS/MS), respectively.Results A total of 328486 high-quality 16S rRNA sequences were obtained from 40 samples including 20 plaque and 20 saliva subjects, which was clustered into 14,076 OTUs, representing 18 phyla, 28 classes, 48 orders, 78 families,135 genera, and 410 species. We found the six most abundant phyla (Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, Actinobacteria, and Candidate division TM7). The Alpha diversity analysis demonstrated that the richness and diversity of the bacterial communities were similar between caries and caries-free children; differences in the bacterial community composition was analyzed by LEfSe. The core microbiome was defined as 18 predominant genera coming from the saliva and plaque of subjects. For the results of salivary proteome analysis, 9135 unique peptides and 1662 proteins group were identified from 20 salivary samples. 258 proteins were differentially expressed between the caries-free and caries-active group, which might be a potential proteinic biomarker of caries and health status.Conclusions Dental caries is a multifactorial disease affecting many children around the world. The result of our study revealed the complexities of the oral bacterial community and confirmed “ecological plaque hypothesis”. In addition, as an important host factor of caries the salivary proteins are different in healthy or carious status. Exploration on microbiological or protein biomarkers is of great significance to prevent dental caries.