BackgroundHuman microbiome dysbiosis is related to various human diseases, and identifying robust and consistent biomarkers that apply in different populations is a key challenge. This challenge arises when identifying key microbial markers of childhood caries.MethodsWe analyzed unstimulated saliva and supragingival plaque samples from children of different ages and sexes, performed 16S rRNA gene sequencing, and sought to identify whether consistent markers exist among subpopulations by using a multivariate linear regression model.ResultsWe found thatAcinetobacterandClostridialesbacterial taxa were associated with caries in plaque and saliva, respectively, whileFirmicutesandClostridiawere found in plaque isolated from children of different ages in preschool and school. These identified bacterial markers largely differ between different populations, leaving onlySaccharibacteriaas a significant caries-associated phylum in children.Saccharibacteriais a newly identified phylum, and our taxonomic assignment database could not be used to identify its specific genus.ConclusionOur data indicated that, in a South China population, oral microbial signatures for dental caries show age and sex differences, butSaccharibacteriamight be a consistent signal and worth further investigation, considering the lack of research on this microbe.